Biology subjects

Sinha, P.

Publications and source records attributed to Sinha, P..

29 records · Page 2Linked to original sources

bioRxiv2021

Stress-responsive Long Non-coding RNA, hsrω, is a genetic modifier of JNK-dependent Intrinsic Tumor Suppression in Drosophila

Host genetics is known to influence cancer susceptibility. However, the specific candidate genes and molecular mechanisms that confer resistance remain poorly understood. Here, we demonstrate the power of haploinsufficiency screen to uncover host genetic regulators of cancer in Drosophila and identify the long noncoding RNA (lncRNA) hsr{omega}, a structural component of nuclear biomolecular condensate known as omega speckles, as a key host cancer susceptibility locus. Loss of hsr{omega} disrupts proteostasis and cell fitness, while its haploinsufficiency accelerates epithelial tumor progression driven by loss of the Lethal giant larvae (Lgl) tumor suppressor. Further validating the breadth of this screening strategy, we independently identified Drosophila STING (innate immunity) and Keap1 (oxidative stress defense) as genetic modifiers of cancer. Moreover, in humans, copy number variations (CNV) in these genes and Sat III (a functional human homolog of hsr{omega}) correlate with poor cancer prognosis, thereby revealing conserved stress pathways as potential host genetic susceptibility regulators.

cancer biology↗

bioRxiv2021

Drosophila Male Accessory Gland Displays Developmental Ground Plan of a Primitive Prostate

Conservation of developmental genetic toolkits of functionally comparable organs from disparate phyla reveals their deep homology, which may help overcome the challenges of their confounding categorization as either homologous or analogous organs. A male accessory sexual organ in mammals, prostate, for instance, is anatomically disparate from its phylogenetically distant counterpart--the male accessory gland (MAG)--in insects like Drosophila. By examining a select set of toolkit gene expression patterns, here we show that Drosophila MAG displays deep homology with the mammalian prostate. Like mammalian prostate, MAG morphogenesis is marked by recruitment of fibroblast growth factor receptor, FGFR, a tubulogenesis toolkit signaling pathway, starting early during its adepithelial genesis. Specialization of the individual domains of the developing MAG tube on the other hand is marked by expression of a posterior Hox gene transcription factor, Abd-B, while Hh-Dpp signaling marks its growth. Drosophila MAG thus reveals developmental design of unitary bud-derived tube--a ground plan that appears to have been reiteratively co-opted during evolutionary diversification of male accessory sexual organs across distant phylogeny.

developmental biology↗

bioRxiv2021

A Serpin27A-dependent Toll Signaling Underlies Host Genetics of Cancer Resistance in Drosophila

Cancer resistance varies amongst individuals, although its host genetic underpinnings remain largely elusive. Remissions of sarcomas were first reported following repeated injections of patients with mixtures of killed bacteria--Coleys toxins--a phenomenon, which was subsequently causally traced to induction of innate immunity. Here we reveal remission of Drosophila epithelial neoplasms by genetically triggered host innate immunity via Toll signaling. These neoplasms display capacities to receive and, in rare instances, induce Toll signaling. A tumor-induced and progressive Toll signaling, however, did not culminate in tumor suppression. By contrast, Drosophila hosts heterozygous for spn27A1 mutation, which constitutively produce activated Toll ligand, SpzAct, displayed comprehensive tumor remission via Toll-induced, NF-{kappa}B-mediated, tumor cell death. Our results reveal a novel node of host genetic cancer resistance via serpin-dependent Toll signaling.

cancer biology↗

bioRxiv2021

Influence of visual feedback persistence on visuo-motor skill improvement

Towards the larger goal of understanding factors relevant for improving visuo-motor control, we investigated the role of visual feedback for modulating the effectiveness of a simple hand-eye training protocol. The regimen comprised a series of curve tracing tasks undertaken over a period of one week by neurologically healthy individuals with their non-dominant hands. Our three subject groups differed in the training they experienced: those who received Persistent visual-feedback by seeing their hand and trace evolve in real-time superimposed upon the reference patterns, those who received Non-Persistent visual-feedback seeing their hand movement but not the emerging trace, and a Control group that underwent no training. Improvements in performance were evaluated along two dimensions - accuracy and steadiness, to assess visuo-motor and motor skills, respectively. We found that persistent feedback leads to a significantly greater improvement in accuracy than non-persistent feedback. Steadiness, on the other hand, benefits from training irrespective of the persistence of feedback. Our results not only demonstrate the feasibility of rapid visuo-motor learning in adulthood, but more specifically, the influence of visual veridicality and a critical role for dynamically emergent visual information.

neuroscience↗

bioRxiv2020

Degenerating Drosophila Larval Epidermal Cells Drive Thorax Closure

Adult thorax formation in Drosophila begins during pre-pupal development by fusion of its two contralateral progenitor halves, the heminotal epithelia (HE). HEs migrate and replace an underlying cell layer of thoracic larval epidermal cells (LECs) during a morphogenetic process called thorax closure. The LEC layer has so far been proposed to be a passive substrate over which HEs migrate before their zipping. By contrast, here we show that the pull forces generated within the LEC layer drive HE migration. During thorax closure, the LECs display actomyosin-mediated contraction, via enrichment of non-muscle myosin-II and actin, besides squamous-to-pseudostratified columnar epithelial transition and tissue shrinkage. This shrinkage of the LEC layer is further accompanied by cell extrusion and death, that prevent overcrowding of LECs, thereby promoting further shrinkage. The pull forces thus generated by the shrinking LEC layer are then relayed to the HEs by their mutual adhesions via {beta}PS1 (Mys) and PS3 (Scb) integrins. Suppression of cell death in the LEC layer by a gain of p35 leads to cell overcrowding, which impedes HE migration and zipping. Further, knockdown of sqh, the light chain of non-muscle myosin II, in LECs or integrins (mys or scb) in either the LEC layer or in the HEs, or both abrogate thorax closure. Mathematical modeling also reveals the biophysical underpinnings of the forces that drive this tissue closure process wherein a degenerating LEC layer mediates its succession by the future adult primodia. These essential principles of thorax closure appear ancient in origin and recur in multiple morphogenetic contexts and tissue repair.

developmental biology↗

bioRxiv2020

Identification and Optimization of cell active 4-anilino-quin(az)oline Inhibitors for Protein Kinase Novel 3 (PKN3)

The development of a small library of 4-anilinoquinolines led to the identification of 7-iodo-N-(3,4,5-trimethoxyphenyl)quinolin-4-amine 16 as a potent inhibitor of Protein Kinase Novel 3 (PKN3) with an IC50 of 1.3 M in cells. Compound 16 presents a useful potential tool compound to study the biology of PKN3 including links to pancreatic and prostate cancer, along with T-cell acute lymphoblastic leukemia. These compounds may be useful tools to explore the therapeutic potential of PKN3 inhibition in prevention of a broad range of infectious and systemic diseases.

pharmacology and toxicology↗

bioRxiv2020

A Drosophila model of oral peptide therapeutics for adult intestinal stem cell tumors

The proto-oncogene YAP /Yki, a transcription co-factor of the Hippo pathway, has been linked to many cancers. YAP interacts with DNA-binding TEAD/Sd proteins to regulate expression of its transcriptional targets. Disruption of YAP-TEAD therefore offers a potential therapeutic strategy. The mammalian Vestigial Like (VGLL) protein, specifically its TONDU domain, has been shown to competitively inhibit YAP-TEAD interaction and a TONDU peptide can suppress YAP-induced cancer. As TONDU could potentially be developed into a therapeutic peptide for multiple cancers, we evaluated its efficacy in Yki-driven adult Intestinal Stem Cell (ISC) tumors in Drosophila. We show that oral uptake of the TONDU peptide is highly effective at inhibiting Yki-driven gut tumors by suppressing YAP-TEAD interaction. Comparative proteomics of early and late stage Yki-driven ISC tumors revealed enrichment of a number of proteins, including members of the integrin signaling pathway, such as Talin, Vinculin and Paxillin. These, in turn displayed a decrease in their levels in TONDU-peptide treated tumors. Further, we show that Sd binds to the regulatory region of integrin-coding gene, mew, which codes for PS1, a key integrin of the ISCs. In support to a possible role of integrins in Yki-driven ISC tumors, we show that genetic downregulation of mew arrests Yki-driven ISC proliferation, reminiscent of the effects of TONDU peptide. Altogether, our findings present a novel platform for screening therapeutic peptides and provide insights into tumor suppression mechanisms. SIGNIFICANCE STATEMENTDiscovering novel strategies to inhibit oncogene activity is a priority in cancer biology. As signaling pathways are widely conserved between mammals and Drosophila, these questions can be effectively addressed in this model organism. Here, we show that progression of Drosophila Intestinal Stem Cell (ISC) tumors induced by gain of an oncogenic form of the transcription co-factor Yki can be suppressed by feeding a peptide corresponding to the conserved TONDU domain of Vestigial (Vg), which blocks binding of Yki to the Sd transcription factor. Further, we show that down regulation of the integrin signaling pathway is causally linked to TONDU-peptide-mediated ISC tumor suppression. Our findings reveal that Drosophila can be successfully used to screen peptides for their therapeutic applications.

cancer biology↗

bioRxiv2019

Transcriptional analysis of sodium valproate in a serotonergic cell line reveals gene regulation through both HDAC inhibition-dependent and independent mechanisms

Sodium valproate (VPA) is a histone deacetylase (HDAC) inhibitor, widely prescribed in the treatment of bipolar disorder, and yet the precise modes of therapeutic action for this drug are not fully understood. After exposure of the rat serotonergic cell line RN46A to VPA, RNA-sequencing (RNA-Seq) analysis showed widespread changes in gene expression. Analysis by multiple pipelines revealed as many as 230 genes were significantly upregulated and 72 genes were significantly downregulated. A subset of 23 differentially expressed genes was selected for validation using the nCounter(R) platform, and of these we obtained robust validation for ADAM23, LSP1, MAOB, MMP13, PAK3, SERPINB2, SNAP91, WNT6, and ZCCHC12. We investigated the effect of lithium on this subset and found four genes, CDKN1C, LSP1, SERPINB2 and WNT6 co-regulated by lithium and VPA. We also explored the effects of other HDAC inhibitors and the VPA analogue valpromide on the subset of 23 selected genes. Expression of eight of these genes, CDKN1C, MAOB, MMP13, NGFR, SHANK3, VGF, WNT6 and ZCCHC12, was modified by HDAC inhibition, whereas others did not appear to respond to several HDAC inhibitors tested. These results suggest VPA may regulate genes through both HDAC-dependent and independent mechanisms. Understanding the broader gene regulatory effects of VPA in this serotonergic cell model should provide insights into how this drug works and whether other HDACi compounds may have similar gene regulatory effects, as well as highlighting molecular processes that may underlie regulation of mood.

genomics↗

bioRxiv2019

dropClust2: An R package for resource efficient analysis of large scale single cell RNA-Seq data

DropClust leverages Locality Sensitive Hashing (LSH) to speed up clustering of large scale single cell expression data. It makes ingenious use of structure persevering sampling and modality based principal component selection to rescue minor cell types. Existing implementation of dropClust involves interfacing with multiple programming languages viz. R, python and C, hindering seamless installation and portability. Here we present dropClust2, a complete R package thats not only fast but also minimally resource intensive. DropClust2 features a novel batch effect removal algorithm that allows integrative analysis of single cell RNA-seq (scRNA-seq) datasets.\n\nAvailability and implementationdropClust2 is freely available at https://debsinha.shinyapps.io/dropClust/ as an online web service and at https://github.com/debsin/dropClust as an R package.

bioinformatics↗

bioRxiv2018

Spatio-Temporal Network Dynamics of Genes Underlying Schizophrenia

Schizophrenia (SZ) is a debilitating mental illness with multigenic etiology and high heritability. Despite extensive genetic studies the molecular etiology stays enigmatic. A systems biology study had suggested a protein-protein interaction (PPI) network for SZ with 504 novel PPIs amongst which several genes happen to be drug targets of existing FDA approved drugs. Although the PPI network presented all possible pairs of interactions (known and novel), it lacks a spatio-temporal information. The onset of psychiatric disorders is predominantly in adolescent and young adult stages, often accompanied by subtle structural abnormalities in multiple regions of the brain. Hence, there is a need to redefine the generic PPI network as a function of time (developmental stages) and space (brain regions). The availability of BrainSpan atlas data allowed us to redefine the SZ interactome as a function of space and time. The absence of non-synonymous variants in centenarians and non-psychiatric ExAC database allowed us to identify the variants of criticality. The expression of candidate genes in different brain regions and during developmental stages, responsible for cognitive processes as well as the onset of disease were studied. A subset of novel interactors detected in the network was further validated using gene-expression data of psychiatric postmortem brains. From the long list of drug targets proposed from the interactome study and based on the microarray gene-expression results, we have shortlisted a probable subset of 10 drug targets (targeted by 34 FDA approved drugs) coalescing into 81 biological pathways, that could be potentially repurposed for neuropsychiatric disorders.

bioinformatics↗

bioRxiv2018

Intronic miRNA Mediated Gene Expression Regulation Controls Protein Crowding Inside the Cell

SUMMARYGene regulatory effects of microRNAs at a posttranscriptional level has been established over the last decade. In this study, we analyze the interaction networks of mRNA translation regulation through intronic miRNA, under various tissue-specific cellular contexts, taking into account the thermodynamic affinity, kinetics, and the presence of competitive interactors. This database, and analysis has been made available through an open-access web-server, miRiam, to promote further exploration.\n\nHere we report that expression of genes involved in Apoptosis Processes, Immune System Processes, Translation Regulator Activities, and Molecular Transport Activities within the cell are predominately regulated by miRNA mediation. Our findings further indicate that this regulatory effect has a profound effect in controlling protein crowding inside the cell. A miRNA mediated gene expression regulation serves as a temporal regulator, allowing the cellular machinery to temporarily pause the translation of mRNA, indicating that the miRNA-mRNA interactions may be important for governing the optimal usage of cell volume.

bioinformatics↗