Stem Cells: Miracle Cure or Hoax? A Review of Present Application and Potential Uses of Stem Cells
By Vita Quintanilla, Genetics 23’
Author’s Note: My purpose in writing this piece is to educate the current safe applications of stem cell as misuse and damage due to the same is so prevalent in the US and abroad. While not detracting from the great advances being made in the field currently this piece is to take stock of the reality of this treatment.
Large segments of the American and world population living with medical conditions that cause significant loss of mobility and quality of life are searching for hope in Stem Cell therapy. The unfortunate reality is that many of these “therapies” are not only ineffective but potentially harmful and the clinics that distribute them are not always properly certified. While stem cell therapies are promising, run away hope for a miracle cure coupled with unethical advertising and untested procedures have caused patients in the United States and beyond to be harmed by a potentially life saving tool. Here we will examine the current state of stem cell investigation, treatment, US Regulation, prospects in the future of medicine, and information for consumers to consider in deciding to receive a stem cell treatment.
Stem cells are undifferentiated cells that are at the start of all cell lines. Embryonic stem cells come from the blastocyst, a small clump of cells that forms several days after conception, and are pluripotent, meaning that they can give rise to any cell type (except specific embryonic tissues not present out of utero). [1] While these are the most often referred to type of stem cells there are also multipotent stem cells that can only give rise to a specific kind of tissue and are present into adulthood. Somatic cells, or differentiated cells, can be reverted to a pluripotent state. Induced pluripotent stem cells (IPS) are a growing area of interest in the field as they carry with them the possibility of culturing tissues for transplant using the existing cells of a patient thus eliminating the possibility of rejection.[2]
IPS exemplify an unfortunate reality in the whole of stem cell research, that at present widespread stem cell therapies are not ready for the general public. While these cells have great potential, a major hurdle is the cost in both time and labor required to culture them in a safe and sterile environment. A single vial of research grade cells that will produce fewer than thirty colonies in five days under ideal circumstances can cost over 1,000 dollars. This does not include the cost of facilities, culture equipment, and labor making these therapies cost prohibitive as the resulting therapy can run as far as 10,000 dollars per treatment. [3&4] Furthermore, colonies of cells are far from fully developed tissues that could potentially be implanted. A patient in critical condition in need of a transplant likely cannot wait for the cells to grow into tissue in culture, even if they can afford it.
Difficulties in access however are not the greatest barrier to stem cell therapy, but rather the lack of widespread testing and approval for the treatment of the diverse conditions for which they are sometimes advertised. While these cells are promising for usage in widespread areas of medicine, at present they do not live up to the claims that many unscrupulous clinics make for them. US Stem Cell Clinic, with a sleek website, and moving testimonials, advertises the use of stem cells as a magical cure that make the old feel young again using stem cells to treat a host of orthopedic maladies. These claims are highly suspicious as the FDA website says, as of January 2019, that only stem cell therapies for blood disorders are approved. [5]
These cells have been proclaimed cure-alls and medical miracles by the mass media but the reality is that the research into the application of stem cells for diverse ailments in humans is not conclusive at the present moment. [5] The FDA only approves stem cell treatments for blood disorders using stem cells from umbilical cord blood or bone marrow, but many clinics are offering stem cell treatments for everything from vision problems to COPD. The FDA recently filed two complaints against US Stem Cell Clinic LLC in Florida and California Stem Cell Treatment Inc. for marketing stem cell products that do not have the proper approval and for having unsafe manufacturing conditions that compromised sterility and patient safety. Patients filed lawsuits against California based stem cell supplier Liveyon who sold umbilical cord stem cells contaminated with E. Coli that resulted in sepsis and several patient hospitalizations after the stem cells were used for unapproved treatments. [6] In a recent lawsuit Florida based US Stem Cell was ordered to cease and desist, destroy all stem cells in their possession and pay for twice annual facilities inspections after taking cells from fat and injecting them into the eyes of patients causing five women to be blinded. In a 2018 statement FDA Commissioner Scott Gottlieb, M.D. said “We support sound, scientific research and regulation of cell-based regenerative medicine, and the FDA has advanced a comprehensive policy framework to promote the approval of regenerative medicine products. But at the same time, the FDA will continue to take enforcement actions against clinics that abuse the trust of patients and endanger their health” [7] The FDA, has in the past been accused of slowing down progress with novel treatments, but in the case of stem cells it is apparent that their actions hold patient safety as first priority, protecting the public from doctors and companies that value monetization over public health.
Patients in the United States have been harmed by these clinics including adverse injection site reactions, migration of cells to the improper location, the failure of cells to work in the desired way, and even the growth of tumors. Clinics that operate these studies may even be operating criminally as the FDA has pressed charges against these clinics in the past in the form of permanent injunction, an order to cease and desist permanently. [7]
Patients are often motivated to take these risky treatments because there is no other hope for a cure, however, unapproved treatments can make the condition worse or even lead to death. The dangers of receiving unapproved therapies is illustrated in the case of a 38-year-old man, who developed a spinal tumor after a stem cell treatment in preformed in Portugal where doctors injected cells taken from his nose into his spine. The treatment was attempting to cure paralysis in his legs and arms. It had no effect on his paralysis, but twelve years later the tumor that formed further limited his mobility and quality of life as his bladder control and motor function in arms steadily declined. Complications have been even more dire as a thirteen-year-old male in Israel who was treated at a clinic in Moscow for Ataxia telangiectasia, which affects the nervous system, died of a tumor that arose from donor cells. These are not isolated instances of unsuccessful treatment in patients that were already ill, the stem cells themselves were directly the cause of degeneration in the patients, and more than 19 deaths confirmed by the National Institute of Health as of 2018. [8&9]
Predatory clinics that perform these unapproved procedures can be especially hard to identify. Many have sleek well-designed websites with official looking personnel and lofty claims of unrealistic success rates and propositions for stem cells as cures for many diverse and at times totally unrelated disorders. Many clinics are located in Florida and Southern California however there are hundreds of clinics across the United States. [10]*** Patients should be advised to do some research into these claims and check to see if the clinic in question as well as the treatment has FDA approval. A good strategy for determining the legitimacy of a clinic is to do research on the main doctors performing the procedure. If a clinic is claiming to be able to cure numerous unrelated and debilitating disorders, the doctors performing these procedures should be of high esteem in the community and have visible external measures to the importance of their work or the prestige of their practice. If this is not the case the patient should proceed with great caution.
The issue of deceptive stem cell clinics is not a mere issue of public health but an example of a greater problem, a break between scientific community and the public perpetuated by a few unscrupulous characters for the sake of profit. Stem cells have the potential to be life saving tools and usher in a whole new chapter of regenerative medicine, but if the reputation of this technology continues to be tarnished by clinics that do not abide by the laws and conventions put in place to keep consumers safe, this technology may never get an opportunity to reach its full potential.While stem cells have great potential for diverse treatments at some point in the future, at present their efficacy and safety for regenerative medicine has not been firmly established in the context of current technology. Not all stem cell treatments are to be feared, stem cell treatments for some blood disorders have been shown to be effective and safe. At some point in the future when culture and delivery techniques improve stem cells could revolutionize transplant and regenerative medicine. At present the best course of action for consumers in regard to these therapies is to partake only in treatments or clinical trials operating with the approval of the FDA, and keep up with developments in the field by reading peer reviewed papers published in reputable journals. Exercise great caution but do not lose hope for the future. Stay current with research and, considering the risks and benefits, consumers may choose to enroll in FDA supervised clinical trials that adhere to the three phase clinical trial process, but always be sure to exclusively receive treatment from FDA regulated and approved clinicians.
Sources
- Yu, Junying, and James Thomson. “Embryonic Stem Cells.”National Institutes of Health, U.S. Department of Health and Human Services, 2016, stemcells.nih.gov/info/Regenerative_Medicine/2006Chapter1.htm.
- “Home.” A Closer Look at Stem Cells, www.closerlookatstemcells.org/learn-about-stem-cells/types-of-stem-cells/.
- McCormack, Kevin. “Patients Beware: Warnings about Shady Clinics and Suspect Treatments.” The Stem Cellar, CRIM, 19 Jan. 2016, blog.cirm.ca.gov/2016/01/19/patients-beware-warnings-about-shady-clinics-and-suspect- treatments/.
- https://www.atcc.org/search?title=Human%20IPS%20(Pluripotent)#q=%40productline%3DL035&sort=relevancy&f:contentTypeFacetATCC=[Products]
- Office of the Commissioner. “Consumer Updates – FDA Warns About Stem Cell Therapies.” U S Food and DrugAdministration Home Page, Center for Drug Evaluation and Research, 16 Nov. 2016, www.fda.gov/ForConsumers/ConsumerUpdates/ucm286155.htm.
- William Wan, Laurie McGinley. “’Miraculous’ Stem Cell Therapy Has Sickened People in Five States.” The Washington Post, WP Company, 27 Feb. 2019, www.washingtonpost.com/national/health-science/miraculous-stem-cell-therapy-has-sickened-people-in-five-states/2019/02/26/c04b23a4-3539-11e9-854a-7a14d7fec96a_story.html.
- Commissioner, Office of the. “FDA Seeks Permanent Injunctions against Two Stem Cell Clinics.” U.S. Food and Drug Administration, FDA, 9 May 2018, www.fda.gov/news-events/press-announcements/fda-seeks-permanent-injunctions-against-two-stem-cell-clinics.
- Bauer, Gerhard, et al. “Concise Review: A Comprehensive Analysis of Reported Adverse Events in Patients Receiving Unproven Stem Cell-Based Interventions.” Stem Cells Translational Medicine, John Wiley & Sons, Inc., Sept. 2018, www.ncbi.nlm.nih.gov/pmc/articles/PMC6127222/#!po=19.4444.
- Flaherty, Brittany, et al. “Case Highlights the Risks of Experimental Stem Cell Therapy.” STAT, Staten News, 11 July 2019, www.statnews.com/2019/07/11/canada-case-long-term-risks-experimental-stem-cell-therapy/.
- https://usstemcellclinic.com/ [10]
- Commissioner, Office of the. “Step 3: Clinical Research.” U.S. Food and Drug Administration, FDA , 4 Jan. 2018, www.fda.gov/patients/drug-development-process/step-3-clinical-research.
- Hiltznik, Micheal. “Column: Judge Throws the Book at a Clinic Offering Unproven Stem Cell ‘Treatments’.” Los Angeles Times, Los Angeles Times, 26 June 2019, www.latimes.com/business/hiltzik/la-fi-hiltzik-stem-cell-injunction-20190626-story.html.
Potential Need for a New Mobile Medical Clinic to Provide ACE-Related Care to the Sacramento County for At-Risk Pediatric Populations
By Tara Allison, Biochemistry and Molecular Biology and Spanish ‘20
Author’s Note: I wrote this document as a UWP 102B assignment to evaluate the societal health care needs of Sacramento County, focusing on an upsetting mental health phenomenon, Adverse Childhood Events (ACEs). This review encompasses an in-depth analysis that illuminates the biological basis of ACEs and their connection to chronic health conditions in adulthood. This review further analyzes several Community Needs Assessments to ascertain that existing health care institutions do not, in fact, provide the proper focus or volume of mental health and ACE-related treatment needed for Sacramento County. The multidisciplinary nature of this paper connects scientific data that suggest a widespread health problem to an effective solution that UC Davis can adopt as a university. My on-campus organization R.I.V.E.R. (Recognizing Illnesses Very Early and Responding) is making progress towards development of this solution, a mobile pediatric ACE clinic.
1. Introduction
This review explores the potential benefits of developing a new mobile pediatric medical clinic that serves the northwest region of Sacramento County through Adverse Childhood Events (ACEs) related care. First, this review provides evidence of the community health needs in Sacramento County, discussed in three sections: what patients need, what currently exists for them, and what they need that is not currently offered. Second, this review examines the correlation between ACEs and future chronic health issues. And finally, this review proposes a solution based on successful existing mobile clinic models and associated limitations. For the studies included in this review, various criteria and characteristics were considered or excluded to achieve an accurate assessment of the ACE-related risk experienced by individuals in Sacramento and Palo Alto. Individuals not primarily living in these specified regions were excluded from these studies.
2. Community Health Needs In Sacramento County
2.a. What Patients Need
The northwest region of Sacramento specifically needs health care services for ACEs and primary care needs despite location and public transportation barriers and access to medical care regardless of insurance status. According to Table 5 of the 2019 Community Health Needs Assessment of Sacramento County, the northwest region of Sacramento lacks many types of health care services. Specifically, this area needs additional mental and behavioral health care services, access to quality primary care, and resources for active living and healthy eating. Additional factors contributing to an underwhelming health care sufficiency are lack of safe and violence-free environments, deficiency of functional mechanisms such as public transportation, reduced services for injury and disease prevention management, and shortage of overall cultural competency [1]. This table also explicitly highlights that youth populations need more mental health and ACE services. For the remainder of this piece, ACE-care can be considered a “mental, behavioral, and substance-abuse” service as indicated by the table.
According to Table 20 of the 2019 Community Health Needs Assessment of Sacramento County, Sacramento County has higher rates of children in poverty and children with single parents than the California averages. The median household income is comparatively lower than the California average, and there is a higher rate of violent crimes and homicides in Sacramento than in California as well [1].
The 2016 Sacramento County Community Needs Assessment establishes that medically underserved areas are localized around several different zip codes in the Sacramento area. Within these regions, pediatric emergency department admission rates are 50 percent higher than county rates due to substance abuse, mental health issues, and asthma [2]. Among the zip codes listed, 95815 and 95841 appear again in the 2019 UCD Community Needs Health Assessment, indicating that from 2016 to 2019 the same regions were consistently in need of improved health care services. This suggests that existing health care organizations are not sufficiently serving these communities.
Table 19 of the 2019 UCD Community Needs Health Assessment indicates varying amounts of clinical care providers in Sacramento County compared to the California average. It reports that portions of Sacramento are in a health professional shortage area (HPSA) for primary care and are generally considered medically underserved. However, the number of mental health providers, psychiatry providers, and primary care physicians is above the ratio for California overall. This may suggest that the location of these providers is potentially inequitable, creating a disparity across various regions of Sacramento by unevenly distributing providers. This disparity is demonstrated by the northwest Sacramento region, which lacks adequate mental health and primary care provisions.
2.b. What Exists Currently
Interestingly, although Sacramento does not lack health care professionals for mental health services compared to the average California benchmark, quality of life indicates that Sacramento residents experience poorer mental and physical health than the average California resident. This suggests that distribution of such health care professionals is inadequate and that care is not being provided to enough regions. The 2019 UCD Community Needs Health Assessment demonstrates this very clearly with data describing existing health organizations. Sacramento County contains 281 existing health care organizations that provide a variety of services. Out of those 281 organizations, only 96 institutions, or 34 percent of them, provide access to mental, behavioral, or substance abuse services. Only 73 of 281 institutions, or 26 percent, provide access to quality primary care services. And only 81 of 281 institutions, or 29 percent, provide access to active living and healthy eating resources [1]. These institutions are distributed across all of Sacramento County, so the actual health care accessibility of specific communities varies. Thus, even though existing organizations are present in Sacramento to provide these services, they are not equitably distributed across the county or provided in a high enough volume to meet expansive geographical demands.
As indicated by Table 5 of the 2019 Community Health Needs Assessment of Sacramento County, additional factors such as quality of public transportation and safety of neighborhoods may also influence patient accessibility to health care [1]. Poorly developed public transportation and frequent crimes may create an environment that encourages potential patients to stay at home, even if they reside nearby a clinic or hospital. Thus, violent environments and reduced transportation combined with inequitably-distributed health care services equate to unmet health care demands. This data indicates that Sacramento may not be well-equipped to address its various medical needs across the county.
It might make sense to conclude that any region containing a higher concentration of health care institutions for mental health should have adequate health care coverage in this category. However, this is not a completely valid assumption. The 2019 UCD Community Needs Health Assessment reports surprising contrasts within particular zip codes. It demonstrates that some areas contain plenty of clinics that provide mental health, behavioral, and substance abuse services, yet these areas are still indicated as regions that are in significant need of those services. For example, within the zip code 95823, 8 of 21 health care institutions provide mental health services in that area. However, according to the 2019 UCD Community Needs Health Assessment, the zip code 95823 resides in a region that still lacks adequate mental health services [1]. Despite that almost half of the health care organizations within 95823 provide mental health services, there is still a demonstrated need for higher volume of service or improved focus on mental health care within community clinics. This data further demonstrates that existing health care organizations are not meeting patients’ needs and could suggest that existing clinics do not provide the correct types of services or adequate volume of care required for the community.
2.c. What is Lacking
There are three primary issues that the northwest region of Sacramento is experiencing. These include health care insurance denial from current providers, location and public transportation barriers to attain proper health care, and lack of primary care access and ACE-related care.
Despite the various health organizations available, the northwest portion of Sacramento still has three unaddressed significant health care needs. In order to address all three issues, a proposal to develop a new pediatric mobile clinic should be considered. To address insurance barriers, the new clinic will provide free services to all patients regardless of insurance status. To address location challenges, the clinic will function in a large mobile vehicle equipped for medical care providers. Not only can new patient locations be reached, but multiple regions can be served by this clinic. And finally, the mobile clinic will provide services to address primary care and ACE-related care needs.
3. Correlation Between Adverse Childhood Events and Chronic Mental, Behavioral, and Physical Health Issues
The Center for Disease Control and Prevention defines ACEs as mentally and emotionally traumatic experiences that affect adolescents before the age of 18. These traumatic experiences can exist in many forms. Some examples include growing up in a household with family members who abuse substances, have mental health problems, are incarcerated, or divorced. Such experiences can undermine children’s sense of stability and safety while simultaneously interfering with their ability to bond with family or friends [3]. Many years of seminal research in this topic demonstrate a myriad of connections between ACEs and chronic health conditions, unsafe health behaviors, and premature death. This discussion will utilize research older than two years ago that is foundational to these health correlations.
3.a. Chronic Health Issues
Chronic health conditions such as autoimmune disease, cancer, chronic obstructive pulmonary disease (COPD), frequent headaches, ischemic heart disease (IHD), prescription drug usage, and liver disease have been proven to result from individuals plagued by ACE-related trauma [4, 5, 6, 7, 8, 9]. Dube and colleagues demonstrate that traumatic events during adolescence correlate with an increased probability of autoimmune disease hospitalization during adulthood [4]. In addition, Ports et al. establish a strong correlation between ACEs and exposure to modifiable cancer risks such as alcohol, chronic inflammation, obesity, UV radiation, and environmental carcinogens. Additionally, this study suggests that addressing ACEs may induce early cancer prevention [5]. Cunningham and colleagues study the correlation between COPD and ACEs such as verbal and sexual abuse, parental separation or divorce, observation of substance-abusing family members, and domestic violence. Their results indicated a higher chance of developing COPD if one or more of these ACEs were experienced in women specifically [6]. Another study by Anda and colleagues studied the relationship between the prevalence of headaches and migraines and the presence of ACEs. The results indicated that, in adulthood, there was a higher frequency of headaches or migraines if the subject had a higher ACE risk score. Subjects with lower or nonexistent ACE risk scores experienced far fewer headaches [7]. Additionally, a study completed by Dong and colleagues illuminates the connection between several types of ACEs and development of IHD. Their results demonstrate a 1.3 to 1.7 fold increase in the chance of developing IHD for patients experiencing more ACEs in comparison to those with a low ACE risk score [8]. In a different study, Dong and colleagues examine correlation of ACEs to risky behaviors that manifest later in life as liver disease. ACEs increased the likelihood of liver disease development by 1.2 to 1.6 times [9]. Beyond chronic health issues, ACEs have been shown to be related to other problems in adulthood such as unsafe health behaviors.
3.b. Unsafe Health Behaviors
Unsafe health behaviors such as alcohol abuse, drug use, obesity, sexual risk behavior, and smoking are health outcomes of ACEs as well [10, 11, 12, 13, 14]. Strine et al. establishes direct correlations between alcohol abuse and ACE-related experiences such as sexual abuse, childhood neglect and emotional abuse, family drug abuse or mental illnesses, and parental divorce. They claim that psychological distress associated with ACEs results in alcohol abuse later in life [10]. Furthermore, Anda and colleagues discovered a 40 percent increase in prescription drug usage in patients with non-zero ACE scores and a positive correlation between a higher ACE risk score and prescriptions across all age groups (18-44, 45-64, and 65-89 years of age) [11]. In another study, Williamson and colleagues identified a correlation between physical and verbal abuse and increased body weight and obesity measurements. Participants that experienced “being hit” were 4.0 kg heavier on average than participants that did not report physical abuse [12]. Additionally, Hillis et al. evaluated the connection between sexual risk behavior and ACE events and discovered a positive correlation between the two as well [13]. Strine and colleagues, in a different study, observed increased risk of smoking habits in women when ACE risk scores are present as well [14]. ACEs have been shown to relate to reduced lifespans as well.
3.c. Premature Death
ACEs correlate with suicide and depression in adulthood, leading to premature death in adulthood [15, 16]. According to Dube and colleagues, suicide rates increased two to five fold in adulthood due to connections regarding ACEs. Factors such as alcoholism and illicit drug use had close ties to the presence of ACEs and path to suicide attempt [15]. Additionally, Chapman et al. established a connection between a higher number of ACE-related events and a greater chance of developing a depressive disorder. The study also suggests that early recognition of childhood trauma may prevent future depression diagnosis [16]. This extensive, yet not exhaustive, collection of studies indicates that ACEs have a very real impact on pediatric mental health and adult health status later in life. In order to address the lack of mental health provision in Sacramento, the proposal to develop a new pediatric mobile clinic specializing in ACE-care and primary care services should be considered.
4. Proposed Solution and Limitations
The northwest region of Sacramento has three primary concerns: health care insurance denial from current providers, location and public transportation barriers to attain proper health care, and lack of primary care access and ACE-related care. In order to address these issues, this paper proposes the implementation of a new mobile medical pediatric clinic. The clinic will provide ACE-related care and primary care services for chronic and acute illnesses. It will mitigate health care insurance barriers by serving uninsured and partially insured residents of Sacramento County as well. Furthermore, the clinic will serve patients in a 26-foot vehicle equipped with two medical examination rooms and ample supplies. In this way, residents can access medical care despite any location or public transportation challenges. As a vehicular clinic, mobility ensures access to multiple communities in Sacramento.
The primary barriers to implementing this mobile clinic include shortage of staffing availability along with annual financial demands. These are not issues unique to a mobile or pediatric ACE-care clinic, so our proposal can model existing clinics to realistically overcome these barriers. First, UC Davis student-run clinics are excellent models to consider. Financially, a volunteer-based operations system will ensure low-cost annual expenditures. Furthermore, grant writing, fundraising, and donor support are effective funding methods these successful clinics utilize as well. Staffing availability can be mitigated by way of a reduced, yet consistent, weekend operations schedule. As physicians may not be available during weekdays due to employment commitments, weekends are an ideal time to volunteer.
We can observe many similarities between this mobile, ACE-care, pediatric clinic proposal and other vehicular clinic models. Existing mobile medical clinics provide similar services in other cities and provide excellent examples to base this proposal on. One especially successful case is the Stanford Teen Van, a mobile medical clinic that primarily serves youth in the Bay Area. The table below from the 2019 Stanford Community Health Needs Assessment indicates that this clinic provides ACE-related care in the form of mental health services in addition to primary care. Furthermore, this establishment has successfully provided improved access for 2,892 individuals that otherwise would experience location-based barriers [17].
The Stanford Teen Van also provides its services and medications for free, thus eliminating any insurance-based discrimination. This model is an excellent comparison to study because this clinic provides identical services to a similarly underserved population in the Bay Area. The Stanford Teen Van, alongside the UC Davis student-run clinics, are phenomenal infrastructures to learn from by way of mobility, service provision, and volunteerism. By analyzing successful practices, this proposal overcomes limitations and provides effective solutions based on existing infrastructures, resulting in a refined and well-rounded project concept.
5. Conclusion
This review discussed the potential benefits of developing a new mobile pediatric medical clinic that would serve the northwest region of Sacramento County. First, this review demonstrated extensive evidence of the community health needs in Sacramento. Second, this review examined the correlation between ACEs and future chronic health issues. Finally, this review discussed a proposed solution following successful existing mobile clinic models and associated limitations. When considering the data holistically, it is clear that a new pediatric mobile clinic would significantly benefit deserving patients in Sacramento. Furthermore, despite the fact that this mobile clinic proposal is built on well-established practices and successful existing infrastructure, this specific combination of ideas has not yet been implemented in Sacramento. While maintaining its merit and validity, this innovative project challenges the existing medical culture of Sacramento by introducing ACE awareness and the expansive versatility of a mobile clinic vehicle.
References
- Ainsworth D, Diaz H, Schmidtlein M, Van T, 2019 Community Health Needs Assessment. 2019 CHNA of Sacramento County 2019. 2019; 1-116.
- Wagner J, Rosenbaum A, Schmidtlein M, Underwood S. Sacramento County Community Health Needs Assessment. Sacramento County CHNA. 2016; 1-40.
- Felitti VJ, Anda RF, Nordenberg D, Williamson DF, Spitz AM, Edwards V, Koss MP, Marks JS. Relationship of Childhood Abuse and Household Dysfunction to Many of the Leading Causes of Death in Adults. American Journal of Preventive Medicine. 1998; Vol 14, Issue 4, 245-258.
- Dube SR, Fairweather D, Pearson WS, Felitti VJ, Anda RF, Croft JB. Cumulative childhood stress and autoimmune disease. Psychol Med. 2009; 71:243–250.
- Ports KA, Holman DM, Guinn A, Pampati S, Dyer K, Merrick MT, Buchanan N, & Metzler M. Association between Adverse Childhood Experiences and Leading Risk Factors for Cancer in Adulthood. Journal of Pediatric Nursing. 2019; 44, 81-96.
- Cunningham TJ, Ford ES, Croft JB, Merrick MT, Rolle IV, Giles WH. Sex-specific relationships between adverse childhood experiences and chronic obstructive pulmonary disease in five states. 2014; 9:1033-42.
- Anda R, Tietjen G, Schulman E, Felitti V, Croft J. Adverse childhood experiences and frequent headaches in adults. Headache. 2010; 50(9):1473-81.
- Dong M, Giles WH, Felitti VJ, Dube, SR, Williams JE, Chapman DP, Anda RF. Insights into causal pathways for ischemic heart disease: adverse childhood experiences study. Circulation. 2004; 110:1761–1766.
- Dong M, Anda RF, Dube SR, Felitti VJ, Giles WH. Adverse childhood experiences and self-reported liver disease: new insights into a causal pathway. Arch Intern Med. 2003; 163:1949–1956.
- Strine TW, Dube SR, Edwards VJ, Prehn AW, Rasmussen S, Wagenfeld M, Dhingra S, Croft JB. Associations between adverse childhood experiences, psychological distress, and adult alcohol problems. Am J Health Behav. 2012; 36(3):408-23.
- Anda RF, Brown DW, Felitti VJ, Dube SR, Giles WH. Adverse childhood experiences and prescription drug use in a cohort study of adult HMO patients. BMC Public Health. 2008; 4; 8:198.
- Williamson DF, Thompson, TJ, Anda, RF, Dietz WH, Felitti VJ. Body weight, obesity, and self-reported abuse in childhood. International Journal of Obesity. 2002; 26:1075–1082.
- Hillis SD, Anda RF, Felitti VJ, Marchbanks PA. Adverse childhood experiences and sexual risk behaviors in women: a retrospective cohort study. Fam Plann Perspect. 2001; 33:206–211.
- Strine TW, Edwards VK, Dube SR, Wagenfeld M, Dhingra S, Prehn AW, Rasmussen S, Mcknight-Eily L, Croft JB. The mediating sex-specific effect of psychological distress on the relationship between adverse childhood experiences and current smoking among adults. Subst Abuse Treat Prev Policy. 2012; 7:30.
- Dube SR, Anda RF, Felitti VJ, Chapman D, Williamson DF, Giles WH. Childhood abuse, household dysfunction and the risk of attempted suicide throughout thelife span: Findings from Adverse Childhood Experiences Study. JAMA. 2001; 286:3089–3096.
- Chapman DP, Anda RF, Felitti VJ, Dube SR, Edwards VJ, Whitfield CL. Adverse childhood experiences and the risk of depressive disorders in adulthood. J Affect Disord. 2004; 82:217–225.
- Espino M, Stelle J. 2019 Community Health Needs Assessment. 2019 Stanford Community Health Needs Assessment. 2019; 1-52.
Gene editing invasive species out of New Zealand
By Jessie Lau, Biochemistry and Molecular Biology ‘20
Authors Note: Since the advent of Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR Associated Protein 9 (CRISPR/Cas9) discovery and biotechnological breakthroughs thereafter, this revolutionary application has been primarily focused on human health, particularly fostering solutions to numerous debilitating ailments. However, the general public has offered little attention towards the use of this engineering feat in a broader ecological system. Upon watching the new Netflix original Unnatural Selection, discussion of considering the use of CRISPR/Cas9 in New Zealand’s effort to completely eradicate invasive species piqued my interest. The following article is an exploration of CRISPR/Cas9 prospect into New Zealand’s bold environmental pursuit and its potential ecological impact.
Abstract
Since it has become feasible to cross oceans to reach unforeseeable land masses, invasive alien species (IAS) are an increasing threat to international biodiversity. Moreover, no other region faces as great of a peril as New Zealand (NZ), which holds the record as the nation with the highest survival rate of threatened avifauna (birds of a particular region) species [5]. In 2012, New Zealand physicist Sir Paul Callaghan introduced a large-scale eradication program to permanently remove eight invasive mammalian predators (rodents: Rattus rattus, Rattus norvegicus, Rattus exulans, Mus musculus; mustelids: Mustela furo, Mustela erminea, Mustela nivalis; and the common brushtail possum: Trichosurus vulpecula) [5]. Four years after this grand proposal, the NZ government committed to a national challenge titled “Predator Free 2050” (PF 2050) to pursue this audacious goal.
Introduction
Approximately 85 million years ago, NZ was one of the first landmasses to split from the supercontinent Gondwana and as it shifted away, it did not carry mammals until bats flew and aquatic species swam to this island. [7]. With the introduction of rodent species initially through Polynesian settlement some 750 years ago and thereafter European seafaring ventures, the endemic species of NZ have been left vulnerable to novel predators. Consequently, at least 51 native bird species that have evolved adaptive skills of remaining close to the ground have been unsuccessful at surviving alongside these rodent predator species [4]. These invasive omnivorous rodents prey on birds, eggs, seeds, snails, lizards, and fruits. As a result, their varied diets prompt competition with the native fauna, further placing pressure on their vulnerable survival [7]. Despite CRISPR/Cas9 modifications offering the greatest potential in gene drive to eliminate these unwanted predators, several techniques implemented to control these invasive populations, such as pesticides, trapping innovations, and biological factors have given favorable results.
Past Successes and Future Endeavors
For decades, the NZ government has pursued eradication initiatives to permanently eliminate foreign invasive species on small local islands. Through concerted efforts, several of these projects have proven successful in the restoration of the natural biodiversity this island nation boasts.
In June of 2009, the NZ Department of Conservation (DOC) undertook a multi-action plan to simultaneously eradicate rodent, rabbit, stout, hedgehog, and cat species in Rangitoto and Motutapu islands. After three years of aerial dispersion of anticoagulant Pestoff 20RTM combined with trapping and indicator dogs, the island witnessed total elimination of the islands’ stoats and four rodent species; declination of rabbit and hedgehog population by 96%; and over 50% reduction in cats [7].
Despite these successful feats, the invasive species fecundity and ability to adapt to these challenges still present an overwhelming challenge to reach the goal of complete eradication. Recently, more direct approaches delving into novel genetic inheritance techniques have been explored to serve as a potential permanent solution. Termed the“Trojan Female Technique” (TFT), the method makes use of the correlation of sperm fitness dependence on the abundance of mitochondrial DNA (mtDNA) [2]. Healthy sperm is dependent on sufficient mitochondrial level for energy production to manage motility and fertilization. For example, experiments conducted on Drosophila melanogaster supports the causation of reduced spermatogenesis and sperm maturation due to induced mutations in cytochrome mitochondrial gene [9]. Contrasting female eggs, the asymmetric greater dependence of sperm on mtDNA for normal functionality results in only male populations to be the sole source of target. Induction of mitochondrial mutations in females to compromise total sperm viability in future male progenies will serve as an effective control to population growth.
Although seemingly promising, TFT is not guaranteed to completely eradicate propagation for several reasons. For starters, males with impaired fertility can still provide sufficient sperm count to fertilize eggs on a population-based scale. Furthermore, in circumstances where females do receive nonviable sperm count, they can still seek adequate functioning sperm through matings with other males. On a larger scale, should the mutation pervade, selection pressures could still inadvertently choose for nuclear modifications to make up for the mitochondrial defects [2]. These flaws raise the need for more pervasive and permanent resolutions.
Daisy Chain CRISPR Gene Drive
The recent biochemical breakthrough underpinning the ability to effectively and precisely modify genes with CRISPR/Cas9 has allowed for potential biotechnology to boom in the realm of ecology. The simple generation of a short RNA sequence into a virus or bacterium to serve as a vector, guides the cutting mechanism of Cas9 to specific regions in the genome to be excised, prompting for these double stranded breaks to be fixed through DNA repair mechanisms. While these fixtures can potentially repair the gene, it can also raise the possibility for the gene to be disabled, introduce a new function, or create an unforeseen mutation. Given the right specific targeting in the germ line, this approach houses the innovation for exterminating entire species through gene drive [6].
The mechanism behind gene drive overthrows the traditional Mendelian sexual reproduction concept of proportional contribution from both the male and female parent. The power comes from the ability of one genetically modified (GM) contributor encoding for the ‘gene drive’ to cut the other set of chromosomes lacking these genes and replace this excision with a self-replicating copy. In effect, this divisive modification would push for an otherwise heterozygous offspring from a wild-type mating with a GM partner to become homozygous for certain genes to be carried on and propagated by future generations. Given that these genetic alterations do not affect the fitness of the organism, dissemination of 1% of the population with CRISPR modified genes can lead to 99% of the local population carrying the genetic indicator in as little as nine generations (The use of gene editing to create gene drives for pest control in New Zealand).
Such a unilateral approach poses political and ethical challenges amongst neighboring nations with diverging ecological approaches to confront pest control. Should this pervasive gene drive program reach beyond its intended border, great difficulty would arise in maintaining this ecological enclosure. For example, possum is on the list of invasive species in NZ while just 2,500 miles west, its neighbor Australia keeps this species of marsupials under protection. As such, scientists have devised a simple model to localize gene alterations, coined The Daisy Chain.
Unlike the original gene drive method in which all components necessary for transformation (CRISPR, edited DNA, and guide RNAs) are provided on the same chromosome, Daisy Chain provides a self-exhaustive means of guaranteeing genetic edits. This tool is designed so that each component required for genetic alteration is dependent on the presence of a different element upstream on the gene found on the same locus to be activated [8]. The most downstream portion of this chain contains the “load” of engineered dominant lethal genes preventing reproduction, which will be promoted to higher frequency in the population within several generations. For instance, should an engineered allele contain three elements A, B, and C, element C would render element B to drive, which will in turn cause element A carrying the final load to drive. The initial element (C in this case) does not actually drive, thus is restricted by the number of altered individuals released into the wild and will be lost via natural selection over time. During initial implementation, the presence of C will increase B in abundance, but B will eventually decline and finally disappear as C is lost in the population. The rapid rise in abundance of B will also cause A to increase in frequency within the local population; however, with the decrease of B, A would not be driven and will ultimately vanish as well [1]. Using MIT Professor Esvelt’s analogy, “… the elements of a daisy drive system are similar to booster stages of a genetic rocket: those at the bottom of the base of the daisy-chain help life the payload until they run out of fuel and are successively lost.”
Challenges with Daisy Chain CRISPR Gene Drive
CRISPR/Cas9 technology’s ability to potentially alter these invasive species’ fecundity provides an avenue of pursuing NZ’s goal of PF 2050. Despite the developed understanding of how to carry out this plan, scientists in NZ are still working to piece together the genomes of stoats and possums in order to understand where to properly facilitate the engineered RNA sequence. Other barriers that must be acknowledged are the unprecedented approach to genetically modify marsupials and the difficulty of implanting hundreds to thousands of oocytes to be dispersed amongst their population.
Beyond these known difficulties, scientists still tread in unknown terrains pertaining to whether these mutations can have pernicious effects in the survival, health, and reproductive success in propagating these mutations within their populations. Further exploration into the development of these modifications, and the potential impacts they can have on these animals, must be investigated on model organisms prior to widespread use.
Of the eight listed mammalian species vied to be permanently eradicated from NZ, Mus musculus holds the most promise, given the extensive knowledge of the Mus musculus genome. With the help of scientists outside of New Zealand, joining in on the efforts to identify which germline gene to focus on, this project has received international attention.
Although the daisy drive provides promising potential, research collaborators at MIT and Harvard have identified a possible risk of, “… DNA encoding a drive component from one element to another, thereby creating a ‘daisy necklace’ capable of a global drive” [1]. Due to this rare recombinatory event arising from the similarity of DNA sequences, these investigators have looked into circumventing the problem by creating numerous alternatives to CRISPR components and selecting the model with the greatest diversity.
Conclusion
From their renowned aviary to reptilian species, New Zealand’s islandic geographical region houses some of the most biodiverse fauna known to man. The arrival of human settlement has introduced predatory species, causing endemic species to experience extinction at concerning rates [4]. With the purpose of preserving their unique remaining diversity, New Zealand has committed to concerted efforts of varying methods to eradicate these invasive vertebrate pests. Investigation into genetic modifications can provide for more expansive and thorough techniques to eliminate these human introduced pests and allow for these endangered species to thrive once again. By further exploring daisy chain CRISPR/Cas9, this effort can be genetically inherited by offspring, allowing for nature to carry out this effort. As opposed to continued efforts of targeting each individual one by one, conservation ecologists can borrow from molecular biologist’s toolkit to revolutionize the means of pursuing pest control and perhaps even pave the road for future endeavors with similar pursuits.
References
- Esvelt, Kevin M. “Daisy Drives.” Sculpting Evolution, www.sculptingevolution.org/daisydrives.
- Gemmell, Neil J., et al. “The Trojan Female Technique: a Novel, Effective and Humane Approach for Pest Population Control.” Proceedings of the Royal Society B: Biological Sciences, vol. 280, no. 1773, 2013, pp. 1–6., doi:10.1098/rspb.2013.2549.
- Griffiths, Richard, et al. “Successful Eradication of Invasive Vertebrates on Rangitoto and Motutapu Islands, New Zealand.” Biological Invasions, vol. 17, no. 5, 2014, pp. 1355–1369., doi:10.1007/s10530-014-0798-7.
- Owens, Brian. “The Big Cull: Can New Zealand Pull off an Audacious Plan to Get Rid of Invasive Predators by 2050?” Nature, vol. 541, 12 Jan. 2017, pp. 148–150.
- Russell, James C., John G. Innes, Philip H. Brown, and Andrea E. Byrom. “Predator-Free New Zealand: Conservation Country.” BioScience 65, no. 5 (October 2015): 520–25. https://doi.org/10.1093/biosci/biv012.
- Saey, Tina Hesman. “Explainer: How CRISPR Works.” Science News for Students, 4 Dec. 2017, www.sciencenewsforstudents.org/article/explainer-how-crispr-works.
- “Why Predator Free 2050?” Department of Conservation. Accessed November 18, 2019. http://www.doc.govt.nz/nature/pests-and-threats/predator-free-2050/why-predator-free-2050/.
- Dearden, Peter K., et al. “The Potential for the Use of Gene Drives for Pest Control in New Zealand: a Perspective.” Journal of the Royal Society of New Zealand, vol. 48, no. 4, 2017, pp. 225–244., doi:10.1080/03036758.2017.1385030.
- Wolff, Jonci N., et al. “Mitonuclear Interactions, MtDNA-Mediated Thermal Plasticity and Implications for the Trojan Female Technique for Pest Control.” Scientific Reports, vol. 6, no. 1, 2016, doi:10.1038/srep30016.
- Min, John, Jason Olejarz, Joanna Buchthal, Alejandro Chavez, Andrea L. Smidler, Erika A. DeBenedictis, George M. Church, Martin A. Nowak, Kevin M. Esvelt, and Charleston Noble. “Daisy-Chain Gene Drives for the Alteration of Local Populations.” PNAS. National Academy of Sciences, April 23, 2019. https://www.pnas.org/content/116/17/8275.
A History of Vaccines and How they Combat Disease
By Vishwanath Prathikanti, Political Science ‘23
Author’s note: The anti-vaccination movement has recently gained traction with many families across the nation and I wanted to tackle the idea of anti-vaccination and where it came from. I also wanted to see if there was any credit due to the anti-vaccinators and see if there was any truth to the idea that more vaccinations might be bad.
In April 2019, public health officials declared a measles outbreak in Los Angeles. To many, this sounded almost absurd; measles was eradicated in the United States in 2000 [4]. The outbreak highlighted the severity of a movement that many had declared irrelevant: the anti-vaccination movement. In light of this event, many had to question: what is the anti-vaccination movement? When did it begin? Is there any truth to the movement?
To understand the anti-vaccination movement, one must first understand vaccines and their history. Centers for Disease Control and Prevention (CDC) defines a vaccination as, “a product that stimulates a person’s immune system to produce immunity to a specific disease, protecting the person from that disease.” [1]. The human immune system uses white blood cells to fight infections in the body; specifically, there are three types of white blood cells that work together to fight infections: macrophages, B-lymphocytes and T-lymphocytes [2]. When a cell becomes infected or dies, it releases a chemical that attracts macrophages, which will engulf and degrade the cell. If the cell was damaged or died due to a virus or bacteria, the macrophage will leave behind antigens, which are recognized by the immune system as harmful [10]. When the immune system recognizes the antigens, B-lymphocytes will produce antibodies to attack the antigens and T-lymphocytes will attack cells in the body that have been infected by the identified antigen. After the infection is dealt with, the immune system will create memory cells that act immediately if the body encounters the same germ again. Vaccines work by imitating an infection; they do not cause illness but they will stimulate the production of T-lymphocytes, B-lymphocytes and memory cells to fight the disease in the future. Most vaccines require multiple doses to ensure full immunity, and how frequent these dosages are required depends on the vaccine [2].
Our knowledge of vaccines has not always been as vast as it is today. Evidence suggests that the earliest form of inoculation was in China during the late 1600s when emperor K’ang Hsi had his children inoculated after surviving smallpox (the process involved grinding smallpox scabs and inhaling them) [5]. The practice of vaccination has grown considerably since then, becoming vastly popular in the West by the 17th century. In 1853, Britain passed a law that made it mandatory for citizens to receive a smallpox vaccination and in 1855, Massachusetts passed the first U.S. law mandating vaccination for smallpox, allowing vaccinations to grow and develop.
In the late 20th century, research on the negative effects of vaccines started to emerge. A 1995 study published in The Lancet linked the measles-mumps-rubella (MMR) vaccine with bowel disease. Wakefield, a gastroenterologist and researcher in the study, went on to further speculate that persistent infection with the vaccine caused disruption of the intestinal tissue that could lead to autism. This led to the study that would capture the attention of parents for decades to come. In 1998, Wakefield and his colleagues published a case series study in which, out of 12 children who had recently been administered their MMR vaccine, eight had the measles virus in their digestive system and were demonstrating symptoms for autism. Wakefield then went on to claim that the combined vaccination led to this, and advocated instead to adopt single-antigen vaccinations as opposed to combined MMR vaccines [3]. He did not, however, list how he came to this conclusion, saying “the combined measles, mumps, and rubella vaccine (rather than monovalent measles vaccine) has been implicated” [3].
The link between autism and the MMR vaccination was studied intensively over the next few years, and no reputable study ever found a similar link. Additionally, a study published in The Journal of Pediatrics, while acknowledging a slightly lower than average antibody count when the combined vaccination was employed, stated that there was no significant reason why single antigen vaccinations should be favored over combined vaccinations. The lower antibody count was deemed irrelevant in light of the fact that failure of the vaccine was extremely rare in fully immunized children [7]. In 2010, The Lancet formally retracted the paper, and three months later, Britain’s General Medical Council banned Wakefield from practicing medicine in Britain. Finally, in 2011, it was revealed that Wakefield had falsified most of his data; in his study, he reported eight children developed symptoms of autism when in reality, there were at most two cases. In addition, two of the children had developmental delays that were not mentioned in the final published work [3].
Despite the study being completely discredited by the scientific community, the damage to society had been done; after the Wakefield paper was published, vaccination rates dropped below 50 percent in some parts of London. Luckily, immunization rates drastically rose since then, with over 90 percent in the UK vaccinated in 2013, with BBC declaring a “universal recovery” [8]. Although vaccination rates are high, the US still faces about 60 cases of the measles every year, caused by international travelers who carry the disease [9]. While the spread of misinformation due to the Wakefield paper has mostly subsided, its legacy continues keeping a minority of children in the US unvaccinated and susceptible to antiquated and preventable diseases.
References
- Centers for Disease Control and Prevention “Immunization: the basics” https://www.cdc.gov/vaccines/vac-gen/imz-basics.htm
- Centers for Disease Control and Prevention “Understanding how vaccines work” https://www.cdc.gov/vaccines/hcp/conversations/downloads/vacsafe-understand-color-office.pdf
- History of Vaccines “Do vaccines cause autism?” https://www.historyofvaccines.org/content/articles/do-vaccines-cause-autism
- Centers for Disease Control and Prevention “History of measles” https://www.cdc.gov/measles/about/history.html
- History of Vaccines “All timelines overview” https://www.historyofvaccines.org/timeline#EVT_1
- Wakefield A, et al. RETRACTED:—Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. Lancet. 1998; 351(9103): 637-641. https://www.thelancet.com/action/showPdf?pii=S0140-6736%2897%2911096-0
- Heinz J. Schmitt, et al. “Primary vaccination of infants with diphtheria-tetanus-acellular pertussis–hepatitis B virus– inactivated polio virus and Haemophilus influenzae type b vaccines given as either separate or mixed injections.” The Journal of Pediatrics. 1999. https://www.sciencedirect.com/science/article/pii/S0022347600260885
- BBC “Measles outbreak in maps and graphics” 2013. https://www.bbc.com/news/health-22277186
- NPR “Fifteen Years After A Vaccine Scare, A Measles Epidemic” 2013. https://www.npr.org/sections/health-shots/2013/05/21/185801259/fifteen-years-after-a-vaccine-scare-a-measles-epidemic
- Arizona State University “Macrophages” https://askabiologist.asu.edu/macrophage
You might have to use more than a microscope, there’s more to genetics than what meets the eye: An interview with Dr. Gerald Quon
By Tannavee Kumar, Genetics & Genomics 20’
Author’s Note: As an undergraduate studying genetics and genomics and computer science, I wanted to interview a former professor to find out the steps he took in order to do computational research in the biological sciences. I was interested in finding out more about the growing field of computational biology and wanted to help shed light on a field to students that may be similarly interested.
Background
You received a Bachelors in Math, then a masters in Biochemistry, then a PhD in Computer Science; did you always know that you wanted to do research in biology? If so, what made you want to start off with a technical education rather than something traditional like biology or chemistry? If not, how did you come to discover applications of computer science in Biology even 15 years ago?
No, I did not start off wanting to do anything related to biology. I started my undergrad thinking I would make computer games. How I kind of got into this was a week before my undergrad, I got an email from my university asking if I wanted to be a part of the first cohort of a bioinformatics program. I initially declined.
As I was looking for my third internship in my co-op program, I had a friend who found a job for a professor in Toronto, and my friend asked if I wanted to work on this cool project about predicting how proteins fold into these 3D structures. I told him I don’t know anything about protein structures, but sure! It was a lot of fun.
Is that what inspired you to pursue Biochemistry for further education?
I think that first internship was very pivotal, because it really nurtured my interest in protein structures. When I finished my undergrad, I was kind of bored of computer science, which is why I thought I would do a PhD studying protein structures.
How do you see life sciences research evolving and progressing in the coming years, given the inclusion of this new field?
In my opinion, we will see more and more blurring of boundaries. In 25 years, there is going to be more undergraduate programs less defined by walls like “life sciences,” “chemistry,” and better recognition that everybody borrows knowledge and skills from many fields. It will be very difficult to do a life sciences degree without learning anything about math or statistics. Similarly, more people in traditional quantitative disciplines will want to take those classes in the life sciences. Essentially there will be fewer walls.
How would undergraduates studying quantitative subjects, like mathematics, statistics, or computer science be made aware of the growing demand for such skills in the Life Sciences?
The classic way to become introduced to such areas would be through coursework, internship with a company, or research with a professor. The last two ways are not very optimal. At the end of the day, in a standard undergraduate program, you have summers, and if you are ambitious you can try to do research during the school year. However, you can only do so many different kinds of internships before you graduate. If you did one every summer of college, and even two before hand, even that would not be sufficient for getting a nice, representative sample for all the things you can work on.
That is where universities need to do a better job of creating opportunities for students to engage with people from industry and research so that they don’t need 4-5 months to figure many essential things out.
Research and Beyond
Can you briefly describe some of the research that your lab does?
We are currently working towards a few different directions. A large project at the moment is studying the genetics of mental disorders and neurodegeneration, for example we look at the genetics of Alzheimer’s disease, schizophrenia, autism, etc. Our main goal is to mechanistically understand how genetic variants associated with these mental conditions modify disease risk. Much of those mechanistic studies currently look at events that happen at the molecular level. This is great and very useful; however, since the majority of the research is geared at the molecular level we don’t have a good understanding of what variants do functionally at the level of the cell. How does it affect the functional properties of the cell, such as neuron electrophysiology? Or, how is the organization of the tissue affected?
Other areas we work on are on building better models to understand how cells are spatially organized in the brain, as well as building models that quantitatively describe cell population behavior. We know that cells behave differently when put into different contexts. It’s of interest to build a model to predict what happens when you put together different kinds of cells in different combinations, orientations, or conditions.
Lastly, a third project being worked on is on the therapeutic end. We are essentially trying to identify the druggable region of the genome. There are a lot of computational problems in trying to determine what is druggable.
How do you think the integration of the computational sciences has shed light on how biological processes are interconnected, and what do they make clear that a molecular approach may not be able to?
In human genetics, computational models play a huge role in hypothesis generation. They do a good job leveraging big data, such as genomics, to prioritize which variants should be tested using molecular approaches, for example, when molecular approaches are costly or too slow to systematically test many variants across a genome. The role of computation is parsing through the many possibilities that you can’t explore molecularly.
For example, a study we worked on four years ago was to try and find a causal variant for obesity. Most human genetic studies only point to a region of the genome where causal variants might hide, but don’t tell you exactly which one is the true causal one. When these regions are big, like hundreds of kilobases long, you need computational tools to identify the precise causal one to test experimentally. In that study, computational tools played the pivotal role of identifying the causal variant that was ultimately tested and shown to drive large changes in obesity risk.
How does computational research like your own lead to the progression of curated care in the health industry?
At a superficial level, in some ways it accelerates some of the biomedical discoveries that are being done today. The obesity study is one example. If you didn’t have the computational resources, you would spend years and years trying to find the right variant. However, we found it relatively quickly with computation.
For healthcare specifically, fields such as machine learning are revolutionizing care today. People from statistics, computer science, and math are working directly with clinicians and hospitals to develop highly accurate ‘digital pathology’ software, they help predict when patients will need to come into the hospital or whether they are high risk for a disease.
Oftentimes, conditions and diseases are misdiagnosed, which leads to inappropriate treatments. How would research in this area begin to remedy this common problem in the healthcare industry?
Most diseases are heterogeneous, which means that a group of people who are diagnosed with the same condition might actually have different underlying conditions, and need different treatments. Many computational approaches based on molecular and clinical data are being developed to identify more homogeneous groups of patients, to help achieve precision medicine. This allows for the most accurate prescription of medication and treatments. This is because these homogenous groups help identify the underlying disease phenotype which means access to better directed medication.
During your time as a PhD student, you also “explored the application of models built from deconvolving gene expression profiles, for personalized medicine.” Can you go more in depth to how these models were built and how it can advance our ability to provide a more accurate prognosis to patients?
During my PhD, we were trying to predict the prognosis of early stage lung cancer patients. If you are diagnosed with early stage lung cancer say stage 1B, clinicians have to make important decisions, such as how much e.g. chemotherapy to give you. If they give you too much, it will get rid of the primary tumor, but you will increase your risk of recurrence. But if you don’t give enough, you don’t get rid of the primary tumor.
Back then, fourteen year ago or so, genome expression profiling was just becoming popular. People were thinking maybe we can predict whether these stage 1B patients were going to be at high risk of recurrence or not. Our motivation for that problem was essentially to build a computational model to predict based on molecular signatures if they should be given extra therapy or not. That in itself is a hard problem. Additionally, before single cell sequencing was available, it was hard to take a sample of a tumor and only sequence the tumor cells. Often times you would have contamination of normal cells that would mess up the signatures you would get. We had to develop a computational method to extract out only the signatures due to tumor cells, and show that once you do that it is much easier to predict prognosis.
Where do you think research will be in the next 10-20 years?
We are going to see a lot more connections across more previously isolated fields. For example, with respect to human psychiatric genetics, a lot of focus right now is at the molecular impact of genetic variants, but in the near future I’d expect there to be much closer integration with clinicians to also study the impact on behavior, and with the experimental biologists to study the impact on brain development and organization.
***Special thanks to Dr. Gerald Quon for this interview
How Are California Bears Doing?
By Timur Katsnelson, Neurobiology, Physiology, and Behavior ‘19
Conservation biology has always been an interesting field to me. After having previously submitted two neuroscience-related articles to the Aggie Transcript, I decided to explore a new topic. The bear-sighting on campus last spring was on my mind, mainly because I began to wonder about the status of bears in our state. Given their symbolic status in California, I imagined that their conservation would be well-documented. This article serves as a brief report of the black bear’s current status in California, and the population genetics methods used by researchers keeping track of the animal.
Shortly before 6 a.m. on June 4, 2019, a very rare occurrence captured the attention of the entire Aggie community. A young, male black bear was spotted wandering near the UC Davis Arboretum’s Redwood Grove [4]. The campus police and fire departments, in conjunction with California’s Department of Fish and Wildlife (CDFW), worked to tranquilize the straggler and release him to the nearest habitat west of the city of Davis. This moment of excitement on campus sparked the curiosity of many who care about wildlife and conservation. According to CDFW, black bear populations have been on the rise over the past quarter-century, so what are the challenges the species face and how do biologists keep track of populations? It is also important to evaluate the evolutionary track of the species to understand if it can withstand changing environments, so what is the genetic diversity of the state’s population of black bears?
California’s history with bears is complicated. Many sports teams in the state are fondly named after them and, most notably, a prominent grizzly roams a patch of grass on the state’s flag. While it is a cherished symbol of the state, the grizzly faced a savage end to its reign as apex predator. The Spanish threw the bears in fights to the death against bulls and dogs, and later American settlers hunted them into oblivion. The last California grizzly was seen in 1924 and has since been extinct [2]. Nearly one hundred years later, environmentalists are aspiring to reintroduce the grizzly bear through back-breeding, cloning, or genetic engineering [2]. Many might consider these to be aspirational long-term goals, and in the meantime have focused on the current population of bears in the state. What is known for sure is that the absence of the grizzly in the state has opened up more room for a different population to flourish [5].
The real challenge in the many decades since the last grizzly has been observing and managing the population of California black bears. Unlike their phylogenetic cousins, black bear populations still exist in the state and are relatively stable. The department estimates that between 25,000 and 30,000 black bears occupy 52,000 square miles in California. There are three subpopulations of the bears which are recognized as the North Coast/Cascade, Sierra, and Central Western/Southwestern regions. Unsurprisingly, about half of the state-wide population of black bears resides in the North Coast/Cascade region [1].
In 2016, a population genetics study of California Black Bears was published by the CDFW in conjunction with the Wildlife Population Health and Genetics Laboratory at the UC Davis School of Veterinary Medicine. The study analyzed the Central Western subpopulation, specifically in Monterey and San Luis Obisbo counties and compared genetic samples to bears in Mono County, which is between Yosemite National Park and the border with Nevada. Research of this sort evaluates abundance of the species and the genetic diversity of small populations to predict migrating patterns, check for genetic bottlenecking and inbreeding, and to examine the overall strength of the genetic pool [3].
One way researchers acquired genetic material was through a hair sampling technique. Two rungs of barbed wire were tied around a circle of trees. At the center of this sample area was fish bait and a sweet scent bait made of honey and berries. As bears approached the bait, their hair would get caught in the wires. The spacing of each sample station was strategically determined from a grid design that considered habitable ranges for the bears and safe distances from human-related dangers such as roads and watch points. DNA extraction and further genotyping was used to identify unique individual bears. From there, most of the work came from computer-programmed statistical tests such as Bayesian genetic clustering algorithms to evaluate the population structure for each data range [3].
Researchers have come to believe that the central coastal population of bears has been in the region for about 50 years and are descendants of the population in the Sierra region that have migrated towards the coast. The report concluded that there are very few bears populating in Monterey County because there has not been enough time for them to disperse adequately within the coastal region. A potential reason for their slow migration towards Monterey County could be urbanization and the construction of highways that provide real physical barriers [3].
A 2009 study (Brown et al.) by researchers at the UC Davis School of Veterinary Medicine also analyzed the population genetics of California’s black bears, this time on a statewide scale. Using historical documents to track translocations of bears by humans, but also the analysis of microsatellite DNA from subpopulations of the bears, the researchers came to similar conclusions as the aforementioned CDFW report. It is believed that the extinction of the California grizzly, which roamed a significant portion of the state’s central coast, made room for the black bear to begin to inhabit regions such as Monterey and San Luis Opisbo [5]. Brown et al. used genetic samples from 540 bears, which were collected between 1990 and 2004 throughout the state. To determine the genetic structure of the California populations, the group used a computer program that “groups individuals into clusters based on genotype without consideration of sampling geography.” Following this, the determined clusters were tested for Hardy-Weinberg equilibrium, one of a handful of tests for genetic populations. This is an evaluation method that assumes no evolutionary changes are taking place in the genetic pool. Doing this makes it possible to simply analyze the allelic frequencies within the population without accounting for potential changes.
Wildlife management is an increasingly important and difficult operation for any organization. Urbanization and global climate change will certainly become more prominent issues in black bear conservation. This is not even considering the laws on hunting or other policy-related challenges that may arise. The CDFW, in conjunction with researchers from around the state, has made a concerted effort to observe this population. If we are to learn a lesson from the past, it would be to not take for granted the abundance of the bear population in California. There has been a lot of excitement about the black bear’s proliferation, but our state will need to be attentive if we are to keep the health of our wildlife in balance.
References
-
- California Department of Fish and Wildlife “Black Bear Biology” https://www.wildlife.ca.gov/Conservation/Mammals/Black-Bear/Biology
- Los Angeles Times “Column: Will the California Grizzly Make a Comeback?” https://www.latimes.com/opinion/op-ed/la-oe-arellano-grizzlies-20180718-story.html
- Sherman et al., “Population Genetics Study of California’s Black Bears” https://lpfw.org/wp-content/uploads/2017/02/Sherman-Ernest-CDFW-Final-Report-Population-Genetics-Study-of-California%E2%80%99s-Black-Bears.pdf
- UC Davis “Bear Caught in the Morning, Freed 5 Hours Later” https://www.ucdavis.edu/news/bear-caught-morning-freed-5-hours-later/
- Brown et al., “Black Bear Population Genetics in California: Signatures of Population Structure, Competitive Release, and Historical Translocation” Journal of Mammalogy https://doi.org/10.1644/08-MAMM-A-193.1
Genetically Engineered Crops: A Food Security Solution?
By Roxanna Pignolet, Biochemistry and Molecular Biology 20’
Author’s Note: Since I started working on plant metabolites as an undergraduate researcher in the Shih Lab, I’ve developed a great appreciation for the power of plant genetic engineering to address a wide variety of problems. A uniquely global and increasingly relevant concern is how to continue to feed the world’s growing population in the face of climate change. I decided to write this paper to provide a snapshot of the current research being done to innovate crop species that will survive in the face of climate change. As part of this review. I also wanted to address ongoing concerns about the safety and impact of GMOs on consumers and the environment, and whether these genetic engineering strategies have the potential to make a positive impact on food security.
Introduction
As the world population continues to rise, climate change is also having an increasingly large impact on agriculture in the form of rising temperatures and intensified weather variations. Population growth is challenging researchers and farmers to find new ways to increase crop yields without access to more land or freshwater. Population is expected to increase from the current 7.7 billion to 9 billion by 2050 (1,2). However, it was found in 2000 that about 70% of the available freshwater was already in use. Meanwhile, climate change is introducing new challenges to crop productivity and stability. By 2050, the global crop demand may increase as much as 110%, which emphasizes the need for new, powerful strategies for crop improvement.
Genetically engineered crops have been used in agriculture since the mid-1990s, and have been instrumental in overcoming serious agricultural challenges such as disease outbreaks and overuse of toxic insecticides (3). In contrast to traditional breeding, genetic engineering allows for a direct transfer of one or more genes of interest from either closely or distantly related organisms. In some cases, a plant is modified solely by turning on or off one of its own genes (4). These methods allow for fast and precise changes that target a specific trait. Since their introduction, numerous studies have measured their potential for health and environmental risks, as well as their benefits. This review will discuss the impacts of genetically engineered crops from an environmental and health perspective. Additionally, I will look at how genetically engineered crops are currently being applied to address food security concerns in the face of climate change.
What is the Impact of Genetically Engineered Crops?
Environment
As genetically engineered crops have now been used in the field for many years, the environmental impacts can be assessed. The most abundant type of genetically engineered crops are insect resistant crops, specifically Bacillus thuringiensis (Bt) resistant corn and cotton. Bt is a soil bacterium which produces proteins that are toxic to certain insects (5). Bt crops have been modified to produce Bt genes as protection against specific pests (3). These crops have been grown commercially since 1996 (2), which has allowed long term environmental studies to be conducted. In a two-year field trial on the impact of transgenic maize on soil fauna, Fan et al. found that there was no impact on biodiversity, abundance or composition of the soil fauna. They compared samples taken in varying conditions from either transgenic maize or non-transgenic maize controls. The researchers found that the insecticide transgene did not affect the soil ecosystem, while factors such as time of year, pH, sampling time, and root-biomass all had significant effects (6). In a 2003 review on Bt crops, Mendelsohn et al. also found that there were no negative impacts observed on species of endangered insects, earthworms, or non-target insects. However, one negative that applies to all insecticides is that pests will eventually gain resistance. Engineering crop varieties to have several different resistance genes has been shown to slow this process (2).
Another class of genetically modified crops that are currently in use are herbicide-tolerant crops. Herbicide-tolerant crops are designed to be tolerant to broad-spectrum herbicides that can be used to control surrounding weeds. Use of herbicide-tolerant corn and soybeans has been shown to decrease the use of highly toxic herbicide sprays in favor of an amino-acid derived, non-toxic alternative (Roundup), and has also encouraged low-till farming practices which have been correlated to significant reductions in greenhouse gasses (2). Weed resistance is a concern with herbicide-resistant crops, especially when a single herbicide gene is overused. In some cases, high selection pressures caused by overuse of a single broad-spectrum herbicide have led to resistant weeds. If unchecked, these resistant weeds can spread across farms and negatively impact crop growth (7). New varieties of crops resistant to multiple types of herbicides should help mitigate this problem by allowing farmers to rotate several types of herbicides. A widespread adaptation of these new varieties and consistent practice of sustainable herbicide application will be important to avoiding negative outcomes of herbicide-tolerant crop use.
Implementing these genetically engineered crops has contributed to overall decreases in the amount of toxic insecticide and herbicide sprayed. Just as with chemical pesticide and herbicide sprays, proper steps must be taken with insect-resistant or herbicide-resistant crops to delay resistance in the affected insect or weed. These steps include rotating planting of herbicide-resistant crops and using weed control tactics with different modes of action to avoid putting high selection pressure on one type of resistance.
Health
The consensus from long term studies carried out to address biosafety concerns of genetically modified crops, is that they are just as safe as their natural counterparts. Genetically engineered crops are subjected to a variety of tests on a case by case basis before they are implemented, and now long term data shows that there have been no side effects from possible unintended chemical compositions of crops, making them just as safe as those derived from traditional breeding. There are, however, concerns about next generation genetic engineering, which targets regulator genes instead of a single functional gene. Targeting regulator genes could allow scientists to target plant stress response pathways, and engineer plants to have multiple desirable traits (8). Additional research must be conducted to assess the plant-wide changes caused by affecting a player in a signaling cascade.
New Approaches to Crop Improvement
While the current genetically engineered crops have been found to have a positive effect on crop yields, the increases are not enough to keep up with projected population growth. Additionally, climate change is predicted to cause stressors to crops such as drought, rising temperatures, and weather variations among other things (2). Therefore, scientists are looking for new and creative genetic engineering techniques to create robust and high-yielding crops for our future.
One of the main targets for genetically engineered crops is adaptions to grow and produce quality yields under higher temperatures. In a study investigating the genes responsible for creating lower quality, chalky rice grains under high temperature conditions, Nakata et al. looked at the role of a starch metabolizing enzyme, known as amylase, in the packing of starch into rice grains. Their team used transgenic rice modified with a reporter gene attached to each isotype of the amylase gene. By comparing the activity of plants overexpressing each variety, they were able to identify specific amylase genes as targets for genetic modification. Rice variants with these modifications would remain higher quality, with tightly packed starch, even if grown under non-optimal higher temperatures (9). Another study tested the responses of a previously created transgenic rice line called HOSUT under high amounts of carbon dioxide (CO2), a heat wave, and nitrogen enriched conditions. They found that the transgenic line, which has enhanced sucrose transport, has a superior yield than the control line (Certo), and that increased CO2 conditions resulted in higher yields in Certo with only minimal increases for HOSUT. They concluded that the minimal response of HOSUT to the increased CO2 was indicative of HOSUT already being saturated due to its optimized transport capabilities. The HOSUT line is already optimized for translocation of carbon, which they were able to show by increases in starch in the grains in HOSUT only. HOSUT also produced more yield in response to increased nitrogen, making it a good option for producing high rice yields under variable climate change conditions (10) The HOSUT line is a great example of how genetic engineering can be used to fortify and optimize crops to both survive under atypical conditions and produce enough yield to keep up with demand.
Another problem that researchers are addressing through genetic engineering, is drought. Selvaraj et al., developed and field tested two drought tolerant rice lines, created by introducing an Arabidopsis stress response gene (galactinol synthase) with a maize promoter. Galactinol synthase produces galactinol, a sugar that functions as an osmoprotectant, keeping water from leaving the cells. These galactinol synthase genes were introduced into two commercially available rice lines and tested in the field under drought and well-watered conditions. Under drought conditions, the collection of galactinol resulted in higher grain yields, while under well-watered conditions no significant yield increase was observed. Galactinol is a sugar that functions as an osmoprotectant, keeping water from leaving the cells. The results of these field trials show that these rice lines are ready to be integrated into ongoing breeding programs (11). Wang et al. also tackled the problem of drought stress caused by global warming on fruit such as apple trees. They transgenically expressed an aquaporin gene found in Fuji apples that has increased expression during fruit growth in tomato. The transgenic plants did have an increased drought tolerance, observed as an increased sensitivity of their stomata to water loss, and a larger fruit size when compared to wild type. This research will be continued in apples next with the goal of producing plants with larger fruits when well-watered, which will also be more tolerant to drought due to increased water transport efficiency (12).
A third target for genetic engineering solutions is circadian rhythms. Understanding and controlling circadian rhythms in crop plants has the potential to adapt plants to radically different environments. One group at the Guru Jambheshwar University of Science and Technology is tackling this challenge in rice. This group expressed an Arabidopsis transcription factor known as Circadian Clock Associated1 (CCA1) under the Timing Of Cab Expression 1 (TOC1) promoter, which are both part of the circadian clock machinery in Arabidopsis. They found that overexpression of the CCA1 in rice had negative results, while repressing it caused positive changes to plant morphology. The researchers used RNAi, which is a biological process where small fragments of RNA are used by the cell to target complementary mRNA for destruction, thus silencing expression of the encoded protein. By comparing RNAi constructs based off of three different parts of the CCA1 gene for silencing the gene expression, they found that the RNAi derived from the 3’-terminal end of the CCA1 gene had the best impact on plant morphology (13). This study is an important first step towards unlocking the power of using circadian clock genes to breed plants better adapted to a changing environment.
One new strategy being considered is a CRISPR/Cas9 genome editing method that could be used to quickly develop improved crop varieties without transgenes. CRISPR/Cas9 can introduce specific changes into a plant genome without being limited by existing variation. Applying this method, scientists will be able to stack multiple edits into a plant within a single generation, resulting in transgene-free progeny. One benefit of this method is that it may allow for more complex changes to polygenetic traits or signaling pathways. For example, this could be helpful for targeting complex plant stress response pathways. This technology is currently limited by the availability of annotated reference genome sequences for plants other than Arabidopsis. Scheben et al. suggest that taking a genomics-based approach would allow for a comparison of species-wide genome diversity, making differences in copy-number visible and thus available for editing. While the authors suggest that this method creates plants that are indistinguishable from those created through natural breeding and random mutations, bans against genetically modified crops may target methodologies rather than the final result (14).
Conclusion
Currently implemented genetically engineered crops, have been shown, through years of testing and trials to be at least as safe, both towards the environment and in terms of human health, as naturally bred varieties. While new transgenic lines must be screened and tested on a case-by-case basis, the overall benefits of this technology make it an important tool that may be necessary to confront upcoming challenges to agriculture. Climate change and population growth are putting steep demands on crops to survive in more hostile environments while also producing higher yields. Current efforts are focusing on vital crops, such as rice, corn, wheat, and fruits, to create drought-tolerant, heat-tolerant, and yield-optimized plants.
References
- “World Population Clock: 7.7 Billion People (2019) – Worldometers.” n.d. Accessed November 18, 2019. https://www.worldometers.info/world-population/.
- Ronald, Pamela. 2011. “Plant Genetics, Sustainable Agriculture and Global Food Security.” Genetics; Bethesda 188 (1): 11–20.
- Mendelsohn, Mike, John Kough, Zigfridais Vaituzis, and Keith Matthews. 2003. “Are Bt Crops Safe?” Nature Biotechnology 21 (9): 1003–9. https://doi.org/10.1038/nbt0903-1003.
- “Genetic Engineering and GM Crops | ISAAA.Org.” n.d. Accessed November 18, 2019. https://www.isaaa.org/resources/publications/pocketk/17/default.asp.
- “Bacillus Thuringiensis (Bt).” n.d. Accessed November 18, 2019. http://npic.orst.edu/ingred/bt.html.
- Fan, Chunmiao, Fengci Wu, Jinye Dong, Baifeng Wang, Junqi Yin, and Xinyuan Song. 2019. “No Impact of Transgenic Cry1Ie Maize on the Diversity, Abundance and Composition of Soil Fauna in a 2-Year Field Trial.” Scientific Reports 9 (1): 1–9. https://doi.org/10.1038/s41598-019-46851-z.
- Resources, University of California, Division of Agriculture and Natural. n.d. “Herbicide Tolerance.” Accessed November 18, 2019. http://sbc.ucdavis.edu/Biotech_for_Sustain_pages/Herbicide_Tolerance.
- Ortiz, R., Andy Jarvis, P. Fox, Pramod K. Aggarwal, and Bruce M. Campbell. 2014. “Plant Genetic Engineering, Climate Change and Food Security.” Working Paper. CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS). https://cgspace.cgiar.org/handle/10568/41934.
- Nakata, Masaru, Yosuke Fukamatsu, Tomomi Miyashita, Makoto Hakata, Rieko Kimura, Yuriko Nakata, Masaharu Kuroda, Takeshi Yamaguchi, and Hiromoto Yamakawa. 2017. “High Temperature-Induced Expression of Rice α-Amylases in Developing Endosperm Produces Chalky Grains.” Frontiers in Plant Science 8. https://doi.org/10.3389/fpls.2017.02089.
- Weichert, Heiko, Petra Högy, Isabel Mora-Ramirez, Jörg Fuchs, Kai Eggert, Peter Koehler, Winfriede Weschke, Andreas Fangmeier, and Hans Weber. 2017. “Grain Yield and Quality Responses of Wheat Expressing a Barley Sucrose Transporter to Combined Climate Change Factors.” Journal of Experimental Botany 68 (20): 5511–25. https://doi.org/10.1093/jxb/erx366.
- Selvaraj, Michael Gomez, et al. “Overexpression of an Arabidopsis Thaliana Galactinol Synthase Gene Improves Drought Tolerance in Transgenic Rice and Increased Grain Yield in the Field.” Plant Biotechnology Journal, vol. 15, no. 11, Nov. 2017, pp. 1465–77. PubMed, doi:10.1111/pbi.12731.
- Wang, Lin, Qing-Tian Li, Qiong Lei, Chao Feng, Xiaodong Zheng, Fangfang Zhou, Lingzi Li, Xuan Liu, Zhi Wang, and Jin Kong. “Ectopically Expressing MdPIP1;3, an Aquaporin Gene, Increased Fruit Size and Enhanced Drought Tolerance of Transgenic Tomatoes.” BMC Plant Biology 17, no. 1 (December 19, 2017): 246. https://doi.org/10.1186/s12870-017-1212-2.
- Chaudhury, Ashok, Anita Devi Dalal, and Nayan Tara Sheoran. 2019. “Isolation, Cloning and Expression of CCA1 Gene in Transgenic Progeny Plants of Japonica Rice Exhibiting Altered Morphological Traits.” PLOS ONE 14 (8): e0220140. https://doi.org/10.1371/journal.pone.0220140.
- Scheben, Armin, Felix Wolter, Jacqueline Batley, Holger Puchta, and David Edwards. 2017. “Towards CRISPR/Cas Crops – Bringing Together Genomics and Genome Editing.” New Phytologist 216 (3): 682–98. https://doi.org/10.1111/nph.14702.
Merging Amputees with their Prostheses
By Brooke B., Computer Science/Design ’22
Author’s Note: As a computer science major, I have always been interested in the concept of an algorithm that can communicate with the brain through manufactured nerve signals. I read about this research in the news and I thought it was a great example of the marriage of biology and computer science, as well as how the two together can improve lives. I wrote this news article in hopes to reach more of the general public to shed light on the strides we’re making in prosthetic technology.
New research was published early October 2019 in Science Translational Medicine with the first prosthesis augmented by sensory feedback for above-the-knee amputees.¹ The findings have helped amputees achieve greater control over their prosthetic limbs. One participant in the clinical study reported feeling as if their prosthesis was their real leg again: “After all of these years, I could feel my leg and foot again, as if it were my own leg,” Djurica Resanovic said, “You don’t need to look at where your leg is to avoid falling.”
Swiss companies ETH Zurich and SensArs Neuroprosthetics developed the sensory feedback technology to improve prosthetic devices. Seven sensors detect signals along the foot of the artificial leg prototype, and one sensor detects the angle of flexion from the knee. These communicate via Bluetooth to an electric conductor, called an electrode, surgically implanted into the stump’s tibial nerve. Co-author of the publication and SensArs Neuroprosthetics co-founder Silvestro Micera has found the approach of piercing an electrode through the nerve rather than wrapping around it to be efficient in other studies performed for bionic hands. The sensors on the limb receive spatial information when moved, which are translated into biosignals by the team’s new algorithm. The electrode implanted to the neuron receives the signals and sends the information through the nervous system to be received at the brain for processing. The better integration of the prosthesis to the body depends on the accuracy of these electrical signals, and how closely they resemble those a real leg would have produced.
Three amputees participated in a clinical trial over a period of three months to test the new technology. “We showed that less mental effort is needed to control the bionic leg because the amputee feels as though their prosthetic limb belongs to their own body,” explained Stanisa Raspopovic, an ETH professor who led the study. “…the feedback is crucial for relieving the mental burden of wearing a prosthetic limb which, in turn, leads to improved performance and ease of use.”
Even blindfolded and wearing earplugs, participants were able to feel their prosthetic prototype. With the improved awareness of the limb in space, navigating through obstacles required less effort and as a result, subjects fell less. With no stimulation in the limb, the average ratio of falls to obstacles was 39 percent, as opposed to the ratio of eight percent with the stimulated prosthesis. On a test with stairs where subjects were tasked with completing laps, the average amount completed with the new technology was 2.28, as opposed to an average of 1.67 laps without it. Additionally, the brain appeared to be less burdened by the prosthesis, exhibiting lower amplitudes in acoustic event-related potentials tests.² These tests pick up small voltages the brain gives off in response to stimuli, thus a lower reading would indicate less mental stimulation involved in maneuvering with the prosthesis.³ Consequently, more focus can be devoted towards other tasks within the amputee’s life.
Silvestro Micera believes the intraneural electrodes implemented in this research hold vast prospects in neuroprosthetic applications. “We believe [they] are key for delivering bio-compatible information to the nervous system… Translation to the market is just around the corner.”
References
- Ecole Polytechnique Fédérale de Lausanne. “Amputees merge with their bionic leg.” ScienceDaily. ScienceDaily, 2 October 2019. <www.sciencedaily.com/releases/2019/10/191002144243.htm>.
- Francesco Maria Petrini, Giacomo Valle, Marko Bumbasirevic, Federica Barberi, Dario Bortolotti, Paul Cvancara, Arthur Hiairrassary, Pavle Mijovic, Atli Örn Sverrisson, Alessandra Pedrocchi, Jean-Louis Divoux, Igor Popovic, Knut Lechler, Bogdan Mijovic, David Guiraud, Thomas Stieglitz, Asgeir Alexandersson, Silvestro Micera, Aleksandar Lesic and Stanisa Raspopovic. Enhancing functional abilities and cognitive integration of the lower limb prosthesis. Science Translational Medicine, 2019 DOI: 10.1126/scitranslmed.aav8939
- Sur, S., & Sinha, V. K. (2009). Event-related potential: An overview. Industrial psychiatry journal, 18(1), 70–73. doi:10.4103/0972-6748.57865
Novel Pathway Elucidates Potential for Nitric-Oxide Produced by Tumor-Associated Macrophages to Confer Resistance to Chemotherapy Drug Cisplatin
By Reshma Kolala, Biochemistry & Molecular Biology ‘22
Authors Note: This past summer I was given the incredible opportunity to work in the Thurmond Lab at the City of Hope where I investigated a point mutant of the Syntaxin 4 protein on -cell function and apoptosis. The following piece reviews a publication that was fundamental to both the understanding and methodology of my project.
Introduction
Cisplatin (CDDP) is a widely used chemotherapy drug that induces apoptosis in solid tumor cells, which are cells that lack cysts or liquid areas such as carcinomas, sarcomas, and lymphomas. The platinum-based chemotherapeutic agent was popularized in the late 1970s as the antitumoral toxicity of platinum compounds became known for their clinical efficacy against solid tumors (1). Although initially promising, many patients suffer a relapse due to the development of cisplatin resistance, largely as a result of their ability to overcome the apoptogenic effects of the drug. To elucidate the underlying mechanisms behind the propagation of cancer progression and chemotherapy resistance, an understanding of the tumor microenvironment is crucial. The tumor microenvironment is comprised of a complex and dynamic milieu that surrounds stromal cells. Among these cells, tumor-associated macrophages (TAMs) represent the largest population of infiltrating inflammatory cells in malignant tumors. TAMs have been suggested to possess a tumor-promoting phenotype that drives multiple mechanisms, most notably tumor cell proliferation and drug resistance (2). Initially, TAMs are in the classically-activated M1 state, in which their proinflammatory characteristics disables tumor growth. As tumors mature, however, they switch to an alternatively-activated M2 state, promoting tumor development and immunosuppression. As M2-like TAMs are major contributors to chemotherapeutic resistance, they are frequently targeted for cancer immunotherapies.
M2-like TAMs are capable of producing nitric oxide (NO) via expression of inducible NO synthase (iNOS). NO is an important cell signaling molecule that is critical for many physiological processes such as neurogenesis and angiogenesis (3). At low levels, NO displays cytoprotective properties, promoting tumor growth, but can be cytotoxic to tumor cells when produced at high levels (4). The cytoprotective tendency of NO has been linked to the inhibition of the sphingomyelin-metabolizing enzyme acid sphingomyelinase (A-SMase). Traditionally, the activation of A-SMase (most commonly by chemotherapeutic drugs such as CDDP) drives the hydrolysis of sphingomyelin to generate ceramide. Ceramide, in coalition with other molecules, forms a cluster that drives transmembrane signaling of apoptotic death to effectively kill tumor cells (5). By contrast, it has been found that at relatively low concentrations NO hinders the beneficial apoptotic effect of A-SMase, resulting in resistance to the chemotherapeutic drug CDDP. The elucidation of this mechanism is the focus of research conducted by Perrotta et al. in 2018.
A study led by Perrotta et al. investigated the potential for NO, a byproduct of TAMs, to be responsible for the mechanism conferring resistance to CDDP (6). An increased concentration of intracellular NO leads to the activation of the membrane-bound protein Syntaxin 4 (STX4) via a pathway that involves the production of cGMP and activation of protein kinase G (PKG). As STX4 aids in the translocation of A-SMase, an enzyme involved in apoptosis, to the plasma membrane, a decrease in the STX4 protein would result in resistance to the intended apoptotic effect of CDDP (Figure 1). However, it was found that a point mutant of the STX4 protein, namely the STX4-S78A mutant, is unable to be phosphorylated by PKG due to the chemical nature of the alanine side chain. This prevents proteasomal degradation, thus leading to successful tumoral apoptosis.
Figure 1: Nitric Oxide (NO)-Mediated Resistance to Apoptotic Effect of Cisplatin
A schematic of the Nitric Oxide-mediated resistance to chemotherapeutic drug CDDP. The introduction of CDDP (1) leads to an increase in the intracellular concentration of NO in TAMs (tumor associated macrophages). (2). This leads to the generation of cGMP via the cGMP pathway (4). This leads to PKG activation (5) and results in STX4-WT phosphorylation at Ser-78 residue (6a) to ultimately allow degradation of STX4 via the proteasome. The STX4-S78A mutant however, cannot be phosphorylated (6b), preventing STX4 degradation by proteasomes. If left intact, the STX4 protein mediates the binding of A-SMase to the plasma membrane (7), resulting in tumor cell death (8).
Methodology & Results
The presence of M2 polarized TAMs in U373 human glioma cells were confirmed through immunostaining of the M2 subtype marker CD206 and iNOS. The presence of double positive cells illustrated the ability for M2-TAMS in glioma cells to produce NO. To investigate the effect of CDDP-induced apoptosis, human glioma cells were cocultured with M2-TAMs and then treated with CDDP in the presence of the iNOS inhibitor L-NAME. Annexin V apoptosis staining data illustrated a three-fold decrease in tumor cell death when CDDP-treated U373 glioma cells were cocultured with M2-TAMs. However, the addition of L-NAME resulted in a roughly two-fold increase in the abundance of dead tumor cells. Similar results were observed in the GL261 murine cells. This demonstrates that NO induces resistance to the apoptotic effect of CDDP as the inhibition of the NO precursor iNOS resulted in increased efficacy of the CDDP treatment.
The NO pathway operates via activation of the cGMP pathway. This was confirmed by administration of ODQ, a guanylate cyclase inhibitor that prevents NO-dependent cGMP generation, and DETA-NO (an NO donor) to U373 cells treated with CDDP. Results indicated a roughly two-fold increase in the percentage of apoptotic cells when treated with cGMP inhibitor ODQ, illustrating that the cGMP pathway is a significant contributor to CDDP. The generation of cGMP is correlated with the inhibition of CDDP-induced apoptosis, therefore, the presence of a cGMP inhibitor (ODQ) should increase levels of apoptosis, which is reflected in the data.
It has been previously demonstrated that acid sphingomyelinase (A-SMase) is activated by CDDP. A-SMase activation often occurs via translocation to the plasma membrane, therefore a cell surface biotinylation assay was used in U373 to confirm increased expression of A-SMase at the plasma membrane 30 minutes post-CDDP treatment. As expected, western blotting data indicated heightened expression of the enzyme when compared to A-SMase expression in U373 cells treated either with DETA-NO or 8Br-cGMP (an activator of cGMP-dependent kinases).
The final step of the pathway conferring resistance to CDDP involves the phosphorylation of Syntaxin 4 (STX4). STX4 is a membrane-bound SNARE protein. SNARE proteins form a SNARE core complex that orchestrate vesicle fusion to the plasma membrane. In tumor cells, STX4 is known to control the trafficking of A-SMase from intracellular compartments to the plasma membrane, allowing the A-SMase to carry out the intended apoptotic effect of CDDP. However, data shows that the phosphorylation of STX4 at the Ser-78 residue promotes its subsequent proteasomal degradation.
Conclusion
It has been found that NO released by M2-polarized TAMS has led to resistance against a widely used chemotherapy drug CDDP. This is achieved via the generation of cGMP and the activation of PKG in response to increased intracellular concentrations of NO. This leads to phosphorylation of the STX4 protein at Ser-78, resulting in its degradation. The decrease of the STX4 protein immobilizes A-SMase, preventing the enzyme from reaching the plasma membrane to initiate tumoral apoptosis.
As previously mentioned, the effect of NO in large quantities yields cytotoxic properties. In smaller concentrations however, NO has exhibited protective effects. The dichotomous behavior of NO on tumor biology could be a result of a myriad of factors, including the conditions of the tumor microenvironment and its origin. The generation of NO by TAMs protects tumor cells from apoptosis through the indirect inhibition of A-SMase activity. It is important to note that this action is dependent on the ability of NO to generate cGMP in tumoral cells and block the CDDP-induced, STX4-dependent translocation of A-SMase to the plasma membrane.
The elucidation of a chemotherapeutic resistance mechanism provides an understanding of Cisplatin’s efficiency and the origin of its drug-resistant tendencies. The observed proteasome-dependent degradation of STX4 may also be relevant to cancer therapies based on proteasome inhibitors. Prevention of the proteasomal degradation mechanism would increase efficacy of many chemotherapeutic treatments. This is due to the preservation of pro-apoptotic factors which would permit the programmed cell death of various proteins, preventing the accumulation of deleterious proteins. Currently, proteasome inhibitors are approved for treating multiple myeloma, a cancer of plasma cells or cells that produce antibodies. As NO is a major signaling molecule in the immune system, the elucidation of the CDDP resistance pathway yields further insight into how NO operates and proliferates. This renders research put forth by Perrotta et al. applicable to various fields of research beyond cancer.
References
- Dasari, S., & Tchounwou, P. B. (2014, October 5). Cisplatin in cancer therapy: molecular mechanisms of action. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4146684/.
- Lin1, Y., & Jianxin. (2019, July 12). Tumor-associated macrophages in tumor metastasis: biological roles and clinical therapeutic applications. Retrieved from https://jhoonline.biomedcentral.com/articles/10.1186/s13045-019-0760-3.
- Nitric Oxide and Cell Stress – Cell Signaling and Neuroscience: Sigma-Aldrich. (n.d.). Retrieved from https://www.sigmaaldrich.com/life-science/cell-biology/cell-biology-products.html?TablePage=9552558.
- XU, W., LIU, L. Z., LOIZIDOU, M., AHMED, M., & CHARLES, I. G. (n.d.). The role of nitric oxide in cancer. Retrieved from https://www.nature.com/articles/7290133.
- Gorelik, A., Illes, K., Heinz, L. X., Superti-Furga, G., & Nagar, B. (2016, July 20). Crystal structure of mammalian acid sphingomyelinase. Retrieved from https://www.nature.com/articles/ncomms12196.
- Perrotta, C., Cervia, D., Di Renzo, I., Moscheni, C., Bassi, M. T., Campana, L., … Clementi, E. (2018, May 29). Nitric Oxide Generated by Tumor-Associated Macrophages Is Responsible for Cancer Resistance to Cisplatin and Correlated With Syntaxin 4 and Acid Sphingomyelinase Inhibition. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5987706/.
How Expectations Shape Perception
By Neha Madugala, Cognitive Science, ‘21
Author’s Note: Previous studies in neuroscience have suggested that our expectations and prior experiences impact how we perceive reality and current tasks. This idea is embedded in Bayesian integration, also referred to as multisensory integration, which essentially studies how the brain combines information obtained from sensory neurons to affect perception and create a distinct outlook on an organism’s surroundings. It defines how we view and think about our environment.
This topic was particularly interesting to me because expectations can serve to aid our further understanding of incoming information, but can also inhibit our understanding if the new information contradicts our predictions.
Scientists classify expectations as essentially creating a placebo effect. The idea is that an individual’s expectations can influence the outcome of a certain treatment, their personal performance, or their feelings towards a person, place, or object. These “prior beliefs” can shape our reality and influence our perception of things we encounter in our daily life. The source of this placebo is argued to either be due to a conditioned response, where a situation has occurred multiple times with the same outcome (behaviorist approach) or that the placebo is a result of expectancy (expectation approach) (4).
In a recent study by MIT, researchers argued for the latter hypothesis suggesting that expectations are the suspect for shaping our interpretation of our surrounding environment. MIT neuroscientists were inspired by the idea of Bayesian integration, which is the process of incorporating prior knowledge with new and uncertain information (6). Jazayeri et al. trained monkeys in a task called “ready-set-go.” The monkeys are shown a starting signal and ending signal. After seeing both signals, they are expected to press a button after the same time interval between the starting and ending code has passed (6). The neuroscientists had short intervals, which spanned from 480 to 800 milliseconds and long intervals, which were 800 to 1,200 milliseconds. The monkeys were given a visual cue at the start of each trial signalling whether the trial would be a “short” or “long” scenario (6).
Monkeys were trained in either the short or long intervals. Each prior condition consisted of four blocks and then was followed by the 800 msec block. When all the monkeys were given an interval of 800 msec, those trained with a shorter interval gave an average response that was a little less than 800 msec and those trained with a longer interval gave an average response that was a little longer than 800 msec (6). These results reveal that monkeys trained under longer time intervals had an expectation for the 800 msec time interval to be longer, and those trained under a shorter time interval had an expectation that the 800 msec time interval would be shorter. This experiment was reproduced in humans and they found similar results (6).
The MIT researchers wanted to further determine which areas of the brain are responsible for the influence of expectations from the short and long trials affected the perception of the length of time for the 800 msce interval. Jazayeri et al, found that prior experiences strengthen a pattern of synaptic connections in a region located in the frontal cortex, which has previously been determined to be involved in temporal resolution (6). These patterns of synaptic connections were further computationally modeled. These models were found to perform the tasks in the same manner as the monkeys used in the previous experiments.
In another study at the University of Wisconsin, researchers conducted a similar study in humans testing how prior expectations of taste can influence an individual’s perception of the taste. Sarinopoulos et al. tested how subjects responded to an aversive taste, which was a diluted solution of quinine hydrochloride, with deceiving and accurate cues to test how placebo altered the participants’ responses. One group was informed that they were about to receive a highly aversive taste, while the other group was deceived and told they would receive a less aversive taste. The group told that they would receive a less aversive taste acted as the experimental group and were used to test whether placebo is altered by expectations or further stated if expectations affect our perception. Sarinopoulos et al. compared the expectancy effect from the highly aversive to less aversive groups by measuring changes in the insula and the amygdala, which are activated by aversive tastes (5).
The insula is associated with pain processing, which explains the presence of many sensory receptors for visceroceptive, referring to signals received from the heart, lungs, stomach, bladder, and other internal organs near the trunk region, and interoceptive inputs, including regions of the brain such as the thalamus, brainstem, insula, somatosensory, and anterior cingulate cortex (2). The amygdala, located near the insula, specifically the medial temporal lobe forms a part of the limbic system and plays a fundamental role in emotion processing, specifically fear and pleasure (1).
The study was conducted using rapid event-related fMRI design. In order to create a basis of comparison, the study included various conditions with different levels of aversion and manipulation – totaling to seven experimental conditions. The wide array of conditions allows Sarinopoulos et al. to eliminate differences if the perception involves a more aversive or less aversive taste by including both aversive and pleasant taste with varying perceptions.
They found that subjects demonstrated a consistent pattern of rostral anterior cingulate cortex (rACC), which plays an important role in decision-making and attention, and orbitofrontal cortex (OFC), which is also involved in decision-making, activation when presented with the misleading cue, followed by a decrease in the bilateral insula responses to the highly aversive taste. It was also associated with a smaller amygdala response. These findings suggest that the rACC and OFC are both correlated with the placebo effect and are associated with the aversive and pleasant perception of taste.
References
- “Amygdala.” ScienceDaily, ScienceDaily, www.sciencedaily.com/terms/amygdala.htm.
- D.P.Papoiu, Alexandru. “Functional MRI Advances to Reveal the Hidden Networks Behind the Cerebral Processing of Itch.” ScienceDirect, Academic Press, 5 Aug. 2016, www.sciencedirect.com/science/article/pii/B9780128028384000285.
- “Figure 2f from: Irimia R, Gottschling M (2016) Taxonomic Revision of Rochefortia Sw. (Ehretiaceae, Boraginales). Biodiversity Data Journal 4: e7720. Https://Doi.org/10.3897/BDJ.4.e7720.” doi:10.3897/bdj.4.e7720.figure2f.
- Haour, France. “Mechanisms of the Placebo Effect and of Conditioning.” Neuroimmunomodulation, vol. 12, no. 4, 2005, pp. 195–200., doi:10.1159/000085651.
- Sarinopoulos, Issidoros, et al. “Brain Mechanisms of Expectation Associated with Insula and Amygdala Response to Aversive Taste: Implications for Placebo.” Brain, Behavior, and Immunity, U.S. National Library of Medicine, Mar. 2006, www.ncbi.nlm.nih.gov/pubmed/16472720.
- Trafton, Anne, and MIT News Office. “How Expectation Influences Perception.” MIT News, 15 July 2019, news.mit.edu/2019/how-expectation-influences-perception-0715.
panelC.A.HanlonL.T.DowdleJ.L.Jones, Author links open overlay, et al. “Biomarkers for Success: Using Neuroimaging to Predict Relapse and Develop Brain Stimulation Treatments for Cocaine-Dependent Individuals.” ScienceDirect, Academic Press, 25 July 2016, www.sciencedirect.com/science/article/pii/S0074774216301131.