Investigating the shared genetic basis and causal relationships between mucosa-associated lymphoid tissue inflammation and psychiatric disorders.

Background: Chronic and acute inflammation of the mucosa-associated lymphoid tissue have been positively linked to the development of psychiatric disorders in observational studies. However, it remains unclear whether this association is causal. In the present study, we investigated this association, using as proxies genetically predicted tonsillectomy, appendectomy and appendicitis on psychiatric disorders including major depressive disorder (MDD), schizophrenia (SCZ), bipolar depression (BD) and anxiety (ANX) via a two-sample Mendelian randomization (MR) analysis. Methods: Genetic association summary statistics for tonsillectomy, appendectomy and appendicitis were sourced from FinnGen Consortium, comprising data from 342,000 participants. Genetic correlations between all exposures and outcome were calculated with Linkage Disequilibrium Score (LDSC) Regression analysis. MR estimates were then calculated to assess their impact on the risk of developing psychiatric disorders. Sensitivity analysis was employed to test for any directional pleiotropy. Results: Our results suggest that there is no direct causal association between tonsillectomy, appendectomy or appendicitis with a heightened risk for development of psychiatric disorders. The robustness of the results of the main MR analysis was further confirmed with additional sensitivity analyses. However, a moderate inverse genetic correlation was observed between tonsillectomy and MDD traits (rg=-0.39, p-value (P)=7.5x10-5). Conclusion: Our findings provide, for the first time, evidence that there is no causal association between tonsillectomy or appendectomy on subsequent vulnerability of developing psychiatric disorders. Future studies using larger sample size GWAS should focus on unraveling the confounding factors and mediators to investigate this relationship further.

Insights into suicidal behavior among psoriatic arthritis patients: A systematic review and a genetic linkage disequilibrium analysis.

OBJECTIVES: To systematically assess the magnitude of suicidal behavior among PsA patients and identify associated risk factors. Also identify common genes or coinherited single nucleotide polymorphisms (SNPs) implicated in suicidal behavior and PsA. METHODS: Based on the PRISMA guidelines, we conducted a systematic literature review of the online databases PubMed/Medline, Web of Science, and EMBASE from inception to May 2022. Full-text original articles that describe suicidal behavior in PsA patients were eligible. All registered genome-wide association study (GWAS) data in the GWAS catalog database for PsA and psychiatric traits, such as suicidal behavior, and depression, were downloaded for further analysis. RESULTS: A total of 48 articles were identified, and 6 were relevant to the study question .Among the 122,160 PsA patients, 700 had suicidal behavior (0,57%). The range of age in one study was between 30 and 49 years, and 64% of PsA patients with suicidal behavior were female. Among 13,899 PsA patients 74 had suicidal ideation (0.53%) and 125 suicide attempts occurred (0.9%). In two studies, among 17,383 patients, 13 complete suicides occurred (0.07%). A genetic haplotype on chromosomal region 6p21.1, spanning from 29,597,596 to 32,251,264 Mb, contains predisposing SNPs for PsA and depression. 6p21.1-6p21.3 is the chromosomal region containing the HLA genes of classes I, II and III. CONCLUSION: Suicide behavior in PsA patients was associated with depression and other psychiatric comorbidities. Further evidence supports a genetic origin, at least partly. Awareness of these findings can help clinicians to recognize suicide behavior and prevent suicide attempts.

Genome-wide association studies reveal shared genetic haplotypes of autoimmune rheumatic and endocrine diseases with psychiatric disorders.

BACKGROUND: Several studies have shown that autoimmune diseases are associated with psychiatric diseases like depression and psychosis. Genetic evidence supports this association. The aim of this study was to investigate if genetic variants predisposing to autoimmune diseases and psychiatric disorders are genetically linked, constructing the common haplotypes. METHODS: All registered single nucleotide polymorphisms (SNPs) in the Genome-wide association studies ("GWAS catalog") having been associated with autoimmune rheumatic and endocrine diseases were investigated for being in linkage disequilibrium with any psychiatric disorders' associated SNPs. Analysis was performed by the LDtrait and LDhap bioinformatics tools. RESULTS: Multiple chromosomal regions have been detected containing rheumatic/endocrine diseases' predisposing SNPs and psychiatric disorders' predisposing SNPs. The genetic haplotypes have been constructed for some of these genetic regions. Six of the autoimmune rheumatic and endocrine diseases examined here share a common haplotype with psychiatric diseases at the HLA locus 6p21-22. CONCLUSION: Our study shows that autoimmune diseases and psychiatric diseases are genetically linked. Genetic haplotypes have been constructed, showing in detail this genetic linkage.

The Role of TP53 in Adaptation and Evolution.

The TP53 gene is a major player in cancer formation, and it is considered the most important tumor suppressor gene. The p53 protein acts as a transcription factor, and it is involved in DNA repair, senescence, cell-cycle control, autophagy, and apoptosis. Beyond cancer, there is evidence that TP53 is associated with fertility, aging, and longevity. Additionally, more evidence exists that genetic variants in TP53 are associated with environmental adaptation. Special TP53 amino-acid residues or pathogenic TP53 mutations seem to be adaptive for animals living in hypoxic and cold environments or having been exposed to starvation, respectively. At the somatic level, it has recently been proven that multiple cancer genes, including TP53, are under positive selection in healthy human tissues. It is not clear why these driver mutations do not transform these tissues into cancerous ones. Other studies have shown that elephants have multiple TP53 copies, probably this being the reason for the very low cancer incidence in these large animals. This may explain the famous Peto's paradox. This review discusses in detail the multilevel role of TP53 in adaptation, according to the published evidence. This role is complicated, and it extends from cells to individuals and to populations.

The double face of cold in cancer.

In a recent paper published in Nature, multiple evidence is provided that cold exposure causes tumor growth restriction in mice, by activating brown adipose tissue metabolism and by subsequent cancer cells' glucose starvation. The paper shows a tumor growth inhibition by 80% for multiple cancer types in mice exposed to 4 °C in comparison with mice exposed to 30 °C. These results are very promising since cost effective protocols could be designed for future clinical trials, for several cancer forms. In this commentary, an extensive analysis is performed on the potential of these results. Some previous published studies are discussed as well, showing differences in tumor growth for mice housed in different external temperatures.

An evolutionary explanation for antibiotics' association with increased colon cancer risk.

: More than 10 studies have confirmed the association of antibiotic overuse with colorectal cancer. The exact cause is unknown, but most authors hypothesize that disturbance of colon microbiota is the main culprit. In this commentary, an evolutionary explanation is proposed. It is well known that antibiotics can induce antibiotic resistance in bacteria through selection of mutators-DNA mismatch repair deficient (dMMR) strains. Mutators have an increased survival potential due to their high mutagenesis rate. Antibiotics can also cause stress in human cells. Selection of dMMR colon cells may be advantageous under this stress, mimicking selection of bacterial mutators. Concomitantly, mismatch repair deficiency is a common cause of cancer, this may explain the increased cancer risk after multiple cycles of oral antibiotics. This proposed rationale is described in detail, along with supporting evidence from the peer-reviewed literature and suggestions for testing hypothesis validity. Treatment schemes could be re-evaluated, considering toxicity and somatic selection mechanisms. Lay Summary: The association of antibiotics with colon cancer is well established but of unknown cause. Under an evolutionary framework, antibiotics may select for stress-resistant cancerous cells that lack mechanisms for DNA mismatch repair (MMR). This mimics the selection of antibiotic resistant 'mutators'-MMR-deficient micro-organisms-highly adaptive due to their increased mutagenesis rate.

TP53 Mutant Versus Wild-Type Zebrafish Larvae Under Starvation Stress: Larvae Can Live Up to 17 Days Post-Fertilization Without Food.

In this study, an experimental protocol has been developed for comparing survival rates of mutant and wild-type zebrafish larvae under extreme starvation. Zebrafish larvae were placed in 96-well plates at fourth day postfertilization (dpf) and larvae were not fed at all from hatching to cease. Zdf1 zebrafish line was used, a strain carrying the (cancer) pathogenic TP53-M214K amino acid substitution. TP53-M214 corresponds to the human TP53-M246 and both residues are located on the DNA-binding domain of the p53 protein. Survival statistical analysis did not show any significant difference in the overall survival rates between homozygous mutant and wild-type larvae. When considering 15 dpf as the endpoint of the experiment (66% of larvae died), a borderline statistical significance was observed for the dominant model of inheritance (p = 0.015; relative hazard = 0.8320). Despite the fact yolk sac of larvae is depleted at 7-8 dpf, 34% of larvae survive until 15 dpf and 1.5% until 17 dpf. Concluding, three main results derive from this study: (1) pathogenic homozygous mutations in TP53 probably do not alter survival rates of zebrafish larvae under starvation; (2) zebrafish larvae can live up to 17 dpf without food, surviving only with their initial nutritional supplies; and (3) an easy and affordable protocol has been developed for estimating survival rates of zebrafish larvae under stressful conditions.

Suicidal behavior in patients with systematic lupus erythematosus: Systematic literature review and genetic linkage disequilibrium analysis.

BACKGROUND: Previous studies suggested that patients with Systematic Lupus Erythematosus (SLE) have a higher risk of suicidal behavior, including suicidal ideation, attempt and complete suicide. Systematic data describing the SLE patients' clinical characteristics and risk factors of suicidal behavior are lacking. OBJECTIVES: To determine the magnitude of suicidal behavior among SLE patients and to examine predictors associated with suicidal behavior. An additional aim was to identify common genes or coinherited single nucleotide polymorphisms (SNP) implicated in suicidal behavior and SLE. METHODS: We conducted a systematic literature review based on PRISMA guidelines using the online databases PubMed/Medline, EMBASE and Web of Science, from inception to August 2021. Full-text original articles that examined the relationship between SLE patients with suicidal behavior were eligible for our review. Two reviewers independently reviewed articles to assess eligibility using the Newcastle-Ottawa Scale and the Joanna Briggs Institute criteria. Systematic reviews, metanalysis, narrative review, case reports, case series, including less than 10 patients, and conference abstracts, were excluded. All registered genome-wide association study (GWAS) data in the GWAS catalog database for SLE and psychiatric traits (suicidal behavior, depression, anxiety, psychosis) were downloaded for further analysis. Special in silico tools were used to examine if any genetic polymorphisms (SNPs) that predispose for SLE or psychiatric traits can be inherited together as a single haplotype. This could be posing a risk factor for a coexisting psychiatric condition in SLE patients. RESULTS: Of the 64 articles identified, 22 were relevant to the study question; cross-sectional (n = 8) and prospective cohorts (n = 6) were the most frequently retrieved studies. Among the 27,106 SLE patients with SLE, 802 had suicidal behavior (2.9%), and of those, 87.9% were female. Suicide attempt occurred in 573/802 (71.4%) and complete suicide in 18/802 (3%). Major depressive disorder was the most frequently reported coexisting psychiatric condition associated with suicidal behavior, followed by psychosis and social phobia. In addition, several clinical manifestations were linked to suicidal behavior, particularly neuropsychiatric lupus, serositis, mucocutaneous, and renal involvement. Further, high scores in disease activity and damage indices were associated with suicidal behavior. A haplotype in chromosomal region 6p21.33 was found to contain a combination of risk alleles predisposing for SLE and depression, the most common psychiatric disorder associated with suicidal behavior. CONCLUSION: Suicide behavior in SLE patients was associated with depression, neuropsychiatric lupus, active disease and damage. Further evidence supports a genetic origin of psychiatric symptoms in SLE patients. Awareness of these findings can guide clinicians to recognize suicide behavior promptly and prevent suicide attempts.

SARS-CoV-2: tracing the origin, tracking the evolution.

The origin of SARS-CoV-2 is uncertain. Findings support a "bat origin" but results are not highly convincing. Studies found evidence that SARS-CoV-2 was around for many years before the pandemic outbreak. Evidence has been published that the progenitor of SARS-CoV-2 already had the capability to bind strongly to the human ACE2 receptor. This may be an indication that many other animal viruses are capable to jump to humans, having already affinity for a human receptor. This is quite worrying since current ecosystems' collapse brings people to high proximity with animals, increasing probabilities for random viral transitions. On the other hand, future adaptation of SARS-CoV-2 is of great concern. Virus-host interactions are complicated and unfortunately, we still do not have accurate tools for predicting viruses' future evolution. Viral adaptation is a multifactorial process and probably SARS-CoV-2 will not become soon, as we wish, a harmless infection. However, humanity is currently under the largest vaccination program and it's of great interest to see if vaccinations will change the evolutionary game against the virus.

Drug Injection-Related Norms and High-Risk Behaviors of People Who Inject Drugs in Athens, Greece.

Drug use involves social interactions. Therefore, norms in the proximal environment of people who inject drugs (PWID) can favor behaviors that may result in HIV transmission. This work aimed at studying drug injection-related norms and their potential association with risky behaviors among PWID in Athens, Greece, in the context of economic recession and political activism that followed the fiscal crisis and soon after a recent HIV outbreak had leveled off. The Transmission Reduction Intervention Project (TRIP) was a social network-based approach (June 2013 to July 2015) that involved two groups of PWID seeds-with recent HIV infection and with long-term HIV infection and one control group of HIV-negative PWID. Network contacts of seeds were also enrolled. TRIP participants answered a questionnaire that included items on injection-related norms and behaviors. TRIP recruited 320 PWID (HIV positive, 44.4%). TRIP participants, especially those without HIV, often recalled or perceived as normative among their partners and in their networks some behaviors that can lead to HIV transmission. TRIP participants who recalled that they were encouraged by their regular drug partners to use an unclean syringe were almost twice as likely to report that they share syringes [odds ratio (OR) = 2.03; 95% confidence interval (CI) = 1.86-2.21], or give syringes to someone else (OR = 1.70; 95% CI = 1.42-2.04) as those who did not recall such an encouragement. Associations were modified by HIV status. HIV negatives, who were reportedly encouraged to share nonsyringe injecting equipment, were almost 4.5 times as likely to share that material as HIV-negative participants who were not encouraged (OR = 4.59, 95% CI = 4.12-5.11). Further research is needed on the multiple determinants (social, economic, and political) of norms in the social environments of PWID. Since peer norms are associated with risky behaviors, interventions should be developed to encourage norms and peer pressure against the sharing of injection equipment.

Directed Evolution. The Legacy of a Nobel Prize.

This article is part of an anniversary issue of Journal of Molecular Evolution, commenting on a paper published on 1999 by the Nobel laureate Frances Arnold and her colleague Kentaro Miyazaki. The paper by Miyazaki and Arnold presented saturation mutagenesis as an alternative method to random mutagenesis for obtaining enzymes with increasing stability. Both techniques were conceived to accomplish directed evolution, an approach honoured by the Nobel Prize of Chemistry 2018. Here, I am commenting on the pros and cons of random and saturation mutagenesis, while also discussing important results from directed evolution. I conclude that molecular evolution is finding new applications in science and it is definitely an integral part of the genomic era's revolution.

Animal-to-Human Viral Transitions: Is SARS-CoV-2 an Evolutionarily Successful One?

Transmission of viruses from one species to another is not unusual in nature. Despite this, evolutionarily successful transmissions are rare. Such events can cause pandemics and are followed by host-virus coevolution procedures that can increase the fitness potential of viruses. In this perspective article, I recognize eight main types of trans-species viral transmission. I consider two of them as evolutionarily successful, explaining why coronavirus SARS-CoV-2 could be one of them.

Antagonistic Pleiotropy in Human Disease.

Between the 1930s and 1950s, scientists developed key principles of population genetics to try and explain the aging process. Almost a century later, these aging theories, including antagonistic pleiotropy and mutation accumulation, have been experimentally validated in animals. Although the theories have been much harder to test in humans despite research dating back to the 1970s, recent research is closing this evidence gap. Here we examine the strength of evidence for antagonistic pleiotropy in humans, one of the leading evolutionary explanations for the retention of genetic risk variation for non-communicable diseases. We discuss the analytical tools and types of data that are used to test for patterns of antagonistic pleiotropy and provide a primer of evolutionary theory on types of selection as a guide for understanding this mechanism and how it may manifest in other diseases. We find an abundance of non-experimental evidence for antagonistic pleiotropy in many diseases. In some cases, several studies have independently found corroborating evidence for this mechanism in the same or related sets of diseases including cancer and neurodegenerative diseases. Recent studies also suggest antagonistic pleiotropy may be involved in cardiovascular disease and diabetes. There are also compelling examples of disease risk variants that confer fitness benefits ranging from resistance to other diseases or survival in extreme environments. This provides increasingly strong support for the theory that antagonistic pleiotropic variants have enabled improved fitness but have been traded for higher burden of disease later in life. Future research in this field is required to better understand how this mechanism influences contemporary disease and possible consequences for their treatment.

Editorial: A New Bright Era for Evolutionary Medicine.

Evolutionary Medicine is a fast-growing research field providing biomedical scientists with valuable information on molecular and pathophysiological mechanisms of disease. Evolutionary theory explains many medical conditions and it can contribute to new innovative treatments. This is the reason that Journal of Molecular Evolution has devoted this issue to Evolutionary Medicine. Nine detailed review papers are included in this issue, analyzing topics that are among the "hottest" subjects of Evolutionary Medicine. All information is up to date and highly valuable for scientists that would like to start their career or get updated on this field.

GWAS studies reveal a possible genetic link between cancer and suicide attempt.

Inuit is the population with the highest incidence of suicide attempt and cancer in the world. Previous studies reported that people attempted suicide have a higher future risk for cancer. In view of these data, the largest available genome wide association studies (GWAS) for four major mental disorder groups were screened here for any common genes with all known cancer associated genes and oncogenes/tumor suppressor genes. A common genetic background came out only between suicide attempt and cancer (cancer associated genes analysis: RR = 1.64, p = 7.83 × 10-5; oncogenes/tumor suppressor genes analysis: RR = 2.55, p = 2.82 × 10-22), this supporting existing epidemiological data. Incidence/prevalence of both conditions was found to correlate with extreme cold geographical regions (adjusted R2 = 0.135, p = 3.00 × 10-4); this is not the case for other mental disorders. Our results show a possible genetic link between suicide attempt and cancer and a possible evolutionary connection of both diseases with extreme cold environments. These data are useful for future molecular studies or even for investigation of possible therapeutic protocols.

Correction to: Evidence that DNA repair genes, a family of tumor suppressor genes, are associated with evolution rate and size of genomes.

In the original publication of this article [1], the Figure 1 and Figure 2 were wrong. The Figure 1 "Heat map showing the quantity of DNA repair genes, from red to blue in ascending order, per species' genome (numbers at the top of the figure represent the species code that is found in Table 1). Each DNA repair gene pathway was analyzed separately in rows. Radiated species' genomes are richer in DNA repair genes. Analytical data can be found in Additional file 2: Table S2. M mammals, B&R birds and reptiles, BF bony fishes" should be the picture of Figure 2. The figure 2 "Linear regression analysis. The number of DNA repair genes is linearly related to genome size and protein number. As a negative control, we show that genome size is not linearly related with protein number" should be the picture of figure 1.

Evidence that DNA repair genes, a family of tumor suppressor genes, are associated with evolution rate and size of genomes.

Adaptive radiation and evolutionary stasis are characterized by very different evolution rates. The main aim of this study was to investigate if any genes have a special role to a high or low evolution rate. The availability of animal genomes permitted comparison of gene content of genomes of 24 vertebrate species that evolved through adaptive radiation (representing high evolutionary rate) and of 20 vertebrate species that are considered as living fossils (representing a slow evolutionary rate or evolutionary stasis). Mammals, birds, reptiles, and bony fishes were included in the analysis. Pathway analysis was performed for genes found to be specific in adaptive radiation or evolutionary stasis respectively. Pathway analysis revealed that DNA repair and cellular response to DNA damage are important (false discovery rate = 8.35 × 10-5; 7.15 × 10-6, respectively) for species evolved through adaptive radiation. This was confirmed by further genetic in silico analysis (p = 5.30 × 10-3). Nucleotide excision repair and base excision repair were the most significant pathways. Additionally, the number of DNA repair genes was found to be linearly related to the genome size and the protein number (proteome) of the 44 animals analyzed (p < 1.00 × 10-4), this being compatible with Drake's rule. This is the first study where radiated and living fossil species have been genetically compared. Evidence has been found that cancer-related genes have a special role in radiated species. Linear association of the number of DNA repair genes with the species genome size has also been revealed. These comparative genetics results can support the idea of punctuated equilibrium evolution.

The "cancer-cold" hypothesis and possible extensions for the Nordic populations.

Cancer incidence is inexplicably high in cold countries. This has been revealed by recent genetic and epidemiological studies. These studies used data from the GLOBOCAN-2012 database, for 186 populations and for a variety of cancer types. Cancer incidence in Nordic people is particularly high for the frequent cancer forms, like breast, prostate and colon cancer. A relationship of cancer with cold is suspected since Inuit and Alaska Indians that live in even more extreme low temperatures have the higher cancer rates in the world. In this article, possible reasons for this phenomenon are discussed. These explanations are related with: evolutionary adaptation to extreme cold, the genetic background of Nordic people, the experimentally proven fast growth and metastasis of tumors at low temperatures, high concentration of certain air pollutants at cold environments, low levels of serum Vitamin D, overdiagnosis by the medical doctors and high quality of the health system in Nordic countries. Lifestyle parameters are not discussed in detail, although these may be equally crucial for cancer risk in cold countries. In conclusion, more studies are needed to elucidate the real causes of this epidemiological pattern.