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Multiomics (RNA-Seq and ATAC-Seq) Forge the Way Towards a Better Understanding of Type 2 Diabetes

By Stuart P. Atkinson, Ph.D.

November 6, 2024

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Introduction: Chromatin Accessibility at the Crossroads Between Genetic Variants and Cell Stress Responses in Type 2 Diabetes

The pathogenesis of type 2 diabetes – characterized by high blood sugar, insulin resistance, and insulin deficiency - involves complex interactions between disease-associated genetic variants and endoplasmic reticulum and inflammatory stress (Halban et al.). Unfortunately, the functional effects of type 2 diabetes genetic variants on stress-induced transcriptional responses by pancreatic islet cells – which produce hormones such as glucagon (a cells) and insulin (b cells) - remain largely unknown even though an association between endoplasmic reticulum and inflammatory stress and islet cell dysfunction in type 2 diabetes has been previously defined.

Notably, a range of studies has revealed that a subset of type 2 diabetes genetic variants can alter chromatin accessibility/effector gene expression at cis-regulatory elements (CREs) – non-coding sequences containing transcription factor binding sites required for proper spatiotemporal expression of an associated gene - in islet cells under steady-state conditions, suggesting a pivotal role for epigenetic mechanisms in the pathogenesis of in type 2 diabetes.

Recently, researchers from the laboratories of Duygu Ucar and Michael L. Stitzel (Jackson Laboratory for Genomic Medicine) mapped genome-wide changes to chromatin accessibility at CREs via assay for transposase-accessible chromatin with sequencing (ATAC-Seq) and gene expression via RNA sequencing (RNA-Seq) in human islets from multiple non-diabetic donors exposed to endoplasmic reticulum and inflammatory stress.

Their findings – published in Cell Metabolism – now provide insight into the transcriptional regulatory circuitry that mediates islet cell stress responses associated with type 2 diabetes pathogenesis (Sokolowski et al.) and describe the context-specific effects of disease-associated genetic variants.

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RNA-Seq and ATAC-Seq Forge the Way Towards a Better Understanding of Type 2 Diabetes

The initial transcriptional analysis of human islets ex vivo exposed to endoplasmic reticulum/inflammatory stress via RNA-Seq revealed multiple transcriptional responses and afforded a comprehensive genome-wide view of modulated genes and pathways. Comparative analyses suggested that the two types of stress elicited distinct, complementary transcriptional responses, inducing multiple stress-specific pathways and repressing islet cell-type-specific functions. Overall, 30% of expressed genes displayed stress-responsive alterations in their levels. Subsequent single-cell RNA-Seq profiling of islets revealed that islet β cells responded more robustly than α cells to endoplasmic reticulum stress (Lee and Lee). Said responses included a transcriptional profile defined by the elevated expression of apoptosis-related genes, which may increase the sensitivity/vulnerability of a β cell subset to endoplasmic reticulum-stress-induced cell death. Of note, these data reveal that α cells also respond to stress, but to a lesser extent, and that their study may offer further insight given that studies have uncovered potential α cell roles in islet pathological responses in diabetes (Bosi et al.).

Comparative whole-islet chromatin accessibility profiling via ATAC-Seq (Buenrostro et al.) (prepared using the Active motif ATAC prep kit) and analysis of stress responses next revealed that endoplasmic reticulum and inflammatory stress substantially remodeled the epigenome, with notable changes to accessibility occurring at distal CREs (14% of islet CREs displayed a stress-responsive alteration in chromatin accessibility). Interestingly, endoplasmic reticulum and inflammatory stress elicited distinct epigenetic restructuring events involving different sets of transcription factors (as the regulatory drivers of islet cell stress responses) whose gene expression was also modulated by the specific stress type. Overall, these data suggested the tight regulation of cellular stress responses in the type 2 diabetes context at the epigenetic level via the activation of critical transcription factors and increased chromatin accessibility at their binding sites.

Sokolowski et al. next sought to identify genetic variants associated with diabetes that might modulate CRE use/activity and associated processes and characterized putative type 2 diabetes genetic variants that overlapped CREs whose chromatin accessibility became altered in response to stress. In total, fifty-two type 2 diabetes genetic variants overlapped thirty-eight stress-responsive CREs (including twenty-one specifically induced by endoplasmic reticulum stress) that may contribute to type 2 diabetes etiology by altering CRE use/activity. Overall, this analysis highlighted a number of putative type 2 diabetes genetic variants with context-specific effects on transcriptional processes modulating islet responses to stress.

Subsequent variant-to-function analyses finally suggested that the type 2 diabetes-associated rs6917676-T risk allele (overlaps a stress-responsive CRE in an islet enhancer hub; Miguel-Escalada et al.) contributed to disease risk/progression by enhancing accessibility at endoplasmic reticulum-stress-responsive islet CREs and increasing the expression of the MAP3K5 gene (encodes an endoplasmic stress-responsive MAP3K5 kinase that promotes apoptosis via JNK/p38 signaling; Pepin et al.) to promote/sensitize/enhance β cell apoptosis. Expression levels of MAP3K5, as the endoplasmic reticulum-stress-responsive putative rs6917676 type 2 diabetes effector gene, correlated inversely with β cell abundance in human islets and became elevated in β cells from type 2 diabetes patients; additionally, pharmacologic MAP3K5 inhibition reduced the level of islet cell apoptosis.

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Conclusion and Future Directions

By combining transcriptomic and chromatin accessibility (thanks to ATAC-Seq) analyses, the authors provided genome-wide insight into the stress responses of human islet cells and the context-specific effects of type 2 diabetes genetic variants. Even given the invaluable insight gained, the authors highlighted the need for additional research, including the study of stress response dynamics and the application of organoid, pancreatic slice, or animal models with transplanted human islets to understand the totality of the factors contributing to islet dysfunction in type 2 diabetes.

For more on how ATAC-Seq can provide new insight into disease pathogenesis, see Cell Metabolism, October 2024.

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About the author

Stuart P. Atkinson, Ph.D.

Stuart was born and grew up in the idyllic town of Lanark (Scotland). He later studied biochemistry at the University of Strathclyde in Glasgow (Scotland) before gaining his Ph.D. in medical oncology; his thesis described the epigenetic regulation of the telomerase gene promoters in cancer cells. Following Post-doctoral stays in Newcastle (England) and Valencia (Spain) where his varied research aims included the exploration of epigenetics in embryonic and induced pluripotent stem cells, Stuart moved into project management and scientific writing/editing where his current interests include polymer chemistry, cancer research, regenerative medicine, and epigenetics. While not glued to his laptop, Stuart enjoys exploring the Spanish mountains and coastlines (and everywhere in between) and the food and drink that it provides!

Contact Stuart on Twitter with any questions

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