Biology subjects

Jain, S.

Publications and source records attributed to Jain, S..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Gene- and domain-aware calibration increases the clinical utility of variant effect predictors

The utility of clinical genetic testing is limited because around 90% of missense variants in ClinVar remain of uncertain clinical significance. Variant effect predictors (VEPs) can score any missense variant, potentially empowering variant classification. Realizing this potential requires calibration to translate predictor scores into evidence. However, genome-wide calibration ignores predictor heterogeneity across genes, causing evidence misassignment. We developed an automated, data-adaptive framework that optimizes two complementary approaches: gene-specific calibration for genes with enough variants for calibration, and domain-aggregate calibration for other disease-associated genes, which groups variants from protein domains with similar predictor score distributions for calibration. Applied to three predictors across 2,769 genes, this framework assigned evidence to 10.6% more variants on average while generally improving evidence accuracy compared to genome-wide calibration. These calibrations and the resulting calibrated computational evidence are available through the PredictMD portal. Our framework substantially increases the clinical utility of VEPs for variant classification.

genetics↗

bioRxiv2026

A scalable approach to resolving variants of uncertain significance

Over 90% of missense variants across [~]4,000 disease-associated genes are variants of uncertain significance (VUS). Experimental variant effect measurements provide critical evidence about pathogenicity and inform disease biology, but most variants lack data and clinical translation has been limited. The Impact of Genomic Variation on Function Consortium generated experimental data for 62,215 variants across ten genes using multiplexed assays and 1,407 variants across 163 genes using arrayed assays, curated 193,139 additional community-generated variant effect measurements across 30 additional genes, and developed automated calibration methods for translating experimental data and variant effect predictions into clinical evidence. To reduce current VUS, we developed a scalable workflow using only experimental and predictive evidence, enabling reclassification of 75% of the 16,115 VUS in these genes as pathogenic or benign with <1% error. To minimize future VUS, we analyzed >90,000 unobserved variants; 62% had enough evidence to be "preclassified" as pathogenic or benign. We validated our data, evidence and classifications using All of Us and created interactive resources to enable clinical use of the calibrated data. Thus, for 40 genes, representing 1% of the clinical genome, we resolve most existing VUS and future variants, illustrating how systematic use of scalable evidence can empower genomic medicine.

genomics↗

bioRxiv2026

RNA degradation by DIS3 is a necessary step in the resolution of backtracked transcription complexes

The RNA exosome is known to participate in transcription, but the contribution of its ribonuclease activities to this process remains unclear. Here we investigated the role of DIS3, one of the exosome ribonucleases, in transcription by RNA polymerase II (RNAPII). Rapid depletion of DIS3 reduced RNA synthesis and induced RNAPII elongation defects that were exacerbated by UV irradiation, a treatment that generates transcription-blocking DNA lesions and promotes RNAPII backtracking. Notably, DIS3 itself was redistributed following UV irradiation in a manner that closely paralleled RNAPII dynamics, which suggested that DIS3 acts in concert with the transcription machinery. We also investigated whether RNA degradation by DIS3 was required for transcription elongation and found that the 3-5 exoribonucleolytic activity of DIS3, but not its endonucleolytic activity, is essential for efficient transcription elongation. More specifically, DIS3 degrades the 3 ends of backtracked RNA, as shown by sequencing of RNA fragments released by TFIIS-induced transcript cleavage in vitro. This DIS3-dependent degradation of backtracked RNA is critical for resolving stalled RNAPII complexes and enabling productive transcription elongation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=169 SRC="FIGDIR/small/703186v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@c080dorg.highwire.dtl.DTLVardef@1e4b375org.highwire.dtl.DTLVardef@1c1f575org.highwire.dtl.DTLVardef@d9d640_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDIS3 depletion leads to severely reduced rates of RNA synthesis in human cells. C_LIO_LITranscription-blocking lesions reveal a critical role for DIS3 in RNA polymerase II elongation. C_LIO_LIThe 3 to 5 exoribonuclease activity of DIS3 is necessary for transcription elongation. C_LIO_LIDIS3-mediated degradation of backtracked RNA is required for the resolution of stalled transcription complexes. C_LI

molecular biology↗

bioRxiv2026

Profibrotic Changes Following Tension Application in a Fetal Lamb Model of Long Gap Esophageal Atresia

IntroductionEsophageal atresia is a common congenital anomaly, occurring in 1 in 3,500 live births. The Foker process has revolutionized the treatment of long gap esophageal atresia (LGEA). It is well established that the Foker process causes tension accelerated growth of the esophagus, but what occurs at the molecular level during tension accelerated growth is still unknown. We aimed to create tension accelerated growth in a fetal lamb model of LGEA in order to answer this question. MethodsFollowing IACUC approval, time-dated fetal lambs (108 to 120 days of gestation) underwent thoracic esophagectomy. Both esophageal ends were ligated and sutured together to create an internal pexy under high tension. Lambs were delivered on postoperative day 2 (POD2) (n=7), POD6 (n=9) or term (n=5). The native esophagus collected at model creation served as control tissue. Specimens were bluntly separated into two layers: inner layer (IL) (epithelium, lamina propria, muscularis mucosa, submucosa) and outer layer (OL) (submucosa, muscle layer, adventitia). RNA sequencing (RNAseq), proteomics, immunohistochemistry, western blotting and real-time qRT-PCR were performed on the specimens. Mann-Whitneys or unpaired t-test were used for statistical analyses. Esophageal fibroblast cell lines established from human biopsy specimens were cultured and stimulated with TGF-beta for in vitro studies on collagen expression. Results23 lambs underwent esophagectomy with tension suture placement at 108 to 120 days gestation. Histologic analysis of tension conditioned compared to control esophagus by trichrome staining demonstrated an increase in collagen deposition in tension conditioned esophagus compared to controls. High throughput bulk RNA sequencing and proteomic analysis were performed with a focus on pathways implicated in fibrosis. GSEA analysis of the inner layer demonstrates upregulation of TGFB signaling, extracellular matrix organization, and collagen deposition at all timepoints. Further analysis was performed to evaluate specific collagen subtypes contributing to this profibrotic phenotype, and COL8A1 and COL12A1 were both significantly upregulated in both RNA and proteomic analysis at all timepoints, with Western blotting confirming up regulation in stretched tissue. In order to evaluate the relationship between TGFB signaling and collagen deposition in the esophagus, we stimulated esophageal fibroblasts with TGFB, qRT-PCR was performed to evaluate the expression of COL8A1, COL12A1, and COL6A3. Expression of all three of these collagen subtypes was noted to be significantly upregulated at all timepoints following TGFB stimulation when compared to non-stimulated controls. ConclusionsTension accelerated growth can safely be achieved in a fetal ovine model of long gap esophageal atresia. Additionally, esophageal atresia can be modeled in the ovine fetus as early as 92 days gestation. Our results demonstrate that esophageal tissue subjected to sustained tension undergoes significant profibrotic changes, as evidenced by upregulation of TGFB signaling, alterations in extracellular matrix organization, and increased collagen deposition. While it is well documented that patients with LGEA have an increased risk of post operative esophageal strictures, these findings provide the first in vivo proof of the role of tension in conferring a profibrotic phenotype in the tension-lengthened esophagus.

developmental biology↗

bioRxiv2026

CRISPR-enabled genetic screens identify synthetic lethal targets across frequently altered cancer drivers

Synthetic lethality (SL) provides a treatment paradigm for targeting cancer with alterations in driver genes that are not conventionally druggable, including loss-of-function (LoF) mutations in tumor suppressor genes and gain-of-function (GoF) alterations in oncogenes. We undertook a series of genome-wide CRISPR screens using functionally validated isogenic cell lines and also conducted a large-scale SL analysis using data from the cancer dependency map (DepMap). We charted SL interactions across 15 genetic alterations characteristic of diseases with high incidence and unmet clinical need: FBXW7, CCNE1, CDK12, ARID1A, KMT2D, DNMT3A, TET2, KEAP1, STK11, IDH1, SF3B1, SRSF2, U2AF1, chromosome 18q loss, and chromosome 13q loss. We show validation of several SL interactions between tractable targets with cancer drivers, including ARID1A and the hexosamine biosynthetic pathway aminotransferase GFPT1, STK11 with CAMK protein kinase family members including MARK2, FBXW7 and the CDK1 regulatory kinase PKMYT1, and CCNE1 amplification and the anaphase promoting complex or cyclosome (APC/C). In summary, this study offers a rich resource of genetic interactions across cancer drivers enabling the discovery of new biological insights and drug targets for future therapeutic development.

cancer biology↗

bioRxiv2026

Dual-inactivation of Regnase-1 and SOCS1 rewires exhausted CD8+ T cell fate to enhance anti-tumor functionality

The solid tumor microenvironment inhibits the functionality of tumor infiltrating T cells recognizing cognate tumor antigen, driving their differentiation towards terminal exhaustion. Interventions are sought to enhance the anti-tumor functionality of tumor-reactive T cells for clinical benefit. The functional genome regulating CD8+ T cell function against solid tumors was mapped by performing genome-wide, focused, and combination in vivo CRISPR/Cas9 screens using OT1 and PMEL TCR transgenic T cells in B16-OVA, MC38-gp100 and EG7-OVA syngeneic tumor models. The ability of the top single hits and combinations, which include Regnase-1 and SOCS1, to enhance CD8+ T cell anti-tumor function was evaluated in the OT1/B16-OVA model with large and established tumors, the disseminated PMEL/B16F10 tumor model, and in a novel murine TIL syngeneic model. The impact of Regnase-1 and SOCS1 single and dual-inactivation on the differentiation of exhausted CD8+ T cell subsets and on long-term persistent memory following tumor clearance was evaluated in OT1 CD8+ T cells in the B16-OVA model. The impact of single and dual-inactivation of Regnase-1 and SOCS1 on the anti-tumor function of experimental human T cell therapeutics was characterized in CRISPR/Cas9-engineered human TIL derived in vitro and in mesothelin-targeting CAR-Ts in vivo. NF-{kappa}B and cytokine signaling were identified as the top pathways regulating CD8+ T cell anti-tumor function, with Regnase-1 and Suppressor of Cytokine Signaling 1 (SOCS1) the top single and combination edits regulating the accumulation of tumor-specific TCR transgenic CD8+ T cells in syngeneic tumor models. Dual-inactivation of Regnase-1 and SOCS1 cooperated through non-redundant mechanisms to strongly expand intermediate (Texint) and effector (Texeff) exhausted CD8+ T cells within lymphoid tissues and tumor, with CD8+ T cells rewired to display an enhanced effector state and suppressed expression of TOX. Dual-edited persistent T effector memory cells (Tem) were formed following tumor clearance. Lastly, Regnase-1 and SOCS1 inactivation enhanced human Tumor Infiltrating Lymphocyte (TIL) and chimeric antigen receptor T cells (CAR-T) therapy functionality. Collectively, this study systematically mapped pathways regulating CD8+ T cell anti-tumor functionality, with Regnase-1 and SOCS1 dual-inactivation found to maximize anti-tumor function through non-redundant mechanisms.

immunology↗

bioRxiv2026

A cross-species single-cell epigenome kidney atlas identifies epithelial cells as a driver of epigenetic aging

Epigenetic aging is a hallmark of chronic diseases, arising from sustained injuries and unresolved repairs. To investigate cell-type-specific epigenetic alterations, we built a cross-species single-cell multi-omics atlas of DNA methylomes, chromatin accessibilities, and transcriptomes on healthy, injured (human) and aging (mouse) kidneys. We identified accelerated epigenetic aging dominated by tubular epithelia in diseased kidneys. The pathological state mirrors transcriptional trajectories observed in normal aging, driven by the preferential dysregulation of lineage-specific genes lacking CpG islands. Spatially, these epigenetic changes mapped to pathological niches of failed repair. Co-profiling of single-cell DNA methylation and 3D genome architecture revealed that epithelial repair states in disease undergo significant higher-order genome reorganizations, activating genes associated with renal decline. Our findings demonstrate that epithelial aging is driven by a collapse of 3D chromatin structure and local methylome integrity, which silences cell identity and promotes a non-resolving repair state.

genomics↗

bioRxiv2025

E1: Retrieval-Augmented Protein Encoder Models

Large language models trained on natural proteins learn powerful representations of protein sequences that are useful for downstream understanding and prediction tasks. Because they are only exposed to individual protein sequences during pretraining without any additional contextual information, conventional protein language models suffer from parameter inefficiencies in learning, baked-in phylogenetic biases, and functional performance issues at larger scales. To address these challenges, we have built Profluent-E1, a family of retrieval-augmented protein language models that explicitly condition on homologous sequences. By integrating retrieved evolutionary context through block-causal multi-sequence attention, E1 captures both general and family-specific constraints without fine-tuning. We train E1 models on four trillion tokens from the Profluent Protein Atlas and achieve state-of-the-art performance across zero-shot fitness and unsupervised contact-map prediction benchmarks - surpassing alternative sequence-only models. Performance scales with model size from 150M to 600M parameters, and E1 can be used flexibly in single-sequence or retrieval-augmented inference mode for fitness prediction, variant ranking, and embeddings for structural tasks. To encourage open science and further development in retrieval-augmented protein language models, we release three models for free research and commercial use at https://github.com/Profluent-AI/E1.

synthetic biology↗

bioRxiv2025

A PLM-Based Method for Predicting Protein Ion Channel Modulators for Drug Discovery and Safety Evaluation

Ion channels are central to regulating neuronal communication, cardiac rhythm, and muscle contraction. Their modulation can induce therapeutic benefits but may also lead to adverse or toxic effects. This study presents IonNTXpred, a protein language model (PLM)-based method for predicting protein ion channel modulators, including channel-specific (Na{square}, K{square}, Ca{superscript 2}{square}, and others) and moonlighting proteins capable of modulating multiple ion channels. We train, test, and evaluate our models on the largest dataset of non-redundant ion channel-modulating proteins, where no two proteins have more than 40% sequence identity. Composition analysis revealed that residues Cys, Gly, and Trp are highly prevalent, whereas Ala, Glu, Leu, Gln, and Val are scarce in ion channel-modulating proteins, with Cys identified as a key discriminative residue. We explored both alignment-based (BLAST, MERCI) and alignment-free (machine learning, deep learning, and PLM-based) approaches. Among these, our evolutionary information-based PLM (ESM2-t33) achieved the best performance, with an AUROC of 0.97 across ion channels, which further improved to 0.98 when integrated with BLAST output. The proposed method outperformed existing approaches on independent datasets. We used IonNTXpred to screen FDA-approved and organismal proteins to identify candidates with ion channel-modulating potential, supporting drug repurposing, discovery of new therapeutic proteins, and safety assessment of existing biologics. We implemented these models in a user-friendly web server, IonNTXpred, which facilitates the design and discovery of ion channel-modulating protein-based drugs and supports the biosafety evaluation of therapeutic proteins through neurotoxin screening (https://webs.iiitd.edu.in/raghava/ionntxpred/). HighlightsO_LIPrediction, design, and large-scale screening of ion channel-modulating proteins. C_LIO_LIIdentifies neurotoxins to support safety evaluation of therapeutic proteins. C_LIO_LIEvolutionary information-based protein language model ESM2-t33 for prediction. C_LIO_LIPredicts moonlighting proteins capable of modulating multiple ion channels. C_LIO_LIProvides standalone software, a web server, and a PyPI package for user accessibility. C_LI

bioinformatics↗

bioRxiv2025

Gut microbial composition modulates food-specific CD4+ T cells in food allergy

The growing food allergy epidemic is thought to be related to changing environmental factors, particularly changes in the gut microbiome. While prior work has demonstrated that food allergy can be modulated by gut microbes, little is known about how food allergen-specific CD4+ T cells are affected by gut microbial composition. Here, we report that food allergy severity differs between mice obtained from two different specific pathogen-free mouse vendors (Jackson Labs [Jax] and Taconic Biosciences [Tac]). Mice from Tac develop diarrhea and anaphylaxis after fewer allergen exposures than mice from Jax. Using food allergen peptide:MHCII tetramers, we also find that Tac mice have fewer allergen-specific regulatory T cells in the small intestine compared to mice from Jax. In addition, Tac mice have a greater abundance of small intestinal mucosal mast cells and increased intestinal permeability. The increased food allergy severity phenotype is transferable via co-housing, which corresponds to a shift in Jax microbial communities towards those found in Tac mice. Our findings demonstrate for the first time that food allergen-specific Treg cells can be modulated by gut microbial community composition, which in turn is correlated to food allergy severity.

immunology↗

bioRxiv2025

Beadex modulates hematopoiesis and innate immune defense against microbial infection in Drosophila melanogaster

Transcription factors play a crucial role during hematopoiesis with implications in leukemia. LIM-domain only proteins (LMO) are also found to be associated with chromosomal translocation in T-cell acute lymphoblastic leukemia and are highly expressed in acute myeloid leukemia, where they correlate with poor prognosis. However, their role in myeloid cell lineage specification and function is poorly understood. Using Drosophila melanogaster, which possesses a single LMO homolog, Beadex (dLMO), and a conserved myeloid-like immune system, we have shown its conserved role in plasmatocytes (equivalent to macrophages) development and innate immunity. Beadex is expressed in progenitor and differentiated plasmatocytes, and its loss reduced lymph gland size, mature plasmatocyte numbers and phagocytic efficiency. The phagocytes of Beadex mutant flies feature reduced filopodia length and lamellipodium area. Mechanistically, Beadex regulates actin remodelling by regulating the expression level of profilin (chickadee/chic), as chic overexpression rescued the defect in phagocytosis. Overexpression of Beadex in hemocytes increased fly susceptibility towards Salmonella enterica serovar Typhimurium infection and this mortality was due to an infection-induced pathology independent of bacterial burden. Bulk RNA sequencing of Beadex knockdown hemocytes revealed transcriptional changes in actin cytoskeleton regulatory genes, phagosome function and immune response pathways. In conclusion, our study identifies Beadex as a key transcriptional regulator impacting multiple aspects of myeloid cell function, ranging from hematopoiesis and cytoskeletal dynamics to host-level immune defense.

immunology↗

bioRxiv2025

Geometric Tuning of Cytokine Receptor Association Modulates Synthetic Agonist Signaling

Cytokines signal by bringing receptor subunits together, but the role of receptor geometry in shaping signaling remains unclear because natural ligands enforce fixed assemblies. Here, we present a de novo protein design platform that rigidly scaffolds receptor-binding domains into defined spatial arrangements. Applying this across IL-7, type I and III interferons, IL-10, gp130, {beta} common, and synthetic receptor pairs, we show that by varying geometry, we can bias pSTAT pathway usage and tune functional outcomes. Geometric control allowed us to decouple pSTAT1 from pSTAT5 in IL-7, separate antigen presentation (MHC-I) from checkpoint induction (PD-L1) in type I interferons, and suppress pro-inflammatory IFN{gamma} secretion while retaining anti-inflammatory activity in IL-10. We further created minimal IL-6 and IL-3 agonists and strengthened synthetic receptor pairings inaccessible with present cytokines. These results establish receptor geometry as a central determinant of cytokine activity and provide a platform for programmable immune modulation.

synthetic biology↗

bioRxiv2025

High-Throughput De Novo Protein Design Yields Novel Immunomodulatory Agonists

Cytokines regulate cell behavior by bringing together specific receptor subunits to trigger downstream signaling. Designed molecules that bring together non-natural receptor pairs could have novel signaling responses and cell specificities. We present a high-throughput de-novo design approach to create novel cytokines by generating and fusing pairs of computationally designed binders. By combining 33 designed receptor-binding domains, we generated over a thousand potential de novo designed "Novokines", of which 75 activated pSTAT signaling in peripheral blood mononuclear cells. We characterized 18 of these, including new pairings of established common receptors, cross-family pairings such as TrkA-{gamma}common, and a series of pairings with interferon receptor-1 (IFNAR1), revealing that IFNAR1 can function as a versatile common receptor similar to {gamma}common or {beta}common. We identify novokines that drive monocyte proliferation, T cell survival and CD4+ T cell-specific proliferation. Our framework provides a blueprint for expanding the understanding of cytokine signaling and generating novel therapeutic proteins.

synthetic biology↗

bioRxiv2025

Degeneration and Impaired Resilience of Skull Bone and Hematopoietic Bone Marrow

Bone marrow health is central to transplantations, blood formation, and cancer progression. However, the bone marrow niche deteriorates with age, impairing haematopoietic stem cell function. Contrary to a recent report1 suggesting skull marrow resists ageing, our multi-laboratory investigation reveals the opposite: the skull marrow is among the vulnerable sites of age-related decline. Ageing skull niches consistently show loss of mesenchymal and osteoprogenitors, suppression of angiogenic and lymphatic programs, adipocyte accumulation, vascular senescence, DNA replication stress, mitochondrial dysfunction, cellular senescence, and heightened inflammation. Proteomic profiling further highlights this vulnerability, demonstrating that vertebral niches--unlike the skull--are relatively spared from these ageing hallmarks. Together, these convergent datasets overturn the notion of skull-specific resilience and instead establish the skull marrow as a fragile, degenerating environment. These findings redefine marrow ageing and highlight the skull as a critical, clinically relevant target for sustaining blood and immune health and reducing vulnerability to haematological disease.

cell biology↗

bioRxiv2025

Establishing a continuum of cell types in the visual cortex

The mammalian cerebral cortex is composed of neurons whose properties vary in a continuous fashion rather than falling into discrete cell types. In the mouse visual cortex, excitatory neurons in layer 2 and 3 (L2/3) form such a continuum along cortical depth, patterned by the graded expression of hundreds of genes. Here we sought to understand how this continuum develops and contributes to cortical wiring. Using single-nucleus multiomics (RNA- and ATAC-Seq) and spatial transcriptomics, we show that the L2/3 continuum is established in two phases. During the first postnatal week, a genetically hardwired program establishes a primitive continuum of cell identities spanning the depth of L2/3. The second program, promoted by visual experience, is later superimposed upon the preexisting continuum. This second phase is driven by activity-regulated transcription factors that drive the L2/3 depth-dependent expression of genes linked to synaptic function and plasticity. We show that neurons at different positions along the L2/3 continuum project preferentially to distinct higher visual areas and that visual deprivation disrupts targeting to some higher visual areas while sparing others. Thus, cortical continua emerge through a stepwise process in which genetic programs and sensory experience specify neuronal identity and sculpt intracortical wiring specificity.

neuroscience↗

bioRxiv2025

A Common PD-Risk GBA1 Variant Disrupts LIMP2 Interaction, Impairs Glucocerebrosidase Function, and Drives Lysosomal and Mitochondrial Dysfunction

Variants in GBA1 cause Gaucher disease (GD), a lysosomal storage disorder, and represent the most common genetic risk factor for Parkinsons disease (PD). While some GBA1 variants are associated with both GD and PD, several coding mutations, including E326K, specifically confer risk for developing PD. It is established that GD-linked variants in {beta}-glucocerebrosidase (GCase), the enzyme encoded by GBA1, are loss-of-function, but it remains unclear whether variants solely associated with PD similarly reduce GCase activity. The mechanisms by which some of these variants impact GCase activity and PD-associated pathways, including lysosomal and mitochondrial function, are also poorly defined. Here, we show that the PD-linked E326K variant significantly reduces lysosomal GCase activity by impairing its delivery to lysosomes via altered interactions with its receptor, LIMP2. Biophysical and structural characterization of this variant, both alone and in complex with LIMP2, reveals a dimeric organization that appears to result from the loss of a key salt bridge between E326 and R329. Restoration of this salt bridge through the introduction of a negatively charged side chain at position 329 promotes monomeric organization and interaction with LIMP2 in cells. GBA1-p.E326K cell models show greater deficits in PD-linked pathways compared to more severe loss of GCase function, including secondary lysosomal lipid storage and mitochondrial dysfunction. We confirm the E326K variant impacts GCase pathway activity in relevant CNS cell types, including iPSC-derived microglia, and in biofluids from heterozygous GBA1-p.E326K variant carriers. Together, our data provide key insights into the nature of GCase dysfunction in GBA1-PD and can inform the development of GCase-targeted therapeutic strategies to treat PD.

cell biology↗

bioRxiv2025

Diploid Hepatocytes Resist Acetaminophen-Induced Liver Injury Through Suppressed JNK Signaling

Background & AimsThe liver contains both diploid and polyploid hepatocytes, but their functional differences remain poorly understood. Emerging evidence suggests that each ploidy state contributes to regeneration in an injury-specific manner. We hypothesized that diploid hepatocytes promote healing after acetaminophen (APAP)-induced liver injury. Approach & ResultsTo study ploidy populations in vivo, we utilized mice with a lifelong liver-specific knockout of E2f7/E2f8 (LKO), which are enriched in diploid hepatocytes (>70%) but otherwise normal. Control and LKO mice were treated with APAP (300 or 600 mg/kg), and injury was assessed over 0-96 hours. Although both groups sustained injury, LKO mice showed improved survival, lower serum liver enzyme levels, and reduced necrosis and DNA fragmentation, indicating resistance to APAP-induced injury. To determine if resistance was due to E2f7/E2f8 loss or increased diploidy, we deleted E2f7/E2f8 in adult hepatocytes (HKO), a model that does not alter ploidy. Injury was similar between controls and HKO, ruling out gene deletion as the protective factor. Transcriptomic and protein analyses revealed minimal baseline differences; however, following APAP treatment, LKO livers exhibited reduced JNK activation and less mitochondrial injury. Finally, APAP-treated wild-type hepatocytes exhibited a shift toward lower ploidy, supporting the idea that diploid cells are more resistant to injury. ConclusionsDiploid hepatocytes resist APAP-induced liver injury through reduced JNK activation and mitochondrial damage. These findings highlight hepatocyte ploidy as a key determinant of injury response and suggest a protective role for diploid hepatocytes in promoting liver resilience and regeneration.

genetics↗

bioRxiv2025

A SWI/SNF-specific Ig-like domain, SWIFT, is a transcription factor binding platform

Mammalian SWI/SNF (BAF) chromatin remodeling complexes modulate DNA accessibility and gene expression, however, their genomic targeting mechanisms remain incompletely understood. Here, we identify SWIFT (SWI/SNF Ig-Fold for Transcription Factor Interactions), a conserved, broad transcription factor (TF) binding platform on the SMARCD subunits. SWIFT is necessary and sufficient for direct engagement with the transactivation domain of PU.1, a single mutation in which disrupts PU.1-mSWI/SNF binding, impairs complex targeting, and attenuates oncogenic transcription and proliferation in PU.1-dependent cancer cells. Dominant expression of the SWIFT domain in isolation sequesters TFs from mSWI/SNF and poisons TF-addicted cancer cells. Finally, TFs across diverse families interact with SMARCD paralog-specific SWIFT domains. These results define a major mechanism of cell type- and disease-specific mSWI/SNF chromatin targeting and inform approaches toward therapeutic modulation.

molecular biology↗