Biology subjects

Nair, R.

Publications and source records attributed to Nair, R..

29 records · Page 2Linked to original sources

bioRxiv2020

Potential consequences of the red blood cell storage lesion on cardiac electrophysiology

The red blood cell (RBC) storage lesion is a series of morphological, functional and metabolic changes that RBCs undergo following collection, processing and refrigerated storage for clinical use. Since the biochemical attributes of the RBC unit shifts with time, transfusion of older blood products may contribute to cardiac complications, including hyperkalemia and cardiac arrest. We measured the direct effect of storage age on cardiac electrophysiology and compared with hyperkalemia, a prominent biomarker of storage lesion severity. Donor RBCs were processed using standard blood banking techniques. The supernatant was collected from RBC units (sRBC), 7-50 days post-donor collection, for evaluation using Langendorff-heart preparations (rat) or human stem-cell derived cardiomyocytes. Cardiac parameters remained stable following exposure to fresh sRBC (day 7: 5.9+0.2 mM K+), but older blood products (day 40: 9.7+0.4 mM K+) caused bradycardia (baseline: 279{+/-}5 vs day 40: 216{+/-}18 BPM), delayed sinus node recovery (baseline: 243{+/-}8 vs day 40: 354{+/-}23 msec), and increased the effective refractory period of the atrioventricular node (baseline: 77+2 vs day 40: 93+7 msec) and ventricle (baseline: 50+3 vs day 40: 98+10 msec) in perfused hearts. Beating rate was also slowed in human cardiomyocytes after exposure to older sRBC (-75+9%, day 40 vs control). Similar effects on automaticity and electrical conduction were observed with hyperkalemia (10-12 mM K+). This is the first study to demonstrate that older blood products directly impact cardiac electrophysiology, using experimental models. These effects are likely due to biochemical alterations in the sRBC that occur over time, including, but not limited to hyperkalemia. Patients receiving large volume and/or rapid transfusions may be sensitive to these effects. New & noteworthyWe demonstrate that red blood cell storage duration time can have downstream effects on cardiac electrophysiology, likely due to biochemical alterations in the blood product. Hyperkalemia and cardiac arrest have been reported following blood transfusions, but this is the first experimental study to show a direct correlation between storage duration and cardiac function. Infant and pediatric patients, and those receiving large volume and/or rapid transfusions may be sensitive to these effects.

physiology↗

bioRxiv2020

Human es-fMRI Resource: Concurrent deep-brain stimulation and whole-brain functional MRI

Mapping the causal effects of one brain region on another (effective connectivity) is a challenging problem in neuroscience, since it requires invasive direct manipulation of brain function, together with whole-brain measurement of the effects produced. Here we establish a unique resource and present data from 26 human patients who underwent electrical stimulation during functional magnetic resonance imaging (es-fMRI). The patients had medically refractory epilepsy requiring surgically implanted intracranial electrodes in cortical and subcortical locations. One or multiple contacts on these electrodes were stimulated while simultaneously recording BOLD-fMRI activity in a block design. Multiple runs exist for patients with different stimulation sites. We describe the resource, data collection process, preprocessing using the fMRIPrep analysis pipeline and management of artifacts, and provide end-user analyses to visualize distal brain activation produced by site-specific electrical stimulation. The data are organized according to the brain imaging data structure (BIDS) specification, and are available for analysis or future dataset contributions on openneuro.org including both raw and preprocessed data.

neuroscience↗

bioRxiv2019

Targeting the Id1-Kif11-Aurka axis in triple negative breast cancer using combination therapy

Evidence points to breast cancer following a hierarchical model, with Cancer Stem Cells (CSCs) driving critical phenotypes of the bulk tumor. Chemoresistant CSCs are not an abstract concept but have clinical consequences as they drive relapse and ultimately lead to mortality in patients, making it imperative to understand how these subpopulations of cells survive. Our previous work (1-2) has demonstrated that the bHLH transcription factor, Inhibitor of Differentiation 1 (Id1) and its closely related family member Id3, have an important role in maintaining the CSC phenotype in the Triple Negative breast cancer (TNBC) subtype. A genetic screen conducted to further elucidate the molecular mechanism underlying the Id (Id1/3) mediated CSC phenotypes in TNBC revealed critical cell cycle genes such as Kif11 and Aurka as putative Id targets. We take this work forward by investigating how alteration in Kif11 and Aurka via Id proteins promotes the CSC phenotype in TNBC. Cells lacking Id are poised in a state of G0/G1 arrest from which they can re-enter the cell cycle. Intriguingly, depletion of Kif11 and Aurka independently did not phenocopy the G0/G1 arrest observed in Id knockdown (Id KD) cells. We have further explored the hypothesis that we can deplete the chemo resistant Id expressing CSC population by combining chemotherapy with targeted therapy using existing small molecule inhibitors (against Id target Kif11) to more effectively debulk the entire tumor. This work opens up exciting new possibilities of targeting Id targets like Kif11, in the TNBC subtype which is currently refractory to chemotherapy.

cancer biology↗

bioRxiv2019

Clinically-relevant cell type cross-talk identified from a human lung tumor microenvironment interactome

Tumors comprise a complex microenvironment of interacting malignant and stromal cell types. Much of our understanding of the tumor microenvironment comes from in vitro studies isolating the interactions between malignant cells and a single stromal cell type, often along a single pathway. To develop a deeper understanding of the interactions between cells within human lung tumors we performed RNA-seq profiling of flow-sorted malignant cells, endothelial cells, immune cells, fibroblasts, and bulk cells from freshly resected human primary non-small-cell lung tumors. We mapped the cell-specific differential expression of prognostically-associated secreted factors and cell surface genes, and computationally reconstructed cross-talk between these cell types to generate a novel resource we call the Lung Tumor Microenvironment Interactome (LTMI). Using this resource, we identified and validated a prognostically unfavorable influence of Gremlin-1 production by fibroblasts on proliferation of malignant lung adenocarcinoma cells. We also found a prognostically favorable association between infiltration of mast cells and less aggressive tumor cell behavior. These results illustrate the utility of the LTMI as a resource for generating hypotheses concerning tumor-microenvironment interactions that may have prognostic and therapeutic relevance.\n\nSummaryRNA-seq profiling of sorted populations from primary lung cancer samples identifies prognostically relevant cross-talk between cell types in the tumor microenvironment.

cancer biology↗

bioRxiv2019

Understanding patterns of abiotic and biotic stress resilience to unleash the potential of crop wild relatives for climate-smart legume breeding

Although new varieties are urgently needed for climate-smart legume production, legume breeding lags behind with cereals and underutilizes wild relatives. This paper provides insights in patterns of abiotic and biotic stress resilience of legume crops and wild relatives to enhance the use and conservation of these genetic resources for climate-smart legume breeding. We focus on Vigna, a pantropical genus with more than 88 taxa including important crops such as cowpea and mung bean. Sources of pest and disease resistance occur in more than 50 percent of the Vigna taxa, which were screened while sources of abiotic stress resilience occur in less than 20 percent of the taxa, which were screened. This difference suggests that Vigna taxa co-evolve with pests and diseases while taxa are more conservative to adapt to climatic changes and salinization. Twenty-two Vigna taxa are poorly conserved in genebanks or not at all. This germplasm is not available for legume breeding and requires urgent germplasm collecting before these taxa extirpate on farm and in the wild. Vigna taxa, which tolerate heat and drought stress are rare compared with taxa, which escape these stresses or tolerate salinity. These rare Vigna taxa should be prioritized for conservation and screening for multifunctional traits of combined abiotic and biotic stress resilience. The high presence of salinity tolerance compared with drought stress tolerance, suggests that Vigna taxa are good at developing salt-tolerant traits compared with drought-tolerant traits. Vigna taxa are therefore of high value for legume production in areas that suffer from salinization.

plant biology↗

bioRxiv2018

Id proteins promote a cancer stem cell phenotype in triple negative breast cancer via Robo1-dependent c-Myc activation

Breast cancers display phenotypic and functional heterogeneity and several lines of evidence support the existence of cancer stem cells (CSCs) in certain breast cancers, a minor population of cells capable of tumor initiation and metastatic dissemination. Identifying factors that regulate the CSC phenotype is therefore important for developing strategies to treat metastatic disease. The Inhibitor of Differentiation Protein 1 (Id1) and its closely related family member Inhibitor of Differentiation 3 (Id3) (collectively termed Id) are expressed by a diversity of stem cells and are required for metastatic dissemination in experimental models of breast cancer. In this study, we show that ID1 is expressed in rare neoplastic cells within ER-negative breast cancers. To address the function of Id1 expressing cells within tumors, we developed two independent murine models of Triple Negative Breast Cancer (TNBC) in which a genetic reporter permitted the prospective isolation of Id1+ cells. Id1+ cells are enriched for self-renewal in tumorsphere assays in vitro and for tumor initiation in vivo. Conversely, depletion of Id1 and Id3 in the 4T1 murine model of TNBC demonstrates that Id1/3 are required for cell proliferation and self-renewal in vitro, as well as primary tumor growth and metastatic colonization of the lung in vivo. Using combined bioinformatic analysis, we have defined a novel mechanism of Id protein function via negative regulation of the Roundabout Axon Guidance Receptor Homolog 1 (Robo1) leading to activation of a Myc transcriptional programme.

cancer biology↗

bioRxiv2018

Selectivity among anti-σ factors by Mycobacterium tuberculosis ClpX influences intracellular levels of Extracytoplasmic Function σ factors

Extracytoplasmic Function {sigma} factors that are stress inducible are often sequestered in an inactive complex with a membrane-associated anti-{sigma} factor. M. tuberculosis membrane-associated anti-{sigma} factors have a small stable RNA gene A-like degron for targeted proteolysis. Interaction between the unfoldase, ClpX, and the substrate with an accessible degron initiates energy-dependent proteolysis. Four anti-{sigma} factors with a mutation in the degron provided a set of natural substrates to evaluate the influence of the degron on degradation strength in ClpX-substrate processivity. We note that a point mutation in the degron (XXX-Ala-Ala) leads to an order of magnitude difference in the dwell time of the substrate on ClpX. Differences in ClpX/anti-{sigma} interactions were correlated with change in unfoldase activity. GFP chimeras or polypeptides of identical length with the anti-{sigma} degron also demonstrate degron-dependent variation in ClpX activity. We show that degron-dependent ClpX activity leads to differences in anti-{sigma} factor degradation thereby regulating the release of free {sigma} from the {sigma}/anti-{sigma} complex. M. tuberculosis ClpX activity thus influences changes in gene expression by modulating the cellular abundance of ECF {sigma} factors.\n\nImportanceThe ability of Mycobacterium tuberculosis to quickly adapt to the changing environmental stimuli occurs by maintaining protein homeostasis. Extra-cytoplasmic function (ECF) {sigma} factors play a significant role in coordinating the transcription profile to changes in environmental conditions. Release of the {sigma} factor from the anti-{sigma} is governed by the ClpXP2P1 assembly. M. tuberculosis ECF anti-{sigma} factors have a ssrA-like degron for targeted degradation. A point mutation in the degron leads to differences in ClpX mediated proteolysis and affects the cellular abundance of ECF {sigma}-factors. ClpX activity thus synchronizes changes in gene expression with environmental stimuli affecting M. tuberculosis physiology.

biochemistry↗

bioRxiv2018

A novel role for the HLH protein Inhibitor of Differentiation 4 (ID4) in the DNA damage response in basal-like breast cancer.

Basal-like breast cancer (BLBC) is a poorly characterised, heterogeneous disease. Patients are diagnosed with aggressive, high-grade tumours and often relapse with chemotherapy resistance. Detailed understanding of the molecular underpinnings of this disease is essential to the development of personalised therapeutic strategies. Inhibitor of Differentiation 4 (ID4) is a helix-loop-helix transcriptional regulator required for mammary gland development. ID4 is overexpressed in a subset of BLBC patients, associating with a stem-like poor prognosis phenotype, and is necessary for the growth of cell line models of BLBC, through unknown mechanisms. Here, we have defined a molecular mechanism of action for ID4 in BLBC and the related disease highgrade serous ovarian cancer (HGSOV), by combining RIME proteomic analysis and ChIP-Seq mapping of genomic binding sites. Remarkably, these studies have revealed novel interactions with DNA damage response proteins, in particular, mediator of DNA damage checkpoint protein 1 (MDC1). Through MDC1, ID4 interacts with other DNA repair proteins ({gamma}H2AX and BRCA1) at fragile chromatin sites. ID4 does not affect transcription at these sites, instead binding to chromatin following DNA damage and regulating DNA damage signalling. Clinical analysis demonstrates that ID4 is amplified and overexpressed at a higher frequency in BRCA1-mutant BLBC compared with sporadic BLBC, providing genetic evidence for an interaction between ID4 and DNA damage repair pathways. These data link the interactions of ID4 with MDC1 to DNA damage repair in the aetiology of BLBC and HGSOV.

cancer biology↗

bioRxiv2018

Single cell transcriptomics reveals molecular subtype and functional heterogeneity in models of breast cancer

Breast cancer has long been classified into a number of molecular subtypes that predict prognosis and therefore influence clinical treatment decisions. Cellular heterogeneity is also evident in breast cancers and plays a key role in the development, evolution and metastatic progression of many cancers. How clinical heterogeneity relates to cellular heterogeneity is poorly understood, so we approached this question using single cell gene expression analysis of well established in vitro and in vivo models of disease.\n\nTo explore the cellular heterogeneity in breast cancer we first examined a panel of genes that define the PAM50 classifier of molecular subtype. Five breast cancer cell line models (MCF7, BT474, SKBR3, MDA-MB-231, and MDA-MB-468) were selected as representatives of the intrinsic molecular subtypes (luminal A and B, basal-like, and Her2-enriched). Single cell multiplex RT-PCR was used to isolate and quantify the gene expression of single cells from each of these models, and the PAM50 classifier applied. Using this approach, we identified heterogeneity of intrinsic subtypes at single-cell level, indicating that cells with different subtypes exist within a cell line. Using the Chromium 10X system, this study was extended into thousands of cells from the MCF7 cell-line and an ER+ patient derived xenograft (PDX) model and again identified significant intra-tumour heterogeneity of molecular subtype.\n\nEstrogen Receptor (ER) is an important driver and therapeutic target in many breast cancers. It is heterogeneously expressed in a proportion of clinical cases but the significance of this to ER activity is unknown. Significant heterogeneity in the transcriptional activation of ER regulated genes was observed within tumours. This differential activation of the ER cistrome aligned with expression of two known transcriptional co-regulatory factors of ER (FOXA1 and PGR).\n\nTo examine the degree of heterogeneity for other important phenotypic traits, we used an unsupervised clustering approach to identify cellular sub-populations with diverse cancer associated transcriptional properties, such as: proliferation; hypoxia; and treatment resistance. In particular, we show that we can identify two distinct sub-populations of cells that may have denovo resistance to endocrine therapies in a treatment naive PDX model of ER+ breast cancer. One of these consists of cells with a non-proliferative transcriptional phenotype that is enriched for transcriptional properties of ERBB2 tumours. The other is heavily enriched for components of the primary cilia. Gene regulatory networks were used to identify transcription factor regulons that are active in each cell, leading us to identify potential transcriptional drivers (such as E2F7, MYB and RFX3) of the cilia associated endocrine resistant cells. This rare subpopulation of cells also has a highly heterogenous mix of intrinsic subtypes highlighting a potential role of intra-tumour subtype heterogeneity in endocrine resistance and metastatic potential.\n\nOverall, These results suggest a high degree of cellular heterogeneity within breast cancer models, even cell lines, that can be functionally dissected into sub-populations of cells with transcriptional phenotypes of potential clinical relevance.

cancer biology↗

bioRxiv2017

Targeting stromal remodeling and cancer stem cell plasticity to overcome chemoresistance in triple negative breast cancer

The cellular and molecular basis of stromal cell recruitment, activation and crosstalk in carcinomas is poorly understood, limiting the development of targeted anti-stromal therapies. In mouse models of triple negative breast cancer (TNBC), Hh ligand produced by neoplastic cells reprogrammed cancer-associated fibroblast (CAF) gene expression, driving tumor growth and metastasis. Hh-activated CAFs upregulated expression of FGF5 and production of fibrillar collagen, leading to FGFR and FAK activation in adjacent neoplastic cells, which then acquired a stem-like, drug-resistant phenotype. Treatment with smoothened inhibitors (SMOi) reversed these phenotypes. Stromal treatment of TNBC patient-derived xenograft (PDX) models with SMOi downregulated the expression of cancer stem cell markers and sensitized tumors to docetaxel, leading to markedly improved survival and reduced metastatic burden. In the phase I clinical trial EDALINE, 3 of 12 patients with metastatic TNBC derived clinical benefit from combination therapy with the SMOi Sonidegib and docetaxel chemotherapy, with one patient experiencing a complete response. Markers of pathway activity correlated with response. These studies identify Hh signaling to CAFs as a novel mediator of cancer stem cell plasticity and an exciting new therapeutic target in TNBC.\n\nSIGNIFICANCECompared to other breast cancer subtypes, TNBCs are associated with significantly worse patient outcomes. Standard of care systemic treatment for patients with non-BRCA1/2 positive TNBC is cytotoxic chemotherapy. However, the failure of 70% of treated TNBCs to attain complete pathological response reflects the relative chemoresistance of these tumors. New therapeutic strategies are needed to improve patient survival and quality of life. Here, we provide new insights into the dynamic interactions between heterotypic cells within a tumor. Specifically, we establish the mechanisms by which CAFs define cancer cell phenotype and demonstrate that the bidirectional CAF-cancer cell crosstalk can be successfully targeted in mice and humans using anti-stromal therapy.

cancer biology↗

bioRxiv2017

Identification Of A Native Novel Oncolytic Immunoglobulin On Exfoliated Colon Epithelial Cells: A Bispecific Heterodimeric Chimera Of IgA/IgG

Understanding the nature of cell surface markers on exfoliated colonic cells is a crucial step in establishing criteria for a normally functioning mucosa. We have found that colonic cells isolated from stool samples (SCSR-010 Fecal Cell Isolation Kit, NonInvasive Technologies, Elkridge, MD), preserved at room temperature for up to one week, with viability of >85% and low levels of apoptosis (8% - 10%) exhibit two distinct cell size subpopulations, in the 2.5M- 5.0 M and 5.0M-8.0M range. In addition to IgA, about 60% of the cells expressed a novel heterodimeric IgA/IgG immunoglobulin that conferred a broad-spectrum cell mediated cytotoxicity against tumor cells. In a cohort of 58 subjects the exclusive absence of this immunoglobulin in two African-Americans was suggestive of a germline deletion. Serial cultures in stem cell medium retained the expression of this heterodimer. Since a majority of the cystic cells expressed the stem cell markers Lgr5 and Musashi-1 we termed these cells as gastrointestinal progenitor stem cells (GIP-C**). CXCR-4, the cytokine co-receptor for HIV was markedly expressed. These cells also expressed CD20, IgA, IgG, CD45, and COX-2. We assume that they originated from mature columnar epithelium by dedifferentiation. Our observations indicate that we have a robust noninvasive method to study mucosal pathophysiology and a direct method to create a database for applications in regenerative medicine.

cell biology↗