Biology subjects

Ghosh, S.

Publications and source records attributed to Ghosh, S..

At least 307 records · Page 17Linked to original sources

bioRxiv2020

Functional dissection of neural circuitry using a genetic reporter for fMRI

The complex connectivity of the mammalian brain underlies its function, but understanding how interconnected brain regions interact in neural processing remains a formidable challenge. Here we address this problem by introducing a genetic probe that permits selective functional imaging of neural circuit elements defined by their synaptic interrelationships throughout the brain. The probe is an engineered enzyme that transduces cytosolic calcium dynamics of probe-expressing cells into localized hemodynamic responses that can be selectively visualized by functional magnetic resonance imaging. Using a viral vector that undergoes retrograde transport, we apply the probe to characterize a brain-wide network of monosynaptic inputs to the striatum activated in a deep brain stimulation paradigm in rats. The results reveal engagement of surprisingly diverse projection sources and inform an integrated model of striatal function relevant to reward behavior and therapeutic neurostimulation approaches. Our work thus establishes a potent strategy for mechanistic analysis of distributed neural systems.

neuroscience↗

bioRxiv2020

Modulation of implanted aortic scaffold- involvement of ECM and immune proteins

Biological scaffold or implant is a popular choice for the preparation of tissue-engineered organs and has the potential to address donor shortage in the clinics. However, biological scaffolds prepared by physical or chemical agents cause damage to the extracellular matrix by potentially inducing immune responses after implantation. The current study explores an alternative route for the preparation of acellular scaffolds and explores the fate of the prepared scaffolds in a milieu of immune cells following implantation without using immunosuppressant. Using the syngeneic (Lewis male-Lewis female) and allogeneic (Brown Norway male-Lewis female) models and different tissue routes (subcutaneous vs omentum) for transplantation, normal blood vascular scaffolds were implanted which was converted to acellular vascular scaffolds by in vivo natural decellularization at the end of 2 months of observation. We also prepared chemically decellularized acellular scaffolds from normal untreated blood vascular scaffolds using a cocktail of chemicals which was also similarly placed in subcutaneous and omentum sites. Here, we applied in-depth quantitative proteomics along with histology and image analysis to comprehensively describe and compare the proteome of the natural and chemically decellularized scaffold. Our data confirm that site-specific advantages exist in modulating the ECM and regulating the immune responses (macrophage and T cells) following implantation, which possibly led to the production of an acellular scaffold (natural decellularization) under in vivo conditions. The current approach opens up the possibility to create tailor-made acellular scaffolds to build functional blood vessels. In addition, the identification of different tissue sites facilitates differential immune response against the scaffolds. This study provides a rich resource aimed toward an enhanced mechanistic understanding to study immune responses under similar settings in the field of transplantation and regenerative medicine. Impact statementThe development of a scaffold helps in the preparation of a functional organ in the clinics. In the current study, we prepared an acellular vascular scaffold by utilizing site specific tissue changes and vis-a-vis compared with a conventionally chemically prepared biological scaffold at genomic and protein level, which helped us to identify immunological trigger following implantation. The current study which was carried out without any immunosuppressive agents could help to establish (a) alternative strategies for preparing biological scaffolds as well as (b) implantable sites as potential bioreactors to circumvent any adverse immune reactions for acceptance of the scaffold/implant post implantation.

bioengineering↗

bioRxiv2020

A Universal Allosteric Mechanism for G Protein Activation

G proteins play a central role in signal transduction and pharmacology. Signaling is initiated by cell-surface receptors, which promote GTP binding and the dissociation of G from the G{beta}{gamma} subunits. Structural studies have revealed the molecular basis for subunit association with receptors, RGS proteins and downstream effectors. In contrast, the mechanism of subunit dissociation is poorly understood. We used cell signaling assays, MD simulations, biochemistry and structural analysis to identify a conserved network of amino acids that dictates subunit release. In the presence of the terminal phosphate of GTP, a glycine forms a polar network with an arginine and glutamate, putting torsional strain on the subunit binding interface. This "G-R-E motif" secures GTP and, through an allosteric link, discharges the G{beta}{gamma} dimer. Replacement of network residues prevents subunit dissociation, regardless of agonist or GTP binding. These findings reveal the molecular basis for the final committed step of G protein activation. HIGHLIGHTSO_LIReceptors promote GTP-GDP exchange and dissociation of G protein and {beta}{gamma} subunits C_LIO_LIWe find an allosteric network linking the {gamma} phosphate of GTP with release of G{beta}{gamma} C_LIO_LIThe network consists of a conserved Gly-Arg-Glu "activation triad" C_LIO_LITriad mutations prevent subunit dissociation, regardless of agonist or GTP binding C_LIO_LITriad mutations are responsible for human endocrine and neurological disorders C_LI

biochemistry↗

bioRxiv2020

Non-transmissibility of Pepper whitefly borne vein yellows virus (PeWBVYV) by the Mediterranean species of Bemisia tabaci and identification of a candidate insect receptor protein for poleroviruses

Recent reports of transmission of poleroviruses by whiteflies is indicative of evolution of new virus-vector relationships. Pepper whitefly-borne vein yellows virus (PeWBVYV), was the first report of a polerovirus infecting pepper in Israel which was transmitted by whiteflies (MEAM1) and not aphids. This study reports the inability of the Mediterranean species (MED, Q biotype) of B. tabaci to transmit PeWBVYV. However we show that non-transmission of PeWBVYV by MED is not due to the lack of interaction with the GroEL protein of the Hamiltonella symbiont. Although not transmitted by MED, PeWBVYV was detected in its hemolymph, indicating its translocation across the MED midgut barrier. The aphid transmitted Pepper vein yellows virus 2 (PeVYV-2) was also detected in the hemolymph of MEAM1 whiteflies but PeWBVYV could not be detected in the aphid hemolymph. Interestingly, relative amounts of PeWBVYV in the hemolymph of the, MED was much lower than in hemolymph of MEAM1 whiteflies. We also identified a candidate receptor protein, complement component 1Q sub-complement binding protein (C1QBP) which interacts with the capsid proteins of PeWBVYV and PeVYV-2 but not with the whitefly transmitted Tomato yellow leaf curl virus by a yeast two-hybrid approach using the minor capsid protein (RTD) as bait to screen for interacting proteins against the whitefly cDNA library. C1QBP, is a known receptor of bacterial and viral pathogens but this is the first report of its interaction with a plant virus.

microbiology↗

bioRxiv2020

One Health, One Hive: A scoping review of honey bees, climate change, pollutants, and antimicrobial resistance

Anthropogenic climate change and increasing antimicrobial resistance (AMR) together threaten the last 50 years of public health gains. Honey bees are a model One Health organism to investigate interactions between climate change and AMR. The objective of this scoping review was to examine the range, extent, and nature of published literature on the relationship between AMR and honey bees in the context of climate change and environmental pollutants. The review followed systematic search methods and reporting guidelines. A protocol was developed a priori in consultation with a research librarian. Resulting Boolean search strings were used to search Embase(R) via Ovid(R), MEDLINE(R), Scopus(R), AGRICOLA and Web of Science databases. Two independent reviewers conducted two-stage screening on retrieved articles. To be included, the article had to examine honey bees, AMR, and either climate change or environmental pollution. Data, in accordance with Joanna Briggs Institute guidelines, were extracted from relevant articles and descriptively synthesized in tables, figures, and narrative form. A total of 21 articles met the inclusion criteria, with almost half of all articles being published in the last five years (n=10). These articles predominantly investigated hive immunocompetence and multi-drug resistance transporter downregulation (n=10), susceptibility to pests (n=15), especially American foul brood (n=9), and hive product augmentation (n=3). This review identified key themes and gaps in the literature, including the need for future interdisciplinary research to explore the link between AMR and environmental change evidence streams in honey bees. We identified three potential linkages between pollutive and climatic factors and risk of AMR. These interconnections reaffirm the necessity of a One Health framework to tackle global threats and investigate complex issues that extend beyond honey bee research into the public health sector. It is integral that we view these "wicked" problems through an interdisciplinary lens to explore long-term strategies for change.

ecology↗

bioRxiv2020

First report of an insilico study of Luciferase in Mycobacterium sp. EPa45

Mycobacterium are a genus of Actinobacteria known to be responsible for several deadly diseases in both humans and animals, including tuberculosis. Luciferase is the primary protein in Mycobacteria that plays a role in bioluminescence. It also plays a role in some bacteria of being a source of energy transference, such as in the case of lumazine proteins. Although studies have been conducted in different luciferase in bacteria, there has been hardly any structural studies on luciferase expressed in Mycobacterium sp. EPa45. Therefore, in this paper we have studied luciferase expressed in Mycobacterium sp. EPa45 by insilico analysis of its structure from its protein sequence. We report the observed differences within luciferase reported from other strains of mycobacterium and pathogenic and non-pathogenic forms of bacteria in terms of their (i) physiochemical characteristics, (ii) protein structure, (iii) multiple sequence alignment and (iv) phylogenetic relationships. We report for the first time the relation of this specific strain of Luciferase in mycobacterium and bacterium at large. HighlightsO_LIMycobacterium sp. EPa45 shows similar characteristics to pathogenic mycobacterium C_LIO_LIAnalysis of Luciferase sequence and protein qualities provides insight to pathogenicity C_LIO_LIThe deadly nature of infectious mycobacterium, especially with luciferase sequences similar to Mycobacterium sp. EPa45, is analyzed C_LI

bioinformatics↗

bioRxiv2020

Biological insights from the whole genome analysis of human embryonic stem cells

There has not yet been a systematic analysis of hESC whole genomes at a single nucleotide resolution. We therefore performed whole genome sequencing (WGS) of 143 hESC lines and annotated their single nucleotide and structural genetic variants. We found that while a substantial fraction of hESC lines contained large deleterious structural variants, finer scale structural and single nucleotide variants (SNVs) that are ascertainable only through WGS analyses were present in hESCs genomes and human blood-derived genomes at similar frequencies. However, WGS did identify SNVs associated with cancer or other diseases that will likely alter cellular phenotypes and may compromise the safety of hESC-derived cellular products transplanted into humans. As a resource to enable reproducible hESC research and safer translation, we provide a user-friendly WGS data portal and a data-driven scheme for cell line maintenance and selection. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/337352v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1c28e3aorg.highwire.dtl.DTLVardef@7a07corg.highwire.dtl.DTLVardef@b95f2borg.highwire.dtl.DTLVardef@1732af_HPS_FORMAT_FIGEXP M_FIG C_FIG IN BRIEFMerkle and Ghosh et al. describe insights from the whole genome sequences of commonly used human embryonic stem cell (hESC) lines. Analyses of these sequences show that while hESC genomes had more large structural variants than humans do from genetic inheritance, hESCs did not have an observable excess of finer-scale variants. However, many hESC lines contained rare loss-of-function variants and combinations of common variants that may profoundly shape their biological phenotypes. Thus, genome sequencing data can be valuable to those selecting cell lines for a given biological or clinical application, and the sequences and analysis reported here should facilitate such choices. HIGHLIGHTSO_LIOne third of hESCs we analysed are siblings, and almost all are of European ancestry C_LIO_LILarge structural variants are common in hESCs, but finer-scale variation is similar to that human populations C_LIO_LIMany strong-effect loss-of-function mutations and cancer-associated mutations are present in specific hESC lines C_LIO_LIWe provide user-friendly resources for rational hESC line selection based on genome sequence C_LI

genomics↗

bioRxiv2020

Altered food habits? Understanding the feeding preference of free-ranging Grey langur (Semnopithecus entellus) within an urban settlement.

Urbanization affects concurrent human-animal movements as a result of altered resource availability and land use pattern, which leads to considerable ecological consequences. While some animals find themselves adrift, homeless with the uncertainty of resources resulting from the urban encroachment, few of them manage to survive by altering their natural behavioural patterns, and co-exist with humans. Folivorous colobines, such as grey langur, whose feeding repertoire largely consists of plant parts, tend to be more attuned to the urban high-calorie food sources to attain maximum fitness benefits within the concrete jungle having an insignificant green cover. However, such a mismatch between their generalized feeding behaviour and specialized gut physiology reminds us of the Liems paradox and demands considerable scientific attention which could tell us the story behind colobines successful co-existence within human settlements. Besides understanding their population dynamics, the effective management of these urbanized, free-ranging, non-human primate populations also depends on their altered feeding preferences, altogether which could lead us to the development of an ecologically sound urban ecosystem. Here, we have used a field-based experimental set up which allows langurs to choose between natural and urban food options, being independent of any inter-specific conflicts over resources due to food scarcity. The multinomial logit model reveals the choice-based decision making of these free-ranging grey langurs in an urban settlement of West Bengal, India, where they have not only learned to approach the human-provisioned urban food items but also shown a keen interest in it. While urbanization imposes tremendous survival challenges to these animals, it also opens up for various alternative options for human-animal co-existence which is reflected in this study, and could guide us for the establishment of a sustainable urban ecosystem in the future. HIGHLIGHTSO_LIThe feeding repertoire of free-ranging grey langurs at Dakshineswar largely consists of urban food items in contrast to the langurs of Nangi, and Nalpur who mostly depend on natural food sources. C_LIO_LIHigh human-langur interactions together with the scarcity of natural plant-based food sources could be considered as an intriguing driving force behind langurs altered feeding habits in Dakhineswar. C_LIO_LIThe field-based experimental set up allows free-ranging langurs to choose between natural and urban food options in an urban settlement like Dakhineswar. C_LIO_LIUrban food items outperformed natural food items as the most chosen one, indicating langurs altered feeding preferences which facilitate their successful co-existence within an urban ecosystem. C_LI

animal behavior and cognition↗

bioRxiv2020

DOT1L primarily acts as a transcriptional repressor in hematopoietic progenitor cells

DOT1L is essential for early hematopoiesis but the precise mechanisms remain largely unclear. The only known function of DOT1L is histone H3 lysine 79 (H3K79) methylation. We generated two mouse models; a Dot1L-knockout (Dot1L-KO), and another possessing a point mutation in its methyltransferase domain (Dot1L-MM) to determine the role of its catalytic activity during early hematopoiesis. We observed that Dot1L-KO embryos suffered from severe anemia, while Dot1L-MM embryos showed minimal to no anemia. However, ex vivo culture of Dot1L-MM hematopoietic progenitors (HPCs) exhibited defective development of myeloid and mixed progenitors. DOT1L is a well-recognized, cell-type specific epigenetic regulator of gene expression. To elucidate the mechanisms underlying such diverse hematopoietic properties of Dot1L-KO and Dot1L-MM HPCs, we examined their whole transcriptomes. Extensively self-renewing erythroblast (ESRE) cultures were established using yolk sac (YS) cells collected on embryonic day 10.5 (E10.5). Dot1l-KO and Dot1l-MM cells expanded significantly less than the wildtype cells and showed slower progression through the cell cycle. Total RNA extracted from the wildtype and Dot1l-mutant ESRE cells were subjected to RNA-seq analyses. We observed that the majority (~82%) of the differentially expressed genes (DEGs) were upregulated in both of the Dot1L-mutants, which suggests that DOT1L predominantly acts as a transcriptional repressor in HPCs. We also observed that about ~40% of the DEGs were unique to either of the mutant group, suggesting that DOT1L possesses both methyltransferase domain-dependent and -independent functions. We further analyzed Gene Ontology and signaling pathways relevant to the DEGs common to both mutant groups and those that were unique to either group. Among the common DEGs, we observed upregulation of CDK inhibitors, which explains the cell cycle arrest in both of the Dot1L-mutant progenitors.

developmental biology↗

bioRxiv2020

Possible transmission flow of SARS-CoV-2 based on ACE2 features

Angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that is engendering the severe coronavirus disease 2019 (COVID-19) pandemic. The spike (S) protein receptor-binding domain (RBD) of SARS-CoV-2 binds to the three sub-domains viz. amino acids (aa) 22-42, aa 79-84, and aa 330-393 of ACE2 on human cells to initiate entry. It was reported earlier that the receptor utilization capacity of ACE2 proteins from different species, such as cats, chimpanzees, dogs, and cattle, are different. A comprehensive analysis of ACE2 receptors of nineteen species was carried out in this study, and the findings propose a possible SARS-CoV-2 transmission flow across these nineteen species.

bioinformatics↗

bioRxiv2020

Granulosa cell genes that regulate ovarian follicle development beyond the antral stage: the role of estrogen receptor β

Follicle development beyond the preantral stage is dependent on gonadotropins. FSH signaling is crucial for the advancement of preantral follicles to the antral stage, and LH signaling is essential for further maturation of preovulatory follicles. Estrogen is intricately tied to gonadotropin signaling during the advanced stages of folliculogenesis. We observed that Er{beta}null ovarian follicles fail to develop beyond the antral stage, even after exogenous gonadotropin stimulation. As ER{beta} is primarily expressed in the granulosa cells (GCs), we explored the gonadotropin-regulated GC genes that induce maturation of antral follicles. Synchronized follicle development was induced by administration of exogenous gonadotropins to wildtype 4-wk-old female rats. The GC transcriptome was analyzed via RNA-sequencing before and after gonadotropin stimulation. An Er{beta}null mutant model that fails to show follicle maturation was also included in order to identify the ER{beta}-regulated genes involved at this step. We observed that specific groups of genes were differentially expressed in response to PMSG or hCG administration in wildtype rats. While some of the PMSG or hCG-induced genes showed a similar expression pattern in Er{beta}null GCs, a subset of PMSG- or hCG-induced genes showed a differential expression in Er{beta}null GCs. These latter ER{beta}-regulated genes included previously known FSH or LH target genes including Lhcgr, Cyp11a1, Cyp19a1, Pgr, Runx2, Egfr, Kiss1, and Ptgs2, which are involved in follicle development, oocyte maturation, and ovulation. We also identified novel ER{beta}-regulated genes including Jaml, Galnt6, Znf750, Dusp9, Wnt16, and Mageb16 that failed to respond to gonadotropin stimulation in Er{beta}null GCs. Our findings indicate that the gonadotropin-induced spatiotemporal pattern of gene expression is essential for ovarian follicle maturation beyond the antral stage. However, expression of a subset of those gonadotropin-induced genes is dependent on transcriptional regulation by ER{beta}.

developmental biology↗

bioRxiv2020

An in-silico study to determine whether changes to mitochondria organization through engineered mitochondrial dynamics can enhance bioenergetics in cardiomyocytes

Mitochondria are the powerhouse of the cell and owing to their unique energetic demands, heart muscles contain a high density of mitochondria. In conditions such as heart failure and diabetes-induced heart disease, changes in the organization of cardiac mitochondria are common. While recent studies have also shown that cardiac mitochondria split and fuse throughout the cell, a mechanistic understanding of how mitochondrial dynamics may affect energy output is lacking. Using a mathematical model that has been fitted to experimental data, we test if briefly altering fission or fusion rates improves ATP production and supply in cardiomyocytes. Unexpectedly, we found that cardiac bioenergetics, e.g., the ADP/ATP ratio, were robust to changes in fusion and fission rates and consequently mitochondria organization. Our study highlights complex nonlinear feedback loops that are at play in the cross-talk between mitochondrial dynamics and bioenergetics. The study motivate further in-silico and experimental investigations to determine the mechanistic basis for new therapies that target mitochondrial dynamics.

systems biology↗

bioRxiv2020

SATB homeobox 1 regulated genes in the mouse ectoplacental cone are important for placental development

SATB homeobox 1 (SATB1) is abundantly expressed in the stem-state of trophoblast cells but downregulated during trophoblast differentiation. It is also expressed in high levels in the mouse ectoplacental cones (EPCs). We detected that SATB1 is involved in maintaining the self-renewal of trophoblast stem cells and inhibiting trophoblast differentiation. In this study, we have identified SATB1-regulated genes in the mouse EPC and analyzed their potential functions. A total of 1618 differentially expressed genes were identified in Satb1null EPCs by mRNA sequencing. Remarkably 90% of the differentially expressed genes were found to be upregulated in Satb1null EPCs suggesting a transcriptional repressor role of SATB1 in mouse trophoblast cells. Ingenuity Pathway Analyses demonstrated that the differentially expressed genes in Satb1null EPCs are particularly linked to WNT and TGF{beta} signaling pathways, which regulate self-renewal of stem cells and cell differentiation. Moreover, twenty-six of the EPC genes that are known to be involved in placental development including Eomes, Epas1, Fgfr2, Cdkn1c, and Plac9 were found dysregulated in Satb1null EPCs due to the loss of SATB1 expression. These genes are particularly involved in the formation of labyrinthine zone. Our results emphasize that SATB1-regulated genes in the mouse EPC contribute to key roles in the regulation of trophoblast differentiation and placental development.

developmental biology↗

bioRxiv2020

GW182 Proteins Restrict Extracellular Vesicle Mediated Selective Export of Used miRNAs In Mammalian Cancer Cells

MicroRNAs are small regulatory RNAs of relatively long half-life in non-proliferative human cells. However, in cancer cells the half-lives of miRNAs are comparatively short. To understand the mechanism of rapid miRNA turn over in cancer cells, we explored the effect of "usage" of specific miRNAs for translation repression of their targets on the abundance of that miRNA. We have noted an accelerated extracellular vesicle mediated export of "used" miRNAs in mammalian cells and the miRNA-export process get retarded by Ago2 interacting protein GW182B. The GW182 group of proteins are localized to GW182 Bodies or RNA Processing Bodies in mammalian cells and GW182B dependent retardation of miRNA export depends on GW-body integrity and is independent of HuR mediated auxiliary pathway of miRNA export. Our data thus support existence of a HuR independent pathway of miRNA export in human cells that can be targeted to increase cellular miRNA levels in cancer cells to induce senescence. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/294488v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1d6e30dorg.highwire.dtl.DTLVardef@d4ab06org.highwire.dtl.DTLVardef@282ad4org.highwire.dtl.DTLVardef@113ef76_HPS_FORMAT_FIGEXP M_FIG C_FIG Key PointsO_LIUsage of miRNA is proportional with its export and turnover C_LIO_LIGW182 proteins cause phase separation of Ago2 to P-bodies and restrict miRNA export via extracellular vesicles (EVs) C_LIO_LIHuR driven auxiliary path of miRNA export is independent of GW182 controlled main path of miRNA exclusion C_LI

molecular biology↗

bioRxiv2020

Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2

The global public health is endangered due to COVID-19 pandemic, which is caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Despite having similar pathology to MERS and SARS-CoV, the infection fatality rate of SARS-CoV-2 is likely lower than 1%. SARS-CoV-2 has been reported to be uniquely characterized by the accessory protein ORF10, which contains eleven cytotoxic T lymphocyte (CTL) epitopes of nine amino acids length each, across various human leukocyte antigen (HLA) subtypes. In this study, all missense mutations found in sequence databases were examined across twnety-two unique SARS-CoV-2 ORF10 variants that could possibly alter viral pathogenicity. Some of these mutations decrease the stability of ORF10, e.g. I4L and V6I were found in the MoRF region of ORF10 which may also possibly contribute to Intrinsic protein disorder. Furthermore, a physicochemical and structural comparative analysis was carried out on SARS-CoV-2 and Pangolin-CoV ORF10 proteins, which share 97.37% amino acid homology. The high degree of physicochemical and structural similarity of ORF10 proteins of SARS-CoV-2 and Pangolin-CoV open questions about the architecture of SARS-CoV-2 due to the disagreement of these two ORF10 proteins over their sub-structure (loop/coil region), solubility, antigenicity and change from the strand to coil at amino acid position 26, where tyrosine is present. Altogether, SARS-CoV-2 ORF10 is a promising pharmaceutical target and a protein which should be monitored for changes which correlate to change pathogenesis and clinical course of COVID-19 infection.

bioinformatics↗

bioRxiv2020

Chromatin State Dynamics Confers Specific Therapeutic Strategies in Enhancer Subtypes of Colorectal Cancer

The extent and function of chromatin state aberrations during colorectal cancer (CRC) progression is not completely understood. Here, by comprehensive epigenomic characterization of 56 tumors, adenomas, and their matched normal tissues, we define the dynamics of chromatin states during the progression of colorectal cancer. H3K27ac-marked active enhancer state could distinguish between different stages of CRC progression. By epigenomic editing, we present evidence that gains of tumor-specific enhancers for crucial oncogenes, such as ASCL2 and FZD10, was crucial for excessive proliferation. Consistently, combination of MEK plus bromodomain (BET) inhibition was found to have synergistic effects in CRC patient-derived xenograft (PDX) models. Probing inter-tumor heterogeneity, we identified four distinct enhancer subtypes (EpiC), three of which correlate well with previously defined transcriptomic subtypes (CMSs). Importantly, CMS2 can be divided into two EpiC subgroups with significant survival differences. Leveraging such correlation, we devised a combinatorial therapeutic strategy of enhancer-blocking bromodomain inhibitors with pathway-specific inhibitors (PARPi, EGFRi, and TGF{beta}i) for three EPIC groups. Our data suggest that the dynamics of active enhancer underlies colorectal cancer progression and the patient-specific active enhancer patterns govern their unique gene expression patterns which can be leveraged for precision combination therapy.

cancer biology↗

bioRxiv2020

IL-4-induced hysteresis in naive T cell activation

Naive T cells are generally considered to be a homogeneous population, but for their unique T cell receptors (TCRs). Naive T cells are activated within a specific cytokine milieu upon interaction with antigen-presenting cells through cognate TCR::MHC-peptide interaction and co-stimulation. Here we demonstrate that naive T cells are transcriptionally heterogeneous, and that the relative proportions of transcriptionally distinct naive T cell subpopulations are modified by immune responses, such as during helminth infection. Not only are cognate naive T cells activated during an immune response, but the cytokine produced - such as IL-4 during helminth infection - changes the transcriptome of bystander naive T cells. Such changes in gene expression and population level heterogeneity in bystander naive T cells result in altered responses to a concurrent immune challenge, for instance, hypo-responsiveness to vaccination. Thus, naive T cell activation is not the result of a singular temporal event, but is characterized by hysteresis. Our studies suggest that antigen-agnostic, cytokine-dependent naive T cell conditioning and resulting hysteresis is a mechanism that integrates input signals from concurrent infections for the regulation of the overall magnitude of the immune response.

immunology↗

bioRxiv2020

A unique view of SARS-CoV-2 through the lens of ORF8 protein

Immune evasion is one of the unique characteristics of COVID-19 attributed to the ORF8 protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This protein is involved in modulating the host adaptive immunity through downregulating MHC (Major Histocompatibility Complex) molecules and innate immune responses by surpassing the interferon mediated antiviral response of the host. To understand the immune perspective of the host with respect to the ORF8 protein, a comprehensive study of the ORF8 protein as well as mutations possessed by it, is performed. Chemical and structural properties of ORF8 proteins from different hosts, that is human, bat and pangolin, suggests that the ORF8 of SARS-CoV-2 and Bat RaTG13-CoV are very much closer related than that of Pangolin-CoV. Eighty-seven mutations across unique variants of ORF8 (SARS-CoV-2) are grouped into four classes based on their predicted effects. Based on geolocations and timescale of collection, a possible flow of mutations was built. Furthermore, conclusive flows of amalgamation of mutations were endorsed upon sequence similarity and amino acid conservation phylogenies. Therefore, this study seeks to highlight the uniqueness of rapid evolving SARS-CoV-2 through the ORF8.

molecular biology↗