Biology subjects

Kaestner, K. H.

Publications and source records attributed to Kaestner, K. H..

At least 19 recordsLinked to original sources

bioRxiv2026

The ortholog of the Human T2D Risk Gene STEAP2 is Required for Glucose Stimulated Insulin Secretion in Mice

Type 2 diabetes is a complex metabolic disease with a strong genetic component, yet this genetic risk is driven by common variants in up to 600 loci with small effect sizes. Variants in the STEAP2 locus, encoding Six-transmembrane epithelial antigen of the prostate-2, are highly associated with altered glycemic traits and type 2 diabetes risk. To elucidate its function in pancreatic beta-cells, we utilized Crisp-Cas9 assisted homologous recombination to derive a conditional null allele for Steap2 (Steap2fl/fl) in mice and crossed this to the rat insulin promoter (Rip)-Cre transgene. Ablation of Steap2 induced glucose intolerance, blunted glucose-stimulated Ca2+ mobilization and stunted first phase glucose-simulated insulin secretion. In contrast, the incretin effect and second phase insulin secretion were not affected. Islet respirometry and transmission electron microscopy (TEM) identified disrupted cristate morphology and impaired glucose-stimulated oxygen consumption as causally responsible for the observed, impaired triggering pathway of insulin secretion. These findings suggest that at least part of the genetic risk for T2D conferred by Steap2 variants is likely due to its function in maintaining optimal mitochondrial respiration in pancreatic beta-cells.

genetics↗

bioRxiv2026

Utilizing single-cell data for per-cell type eQTL mapping in the human pancreas

Aims/hypothesis The human pancreas is a central organ for metabolic regulation that is comprised of diverse cell types that uniquely contribute to its function. Previous studies have performed expression quantitative trail loci (eQTL) discovery in either whole pancreas or in pancreatic islets, but due to differences between pancreatic cell types, this approach does not reveal cell type-specific effects. In this study, we sought to either implicate the cell type of action for known eQTLs or identify new eQTLs that may have been masked in bulk studies by performing eQTL discovery in individual pancreatic cell types. Methods We clustered 153,018 single-cell RNA sequencing (scRNA-seq) data from 71 pancreatic islet donors from the Human Pancreas Analysis Program (HPAP). We performed eQTL discovery in six pancreatic cell types using this resource directly. We further utilized this single cell resource as a reference to deconvolute bulk pancreatic RNA sequencing data from 305 Genotype Tissue Expression (GTEx) project donors and performed eQTL discovery in four pancreatic cell types. Finally, we performed fine-mapping and co-localization of pancreatic cell type eQTLs with metabolic GWAS to connect our findings to metabolic disease risk. Results From analyzing 71 individuals with single cell profiles, we identified 112 unique eGenes across six pancreatic cell types, 99 of which had been identified previously and 13 unique to this study. From the deconvoluted eQTLs, we identified 3,134 unique eGenes across four pancreatic cell types, 116 of which were unique to our study. Fine-mapping and co-localization of eQTLs with metabolic GWAS yielded key leads that warrant further investigation, such as the association of rs2168101 with LMO1 expression in alpha cells. Conclusions/interpretation We identified new signals that were previously not found in bulk pancreatic eQTL studies and potential cell type of action for several signals that were identified previously. Although there are limitations to the power, and therefore, discoverability of this study, it provides insights into how individual pancreatic cells differently contribute to metabolic disease.

genetics↗

bioRxiv2025

Human length telomeres restrict the regenerative potential of hematopoietic stem cells in mice

Extremely short telomeres cause bone marrow failure in telomere biology disorder (TBDs) patients. Here, we employed the recently developed Telomouse with human-length telomeres resulting from a single amino acid substitution in the helicase Rtel1 (Rtel1M492K/M492K) to determine the effects of the short telomeres on the bone marrow and hematopoiesis. Under homeostatic conditions, Telomice have notably short telomeres but normal hematopoiesis. However, when forced to repopulate following repeated treatment with 5-fluoro-uracil or upon bone marrow transplantation into lethally irradiated mice, bone marrow progenitor cells are significantly depleted in Telomice compared to wild-type controls. This effect is associated with increased frequency of telomere repeat arrays too short to be detected by fluorescence in situ hybridization in the bone marrow of Telomice.

genetics↗

bioRxiv2025

Epigenetic adaptation of beta cells across lifespan and disease: age-related demethylation is advanced in type 2 diabetes

Although the prevalence of type 2 diabetes (T2D) increases with age, most adults maintain normoglycemia despite rising insulin resistance, largely due to the adaptive capacity of pancreatic beta cells to meet increased metabolic demand. However, persistent insulin resistance can lead to beta cell dysfunction and T2D onset. Here, leveraging cell-type-specific methylome data from the Human Pancreas Analysis Program (HPAP), we investigate the epigenomic basis of beta cell adaptation by mapping genome-wide DNA methylation (DNAm) patterns across the human lifespan. In healthy donors, we identify progressive age-related demethylation enriched in cis- regulatory elements at beta cell identity and function genes, suggesting that epigenetic remodeling supports functional adaptation to metabolic demand over time. In contrast, alpha cells show the opposite trajectory, with subtle, age-related hypermethylation. In T2D beta but not alpha cells we observed further demethylation compared to healthy controls, underscoring a unique capacity of beta cells to respond to changes in metabolic demand. Together, our findings suggest that DNAm remodeling in healthy beta cells reflects a long-term adaptation to metabolic demand, which in T2D is accelerated as part of a compensatory response that ultimately fails under sustained insulin resistance.

genomics↗

bioRxiv2025

Spatial transcriptomics from pancreas and local draining lymph node tissue reveals a lymphotoxin-β signature in human type 1 diabetes

This study explores the inflammatory response observed in pancreata and pancreatic lymph node (pLN) samples obtained throughout the natural history of type 1 diabetes (T1D) including non-diabetic individuals and non-diabetic autoantibody positive individuals with high susceptibility using spatial transcriptomics (ST). Integration of ST with public single-cell RNA sequencing data enabled interrogation of transcriptional alterations in T1D pathogenesis across both tissues and cellular scales. In the T1D pancreas, we observed global upregulation of multiple inflammation-associated transcripts, including regenerating islet-derived (REG) family genes, complement factor 3 (C3), SOD2, and OLFM4, and highlighted cellular candidates potentially contributing to these signatures. Within the T1D pLN, we observed spatially restricted upregulation of lymphotoxin-{beta} (LTB) alongside follicular dendritic cell (FDC)-associated transcripts including FDCSP, CLU, and FCER2. Collectively, these findings highlight distinct inflammation signatures in the pancreas and regional pLN which can help inform the development of future therapeutic interventions.

immunology↗

bioRxiv2025

IFN-α Induces Heterogenous ROS Production in Human β-Cells

Type 1 diabetes (T1D) is a multifactorial disease involving genetic and environmental factors, including viral infection. We investigated the impact of interferon alpha (IFN-), a cytokine produced during the immune response to viral infection or the presence of un-edited endogenous double-stranded RNAs, on human {beta}-cell physiology. Intravital microscopy on transplanted human islets using a {beta}-cell-selective reactive oxygen species (ROS) biosensor (RIP1-GRX1-roGFP2), revealed a subset of human {beta}-cells that acutely produce ROS in response to IFN-. Comparison to Integrated Islet Distribution Program (IIDP) phenotypic data revealed that healthier donors had more ROS accumulating cells. In vitro IFN- treatment of human islets similarly elicited a heterogenous increase in superoxide production that originated in the mitochondria. To determine the unique molecular signature predisposing cells to IFN- stimulated ROS production, we flow sorted human islets treated with IFN-. RNA sequencing identified genes involved in inflammatory and immune response in the ROS-producing cells. Comparison with single cell RNA-Seq datasets available through the Human Pancreas Analysis Program (HPAP) showed that genes upregulated in ROS-producing cells are enriched in control {beta}-cells rather than T1D donors. Combined, these data suggest that IFN- stimulates mitochondrial ROS production in healthy human {beta}-cells, potentially predicting a more efficient antiviral response.

cell biology↗

bioRxiv2025

Single-cell multiome analysis supports α-to-β transdifferentiation in human pancreas

Spontaneous transdifferentiation of pancreatic glucagon-producing alpha to insulin-secreting beta-cells has been observed in mouse but not in human islets1. Here, we analyzed the largest single-cell dataset of human islets to date, composed of 650,000 cells across 121 deceased organ donors, in search of transitional cell states. By integrating single-cell RNA-seq, single-nucleus ATAC-seq and single-nucleus multiome (joint RNA and ATAC profiling) datasets generated by the Human Pancreas Analysis Program (HPAP)2,3 we identified two previously undescribed cell populations (c11 and c13 cells), which together represent transitional states between alpha- and beta-cells. Some c11 cells are insulin-positive while others are glucagon positive, but none are double-positive. C11 cells repress alpha-cell identity genes and activate beta-cell specific genes. Moreover, the transcriptomic and epigenetic profiles of c11 and c13 cells indicate a transitioning phenotype driven by lineage-specific transcription factors. Genetic lineage tracing in primary human islet cells confirmed alpha-to-beta cell transdifferentiation. C11 and c13 cells exist in all islet samples regardless of disease statuses, with type 2 diabetic samples having significantly more transitioning cells than matched non-diabetic controls. The discovery of these transitional cell types suggests a possibility for future therapy - transdifferentiating alpha-cells to beta-cell through activation of the c11 gene program.

systems biology↗

bioRxiv2024

TNFSF13 insufficiency disrupts human colonic epithelial cell-mediated B cell differentiation

Cytokines mediating epithelial and immune cell interactions modulate mucosal healing-a process that goes awry with chronic inflammation as in inflammatory bowel disease. TNFSF13 is a cytokine important for B cell maturation and function, but roles for epithelial TNFSF13 and putative contribution to inflammatory bowel disease are poorly understood. We evaluated functional consequences of a novel monoallelic TNFSF13 variant using biopsies, tissue-derived colonoids and induced pluripotent stem cell (iPSC)-derived colon organoids. TNFSF13 variant colonoids exhibited a >50% reduction in secreted TNFSF13, increased epithelial proliferation, and reduced apoptosis, which was confirmed in iPSC-derived colon organoids. Single cell RNA-sequencing, flow cytometry, and co-immunoprecipitation identified FAS as the predominant colonic epithelial receptor for TNFSF13. Imaging mass cytometry revealed an increase in epithelial-associated B cells in TNFSF13 variant colon tissue sections. Finally, TNFSF13 variant colonoids co-cultured with memory B cells demonstrated a reduction in the production of IgA+ plasma cells compared to control colonoid co-cultures. Our findings support a role for epithelial TNFSF13 as a regulator of colonic epithelial growth and epithelial crosstalk with B cells. SUMMARYEpithelial TNFSF13 regulates colonic epithelial growth and epithelial-B cell interactions. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/614260v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1e5b892org.highwire.dtl.DTLVardef@b8857forg.highwire.dtl.DTLVardef@448b95org.highwire.dtl.DTLVardef@2820e2_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

Aberrant TNF signaling in pancreatic lymph nodes of patients with Type 1 Diabetes

The therapeutic landscape for Type 1 Diabetes (T1D) is rapidly changing as ongoing clinical trials aim to delay beta-cell loss by inhibiting proinflammatory cytokines. However, the precise timing and cellular contexts of cytokine dysregulation remains unknown. We generated the largest existing measurement of gene expression and chromatin accessibility in [~]1 million immune cells from the pancreatic lymph nodes and spleens of 34 T1D and non-diabetic organ donors. Our study revealed heightened gene activity of the tumor necrosis factor (TNF) pathway and subsequent chromatin remodeling in central memory CD4+ T cells residing in the pancreatic lymph nodes of T1D and non-diabetic islet-autoantibody positive donors. These findings, validated in mice, offer a mechanism underlying the efficacy of TNF inhibitors, currently undergoing clinical trials to delay T1D onset.

immunology↗

bioRxiv2024

Immune perturbations in human pancreas lymphatic tissues prior to and after type 1 diabetes onset

Autoimmune destruction of pancreatic {beta} cells results in type 1 diabetes (T1D), with pancreatic immune infiltrate representing a key feature in this process. Studies of human T1D immunobiology have predominantly focused on circulating immune cells in the blood, while mouse models suggest diabetogenic lymphocytes primarily reside in pancreas-draining lymph nodes (pLN). A comprehensive study of immune cells in human T1D was conducted using pancreas draining lymphatic tissues, including pLN and mesenteric lymph nodes, and the spleen from non-diabetic control, {beta} cell autoantibody positive non-diabetic (AAb+), and T1D organ donors using complementary approaches of high parameter flow cytometry and CITEseq. Immune perturbations suggestive of a proinflammatory environment were specific for T1D pLN and AAb+ pLN. In addition, certain immune populations correlated with high T1D genetic risk independent of disease state. These datasets form an extensive resource for profiling human lymphatic tissue immune cells in the context of autoimmunity and T1D.

immunology↗

bioRxiv2024

Separation of telomere protection from length regulation by two different point mutations at amino acid 492 of RTEL1

RTEL1 is an essential DNA helicase that plays multiple roles in genome stability and telomere length regulation. A variant of RTEL1 with a lysine at position 492 is associated with short telomeres in Mus spretus, while a conserved methionine at this position is found in M. musculus, which has ultra-long telomeres. In humans, a missense mutation at this position (Rtel1M492I) causes a fatal telomere biology disease termed Hoyeraal-Hreidarsson syndrome (HHS). Introducing the Rtel1M492K mutation into M. musculus shortened the telomeres of the resulting strain, termed Telomouse, to the length of human telomeres. Here, we report on a mouse strain carrying the Rtel1M492I mutation, termed HHS mouse. The HHS mouse telomeres are not as short as those of Telomice but nevertheless they display higher levels of telomeric DNA damage, fragility and recombination, associated with anaphase bridges and micronuclei. These observations indicate that the two mutations separate critical functions of RTEL1: M492K mainly reduces the telomere length setpoint, while M492I predominantly disrupts telomere protection. The two mouse models enable dissecting the mechanistic roles of RTEL1 and the different contributions of short telomeres and DNA damage to telomere biology diseases, genomic instability, cancer, and aging.

genetics↗

bioRxiv2023

G6PC2 controls glucagon secretion by defining the setpoint for glucose in pancreatic α-cells

Impaired glucose suppression of glucagon secretion (GSGS) is a hallmark of type 2 diabetes. A critical role for -cell intrinsic mechanisms in regulating glucagon secretion was previously established through genetic manipulation of the glycolytic enzyme glucokinase (GCK) in mice. Genetic variation at the G6PC2 locus, encoding an enzyme that opposes GCK, has been reproducibly associated with fasting blood glucose and hemoglobin A1c levels. Here, we find that trait-associated variants in the G6PC2 promoter are located in open chromatin not just in {beta}- but also in -cells, and document allele-specific G6PC2 expression of linked variants in human - cells. Using -cell specific gene ablation of G6pc2 in mice, we show that this gene plays a critical role in controlling glucagon secretion independent of alterations in insulin output, islet hormone content, or islet morphology; findings we confirmed in primary human -cells. Collectively, our data demonstrate that G6PC2 impacts glycemic control via its action in -cells and suggest that G6PC2 inhibitors could help control blood glucose through a novel, bi-hormonal mechanism.

genetics↗

bioRxiv2023

Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data

Single-cell RNA-sequencing (scRNA-seq) measures gene expression in single cells, while single-nucleus ATAC-sequencing (snATAC-seq) enables the quantification of chromatin accessibility in single nuclei. These two data types provide complementary information for deciphering cell types/states. However, when analyzed individually, scRNA-seq and snATAC-seq data often produce conflicting results regarding cell type/state assignment. In addition, there is a loss of power as the two modalities reflect the same underlying cell types/states. Recently, it has become possible to measure both gene expression and chromatin accessibility from the same nucleus. Such paired data make it possible to directly model the relationships between the two modalities. However, given the availability of the vast amount of single-modality data, it is desirable to integrate the paired and unpaired single-modality data to gain a comprehensive view of the cellular complexity. Here, we benchmarked the performance of seven existing single-cell multi-omic data integration methods. Specifically, we evaluated whether these methods are able to uncover peak-gene associations from single-modality data, and to what extent the multiome data can provide additional guidance for the analysis of the existing single-modality data. Our results indicate that multiome data are helpful for annotating single-modality data, but the number of cells in the multiome data is critical to ensure a good cell type annotation. Additionally, when generating a multiome dataset, the number of cells is more important than sequencing depth for cell type annotation. Lastly, Seurat v4 is the best at integrating scRNA-seq, snATAC-seq, and multiome data even in the presence of complex batch effects.

bioinformatics↗

bioRxiv2023

AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics

Cellular composition and anatomical organization influence normal and aberrant organ functions. Emerging spatial single-cell proteomic assays such as Image Mass Cytometry (IMC) and Co-Detection by Indexing (CODEX) have facilitated the study of cellular composition and organization by enabling high-throughput measurement of cells and their localization directly in intact tissues. However, annotation of cell types and quantification of their relative localization in tissues remain challenging. To address these unmet needs, we developed AnnoSpat (Annotator and Spatial Pattern Finder) that uses neural network and point process algorithms to automatically identify cell types and quantify cell-cell proximity relationships. Our study of data from IMC and CODEX show the superior performance of AnnoSpat in rapid and accurate annotation of cell types compared to alternative approaches. Moreover, the application of AnnoSpat to type 1 diabetic, non-diabetic autoantibody-positive, and non-diabetic organ donor cohorts recapitulated known islet pathobiology and showed differential dynamics of pancreatic polypeptide (PP) cell abundance and CD8+ T cells infiltration in islets during type 1 diabetes progression.

bioinformatics↗

bioRxiv2021

The three-dimensional chromatin structure of the major human pancreatic cell types reveals lineage-specific regulatory architecture of T2D risk

Three-dimensional (3D) chromatin organization maps help to dissect cell type-specific gene regulatory programs. Furthermore, 3D chromatin maps have contributed to elucidating the pathogenesis of complex genetic diseases by connecting distal regulatory regions and genetic risk variants to their respective target genes. To understand the cell type-specific regulatory architecture of diabetes risk, we generated transcriptomic and 3D epigenomic profiles of human pancreatic acinar, alpha, and beta cells using single-cell RNA-seq, single-cell ATAC-seq, and high-resolution Hi-C of sorted cells. Comparisons of these profiles revealed differential A/B (open/closed) chromatin compartmentalization, chromatin looping, and transcriptional factor mediated control of cell type-specific gene regulatory programs. We identified a total of 4,750 putative causal-variant-target-gene pairs at 194 type 2 diabetes GWAS signals using pancreatic 3D chromatin maps. We found that the connections between candidate causal variants and their putative target effector genes are cell-type stratified and emphasize previously underappreciated roles for alpha and acinar cells in diabetes pathogenesis.

genetics↗

bioRxiv2021

Alpha cell dysfunction in early type 1 diabetes

Multiple islet autoantibodies (AAb) predict type 1 diabetes (T1D) and hyperglycemia within 10 years. By contrast, T1D develops in just [~]15% of single AAb+ (generally against glutamic acid decarboxylase, GADA+) individuals; hence the single GADA+ state may represent an early stage of T1D amenable to interventions. Here, we functionally, histologically, and molecularly phenotype human islets from non-diabetic, GADA+ and T1D donors. Similar to the few remaining beta cells in T1D islets, GADA+ donor islets demonstrated a preserved insulin secretory response. By contrast, alpha cell glucagon secretion was dysregulated in both T1D and GADA+ islets with impaired glucose suppression of glucagon secretion. Single cell RNA sequencing (scRNASeq) of GADA+ alpha cells revealed distinct abnormalities in glycolysis and oxidative phosphorylation pathways and a marked downregulation of PKIB, providing a molecular basis for the loss of glucose suppression and the increased effect of IBMX observed in GADA+ donor islets. The striking observation of a distinct early defect in alpha cell function that precedes beta cell loss in T1D suggests that not only overt disease, but also the progression to T1D itself, is bihormonal in nature.

physiology↗

bioRxiv2021

A single amino acid in RTEL1 determines telomere length in mice

Telomeres, the ends of eukaryotic chromosomes, protect genome integrity and enable cell proliferation. Maintaining optimal telomere length in the germline and throughout life limits the risk of cancer and enables healthy aging. Telomeres in the house mouse, Mus musculus, are about five times longer than human telomeres, limiting the use of this common laboratory animal for studying the contribution of telomere biology to aging and cancer. We identified a key amino acid variation in the helicase RTEL1, naturally occurring in the short-telomere mouse species M. spretus. Introducing this variation into M. musculus is sufficient to reduce the telomere length set point in the germline and generate mice with human-length telomeres. While these mice are fertile and appear healthy, the regenerative capacity of their colonic epithelium is compromised. The engineered Telomouse reported here demonstrates a dominant role of RTEL1 in telomere length regulation and provides a unique model for aging and cancer.

genetics↗

bioRxiv2021

Adaptation to chronic ER stress enforces pancreatic β-cell plasticity

Pancreatic {beta}-cells undergo high levels of endoplasmic reticulum (ER) stress due to their role in insulin secretion. Hence, they require sustainable and efficient adaptive stress responses to cope with the stress. Whether duration and episodes of chronic ER stress directly compromises {beta}-cell identity is largely unknown. We show that under reversible, chronic ER stress, {beta}-cells undergo a distinct transcriptional and translational reprogramming. During reprogramming, expression of master regulators of {beta}-cell function and identity and proinsulin processing is impaired. Upon recovery from stress, {beta}-cells regain their identity, highlighting a high-degree of adaptive {beta}-cell plasticity. Remarkably, when stress episodes exceed a certain threshold, {beta}-cell identity is gradually lost. Single cell RNA-seq analysis of islets from type 1 diabetes (T1D) patients, identifies the severe deregulation of the chronic stress-adaptation program, and reveals novel biomarkers for progression of T1D. Our results suggest {beta}-cell adaptive exhaustion ({beta}EAR) is a significant component of the pathogenesis of T1D.

systems biology↗