Biology subjects

Ishahak, M.

Publications and source records attributed to Ishahak, M..

7 recordsLinked to original sources

bioRxiv2026

A digital twin of pancreatic islet differentiation predicts cell fate

The controlled generation of mature stem cell-derived islets (SC-islets) remains a barrier to scalable cell therapy for diabetes. Here, we develop a predictive digital model defining the cell-state-specific regulatory logic governing fate specification during human SC-islet differentiation. We integrate 400,603 cells from 9 original single-cell multiomic datasets and 52 public single-cell RNA-seq and ATAC-seq datasets across 4 cell lines and 7 differentiation protocols. This model resolves transcriptional and chromatin accessibility dynamics while enabling time-resolved inference and in silico perturbation of cell-state-specific gene regulatory networks. We identify regulators across trajectories from endoderm progenitors to pancreatic exocrine and endocrine lineages, nominating new candidate regulators. Among these candidates, we validate previously unreported roles for STAT1 as an exocrine driver and ZEB1 as a dynamic regulator of early endocrine specification and later off-target serotonergic islet cell fate. This work provides an experimentally supported predictive framework and an interactive resource comprising 1,116 simulations to prioritize transcription factors and intervention windows for refining SC-islet differentiation.

cell biology↗

bioRxiv2026

Optimizing Post-Transplantation Detection of Subcutaneously Transplanted Islets Using Dithizone Staining

IntroductionPancreatic islet transplantation is a promising therapeutic strategy to restore insulin independence in patients with type 1 diabetes mellitus. In addition to primary human islets, human pluripotent stem cell-derived islets have shown clinical promise. However, optimizing transplantation sites and improving methods for standardized islet dosing and post-transplant graft localization are key limitations. The subcutaneous space offers an alternative site for transplantation due to its accessibility and minimally invasive nature; nevertheless, poor vascularization and difficulty locating engrafted islets limit its experimental utility. The use of dithizone, a zinc-chelating dye that selectively binds the high intracellular zinc concentrations of insulin-producing {beta}-cells, may enable rapid graft localization through selective staining. Here, we investigate whether dithizone staining can reliably localize transplanted islet grafts within the subcutaneous space of murine models. MethodsSC-islets were generated from HUES8 stem cells and functionally validated using glucose-stimulated insulin secretion. Islet volume was standardized prior to transplantation using automated islet equivalent quantification with the BioRep Islet Cell Counter. Approximately 4,000 islet equivalents of either SC-islets or primary human islets were transplanted into the subcutaneous space of immunodeficient mice. Graft function was assessed longitudinally via blood glucose monitoring, glucose tolerance testing, and human C-peptide measurements. Four weeks post-transplantation, dithizone staining was applied to harvested skin tissue to localize islet grafts, and immunohistochemical validation was performed. ResultsAutomated quantification of islet equivalents enabled consistent dosing across transplantation groups. Transplanted islets maintained function in vivo, as demonstrated by reduced blood glucose levels, preserved glucose tolerance, and detectable human C-peptide. Dithizone staining produced clear and selective red labeling of insulin-producing {beta}-cell grafts within the subcutaneous tissue, enabling reliable localization and recovery of engrafted islets. Immunohistochemical analyses confirmed the presence of insulin-expressing cells at isolated islet grafts. DiscussionDithizone staining is a rapid, cost-effective approach to identify subcutaneous islet grafts and enables downstream analyses, addressing a significant limitation in islet transplantation research. When combined with standardized pre-transplant islet quantification, this approach provides a cohesive and reproducible framework for evaluating subcutaneous islet transplantation. Future studies could complement these results by assessing the potential effects of dithizone exposure and exploring its applicability across other transplantation sites and imaging modalities.

cell biology↗

bioRxiv2025

Divergent Cell-Type Specific Hypoxia Responses in Human Stem Cell-Derived and Primary Islets

BackgroundThe success of stem cell-derived islet (SC-islet) therapy for type 1 diabetes is limited by poor graft survival in the hypoxic post-transplantation microenvironment. While the response of SC-islets to chronic hypoxia has been studied, a direct comparison to primary human islets during the acute hypoxic phase has not been performed. Here, we conduct a comparative single-cell transcriptomic and functional analysis of human SC-islets and primary islets exposed to acute hypoxia (1% O2) over 48 hours. ResultsOur analysis reveals two divergent response patterns. Primary islets exhibit an energy-conserving response, characterized by a {beta}-cell-specific suppression of identity genes (PDX1, MAFA) and pro-apoptotic factors like DDIT3, alongside a shift toward metabolic quiescence. In contrast, the SC-islet response is characterized by lineage instability, a significant metabolic shift toward glycolysis, and the activation of pro-apoptotic pathways. Functionally, these transcriptomic differences result in a loss of glucose-stimulated insulin secretion in both islet types, but through different mechanisms: a suppression of secretion in primary islets versus dysregulated, glucose-unresponsive insulin release in SC-islets. ConclusionThese findings demonstrate that SC-islets are particularly vulnerable under hypoxic stress, exhibiting an unstable, plastic phenotype. This comparative dataset provides a resource for developing source-specific therapeutic interventions to overcome the hypoxic barrier and improve the efficacy of cell replacement therapies.

cell biology↗

bioRxiv2024

Modeling glioblastoma tumor progression via CRISPR-engineered brain organoids

Glioblastoma (GBM) is an aggressive form of brain cancer that is highly resistant to therapy due to significant intra-tumoral heterogeneity. The lack of robust in vitro models to study early tumor progression has hindered the development of effective therapies. Here, we develop engineered GBM organoids (eGBOs) harboring GBM subtype-specific oncogenic mutations to investigate the underlying transcriptional regulation of tumor progression. Single-cell and spatial transcriptomic analyses revealed that these mutations disrupt normal neurodevelopment gene regulatory networks resulting in changes in cellular composition and spatial organization. Upon xenotransplantation into immunodeficient mice, eGBOs form tumors that recapitulate the transcriptional and spatial landscape of human GBM samples. Integrative single-cell trajectory analysis of both eGBO-derived tumor cells and patient GBM samples revealed the dynamic gene expression changes in developmental cell states underlying tumor progression. This analysis of eGBOs provides an important validation of engineered cancer organoid models and demonstrates their utility as a model of GBM tumorigenesis for future preclinical development of therapeutics.

bioengineering↗

bioRxiv2023

Comparative and Integrative Single Cell Analysis Reveals New Insights into the Transcriptional Immaturity of Stem Cell-Derived β Cells

Diabetes cell replacement therapy has the potential to be transformed by human pluripotent stem cell-derived {beta} cells (SC-{beta} cells). However, the precise identity of SC-{beta} cells in relationship to primary fetal and adult {beta}-cells remains unclear. Here, we used single-cell sequencing datasets to characterize the transcriptional identity of islets from in vitro differentiation, fetal islets, and adult islets. Our analysis revealed that SC-{beta} cells share a core {beta}-cell transcriptional identity with human adult and fetal {beta}-cells, however SC-{beta} cells possess a unique transcriptional profile characterized by the persistent expression and activation of progenitor and neural-biased gene networks. These networks are present in SC-{beta} cells, irrespective of the derivation protocol used. Notably, fetal {beta}-cells also exhibit this neural signature at the transcriptional level. Our findings offer insights into the transcriptional identity of SC-{beta} cells and underscore the need for further investigation of the role of neural transcriptional networks in their development.

cell biology↗

bioRxiv2022

Multiomic profiling defines cell fate plasticity of in vitro-derived islets

Transplantation of insulin-secreting {beta}-cells differentiated from human pluripotent stem cells holds great potential as a cell therapy for treating insulin-dependent diabetes. While these stem cell-derived islets (SC-islets) are able to reverse diabetes in animal models, they are not fully equivalent to their in vivo counterparts. To better define the state of the cell types generated within these SC-islets and provide a resource for identifying deficiencies in lineage specification, we used single-cell multiomic sequencing to simultaneously measure the chromatin accessibility and transcriptional profiles of SC-islets at multiple time points as well as primary human islets. The integrated analysis of both the transcriptional and chromatin landscape for each cell provided greater resolution for defining cell identity, allowing us to derive novel gene lists for identifying each islet cell type. Furthermore, this multiomic analysis revealed that the difference between SC-{beta} cells and enterochromaffin-like cells, which are a major off-target from in vitro differentiation, is a gradient of progressive cell states rather than a stark difference in identity. The chromatin landscape of primary human islets was much more restricted, suggesting that stem cell-derived cells are not fully locked into their cell fate. While long term culture of SC-islets both in vitro and in vivo does close overall chromatin state, only in vivo transplantation directs cells toward their correct identities. Collectively, our multiomic analysis demonstrates that both the chromatin and transcriptional landscapes play significant roles in islet cell identity, and these data can be used as a resource to identify specific deficiencies in the chromatin and transcriptional state of SC-islet cell types.

cell biology↗

bioRxiv2019

Human pseudoislet system enables detection of differences in G-protein-coupled-receptor signaling pathways between α and β cells

G-protein-coupled-receptors (GPCRs) modulate insulin secretion from {beta} cells and glucagon secretion from cells. Here, we developed an integrated approach to study the function of primary human islet cells using genetically modified pseudoislets that resemble native islets across multiple parameters. We studied the Gi and Gq GPCR pathways by expressing the designer receptors exclusively activated by designer drugs (DREADDs) hM4Di or hM3Dq. Activation of Gi signaling reduced insulin and glucagon secretion, while activation of Gq signaling stimulated glucagon secretion but had both stimulatory and inhibitory effects on insulin secretion. Further, we developed a microperifusion system that allowed synchronous acquisition of GCaMP6f biosensor signal and hormone secretory profiles and showed that the dual effects for Gq signaling occur through changes in intracellular Ca2+. By combining pseudoislets with a microfluidic system, we co-registered intracellular signaling dynamics and hormone secretion and demonstrated differences in GPCR signaling pathways between human {beta} and cells.

cell biology↗