Biology subjects

Sahoo, S.

Publications and source records attributed to Sahoo, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Inflammation is an essential trigger for POLE-driven ultramutated colorectal cancer

Pathogenic variants in the exonuclease (proofreading) domain of DNA polymerase {varepsilon} (POLE) are frequently detected in colorectal cancers (CRC) with high tumor mutational burden (TMB), yet their functional role in intestinal tumorigenesis remains unknown. Here, we investigated the impact of mutation in POLE on intestinal homeostasis using a conditional mouse model expressing the PoleP286R pathogenic driver in intestinal epithelial cells. PoleP286R mutant mice developed invasive adenocarcinomas in the small intestine with incomplete penetrance and extremely long latency but did not spontaneously develop colorectal tumors. However, induction of colitis with dextran sodium sulfate (DSS) resulted in a striking phenotypic shift to colorectal adenocarcinomas at high frequency. Molecular and histological analyses revealed hyperactivation of Wnt/{beta}-catenin, NF-{kappa}B, ERK and STAT3 pathways, accompanied by markedly higher proliferation of intestinal epithelial cells, in DSS-treated PoleP286R mutant mouse colons. Whole genome sequencing of the tumor demonstrated exceptionally high TMB (>100 mutations/megabase) and characteristic trinucleotide signatures, consistent with human POLE tumors. Recurrent mutations in Apc and Ctnnb1 underscored the central role of Wnt signaling in POLE-driven hypermutated CRC. In addition, intestinal organoids derived from PoleP286R mutant mice exhibited accelerated growth and increased expression of pro-proliferative genes. Together, these findings highlight POLE as a gatekeeper of intestinal genomic integrity and identify inflammation as the key driver that unleashes POLE-mutant CRC. Furthermore, this work establishes a mechanistically faithful preclinical platform for studying the molecular pathogenesis of CRC and advancing therapeutic drug discovery.

cancer biology↗

bioRxiv2026

MHC-I downregulation is associated with immune-evasion in breast cancers with heterogeneous activation of epithelial-mesenchymal plasticity

Cancer cell-intrinsic epithelial-mesenchymal plasticity (EMP) drives carcinoma progression through increased intratumoral heterogeneity and an immunosuppressive tumor microenvironment (TME). Specifically, EMP activation in murine mammary carcinomas results in exclusion of CD8+ T-cells and recruitment of immunosuppressive M2-like macrophages, resulting in resistance to anti-CTLA-4 immune checkpoint blockade (ICB) therapy. Notably, mixed E-qM tumors in which only 10% of cancer cells have activated EMP are resistant anti-CTLA-4 immune checkpoint blockade (ICB) therapy. This suggests that minority fractions of qM cancer cells could, in theory, exert immunosuppressive effects on surrounding E cancer and immune cells to shield the entire heterogeneous tumor against immune attack. However, this has not yet been demonstrated. Here, we use spatial transcriptomic profiling to demonstrate that mixed E-qM tumors assemble immunosuppressive cellular niches. Furthermore, E cancer cells within mixed E-qM tumors experience long-term MHC-I downregulation leading to resistance to elimination by CD8+ T-cells. This is associated with the exclusion of T-cells from the tumor core and a dysfunctional phenotype in the remaining CD8+ T-cells. qM cancer cells recruit immunosuppressive M2-like macrophages to mixed tumors, which further downregulates E cancer cell-intrinsic MHC-I levels. Finally, we demonstrate that human triple-negative breast cancers with increased EMP activation exclude T-cells from the tumor core. Together, these findings reveal that qM cancer cells modulate the immune infiltrate of mixed tumors, promoting MHC-I downregulation and evasion of immunological control by CD8+ T-cells.

cancer biology↗

bioRxiv2026

Cyclic Hypoxia drives Wnt5a-ROR1 stroma-tumor crosstalk promoting breast cancer growth

Tumor hypoxia can be stable, or cyclic based on proximity to vasculature, and affects not just the cancer cells, but also other cells in the tumor microenvironment (TME). Although cyclic hypoxia can affect cells in the tumor microenvironment differently from stable hypoxia, its effect on non-malignant cells in the tumor microenvironment (TME) is unclear. Here, using single cell RNA ATAC sequencing of multicellular co-culture model of triple-negative breast cancer (TNBC), comprising MDA-MB-231 cells, fibroblasts (Fbs), mesenchymal stromal cells (MSCs), endothelial cells, and macrophages, we systemically map the transcriptomic response shaped by dynamic oxygen regimes. Cyclic hypoxia induced a distinct transcriptional program compared to stable hypoxia in a cell type specific manner, regulating cell subpopulation proportions with key phenotypic implications. In TNBC, cyclic hypoxia reversed chronic hypoxia-induced cell cycle arrest, and reversed the enrichment of a highly mesenchymal WNT5A+/COL6+ subpopulation stabilized in hypoxia. Furthermore, cyclic hypoxia increased fibroblast activation, but suppressed MSC proliferation. Mechanistically, cyclic hypoxia coordinated paracrine WNT5A/B-ROR1 signaling between fibroblasts and TNBCs. In a mouse breast CAF-TNBC co-xenograft model, disrupting this cyclic hypoxia driven WNT5A-ROR1 stroma-cancer crosstalk reduced tumor growth in vivo. Together, our findings highlight dynamics in oxygen regimen as distinct microenvironmental cues, reprograming the TME compartments to accelerate cancer growth and invasion.

cancer biology↗

bioRxiv2026

Answering clinicians' questions over trial evidence tables with verifiable, feedback-driven language models

Systematic reviews condense clinical trials into evidence tables, yet clinicians can interrogate these tables only through database queries, and many questions concern attributes that the table does not record, such as a drug's target class or a harmonised endpoint. Here we introduce FD-SCoPE, a language-model framework that answers both kinds of question, exposes the query, the selected trials and the derivation rule behind every answer, and learns from expert corrections. On an oncology evidence table of 159 immune checkpoint inhibitor trial records, FD-SCoPE completed all 140 clinician-style tasks (alternatives, 90.7--97.9%). For questions needing derived attributes it retrieved 99.3% of relevant trial records at a positive predictive value of 89.8% and outperformed four alternative approaches (derived-value F1 77.7% versus 64.8--73.4%). Corrections on 299 questions, simulated from reference answers, raised F1 on 1,201 unseen questions from 77.9% to 84.9%. Language models coupled with executable queries, verified programs and expert feedback can give clinicians auditable access to trial evidence.

bioengineering↗

bioRxiv2026

A Nanomechanical Fingerprint of Centromeric Methylation Co-Localization in TNBC Chromosomal Instability

Centromeric heterochromatin is maintained by a self-reinforcing loop between DNA methylation (5mC) and histone H3 lysine 9 trimethylation (H3K9me3), yet whether this coupling is preserved at the level of individual chromosomes in cancer has been inaccessible to conventional epigenomic assays, which average signals across cell populations and cannot resolve single-chromosome heterogeneity. Here, we use antibody-functionalized atomic force spectroscopy to simultaneously map 5mC and H3K9me3 at the centromeres of individual metaphase chromosomes from non-tumorigenic, luminal, and triple-negative breast cancer (TNBC) cell models. Co-localized 5mC/H3K9me3 sites are mechanically stiffer than sites carrying either mark alone across the panel, revealing a cooperative biophysical signature of epigenetic crosstalk. Luminal chromosomes acquire the highest mark density, co-localization, and stiffness, whereas TNBC chromosomes show reduced density and diminished, though not absent, co-localization and stiffness, converging toward the low baseline of non-tumorigenic epithelium. TGF-{beta}1-induced epithelial-mesenchymal transition reproduces this attenuated phenotype in luminal cells, linking it directly to a process central to TNBC aggressiveness. These biophysical parameters classify cancer versus non-tumorigenic chromosomes with near-perfect, cross-validated accuracy, and further resolve the two TNBC subtypes using colocalization-derived features alone (macro-F1 = 0.933). These results establish the mechanical consequence of epigenetic mark co-localization as a single-chromosome-resolvable signature of centromeric organization, attenuated in aggressive breast cancer, and demonstrate a force-spectroscopy platform for mechano-epigenetic profiling of cancer chromosomes.

biophysics↗

bioRxiv2026

Spatially Organized Tertiary Lymphoid Structures Emerge in Small Cell Lung Cancer and Associate with Improved Survival

Tertiary lymphoid structures (TLS) are ectopic immune aggregates associated with improved prognosis and response to immunotherapy in multiple solid tumors. However, their presence, spatial organization, and functional relevance in small cell lung cancer (SCLC), a malignancy characterized by profound immune evasion, remain poorly understood. Using imaging mass cytometry (IMC) across 320 regions of interest spanning primary lung tumor, tumor-adjacent lung, liver and lymph node metastasis, complemented by Visium HD spatial transcriptomics, we characterized the cellular architecture and molecular programs of TLS-like niches in SCLC. TLS-like niches were identified in a subset of SCLC samples, predominantly primary lung tumor tissues and adjacent lung, spanning a continuum from loose lymphoid aggregates to compact follicle-like immune structures. Organized TLS-like niches contained CD20+ B-cell cores, closely associated with CD4+ and CD8A+ T cells, proliferating lymphocytes, HLA-DR+ antigen-presenting compartments, and SMA+ stromal scaffolds, and were enriched for canonical TLS organizer signals (CXCL13, LTB, FDCSP). Patients with TLS-positive tumors demonstrated improved overall survival, and core TLS-associated transcriptional programs were associated with favorable survival in an independent bulk RNA-seq cohort. To our knowledge, this represents one of the first spatially resolved analyses of TLS-like immune architecture in SCLC, demonstrating that organized lymphoid immunity can emerge in this classically immune-evasive disease and is associated with improved survival.

cancer biology↗

bioRxiv2026

Hepatobiliary Progenitor-like Reprogramming in Liver Metastases

Metastatic progression requires cancer cells to adapt to the unique constraints of distant organ microenvironments, yet the mechanisms that drive organ-specific adaptations remain poorly understood. Here, we show that the liver actively rewrites metastatic cancer cell identity, driving tumor cells toward a hepatobiliary progenitor-like state. Through integrated transcriptomic, proteomic, metabolomic, and epigenomic analyses of patient-derived rapid-autopsy samples and experimental models, we identify this state as selectively enriched in liver metastases. It is characterized by co-activation of hepatic and biliary/progenitor regulators HNF4A and SOX9 and is observed across multiple epithelial cancers, indicating a conserved response to the hepatic niche. Mechanistically, hepatocyte-derived TGF-{beta} and hypoxia converge to activate a HIF-1-ACLY axis, increasing nuclear acetyl-coenzyme A availability and histone acetylation at hepatic lineage regulatory elements to drive hepatobiliary reprogramming. This coordinated niche-response program can be captured transcriptionally and is associated with inferior overall survival. Disruption of this pathway suppresses hepatic reprogramming and impairs liver metastatic fitness. These findings identify the liver as an active determinant of metastatic cell fate, linking microenvironmental signaling to metabolic and chromatin remodeling programs that enable lineage plasticity. More broadly, they reveal organ-specific reprogramming as a fundamental principle of metastasis and a therapeutic vulnerability in liver metastases.

cancer biology↗

bioRxiv2026

Residue-specific dominant-negative mutant of ubiquitin reveals functional selectivity as Ubp14 deubiquitinase inhibitor

Multifunctional proteins encode specificity through nuanced molecular interactions that operate in the presence of abundant wild-type molecules. Previous studies on multifunctional proteins have shown how certain regulated interactions parse complex biological activities into discrete functional modules. Discrete interaction edges can function as regulatory nodes whose perturbations selectively remodel proteostasis output, especially under disease conditions. However, whether such interaction specificity can be harnessed to selectively manipulate functional modules and reveal residue-level control principles, remains largely unexplored. Here, we screened for dominant negative mutations that impact partner-selective functions linked to Leu8, a critical binding residue on ubiquitin. Our results reveal that the Leu8Ala mutation specifically leads to accumulation of polyubiquitinated proteins and decreased levels of free ubiquitin suggesting loss of deubiquitinase function in yeast cells. Cellular and biochemical analyses establish that the Leu8Ala variant of ubiquitin specifically inhibits the yeast deubiquitinase, Ubp14, and its human homolog, USP5. We further demonstrate remodelling of the binding interface with increased interface contacts for the variant and Ubp14 complex. The variant shows a higher inhibitory potency compared to the wild-type ubiquitin and can inhibit Ubp14 both as unconjugated and as conjugated ubiquitin chain indicating the strength of its inhibitory function. Our results provide mechanistic insight into how edge perturbations in ubiquitin can reveal critical nodes that impact selective functions and thus fine-tune the cellular proteostasis network for therapeutic benefit.

biochemistry↗

bioRxiv2026

Endocrine therapy-specific lineage and partial epithelial-mesenchymal reprogramming defines divergent resistant cell-states in ER+ breast cancer

Acquired resistance to endocrine therapy remains a primary obstacle in the clinical management of estrogen receptor-positive (ER+) breast cancer. While resistance is frequently accompanied by transcriptional rewiring and lineage plasticity, how specific pharmacological modalities dictate divergent resistance trajectories remains poorly understood. Here, we integrate multi-omic profiling, spanning bulk and single-cell transcriptome, chromatin architecture (Hi-C), and the cistrome, to systematically compare the mechanisms involved in adaptive resistance to selective estrogen receptor modulators (SERMs, e.g., tamoxifen) and degraders (SERDs, e.g., fulvestrant), and the mechanism driven by constitutive ESR1 mutation, to characterize how mode of ER perturbation influences lineage identity and epithelial-mesenchymal state. We found that tamoxifen resistant (TamR) cells occupy a distinct transcriptional state characterized by coordinated luminal erosion, partial basal lineage activation, and stabilization of a partial epithelial-mesenchymal (pEMT) program. In contrast, fulvestrant resistant (FulR) cells primarily suppress ER signaling without extensive lineage reprogramming. Finally, ESR1 mutant cells recapitulate ligand-driven ER hyperactivation with limited engagement of mesenchymal and basal gene expression programs. Chromatin profiling further revealed that SERM resistance is accompanied by higher-order genome reorganization, including A-to-B compartment switching at luminal regulators such as GATA3 and ESR1, redistribution of ER and FOXA1 binding, and consequent activation of a pEMT program. Furthermore, we show that SERM-induced reprogramming is accompanied by a distinct mode of immune evasion where the reprogrammed cells do not engage classical T-cell exhaustion programs but instead exhibit coordinated loss of major histocompatibility complex (MHC) class I antigen presentation and establishment of a pro-tumorigenic signaling that strongly predicts adverse survival outcomes in patient cohorts. Together, these findings indicate that endocrine resistance does not converge on a single molecular endpoint but instead reflects drug-specific adaptive states defined by ER signaling context, lineage identity, and chromatin architecture. Our study establishes the basal-pEMT axis as a coordinated, epigenetically encoded module of SERM-induced plasticity and reframes endocrine resistance as a multidimensional evolutionary process shaped by therapeutic mechanisms of action.

cancer biology↗

bioRxiv2026

Exosome-like biogenesis from the Golgi releases extracellular vesicles lacking conventional tetraspanins that mediate immune evasion in cancer

Immunotherapy has improved survival across multiple malignancies but remains largely ineffective in solid cancers such as lung, breast, and pancreatic cancer. A key driver of resistance is the immunosuppressive tumor microenvironment (TME). Although numerous mediators of TME immunosuppression have been identified, therapeutic targeting has provided limited clinical benefit. Tumor-derived extracellular vesicles (EVs) have recently emerged as contributors to resistance, yet their mechanisms remain unclear. We developed human non-small cell lung cancer models to investigate EV-mediated immunosuppression. We identified a distinct Golgi-derived EV subpopulation that potently suppress T cell function and tumor infiltration. These EVs express the trans-Golgi network marker TGOLN2, and exhibit minimal levels of canonical EV markers. TGOLN2 overexpression drives this suppressive phenotype. Clinically, elevated TGOLN2 associates with poor survival and correlate with an immunosuppressive TME signature across more than 20 cancer types, including NSCLC. Collectively, this work defines a previously unrecognized mechanism of TGOLN2-driven, EV-mediated immunosuppression. Statement of SignificanceWe revealed TGOLN2 overexpression as a new immune evasion mechanism that mediates T cell suppression through increased secretion of a Golgi-derived extracellular vesicle (EV) subpopulation. These findings redefine current paradigms of EV biology and nominate TGOLN2 as a potential biomarker and therapeutic target in immunosuppressive cancers.

cell biology↗

bioRxiv2026

Distinct complexes of RAD51 paralogs participate in different fork protection pathways

Error-free genome duplication is critical for cellular homeostasis and genome maintenance. Stalled forks undergo remodeling during replication stress, and unprotected forks undergo degradation by nucleases. RAD51 paralogs are evolutionarily conserved essential proteins for genome maintenance with diverse roles ranging from homologous recombination (HR) to replication stress responses. However, the mechanisms underlying their participation in fork maintenance remain unclear. Here, we demonstrate that the RAD51 paralogs do not participate in the canonical SMARCAL1-BRCA2 axis of fork protection. Instead, RAD51D-XRCC2 (DX2) and RAD51C-XRCC3 (CX3) complexes protect forks remodeled by the FBH1 helicase, whereas the RAD51B-RAD51C (BC) subcomplex but not BRCA2 safeguards forks remodeled by the FANCM translocase, revealing a new FANCM-mediated pathway of fork remodeling which is protected by the BC sub-complex. Mechanistically, we show that FANCM-mediated fork reversal is RAD51-dependent and generates substrates for MRE11-, EXO1-, and DNA2-mediated degradation in the absence of RAD51B/C. Our findings establish the participation of the RAD51 paralogs in multiple fork protection pathways in a fork-remodeler-specific manner, highlighting the existence of several independent fork remodeling and protection mechanisms for maintaining genomic stability under replication stress.

cell biology↗

bioRxiv2026

Translation of a four-codon ORF in the 3'UTR of MAP3K10 regulates its expression

Several eukaryotic mRNAs are polycistronic because of translatable open reading frames (ORFs) embedded in their untranslated regions (UTRs), in addition to the primary ORF (i.e., the coding sequence). While 5'UTR upstream ORFs (uORFs) are mechanistically and functionally well studied, 3'UTR downstream ORFs (dORFs) remain poorly understood. Here, we identify and characterize a short, translatable dORF in the 3'UTR of MAP3K10, which encodes a serine/threonine kinase involved in JNK signalling. A stringent computational screen predicted a conserved RNA G-quadruplex (rG4) within the 3'UTR of MAP3K10. Biophysical assays provided more evidence for rG4 formation, which drives translation of a conserved four-codon dORF. Disruption of the rG4 by point mutations or by an rG4-binding ligand reduced dORF translation. Reporter assays using constructs with strategically placed hairpin structures show that translation of the dORF is independent of both the 5 cap and the translation of the canonical ORF. Notably, deletion of the rG4-dORF module, either in exogenous constructs or in CRISPR-edited cells, led to reduced MAP3K10 expression. Together, these results provide evidence for the regulation of MAP3K10 expression by rG4-driven translation of a dORF. Thus, our study contributes to the growing body of evidence suggesting that dORF translation can regulate gene expression.

molecular biology↗

bioRxiv2026

Whole-genome pre-amplification as a viable approach for genomic screening of FFPE-derived DNA samples

Whole-genome sequencing (WGS) enables comprehensive analysis of tumour genomes, but its use in formalin-fixed paraffin-embedded (FFPE) samples is limited by DNA fragmentation and low yields. Whole-genome amplification (WGA) methods such as multiple displacement amplification (MDA) can boost DNA availability but distort copy-number alteration (CNA) profiles. DNA ligation-mediated MDA (DLMDA) mitigates this bias by reconstituting fragmented templates, yet its performance in FFPE-derived DNA remains uncertain. We compared paired DLMDA pre-amplified (2h, 8h) and non-pre-amplified FFPE prostate tumour samples from 22 archival blocks (5, 15 and 20 years old). DLMDA increased DNA yield by 42- to 86-fold, with global CNA patterns largely preserved. However, DLMDA significantly reduced the number of detected CNA deletions and amplifications. These effects were independent of both block age and reaction time. CNA dropouts were randomly distributed across the genome, indicating that DLMDA does not introduce regional bias. Our results show that DLMDA enables robust DNA yield recovery and avoids false-positive CNA artefacts, but at the cost of reduced CNA sensitivity. While suitable for CNA screening pipelines through WGS, further improvements are required to minimise the false-negative risk and improve the techniques sensitivity for FFPE-based genomics.

molecular biology↗

bioRxiv2026

Systems-level analysis identifies IRF6 as an inhibitor of epithelial-mesenchymal transition

BackgroundEpithelial-mesenchymal transition (EMT) and its reverse process Mesenchymal-Epithelial Transition (MET) are crucial during metastasis and therapy resistance. While the dynamics and master regulators of EMT are well-studied, the transcription factors that can prevent EMT or promote MET are relatively less understood. ResultsHere, by integrating bulk and spatial transcriptomic data analysis from cell lines and patient samples, with mechanism-based dynamical modelling, we identify IRF6 as a factor that strongly associates with an epithelial phenotype and is often inhibited during EMT. In vitro experiments in multiple cancer cell lines demonstrate the progression to a mesenchymal phenotype upon IRF6 knock-down, suggesting a role as an inhibitor of EMT. Finally, we observe that IRF6 expression levels correlates with worse patient survival in a subset of solid tumour types. ConclusionOur integrated computational-experimental systems-level analysis suggests that IRF6 is frequently downregulated during EMT and can also prevent the progression towards a complete EMT, underscoring its role as an MET stabilizing factor.

systems biology↗

bioRxiv2025

Multi-omics investigation reveals molecular determinants of cancer cell evolution on soft extracellular matrix

Cancer cell adaptation to their physical tumor microenvironment is a key driver of malignancy. Recent experimental evolution experiments show that the soft extracellular matrix (ECM) can impose a selection pressure on genetically variable tumor populations. Over months of sustained culture, the selection pressure leads to enrichment of specific genetic variants with high fitness, but the mechanisms underlying the high fitness of these soft-selected clones are not fully understood. Here, we used a combination of RNA-seq, ATAC-seq, and RRBS-seq to compare soft-selected populations with non-selected ancestral populations cultured on soft ECM. We demonstrate that ancestral populations grown on soft ECM for short durations are characterized by a stressed cell state with low fitness marked by cell cycle arrest and distinct metabolic shifts, whereas sustained culture selects for a robust proliferative phenotype. Mechanistically, selected cells exhibit a silenced ancestral stress response through epigenetic modifications, characterized by reduced chromatin accessibility and de novo DNA methylation, including CDH1 promoter hypermethylation. This repressive landscape supports a high-fitness state defined by elevated MYBL2 and FAK levels. An in-silico mechanism-based model shows that these molecular differences, together with high YAP1 nuclear localization in soft-selected cells, are salient features of genetic clones capable of FAK upregulation. These findings uncover a coordinated genetic and epigenetic mechanism driving cancer cell evolution in mechanically soft microenvironments.

systems biology↗

bioRxiv2025

The non-kinase function of CDK6 is a key driver of acquired resistance to CDK4/6 inhibitors in Estrogen Receptor-positive breast cancer

The therapeutic efficacy of CDK4/6 inhibitors in ER+ breast cancer (BC) patients is presumed to arise from inhibition of the kinase function of CDK4 and 6 proteins. Despite their initial efficacy, development of acquired resistance to CDK4/6 inhibitors in metastatic ER+ BC patients is nearly universal, commonly through compensatory overexpression of CDK6. Here, we show that primary ER+ tumors show high CDK4 but very low to undetectable expression of CDK6, which suggests that the therapeutic efficacy of CDK4/6 inhibitors in ER+ BC patients is largely driven by inhibition of CDK4, rather than CDK6. Furthermore, we show that overexpression of CDK6 confers acquired resistance to CDK4/6 inhibitors, largely, through a kinase-independent function. Our findings challenge the dogma that CDK4/6-mediated phosphorylation of retinoblastoma protein (pRB) is necessary to ER+ BC cells to progress from G1 to S phase of cell cycle. Consequently, by taking advantage of the non-kinase function of CDK6, ER+ BC cells acquire independence from the kinase function of CDK4 and 6 for cell cycle progression. These findings highlight the limitations of the current standard-of-care treatments, which focus on merely inhibiting the kinase function of CDK4 and 6, and uncover the non-kinase function of CDK6 as a new targetable vulnerability to overcome acquired resistance to CDK4/6 inhibitors in ER+ BC.

cancer biology↗

bioRxiv2025

Tissue specific de novo transcriptome sequencing and expression analysis of candidate genes for terpenoid biosynthesis in Piper longum.

Piper longum L. an economically important plant lacks adequate molecular resources towards unmasking molecular mechanisms for terpenoid biosynthesis. The transcriptome profiling generated 36.91 and 36.24 million raw reads in leaf and fruit tissue respectively. The de novo transcriptome assembly was performed with 36,688,460 and 36,011,305 clean reads, which subsequently produced 40,033 and 44,025 coding sequences (CDS) in leaf and fruit samples, respectively. The CDS were annotated using different databases such as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). These annotations resulted mining of various trait specific genes including important terpenoid biosynthesis genes. Presence of 53 and 58 terpenoid compounds in essential oils of leaf and fruit of long pepper have also been identified using GC-MS. Additionally, relative gene expression of eight terpenoid biosynthesis genes each for both leaf and fruit were conducted using real-time polymerase chain reaction (RT-PCR). For further genetic diversity study, 4085 and 4564 number of SSRs were identified in leaf and fruit, respectively. This study significantly contributes to the understanding of long pepper at the molecular level by expanding the available genetic resources. This paves the way to improve long pepper varieties and develop new genotype with desirable quality traits.

plant biology↗

bioRxiv2025

Proinflammatory circulating extracellular vesicles from type 1 diabetes patients contribute to beta cell cytotoxicity and disease pathogenicity

In Type 1 diabetes (T1D), {beta}-cell loss and autoimmunity initiate years before disease diagnosis. However, the mechanisms remain unknown. Here, we investigated the role and mechanisms of circulating extracellular vesicles (cEVs) on T1D pathogenesis and {beta}-cell cytotoxicity. We used cEVs isolated from healthy donors (HD), T1D, multiple autoantibody-positive (AAb+), pre- and post-islet transplantation T1D subjects, NOD-T1D mice, and T1D PBMCs. Patient T1D-cEVs significantly induced apoptosis in vitro in human {beta}-cells but not -cells compared to HD-cEVs. cEVs from AAb+ subjects and pre-diabetic mice were cytotoxic, demonstrating that cEV-induced {beta}-cell cytotoxicity precedes T1D onset and diagnosis. cEV reduction in prediabetic NOD-T1D mice improved {beta}-cell health implying cEV contribution to T1D development. Proteomic analysis of patient T1D-cEVs found several proinflammatory proteins, including interferon gamma, which induced {beta}-cell cytotoxicity. Our data using cEVs from pre- and post-islet transplant and PBMC-EVs from T1D patients implicated immune cells as a potential cellular source of cytotoxic cEVs in T1D. Collectively, our data using T1D patient samples coupled with studies in mice demonstrate that cEVs contribute to {beta}-cell cytotoxicity and to the progression of T1D pathogenicity. Our study is one of the first to demonstrate a functional role of the proinflammatory cEV protein cargo on glucose homeostasis, {beta}-cell health, and insulitis. Our studies on T1D-cEVs may lead to discovery of novel biomarkers and therapeutic targets for T1D.

cell biology↗