Biology subjects

Balboa, D.

Publications and source records attributed to Balboa, D..

12 recordsLinked to original sources

bioRxiv2026

The Human Pancreas Cell Atlas defines a healthy reference framework for disease contextualization and translational benchmarking

A central challenge in single-cell biology is distinguishing disease-associated remodeling from normal cellular heterogeneity. Addressing this challenge requires healthy reference frameworks that capture cellular diversity across individuals, technologies, and biological contexts. Here we present the Human Pancreas Cell Atlas (HPCA), a reference atlas of the healthy human pancreas integrating 815,126 single-cell and single-nucleus transcriptomes from 109 donors across 12 studies, diverse technologies, and demographics. Using benchmarked integration and community-driven annotations, HPCA defines 94 cell types and transcriptional states spanning endocrine, exocrine, immune, and stromal compartments. The atlas identifies rare endocrine populations, including a putative, spatially supported polyhormonal alpha-beta-delta state, and provides a unified framework for interpreting pancreatic cellular variation across diverse biological and demographic covariates. Projection of disease and model-system datasets onto HPCA contextualized endocrine and epithelial remodeling relative to healthy pancreatic states. Diabetes-associated endocrine cells remained embedded within the healthy endocrine state space while exhibiting disease-specific changes, as supported by spatial and eQTL concordance analyses. Integration with a pancreatic ductal adenocarcinoma atlas resolved injury-associated and malignant epithelial ecosystem regions across donors. Finally, the HPCA enables quantitative benchmarking of murine diabetes models and stem-cell-derived islets against human pancreatic reference states. Together, the HPCA establishes a healthy transcriptional coordinate system for interpreting disease-associated pathophysiology, experimental perturbation, and regenerative fidelity, illustrating how reference atlases can function as analytical frameworks rather than static cell catalogs.

bioinformatics↗

bioRxiv2026

Scinderin-driven Golgi Actin Remodeling coordinates GLP-1 and insulin secretion to regulate glucose homeostasis

Maintenance of glucose homeostasis requires coordinated hormone secretion from intestinal enteroendocrine cells and pancreatic {beta}-cells, yet the intracellular mechanisms that couple nutrient sensing to endocrine output remain poorly defined. Here, we identify the actin remodeler Scinderin (SCIN) as a shared regulator of hormone secretion across these systems. SCIN is selectively expressed in enteroendocrine L-cells and pancreatic {beta}-cells, where it localizes to phosphatidylinositol-4-phosphate (PI(4)P)-enriched Golgi membranes and controls Golgi-associated actin dynamics. Loss of SCIN disrupts Golgi organization, impairs prohormone trafficking, and reduces secretory granule formation, resulting in defective nutrient-stimulated GLP-1 and insulin secretion while preserving cAMP-dependent amplification pathways. In vivo, tissue-specific deletion of Scin compromises incretin responses, {beta}-cell insulin secretion, and systemic glucose homeostasis. Consistent with these findings, SCIN expression is reduced in human diabetic {beta}-cells and associates with stress-related loss of {beta}-cell maturity. Transcriptomic analyses reveal a conserved Golgi stress program upon SCIN loss, linking intracellular trafficking defects to endocrine dysfunction. Together, our results identify SCIN-dependent Golgi actin remodeling as a rate-limiting intracellular mechanism coordinating enteroendocrine and pancreatic hormone secretion. This work uncovers a shared, targetable node controlling endocrine output, providing a mechanistic link between secretory pathway dysfunction and diabetes.

cell biology↗

bioRxiv2026

Sodium tungstate promotes vascularization to support beta bell replacement in diabetes

Insufficient vascularization remains a major obstacle to the success of cell-based therapies for diabetes. Building on prior findings that loss of the phosphatase PTP1B enhances VEGFA production and improves graft vascularization, we investigated sodium tungstate (NaW), a pharmacological phosphatase inhibitor, as a strategy to improve transplantation outcomes. Using human fibroblast-derived insulin-producing cells and human stem cell-derived islets transplanted into the anterior chamber of the eye in immunodeficient mice, we show that NaW treatment significantly increases both vascularized area and insulin-positive tissue area, while reducing apoptosis within transplanted cells. Mechanistically, NaW upregulates VEGFA expression in transplanted cells and amplifies VEGFA-induced endothelial cell proliferation, migration, and tubulogenesis via MAPK/ERK signalling. These dual effects, which encompass stimulating both endocrine and endothelial compartments, lead to enhanced integration and function of transplanted cells. Importantly, the pro-angiogenic effects of NaW occur independently of exogenous endothelial cell supplementation, relying solely on the hosts endogenous endothelial cells. These findings position NaW, and potentially other phosphatase inhibitors, as promising adjuncts to improve vascularization, survival, and therapeutic efficacy in clinical cell-based transplantation protocols for diabetes. One-sentence summaryProangiogenic role of sodium tungstate in transplantation

physiology↗

bioRxiv2025

Latent plasticity of the human pancreas across development, health, and disease.

The pancreas plays a central role in major human diseases, yet our understanding of its cellular diversity and plasticity remains incomplete. Here, we present a single-cell multiomics atlas of the human pancreas, profiling over four million cells and nuclei from 57 donors across fetal development, adult homeostasis, and type 2 diabetes (T2D). Integrating sc/snRNA-seq, snATAC-seq, VASA-seq, spatial transcriptomics (Xenium), and multiplexed proteomics (CODEX), we resolve gene expression, chromatin accessibility, and spatial organization at high resolution. We identify transcriptionally plastic centroacinar-like cells (pCACs) in adults with fetal-like features, delineate endocrine and exocrine lineage trajectories during development, and uncover HNF1A-defined beta cell epigenetic states. In T2D, we observe shifts in beta cell subtypes and altered regulatory programs. Glucose perturbation of healthy islets reveals cell-type-specific adaptation and stress responses. This atlas provides a foundational framework to understand pancreas biology and the role of cellular plasticity in regeneration and disease.

genomics↗

bioRxiv2025

Ghrelin and relamorelin alleviate hypoglycaemia in humanised mice with congenital hyperinsulinism

KATP-channel related hyperinsulinism (KATPHI) is a genetic disorder of the pancreatic beta cells, manifesting as life-threatening hypoglycaemia in neonates due to dysregulated insulin secretion. Management of the severe diffuse form of KATPHI currently lacks treatment options, as the first-line therapy octreotide is often insufficiently effective, necessitating radical pancreatectomy in many patients. In this study, we applied stem cell derived islets carrying KATPHI-causing mutation KCNJ11-/- to develop new pharmaceutical therapies for KATPHI. We tested seven candidate molecules in vitro, identifying three that reduced insulin secretion in KCNJ11-/- stem cell derived islets. Of these, we tested acyl-ghrelin and its long-acting analogue relamorelin in mice that became hypoglycaemic due to carrying human KCNJ11-/- stem cell derived grafts. Acyl-ghrelin and relamorelin alone increased fasting glycaemia. Combining relamorelin with octreotide increased blood glucose more than the sum of each drug alone, reversing hypoglycaemia to normoglycaemia. In conclusion, we show that ghrelin receptor agonists have acute anti-hypoglycaemic effects in a humanised mouse model of KATPHI, especially when combined with octreotide. Relamorelin has been tested in >650 diabetic adults with little side effects, leading us to propose relamorelin - octreotide combination as a novel therapeutic candidate for severe KATPHI patients.

physiology↗

bioRxiv2023

Quantifying stem cell derived islet graft volume and composition with FDOPA positron emission tomography

Stem cell derived islets (SC-islets) are being developed as a novel source of beta cells that would enable large scale cell replacement therapy for insulin dependent diabetes. Therapeutic use of SC-islets carries an inherent risk of unwanted growth; and multiple strategies are being explored for optimizing long-term SC-islet graft effectiveness. However, a method for noninvasive in vivo monitoring for SC-islet graft safety and efficacy is lacking, as current insulin secretion measurements are inadequate. Here, we demonstrate the potential of positron emission tomography (PET) for monitoring SC-islet grafts using two tracers: GLP1-receptor binding [18F]F-DBCO-exendin and dopamine precursor [18F]FDOPA. We could detect and longitudinally monitor human SC-islet grafts in calf muscles of immunocompromised mice. Importantly, graft volume quantified with PET strongly correlated with actual graft volume (r2=0.91 for [18F]F-DBCO-exendin). PET using [18F]F-DBCO-exendin allowed delineation of cystic structures and its uptake correlated with graft beta cell proportion, enabling study of SC-islet graft purity noninvasively. [18F]FDOPA performed similarly to [18F]F-DBCO-exendin, but with slightly weaker sensitivity. Uptake of neither tracer was biased in SC-islet grafts genetically rendered hyper- or hypoactive. Insulin secretion measurements under fasted, glucose-stimulated or hypoglycemic conditions did not correlate with graft volume. In conclusion, [18F]F-DBCO-exendin and [18F]FDOPA PET constitute powerful approaches to noninvasively assess SC-islet graft volume and composition regardless of their functionality. PET imaging could therefore be leveraged for optimizing safety and effectiveness of SC-islet grafts in patients with insulin dependent diabetes.

cell biology↗

bioRxiv2023

RFX6 haploinsufficiency predisposes to diabetes through impaired beta cell functionality

Regulatory factor X 6 (RFX6) is indispensable for pancreatic endocrine development and differentiation. The RFX6 protein-truncating variant p.His293LeufsTer7 is significantly enriched in the Finnish population with almost 1:250 individuals as a carrier. Importantly, the FinnGen study indicates a high predisposition for heterozygous carriers to develop type 2 diabetes (T2D) and gestational diabetes. To understand the role of this variant in {beta}-cell development and function, we generated allelic series of isogenic pluripotent stem cell models and directed them into pancreatic islet lineages (SC-islets). Expectedly, in-vitro models of the homozygous RFX6-/- variant failed to generate pancreatic endocrine cells, recapitulating the phenotype in Mitchell-Riley syndrome. Notably, heterozygous RFX6+/- derived SC-islets showed reduced {beta}-cell maturation markers and calcium oscillations, resulting in defective insulin secretion, without affecting {beta}-cell number or insulin content. The reduced insulin secretion is sustained during in-vivo implantation studies, consistent with the susceptibility of the carriers to develop diabetes. TeaserModeling RFX6-assocciated neonatal and type-2 diabetes using allelic series stem cell-derived islets in-vitro and in-vivo.

cell biology↗

bioRxiv2022

Supernumerary proteins of the human mitochondrial ribosomal small subunit are integral for assembly and translation

Mitochondrial ribosomes (mitoribosomes) have undergone substantial structural remodelling throughout evolution. Compared to their prokaryotic counterparts, mitoribosomes show a substantial loss of ribosomal RNA, whilst acquiring unique protein subunits located on the periphery of the ribosomal subunit structures. We set out to investigate the functional properties of all 14 unique (mitochondrial-specific or supernumerary) human mitoribosomal proteins in the small subunit. Using genome editing with CRISPR-Cas9, we made knockouts for each subunit in HEK293 cells to study the effect on mitoribosome assembly and function in protein synthesis. Unexpectedly, we show that each supernumerary knockout leads to a unique mitoribosome assembly defect with variable impact on mitochondrial protein synthesis. Our data demonstrates that all supernumerary subunits are essential structural components except mS37. Surprisingly, we found the stability of mS37 was reduced in all our supernumerary knockouts of the small and large ribosomal subunits as well as patient-derived lines with mitoribosome assembly defects. We identified that a redox regulated CX9C motif in mS37 was essential for protein stability, suggesting a potential mechanism to regulate mitochondrial protein synthesis. Together, our findings support a modular assembly of the human mitochondrial small ribosomal subunit mediated by essential supernumerary subunits and identify a redox regulatory role involving mS37 in mitochondrial protein synthesis in health and disease.

molecular biology↗

bioRxiv2022

The type 1 diabetes gene TYK2 regulates β-cell development and its responses to interferon-α

Type 1 diabetes (T1D) is an autoimmune disease that results in the destruction of insulin producing pancreatic {beta}-cells. One of the genes associated with T1D is TYK2, which encodes a Janus kinase with critical roles in type-I interferon (IFN) mediated intracellular signaling. To study the role of TYK2 in human pancreatic {beta}-cell development and response to IFN, we generated TYK2 knockout human iPSCs and directed them into the pancreatic endocrine lineage. Here we show that loss of TYK2 compromised the emergence of endocrine precursors by regulating KRAS expression while mature stem cell-islets (SC-islets) function was not affected. In the maturing SC-islets, the loss or inhibition of TYK2 prevented IFN-induced antigen processing and presentation, including MHC Class I expression in pancreatic endocrine and progenitor cells. Furthermore, in a CD8+ cytotoxic T-cell co-culture model, the survival of {beta}-cells was enhanced by a selective TYK2 inhibitor. These results identify an unsuspected role for TYK2 on {beta}-cell development and support TYK2 inhibition in adult {beta}-cells as a potent therapeutic target to halt T1D progression.

molecular biology↗

bioRxiv2021

Functional, metabolic and transcriptional maturation of stem cell derived beta cells

Transplantation of pancreatic islet cells derived from human pluripotent stem cells is a promising treatment for diabetes. Despite progress in stem cell-derived islet (SC-islet) generation, detailed characterization of their functional properties has not been conducted. Here, we generated functionally mature SC-islets using an optimized protocol and comprehensively benchmarked them against primary adult islets. Biphasic glucose stimulated insulin secretion developed during in vitro maturation, associated with cytoarchitectural reorganization and increased alpha cells. Electrophysiology and exocytosis of SC-islets were comparable to adult islets. Glucose-responsive insulin secretion was achieved despite differences in glycolytic and mitochondrial glucose metabolism. Single-cell transcriptomics of SC-islets in vitro and throughout 6 months of murine engraftment revealed a continuous maturation trajectory culminating in a transcriptional landscape closely resembling that of primary islets. Our thorough evaluation of SC-islet maturation highlights their advanced degree of functionality and supports their use in further efforts to understand and combat diabetes.

developmental biology↗

bioRxiv2019

Maturation of Neuronal Activity in Caudalized Human Brain Organoids

Human brain organoids are an emerging tool to study functional neuronal networks in health and disease. A critical challenge is the engineering of brain organoids with defined regional identity and developmental stage. Here we describe a protocol for generating hindbrain-like organoids from human pluripotent stem cells. We first generated a stable pool of caudalized stem cells that expressed hindbrain identity transcription factors and differentiated into tissue containing neurons and astrocytes. After maturation, caudalized brain organoids presented synaptically connected networks consisting of glutamate-, GABA-, and serotoninergic postmitotic neurons. These mature neurons displayed electric properties and dendritic trees resembling medulla oblongata neurons. They fired spontaneous and evoked repetitive action potentials, released serotonin and displayed excitatory and inhibitory synaptic currents, functionally resembling the activity patterns observed in normal human fetal brain. Reminiscent of infected human fetal brain, infection with Zika virus hampered organoid development, while the treatment with anticonvulsant drugs - carbamazepine and valproic acid - reduced organoid growth. Neuronal maturation also occurred in the grafted organoids in vivo. In conclusion, our approach enables efficient derivation of caudalized neuronal stem cells that differentiate into mature and functional neurons in organoids with hindbrain identity following human developmental trajectory. The organoids provide excellent model to study congenital abnormalities in brain development and for drug testing.

neuroscience↗

bioRxiv2017

Human pluripotent reprogramming with CRISPR activators

CRISPR/Cas9 based gene activation (CRISPRa) is an attractive tool for cellular reprogramming applications due to its high multiplexing capacity and direct targeting of endogenous loci. Here we present the reprogramming of primary human skin fibroblasts into induced pluripotent stem cells (iPSC) using CRISPRa, targeting endogenous OCT4, SOX2, KLF4, MYC and LIN28A promoters. The basal reprogramming efficiency can be improved by an order of magnitude by additionally targeting a conserved Alu-motif, enriched near genes involved in embryo genome activation (EEA-motif). This effect is mediated in part by more efficient activation of NANOG and REX1. These data constitute a proof of principle that somatic cells can be reprogrammed into iPSC using only CRISPRa. Furthermore, the results unravel previously uncharacterized involvement of EEA-motif-associated mechanisms in cellular reprogramming.

cell biology↗