Biology subjects

Sahoo, D.

Publications and source records attributed to Sahoo, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Catestatin ameliorates tauopathy and amyloidogenesis via adrenergic inhibition

Neurodegenerative disorders like Alzheimers disease (AD), Corticobasal Degeneration (CBD), and Progressive Supranuclear Palsy (PSP) are characterized by Tau aggregation, synaptic dysfunction, neuroinflammation, and progressive cognitive decline. Although metabolic dysregulation and neuropeptide imbalance have been linked to these disorders, the functional consequences of such imbalance and its potential for therapeutic reversal remain poorly understood. Our previous work identified chromogranin A (CgA), which encodes a pro-hormone for several metabolic peptides, as a key regulator of Tau pathology. Here, we investigate Catestatin (CST), a CgA-derived peptide that is a potent inhibitor of catecholamine release and has been shown to increase insulin sensitivity and lower peripheral blood pressure. We report significant reductions in CST levels in the hippocampus and cortex of AD brains, as well as in the frontal cortex of CBD and the basal ganglia of PSP. Supplementing CST in cortical neuronal cultures and organotypic slice cultures (OTSC) decreased Tau phosphorylation and aggregation. In vivo, CST administration in PS19 Tauopathy mice reduced pathological Tau species, attenuated gliosis, and improved cognitive function. CST treatment also lowered amyloid plaque burden and neuroinflammation in 5xFAD mice. Mechanistically, CST decreased epinephrine (EPI) levels in both PS19 and 5xFAD mice and suppressed downstream protein kinase A (PKA) hyperactivation in PS19 and OTSC. These findings reveal a previously unrecognized neuropeptidergic mechanism linking CST deficiency to elevated adrenergic receptor (ADR)-EPI-PKA stress signaling and Tauopathy-driven neurodegeneration, suggesting CST replacement as a promising therapeutic approach.

neuroscience↗

bioRxiv2025

Alternative NADH:ubiquinone oxidoreductase modulates disease susceptibility in rice by interfering ROS homeostasis and ferroptosis

Necrotrophic fungal pathogens, such as Rhizoctonia solani, the causal agent of sheath blight disease (SBD) in rice, enhance the production of reactive oxygen species (ROS) to induce necrosis and infect a broad range of plant species. Here, we present evidence that the upregulation of host alternative NADH:ubiquinone oxidoreductase (OsNUOR) is important for R. solani to induce ROS production and cause SBD in rice. The knock-out lines developed through genome editing are defective in ROS accumulation and demonstrate SBD resistance, whereas the overexpression lines exhibit enhanced disease susceptibility. We emphasize that the cross-talk between OsNUOR and ROS signaling is important for the suppression of antioxidant defense, followed by enhancement of lipid peroxidation and accumulation of ferric ions in rice under R. solani-infected conditions. Considering that treatment with deferoxamine, an iron chelator, and ferrostatin-1, a lipid peroxidation inhibitor, prevents SBD disease, whereas FeCl3 enhances disease severity, we propose that R. solani induces iron-dependent cell death, referred to as ferroptosis, in rice. As agronomic traits of OsNUOR-edited lines are comparable to wild-type lines, we emphasize that editing of OsNUOR and additional genes in ferroptotic pathway can be utilized as biotechnological interventions for control of SBD, for which effective control measures remain a challenge.

plant biology↗

bioRxiv2025

Time-Restricted Feeding Attenuates Kidney Damage and Preserves Renal Function in Mouse Model of Chronic Kidney Disease

Chronic kidney disease (CKD) is a highly disabling and potentially deadly condition for which there is no cure. With renal damage risk factors such as hypertension, metabolic syndrome and type 2 diabetes on the rise, the prevalence of CKD is increasing worldwide. New therapeutic approaches to CKD management are thus warranted. Time-restricted feeding, a dietary intervention in which daily food intake is limited to a consistent time window, has shown benefits in the context of metabolic disease management. Boolean implication network model of human CKD gene expression data and data from mouse TRF kidney implied TRF could attenuate kidney injury from CKD. We tested the effect of TRF in mouse models of kidney damage under high-fat high-sucrose feeding to induce a metabolic-disease prone environment. Using gold standard pre-clinical models of renal fibrosis, we discovered that TRF protected from kidney damage and clinical features of CKD. At the molecular level, the effects of TRF were pleiotropic with benefits in pathways involved in renal inflammation, fibrosis, and ER stress. Importantly, our results also suggest that TRF can confer early protection from metabolic alterations implicated in kidney damage.

pathology↗

bioRxiv2025

Germline stem cell isolation, lineage tracing, and aging in a protochordate

Germline stem cells (GSCs), the source of gametes, are the only stem cells capable of passing genes to future generations and are therefore considered units of natural selection. Yet, the factors that influence GSC fitness, and thus govern GSC competition, which exist in both protochordates and mammals, remain poorly understood. We studied how aging affects GSC fitness in the protochordate Botryllus schlosseri, an evolutionary crosspoint between invertebrates and vertebrates. GSCs were isolated and distinguished from developing and mature gametes using flow cytometry and scRNA-Seq, facilitated by a new PacBio genome assembly. Moreover, their function was validated through a novel lineage tracing approach that combines membrane-labeled GSC transplantation with scRNA-Seq. Leveraging our method to isolate them, single-cell transcriptomics showed significant age-related changes between young and old GSCs. Spermatids and sperm, however, showed minimal changes, suggesting that reproductive aging is governed by GSCs rather than by gametes. Reduced expressions of markers like DDX4 and PIWIL1 in aged GSCs mirrored trends in mammalian datasets, pointing to a conserved GSC-driven aging mechanism across chordate evolution. This study provides new techniques that lay the foundation to investigate further drivers of GSC fitness and highlights fertility-related genes as promising targets for therapies to preserve reproductive health.

cell biology↗

bioRxiv2025

Boolean Network Modeling Identifies Cognitive Resilience in the First Murine Model of Asymptomatic Alzheimer Disease

Alzheimers disease (AD) is a progressive neurodegenerative disorder defined by amyloid beta (A{beta}) plaques and neurofibrillary tangles (NFTs), yet approximately 20-30% of aged individuals exhibit these hallmark lesions without developing cognitive impairment--a clinically silent condition termed asymptomatic AD (AsymAD). The molecular basis of this cognitive resilience remains poorly understood due to a lack of mechanistic models. Here, we integrate systems-level Boolean network modeling with in vivo validation to define the transcriptomic logic of AsymAD and uncover a novel preclinical model. Using Boolean implication networks trained on large-scale human cortical RNA-seq datasets, we identified a robust and invariant AD gene signature that accurately stratifies disease states across independent datasets. Application of this signature to Chromogranin A- deficient PS19 mice (CgA-KO/PS19) revealed a unique resilience phenotype: male mice developed AD-like molecular and neuropathological profiles in the pre-frontal cortex yet retained intact learning and memory. Female CgA-KO/PS19 mice displayed even greater protection, including reduced Tau phosphorylation and preserved synaptic ultrastructure. These findings establish the first validated murine model of AsymAD and identify CgA as a modifiable node linking neuroendocrine signaling, Tauopathy, and cognitive preservation. This work provides a scalable platform to probe sex-specific resilience, uncover early-stage biomarkers, and accelerate preventive therapeutic development in AD.

neuroscience↗

bioRxiv2025

Optimizing Oyster Breeding with Machine Learning and BigData for Superior Quality

1.Oyster aquaculture is a vital component of global marine ecosystems and food production, yet winter mortality events threaten both ecological stability and economic viability. Traditional selective breeding methods, reliant on phenotypic traits and slow generational cycles, struggle to address these challenges efficiently. This study introduces an innovative approach integrating machine learning with multi-omics data genomics, transcriptomics, and proteomics to optimize oyster breeding for resilience and quality. By analyzing high-resolution datasets encompassing genetic markers, environmental stressors, and survival metrics, our ML models identified key SNPs linked to cold tolerance and disease resistance. Marker-assisted selection (MAS) accelerated breeding cycles, while predictive algorithms achieved 92.4% accuracy in forecasting survival and growth traits. Controlled trials demonstrated a 30% reduction in winter mortality and a 25% improvement in growth rates among ML-selected oyster lineages compared to traditional methods. Additionally, a smartphone-based diagnostic tool was developed to enable real-time monitoring of oyster health, empowering farmers to adapt feeding and environmental strategies dynamically. This research bridges the gap between conventional aquaculture and computational innovation, offering a scalable framework to enhance genetic diversity, sustainability, and yield. By replacing trial-and-error practices with data-driven precision, our approach not only mitigates immediate industry challenges but also establishes a pathway for climate-resilient aquaculture. The fusion of ML with multi-omics technologies marks a transformative shift, enabling breeders to make rapid, evidence-based decisions that harmonize ecological stewardship with commercial demands.

bioinformatics↗

bioRxiv2025

Electrical Stimulation Rejuvenates Tunicates: Altered Stem Cell and Immune Activity

Applicable methods of rejuvenating organisms and improving resistance to environmental stimuli are needed. During attempts to synchronize heart rates in unhealthy colonial chordates, we observed morphological rejuvenation. While the importance of endogenously generated bioelectric currents in development is well-established1,2, and exogenously applied current has shown promise in regenerative medicine3,4,5,6,7,8,9, a model that robustly increases longevity and fertility while providing detailed mechanistic insights has not been reported. Here, we report the establishment of such a model using pulsatile electrical current (PEC) in Botryllus schlosseri, an established colonial chordate model10,11,12,13,14,15. PEC treatment significantly improved survival, morphological integrity, stem cell mediated regeneration, and gonad production in Botryllus. Transcriptomic analysis revealed pathway changes associated with cellular metabolism, cell cycle, stem cell activity, DNA repair, and immune modulation. Notably, PEC-induced expression patterns resemble the exercise-induced macrophage-associated transcriptional response previously observed across several mammalian species16,17. This transcriptomic signature correlated with an increase in immune-cell-containing populations. These findings demonstrate that PEC can improve longevity, vitality, and reproduction in an established model renowned for defining broadly applicable biological principles. These studies offer insights into novel strategies for promoting healthy aging and organismal survival.

developmental biology↗

bioRxiv2025

Distinct Colitis-Associated Macrophages Drive NOD2-DependentBacterial Sensing and Gut Homeostasis

Single-cell studies have revealed that intestinal macrophages maintain gut homeostasis through the balanced actions of reactive (inflammatory) and tolerant (non-inflammatory) subpopulations. How such balance is impaired in inflammatory bowel diseases (IBD), including Crohns disease (CD) and ulcerative colitis (UC), remains unresolved. Here, we define colon-specific macrophage states and reveal the critical role of non-inflammatory colon-associated macrophages (niColAMs) in IBD recovery. Through trans-scale analyses--integrating computational transcriptomics, proteomics, and in vivo interventional studies--we identified GIV (CCDC88A) as a key regulator of niColAMs. GIV emerged as the top-ranked gene in niColAMs that physically and functionally interacts with NOD2, an innate immune sensor implicated in CD and UC. Myeloid-specific GIV depletion exacerbates infectious colitis, prolongs disease, and abolishes the protective effects of the NOD2 ligand, muramyl dipeptide, in colitis and sepsis models. Mechanistically, GIVs C-terminus binds the terminal leucine-rich repeat (LRR#10) of NOD2 and is required for NOD2 to dampen inflammation and clear microbes. The CD-associated 1007fs NOD2-variant, which lacks LRR#10, cannot bind GIV--providing critical insights into how this clinically relevant variant impairs microbial sensing and clearance. These findings illuminate a critical GIV-NOD2 axis essential for gut homeostasis and highlight its disruption as a driver of dysbiosis and inflammation in IBD.

immunology↗

bioRxiv2025

The E2F4 transcriptional repressor is a key mechanistic regulator of colon cancer resistance to irinotecan (CPT-11).

Background. Colorectal carcinomas (CRCs) are seldom eradicated by cytotoxic chemotherapy. Cancer cells with stem-like functional properties, often referred to as "cancer stem cells" (CSCs), display preferential resistance to several anti-tumor agents used in cancer chemotherapy, but the molecular mechanisms underpinning their selective survival remain only partially understood. Methods. In this study, we used Transcription Factor Target Genes (TFTG) enrichment analysis to identify transcriptional regulators (activators or repressors) that undergo preferential activation by chemotherapy in CRC cells with a "bottom-of-the-crypt" phenotype (EPCAM+/CD44+/CD166+; CSC-enriched) as compared to CRC cells with a "top-of-the-crypt" phenotype (EPCAM+/CD44neg/CD166neg; CSC-depleted). The two cell populations were purified in parallel by fluorescence-activated cell sorting (FACS) from a patient-derived xenograft (PDX) line representative of a moderately differentiated human CRC, following in vivo chemotherapy with irinotecan (CPT-11). The transcriptional regulators identified as differentially activated were tested for differential expression in normal vs. cancer tissues, and in cell populations enriched in stem/progenitor cell-types as compared to differentiated lineages (goblet cells, enterocytes) in the mouse colon epithelium. Finally, the top candidate was tested for mechanistic contribution to drug-resistance by selective down-regulation using short-hairpin RNAs (shRNAs). Results. Our analysis identified E2F4 and TFDP1, two core components of the DREAM transcriptional repression complex, as transcriptional modulators preferentially activated by irinotecan in EPCAM+/CD44+/CD166+ as compared to EPCAM+/CD44neg/CD166neg cancer cells. The expression levels of both genes (E2F4, TFDP1) were found up-regulated in CRCs as compared to human normal colon tissues, and in a sub-population of mouse colon epithelial cells enriched in stem/progenitor elements (Epcam+/Cd44+/Cd66alow/Kitneg) as compared to other sub-populations enriched in either goblet cells (Epcam+/Cd44+/Cd66alow/Kit+) or enterocytes (Epcam+/Cd44neg/Cd66ahigh). Most importantly, E2F4 down-regulation using shRNAs dramatically enhanced the sensitivity of human CRCs to in vivo treatment with irinotecan, across three independent PDX models. Conclusions. Our data identified E2F4 and the DREAM repressor complex as critical regulators of human CRC resistance to irinotecan, and as candidate targets for the development of chemo-sensitizing agents.

cancer biology↗

bioRxiv2024

Catestatin improves heart metabolic flexibility by promoting mitochondrial structure and function

Hypertension, a major cause of cardiomyopathy, is one of the most critical risk factors for heart failure and mortality worldwide. Loss of metabolic flexibility of cardiomyocytes is one of the major causes of heart failure. Although Catestatin (CST) treatment is known to be both hypotensive and cardioprotective, its effect on cardiac metabolism is unknown. In this study, we undertook a transcriptomic approach to identify differentially expressed genes that were filtered using Boolean implication relationships to develop a model of gene regulation in saline or CST-supplemented CST knockout (CST-KO) mice. The analysis revealed a set of gene signatures (fibroblast, cardiomyocyte, and macrophage) rescued after CST supplemented CST-KO mice compared to wild-type. Furthermore, we independently validated these gene signature models using publicly available patient datasets. Since the gene signature includes genes related to glucose, fatty acid metabolism, and mitochondrial function, we assessed the glucose and fatty acid uptake after CST treatment. We found that CST treatment can restore the cardiac metabolic inflexibility in CST-KO heart due to the metabolic shift of glucose utilization to fatty acid as energy source. Binding studies after immunoprecipitation and mass spectrometry revealed CST binding with ATP synthase, supported by molecular simulation and computational modeling that predicted CST binding to /{beta} subunit of ATP synthase. Colocalization of CST with mitochondria and increased mitochondrial membrane potential and ATP production upon CST treatment in neonatal cardiomyocytes further exhibit CST as a key regulator of cardiac metabolism and mitochondrial function.

physiology↗

bioRxiv2024

Molecular Signatures for Microbe-Associated Colorectal Cancers

BackgroundGenetic factors and microbial imbalances play crucial roles in colorectal cancers (CRCs), yet the impact of infections on cancer initiation remains poorly understood. While bioinformatic approaches offer valuable insights, the rising incidence of CRCs creates a pressing need to precisely identify early CRC events. We constructed a network model to identify continuum states during CRC initiation spanning normal colonic tissue to pre-cancer lesions (adenomatous polyps) and examined the influence of microbes and host genetics. MethodsA Boolean network was built using a publicly available transcriptomic dataset from healthy and adenoma affected patients to identify an invariant Microbe-Associated Colorectal Cancer Signature (MACS). We focused on Fusobacterium nucleatum (Fn), a CRC-associated microbe, as a model bacterium. MACS-associated genes and proteins were validated by RT-qPCR, RNA seq, ELISA, IF and IHCs in tissues and colon-derived organoids from genetically predisposed mice (CPC-APCMin+/-) and patients (FAP, Lynch Syndrome, PJS, and JPS). ResultsThe MACS that is upregulated in adenomas consists of four core genes/proteins: CLDN2/Claudin-2 (leakiness), LGR5/leucine-rich repeat-containing receptor (stemness), CEMIP/cell migration-inducing and hyaluronan-binding protein (epithelial-mesenchymal transition) and IL8/Interleukin-8 (inflammation). MACS was induced upon Fn infection, but not in response to infection with other enteric bacteria or probiotics. MACS induction upon Fn infection was higher in CPC-APCMin+/- organoids compared to WT controls. The degree of MACS expression in the patient-derived organoids (PDOs) generally corresponded with the known lifetime risk of CRCs. ConclusionsComputational prediction followed by validation in the organoid-based disease model identified the early events in CRC initiation. MACS reveals that the CRC-associated microbes induce a greater risk in the genetically predisposed hosts, suggesting its potential use for risk prediction and targeted cancer prevention.

microbiology↗

bioRxiv2024

Macrophage Polarizations in the Placenta and Lung are Associated with Bronchopulmonary Dysplasia

The intricate interplay between macrophage polarization and placenta vascular dysfunction has garnered increasing attention in the context of placental inflammatory diseases. This study delves into the complex relationship between macrophage polarization within the placenta and its potential impact on the development of vascular dysfunction and inflammatory conditions. The placenta, a crucial organ in fetal development, relies on a finely tuned balance of immune responses for proper functioning. Disruptions in this delicate equilibrium can lead to pathological conditions, including inflammatory diseases affecting the fetus and newborn infant. We explored the interconnectedness between placental macrophage polarization and its relevance to lung macrophages, particularly in the context of early life lung development. Bronchopulmonary dysplasia (BPD), the most common chronic lung disease of prematurity, has been associated with abnormal immune responses, and understanding the role of macrophages in this context is pivotal. The investigation aims to shed light on how alterations in placental macrophage polarization may contribute to lung macrophage behavior and, consequently, influence the development of BPD. By unraveling the intricate mechanisms linking macrophage polarization, placental dysfunction and BPD, this research seeks to provide insights that could pave the way for targeted therapeutic interventions. The findings may offer novel perspectives on preventing and managing placental and lung-related pathologies, ultimately contributing to improved maternal and neonatal health outcomes.

systems biology↗

bioRxiv2024

C1QA is an invariant biomarker for tissue macrophages

Macrophages play a pivotal role in immune responses, particularly in the context of combating microbial threats within tissues. The identification of reliable biomarkers associated with macrophage function is essential for understanding their diverse roles in host defense. This study investigates the potential of C1QA as an invariant biomarker for tissue macrophages, focusing on its correlation with the anti-microbial pathway. C1QA, a component of the complement system, has been previously implicated in various immune functions. Our research delves into the specific association of C1QA with tissue-resident macrophages and its implications in the context of anti-microbial responses. Through comprehensive systems biology and Boolean analysis of gene expression, we aim to establish C1QA as a consistent and reliable marker for identifying tissue macrophages. Furthermore, we explore the functional significance of C1QA in the anti-microbial pathway. This research seeks to provide valuable insights into the molecular mechanisms underlying the anti-microbial functions of tissue macrophages, with C1QA emerging as a potential key player in this intricate regulatory network. Understanding the relationship between C1QA, tissue macrophages, and the anti-microbial pathway could pave the way for the development of targeted therapeutic strategies aimed at enhancing the hosts ability to combat infections. Ultimately, our findings contribute to the expanding knowledge of macrophage biology and may have implications for the diagnosis and treatment of infectious diseases. One Sentence SummaryC1QA is a fundamental biomarker of tissue macrophages

systems biology↗

bioRxiv2023

Reinstatement of CDX2 as a differentiation therapy for colorectal cancers

Despite advances in artificial intelligence (AI) within cancer research, its application toward realizing differentiation therapy in solid tumors remains limited. Using colorectal cancer (CRC) as a model, we developed a machine learning (ML) framework, CANDiT (Cancer Associated Nodes for Differentiation Targeting), to selectively induce differentiation and death of cancer stem cells (CSCs)--a key obstacle to durable response. Centering on one node, CDX2, a master differentiation factor lost in high-risk, poorly differentiated CRCs, we built a transcriptomic network to identify therapeutic strategies for CDX2 restoration. Network-based prioritization identified PRKAB1, a stress polarity sensor, as a top target. A clinical-grade PRKAB1 agonist reprogrammed transcriptional networks, induced crypt differentiation, and selectively eliminated CDX2-low CSCs in CRC cell lines, xenografts and patient-derived organoids (PDOs). Multivariate analyses in PDOs revealed a strong therapeutic index, linking efficacy (IC) to the biomarker-defined CDX2-low state. A 50-gene response signature--derived from an integrated analyses of all three models and trained across multiple datasets--revealed that CDX2 restoration therapy may translate into a [~]50% reduction in recurrence and mortality risk. Mechanistically, treatment activated a differentiation-associated stress polarity signaling axis while dismantling Wnt and YAP-driven stemness programs essential to CSC survival. Thus, CANDiT offers a scalable path to CSC-directed therapy in solid tumors by translating transcriptomic vulnerabilities into precision treatments. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=174 SRC="FIGDIR/small/557628v4_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@16eeb1eorg.highwire.dtl.DTLVardef@10e308borg.highwire.dtl.DTLVardef@9512f0org.highwire.dtl.DTLVardef@10e74eb_HPS_FORMAT_FIGEXP M_FIG C_FIG One sentence summaryIn this work, Sinha et al. introduce a machine learning-guided framework to identify and target transcriptomic vulnerabilities in colorectal cancer, demonstrating that differentiation therapy selectively eliminates cancer stem cells and reduces recurrence risk. HighlightsO_LIAn ML framework (CANDiT) identifies target for differentiation therapy for CRCs C_LIO_LITherapy induces crypt differentiation and CSC-specific cytotoxicity C_LIO_LICDX2-low state predicts therapeutic response; restoration improves prognosis C_LIO_LITherapy dismantles stemness via reactivation of stress polarity signaling C_LI

cancer biology↗

bioRxiv2023

Scavenger receptor class B type I is required for efficient glucose uptake and metabolic homeostasis in adipocytes

Obesity is a worldwide epidemic and places individuals at a higher risk for developing comorbidities that include cardiovascular disease and type 2 diabetes. Adipose tissue contains adipocytes that are responsible for lipid metabolism and reducing misdirected lipid storage. Adipocytes facilitate this process through insulin-mediated uptake of glucose and its subsequent metabolism into triglycerides for storage. During obesity, adipocytes become insulin resistant and have a reduced ability to mediate glucose import, thus resulting in whole-body metabolic dysfunction. Scavenger receptor class B type I (SR-BI) has been implicated in glucose uptake in skeletal muscle and adipocytes via its native ligands, apolipoprotein A-1 and high-density lipoproteins. Further, SR-BI translocation to the cell surface in adipocytes is sensitive to insulin stimulation. Using adipocytes differentiated from ear mesenchymal stem cells isolated from wild-type and SR-BI knockout (SR-BI-/-) mice as our model system, we tested the hypothesis that SR-BI is required for insulin-mediated glucose uptake and regulation of energy balance in adipocytes. We demonstrated that loss of SR-BI in adipocytes resulted in inefficient glucose uptake regardless of cell surface expression levels of glucose transporter 4 compared to WT adipocytes. We also observed reduced glycolytic capacity, increased lipid biosynthesis, and dysregulated expression of lipid metabolism genes in SR-BI-/- adipocytes compared to WT adipocytes. These results partially support our hypothesis and suggest a novel role for SR-BI in glucose uptake and metabolic homeostasis in adipocytes.

biochemistry↗

bioRxiv2023

An AI-assisted Investigation of Tumor-Associated Macrophages and their Polarization in Colorectal Cancer

Tumor-associated Macrophages (or TAMs) are amongst the most common cells that play a significant role in the initiation and progression of colorectal cancer (CRC). [Ghosh et al., 2023] have built a Boolean-logic dependent model to propose a set of gene signatures capable of identifying macrophage polarization states. The signature, called the Signature of Macrophage Reactivity and Tolerance (SMaRT), comprises of 338 human genes (equivalently, 298 mouse genes). The SMaRT signature was constructed using datasets that were not specialized towards any particular disease. To specifically investigate macrophage polarization in CRC, in this paper, we (a) perform a comprehensive analysis of the SMaRT signature on single-cell human and mouse colorectal cancer RNA-seq datasets and (b) adopt transfer learning to construct a "refined" SMaRT signature that specifically characterizes TAM polarization in the CRC tumor microenvironment. Towards validation of our refined gene signature, we use: (a) 5 RNA-seq datasets derived from single-cell human datasets; and (b) 5 large-cohort microarray datasets from humans. Furthermore, we propose the translational potential of our refined gene signature while investigating microsatellite stability and CpG island methylator phenotype (CIMP) in colorectal cancer. Overall, our refined gene signature and its extensive validation provide a path for its adoption in clinical practice in diagnosing colorectal cancer and associated attributes. Availability and ImplementationThe data, codes, and software packages used in our research are linked and shared publicly at https://github.com/tirtharajdash/TAMs-CRC.

bioinformatics↗

bioRxiv2023

A Living Organoid Biobank of Crohn's Disease Patients Reveals Molecular Subtypes for Personalized Therapeutics

ABSTRACT (Structured)Crohns disease (CD) is a complex, clinically heterogeneous disease of multifactorial origin; there is no perfect pre-clinical model, little insight into the basis for such heterogeneity, and still no cure. To address these unmet needs, we sought to explore the translational potential of adult stem cell-derived organoids that not only retain their tissue identity, but also their genetic and epigenetic disease-driving traits. We prospectively created a biobank of CD patient-derived organoid cultures (PDOs) using biopsied tissues from colons of 34 consecutive subjects representing all clinical subtypes (Montreal Classification B1-B3 and perianal disease). PDOs were generated also from healthy subjects. Comparative gene expression analyses enabled benchmarking of PDOs as tools for modeling the colonic epithelium in active disease and revealed that despite the clinical heterogeneity there are two major molecular subtypes: immune-deficient infectious-CD [IDICD] and stress and senescence-induced fibrostenotic-CD [S2FCD]. The transcriptome, genome and phenome show a surprising degree of internal consistency within each molecular subtype. The spectrum of morphometric, phenotypic, and functional changes within the "living biobank" reveals distinct differences between the molecular subtypes. These insights enabled drug screens that reversed subtype-specific phenotypes, e.g., impaired microbial clearance in IDICD was reversed using agonists for nuclear receptors, and senescence in S2FCD was rectified using senotherapeutics, but not vice versa. Phenotyped-genotyped CD-PDOs may fill the gap between basic biology and patient trials by enabling pre-clinical Phase 0 human trials for personalized therapeutics. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/532245v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@1edcea0org.highwire.dtl.DTLVardef@198a3c8org.highwire.dtl.DTLVardef@28d394org.highwire.dtl.DTLVardef@5a9dbb_HPS_FORMAT_FIGEXP M_FIG C_FIG In BriefThis work creates a prospectively biobanked phenotyped-genotyped Crohns disease patient-derived organoids (CD-PDOs) as platforms for molecular subtyping of disease and for ushering personalized therapeutics. HIGHLIGHTSO_LIProspectively biobanked CD-organoids recapitulate the disease epithelium in patients C_LIO_LIThe phenome-transcriptome-genome of CD-organoids converge on two molecular subtypes C_LIO_LIOne subtype shows impaired microbial clearance, another increased cellular senescence C_LIO_LIPhenotyped-genotyped PDOs are then used for integrative and personalized therapeutics C_LI

immunology↗

bioRxiv2022

Growth Signaling Autonomy in Circulating Tumor Cells Aids Metastatic Seeding

Self-sufficiency (autonomy) in growth signaling, the earliest recognized hallmark of cancer, is fueled by the tumor cells ability to secrete-and-sense growth factors; this translates into cell survival and proliferation that is self-sustained by auto-/paracrine secretion. A Golgi-localized circuitry comprised of two GTPase switches has recently been implicated in the orchestration of growth signaling autonomy. Using breast cancer cells that are either endowed or impaired (by gene editing) in their ability to assemble the circuitry for growth signaling autonomy, here we define the transcriptome, proteome, and phenome of such autonomous state, and unravel its role during cancer progression. We show that autonomy is associated with enhanced molecular programs for stemness, proliferation, and epithelial-mesenchymal plasticity (EMP). Autonomy is both necessary and sufficient for anchorage-independent growth factor-restricted proliferation and resistance to anti-cancer drugs and is required for metastatic progression. Transcriptomic and proteomic studies show that autonomy is associated, with a surprising degree of specificity, to self-sustained EGFR/ErbB signaling. Derivation of a gene expression signature for autonomy revealed that growth signaling autonomy is uniquely induced in circulating tumor cells (CTCs), the harshest phase in the life of tumor cells when it is deprived of biologically available EGF. We also show that autonomy in CTCs tracks therapeutic response and prognosticates outcome. These data support a role for growth signaling autonomy in multiple processes essential for the blood-borne dissemination of human breast cancer. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/518910v2_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@167b370org.highwire.dtl.DTLVardef@135b62dorg.highwire.dtl.DTLVardef@14b5e9forg.highwire.dtl.DTLVardef@1311e84_HPS_FORMAT_FIGEXP M_FIG C_FIG Significance StatementA Golgi-localized molecular circuitry has been recently implicated in the orchestration of secrete-and-sense auto-/paracrine loops that impart self-sufficiency in growth signaling, a.k.a., growth signaling autonomy. Using a transdisciplinary approach, this work shows that growth signaling autonomy is uniquely induced in tumor cells that are in circulation. Circulating tumor cells (CTCs) represent a brutish and risky phase in the lifetime of tumor cells when they are exposed to the immune system and hemodynamic sheer forces, all in the setting of growth factor starvation. Cancer cells appear to rely on the autonomy circuit to survive and enhance their fitness to seed metastases. Autonomy generates the kind of eat-what-you-kill entrepreneurial spirit which minimizes the risk of CTCs dying on an otherwise risky journey.

cancer biology↗