Periodic Reporting for period 4 - DecodeDiabetes (Expanding the genetic etiological and diagnostic spectrum of monogenic diabetes mellitus)
Période du rapport: 2023-05-01 au 2024-10-31
Whole genome sequencing is quickly becoming a routine clinical instrument. However, our ability to decipher DNA variants is still largely limited to protein-coding exons, which comprise 1% of the genome. Most known Mendelian mutations are in exons, yet genetic testing still fails to show causal coding mutations in more than 50% of well-characterized Mendelian disorders. This defines a pressing need to interpret noncoding genome sequences, and to establish the role of noncoding mutations in genetically inherited diseases.
Recent examples have highlighted that mutations in enhancers can not only predispose to polygenic disorders but also cause Mendelian defects. Based on these studies, we have tried to address the following questions: (i) what is the overall impact of penetrant regulatory mutations in human diabetes? (ii) do regulatory mutations cause distinct forms of diabetes? (iii) more generally, can we develop a strategy to systematically tackle regulatory variation in diverse forms of human disease?
Our project has addressed these questions with unique resources. First, we have created epigenomic and functional perturbation resources to interpret the regulatory genome in beta cells, which are critically important for human diabetes. We have also used experimental models to uncover the essential role of noncoding regions, and to identify new types of cis-regulatory elements that play a key role in beta cell genome regulation. Finally, we have sequenced >1300 index patients with a clinical phenotype consistent with monogenic diabetes, yet lacking mutations in known gene culprits after genetic testing, and therefore with increased likelihood of harboring noncoding mutations. This resource has uncovered insights into the genetic underpinnings of young-onset diabetes, and into genetic regulators of diabetes-relevant networks
Recent examples have highlighted that mutations in enhancers can not only predispose to polygenic disorders but also cause Mendelian defects. Based on these studies, we have tried to address the following questions: (i) what is the overall impact of penetrant regulatory mutations in human diabetes? (ii) do regulatory mutations cause distinct forms of diabetes? (iii) more generally, can we develop a strategy to systematically tackle regulatory variation in diverse forms of human disease?
Our project has addressed these questions with unique resources. First, we have created epigenomic and functional perturbation resources to interpret the regulatory genome in beta cells, which are critically important for human diabetes. We have also used experimental models to uncover the essential role of noncoding regions, and to identify new types of cis-regulatory elements that play a key role in beta cell genome regulation. Finally, we have sequenced >1300 index patients with a clinical phenotype consistent with monogenic diabetes, yet lacking mutations in known gene culprits after genetic testing, and therefore with increased likelihood of harboring noncoding mutations. This resource has uncovered insights into the genetic underpinnings of young-onset diabetes, and into genetic regulators of diabetes-relevant networks
The team has led three major studies linking noncoding variants to type 2 diabetes (T2D). The first, Miguel-Escalada et al. (Nature Genetics, 2019), created a 3D chromatin interaction map in human pancreatic islets, enabling linkage of noncoding risk variants to target genes by physical proximity. Over 1,300 enhancer hubs enriched for T2D variants were identified, explaining a substantial portion of heritability. CRISPR validation confirmed these enhancers regulate diabetes-related genes, including previously unlinked ones. Incorporating enhancer-based polygenic risk scores improved T2D prediction, especially in lean, early-onset individuals. This work provided a framework for interpreting noncoding variants in islet gene regulation. In Atla et al. (Genome Biology, 2022), we examined RNA splicing as a regulatory layer, analyzing splicing QTLs (sQTLs) in islets from ~400 donors. Many sQTLs overlapped with T2D risk loci, indicating altered splicing as a contributor to disease mechanisms. A third study, co-led with the Hansen team and published in Nature Metabolism (2024), analyzed β-cell function genetics using GWAS data from ~26,000 individuals. We identified 55 associations at 44 loci influencing insulin secretion dynamics. By integrating genetic data with islet transcriptomic and epigenomic maps, we uncovered 92 candidate effector genes regulating insulin secretion. These findings link genetic control of β-cell function to distinct T2D risk pathways.
In studies to understand why certain cis regulatory elements are vulnerable to diabetes-causing mutations, we discovered that rare enhancer mutations upstream of PTF1A causing pancreatic agenesis disrupt a lead enhancer that activates an entire enhancer cluster (Developmental Cell., 2022). This work sets a clear example of a single enhancer mutation causing monogenic disease, providing an underlying mechanism.
In a separate study we identified a noncanonical regulatory element essential for maintaining proper HNF1A levels, critical for β-cell function. Rather than acting as an enhancer or silencer, this element—named HASTER—functions as a transcriptional stabilizer that buffers HNF1A via a feedback loop. Published in Nature Cell Biology (2022) and reviewed in Nature Reviews Molecular Cell Biology (2024), this work establishes transcriptional stability as a distinct regulatory mechanism separate from traditional activation or repression.
During this period we have also dissected beta cell networks linked to human diabetes. We discovered that the beta cell transcriptional regulator HNF1A, which carries causal variants for monogenic diabetes as well as forpolygenic diabetes susceptibility, controls a broad RNA splicing program in beta cells, and incriminates this transcription-splicing regulatory axis in human diabetes.
Finally, this grant enabled the DecodeDiabetes Study, which is perhaps the largest genomic dataset of patients with clinical diagnosis of monogenic diabetes but no known gene mutations. This work is ongoing and has led to an overall strategy for noncoding variant interpretation, and uncovered insights into the genetic underpinnings of young-onset diabetes,as well as into genetic regulators of diabetes-relevant networks
In studies to understand why certain cis regulatory elements are vulnerable to diabetes-causing mutations, we discovered that rare enhancer mutations upstream of PTF1A causing pancreatic agenesis disrupt a lead enhancer that activates an entire enhancer cluster (Developmental Cell., 2022). This work sets a clear example of a single enhancer mutation causing monogenic disease, providing an underlying mechanism.
In a separate study we identified a noncanonical regulatory element essential for maintaining proper HNF1A levels, critical for β-cell function. Rather than acting as an enhancer or silencer, this element—named HASTER—functions as a transcriptional stabilizer that buffers HNF1A via a feedback loop. Published in Nature Cell Biology (2022) and reviewed in Nature Reviews Molecular Cell Biology (2024), this work establishes transcriptional stability as a distinct regulatory mechanism separate from traditional activation or repression.
During this period we have also dissected beta cell networks linked to human diabetes. We discovered that the beta cell transcriptional regulator HNF1A, which carries causal variants for monogenic diabetes as well as forpolygenic diabetes susceptibility, controls a broad RNA splicing program in beta cells, and incriminates this transcription-splicing regulatory axis in human diabetes.
Finally, this grant enabled the DecodeDiabetes Study, which is perhaps the largest genomic dataset of patients with clinical diagnosis of monogenic diabetes but no known gene mutations. This work is ongoing and has led to an overall strategy for noncoding variant interpretation, and uncovered insights into the genetic underpinnings of young-onset diabetes,as well as into genetic regulators of diabetes-relevant networks
The expansion of defects underlying human Mendelian diseases from coding to noncoding genomic space represents a major milestone in human genetics. This project is expected to make major contributions to this endeavour.