Biology subjects

Khurana, P.

Publications and source records attributed to Khurana, P..

7 recordsLinked to original sources

bioRxiv2023

Two splice forms of OsbZIP1, a homolog of AtHY5, function to regulate skoto- and photo-morphogenesis in rice

Plants possess well-developed light sensing mechanisms and signal transduction systems for regulating photomorphogenesis. ELONGATED HYOCOTYL 5 (HY5), a basic leucine zipper transcription factor, has been extensively characterized in dicot plants. In this study, we have shown that OsbZIP1 is a functional homolog of Arabidopsis HY5 (AtHY5) and is important for light-mediated regulation of seedling and mature plant development in rice. Ectopic expression of OsbZIP1 in rice reduces plant height and leaf length without affecting plant fertility, which is in contrast to OsbZIP48, another HY5 homolog we characterised earlier. OsbZIP1 is alternatively spliced and the isoform OsbZIP1.2 lacking COP1 binding domain regulates seedling development in dark; this is unique since AtHY5 lacking COP1 binding domain does not display such a phenotype. Rice seedlings overexpressing OsbZIP1 were found to be shorter than vector control under white and monochromatic light conditions whereas RNAi seedlings displayed completely opposite phenotype. While OsbZIP1.1 is light regulated, OsbZIP1.2 shows similar protein profile in both light and dark conditions. Due to its interaction with OsCOP1, OsbZIP1.1 undergoes degradation via 26S proteasome under dark conditions. Also, OsbZIP1.1 interacts with CASEIN KINASE 2 (OsCK2[a]3) and consequently undergoes phosphorylation. In comparison, OsbZIP1.2 did not show any interaction with COP1 and OsCK2[a]3. We propose that OsbZIP1.1 most likely works under low fluence of blue light (15 mol/m{superscript 2}/s) while OsbZIP1.2 becomes dominant as the fluence is increased to 30 mol/m{superscript 2}/s. Data presented in this study reveal that AtHY5 homologs in rice have undergone neofunctionalization and alternative splicing (AS) of OsbZIP1 has increased the repertoire of its functions. One sentence summaryAlternative spliced forms of OsbZIP1, an AtHY5 homolog in rice, regulate seedling development in response to light and dark

plant biology↗

bioRxiv2021

Anti-GD2 antibody therapy alters the neuroblastoma tumor microenvironment and extends survival in TH-MYCN mice

BackgroundNeuroblastoma is a commonly lethal solid tumor of childhood and intensive chemoradiotherapy treatment cures ~50% of children with high-risk disease. The addition of immunotherapy using dinutuximab, a monoclonal antibody directed against the GD2 disialoganglioside expressed on neuroblasts, improves survival when incorporated into front-line therapy and shows robust activity in regressing relapsed disease when combined with chemotherapy. Still, many children succumb to neuroblastoma despite receiving dinutuximab-based immunotherapy, and efforts to counteract the immune suppressive signals responsible are warranted. Animal models of human cancers provide useful platforms to study immunotherapies. TH-MYCN transgenic mice are immunocompetent and develop neuroblastomas at autochthonous sites due to enforced MYCN expression in developing neural crest tissues. However, GD2-directed immunotherapy in this model has been underutilized due to the prevailing notion that TH-MYCN neuroblasts express insufficient GD2 to be targeted. MethodsTH-MYCN mice were treated with 14G2a (anti-GD2 antibody), isotype antibody, or phosphate buffered saline from day 14 of life until day 100 or signs of morbidity. Survival was recorded, and tumors were isolated in terminal surgeries for analysis of GD2 expression and immune cell frequencies. Tumors from untreated mice were explanted for generation into cell lines, and GD2 expression was recorded with serial passage in tissue culture. Immunocytology and immunoblotting were performed to evaluate for adrenergic and mesenchymal markers of neuroblasts. Survival curves compared using Kaplan-Meier method with a log-rank test for significance. Unpaired two-tailed Students t-tests used for comparison of groups in flow cytometry analysis. Results14G2a markedly extends survival in such TH-MYCN mice. Additionally, neuroblasts in 14G2a-treated mice have reduced GD2 expression and fewer macrophage and myeloid-derived suppressor cells in their tumor microenvironments. Neuroblasts in TH-MYCN-driven tumors express GD2 at levels comparable to human neuroblastomas but rapidly lose GD2 expression when explanted ex vivo to establish tumor cell lines. The loss of GD2 expression ex vivo is associated with a transition from an adrenergic to mesenchymal state that is maintained when reimplanted in vivo. ConclusionsOur findings support the utility of the TH-MYCN model to inform GD2-directed immunotherapy approaches for neuroblastoma as well as opportunities to investigate drivers of adrenergic to mesenchymal fate decisions.

cancer biology↗

bioRxiv2021

Distinct bioenergetic features of human invariant natural killer T (iNKT) cells enable retained functions in nutrient-deprived states

Invariant natural killer T (iNKT) cells comprise a unique subset of lymphocytes that are primed for activation and possess innate NK-like functional features. Currently, iNKT cell-based immunotherapies remain in early clinical stages, and little is known about the ability of these cells to survive and retain effector functions within the solid tumor microenvironment (TME) long-term. In conventional T cells (TCONV), cellular metabolism is linked to effector functions and their ability to adapt to the nutrient-poor TME. In contrast, the bioenergetic requirements of iNKT cells - particularly those of human iNKT cells - at baseline and upon stimulation are not well understood; neither is how these requirements affect cytokine production or anti-tumor effector functions. We find that unlike TCONV, human iNKT cells are not dependent upon glucose or glutamine for cytokine production and cytotoxicity upon stimulation with anti-CD3 and anti-CD28. Additionally, transcriptional profiling revealed that stimulated human iNKT cells are less glycolytic than TCONV and display higher expression of fatty acid oxidation (FAO) and adenosine monophosphate-activated protein kinase (AMPK) pathway genes. Furthermore, stimulated iNKT cells displayed higher mitochondrial mass and membrane potential relative to TCONV. Real-time Seahorse metabolic flux analysis revealed that stimulated human iNKT cells utilize fatty acids as substrates for oxidation more than stimulated TCONV. Together, our data suggest that human iNKT cells possess different bioenergetic requirements from TCONV and display a more memory-like metabolic program relative to effector TCONV. Importantly, iNKT cell-based immunotherapeutic strategies could co-opt such unique features of iNKT cells to improve their efficacy and longevity of anti-tumor responses.

immunology↗

bioRxiv2020

HAHmiR.DB : A Server Platform For High Altitude Human miRNA-Gene Coregulatory Networks And Associated Regulatory-Circuits.

Rapid ascent to High Altitude (HA) can cause severe damage to body organs and may lead to many fatal disorders. During induction to HA, human body undergoes various physiological, biochemical, hematological and molecular changes to adapt to the extreme environmental conditions. Many literature references hint that gene-expression-regulation and regulatory molecules like microRNAs (miRNAs) and Transcription Factors (TFs) control adaptive responses during HA-stress. These biomolecules are known to interact in a complex combinatorial manner to fine-tune the gene expression and help in controlling the molecular responses during this stress and ultimately help in acclimatization. HAHmiR.DB (High-Altitude Human miRNA Database) is a unique, comprehensive, curated collection of miRNAs that have been experimentally validated to be associated with HA-stress; their level of expression in different altitudes, fold change, experiment duration, biomarker association, disease and drug association, tissue-specific expression level, Gene Ontology (GO) and Kyoto Encyclopaedia of Gene and Genomes (KEGG) pathway associations. As a server platform it also uniquely constructs and analyses interactive miRNA-TF-Gene coregulatory networks and extracts regulatory-circuits/Feed Forward Loops (FFLs) using in-house scripts. These regulatory circuits help to offer mechanistic insights in complex regulatory mechanisms during HA stress. The server can also build these regulatory networks between two and more miRNAs of the database and also identify the regulatory-circuits from this network. Hence HAHmiR.DB is the first-of its-kind database in HA research which a reliable platform to explore, compare, analyse and retrieve miRNAs associated with HA stress, their coregulatory networks and FFL regulatory circuits. HAHmiR.DB is freely accessible at http://www.hahmirdb.in

bioinformatics↗

bioRxiv2020

miRFFLDB - An integrated resource for human miRNA-Transcription Factor-Target Gene coregulatory networks and associated Feed Forward Loops.

Gene regulation is viewed as a complex process where regulatory elements and their targets form highly complex network interactions thus affecting normal biological physiology and also disease-initiation and progress. Transcription factors (TF) and microRNA (miRNA) are fundamental transcriptional and post-transcriptional regulators of the gene expression controlling important biological processes. In recent years, many high throughput studies revealed that the complex regulatory interactions are mediated by the complex interplay between miRNA and TF regulating a Target Gene (TG) in conjunction. miRNAs and TFs are also known to regulate each other. This complex coregulatory mechanism may be represented in the form of miRNA:TF:TG coregulatory network. This network can be used to identify several small recurring subgraphs known as regulatory-circuits. One of these regulatory-circuits also called the Feed-Forward Loops (FFLs) is a three-node pattern which is composed of a miRNA and a TF, one of which regulates the other and both jointly regulate a TG. These regulatory-circuits have proven useful in elucidating the complex interplay of gene regulation during many physiological and pathological conditions. Human.miRFFL.DB is a comprehensive integrated resource for human miRNA:TF:TG coregulatory directed networks and their associated regulatory-circuits. In-house scripts based on the graph theory principle have been used to identify both types of FFL motifs i.e. miRNA-FFL and TF-FFL. The database additionally provides an interactive visualization of the coregulatory networks and associated FFLs. Human.miRFFL.DB can be used as a comprehensive ready reference for human miRNA:TF:TG coregulatory networks and associated FFLs for decrypting complex cellular interactions of these regulatory biomolecules. Human.miRFFL.DB is available online at http://mirffldb.in/human/

bioinformatics↗

bioRxiv2019

LIN28B-PDZ Binding Kinase Signaling Promotes Neuroblastoma Metastasis

Neuroblastoma is an aggressive pediatric malignancy of the neural crest with suboptimal cure rates and a striking predilection for widespread metastases, underscoring the need to identify novel therapeutic vulnerabilities. We recently identified the RNA binding protein LIN28B as a driver in high-risk neuroblastoma and demonstrated it promotes oncogenic cell proliferation by coordinating a RAN-Aurora kinase A network. Here, we demonstrate that LIN28B influences another key hallmark of cancer, metastatic dissemination. Using a murine xenograft model of neuroblastoma dissemination, we show that LIN28B promotes metastasis. We demonstrate that this is in part due to the effects of LIN28B on self-renewal and migration, providing an understanding of how LIN28B shapes the metastatic phenotype. Our studies reveal that the let-7 family, which LIN28B inhibits, opposes the effects of LIN28B. Next, we identify PDZ Binding Kinase (PBK) as a novel LIN28B target. PBK is a serine/threonine kinase that promotes the proliferation and self-renewal of neural stem cells and serves as an oncogenic driver in multiple aggressive malignancies. We demonstrate that PBK is both a novel direct target of let-7 and that MYCN regulates PBK expression, thus elucidating two oncogenic drivers that converge on PBK. Functionally, PBK promotes self-renewal and migration, phenocopying LIN28B. Taken together, our findings define a role for LIN28B in neuroblastoma metastasis and define the targetable kinase PBK as a potential novel vulnerability in metastatic neuroblastoma.

cancer biology↗

bioRxiv2019

Functional characterization of RNase H1 proteins in Arabidopsis thaliana

ABSTRACTRNase H1 is an endonuclease specific towards RNA:DNA hybrids. Members of this protein family are present in most living organisms and are essential for removing RNA that base pairs with DNA. It prevents detrimental effects of RNA:DNA hybrids and is involved in several biological processes. We show that Arabidopsis thaliana contains four RNase H1-like proteins originating from two gene duplication events and alternative splicing. These proteins have the canonical RNase H1 activity, which requires at least four ribonucleotides for activity. Two of those proteins are nuclear, one is localized to mitochondria and one to plastids. While the nuclear RNases H1 are dispensable, the presence of at least one organellar RNase H1 is required for embryonic development. The plastid protein RNH1C affects plastid DNA copy number and sensitivity to hydroxyurea. This indicates that three genomes present in each plant cell are served by at least one specialized RNase H1 protein.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗