INTRODUCTION The main objective was to carry out a global DNA methylation analysis in a population with gender incongruence before gender-affirming hormone treatment (GAHT), in comparison to a cisgender population. METHODS A global CpG (cytosine-phosphate-guanine) methylation analysis was performed on blood from 16 transgender people before GAHT vs. 16 cisgender people using the Illumina© Infinium Human Methylation 850k BeadChip, after bisulfite conversion. Changes in the DNA methylome in cisgender vs. transgender populations were analyzed with the Partek® Genomics Suite program by a 2-way ANOVA test comparing populations by group and their sex assigned at birth. RESULTS The principal components analysis (PCA) showed that both populations (cis and trans) differ in the degree of global CpG methylation prior to GAHT. The 2-way ANOVA test showed 71,515 CpGs that passed the criterion FDR p < 0.05. Subsequently, in male assigned at birth population we found 87 CpGs that passed both criteria (FDR p < 0.05; fold change ≥ ± 2) of which 22 were located in islands. The most significant CpGs were related to genes: WDR45B, SLC6A20, NHLH1, PLEKHA5, UBALD1, SLC37A1, ARL6IP1, GRASP, and NCOA6. Regarding the female assigned at birth populations, we found 2 CpGs that passed both criteria (FDR p < 0.05; fold change ≥ ± 2), but none were located in islands. One of these CpGs, related to the MPPED2 gene, is shared by both, trans men and trans women. The enrichment analysis showed that these genes are involved in functions such as negative regulation of gene expression (GO:0010629), central nervous system development (GO:0007417), brain development (GO:0007420), ribonucleotide binding (GO:0032553), and RNA binding (GO:0003723), among others. STRENGTHS AND LIMITATIONS It is the first time that a global CpG methylation analysis has been carried out in a population with gender incongruence before GAHT. A prospective study before/during GAHT would provide a better understanding of the influence of epigenetics in this process. CONCLUSION The main finding of this study is that the cis and trans populations have different global CpG methylation profiles prior to GAHT. Therefore, our results suggest that epigenetics may be involved in the etiology of gender incongruence.

中文翻译：

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表观遗传学与性别不一致的基础有关：表观基因组范围的关联分析。

引言 主要目的是在性别确认激素治疗 (GAHT) 之前对性别不一致的人群与顺性别人群进行全球 DNA 甲基化分析。方法 在亚硫酸氢盐转化后，使用 Illumina© Infinium Human Methylation 850k BeadChip 对 GAHT 之前的 16 名跨性别者与 16 名顺性别者的血液进行全局 CpG（胞嘧啶-磷酸-鸟嘌呤）甲基化分析。使用 Partek® Genomics Suite 程序分析顺性别与跨性别人群中 DNA 甲基化组的变化，通过 2 路方差分析测试按组比较人群及其出生时分配的性别。结果 主成分分析 (PCA) 表明，两个群体（顺式和反式）在 GAHT 之前的全局 CpG 甲基化程度不同。2-way ANOVA 测试显示 71, 通过标准 FDR p < 0.05 的 515 个 CpG。随后，在出生时分配的男性群体中，我们发现 87 个 CpGs 通过了这两个标准（FDR p < 0.05；倍数变化 ≥ ± 2），其中 22 个位于岛屿中。最重要的 CpG 与基因有关：WDR45B、SLC6A20、NHLH1、PLEKHA5、UBALD1、SLC37A1、ARL6IP1、GRASP 和 NCOA6。关于出生时分配的女性群体，我们发现 2 个 CpG 通过了这两个标准（FDR p < 0.05；倍数变化 ≥ ± 2），但没有一个位于岛屿中。其中一个与 MPPED2 基因相关的 CpG 由跨性别男性和跨性别女性共享。富集分析表明，这些基因参与了基因表达负调控（GO:0010629）、中枢神经系统发育（GO:0007417）、大脑发育（GO:0007420）、核糖核苷酸结合（GO:0032553）、和 RNA 结合 (GO:0003723) 等。优势和局限 这是首次在 GAHT 之前对性别不一致的人群进行全球 CpG 甲基化分析。GAHT 之前/期间的前瞻性研究将更好地理解表观遗传学在这一过程中的影响。结论 本研究的主要发现是顺式和反式群体在 GAHT 之前具有不同的全局 CpG 甲基化谱。因此，我们的研究结果表明，表观遗传学可能与性别不一致的病因有关。GAHT 之前/期间的前瞻性研究将更好地理解表观遗传学在这一过程中的影响。结论 本研究的主要发现是顺式和反式群体在 GAHT 之前具有不同的全局 CpG 甲基化谱。因此，我们的研究结果表明，表观遗传学可能与性别不一致的病因有关。GAHT 之前/期间的前瞻性研究将更好地理解表观遗传学在这一过程中的影响。结论 本研究的主要发现是顺式和反式群体在 GAHT 之前具有不同的全局 CpG 甲基化谱。因此，我们的研究结果表明，表观遗传学可能与性别不一致的病因有关。