Biology subjects

Hashmi, A.

Publications and source records attributed to Hashmi, A..

7 recordsLinked to original sources

bioRxiv2026

Predicting Pre-treatment Resistance or Post-treatment Effect? A Systematic Benchmarking of Single-Cell Drug Response Models

Intratumoral heterogeneity drives variable drug responses in cancer. Single-cell RNA sequencing (scRNA-seq) enables characterization of such heterogeneity and prediction of drug response at single-cell resolution. Accordingly, various computational models have been developed to infer drug response from scRNA-seq data. However, their performance, robustness, and generalizability across different biological contexts remain insufficiently evaluated. To address this gap, we benchmarked representative single-cell drug response prediction models using 26 curated datasets comprising over 760,000 cells across 12 cancer types and 21 therapeutic agents. We constructed balanced and imbalanced scenarios to reflect realistic drug-response label distributions. To address the lack of ground-truth labels in conventional scRNA-seq datasets, we incorporated lineage-tracing data with experimentally validated drug-response annotations, enabling evaluation in a clinically relevant pre-treatment prediction setting. Our results show that prediction performance was markedly higher in cell lines than in tissue samples. Under imbalanced conditions, most methods exhibited sharp performance declines, whereas scDEAL demonstrated the highest robustness. Independent validation using an in-house pancreatic ductal adenocarcinoma dataset further confirmed scDEALs robustness and ability to capture biologically meaningful state transitions. Label-substitution experiment revealed that this robustness was partially driven by the models specific training-label construction. However, benchmarking with lineage-tracing data revealed a fundamental limitation: most models capture drug-induced transcriptional changes but struggled to predict intrinsic resistance before treatment. In summary, our study defines the performance boundaries of current approaches and highlights their limitations in addressing intratumoral heterogeneity, class imbalance, and intrinsic resistance prediction, emphasizing the need for the next-generation single-cell drug response models with stronger clinical relevance.

bioinformatics↗

bioRxiv2026

Isoform-Resolved Genetic Architecture of Epilepsy and SUDEP Reveals Divergent Brain and Heart Channelopathy Signatures

Sudden unexpected death in epilepsy (SUDEP) is the most devastating complication of epilepsy, yet the molecular features distinguishing individuals at risk remain poorly defined. Although epilepsy and SUDEP share substantial genetic overlap, fatal outcomes may arise when shared risk genes are differentially deployed across neuronal and cardiac systems. Here, we identify tissue- and isoform-level regulation as a key determinant of divergence between epilepsy and SUDEP risk. We performed a large-scale integrated analysis of genetic variants reported in epilepsy and SUDEP across 419 sequencing-based studies encompassing 35,659 individuals, and quantified gene-level burden using a Bayesian Poisson-Gamma rate ratio framework. This analysis revealed preferential enrichment of genes related to cardiac electrophysiology and contractile function in SUDEP, whereas epilepsy was dominated by genes involved in neuronal excitability and synaptic signaling. To determine how shared genetic loci are deployed across tissues, we integrated GTEx-based tissue expression profiles with long-read single-cell transcriptomic datasets from human heart and brain to resolve isoform-level expression patterns. These analyses revealed pronounced tissue-specific transcript architectures. Cardiac-associated genes, including HCN4, KCNH2, KCNE1, MYH6, MYO18B, and ATP1A2, showed heart-restricted isoform expression, whereas neuronal genes such as ADGRV1, CACNA1A, GRIN2B, HCN1, HCN2, KCNA1, SCN1A, SCN2A, and SCN8A. Importantly, several shared genes exhibited tissue-partitioned isoform expression, with distinct transcript repertoires in heart and brain, particularly across pathways related to ion transport, signaling, metabolism, and structural organization. Consistent patterns were observed in iPSC-derived cardiomyocytes and neurons, indicating that lineage-dependent deployment of shared genes is preserved in controlled systems. Together, these findings suggest that tissue-specific isoform regulation provides a mechanistic basis linking shared epilepsy genetics to SUDEP susceptibility, whereby the same genetic loci contribute to neuronal dysfunction in epilepsy and to cardiac vulnerability in SUDEP. This positions SUDEP as a neuro-cardiac interface disorder shaped by isoform-level regulatory divergence.

genetics↗

bioRxiv2026

Lung microvascular rarefaction impairs pulmonary gas exchange and exacerbates heart failure with preserved ejection fraction

BackgroundDyspnea and exercise intolerance are the primary clinical symptoms of heart failure. Heart failure patients experience frequent hypoxemic episodes, yet underlying mechanisms and relevance remain poorly understood. In a cohort of heart failure patients and multiple animal models, we identify pulmonary capillary rarefaction driven by excessive autophagy in endothelial cells as a novel mechanism of hypoxemia and cardiac disease progression. MethodsA cohort of heart failure with preserved ejection fraction (HFpEF) patients was analyzed for parameters of left ventricular (LV) dysfunction and pulmonary gas exchange. Morphological and cellular mechanisms of impaired pulmonary oxygenation were assessed in three animal models of heart failure, namely two HFpEF models, SU5416-treated ZSF1 obese rats and high fat diet/L-NAME treated mice, and in rats subjected to aortic banding. Lung microvascular rarefaction was quantified by micro-computed tomography, stereology, flow cytometry and dye efflux. Cellular mechanisms of capillary loss were analyzed by single-cell transcriptomics, electron microscopy and immunofluorescence, and in mice with endothelial-specific deletion of the autophagy gene Atg7 (Atg7EN-KO). ResultsIn 234 HFpEF patients, advancing NYHA class was associated with progressive worsening of arterial oxygen saturation at rest and during exercise and a reduced lung diffusing capacity. Impaired gas diffusion correlated with indices of LV diastolic dysfunction. Impaired oxygenation and reduced exercise capacity were similarly evident in animal models of left heart disease, which showed a distinct loss of pulmonary microvessels and capillaries. Lung microvascular endothelial cells in HFpEF showed characteristics of increased autophagic flux and apoptosis. Relative to their wild type HFpEF controls, Atg7EN-KO mice had less capillary loss, restored normoxemia, improved exercise tolerance, and mitigated LV diastolic dysfunction. Additional studies in HFpEF mice corroborated the functional relevance of impaired gas exchange for the progression of left heart disease by demonstrating that additional hypoxia aggravated, whereas moderate hyperoxia improved LV function. ConclusionOur findings identify pulmonary microvascular rarefaction as a novel pathomechanism in heart failure that i) contributes to dyspnea and exercise intolerance, ii) impairs pulmonary gas exchange and iii) accelerates LV disease progression. Strategies targeting this axis such as moderate oxygen therapy may mitigate cardiopulmonary morbidity in heart failure. Clinical Trial RegistrationRegistered in the DRKS (Deutsches Register fur klinische Studien) as trial# DRKS00032974 at https://drks.de/search/en/trial/DRKS00032974.

physiology↗

bioRxiv2025

α-Parvin regulation of cell re-arrangement is critical for ureteric bud branching morphogenesis

All branched tubular structures, including the kidney collecting system, are formed by branching morphogenesis, a process that includes tip branching and trunk narrowing. Tight control of cell movement and rearrangements is a prerequisite for branching morphogenesis. The role of integrin-associated adhesion proteins in coordinating actin dynamics and cell rearrangements during branching morphogenesis is poorly understood. Here we used 3D live imaging of mouse ureteric bud branching to show that -parvin, a component of the integrin binding ILK-PINCH-Parvin (IPP) complex, regulates tip branching and tubule thinning by inhibiting excessive cell adhesion and actin polymerization. Mechanistically, -parvin promotes actin turnover by inhibiting activation of the small GTPases RhoA and Cdc42, which in turn enhances the severing function of the actin regulatory protein, cofilin. These results underscore the importance of adhesion protein-regulated actin dynamics in the critical process of cell rearrangement, which is required for branching morphogenesis. TeaserScaffold protein -parvin limits cell adhesion and actin polymerization, enabling cell rearrangements that drive kidney branching

developmental biology↗

bioRxiv2025

PanScan: A Tool for Tertiary Analysis of Human Pangenome Graphs

The genomic representation of populations across the globe is critical to ensuring a comprehensive and equitable human reference. Constructing a pangenome graph reference for different populations is the best approach to addressing local genomic diversities. Although major initiatives across continents are underway to construct pangenome graph references, the field lacks the necessary toolsets for tertiary analysis to characterize telomere-to-telomere (T2T) assemblies and the complexity of haplotypes. PanScan is a bioinformatics software package developed for human pangenome tertiary analysis. It includes multiple modules designed to detect duplicated gene sets from T2T assemblies, identify novel variants and sequences, as well as detect and visualize complex genomic regions through pangenome graph haplotype loops. We have used multiple pangenomes across different populations to assess the tertiary analysis and their accuracy. The tool is designed to streamline tertiary analysis and is compatible with multiple pangenome graph construction algorithms. PanScan is freely available on GitHub (https://github.com/CATG-Github/panscan), where users can provide human pangenome assemblies or VCF files as inputs for automated analyses through command-line operations on Linux systems. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/651685v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@16cc212org.highwire.dtl.DTLVardef@13961d0org.highwire.dtl.DTLVardef@44d194org.highwire.dtl.DTLVardef@1b72aa_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2022

Mechanical forces across compartments coordinate cell shape and fate transitions to generate tissue architecture

Morphogenesis and cell state transitions must be coordinated in time and space to produce a functional tissue. An excellent paradigm to understand the coupling of these processes is mammalian hair follicle development, initiated by the formation of an epithelial invagination - termed placode - that coincides with the emergence of a designated hair follicle stem cell population. The mechanisms directing the deformation of the epithelium, cell state transitions, and physical compartmentalization of the placode are unknown. Here, we identify a key role for coordinated mechanical forces stemming from contractile, proliferative, and proteolytic activities across the epithelial and mesenchymal compartments in generating the placode structure. A ring of fibroblast cells gradually wraps around the placode cells to generate centripetal contractile forces, which in collaboration with polarized epithelial myosin activity promote elongation and local tissue thickening. These mechanical stresses further enhance and compartmentalize Sox9 expression to promote stem cell positioning. Subsequently, proteolytic remodeling locally softens the basement membrane to facilitate release of pressure on the placode, enabling localized cell divisions, tissue fluidification, and epithelial invagination into the underlying mesenchyme. Together, our experiments and modeling identify dynamic cell shape transformations and tissue-scale mechanical co-operation as key factors for orchestrating organ formation.

developmental biology↗

bioRxiv2020

Cell state transitions and collective cell movement generate an endoderm-like region in gastruloids

Shaping the animal body plan is a complex process that involves the spatial organization and patterning of the different germ layers. Recent advances in live imaging have started to unravel the cellular choreography underlying this process in mammals, however, the sequence of events transforming an unpatterned cell ensemble into structured territories is largely unknown. Here, using gastruloids -3D aggregates of mouse embryonic stem cells-we study the formation of one of the three germ layers, the endoderm. We show that the endoderm is generated from an epiblast-like homogeneous state by a three-step mechanism: (i) a loss of E-cadherin mediated contacts in parts of the aggregate leading to the appearance of islands of E-cadherin expressing cells surrounded by cells devoid of E-cadherin, (ii) a separation of these two populations with islands of E-cadherin expressing cells flowing toward the aggregate tip, and (iii) their differentiation into an endoderm population. During the flow, the islands of E-cadherin expressing cells are surrounded by cells expressing T-Brachyury, reminiscent of the process occurring at the primitive streak. Consistent with recent in vivo observations, the endoderm formation in the gastruloids does not require an epithelial-to-mesenchymal transition, but rather a maintenance of an epithelial state for a subset of cells coupled with fragmentation of E-cadherin contacts in the vicinity, and a sorting process. Our data emphasize the role of signaling and tissue flows in the establishment of the body plan.

developmental biology↗