Epigenetics Is Implicated in the Basis of Gender Incongruence: An Epigenome-Wide Association Analysis

After the trans brain: a critique of the neurobiological accounts of embodied trans* identities

This paper critically analyses three main neurobiological hypotheses on trans* identities: the neurobiological theory about the origin of gender dysphoria, the neurodevelopmental cortical hypothesis, and the alternative hypothesis of self-referential thinking and body perception. In this study I focus then the attention on three elements: the issue of (de)pathologisation, the idea of the trans brain, and the aetiology of trans* identities. While the neurobiological theory about the origin of gender dysphoria and the neurodevelopmental cortical hypothesis claim the existence of the trans brain, each offering its own neurobiological depiction, the hypothesis of self-referential thinking and body perception doesn't postulate a distinctive neurobiological trait for all trans* people. I problematize both portrayals of the trans brain departing from the findings and conceptualizations of the paradigm shifting brain mosaicism. Unlike the hypothesis of self-referential thinking and body perception that keeps the question of causation open, both the neurobiological theory about the origin of gender dysphoria and the neurodevelopmental cortical hypothesis situate the origin of trans* identities in the neurobiological domain. I challenge the biological deterministic framework in which this aetiology is inscribed from a dynamic processual entanglement perspective. Finally, concerning the issue of (de)pathologisation of trans* identities, an evolution can be seen in each of the hypothesis and among them, from the least to the most depathologising. However, I question their complete departure from a pathologising framework.

Early Female Transgender Identity after Prenatal Exposure to Diethylstilbestrol: Report from a French National Diethylstilbestrol (DES) Cohort

Diagnostic of transsexualism and gender incongruence are terms to describe individuals whose self-identity does not match their sex assignment at birth. A transgender woman is an individual assigned male at birth (AMAB) on the basis of the external or internal genitalia who identifies and lives as a woman. In recent decades, a significant increase in the number of transgender people has been reported. Although, its etiology is unknown, biological, anatomical, genetic, environmental and cultural factors have been suggested to contribute to gender variation. In XY animals, it has been shown that environmental endocrine disruptors, through their anti-androgenic activity, induce a female identity. In this work, we described four XY individuals who were exposed in utero to the xenoestrogen diethylstilbesterol (DES) and were part of the French HHORAGES cohort. They all reported a female transgender identity starting from childhood and adolescence. This high prevalence of male to female transgenderism (1.58%) in our cohort of 253 DES sons suggests that exposure to chemicals with xenoestrogen activity during fetal life may affect the male sex identity and behavior.

CBLL1 is hypomethylated and correlates with cortical thickness in transgender men before gender affirming hormone treatment

Gender identity refers to the consciousness of being a man, a woman or other condition. Although it is generally congruent with the sex assigned at birth, for some people it is not. If the incongruity is distressing, it is defined as gender dysphoria (GD). Here, we measured whole-genome DNA methylation by the Illumina © Infinium Human Methylation 850k array and reported its correlation with cortical thickness (CTh) in 22 transgender men (TM) experiencing GD versus 25 cisgender men (CM) and 28 cisgender women (CW). With respect to the methylation analysis, TM vs. CW showed significant differences in 35 CpGs, while 2155 CpGs were found when TM vs. CM were compared. With respect to correlation analysis, TM showed differences in methylation of CBLL1 and DLG1 genes that correlated with global and left hemisphere CTh. Both genes were hypomethylated in TM compared to the cisgender groups. Early onset TM showed a positive correlation between CBLL1 and several cortical regions in the frontal (left caudal middle frontal), temporal (right inferior temporal, left fusiform) and parietal cortices (left supramarginal and right paracentral). This is the first study relating CBLL1 methylation with CTh in transgender persons and supports a neurodevelopmental hypothesis of gender identity.

Precision oncology: Artificial intelligence, circulating cell-free DNA, and the minimally invasive detection of pancreatic cancer-A pilot study

BACKGROUND

Pancreatic cancer (PC) is among the most lethal cancers. The lack of effective tools for early detection results in late tumor detection and, consequently, high mortality rate. Precision oncology aims to develop targeted individual treatments based on advanced computational approaches of omics data. Biomarkers, such as global alteration of cytosine (CpG) methylation, can be pivotal for these objectives. In this study, we performed DNA methylation profiling of pancreatic cancer patients using circulating cell-free DNA (cfDNA) and artificial intelligence (AI) including Deep Learning (DL) for minimally invasive detection to elucidate the epigenetic pathogenesis of PC.

METHODS

The Illumina Infinium HD Assay was used for genome-wide DNA methylation profiling of cfDNA in treatment-naïve patients. Six AI algorithms were used to determine PC detection accuracy based on cytosine (CpG) methylation markers. Additional strategies for minimizing overfitting were employed. The molecular pathogenesis was interrogated using enrichment analysis.

RESULTS

In total, we identified 4556 significantly differentially methylated CpGs (q-value < 0.05; Bonferroni correction) in PC versus controls. Highly accurate PC detection was achieved with all 6 AI platforms (Area under the receiver operator characteristics curve [0.90-1.00]). For example, DL achieved AUC (95% CI): 1.00 (0.95-1.00), with a sensitivity and specificity of 100%. A separate modeling approach based on logistic regression-based yielded an AUC (95% CI) 1.0 (1.0-1.0) with a sensitivity and specificity of 100% for PC detection. The top four biological pathways that were epigenetically altered in PC and are known to be linked with cancer are discussed.

CONCLUSION

Using a minimally invasive approach, AI, and epigenetic analysis of circulating cfDNA, high predictive accuracy for PC was achieved. From a clinical perspective, our findings suggest that that early detection leading to improved overall survival may be achievable in the future.

Neuronal expression in Drosophila of an evolutionarily conserved metallophosphodiesterase reveals pleiotropic roles in longevity and odorant response

Evolutionarily conserved genes often play critical roles in organismal physiology. Here, we describe multiple roles of a previously uncharacterized Class III metallophosphodiesterase in Drosophila, an ortholog of the MPPED1 and MPPED2 proteins expressed in the mammalian brain. dMpped, the product of CG16717, hydrolyzed phosphodiester substrates including cAMP and cGMP in a metal-dependent manner. dMpped is expressed during development and in the adult fly. RNA-seq analysis of dMppedKO flies revealed misregulation of innate immune pathways. dMppedKO flies showed a reduced lifespan, which could be restored in Dredd hypomorphs, indicating that excessive production of antimicrobial peptides contributed to reduced longevity. Elevated levels of cAMP and cGMP in the brain of dMppedKO flies was restored on neuronal expression of dMpped, with a concomitant reduction in levels of antimicrobial peptides and restoration of normal life span. We observed that dMpped is expressed in the antennal lobe in the fly brain. dMppedKO flies showed defective specific attractant perception and desiccation sensitivity, correlated with the overexpression of Obp28 and Obp59 in knock-out flies. Importantly, neuronal expression of mammalian MPPED2 restored lifespan in dMppedKO flies. This is the first description of the pleiotropic roles of an evolutionarily conserved metallophosphodiesterase that may moonlight in diverse signaling pathways in an organism.

Exploring gender dysphoria and related outcomes in a prospective cohort study: protocol for the Swedish Gender Dysphoria Study (SKDS)

INTRODUCTION

There has been a drastic increase in the reported number of people seeking help for gender dysphoria in many countries over the last two decades. Yet, our knowledge of gender dysphoria and related outcomes is restricted due to the lack of high-quality studies employing comprehensive approaches. This longitudinal study aims to enhance our knowledge of gender dysphoria; different aspects will be scrutinised, focusing primarily on the psychosocial and mental health outcomes, prognostic markers and, secondarily, on the underlying mechanisms for its origin.

METHODS AND ANALYSIS

The Swedish Gender Dysphoria Study is an ongoing multicentre longitudinal cohort study with 501 registered participants with gender dysphoria who are 15 years old or older. Participants at different phases of their clinical evaluation process can enter the study, and the expected follow-up duration is three years. The study also includes a comparison group of 458 age- and county-matched individuals without gender dysphoria. Data on the core outcomes of the study, which are gender incongruence and experienced gender dysphoria, body satisfaction and satisfaction with gender-affirming treatments, as well as other relevant outcomes, including mental health, social functioning and life satisfaction, are collected via web surveys. Two different research visits, before and after starting on gender-affirming hormonal treatment (if applicable), are planned to collect respective biological and cognitive measures. Data analysis will be performed using appropriate biostatistical methods. A power analysis showed that the current sample size is big enough to analyse continuous and categorical outcomes, and participant recruitment will continue until December 2022.

ETHICS AND DISSEMINATION

The ethical permission for this study was obtained from the Local Ethical Review Board in Uppsala, Sweden. Results of the study will be presented at national and international conferences and published in peer-reviewed journals. Dissemination will also be implemented through the Swedish Gender Dysphoria Study network in Sweden.

DNA-Methylation Signatures of Tobacco Smoking in a High Cardiovascular Risk Population: Modulation by the Mediterranean Diet

Biomarkers based on DNA methylation are relevant in the field of environmental health for precision health. Although tobacco smoking is one of the factors with a strong and consistent impact on DNA methylation, there are very few studies analyzing its methylation signature in southern European populations and none examining its modulation by the Mediterranean diet at the epigenome-wide level. We examined blood methylation smoking signatures on the EPIC 850 K array in this population (n = 414 high cardiovascular risk subjects). Epigenome-wide methylation studies (EWASs) were performed analyzing differential methylation CpG sites by smoking status (never, former, and current smokers) and the modulation by adherence to a Mediterranean diet score was explored. Gene-set enrichment analysis was performed for biological and functional interpretation. The predictive value of the top differentially methylated CpGs was analyzed using receiver operative curves. We characterized the DNA methylation signature of smoking in this Mediterranean population by identifying 46 differentially methylated CpGs at the EWAS level in the whole population. The strongest association was observed at the cg21566642 (p = 2.2 × 10-32) in the 2q37.1 region. We also detected other CpGs that have been consistently reported in prior research and discovered some novel differentially methylated CpG sites in subgroup analyses. In addition, we found distinct methylation profiles based on the adherence to the Mediterranean diet. Particularly, we obtained a significant interaction between smoking and diet modulating the cg5575921 methylation in the AHRR gene. In conclusion, we have characterized biomarkers of the methylation signature of tobacco smoking in this population, and suggest that the Mediterranean diet can increase methylation of certain hypomethylated sites.

Alzheimer's Precision Neurology: Epigenetics of Cytochrome P450 Genes in Circulating Cell-Free DNA for Disease Prediction and Mechanism

Precision neurology combines high-throughput technologies and statistical modeling to identify novel disease pathways and predictive biomarkers in Alzheimer's disease (AD). Brain cytochrome P450 (CYP) genes are major regulators of cholesterol, sex hormone, and xenobiotic metabolism, and they could play important roles in neurodegenerative disorders. Increasing evidence suggests that epigenetic factors contribute to AD development. We evaluated cytosine ('CpG')-based DNA methylation changes in AD using circulating cell-free DNA (cfDNA), to which neuronal cells are known to contribute. We investigated CYP-based mechanisms for AD pathogenesis and epigenetic biomarkers for disease detection. We performed a case-control study using 25 patients with AD and 23 cognitively healthy controls using the cfDNA of CYP genes. We performed a logistic regression analysis using the MetaboAnalyst software computer program and a molecular pathway analysis based on epigenetically altered CYP genes using the Cytoscape program. We identified 130 significantly (false discovery rate correction q-value < 0.05) differentially methylated CpG sites within the CYP genes. The top two differentially methylated genes identified were CYP51A1 and CYP2S1. The significant molecular pathways that were perturbed in AD cfDNA were (i) androgen and estrogen biosynthesis and metabolism, (ii) C21 steroid hormone biosynthesis and metabolism, and (iii) arachidonic acid metabolism. Existing evidence suggests a potential role of each of these biochemical pathways in AD pathogenesis. Next, we randomly divided the study group into discovery and validation sub-sets, each consisting of patients with AD and control patients. Regression models for AD prediction based on CYP CpG methylation markers were developed in the discovery or training group and tested in the independent validation group. The CYP biomarkers achieved a high predictive accuracy. After a 10-fold cross-validation, the combination of cg17852385/cg23101118 + cg14355428/cg22536554 achieved an AUC (95% CI) of 0.928 (0.787~1.00), with 100% sensitivity and 92.3% specificity for AD detection in the discovery group. The performance remained high in the independent validation or test group, achieving an AUC (95% CI) of 0.942 (0.905~0.979) with a 90% sensitivity and specificity. Our findings suggest that the epigenetic modification of CYP genes may play an important role in AD pathogenesis and that circulating CYP-based cfDNA biomarkers have the potential to accurately and non-invasively detect AD.

Concordance for Gender Dysphoria in Genetic Female Monozygotic (Identical) Triplets

The biopsychosocial etiology of gender dysphoria is poorly understood, but current thought suggests a complex interaction of genetic, hormonal, environmental, and differences in brain development and physiology. Twin studies have implicated a genetic role in the formation of gender identity. Congruence for gender dysphoria is more common among monozygotic twins compared to dizygotic twins. We present a case of monozygotic (identical) triplets who have each transitioned from female to male under the care of a university transgender health service. Each triplet experienced gender dysphoria from childhood and has undergone transitional endocrine care and various aspects of gender-affirming surgery. Although a pure genetic or biological component cannot be attributed as a cause of their gender dysphoria with absolute certainty since the triplets were raised together, this unusual case of gender dysphoria among a set of monozygotic triplets adds support for a heritable role in gender identity formation.

Sex-specific DNA methylation: impact on human health and development

Human evolution has shaped gender differences between males and females. Over the years, scientific studies have proposed that epigenetic modifications significantly influence sex-specific differences. The evolution of sex chromosomes with epigenetics as the driving force may have led to one sex being more adaptable than the other when exposed to various factors over time. Identifying and understanding sex-specific differences, particularly in DNA methylation, will help determine how each gender responds to factors, such as disease susceptibility, environmental exposure, brain development and neurodegeneration. From a medicine and health standpoint, sex-specific methylation studies have shed light on human disease severity, progression, and response to therapeutic intervention. Interesting findings in gender incongruent individuals highlight the role of genetic makeup in influencing DNA methylation differences. Sex-specific DNA methylation studies will empower the biotechnology and pharmaceutical industry with more knowledge to identify biomarkers, design and develop sex bias drugs leading to better treatment in men and women based on their response to different diseases.

Artificial Intelligence and Circulating Cell-Free DNA Methylation Profiling: Mechanism and Detection of Alzheimer's Disease

Background: Despite extensive efforts, significant gaps remain in our understanding of Alzheimer’s disease (AD) pathophysiology. Novel approaches using circulating cell-free DNA (cfDNA) have the potential to revolutionize our understanding of neurodegenerative disorders. Methods: We performed DNA methylation profiling of cfDNA from AD patients and compared them to cognitively normal controls. Six Artificial Intelligence (AI) platforms were utilized for the diagnosis of AD while enrichment analysis was used to elucidate the pathogenesis of AD. Results: A total of 3684 CpGs were significantly (adj. p-value < 0.05) differentially methylated in AD versus controls. All six AI algorithms achieved high predictive accuracy (AUC = 0.949−0.998) in an independent test group. As an example, Deep Learning (DL) achieved an AUC (95% CI) = 0.99 (0.95−1.0), with 94.5% sensitivity and specificity. Conclusion: We describe numerous epigenetically altered genes which were previously reported to be differentially expressed in the brain of AD sufferers. Genes identified by AI to be the best predictors of AD were either known to be expressed in the brain or have been previously linked to AD. We highlight enrichment in the Calcium signaling pathway, Glutamatergic synapse, Hedgehog signaling pathway, Axon guidance and Olfactory transduction in AD sufferers. To the best of our knowledge, this is the first reported genome-wide DNA methylation study using cfDNA to detect AD.

Gender-affirming hormone therapy induces specific DNA methylation changes in blood

Background

DNA methylation is an epigenetic mark that is influenced by underlying genetic profile, environment, and ageing. In addition to X-linked DNA methylation, sex-specific methylation patterns are widespread across autosomal chromosomes and can be present from birth or arise over time. In individuals where gender identity and sex assigned at birth are markedly incongruent, as in the case of transgender people, feminization or masculinization may be sought through gender-affirming hormone therapy (GAHT). GAHT is a cornerstone of transgender care, yet no studies to date have investigated its effect on genome-wide methylation. We profiled genome-wide DNA methylation in blood of transgender women (n = 13) and transgender men (n = 13) before and during GAHT (6 months and 12 months into feminizing or masculinizing hormone therapy).

Results

We identified several thousand differentially methylated CpG sites (DMPs) (Δβ ≥ 0.02, unadjusted p value < 0.05) and several differentially methylated regions (DMRs) in both people undergoing feminizing and masculinizing GAHT, the vast majority of which were progressive changes over time. X chromosome and sex-specific autosomal DNA methylation patterns established in early development are largely refractory to change in association with GAHT, with only 3% affected (Δβ ≥ 0.02, unadjusted p value < 0.05). The small number of sex-specific DMPs that were affected by GAHT were those that become sex-specific during the lifetime, known as sex-and-age DMPs, including DMRs in PRR4 and VMP1 genes. The GAHT-induced changes at these sex-associated probes consistently demonstrated a shift towards the methylation signature of the GAHT-naïve opposite sex, and we observed enrichment of previously reported adolescence-associated methylation changes.

Conclusion

We provide evidence for GAHT inducing a unique blood methylation signature in transgender people. This study advances our understanding of the complex interplay between sex hormones, sex chromosomes, and DNA methylation in the context of immunity. We highlight the need to broaden the field of ‘sex-specific’ immunity beyond cisgender males and cisgender females, as transgender people on GAHT exhibit a unique molecular profile.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13148-022-01236-4.

Rodent Model of Gender-Affirming Hormone Therapies as Specific Tool for Identifying Susceptibility and Vulnerability of Transgender People and Future Applications for Risk Assessment

Transgenders (TGs) are individuals with gender identity and behaviour different from the social norms; they often undergo gender-affirming hormone therapy (HT). HT for TG men involves testosterone treatment and, for TG women, oestrogen plus androgen-lowering agents. Due-but not limited-to the lifelong lasting HT, usually TG people experience several physical and behavioural conditions leading to different and specific susceptibility and vulnerability in comparison to general population, including the response to chemical contaminants present in daily life. In particular, the exposure to the widespread endocrine disrupters (EDs) may affect hormonal and metabolic processes, leading to tissue and organ damage. Since the endocrine system of TG people is overstimulated by HT and, often, the targets overlap with ED, it is reasonable to hypothesize that TG health deserves special attention. At present, no specific tools are available to study the toxicological effects of environmental contaminants, including EDs, and the potential long-term consequences of HT on TG people. In this context, the development of adequate and innovative animal models to mimic gender-affirming HT have a high priority, since they can provide robust data for hazard identification in TG women and men, leading to more reliable risk assessment.