Biology subjects

Shukla, N.

Publications and source records attributed to Shukla, N..

27 records · Page 2Linked to original sources

bioRxiv2023

Novel CAF-identifiers via transcriptomic analysis in oral cancer patients

BackgroundCancer-associated fibroblasts (CAFs), a prominent component of the tumor microenvironment, plays an important role in tumor development, invasion, and drug resistance. The expression of distinct "CAF markers," which separates CAFs from normal fibroblasts and epithelial cells, have traditionally been used to identify them. These commonly used CAF markers have been reported to differ greatly across microenvironmental subpopulations even within a cancer site. MethodsUsing an unbiased data analysis approach utilizing publicly available and in-house gene expression data from patient derived novel CAF cells, we identified a collection of markers in oral cancer to distinguish CAF populations from tumor epithelia and normal oral fibroblasts. ResultsCOL1A1, SPARC, COL1A2, COL3A1 and TIMP-1 were identified as potential markers which can be utilized to differentiate cancer associated fibroblast from all other cell types including normal fibroblasts in oral cancer.

cancer biology↗

bioRxiv2022

Clonal evolution during metastatic spread in high-risk neuroblastoma

High-risk neuroblastoma is generally metastatic and often lethal. Using genomic profiling of 470 sequential and spatially separated samples from 283 patients, we characterize subtype-specific genetic evolutionary trajectories from diagnosis, through progression and end-stage metastatic disease. Clonal tracing timed disease initiation to embryogenesis. Continuous acquisition of structural variants at disease defining loci (MYCN, TERT, MDM2-CDK4) followed by convergent evolution of mutations targeting shared pathways emerged as the predominant feature of progression. At diagnosis metastatic clones were already established at distant sites where they could stay dormant, only to cause relapses years later and spread via metastasis-to-metastasis and polyclonal seeding after therapy.

genomics↗

bioRxiv2022

A complex role of Arabidopsis CDKD;3 in meiotic progression and cytokinesis

Meiosis is a specialized cell division that halves the number of chromosomes in two consecutive rounds of chromosome segregation. In angiosperm plants is meiosis followed by mitotic divisions to form rudimentary haploid gametophytes. In Arabidopsis, termination of meiosis and transition to gametophytic development is governed by TDM1 and SMG7 that mediate inhibition of translation. Mutants deficient in this mechanism do not form tetrads, but instead undergo multiple cycles of aberrant nuclear divisions, that are likely caused by the failure to downregulate cyclin dependent kinases during meiotic exit. A suppressor screen to identify genes that contribute to meiotic exit uncovered a mutation in CDKD;3 that alleviates meiotic defects in smg7 deficient plants. The CDKD;3 deficiency prevents aberrant meiotic divisions observed in smg7 mutants, or delays their onset after initiation of cytokinesis, which permits formation of functional microspores. Although CDKD;3 acts as an activator of CDKA;1, the main cyclin dependent kinase that regulates meiosis, cdkd;3 mutation appears to promote meiotic exit independently of CDKA;1. Furthermore, analysis of CDKD;3 interactome revealed enrichment for proteins implicated in cytokinesis suggesting a more complex function of CDKD;3 in cell cycle regulation.

plant biology↗

bioRxiv2022

Expanded ACE2 dependencies of diverse SARS-like coronavirus receptor binding domains

Viral spillover from animal reservoirs can trigger public health crises and cripple the world economy. Knowing which viruses are primed for zoonotic transmission can focus surveillance efforts and mitigation strategies for future pandemics. Successful engagement of receptor protein orthologs is necessary during cross-species transmission. The clade 1 sarbecoviruses including SARS-CoV and SARS-CoV-2 enter cells via engagement of ACE2, while the receptor for clade 2 and clade 3 remains largely uncharacterized. We developed a mixed cell pseudotyped virus infection assay to determine whether various clade 2 and 3 sarbecovirus spike proteins can enter HEK 293T cells expressing human or Rhinolophus horseshoe bat ACE2 proteins. The receptor binding domains from BtKY72 and Khosta-2 used human ACE2 for entry, while BtKY72 and Khosta-1 exhibited widespread use of diverse rhinolophid ACE2s. A lysine at ACE2 position 31 appeared to be a major determinant of the inability of these RBDs to use a certain ACE2 sequence. The ACE2 protein from R. alcyone engaged all known clade 3 and clade 1 receptor binding domains. We observed little use of Rhinolophus ACE2 orthologs by the clade 2 viruses, supporting the likely use of a separate, unknown receptor. Our results suggest that clade 3 sarbecoviruses from Africa and Europe use Rhinolophus ACE2 for entry, and their spike proteins appear primed to contribute to zoonosis under the right conditions.

microbiology↗

bioRxiv2021

Genetic diversity in chimpanzee transcriptomics does not represent wild populations

Chimpanzees (Pan troglodytes) are a genetically diverse species, consisting of 4 highly distinct subspecies. As humans closest living relative they have been a key model organism in the study of human evolution, and comparisons of human and chimpanzee transcriptomes have been widely used to characterise differences in gene expression levels that could underlie the phenotypic differences between the two species. However, the subspecies from which these transcriptomic datasets have been derived is not recorded in metadata available in the public NCBI Sequence Read Archive (SRA). Furthermore, labelling of RNA-seq samples is for the most part inconsistent across studies, and the true number of individuals from whom transcriptomic data is available is difficult to ascertain. Thus we have evaluated genetic diversity at the subspecies and individual level in 486 public RNA-seq samples available in the SRA, spanning the vast majority of public chimpanzee transcriptomic data. Using multiple population genetics approaches we find that nearly all samples (96.6%) have some degree of Western chimpanzee ancestry. At the individual donor level, we identify multiple samples that have been repeatedly analysed across different studies, and identify a total of 135 genetically distinct individuals within our data, a number that falls to 89 when we exclude likely first and second-degree relatives. Altogether, our results show that current transcriptomic data from chimpanzees is capturing low levels of genetic diversity relative to what exists in wild chimpanzee populations. These findings provide important context to current comparative transcriptomics research involving chimpanzees.

genomics↗

bioRxiv2020

Continuous variable response, kinetic gating and connectivity that govern IS topology are perturbed in hyperinsulinemia

Understanding kinetic control of biological processes is as important as identifying components that constitute pathways. Insulin-signaling (IS) is central for almost all metazoans and its perturbations are associated with various diseases and aging. While temporal phosphorylation changes and kinetic constants have provided some insights, constant or variable parameters that establish and maintain signal topology are poorly understood. Our iterative experimental and mathematical simulation-based approaches reveal novel kinetic parameters that encode concentration and nutrient dependent information. Further, we find that pulsatile fasting insulin rewires IS akin to memory and in anticipation of a fed response. Importantly, selective kinetic gating of signals and maximum connectivity, between metabolic and growth-factor arms under normo-insulinemic states, maintains network topology. In addition to unraveling kinetic constraints that determine cascade architecture, our findings will help in identifying novel therapeutic strategies that conserve coupling between metabolic and growth-factor arms, which is lost in diseases and conditions of hyperinsulinemia.

bioinformatics↗

bioRxiv2020

Continuous variable response, kinetic gating and connectivity that determine topology of insulin signaling are perturbed in hyper-insulinemic states

Understanding kinetic control of biological processes is as important as identifying components that constitute pathways. Insulin signaling (IS) is central for almost all metazoans and its perturbations are associated with various diseases and aging. While temporal phosphorylation changes and kinetic constants have provided some insights, constant or variable parameters that establish and maintain signal topology are poorly understood. Our iterative experimental and mathematical simulation-based approaches reveal novel kinetic parameters of IS that encode concentration and nutrient dependent information. Further, we find that pulsatile fasting insulin rewires IS akin to memory and in anticipation of a fed response. Importantly, selective kinetic gating of signals and maximum connectivity, between metabolic and growth-factor arms under normo-insulinemic states, maintains network topology. In addition to unraveling kinetic constraints that determine cascade architecture, our findings will help in identifying novel therapeutic strategies that conserve coupling between metabolic and growth-factor arms, which is lost in diseases and conditions of hyperinsulinemia.

systems biology↗

bioRxiv2020

Regulation of peroxisome and lipid droplet hitchhiking by PxdA and the DipA phosphatase

In canonical microtubule-based transport, adaptor proteins link cargos to the molecular motors dynein and kinesin. Recently, an alternative mode of transport known as hitchhiking was discovered, in which a cargo achieves motility by hitching a ride on an already-motile cargo, rather than attaching to a motor protein. Hitchhiking has been best-studied in two filamentous fungi, Aspergillus nidulans and Ustilago maydis. In U. maydis, ribonucleoprotein complexes, peroxisomes, lipid droplets, and endoplasmic reticulum all hitchhike on early endosomes. In A. nidulans, peroxisomes hitchhike using a putative molecular linker, PxdA, that associates with early endosomes. However, whether other organelles use PxdA to hitchhike on early endosomes is unclear, as are the molecular mechanisms that regulate hitchhiking in A. nidulans. Here we find that the proper distribution of lipid droplets, mitochondria and autophagosomes do not require PxdA, suggesting that PxdA is a molecular linker specific to peroxisomes. We also identify two new pxdA alleles, including a point mutation (R2044P) that disrupts PxdAs ability to associate with early endosomes and reduces peroxisome movement. Finally, we identify a novel regulator of peroxisome hitchhiking, the phosphatase DipA. DipA co-localizes with early endosomes and its early endosome-association relies on PxdA.

cell biology↗

bioRxiv2019

Temporal gating of SIRT1 functions by O-GlcNAcylation prevents hyperglycemia and enables physiological transitions in liver

Inefficient fasted-to-refed transitions are known to cause metabolic diseases. Thus, identifying mechanisms that may constitute molecular switches during such physiological transitions become crucial. Specifically, whether nutrients program a relay of interactions in master regulators, such as SIRT1, and affect their stability is underexplored. Here, we elucidate nutrient-dependent O-GlcNAcylation of SIRT1, within its N-terminal domain, as a key determinant of hepatic glucose- and fat-metabolism, and insulin signaling. SIRT1 glycosylation dictates interactions with PPAR/FOXO1/PGC1/SREBP1, to exert a temporal control over transcription of genes during fasted-to-refed transitions. Interestingly, glycosylation-dependent cytosolic export of SIRT1 promotes a transient interaction with AKT and subsequent proteasomal degradation. Loss of glycosylation discomposes these interactions and enhances stability of SIRT1 even upon refeeding, which causes insulin resistance, hyperglycemia and hepatic-inflammation. Aberrant glycosylation of SIRT1 is associated with aging and/or metabolic diseases. Thus, nutrient-dependent glycosylation constrains spatio-temporal dynamics of SIRT1 and gates its functions to maintain metabolic homeostasis.

physiology↗