Biology subjects

Goswami, S.

Publications and source records attributed to Goswami, S..

42 records · Page 3Linked to original sources

bioRxiv2020

Role of RBC membrane protein palmitoylation in regulation of molecular topology and susceptibility to Plasmodium falciparum invasion

Squeezability of biconcave RBC raises a fundamental query, about, how it can restructure its bendable cytoskeleton for efficient micro-circulation. We report for the first time, the existence of dynamic palmitoylome in RBC composed of 118 palmitoylated proteins that reduced to 42 upon treatment with 2BP, a generic inhibitor of palmitoylation. In-depth analysis revealed that Semaphorin7A, CR1 and ABCB6, the known RBC receptors for P. falciparum were reduced to negligible in 2BP-treated RBCs, suggesting palmitoylation-dependent recruitment of parasite-specific receptors. Interestingly, Kell, a single disulphide-linked co-partner in Kell-Kx complex was undetected in 2BP-treated RBCs, while Kx remained intact. RBCs-blocked with anti-Kell antibody demonstrated signficant reduction in parasite invasion, thus suggesting it as a receptor proto-type for P. falciparum invasion. Finally, reduced expression of Kell in palmitoylated protein pool of sickle-cell RBC ghost, with its diminished surface representation in these RBCs, proposed Kell, as one of the novel receptor-prototype for P. falciparum invasion.

cell biology↗

bioRxiv2019

GO: A functional reporter system to identify and enrich base editing activity

Base editing (BE) is a powerful tool for engineering single nucleotide variants (SNVs) and has been used to create targeted mutations in cell lines, organoids, and animal models. Recent development of new BE enzymes has provided an extensive toolkit for genome modification; however, identifying and isolating edited cells for analysis has proven challenging. Here we report a "Gene On" (GO) reporter system that indicates precise cytosine or adenine base editing in situ with high sensitivity and specificity. We test GO using an activatable GFP and use it to measure the kinetics, efficiency, and PAM specificity of a range of new BE variants. Further, GO is flexible and can be easily adapted to induce expression of numerous genetically encoded markers, antibiotic resistance genes, or enzymes such as Cre recombinase. With these tools, GO can be exploited to functionally link BE events at endogenous genomic loci to cellular enzymatic activities in human and mouse cell lines and organoids. Thus, GO provides a powerful approach to increase the practicality and feasibility of implementing CRISPR BE in biomedical research.

bioengineering↗

bioRxiv2019

An in vivo KRAS allelic series reveals distinct phenotypes of common oncogenic variants

KRAS is the most frequently mutated oncogene in cancer. Tumor sequencing has revealed a complex spectrum of KRAS mutations across different cancer types, yet there is little understanding how specific KRAS alterations impact tumor in initiation, progression, or therapy response. Using high-fidelity CRISPR-based engineering, we created an allelic series of new LSL-Kras mutant mice, reflecting codon 12 and 13 mutations that are highly prevalent in lung (KRASG12C), pancreas (KRASG12R) and colon (KRASG13D) cancers. Induction of each mutation in the developing mouse pancreas reveal striking quantitative and qualitative differences in the degree of ductal transformation and pre-malignant progression. Further, using organoid models we show that KRASG13D mutants respond to EGFR inhibition, while the anti-proliferative effect of KRASG12C-selective inhibitors can be overcome by upstream EGFR signaling. Together, these new mouse strains provide an ideal for investigating KRAS biology in vivo, and for developing pre-clinical precision oncology models of KRAS-mutant pancreas (G12R), colon (G13D), and lung (G12C) cancers.

cancer biology↗

bioRxiv2019

Tankyrase inhibition sensitizes cells to CDK4 blockade

Tankyrase (TNKS) 1/2 are positive regulators of WNT signaling by controlling the activity of the {beta}-catenin destruction complex. TNKS inhibitors provide an opportunity to suppress hyperactive WNT signaling in tumors, however, they have shown limited anti-proliferative activity as a monotherapy in human cancer cell lines. Here we perform a kinome-focused CRISPR screen to identify potential effective drug combinations with TNKS inhibition. We show that the loss of CDK4, but not CDK6, synergizes with TNKS1/2 blockade to drive G1 cell cycle arrest and senescence. Through precise modelling of cancer-associated mutations using cytidine base editors, we show that this therapeutic approach is absolutely dependent on suppression of canonical WNT signaling by TNKS inhibitors and is effective in cells from multiple epithelial cancer types. Together, our results suggest that combined WNT and CDK4 inhibition might provide a potential therapeutic strategy for difficult-to-treat epithelial tumors.

cancer biology↗

bioRxiv2018

An optimized toolkit for precision base editing

CRISPR base editing is a potentially powerful technology that enables the creation of genetic mutations with single base pair resolution. By re-engineering both DNA and protein sequences, we developed a collection of constitutive and inducible base editing vector systems that dramatically improve the ease and efficiency by which single nucleotide variants can be created. This new toolkit is effective in a wide range of model systems, and provides a means for efficient in vivo somatic base editing.

bioengineering↗

bioRxiv2017

Five years of land surface phenology in a large-scale flooding and draining manipulation in a coastal Arctic ecosystem

This study was motivated by the knowledge gap for observing the complex interplay between surface hydrology and plant phenology in arctic landscapes and was conducted as part of a large scale, multi investigator flooding and draining experiment near Barrow, Alaska (71{degrees}1701\" N, 156{degrees}3548\" W) during 2005 - 2009. Hyperspectral reflectance data were collected in the visible to near IR region of the spectrum using a robotic tram system that operated along a 300m transects during the snow free growing period between June and August, 2005-09. Interannual patterns of land-surface phenology (NDVI) unexpectedly lacked marked differences under experimental conditions. Measurement of NDVI was, however, compromised for presence of surface water. Land-surface phenology and surface water was negatively correlated, which held when scaled to a 2km by 2km MODIS subset of the study area. This result suggested that published findings of greening of the Arctic may relate to a drying of the Arctic i.e. reduced surface water in vegetated high-latitude landscapes where surface water is close to ground level.

ecology↗