Monthly Archives: November 2021

Genetic data and Global populations: Do we have enough data to do a genetic study on the correlation between mental illness and drug use in a South African population?

by Mellie Msipa

Studies into Crystal Meth and its association with Schizophrenia

We all know that drug abuse is “bad”. Cocaine, Benzodiazepines and Methamphetamine (Crystal Meth) are just some of the drugs that people abuse, and if you were like me and grew up around people that weren’t always politically correct, then you probably heard the saying that ‘drugs kill your brain cells, and make you mentally ill’. Although phrases like this are often thrown at children and adolescence as a scare tactic to deter them from experimenting with opioids, some researchers in South Africa, Germany and the United States may have taken it quite literally, when they investigated and later published their paper on, “Schizophrenia Polygenic Risk and Brain Structural Changes in Methamphetamine-Associated Psychosis in a South African Population” (Passchier, et al., 2020).

How was the investigation conducted?

Saliva samples were collected for various cases and controls. The cases included patients that had Methamphetamine-associated psychosis (MAP) and patients who had a methamphetamine dependence (MD) and no psychosis. Healthy controls (HC) were also investigated for comparative purposes (Passchier, et al., 2020). The samples were genotyped, and quality control was performed on the data. Principal component analysis was performed to account for stratification, Structural brain imaging was performed to investigate the brain regions that have been linked to MAP and schizophrenia (Passchier, et al., 2020). Polygenic risk scoring was performed to determine the effect of the risk variants on the phenotype/ disease. Statistical analysis was then performed using tests, one of which included a t-test that tested the differences between the two case groups and the healthy group.

The results found the following:

The aim of the study was to determine how the polygenic risk scoring data from a European ethnicity based GWAS study on MAP compared with the brain measurement volumes tested in the South African MAP patients (Passchier, et al., 2020). The results of the investigation showed no significant association between Schizophrenia-derived risk scoring and the MAP disease diagnosis in patients.

The researchers also found that there was no correlation between the polygenic risk scoring and the volume measures from the different parts of the brain in the patients. The paper explains that that the negative result could be since Schizophrenia polygenic risk scores have no relation to the brain volume measurements seen in the case samples (Passchier, et al., 2020).

Due to the lack of GWAS data available for patients of African descent, the researchers found that people of African descent had the lowest polygenic score performance, and they concluded that the Polygenic risk score data from European population based studies were not applicable for the South African patients studied in this paper (Passchier, et al., 2020).

Ultimately the results for the study were inconclusive due to the limitations due to sample size, stratification bias and the risk of misclassification from the diagnostic interviews.

Impact of this research:

African health care systems like South Africa saw that mental and substance used disorders like schizophrenia increased by over 50% in the different populations just between the years 2000 and 2015 (Sankoh, et al., 2018). Diseases like Schizophrenia have led to over 14% of deaths globally and previous studies have found 145 genome wide significant loci for Schizophrenia ( Stevenson, et al., 2019). Mental health is a global problem, however very little genetic data is available/ recorded for mental health diseases that plague non-white populations. While the results of the study could not show any strong correlation between Schizophrenia and Crystal Meth use, the design of the study highlighted the need for more studies into non-European populations, like African populations that could uncover new risk variants.

References:

Stevenson, A. et al., 2019. Populations-Psychosis (NeuroGAP- Psychosis): a case-control study protocol and GWAS in Ethiopia, Kenya, South Africa and Uganda. BMJ, Volume 9, pp. 1- 9.

Passchier, R. V. et al., 2020. Schizophrenia Polygenic Risk and Brain Structural Changes in Methamphetamine-Associated Psychosis in South African Population. Fronteirs in Genetics, Volume 11, pp. 1- 7.

Sankoh, O., Sevalie, S. & Weston, M., 2018. Mental health in Africa. The Lancet Global Health, Volume 6, pp. 954- 955.

Burn wounds and P-fibrin

by Alexander Geragotellis

Background:

Burns are a global public health challenge and claim the lives of ±180 000 people each year [1]. The vast majority (±90-95%) of these deaths occur in LMICs and disproportionately afflict African children under the age of 5 years, who carry double the incidence of burn deaths compared to children under the age of 5 years worldwide [1]. Despite the extensive catalogue of burn wound coverage options, skin repair could still be defective owing to the complexity of the healing process. Cell-mediated treatment achieved through bioengineered constructs may provide alternative and more effective avenues to resolve burn wounds. Hydrogels are valuable tools in tissue engineering and regenerative medicine for stabilising tissue, and for delivering growth factors, bioactive ingredients and stem cells. The polymers used to make hydrogels can be natural [2], synthetic [3] or hybridised using both polymer types to infuse the desirable properties into one construct. The group who published the current research paper have previously reported on the advantageous properties of the poly(ethylene-glycol)-fibrin hybrid hydrogels [4]. Figure 1 offers a resource with further clarity on relevant tissue engineering terminology.

Aim:

The current study [5] aimed to evaluate the burn-wound healing potential of a bio-engineered 3D PEGylated-fibrin (P-fibrin) hybrid hydrogel as a scaffold to deliver adipocyte derived stem-cell (ASCs) using a rat model. The synthesis scheme has been summarised in Figure 2.

Figure 1 – Glossary of useful terminology to guide interpretation of the paper and results.

Figure 2 – Synthesis scheme for the ASC-embedded P-fibrin hybrid hydrogels used in the study [5]. ASCs were embedded within the hydrogels to try further augment the pro-regenerative activity of the P-fibrin hydrogels.

Objectives:

Methods used to achieve objectives have been summarised in Figure 3. By comparing burns wounds (i) untreated, or treated with either (ii) P-fibrin or (iii) P-fibrin with embedded ASCs between 7-21 days post- burn injury, authors set out to determine:

  1. Whether or not the application of the gels negatively affected burn wound closure.
  2. Characterise wound coverage and wound integration of the hydrogels using light and fluorescent microscopy.
  3. Explore angiogenic potential via immunohistochemical analysis of burn wounds to quantify blood vessels.
  4. Evaluate macrophage activation status of regenerating wounds, and how it is impacted by hydrogel application using immunohistochemistry.
  5. Assess collagen deposition and organisation 21 days post-injury to understand longer-term recovery phenotype.

Figure 3 – Rat burn model, adapted from Chung et. al [5], and accompanying methodologies used to achieve the objectives of the study.

Take home messages:

  • The major value of using a P-fibrin hydrogel appears to be with the increased cellularity of the granulation tissue at one week post-burn, suggesting an increase in tissue regeneration capability. The increased cellularity was similar to that observed when the P-fibrin was embedded with ASCs, indicating that the scaffold itself was the responsible factor and that the ASCs had little effect.
  • Angiogenesis is central process in tissue regeneration. The major value of embedding ASCs within the P-fibrin scaffolds was the bolstered neovascularisation observed at 7 days post-burn, which was significantly superior to the small increase observed with the P-fibrin only group. This would support the authors’ supplementary findings that suggest a role of the ASC secretome upregulating pro-angiogenic genes [5]. Although not fully studied, it is likely that the ASCs influence the population diversity of regenerative cells recruited to the burn wound to influence this superior angiogenic response.
  • To this end, there is some evidence in the present study to suggest that embedded ASCs can inflict a local tolerising pro-regenerative phenotype. Specifically, wounds treated with P-Fibrin embedded with ASCs showed a drastically greater coverage of the M2 immunosuppressive, pro-regenerative macrophages than when the wounds were treated with P-Fibrin gel alone.
  • It is encouraging that the wound thickness, collagen deposition and organisation between the studied hydrogel groups did not vary significantly, because this suggests that the hydrogels only accelerate but do not change the orchestrated sequence of the in-vivo regenerative response to full-thickness burns.
  • P-fibrin hydrogels hold great promise for burn wound healing applications, especially when conjugated with biological agents. Infection control is a crucial consideration in the burn wound healing process, and was not explored in the present study [5]. Interestingly, a recent study found that both infection control and neovascularisation post-burn can be enhanced through sequential delivery of P-fibrin embedded silver sulfadiazine loaded chitosan microspheres followed by P-fibrin embedded ASCs [6]. Future studies will likely focus on further characterising similar functional hydrogel constructs prior to progressing to more advanced trials.

References:

  1. World Health Organisation. 2018. Burns. Online: https://www.who.int/news-room/fact-sheets/detail/burns
  2. Janmey PA, Winer JP, Weisel JW. Fibrin gels and their clinical and bioengineering applications. J R Soc Interface. 2009;6(30):1-10.
  3. Overby RJ, Feldman DS. Influence of Poly (Ethylene Glycol) End Groups on Poly (Ethylene Glycol)-Albumin System Properties as a Potential Degradable Tissue Scaffold. Journal of Functional Biomaterials. 2019;10:1.
  4. Nam SY, Chung E, Suggs LJ, Emelianov SY. Combined ultrasound and photoacoustic imaging to noninvasively assess burn injury and selectively monitor a regenerative tissue-engineered construct. Tissue Eng Part C Methods. 2015;21(6):557-566.
  5. Chung E, Rybalko VY, Hsieh PL, Leal SL, Samano MA, Willauer AN, et al. Fibrin-based stem cell containing scaffold improves the dynamics of burn wound healing. Wound Repair Regen 2016;24:810–9.
  6. Banerjee J, Seetharaman S, Wrice NL, Christy RJ, Natesan S. Delivery of silver sulfadiazine and adipose derived stem cells using fibrin hydrogel improves infected burn wound regeneration. PLoS One. 2019;14(6):e0217965.

The Science of Human Sexuality

by Sesethu Mbunge

What better time, than the time of the release of the ever so controversial Lil Nas X’s music video for his single titled “Industry Baby”, to write about the neurobiology that underpins human sexuality? This masterpiece features an iconic shower scene, with a group of male bodies dancing in the nude, that had naysayers claiming that Lil Nas X is “turning people gay”. Contrary to popular belief, the nuance subject matter of gender identity and sexual orientation is not as simple as deciding to be gay. Although there is a huge gap in the understanding of the biological underpinnings of human sexuality, many studies have suggested that the prenatal environment, including the maternal immune environment as well as exposure to certain sex hormones, may play a role in gender identity and sexual orientation of the developing foetus. Further studies hypothesize that there is a genetic determinant of human sexuality, although these studies have been difficult to reproduce. It is believed that this resultant maternal, and potentially genetic, environment results in the organizational differentiation of the developing foetal brain. In simple terms, this means that these factors contribute to the structural differences in certain regions of the brain, and that these differences are what is attributed to the difference in the human sexual identity. The assumption with many of these studies was that sexuality is categorizable and binary. For the sake of cohesiveness, this summary will also be written under this assumption, although it is understood that sexuality is a spectrum.

Human sexual identity is categorized as gender identity and sexual orientation. Gender identity refers to one’s perception of oneself as male, female, or non-binary and this can be the same, or different from one’s biological sex. Sexual orientation refers to the pattern of emotional and/or sexual and romantic attractions to males, females, or both. To understand the effects of different factors on sexuality, let’s look at these factors individually.

Pre- and Perinatal Hormone Environment:

Animal studies have demonstrated that prenatal exposure to testosterone resulted in masculinization (male-type development) and that in the absence of testosterone feminization (female-type development) occurred. Masculinization results in permanent neural structural differentiation and occurs within the period when the brain is most sensitive to testosterone. Brain areas that are affected by testosterone levels are thought to be important for sexual differences in various adult behaviours including sexual behaviour, aggression, and cognition as well as gender identity and sexual orientation. Clinical studies have shown that in XY (typical male genotype) children that were born with ambiguous genitals developed into males when exposed to testosterone prenatally, but that if they had an androgen receptor (receptor for testosterone) mutation, they were phenotypically female and identified as female.

Studies in several animal models have shown that perinatal exposure to testosterone resulted in female partner preferences, whereas testosterone deprivation resulted in male partner preferences. In humans, it has been observed that women that were born with congenital adrenal hyperplasia (were exposed to an elevated amount of testosterone) developed masculinized genitals and behaviours and were less likely to be exclusively heterosexual in comparison to unaffected women.

Genetic Factors:

It is difficult to analyse the biological basis of gender identity in animal models, thus this is best studied in individuals that identify with a gender that is different from their biological sex. Although there is very limited evidence, it has been observed that in female-to-male transsexual individuals, there was a higher incidence of the A2 allele polymorphism for the gene that codes for a testosterone-synthesis catalysing enzyme, CYP17A1, compared to male-to-female transsexual individuals.

Familial and twin studies have shown that sexual orientation is moderately accounted for by a genetic component. A recent study approximated that about 40% and 20% of the variance in sexual orientation in men and women respectively was due to a genetic component. In a linkage study performed by Hamer in 1993, it was hypothesised that a locus, namely Xq28, on the X chromosome contained a gene that was loosely associated with homosexuality in men. This was then also confirmed in a larger genome-wide study, and it was also found that there were associations with chromosome 7 and 8. No specific genetic locus has been identified as associated with sexuality yet.

Neuroanatomy:

Studies have found that transgender individuals had structural and functional brain features that are more similar with individuals of the same gender identity, rather than with individuals with the same biological sex.

Rodent models have identified the sexually dimorphic preoptic nucleus (SDN) of the brain as the region associated with sexual partner preferences. In male rodents it was found that the larger the SDN was, the greater its attraction to female rats. It was also subsequently found that destruction of the SDN in male rats and ferrets either resulted in neutral or male preferences. This finding was also confirmed in sheep models, where they found that larger the ovine sexually dimorphic nuclei (oSDN) were associated with more female-oriented rams, whereas male-oriented rams had smaller oSDN. It was found that oSDN due to prenatal exposure to testosterone. Exposure of female lamb foetuses at the proper time was shown to alter oSDN size independently of genetic and phenotypic sex.

In humans, the third interstitial nucleus of the anterior hypothalamus (INAH3) has been implicated in sexuality. Based on its localization and the structure of its cytoskeleton, this nucleus resembles the oSDN of sheep. Studies have shown the INAH3 is smaller in homosexual men in comparison to heterosexual men, and the INAH3 in homosexual men is similar in size to that of women.

Maternal Immune Environment:

One interesting observation that has been made is the effect that the maternal immune environment has been shown to affect the sexual orientation of the developing foetus. It has been observed that homosexual men have, on average, more older brothers that heterosexual men. This is referred to as the fraternal birth order, and incidence of homosexuality increase by about 33% with each older brother. This is hypothesised to be due to the mother developing antibodies against a gene on the Y-chromosome that is a key factor in male brain development, and this immune response increases with each male pregnancy. This is subsequently thought to alter the neural structures that affect sexual orientation in boys that are conceived later. It was found that the mothers of homosexual sons that had many brothers, had a concentration of antibodies against neurolignin 4 (NLGN4Y), a gene that codes for a protein that is assumed to play a role in foetal brain development.

These factors are an indication that the events and environments that occur during early foetal development play a crucial role in determining the sexual identity of the developing foetus. Animal models have been found to display the causality of the effects of prenatal hormones on sexual orientation, but this however has not translated to gender identity. There are so many more biological processes that are implicated in sexual development that are yet to be understood or discovered. As such, it is biologically incorrect to reduce sexuality and sexual identity to a mere choice!

Reference:

Roselli, C., 2018. Neurobiology of gender identity and sexual orientation. Journal of Neuroendocrinology, 30(7).

Facts, some realistic heartbreak story, and an outrageous ending paragraph

by Sagel Kundieko 


At first, I thought it was a new virus that was practically wiping out the Chinese population. It was unrealistic that it would actually spread to the entire continent and cover all the many kilometres that there is to cover. Then we heard of Italy and the consequences of their stubbornness. Then finally it hit us too, in waves and lockdowns. It is really scary to think about how the economy has plummeted in this very short period of time. Also, how easily a virus from one corner of the world was easily able to cross barriers at such an overwhelming rate. On the other hand, the global pandemic aspect of it brings a sense of “we are all on this earth together” at the end of the day.  

The recent lootings and taxi violence is an offspring of the (increased) poverty, depression, and frustration from the lockdowns. It is clear that those most affected are from the black community because they have to commute to work and do not (literally) have pantries full of food or big companies that can make them money while they lockdown at home. This is not even considering that some do not have “homes” conducive for a lockdown or quarantine. Acknowledging that the lockdown was necessary, the inadequacy of the government in providing the necessary food to those who needed it, was problematic. 

On my immediate hand (usually written as on the other hand), the lockdown meant that I could not pursue my driver’s license because our documents needed to be renewed by the Home Affairs. In the grander scheme of things, that seems like a minimal issue, but the sense of unfulfillment still lingers, getting behind on an imaginary timeline I had set for myself. 

Furthermore, last year started off on a left foot (in the heat of the rising cases and lockdowns). I always felt that a problem is only a problem in relation to the other problems at hand. I imagined that something worse than my heartbreak would happen and I would forget about the man that broke my heart and move on, and it did. The idea of the possible end of the world or how insignificant and fragile our bodies are and how my life is worth nothing more than a statistic if I and those around me were to die, cured me of my heartbreak. A terrible parallel to draw between actual real world problems to a common heartbreak, it is unforgivable really. It is not even a parallel if you think of it, it is more of a mountain and me realising that because I am a pebble, then my problems must be a grain of sand, thus nothing to ponder ever so deeply on. I am more motivated now to do better, study harder, work harder, love God more, help those in need, go after my dreams and goals, and as I find true love, I experience it to the fullest of its capacities, because we do not know when another virus will head our way and who it will want to claim. I pray we survive through this as a world and do better for the future (do better in reference to the social class structures that have governed our countries, now we should realise that we are more the same than different and more together than apart).  

I also realise that the virus is the main topic at hand, but everything else that was wrong with the world before still exists. Even more so, humans are the deadliest virus this planet has ever been invaded by. That is an undeniable and uncontained fact.

A Whole New World

by Jesmika Singh

Am I really writing a piece about being in HONOURS? I still feel like I was just yesterday sending in applications for my first year of university. When they say university is over before you know it, they really weren’t joking. Regardless, it has been an exciting ride (even though parts of it have been stressful).

Throughout my schooling career and general social life, I have been someone that gets stressed very easily. I put a lot of pressure on myself to achieve my academic goals. Particularly in the third year of my undergraduate degree in 2020, I felt an even stronger need to push myself and put all my time and effort into my studies since everything was done through remote learning. As a result, the stress I felt during that year was unexplainable. Directly following that, I came into honours with the expectation that my stress would be even worse- I was moving to Cape Town from Durban; gaining more independence; being isolated from the majority of my loved ones and having to begin what I was told would be the hardest year of my university career. Granted, these things have been as challenging as expected, yet, I’m surprised to say that this has been one of the least stressful academic years I have had- perhaps I have gotten used to the stress or lost my ability to stress my usual amounts.

Honours is a year that I was told would push me to my breaking point- granted the year is far from over and there is still plenty of time left for that, somehow I have enjoyed the academic aspect of this year much more than any previous academic year. To be fair, if it were not for online learning, recorded lectures (I don’t know where I would be without these), teamwork and the lecturers, I doubt I would have been able to cope.

Something I have admired greatly about how this course has been run and kept my morale up- is how we are assessed. Unlike previous years, we were allowed (in some cases) to indicate the type of assessment we felt would best showcase our understanding of work and the way we were marked has been one of my favourite parts of the year. From the time I started school if your answer was not exactly what was in the memo, you didn’t get the mark- that was not the case this year. The lecturers took their time with each individual script/assignment to determine whether someone understood the work or not. If we didn’t get the correct answer but showed understanding, we could still do well. This kind of teaching and learning has helped me better understand my work, but more than that, it has helped me grow my confidence. If I had been marked like this for my entire schooling career, perhaps I wouldn’t have been so stressed and I may have been able to retain my work better. Being able to chase knowledge and understanding over answers from an unseen memo, has made a big difference in the way I take in knowledge.

I was also very fortunate to get a very helpful supervisor and co-supervisor this year. Without the constant guidance, kindness and willingness to assist from my co-supervisor, I don’t think I would have managed half of the challenges phased by my project and even the modules. By allowing me to ask questions at any time of the day and equipping me with the ability to solve problems I had myself, she has also assisted in helping me deal with the stress of Honours.

I am very grateful for being given this opportunity to do this incredible degree this year. I have made great friends, met highly accomplished academics, and opened doors for my career goals that I didn’t think possible.

If there was anything I would change about the way I handled this year, I would go into every assessment to aiming show my full understanding of topics rather than just putting down answers I thought were wanted.

To every individual that has helped me along my way through this Whole New World of Honours at UCT- Thank you!

CANCER RISK ESTIMATION USING COLONOSCOPIC SURVELLANCE AND MMR GENE MUTATIONS

by Kelly-Robyn Singh

Lynch syndrome is an autosomal dominantly inherited cancer syndrome which predisposes individuals to a wide range of cancers, most commonly, cancer of the colon and/or rectum (colorectal cancer- CRC). It presents as colonic adenomas (benign epithelial tissue tumor) at an early age of onset that is averagely seen in other cancers. Lynch syndrome is the most common type of hereditary colon cancer, and it is estimated that approximately 1 in every 300 people carry mutations which are associated with Lynch syndrome. These associated mutations are found in the mismatch repair (MMR) genes, MLH1, MSH2, MSH6 or PMS2. Consider the following analogy: the MMR genes encode the MMR machinery, which we can think of as the police-force of the genetic code, in the sense that they recognize inconsistencies in the genetic code which may have arisen during DNA synthesis, and they repair it to restore genetic stability, much like a policeman/woman would in the instance of crime. In a society without the police to maintain law and order, there would be chaos, much like there is when the mutated MMR genes cause non-functional MMR and subsequently, deleterious mutations are allowed to accumulate in the genetic code, uninterrupted.

The question is, could mutations in some of these mismatch repair genes have a more severe effect than others? Is colonic surveillance and removal of pre-cancerous adenomas an effective strategy to manage CRC risk and incidence? The paper by Møller et al. aims to investigate the effects of surveillance in individuals carrying Lynch Syndrome associated mutations and their risk of cancer in more effective and accurate estimates than the usual risk estimation approaches which mainly involve retrospective studies.

To accomplish this, a cohort of patients carrying mutations in the mismatch repair (MMR) genes, MLH1, MSH2, MSH6 and PMS2 were studied and monitored on an Oracle regional database, with the aim to correlate data across categories like age, sex and mutated gene as the data develops to identify significant trends.

The findings were that 314 patients had developed cancer out of 1942 mutation carriers with no prior history of cancer. The cancers were found were mostly CRC, followed by endometrial and ovarian. Interestingly, carriers with mutations in the MLH1 and MSH2 had an earlier age of onset (25 years) as compared to that of MSH6 and PMS2 carriers (40 years). The cumulative cancer incidence rates at 70 years (patient age)for each gene as well as ten-year crude survival can be found below.

Table 1: Cumulative cancer incidences for each MMR gene and ten-year crude survivals for their respective cancers

Figure 1: Cumulative incidences by age and mutated MMR gene for any cancer

These findings conclude that there are varied penetrance and expression patterns of each of the mismatch repair genes, with that of MLH1 and MSH2 being higher and therefore causing an earlier age of onset as well as incidence. The results of this paper conclude that colonoscopic surveillance did not significantly decrease the incidence of CRC, but it did result in a lower mortality rate. The early detection of pre-cancerous adenomas is therefore imperative to prevention and the prolonging of life.

References:

Møller P, Seppälä T, Bernstein I, Holinski-Feder E, Sala P, Evans DG, Lindblom A, Macrae F, Blanco I, Sijmons R, Jeffries J, Vasen H, Burn J, Nakken S, Hovig E, Rødland EA, Tharmaratnam K, de Vos Tot Nederveen Cappel WH, Hill J, Wijnen J, Green K, Lalloo F, Sunde L, Mints M, Bertario L, Pineda M, Navarro M, Morak M, Renkonen-Sinisalo L, Frayling IM, Plazzer JP, Pylvanainen K, Sampson JR, Capella G, Mecklin JP, Möslein G; Mallorca Group (http://mallorca-group.eu). Cancer incidence and survival in Lynch syndrome patients receiving colonoscopic and gynaecological surveillance: first report from the prospective Lynch syndrome database. Gut. 2017 Mar;66(3):464-472. doi: 10.1136/gutjnl-2015-309675. Epub 2015 Dec 9. PMID: 26657901; PMCID: PMC5534760.

« Older Entries