Generation of human islet cell type-specific identity genesets

Gurp, Léon van; Fodoulian, Leon; Oropeza, Daniel; Furuyama, Kenichiro; Bru-Tarí, Eva; Vu, Anh Nguyet; Kaddis, John S.; Rodríguez, Iván; Thorel, Fabrizio; Herrera, Pedro Luis

doi:10.1038/s41467-022-29588-8

Cited by 50 publications

(59 citation statements)

References 74 publications

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“…scRNA-seq of human islets cells and human pancreas has identified genes associated with Type 1 (T1D) and Type 2 diabetes (T2D) (5)(6)(7), genes important for islet cell development and maturation (8,9), for islet dysfunction and dedifferentiation (10,11), for aging (12), and genes involved in the transdifferentiation among islet cells (13,14). These studies typically use canonical gene sets to annotate different islet cell populations, but new gene sets are continuously identified that more precisely define islet cell subtypes as they passage from development, stem cell differentiation to maturation (15). scRNA-seq has also confirmed the presence of heterogeneity among human β-cells defining several β-cell subtypes with different gene profiles (16,17).…”

Section: Introductionmentioning

confidence: 99%

Single Nucleus RNA Sequencing of Human Pancreatic Islets In Vitro and In Vivo Identifies New Gene Sets and Three β-Cell Subpopulations with Different Transcriptional Profile

Kang

Rosselot

et al. 2022

Preprint

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Single-cell RNA sequencing (scRNA-seq) has provided valuable insights into human islet cell types and their corresponding stable gene expression profiles. However, this approach requires cell dissociation that complicates its utility in vivo and provides limited information on the active transcriptional status of islet cells. On the other hand, single-nucleus RNA sequencing (snRNA-seq) does not require cell dissociation and affords enhanced information from intronic sequences that can be leveraged to identify actively transcribing genes in islet cell populations. Here, we first sought to compare scRNA-seq and snRNA-seq analysis of human islets in vitro using exon reads or combined exon and intron reads, respectively. Datasets reveal similar human islet cell clusters using both approaches. In the snRNA-seq data, however, the top differentially expressed genes in human islet endocrine cells are not the canonical genes but a new set of non-canonical gene markers including ZNF385D, TRPM3, LRFN2, PLUT (β cells), PTPRT, FAP, PDK4, LOXL4 (α cells), LRFN5, ADARB2, ERBB4, KCNT2 (δ cells) and CACNA2D3, THSD7A, CNTNAP5, RBFOX3 (γ cells). Notably, these markers also accurately define endocrine cell populations in human islet grafts in vivo. Further, by integrating the information from nuclear and cytoplasmic transcriptomes, we identify three β-cell sub-clusters: an active INS mRNA transcribing cluster (β1), an intermediate INS mRNA-transcribing cluster (β2), and a mature INS mRNA rich cluster (β3). These display distinct gene expression patterns representing different biological dynamic states both in vitro and in vivo. Interestingly, the INS mRNA rich cluster (β3) becomes the predominant sub-cluster in vivo. In summary, snRNA-seq analysis of human islet cells is a previously unrecognized tool that can be accurately employed for improved identification of human islet cell types and their transcriptional status in vivo.

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Section: Introductionmentioning

confidence: 99%

Single Nucleus RNA Sequencing of Human Pancreatic Islets In Vitro and In Vivo Identifies New Gene Sets and Three β-Cell Subpopulations with Different Transcriptional Profile

Kang

Rosselot

et al. 2022

Preprint

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“…1f). Highly active transcription factors in SC-β cells include of RFX1, PDX1 and PAX6, which have been previously reported to be important for β-cell identity 27, 35 . Other highly active transcription factors, such as MAFG, EBF1, ISX, and PLAGL2, have not been highlighted in previous studies, demonstrating the utility of using both mRNA and chromatin accessibility data for identifying cell types.…”

Section: Introductionmentioning

confidence: 99%

Defining the chromatin and transcriptional landscape of stem cell-derived islets

Augsornworawat

Hogrebe²,

Ishahak

et al. 2022

Preprint

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Insulin-secreting β-cells within the pancreatic islets of Langerhans are lost in patients with type 1 diabetes1. Islets can be generated in vitro by differentiation of human pluripotent stem cells2-5, but understanding of the molecular events governing this process is limited. Here, we use single-cell multiomics to measure chromatin accessibility and transcriptional profiles of 120,064 cells to characterize and delineate maturation of islets from in vitro differentiation. We find distinguishing chromatin accessibility and gene expression signatures as well as dynamic profiles for each major islet cell type produced from in vitro differentiation. Furthermore, based on chromatin accessibility, β, α, and δ cells from in vitro differentiation are more ambiguous in their cellular identity than from isolated primary islets. However, extended time in vitro or with transplantation into mice drives more distinct states of chromatin accessibility for each cell type. Modulation of CTCF expression redirects cell fate from pancreatic islet endocrine to an intestinal enteroendocrine-like cell type. Additionally, knockdown of ARID1B enhances β-cell maturation transcriptionally and by chromatin accessibility. These results provide a comprehensive atlas and insights into cell fate identity and maturation of stem cell-derived islets, which will inform on their utility for therapy and disease modeling6-8.

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“…To determine the transcriptional similarity of our four pNET tumors to healthy, mature pancreatic islet cells, we scored malignant cells from each tumor with curated gene signatures specific to alpha, beta, gamma, and delta cells in mature human pancreatic islets ( Figure 2E )( 26 ). Tumor cells from pnet1 displayed robust expression of alpha cell and gamma cell gene signatures, with lower expression of the delta cell signature ( Figure 2E ); these findings are consistent with the robust expression of gamma and delta cell hormones PPY and VIP and elevated ARX TF activity identified in our previous analyses.…”

Section: Resultsmentioning

confidence: 99%

Intertumoral lineage diversity and immunosuppressive transcriptional programs in well-differentiated gastroenteropancreatic neuroendocrine tumors

Hoffman

Dowrey

Martin

et al. 2022

Preprint

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Neuroendocrine tumors (NETs) are rare cancers that may arise in the gastrointestinal tract and pancreas. The fundamental mechanisms driving gastroenteropancreatic (GEP) NET growth remain incompletely elucidated; however, the heterogeneous clinical behavior of GEP-NETs suggests that both cellular lineage dynamics and tumor microenvironment influence tumor pathophysiology. Here, we investigated the single-cell transcriptomes of tumor and immune cells from patients with gastroenteropancreatic NETs. Malignant GEP-NET cells expressed genes and regulons associated with normal, gastrointestinal endocrine cell differentiation and fate determination stages. While tumor and lymphoid compartments sparsely expressed immunosuppressive targets, infiltrating myeloid cells were enriched for alternative immunotherapy pathways including VSIR, Tim3/Gal9, and SIGLEC10. Finally, analysis of paired primary and metastatic tissue specimens from small intestinal NETs demonstrated transcriptional transformation between the primary tumor and its distant metastasis. Our findings highlight the transcriptomic heterogeneity that distinguishes the cellular landscapes of GEP-NET anatomic subtypes and reveal potential avenues for future precision medicine therapeutics.

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Generation of human islet cell type-specific identity genesets

Cited by 50 publications

References 74 publications

Single Nucleus RNA Sequencing of Human Pancreatic Islets In Vitro and In Vivo Identifies New Gene Sets and Three β-Cell Subpopulations with Different Transcriptional Profile

Single Nucleus RNA Sequencing of Human Pancreatic Islets In Vitro and In Vivo Identifies New Gene Sets and Three β-Cell Subpopulations with Different Transcriptional Profile

Defining the chromatin and transcriptional landscape of stem cell-derived islets

Intertumoral lineage diversity and immunosuppressive transcriptional programs in well-differentiated gastroenteropancreatic neuroendocrine tumors

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