SUDARSHANA BASU - Academia.edu (original) (raw)

Papers by SUDARSHANA BASU

Early-Onset Colorectal Carcinoma (EOCRC) is a growing concern as reports indicate a worldwide inc... more Early-Onset Colorectal Carcinoma (EOCRC) is a growing concern as reports indicate a worldwide increase in the incidence of CRC among young adults (<50 years old). In an effort to understand the different mode of pathogenesis in young-onset CRC, we performed a pilot study wherein we looked at colorectal tumors from both young (< 50 years old) and old patients (>55 years old) and screened them to eliminate tumors positive for Microsatellite Instability (MSI) and showing activation of the Wnt pathway, known canonical factors in CRC pathogenesis. RNA isolated from EOCRC and Late-Onset (LOCRC) tumors and paired normal tissues without MSI, nuclear β-catenin and APC mutations were sent for small RNA seq to identify miRNA alterations between the two subsets. Comparative analysis revealed differential expression of 23 miRNAs specific to EOCRC and 11 miRNAs specific to LOCRC. We validated the top 10 EOCRC DEMs in TCGA-COAD cohorts followed by validation in additional EOCRC and LOCRC ...

Pathology - Research and Practice

Toxicology and Applied Pharmacology, 2022

Chemoresistance is an imminent therapeutic challenge for breast cancer. Previous evidence suggest... more Chemoresistance is an imminent therapeutic challenge for breast cancer. Previous evidence suggests that breast cancer stem cells (BCSC) develop resistance through upregulation of stemness and chemo-evasion markers viz. SOX2, OCT4, NANOG, MDR1 and CD44, following anticancer chemotherapeutic treatments. Early studies suggest an inhibitory role of Kaempferol in BCSC propagation through downregulation of epithelial to mesenchymal transition. We hypothesized that the pathway involved in chemoresistance could be effectively addressed through Kaempferol (K), alone or in combination with Verapamil (V), which is an inhibitor of MDR1. We used K in combination with V, in multiple assays to determine if there was an inhibitory effect on BCSC. Both K and KV attenuated pH-dependent mammosphere formation in primary BCSC and MDA-MB-231 cells. RNA and protein (immunocytochemistry, western blot) expression of candidate markers viz. SOX2, OCT4, NANOG, MDR1 and CD44 were carried out in the presence or absence of candidate drugs in ex-vivo grown primary BCSC and MDA-MB-231 cell line. Immunoprecipitation assay, cell cycle analysis was carried out in MDA-MB-231. Our candidate drugs were not only anti-proliferative, but also downregulated candidate genes expression at RNA and protein level in both settings, with more robust efficacy in KV treatment than K; induced G2/M dependent cell cycle arrest, and interrupted physical association of CD44 with NANOG as well as MDR1 in MDA-MB-231. In primary tumor explant but not in adjacent normal tissue, our candidate drugs K and KV induced robust γH2AX expression. Thus, our candidate drugs are effective in attenuating BCSC survival.

JOURNAL OF CLINICAL AND BIOMEDICAL SCIENCES

This article reviews and compares various currently available non-invasive, molecular biomarker-b... more This article reviews and compares various currently available non-invasive, molecular biomarker-based tests for bladder cancer (BC) detection, and evaluates other potential molecules that may be used for BC diagnosis and surveillance. Currently, urinary cytology and periodic cystoscopies are clinically recommended for the diagnosis and monitoring of BC. Though highly specific, urinary cytology lacks sensitivity, whereas cystoscopies are invasive tests that are uncomfortable for the patient. Molecular biomarkers associated with BC progression form the basis for various available non-invasive tests. Urinary proteins like NMP22, MCM5 and Human complement factor-H related protein (BTA) are detected by ELISA/Immunochromatographic assay devices (NMP22, BTA, ADXBLADDER). Chromosomal abnormalities reported in BC-aneuploidy in chromosomes 3, 7, and 17 and deletions in chromosome 9-are detected by the Fluorescence in situ Hybridization based UroVysion test. Tumor antigens like sulfated mucin glycoproteins and glycosylated CEA help to light up urothelial carcinoma cells exfoliated into urine (uCyt+). Mutations in TERTp, FGFR3, KRAS, HRAS, TP53, CDKN2A, ERBB2 and PIK3CA contribute to BC progression and these are detected in tumor DNA by RT-qPCR, NGS and/or Sanger sequencing-based assays (Uromonitor, UroSEEK, AssureMDX). mRNA levels of genomic markers frequently deregulated in BC like IGFBP5, HOXA13, MDK, CDC2, CXCR5, IGF2, ABL1, CRH, UPK1B and ANXA10 are assesed by CxBladder and Xpert Bladder Cancer Monitor. BC associated changes in DNA methylation are detected by real time PCR and NGS based assays (EpiCheck, UroMark, AssureMDX). These tests have not yet been formally indicted into clinical practice but can serve as sensitive indicators for early diagnosis, disease monitoring, and treatment response in BC.

Leishmania, a dimorphic protozoan parasite of the order kinetoplastida is the causative agent for... more Leishmania, a dimorphic protozoan parasite of the order kinetoplastida is the causative agent for a large number of diseases ranging from self-healing skin ulcers to severe pathologies associated with visceral leishmaniasis. The parasite exists as a flagellated mobile promastigote form in the sand-fly vector and as a sessile amastigote form in the mammalian host. The transformation from one form to the other occurs in the phagolysosomal compartment of host macrophages. One characteristic feature of these parasites is that, their mitochondrial genome does not have any tRNA encoding genes. Therefore, to carry out mitochondrial protein synthesis, the entire set of tRNAs have to be imported into the mitochondria from the cytosol. An in vitro assay system had been previously developed in this laboratory using purified Leishmania mitochondria (311,313,328). This assay system demonstrated that mitochondrial tRNA import in Leishmania is ATP dependent and driven by the proton motive force ge...

miR-122 is a liver specific miRNA that plays an important role in controlling metabolic homeostas... more miR-122 is a liver specific miRNA that plays an important role in controlling metabolic homeostasis in mammalian liver cells. Interestingly, miR-122 on exposure to lipotoxic stress is reduced in liver cells. To fight stress, miRNA processor Dicer1 is depleted to cause reduced miR-122 production and the lowering of miRNA level ensures a better stress response in hepatocytes under lipotoxic stress. Interestingly, lipid droplets, formed in the liver cells on exposure to high fat, ensure cytoplasmic phase separation of Ago2 and prevent interaction of Ago2 with Dicer1. Lipid droplets bind miRNA and enhance miRNA-Ago2 uncoupling and Ago2 phase separation. Loss of interaction between Ago2 and Dicer1 eventually facilitates export and lowering of cellular Dicer1, a process also dependent on the endosomal maturation controller protein Alix, thereby ceasing pre-miRNA processing by Dicer1 in lipid exposed cells. Depletion of lipid droplets by downregulation of Perilipins with siRNAs resulted in...

Leishmania: Current Biology and Control, 2015

Nucleic acids research, 2003

Import of nucleus-encoded tRNAs into the mitochondria of the kinetoplastid protozoon Leishmania i... more Import of nucleus-encoded tRNAs into the mitochondria of the kinetoplastid protozoon Leishmania involves recognition of specific import signals by the membrane-bound import machinery. Multiple signals on different tRNA domains may be present, and further, importable RNAs interact positively (Type I) or negatively (Type II) with one another at the inner membrane in vitro. By co-transfection assays, it is shown here that tRNA(Tyr) (Type I) transiently stimulates the rate of entry of tRNA(Ile) (Type II) into Leishmania mitochondria in transfected cells, and conversely, is inhibited by tRNA(Ile). Truncation and mutagenesis experiments led to the co-localization of the effector and import activities of tRNA(Tyr) to the D domain, and those of tRNA(Ile) to the variable region-T domain (V-T region), indicating that both activities originate from a single RNA-receptor interaction. A third tRNA, human tRNA(Lys), is imported into Leishmania mitochondria in vitro as well as in vivo. This tRNA h...

EMBO reports, 2011

The mechanism of active transport of transfer RNA (tRNA) across membranes is largely unknown. Fac... more The mechanism of active transport of transfer RNA (tRNA) across membranes is largely unknown. Factors mediating the import of tRNA into the kinetoplast mitochondrion of the protozoon Leishmania tropica are organized into a multiprotein RNA import complex (RIC) at the inner membrane. Here, we present the complete characterization of the identities and functions of the subunits of this complex. The complex contains three mitochondrion-and eight nuclear-encoded subunits; six of the latter are necessary and sufficient for import. Antisense-mediated knockdown of essential subunits resulted in the depletion of mitochondrial tRNAs and inhibition of organellar translation. Functional complexes were reconstituted with recombinant subunits expressed in Escherichia coli. Several essential RIC subunits are identical to specific subunits of respiratory complexes. These findings provide new information on the evolution of tRNA import and the foundation for detailed structural and mechanistic studies.

Differentiation, 2003

Differentiation of kinetoplastid protozoa during their complex life cycles is accompanied by step... more Differentiation of kinetoplastid protozoa during their complex life cycles is accompanied by stepwise changes in mitochondrial functions. Recent studies have begun to reveal multilevel post-transcriptional regulatory mechanisms by which the expression of the nuclear and mitochondrially encoded components of respiratory enzymes is coordinated, as well as the identities of some general and gene-specific factors controlling mitochondrial differentiation.

Nucleic acids research, 2014

miRNAs are 20-22 nt long post-transcriptional regulators in metazoan cells that repress protein e... more miRNAs are 20-22 nt long post-transcriptional regulators in metazoan cells that repress protein expression from their target mRNAs. These tiny regulatory RNAs follow tissue and cell-type specific expression pattern, aberrations of which are associated with various diseases. miR-122 is a liver-specific anti-proliferative miRNA that, we found, can be transferred via exosomes between human hepatoma cells, Huh7 and HepG2, grown in co-culture. Exosomal miR-122, expressed and released by Huh7 cells and taken by miR-122 deficient HepG2 cells, was found to be effective in repression of target mRNAs and to reduce growth and proliferation of recipient HepG2 cells. Interestingly, in a reciprocal process, HepG2 secretes Insulin-like Growth Factor 1 (IGF1) that decreases miR-122 expression in Huh7 cells. Our observations suggest existence of a reciprocal interaction between two different hepatic cells with distinct miR-122 expression profiles. This interaction is mediated via intercellular exoso...

Nucleic Acids Research, 2008

The RNA import complex (RIC) from the mitochon- drion of the kinetoplastid protozoan Leishmania t... more The RNA import complex (RIC) from the mitochon- drion of the kinetoplastid protozoan Leishmania tropica contains two subunits that directly bind to import signals on two distinct subsets of tRNA and interact with each other allosterically. What happens to the tRNA subsequent to its loading on the complex is unknown. A third subunit—RIC9—has intrinsic affinity for both types of tRNA