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Rai, K.

Publications and source records attributed to Rai, K..

At least 19 recordsLinked to original sources

Repeated within-session rule switching in the marmoset: a paradigm for tracking the dynamics of cognitive flexibility

Adapting behaviour when reward contingencies change is a core function of cognitive control, but the underlying trial-by-trial computations are hard to observe when tasks cue each rule or allow only one switch per session. We developed the Feature-Rule Switching Task (FRST), in which common marmosets (Callithrix jacchus) repeatedly switch, without cues and under a fixed stimulus set, among the visual features that earn reward, inferring each switch from feedback alone. All four animals acquired the task within two days and sustained several switches per session across months of testing. A reinforcement-learning model with a learned weighting of stimulus dimensions best explained choices in every animal, outperforming complexity-matched perseveration controls. Learning-rate estimates fell within the human range, and in almost every session the animals weighted a stimulus dimension rather than individual features alone, with a dimensional commitment comparable in strength to that of humans. FRST thus provides a primate paradigm, amenable to laminar recording, for tracking the dynamics of cognitive flexibility.

animal behavior and cognition↗

Chromatin Landscape of Cancer Cell Lines Identifies Enhancer Subtypes

Epigenetic aberrations are a hallmark of cancer; however, systematic chromatin state maps of cancer cells are unavailable. We generated and analyzed 803 histone mark profiles in 142 cancer cell lines and 114 human tumors belonging to 9 solid tumor types. Irrespective of their cell-of-origin, cancer cells segregate from normal tissues based on their enhancer patterns, suggesting enhancer deregulation is a fundamental epigenetic feature in cancer. Enhancer based clustering defined 5 distinct subgroups of cancer cells (EpiC1-5) with unique developmental trajectories, molecular features and dependencies. Importantly, we define a set of core TFs that are critical for EpiC-specific enhancer patterns and survival. Notably, EpiC4 represented a predominantly epigenetic, pan-cancer subtype that displays poor survival, activation and dependence on a FN1-CAV1-SRC-PI3K-AKT signaling network. Together, these data uncover enhancer heterogeneity in pan-cancer systems with identification of a novel enhancer-based subtype and identify potential new therapeutic targets associated with unique epigenetic features.

cancer biology↗

Cross-species Study of Canine and Human Peripheral Nerve Sheath Tumors: Clinical and Molecular Perspectives

Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas. An obstacle to treating MPNSTs is a lack of effective systemic therapies. Although over 70% of human MPNSTs have lost or inactivated the epigenome regulator polycomb repressive complex 2 (PRC2), its activity and contribution to canine PNST progression remain unclear. This study compared canine peripheral nerve sheath tumors (PNSTs) and human MPNSTs across biological and clinical features, including PRC2 activity. Immunohistochemical analysis was performed for a human tissue microarray of 54 neurofibromas and 139 MPNSTs, and 63 canine PNSTs for H3K27me3, a repressive histone mark deposited by intact PRC2, and H3K27ac, which increases globally upon H3K27me3 loss. To understand the genomic alterations present in canine PNSTs, we analyzed tumor mutation burden, copy number alteration, and transcriptomes of eight canine PNST/normal pairs. The results suggested that H3K27me3 loss and associated gain of H3K27ac epigenetically drive human and canine tumors. These findings warrant further studies to evaluate whether these epigenetic deregulations alter similar gene signatures across species.

cancer biology↗

NanoCellAnnotator: Formalizing Expert Cell Type Annotation with Large Language Models

MotivationCell-type annotation in spatial transcriptomics is challenging due to sparse gene panels, spatial heterogeneity, and limited availability of tissue-matched reference atlases. Recent approaches have explored large language models (LLMs) for integrating biological knowledge during annotation, but unconstrained inference can produce biologically unsupported predictions and hallucinated cell types. In addition, many LLM-based pipelines rely on large cloud-hosted models that limit reproducibility and deployment in privacy-sensitive environments. ResultsWe introduce NanoCellAnnotator, a biologically constrained and confidence-aware framework for automated cell-type annotation in spatial transcriptomics. The framework de-couples spatial structure discovery, deterministic biological evidence construction, and language-model-based semantic inference. Spatial clusters are identified using hybrid spatially regularized non-negative matrix factorization (hSNMF), after which cluster-level marker genes are abstracted into ontology-derived functional programs using Gene Ontology enrichment and GO-slim projection. A lightweight locally executable language model performs constrained label selection within a curated admissible label space derived from PanglaoDB and CellMarker. Annotation confidence is estimated independently using marker support strength and lineage separation, enabling ambiguous or heterogeneous clusters to be explicitly flagged. We evaluate NanoCellAnnotator on Xenium spatial transcriptomics data from intrahepatic cholangiocarcinoma and an independent breast cancer spatial transcriptomics dataset. The framework recovers canonical cell populations with high confidence while identifying heterogeneous or transitional spatial domains as ambiguous. Agreement with manual annotations was evaluated using accuracy and adjusted Rand index. AvailabilityCode available at https://github.com/ishtyaqmahmud/NanoCellAnnotator.

bioinformatics↗

Ambiguity-Aware Multi-Stage Cell-Type Annotation for Spatial Transcriptomics

Spatial transcriptomics enables characterization of cellular organization in intact tissue, but robust cell-type annotation remains challenging due to heterogeneous expression profiles, mixed populations, and transitional states. Existing methods often enforce a single label per cluster, obscuring biologically meaningful ambiguity and producing overconfident assignments. We propose an ambiguity-aware, multi-stage framework for spatial cell-type annotation. The method combines hybrid spatial-feature clustering with constrained language-model inference over curated label sets, and assigns confidence scores based on marker coverage, candidate separation, and entropy. Low-confidence clusters are selectively refined via local reclustering of ambiguous regions, while unresolved clusters are preserved as mixed rather than forcibly labeled. Applied to 10x Genomics Xenium spatial transcriptomics data from cholangiocarcinoma, the proposed refinement reduces cluster-level ambiguity from 16.1% to 2.27% and cell-level ambiguity from 18.4% to 0.86%, while improving confidence calibration. Spatial ablation confirms that topological integration resolves structural ambiguity over feature-only baselines, while constrained inference via a lightweight language model ensures scalable and biologically coherent annotations. These results highlight the importance of explicit ambiguity handling for reliable spatial annotation in heterogeneous tumors.

bioinformatics↗

Development of a Staining-based Electrophoretic Mobility Shift Assay for Analyzing Pbx1, DNA and HoxA9 Interactions

Transcription factors (TFs) are master regulators of gene expression and control a wide range of cellular functions including embryonic development, signaling pathways, immune response, and differentiation. A tight regulation of gene expression is crucial during all stages of life and changes in the TF function can lead to developmental abnormalities, diseases such as cancer, or resistance to treatment. Therefore, TFs are a promising class of drug targets, and the techniques that would contribute to the development of TF modulators are critical. Electrophoretic Mobility Shift Assay (EMSA) has been a primary tool to verify protein-DNA interactions, where a fluorescent, biotin, or isotope end-labelled DNA probe is used to quantify binding. Such labeling techniques, however, can be costly, time consuming, possess safety hazard risks and require capital equipment for imaging. Here, we optimized a label-free, staining-based EMSA to characterize a potential drug target, homeodomain (HD) TF Pre-B-cell leukemia homeobox-1 (Pbx1) and its binding partner Homeobox A9 (HoxA9). Staining the polyacrylamide EMSA gel with a DNA intercalating green cyanine dye - SYBR safe - allowed the visualization of Pbx1 homeodomain interactions with DNA at nanomolar concentrations and enabled quantitative determination of protein-DNA apparent binding affinity in the sub-micromolar range. Furthermore, a ternary complex of homeodomains of Pbx1 with HoxA9 and the DNA was also visible in the assay. We have shown that the staining-based EMSA can be used to evaluate inhibitors of Pbx1 that block the interaction with DNA. We have further validated the data from our assay with fluorophore labeling-based EMSA. Overall, using HD transcription factors Pbx1 and HoxA9 as a model, we have optimized a reliable and cost-effective staining-based EMSA that enables the high-sensitivity visualization and quantitative evaluation of transcription factor-DNA complexes without the need for end-labeled DNA probes. The streamlined workflow could be readily adapted to other DNA-binding proteins to study their interactions with the DNA, inhibitors, and other proteins.

biochemistry↗

Spatially-Resolved Multiomic Atlas of Leiomyosarcoma Identifies Two Clinically Relevant Epigenetically-Driven Cell States

Leiomyosarcoma is a smooth muscle-derived malignancy marked by significant clinical heterogeneity. The extent and nature of cellular heterogeneity and molecular underpinnings remain poorly understood. To address this at transcriptomic and epigenomic levels, we performed single-nucleus multiome sequencing on untreated primary leiomyosarcoma tissues. Malignant cells segregated almost exclusively into two previously unrecognized and epigenetically distinct states: a dedifferentiated, mesenchymal-like subtype (MES) and a differentiated smooth muscle-enriched subtype (SMC). Chromatin accessibility profiling revealed strong enrichment of nuclear factor I (NFI) transcription factor motifs in MES cells, whereas AP-1 family motifs--most prominently FOSL2--were selectively accessible in SMC cells. Established leiomyosarcoma cell lines faithfully recapitulated these subtypes, and targeted depletion of NFI or AP-1 factors suppressed proliferation, invasion, and in vivo tumor growth, demonstrating functional dependency on these transcriptional programs. Spatial transcriptomics across 328 tissue cores from 128 leiomyosarcomas showed that immunosuppressive macrophages preferentially cluster around MES regions, revealing a subtype-specific tumor-immune niche. Clinically, MES-dominant tumors were associated with significantly worse patient outcomes. Through an epigenetic inhibitor screen, we identify and validate SMARCA4/2 inhibition as a promising therapeutic vulnerability for MES leiomyosarcomas. Together, this work defines two epigenetically driven, transcription factor-regulated, and clinically relevant states of leiomyosarcoma, revealing mechanistic underpinnings of tumor heterogeneity and uncovering actionable therapeutic strategies. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=93 HEIGHT=200 SRC="FIGDIR/small/726988v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@132928eorg.highwire.dtl.DTLVardef@133e3b7org.highwire.dtl.DTLVardef@1ab4398org.highwire.dtl.DTLVardef@e2de25_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

Cellular stemness identifies high-risk ductal carcinoma in situ and offers a therapeutic interception opportunity

Ductal carcinoma in situ (DCIS) exhibits substantial heterogeneity in its risk of progression to invasive breast cancer, yet the cellular and molecular determinants of high-risk lesions remain incompletely defined. Using spatially resolved single-cell transcriptomic and epigenomic profiling of 43 patient-derived DCIS and DCIS/invasive ductal carcinoma (IDC) samples, we delineate cellular programs, spatial organization, and epigenetic regulatory mechanisms associated with invasive potential. We identify an epithelial population with stemness features within luminal hormone-responsive (LumHR) cells that progressively expands from benign tissue to DCIS and IDC, and is strongly associated with invasive progression and recurrence-linked transcriptional programs. Spatial mapping reveals discrete DCIS niches enriched for stem-like LumHR cells, characterized by elevated CEACAM6 expression and enhanced ligand-receptor interactions, including CEACAM6-EGFR signaling between epithelial and stromal compartments, including cancer-associated fibroblasts, macrophages (APOC1-positive) and perivascular cells. These niches define a microenvironmental context that supports stemness and invasive potential. Epigenomic analyses implicate FOXA1 as a key regulator of these stem-like transcriptional states. Pharmacologic disruption of FOXA1-regulatory network using LSD1 inhibition suppresses stemness-associated transcriptional programs in vitro and significantly restrains tumor growth in vivo. Collectively, these findings define high-risk DCIS as a stemness-driven disease embedded within specialized microenvironments, and identify associated regulatory networks as candidate biomarkers and therapeutic vulnerabilities.

cancer biology↗

Characterization of genetically effective cells and EMS mutagenesis on the novel winter oil seed Pennycress (Thlaspi arvense)

Pennycress (Thlaspi arvense L.) is an intermediate winter oilseed crop that has only recently been domesticated for agronomic use. Improving agronomic traits requires sources of genetic variation, and mutagenesis is frequently used to help overcome the limitations of natural populations. We investigate the impact of Ethyl methanesulfonate (EMS) on genetically effective cells (GECs) to characterize the intra-individual genetic variation of EMS mutagenesis in pennycress. We identified that pennycress contains at least 4 GECs which, when treated with EMS, create unique mutations across different branches within the same individual plant. We then propagated the M2 plants for whole genome sequencing, providing extensive characterization of the EMS mutation profile and developing a gene index as a resource for future reverse genetic screenings. Article SummaryPennycress is an emerging winter oil seed crop in the American Midwest. Domestication efforts have advanced rapidly through a combination of genetic techniques. One of the most successful methods has been the use of a mutant gene index, a large collection of pennycress seed where new genetic variation has been created through Ethyl methanesulfonate (EMS). EMS mutations are not uniform however, and a single treated seed can have wide genetic variation within the resulting plant. We investigate the role of genetically effective cells on EMS variation, and present the full EMS population as a resource for further pennycress domestication efforts.

genomics↗

Counterfactual Modeling of Directional Cell Cell Influence in Spatial Transcriptomics

Understanding how neighboring cells influence cellular states is central to spatial transcriptomics, yet most existing methods rely on correlation or predefined ligand-receptor (LR) pairs and do not explicitly test directionality. We introduce a counterfactual, intervention-based framework for inferring directional cell-cell influence that is LR-agnostic and tests sender specificity. A neighborhood-conditioned graph model predicts receiver cell state from local spatial context. Directional influence is quantified by counterfactually replacing neighbors of a candidate sender type and measuring the resulting displacement in predicted receiver state. We define a Counterfactual Directionality Score (CDS) that quantifies directional influence, and compute pair-level CDS by aggregating across receiver cells and test cores for each ordered sender-receiver pair. Applied to Xenium cholangiocarcinoma tissue microarrays (38 cores), the framework identified reproducible, asymmetric interactions between tumor, immune, and stromal compartments, most prominently Tumor-EMT [->] Macrophage (CDS = 0.0828) and Fibroblast [->] Macrophage (CDS = 0.0582). Effects exceeded label-permutation and spatial-shuffle null models (p < 0.001, FDR-controlled) and remained stable under core-level bootstrap resampling. Inferred directional strengths correlated strongly with matched LR scores (r = 0.758, p = 0.0027), supporting biological concordance. These results demonstrate counterfactual testing as a statistically rigorous and scalable approach for directional cell-cell communication analysis in spatial transcriptomics.

cell biology↗

Spatially Anchored Regulatory State Inference in Melanoma

Spatial transcriptomics (ST) captures gene expression within tissue architecture but lacks direct regulatory information, while single-cell multiome assays profile transcriptional and chromatin states without spatial context. We present a framework for spatially anchored regulatory inference that integrates Visium ST with single-cell multiome data to infer spatially resolved regulatory programs. Building upon GraphST, we introduce spatially regularized cell-to-spot mapping and propagate chromatin accessibility and transcription factor motif activity into tissue space. Regulatory analysis is performed at the spatial domain level via joint differential expression and accessibility testing, along with quantitative concordance assessment. Applied to melanoma tissue sections, the framework reveals spatially localized regulatory programs and shows that assignment strategy substantially affects downstream regulatory stability. This modular approach enables interpretable gene-, peak-, and transcription factor-level outputs for multimodal spatial analysis.

bioinformatics↗

Spatially-resolved single cell atlas of liposarcoma reveals lineage hierarchies, immune niches, and regulatory circuits

Well-differentiated and dedifferentiated liposarcoma (WDLPS and DDLPS) exhibit markedly different clinical behaviors, with DDLPS showing greater aggressiveness, higher recurrence and metastasis rates, and worse outcomes. Using single-nucleus multiome sequencing, epigenomic profiling, and spatial transcriptomics, we characterized cellular and epigenetic heterogeneity between these subtypes at single-cell and spatial resolution. We found distinct phenotypic states reflecting altered lineage differentiation and plasticity: DDLPS is dominated by early-differentiated progenitor-like cells, sclerotic WDLPS displays broader mesenchymal lineage plasticity, and adipocytic WDLPS contains abundant committed adipocytes. The DDLPS immune microenvironment was dominated by immunosuppressive macrophages, whereas WDLPS harbored more T cells and inflammatory macrophages. Notably, sclerotic WDLPS displayed intermediate cellular and molecular features, suggesting it may represent a distinct WDLPS subtype. Importantly, we identified novel gene regulatory circuits underlying each state, including FABP4/PPARG programs in adipocytic WDLPS, GLI2/TCF7L2/RBPJ/KLF7 programs in sclerotic WDLPS, and KLF7/FOSL2/SP3/GLI2/RBPJ programs in DDLPS. H3K27ac-marked enhancers were enriched near adipocytic marker genes in WDLPS and mesenchymal markers in DDLPS. Together, these findings reveal the cellular heterogeneity of tumor and immune compartments across liposarcoma subtypes and identify regulatory programs driving their differentiation states. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/713651v1_ufig1.gif" ALT="Figure 1"> View larger version (73K): org.highwire.dtl.DTLVardef@1c84ee1org.highwire.dtl.DTLVardef@1b2ad42org.highwire.dtl.DTLVardef@18ce5a6org.highwire.dtl.DTLVardef@138f615_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

Fasting primes small intestinal regeneration after damage via a microbiome metabolite chromatin axis

Fasting enhances small intestinal regeneration after radiation but the contribution of the gut microbiome to this process remains uncharacterized. We identify Akkermansia muciniphila (AKK) as a key mediator of this response. AKK was enriched in fasted mice and its antibiotic depletion abrogated radioprotection whereas reintroduction restored both organismal survival and intestinal integrity. Fasting elevated propionic acid, consistent with AKKs metabolic output. AKK-conditioned medium and propionate induced histone H3 acetylation in intestinal stem cell cultures while in vivo fasting induced AKK-dependent H3K27ac and H3K9ac, remodeling promoter-enhancer landscapes in crypt epithelial cells. Epigenetic profiling revealed a rewired core regulatory program enriched for pioneer transcription factors (Foxa, Gata, Klf), architectural organizers (Ctcf, Boris), and lineage-defining and metabolic regulators (Cdx2, Hnf4). This program supports expansion of a population of persister stem cells characterized by open chromatin accessibility at key stem and regenerative-associated loci including Clu, Olfm4, Lgr5, Ascl2, Lrig1, Sox9, Rnf43, and Axin2. These findings define a fasting-induced microbiome-metabolite-chromatin axis that epigenetically primes highly plastic persister stem cells for rapid regeneration of the intestinal epithelium following radiation-induced injury. Significance StatementFasting changes the gut microbiome, but how these changes help the body recover from damage is not well understood. We found that fasting increases a helpful bacterium, Akkermansia muciniphila, which produces propionate, which drives epigenetic changes by modifying histones and regulating gene activity. These changes promote the expansion of persister stem cells that help the intestine recover after radiation. This study shows how fasting and gut bacteria work together to protect healthy tissue and suggests that diet or microbial treatments could help reduce side effects of cancer radiotherapy.

cell biology↗

A poly(A) isoform-aware single-cell and spatial atlas defines fibroblast niches in the human bladder

Bladder function relies on coordinated interactions among epithelial, stromal, vascular, and neural compartments, but high-resolution molecular and spatial features remain undefined. We generated a publicly accessible, poly(A) isoform-aware single-nucleus and spatial reference of the adult human bladder spanning four anatomical regions and both sexes. Integrating 74,694 snRNA-seq profiles with 168,476 Xenium-resolved cells, we identified 22 cell types and 23,489 polyadenylation sites, with isoform usage improving stromal resolution beyond gene expression alone. Spatial mapping revealed layered fibroblast niches aligned with epithelial, vascular, and neural structures, supported by Visium data. This multimodal reference links isoform regulation to anatomical context and provides a reusable framework for cell-type annotation, cross-study integration, and analyses of bladder physiology and disease.

molecular biology↗

ATRX Loss Predicts Poor Outcomes and Reveals a Therapeutic Vulnerability to TEAD Inhibition in Soft Tissue Sarcomas

ATRX is one of the most frequently altered genes in sarcoma and encodes an ATP-dependent chromatin remodeler implicated in maintaining heterochromatin. However, ATRX alterations have not been leveraged for sarcoma treatment. We observed loss of ATRX protein in 14% of soft tissue leiomyosarcoma (STLMS, n =127), 53% of uterine leiomyosarcoma (ULMS, n = 95), 37% of undifferentiated pleomorphic sarcoma (UPS, n = 82), and 8% of dedifferentiated liposarcoma (DDLPS, n = 84). ATRX loss was associated with significantly worse outcomes in ULMS, UPS, and DDLPS. ATRX knockout in sarcoma cells increased proliferation in cooperation with TP53 deletion. ATRX knockout led to chromatin de-repression and enrichment of PRDM4 and NFIX transcription factor (TF) motifs. PRDM4 and NFIX knockdown in ATRX-mutant sarcoma lines resulted in reduced proliferation and invasion suggesting epistatic relationship. Consistent with the known functional relationship between PRMD4 and YAP1, we observed that ATRX/TP53 KO cells were more sensitive to the TEAD inhibitor VT103 compared to TP53 KO and ATRX WT controls. Overall, our results identify ATRX loss as a prognostic factor of worse outcomes, implicate the ATRX-PRDM4-YAP1 axis as a novel underlying mechanism, and suggest use of TEAD inhibition as a potential therapeutic strategy for ATRX-deficient sarcomas. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=45 SRC="FIGDIR/small/689992v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@a759ecorg.highwire.dtl.DTLVardef@100c580org.highwire.dtl.DTLVardef@1a675c9org.highwire.dtl.DTLVardef@17f1f91_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

The Microbiotas Response to Host Adaptive Evolution

Over the past two decades, experimental evolution has significantly advanced our understanding of evolutionary patterns and mechanisms of genomic change. One critically underexplored dimension is the role of microbiota in host adaptive evolution. In this research we investigate the microbiota from forty laboratory-selected Drosophila melanogaster populations exhibiting four distinct aging trajectories, ranging from extremely-short lifespans to -long lifespans. Using metagenomic sequencing and colony forming unit (CFU) counts in both conventional and gnotobiotic conditions, we uncover substantial microbiota differentiation among these populations. The most striking pattern is the consistent loss of Wolbachia in populations selected for rapid aging, in contrast to its near complete dominance in long-lived populations. This suggests a positive association between relative abundance of Wolbachia and lifespan, alongside a negative correlation between Wolbachia and Acetic Acid Bacteria (AAB) titres. These findings position the microbiota, and particularly Wolbachia, as a potentially integral component in host life history evolution, with implications for understanding the microbial contributions to aging and adaptation. SignificanceFruit flies bred for short lifespans consistently lose the bacterial symbiote Wolbachia, while the microbiota of long-lived flies are almost entirely dominated by it. There is a stable, recurring link between this microbe and lifespan, and traits associated with lifespan. This persistent pattern suggests that microbiota, Wolbachia in particular, may play a direct role in shaping the evolution of lifespan.

microbiology↗

Association of haplotypes of AAP family amino acid transporters with nitrogen response and nitrogen use efficiency in rice grown under hydroponics and field conditions

The low nitrogen use efficiency (NUE) of staple food crops like rice has both economic and environmental impact. Amino acids taken up from soil or synthesized in source tissues and transported to sink tissues influence plant development and NUE. Amino acid permeases (AAPs) mediate amino acid uptake and transport and influence plant development, yield and NUE. NUE is a complex trait critical for improving rice productivity under variable N supply. Amino acid permeases such as OsAAP3, OsAAP5, and OsAAP11 have been shown to function as negative regulators of NUE in Japonica rice, yet their roles in Indica rice remain to be fully elucidated. In this study, we evaluated selected Indica genotypes under contrasting N regimes--seedlings were tested under high nitrate (HN), high ammonium (HA), and low N (LN) conditions, and field performance was assessed under N120 (optimum N) and N0 (low N). Our aim was to relate performance differences to the SNP status in these three genes, thereby clarifying their influence on N uptake, assimilation, yield potential, and N stress adaptation. ARC 10799 had non-synonymous SNP in OsAAP3, OsAAP5 and OsAAP11. Rice accessions like "Local," "NCS901," and "Bhainsa Mundariya," showed superior biomass accumulation relative to MTU1010. Interestingly, the trend observed in the NUE calculated in seedling stage was similar to those proven in field evaluation and this proves that in general, genotypes with non-synonymous mutation in AAP3, AAP5 and AAP11 in comparison to Japonica showed better growth and N content. Data suggests an N induced regulation of physiological parameters and the changes in NUE parameters was at least in part, related to variation in biomass, plant height, photosynthesis and pigment content related parameters. The comparatively dissimilar trends in shown by different AAP haplotypes indicates the possibility of high or low correlation trait-wise, offering an opportunity to identify significant contrasts in a divergent set of AAP haplotypes. The previous reports and current findings opens new avenues and insights for improving rice yield, quality and NUE by changes in AAP haplotypes that occur naturally or created by precise genome editing.

plant biology↗

Reprogramming of Cellular Plasticity via ETS and MYC Core-regulatory Circuits During Response to MAPK Inhibition in BRAF-mutant Colorectal Cancer

BackgroundAberrant enhancer dynamics play a critical role in the initiation and progression of colorectal cancer (CRC). BRAFV600E-mutated metastatic CRC may be a unique subtype, exhibiting a strong epigenetic phenotype. Interestingly, bromodomain 2, a reader protein for H3K27ac-marked enhancers, was found to be synthetically lethal in CRC with BRAF + EGFR inhibition. DesignWe evaluated the effectiveness of targeting aberrant enhancers with bromodomain and extraterminal (BET) + MAPK pathway inhibitors in patient-derived xenograft models of metastatic CRC, followed by comprehensive profiling of transcriptomic and chromatin dynamics upon BET inhibitor combination treatment. ResultsThe combination of BET and standard MAPK inhibitors has demonstrated improved efficacy against BRAFV600E CRC and selective improvements against RAS-mutant CRC in vivo. We showed that BET + MAPK inhibition induced a profound downregulation of the MAPK signaling pathway compared to MAPK inhibition alone. The loss of activation signal on enhancers, as determined by H3K27ac, led to dysregulation of core-regulatory circuitries of CRC, especially loss of the auto-regulatory mechanism of the MAPK downstream E26 transformation-specific transcription factor family. Single nucleus multiome (RNA + ATAC) sequencing further distinguished differential transcriptomic and chromatin dynamics at cell type levels. Profound downregulation of well-differentiated cell types confirmed deep inhibition of MAPK signaling and downstream transcription factors. On the other hand, dedifferentiated cell populations were abundant after MAPK or combination inhibition, suggesting therapy-induced cell state switching and adaptation. ConclusionWe are evaluating BET + BRAF + EGFR inhibition in patients with treatment-refractory BRAFV600E metastatic CRC. ClinicalTrial.gov identifier: NCT06102902. What is already known on this topicEnhancer aberrations emerge as critical epigenetic features in the progression of colorectal cancer (CRC). However, the dynamics of active enhancer and the therapeutic potential of enhancer blockade, particularly in CRC tumors with BRAFV600E mutation, is not well understood. What this study addsThis study demonstrates improved efficacy of BET inhibitor combination therapies in diverse patient-derived models and reveals epigenetic reprogramming driven cellular plasticity in BRAFV600E-mutated CRC. How this study might affect research, practice or policyOur findings support treatment with BET + BRAF + EGFR inhibitors for patients with BRAFV600E-mutant mCRC [NCT06102902]. This study also highlights the potential of combining epigenetic agents to standard targeted therapy, offering a novel treatment option for this subset of patients.

cancer biology↗