Biology subjects

Kirov, S.

Publications and source records attributed to Kirov, S..

5 recordsLinked to original sources

bioRxiv2022

Frameshifts may carry oncogenic potential beyond loss of function and categorize genes role in tumor development

In this work I present evidence that frameshift mutations represent substantial oncogenic potential across multiple tumor types and may change our understanding of the function of some genes with well established tumor suppressor. I analyzed data deposited in Cbio portal and show that frameshifts, even when they result in the removal of a substantial part of a protein have the potential to create recurring large domains with unknown function. Based on this analysis I propose a novel categorization of genes according to their association with cancer that is more reflective of a complex nature that goes beyond the simple division to tumor suppressors and oncogenes.

genomics↗

bioRxiv2022

Cholinergic forebrain activation improves cognition, boosts neurotrophin receptors, and lowers Aβ42 levels in the cerebral cortex of 5xFAD mice.

The biological basis of Alzheimers dementia has been hypothesized in terms of basal forebrain cholinergic decline, and in terms reflecting the neuropathologies surrounding beta amyloid and tau. To shed light on the contributions of these different biological elements, we performed five month intermittent stimulation of the basal forebrain, which projects to the cortical mantle, in 5xFAD Alzheimers model mice and wild-type littermates, and subjected mice to behavioral testing and tissue analysis. The 5xFAD mice performed worse in water maze testing than their littermates. Stimulation improved both classes of mice, and removed performance differences between genotypes by the fifth testing day. Stimulated groups had two to four-fold increases in immunoblot measures of each of the neurotrophin receptors tropomyosin receptor kinase A and B. Stimulation also led to lower tissue A{beta}42 and beta amyloid cleavage enzyme 1 in 5xFAD mice. Despite the lack of strong direct projections from the basal forebrain stimulation region to the hippocampus, the hippocampal tissues in stimulated mice had more nerve growth factor receptor, and lower levels of beta secretase for amyloid. These data support a causal relation between forebrain cholinergic pathways and cognitive decline dependent on A{beta}42. Activation of cholinergic brain pathways improves neurotrophin pathways and reduces A{beta}42 accumulation. The recruitment of both classes of neurotrophin receptors in the process suggests a serine protease cleavage intermediary between cholinergic response and neurotrophin activation.

neuroscience↗

bioRxiv2020

Mis-annotated multi nucleotide variants in public cancer genomics datasets can lead to inaccurate mutation calls with significant implications

BackgroundNext generation sequencing is widely used in cancer to profile tumors and detect variants. Most somatic variant callers used in these pipelines identify variants at the lowest possible granularity - single nucleotide variants (SNVs). As a result, multiple adjacent SNVs are called individually instead of as a multi-nucleotide variant (MNV). The problem with this level of granularity is that the amino acid change from the individual SNVs within a codon could be different from the amino acid change based on the MNV that results from combining the SNVs. Most variant annotation tools do not account for this, leading to incorrect conclusions about the downstream effects of the variants. MethodHere, we used Variant Call Files (VCFs) from the TCGA Mutect2 caller, and developed a solution to merge SNVs to MNVs. Our custom script takes the phasing information from the SNV VCFs and based on a gene model, determines if SNVs are at the same codon and need to be merged into a MNV prior to variant annotation. ResultsWe analyzed 10,383 VCFs from TCGA and found 12,141 MNVs that were incorrectly annotated. Strikingly, the analysis of seven commonly mutated genes from 178 studies from cBioPortal revealed that MNVs were consistently missed in 20 of these studies, while they were correctly annotated in 15 more recent studies. The best and most common example of MNVs was found at the BRAF V600 locus, where several public datasets reported separate BRAF V600E and BRAF V600M variants, instead of a single merged V600K variant. ConclusionWhile some datasets merged MNVs correctly, many public datasets have not been corrected for this problem. As a best practice for variant calling, we recommend that MNVs be accounted for in NGS processing pipelines, thus improving analyses on the impact of somatic variants in cancer genomics.

genomics↗

bioRxiv2019

Bioinformatic Methods and Bridging of Assay Results for Reliable Tumor Mutational Burden Assessment in Non-Small Cell Lung Cancer

IntroductionTumor mutational burden (TMB) has emerged as a clinically relevant biomarker that may be associated with immune checkpoint inhibitor efficacy. Standardization of TMB measurement is essential for implementing diagnostic tools to guide treatment.\n\nObjectiveHere we describe the in-depth evaluation of bioinformatic TMB analysis by whole exome sequencing (WES) in formalin-fixed, paraffin-embedded samples from a phase 3 clinical trial.\n\nMethodsIn the CheckMate 026 clinical trial, TMB was retrospectively assessed in 312 patients with non-small cell lung cancer (58% of the intent-to-treat population) who received first-line nivolumab treatment or standard-of-care chemotherapy. We examined the sensitivity of TMB assessment to bioinformatic filtering methods and assessed concordance between TMB data derived by WES and the FoundationOne(R) CDx assay.\n\nResultsTMB scores comprising synonymous, indel, frameshift, and nonsense mutations (all mutations) were 3.1-fold higher than data including missense mutations only, but values were highly correlated (Spearmans r = 0.99). Scores from CheckMate 026 samples including missense mutations only were similar to those generated from data in The Cancer Genome Atlas, but those including all mutations were generally higher. Using databases for germline subtraction (instead of matched controls) showed a trend for race-dependent increases in TMB scores. WES and FoundationOne CDx outputs were highly correlated (Spearmans r = 0.90).\n\nConclusionsParameter variation can impact TMB calculations, highlighting the need for standardization. Encouragingly, differences between assays could be accounted for by empirical calibration, suggesting that reliable TMB assessment across assays, platforms, and centers is achievable.\n\nKey PointsO_LITumor mutational burden (TMB) is a clinically relevant biomarker for efficacy of immunotherapy in patients with cancer\nC_LIO_LIVariations in TMB assessment parameters can shift the final TMB value. Harmonization and standardization are important to the successful clinical implementation of TMB testing\nC_LIO_LITMB values assessed by different methods are highly correlated. Harmonization of TMB testing in patients with cancer is therefore achievable\nC_LI

bioinformatics↗

bioRxiv2018

Degradation of the extracellular matrix is part of the pathology of ulcerative colitis

The scientific value of re-analyzing existing datasets is often proportional to the complexity of the data. Proteomics data are inherently complex and can be analyzed at many levels, including proteins, peptides, and post-translational modifications to verify and/or develop new hypotheses. In this paper, we present our re-analysis of a previously published study comparing colon biopsy samples from ulcerative colitis (UC) patients to non-affected controls. In addition to confirming and reinforcing the original finding of upregulation of neutrophil extracellular traps (NETs), we report novel findings, including that Extracellular Matrix (ECM) degradation and neutrophil maturation are involved in the pathology of UC. The pharmaceutically most relevant differential protein expressions were confirmed using immunohistochemistry as an orthogonal method. As part of this study, we also compared proteomics data to previously published mRNA expression data. These comparisons indicated compensatory regulation at transcription levels of the ECM proteins we identified and open possible new venues for drug discovery.

molecular biology↗