Studies in Cancer Epigenetics through a Sex and Gendered Lens: A Comprehensive Scoping Review.

Background: Sex and gender are vitally important in the study of epigenetic mechanisms for various types of cancer. However, little has been done to assess the state of sex and gender-based analyses (SGBA) in this field. The aim was to undertake a critical evaluation of sex and gender representation, discussion, and data analysis within the cancer epigenetics field since 2010. Methods: A PRISMA-ScR scoping review was conducted with 111 peer-reviewed studies comprising of colorectal, gastric, head and neck, hepatocellular carcinoma, and lung cancers. Data extraction and a quality appraisal were performed by a team of epidemiologists and bioethicists. Results: Of the 111 included studies, only 17 studies (15.3%) explicitly stated sex and gender analysis to be their primary aim. A total of 103 studies (92.8%) provided a detailed analysis of sex/gender as a biological or social variable, while the remaining 8 studies (7.2%) only stratified results by sex/gender. Although sex and gender were a key facet in all the eligible studies, only 7 studies (6.3%) provided an explicit definition of the terms "sex" or "gender", while the remaining 104 studies (93.7%) used the words "sex" or "gender" without providing a definition. A total of 84 studies (75.7%) conflated the concepts of "sex" and "gender", while 44 studies (39.6%) were inconsistent with their usage of the "sex" and "gender" terms. Conclusions: Very few studies offered a robust analysis of sex/gender data according to SAGER guidelines. We call for clear and directed guidelines regarding the use of sex/gender as a variable in epigenetics research.

Prevalence of cancer risk factors among transgender and gender diverse individuals: a cross-sectional analysis using UK primary care data.

BACKGROUND: Transgender and gender diverse (TGD) individuals experience an incongruence between their assigned birth sex and gender identity. They may have a higher prevalence of health conditions associated with cancer risk than cisgender people. AIM: To examine the prevalence of several cancer risk factors among TGD individuals compared with cisgender individuals. DESIGN AND SETTING: A cross-sectional analysis was conducted using data from the UK's Clinical Practice Research Datalink to identify TGD individuals between 1988-2020, matched to 20 cisgender men and 20 cisgender women on index date (date of diagnosis with gender incongruence), practice, and index age (age at index date). Assigned birth sex was determined from gender-affirming hormone use and procedures, and sex-specific diagnoses documented in the medical record. METHOD: The prevalence of each cancer risk factor was calculated and the prevalence ratio by gender identity was estimated using log binomial or Poisson regression models adjusted for age and year at study entry, and obesity where appropriate. RESULTS: There were 3474 transfeminine (assigned male at birth) individuals, 3591 transmasculine (assigned female at birth) individuals, 131 747 cisgender men, and 131 827 cisgender women. Transmasculine people had the highest prevalence of obesity (27.5%) and 'ever smoking' (60.2%). Transfeminine people had the highest prevalence of dyslipidaemia (15.1%), diabetes (5.4%), hepatitis C infection (0.7%), hepatitis B infection (0.4%), and HIV infection (0.8%). These prevalence estimates remained elevated in the TGD populations compared with cisgender persons in the multivariable models. CONCLUSION: Multiple cancer risk factors are more prevalent among TGD individuals compared with cisgender individuals. Future research should examine how minority stress contributes to the increased prevalence of cancer risk factors in this population.

Cancer researchers' perceptions of the importance of the sex of cell lines, animals, and human samples for cancer biology research.

Sex differences in cancer risk and outcome are currently a topic of major interest in clinical oncology. It is however unknown to what extent cancer researchers consider sex as a biological variable for their research. We conducted an international survey among 1243 academic cancer researchers and collected both quantitative and qualitative data. Although most of the participants indicated that they were familiar with the concept of studying sex differences in cancer biology, they did not think it was important to investigate sex differences in every context of cancer research nor in all tumor types. This is in stark contrast to the current recommendations and guidelines and illustrates the need for increased awareness among cancer researchers regarding the potential impact of the sex of cell lines, animals, and human samples in their studies.

Evolutionary and immune microenvironment dynamics during neoadjuvant treatment of oesophagael adenocarcinoma.

Locally advanced oesophageal adenocarcinoma (EAC) remains difficult to treat because of common resistance to neoadjuvant therapy and high recurrence rates. The ecological and evolutionary dynamics responsible for treatment failure are incompletely understood. Here, we performed a comprehensive multi-omic analysis of samples collected from EAC patients in the MEMORI clinical trial, revealing major changes in gene expression profiles and immune microenvironment composition that did not appear to be driven by changes in clonal composition. Multi-region multi-timepoint whole exome (300x depth) and paired transcriptome sequencing was performed on 27 patients pre-, during and after neoadjuvant treatment. EAC showed major transcriptomic changes during treatment with upregulation of immune and stromal pathways and oncogenic pathways such as KRAS, Hedgehog and WNT. However, genetic data revealed that clonal sweeps were rare, suggesting that gene expression changes were not clonally driven. Additional longitudinal image mass cytometry was performed in a subset of 15 patients and T-cell receptor sequencing in 10 patients, revealing remodelling of the T-cell compartment during treatment and other shifts in microenvironment composition. The presence of immune escape mechanisms and a lack of clonal T-cell expansions were linked to poor clinical treatment response. This study identifies profound transcriptional changes during treatment with limited evidence that clonal replacement is the cause, suggesting phenotypic plasticity and immune dynamics as mechanisms for therapy resistance with pharmacological relevance.

Demographic characteristics, long-term health conditions and healthcare experiences of 6333 trans and non-binary adults in England: nationally representative evidence from the 2021 GP Patient Survey.

OBJECTIVE: In order to address the lack of data on the health and healthcare needs of trans and non-binary adults, NHS England includes questions asking about both gender and trans status in its surveys to support quality improvement programmes.We used self-reported data from the GP Patient Survey to answer the research question: what are the demographic characteristics, health conditions and healthcare experiences of trans and non-binary adults in England? DESIGN/SETTING: Nationally representative, population-based cross-sectional survey in England with survey data collection from January to March 2021. PARTICIPANTS: 840 691 survey respondents including 6333 trans and non-binary adults. OUTCOMES: We calculated weighted descriptive statistics, and using logistic regression explored 15 long-term physical and mental health conditions, and 18 patient experience items, covering overall experience, access, communication and continuity. RESULTS: Trans and non-binary adults were younger, more likely to be from Asian, black, mixed or other ethnic groups and more likely to live in more deprived parts of the country. Age-specific patterns of long-term conditions were broadly similar among trans and non-binary adults compared with all other survey respondents, with some variation by condition. Overall, inequalities in long-term health conditions were largest for autism: OR (95% CI), 5.8 (5.0 to 6.6), dementia: 3.1 (2.5 to 3.9), learning disabilities: 2.8 (2.4 to 3.2) and mental health: 2.0 (1.9 to 2.2), with variation by age. In healthcare experience, disparities are much greater for interpersonal communication (OR for reporting a positive experience, range 0.4 to 0.7 across items) than access (OR range 0.8 to 1.2). Additionally, trans and non-binary adults report much higher preference for continuity 1.7 (1.6 to 1.8), with no evidence of any differences in being able to see or speak to a preferred general practitioner. CONCLUSION: This research adds up to date evidence about population demographics, health and healthcare needs to support healthcare improvement for trans and non-binary adults.

Analysis of Mortality Among Transgender and Gender Diverse Adults in England.

Importance: Limited prior research suggests that transgender and gender diverse (TGD) people may have higher mortality rates than cisgender people. Objective: To estimate overall and cause-specific mortality among TGD persons compared with cisgender persons. Design, Setting, and Participants: This population-based cohort study used data from general practices in England contributing to the UK's Clinical Practice Research Datalink GOLD and Aurum databases. Transfeminine (assigned male at birth) and transmasculine (assigned female at birth) individuals were identified using diagnosis codes for gender incongruence, between 1988 and 2019, and were matched to cisgender men and women according to birth year, practice, and practice registration date and linked to the Office of National Statistics death registration. Data analysis was performed from February to June 2022. Main Outcomes and Measures: Cause-specific mortality counts were calculated for categories of disease as defined by International Statistical Classification of Diseases and Related Health Problems, Tenth Revision chapters. Overall and cause-specific mortality rate ratios (MRRs) were estimated using Poisson models, adjusted for index age, index year, race and ethnicity, Index of Multiple Deprivation, smoking status, alcohol use, and body mass index. Results: A total of 1951 transfeminine (mean [SE] age, 36.90 [0.34] years; 1801 White [92.3%]) and 1364 transmasculine (mean [SE] age, 29.20 [0.36] years; 1235 White [90.4%]) individuals were matched with 68 165 cisgender men (mean [SE] age, 33.60 [0.05] years; 59 136 White [86.8%]) and 68 004 cisgender women (mean [SE] age, 33.50 [0.05] years; 57 762 White [84.9%]). The mortality rate was 528.11 deaths per 100 000 person-years (102 deaths) for transfeminine persons, 325.86 deaths per 100 000 person-years (34 deaths) for transmasculine persons, 315.32 deaths per 100 000 person-years (1951 deaths) for cisgender men, and 260.61 deaths per 100 000 person-years (1608 deaths) for cisgender women. Transfeminine persons had a higher overall mortality risk compared with cisgender men (MRR, 1.34; 95% CI, 1.06-1.68) and cisgender women (MRR, 1.60; 95% CI, 1.27-2.01). For transmasculine persons, the overall MMR was 1.43 (95% CI, 0.87-2.33) compared with cisgender men and was 1.75 (95% CI, 1.08-2.83) compared with cisgender women. Transfeminine individuals had lower cancer mortality than cisgender women (MRR, 0.52; 95% CI, 0.32-0.83) but an increased risk of external causes of death (MRR, 1.92; 95% CI, 1.05-3.50). Transmasculine persons had higher mortality from external causes of death than cisgender women (MRR, 2.77; 95% CI, 1.15-6.65). Compared with cisgender men, neither transfeminine nor transmasculine adults had a significantly increased risk of deaths due to external causes. Conclusions and Relevance: In this cohort study of primary care data, TGD persons had elevated mortality rates compared with cisgender persons, particularly for deaths due to external causes. Further research is needed to examine how minority stress may be contributing to deaths among TGD individuals to reduce mortality.

The co-evolution of the genome and epigenome in colorectal cancer.

Colorectal malignancies are a leading cause of cancer-related death1 and have undergone extensive genomic study2,3. However, DNA mutations alone do not fully explain malignant transformation4-7. Here we investigate the co-evolution of the genome and epigenome of colorectal tumours at single-clone resolution using spatial multi-omic profiling of individual glands. We collected 1,370 samples from 30 primary cancers and 8 concomitant adenomas and generated 1,207 chromatin accessibility profiles, 527 whole genomes and 297 whole transcriptomes. We found positive selection for DNA mutations in chromatin modifier genes and recurrent somatic chromatin accessibility alterations, including in regulatory regions of cancer driver genes that were otherwise devoid of genetic mutations. Genome-wide alterations in accessibility for transcription factor binding involved CTCF, downregulation of interferon and increased accessibility for SOX and HOX transcription factor families, suggesting the involvement of developmental genes during tumourigenesis. Somatic chromatin accessibility alterations were heritable and distinguished adenomas from cancers. Mutational signature analysis showed that the epigenome in turn influences the accumulation of DNA mutations. This study provides a map of genetic and epigenetic tumour heterogeneity, with fundamental implications for understanding colorectal cancer biology.

Phenotypic plasticity and genetic control in colorectal cancer evolution.

Genetic and epigenetic variation, together with transcriptional plasticity, contribute to intratumour heterogeneity1. The interplay of these biological processes and their respective contributions to tumour evolution remain unknown. Here we show that intratumour genetic ancestry only infrequently affects gene expression traits and subclonal evolution in colorectal cancer (CRC). Using spatially resolved paired whole-genome and transcriptome sequencing, we find that the majority of intratumour variation in gene expression is not strongly heritable but rather 'plastic'. Somatic expression quantitative trait loci analysis identified a number of putative genetic controls of expression by cis-acting coding and non-coding mutations, the majority of which were clonal within a tumour, alongside frequent structural alterations. Consistently, computational inference on the spatial patterning of tumour phylogenies finds that a considerable proportion of CRCs did not show evidence of subclonal selection, with only a subset of putative genetic drivers associated with subclone expansions. Spatial intermixing of clones is common, with some tumours growing exponentially and others only at the periphery. Together, our data suggest that most genetic intratumour variation in CRC has no major phenotypic consequence and that transcriptional plasticity is, instead, widespread within a tumour.

Researcher perspectives on ethics considerations in epigenetics: an international survey.

Over the past decade, bioethicists, legal scholars and social scientists have started to investigate the potential implications of epigenetic research and technologies on medicine and society. There is growing literature discussing the most promising opportunities, as well as arising ethical, legal and social issues (ELSI). This paper explores the views of epigenetic researchers about some of these discussions. From January to March 2020, we conducted an online survey of 189 epigenetic researchers working in 31 countries. We questioned them about the scope of their field, opportunities in different areas of specialization, and ELSI in the conduct of research and knowledge translation. We also assessed their level of concern regarding four emerging non-medical applications of epigenetic testing-i.e., in life insurance, forensics, immigration and direct-to-consumer testing. Although there was strong agreement on DNA methylation, histone modifications, 3D structure of chromatin and nucleosomes being integral elements of the field, there was considerable disagreement on transcription factors, RNA interference, RNA splicing and prions. The most prevalent ELSI experienced or witnessed by respondents were in obtaining timely access to epigenetic data in existing databases, and in the communication of epigenetic findings by the media. They expressed high levels of concern regarding non-medical applications of epigenetics, echoing cautionary appraisals in the social sciences and humanities literature.

Knowing to Ask and Feeling Safe to Tell - Understanding the Influences of HCP-Patient Interactions in Cancer Care for LGBTQ+ Children and Young People.

Background: Lesbian, gay, bisexual, transgender, queer or questioning (LGBTQ+) people experience healthcare inequalities in cancer care. Previous studies have focused on knowledge, attitudes and behaviours of healthcare professionals (HCPs) treating adults with cancer and how these contribute to inequalities. To date, no research has focused on HCPs treating LGBTQ+ children and adolescents with cancer in the UK. This is important given that this group may be at a critical time for exploring their gender identity and sexual orientation, whilst also facing a cancer diagnosis. We aimed to explore the knowledge, attitudes and behaviours of paediatric, teenage and young adult oncology HCPs treating LGBTQ+ patients in the UK. Methods: We carried out semi-structured interviews with 8 HCPs in paediatric, teenage and young adult (TYA) oncology from the Royal Marsden NHS Foundation Trust. Eight questions were asked, which centred around participants' knowledge, attitudes and behaviours regarding management of LGBTQ+ patients in oncology. Interview transcripts were analysed by inductive thematic analysis. Results: We identified 10 themes, including novel themes (how HCPs acquire knowledge and expectations of a 'third party' to be the expert) which may underlie previously observed trends in knowledge, attitudes and behaviours of HCPs. We highlight other themes and HCP concerns specific to care of LGBTQ+ patients in paediatrics (influence of the parental-carer dynamic, concerns around patient age and development as a barrier to disclosure) which require further research. We found evidence of the interrelatedness of HCP knowledge, attitudes and behaviours and the ability of these elements to positively influence each other. We mapped our themes across these elements to form a new suggested framework for improving HCP-patient interactions in LGBTQ+ Cancer Care. We found a need both for individual HCP education and organisational change, with creation of a culture of psychological safety to improve patient care. Conclusion: Knowledge, attitudes and behaviours of HCPs are closely interdependent when providing care to young LGBTQ+ patients with cancer. The authors suggest that future efforts to improve care of these patients address this complexity by spanning the domains of our suggested framework. Whilst HCP education is essential, change must also occur at an organisational level.

Auditing the Editor: A Review of Key Translational Issues in Epigenetic Editing.

Currently, most advances in site-specific epigenetic editing for human use are concentrated in basic research, yet, there is considerable interest to translate this technology beyond the bench. This review highlights recent developments with epigenetic editing technology in comparison with the canonical CRISPR-Cas genome editing, as well as the epistemic and ethical considerations with preemptive translation of epigenetic editing into clinical or commercial use in humans. Key considerations in safety, equity, and access to epigenetic editing are highlighted, with a spotlight on the ethical, legal, and social issues of this technology in the context of global health equity.

Understanding the role of sex hormones in cancer for the transgender community.

Sex hormones are crucial for the body's development and function. Therefore, many transgender people seek hormone therapy as part of their transition. However, sex hormones modulate cancer risk. Studying sex hormones in cisgender and transgender populations will improve our knowledge of their biological role in cancer and reduce health disparities.

Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues.

Molecular clocks that record cell ancestry mutate too slowly to measure the short-timescale dynamics of cell renewal in adult tissues. Here, we show that fluctuating DNA methylation marks can be used as clocks in cells where ongoing methylation and demethylation cause repeated 'flip-flops' between methylated and unmethylated states. We identify endogenous fluctuating CpG (fCpG) sites using standard methylation arrays and develop a mathematical model to quantitatively measure human adult stem cell dynamics from these data. Small intestinal crypts were inferred to contain slightly more stem cells than the colon, with slower stem cell replacement in the small intestine. Germline APC mutation increased the number of replacements per crypt. In blood, we measured rapid expansion of acute leukemia and slower growth of chronic disease. Thus, the patterns of human somatic cell birth and death are measurable with fluctuating methylation clocks (FMCs).

Attitudes of transgender men and non-binary people to cervical screening: a cross-sectional mixed-methods study in the UK.

BACKGROUND: Transgender men and non-binary people assigned female at birth (TMNB) who have not had surgery to remove the cervix are recommended to undertake cervical screening with the same frequency as cisgender women, but evidence suggests that TMNB have lower odds of lifetime and up-to-date cervical screening uptake. AIM: To understand the attitudes towards and preferences for cervical screening among UK-based TMNB. DESIGN AND SETTING: Cross-sectional survey of TMNB at an NHS gender identity clinic (GIC) and an NHS sexual health service specialising in care of transgender people. METHOD: Recruitment was via email invitations to patients of the GIC and sexual health service. Inclusion criteria were: female sex assigned at birth; transgender man, masculine, or non-binary gender identity; aged ≥18 years; and UK resident. Quantitative results were analysed using descriptive statistics, and free-text comments were analysed thematically. RESULTS: In total there were 137 participants; 80% identified as transmasculine,18% as non-binary, and the remaining participants reported other noncisgender identities. Sixty-four participants (47%) were eligible for cervical screening and 37 (58%) of those had been screened. Only 34 (53%) of those eligible felt they had sufficient information about cervical screening. Just over half (n = 71/134, 53%) stated they would like the option to self-swab for high-risk human papillomavirus. Only half (n = 68/134, 51%) of participants were in favour of an automatic invitation for cervical screening. Thematic analysis identified a number of additional barriers to and facilitators of screening. CONCLUSION: TMNB have identified numerous potential areas for change that may improve cervical screening uptake and patient experience.

An evaluation of self-perceived knowledge, attitudes and behaviours of UK oncologists about LGBTQ+ patients with cancer.

INTRODUCTION: Over one million people in the UK identify as LGBTQ+ (lesbian, gay, bisexual, transgender, queer or questioning). Research has shown that this population experience differing cancer risk factors compared with non-LGBTQ+ patients and persistent inequalities in cancer care. Literature concerning the knowledge of oncologists of this group's healthcare needs is limited; our study aimed to evaluate knowledge, attitudes and behaviours of UK oncologists about LGBTQ+ patients. METHODS: A 53-question survey was delivered via a secure online platform. Questions covered respondent demographics, knowledge, attitudes and behaviours with the majority of responses on a Likert scale. Oncologists were recruited via email from professional bodies and social media promotion. Informed consent was sought and responses fully anonymised. Multifactorial ordinal logistic regression and Fisher's exact test were used to assess for interactions between demographics and responses with Holm-Bonferroni multiple testing correction. RESULTS: 258 fully completed responses were received. Respondents had a median age of 43 years (range 28-69); 65% consultants and 35% registrars; 42% medical, and 54% clinical, oncologists. 84% felt comfortable treating LGBTQ+ patients but only 8% agreed that they were confident in their knowledge of specific LGBTQ+ patient healthcare needs. There were low rates of routine enquiry about sexual orientation (5%), gender identity (3%) and preferred pronouns (2%). 68% of oncologists felt LGBTQ+ healthcare needs should be a mandatory component of postgraduate training. CONCLUSIONS: This survey showed that UK oncologists feel comfortable treating LGBTQ+ patients but may fail to identify these patients in their clinic, making it more difficult to meet LGBTQ+ healthcare needs. There is self-awareness of deficits in knowledge of LGBTQ+ healthcare and a willingness to address this through postgraduate training. Educational resources collated and developed in accordance with this study would potentially improve the confidence of oncologists in treating LGBTQ+ patients and the cancer care these patients receive.