Biology subjects

Seetharaman, A.

Publications and source records attributed to Seetharaman, A..

4 recordsLinked to original sources

bioRxiv2026

Targeting AXL Overcomes Adaptive Resistance to KRAS Inhibition in KRAS-Driven Cancer

Direct KRAS inhibitors have established mutant KRAS as a clinically actionable target, yet adaptive resistance remains a major barrier to durable responses. To identify therapeutically actionable resistance mechanisms, we performed an unbiased in vivo CRISPR activation screen in an autochthonous lung adenocarcinoma model, identifying the receptor tyrosine kinase AXL as a dominant adaptive resistance driver. Pharmacologic AXL inhibition enhanced the efficacy of both allele-specific inhibition and the RAS(ON) multi-selective inhibitor daraxonrasib across lung and pancreatic cancer models, resulting in deeper and more durable suppression of MAPK signaling and improved tumor control. Beyond tumor-intrinsic effects, combined KRAS and AXL inhibition remodeled the tumor immune microenvironment, promoting an IFN{gamma}-responsive program, increased recruitment of cytotoxic T cells and sensitization to FAS-mediated apoptosis. Collectively, our findings identify AXL as a convergence point for adaptive resistance to KRAS inhibition and provide a mechanistically informed combination strategy to extend the durability of KRAS-directed therapies. Statement of SignificanceAn unbiased in vivo functional (CRISPR activation) screen identifies AXL as a convergence point for adaptive resistance to KRAS inhibition. By integrating adaptive response to KRAS inhibition with anti-tumor immunity, AXL represents a mechanistically actionable vulnerability whose inhibition deepens and prolongs responses to both allele-specific and pan-KRAS-targeted therapies.

cancer biology↗

bioRxiv2024

Caenorhabditis elegans SynMuv B gene activity is down-regulated during a viral infection to enhance RNA interference

Small RNA pathways regulate eukaryotic antiviral defense. Many of the Caenorhabditis elegans mutations that were identified based on their enhanced RNAi, the synMuv B genes, also emerged from unrelated genetic screens for increased growth factor signaling. The dozen synMuv B genes encode homologues of the mammalian dREAM complex found in nearly all animals and plants, which includes the lin-35/retinoblastoma oncogene. We show that a set of highly induced mRNAs in synMuv B mutants is congruent with mRNAs induced by Orsay RNA virus infection of C. elegans. In wild type animals, a combination of a synMuv A mutation and a synMuv B mutation are required for the Muv phenotype of increased growth factor signaling. But we show that Orsay virus infection of a single synMuv A mutant can induce a Muv phenotype, unlike the uninfected single synMuv A mutant. This suggests that decreased synMuv B activity, which activates the antiviral RNAi pathway, is a defense response to viral infection. Small RNA deep sequencing analysis of various dREAM complex mutants uncovers distinct siRNA profiles indicative of such an siRNA response. We conclude that the synMuv B mutants maintain an antiviral readiness state even in the absence of actual infection. The enhanced RNAi and conservation of the dREAM complex mutants suggests new therapeutic avenues to boost antiviral defenses.

genetics↗

bioRxiv2021

Crystal Structures of Ferritin Grown by the Microbatch Method in the Presence of Agarose and Electric Field Shows Enhanced Metal Binding

Ferritin is an ubiquitous iron storage protein found in all kingdoms of life. Ferritin is essential for iron homeostasis and is involved in a wide range of physiological and pathological processes. Several structures of ferritin in complex with small molecules and metal ions have been reported. Here we report the crystal structures of Horse Spleen Ferritin, in which the crystals were grown by employing a novel approach adopting the microbatch experiments performed in the presence and absence of electric field using a 2% agarose pellet of CdSO4. We observed that 1) these structures contain increased number of Cd ions as compared to the crystallization of same protein by others using different methods. 2) The externally applied electric field reduced the number of nucleation and with fewer nucleation the size of the crystals increased. 3) There is no significant conformational change observed among these structures. 4) Irrespective of the externally applied electric field, this agarose microbatch crystallization method facilitates the retaining of increased number of bound metal ions with ferritin to mimic the possible in vivo environment.

biochemistry↗

bioRxiv2017

Evaluation and Design of Genome-wide CRISPR/Cas9 Knockout Screens

The adaptation of CRISPR/Cas9 technology to mammalian cell lines is transforming the study of human functional genomics. Pooled libraries of CRISPR guide RNAs (gRNAs), targeting human protein-coding genes and encoded in viral vectors, have been used to systematically create gene knockouts in a variety of human cancer and immortalized cell lines, in an effort to identify whether these knockouts cause cellular fitness defects. Previous work has shown that CRISPR screens are more sensitive and specific than pooled library shRNA screens in similar assays, but currently there exists significant variability across CRISPR library designs and experimental protocols. In this study, we re-analyze 17 genome-scale knockout screens in human cell lines from three research groups using three different genome-scale gRNA libraries, using the Bayesian Analysis of Gene Essentiality (BAGEL) algorithm to identify essential genes, to refine and expand our previously defined set of human core essential genes, from 360 to 684 genes. We use this expanded set of reference Core Essential Genes (CEG2), plus empirical data from six CRISPR knockout screens, to guide the design of a sequence-optimized gRNA library, the Toronto KnockOut version 3.0 (TKOv3) library. We demonstrate the high effectiveness of the library relative to reference sets of essential and nonessential genes as well as other screens using similar approaches. The optimized TKOv3 library, combined with the CEG2 reference set, provide an efficient, highly optimized platform for performing and assessing gene knockout screens in human cell lines.

systems biology↗