Biology subjects

Dandage, R.

Publications and source records attributed to Dandage, R..

11 recordsLinked to original sources

bioRxiv2026

Recursive mutational robustness in cancer through intra- and inter-genic compensation

Mutational robustness is a fundamental property of biological systems allowing phenotypic stability against genotypic perturbation. At the gene level, this is primarily attributed to inter-genic functional redundancy driven by paralogs. Here, we show that intra-genic functional redundancy, driven by alternatively spliced isoforms, is another prevalent source of mutational robustness. Integrating isoform-resolved pan-cancer genomics and transcriptomics data across tumors and cancer cell lines, we show that alternative isoforms often bypass deleterious somatic mutations. Mutation-skipping isoforms exhibit compensatory upregulation indicative of robustness against deleterious effects, especially in highly expressed genes. We found that intra-genic robustness is strongly associated with perturbation tolerance, is highly context-specific and, notably, can be complemented and augmented recursively by inter-genic robustness. Non-tumour-suppressor genes generally show higher robustness than tumour suppressor genes, and intra-genic compensation of their mutations is associated with worse disease outcome in most cancer types. Furthermore, intra-genic compensation by mutation-skipping isoforms associates with differential isoform usage among proximal interactors, suggesting restorative protein interaction rewiring at isoform-level. Mechanistically, self-transcriptional adaptation (self-TA) following nonsense-mediated decay of perturbed isoforms provides an explanation for the observed up-regulation of mutation-skipping isoforms. Overall, the proposed recursive mutational robustness framework opens new avenues for deeper mechanistic investigation into cancer evolution and identification of selective vulnerabilities in cancer cells. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/727768v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1b0f79aorg.highwire.dtl.DTLVardef@14fa261org.highwire.dtl.DTLVardef@12da16aorg.highwire.dtl.DTLVardef@c03dee_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

Integrated Metabolic Complex Genetic Interaction 1 Network of Chromosome 4p Loss in Basal Breast Cancer

Basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and exhibits a recurrent large chromosomal deletion in chromosome 4p (chr4p). Chr4p loss is associated with poor survival, evolves early in tumorigenesis and confers on cells a proliferative state. Here, we map the integrated metabolic complex genetic interaction network of chr4p in basal breast cancer to identify targetable vulnerabilities. Differential gene expression analysis of patient derived xenografts and cancer cell models revealed that chr4p loss is associated with changes in cellular energetics and reduction/oxidation balance. Analysis of DepMap pooled genome-wide CRISPR-Cas9 screens identified complex genetic interactions specific to chr4p deletion in basal breast cancer cell models. Functional assays revealed that chr4p loss is associated with disrupted mitochondrial respiratory function and reduced glycolytic capacity, suggesting metabolic rewiring. Increased reactive oxygen species and lipid peroxidation compromised antioxidant defense mechanisms. Ultimately, this study sheds light on targeted therapies for basal breast cancer harboring large chromosomal deletions.

genomics↗

bioRxiv2025

PARPAL: PARalog Protein Redistribution using Abundance and Localization in Yeast Database

Whole-genome duplication (WGD) events are common across various organisms however the retention and evolution of WGD paralogs is not fully understood. Quantitative measure of protein redistribution in response to the deletion of their WGD paralog provides insight into sources of gene retention. Here, we describe PARPAL (PARalog Protein Retribution using Abundance and Localization in Yeast), a web database that houses results of high-content screening and deep learning neural network analysis of the redistribution of 164 proteins reflecting how their subcellular localization and protein abundance change in response to their paralog deletion. We interrogated a total of 82 paralog pairs in two genetic backgrounds for a total of [~]3,500 micrographs of [~]460,000 cells. PARPAL also links to other studies on trigenic interactions, protein-protein interactions and protein abundance. PARPAL is available at https://parpal.c3g-app.sd4h.ca and is a valuable resource for the yeast community interested in understanding the retention and evolution of paralogs and can help researchers to investigate protein dynamics of paralogs in other organisms.

systems biology↗

bioRxiv2023

Single-cell imaging of protein dynamics of paralogs reveals mechanisms of gene retention

Gene duplication is common across the tree of life, including yeast and humans, and contributes to genomic robustness. In this study, we examined changes in the subcellular localization and abundance of proteins in response to the deletion of their paralogs originating from the whole-genome duplication event, which is a largely unexplored mechanism of functional divergence. We performed a systematic single-cell imaging analysis of protein dynamics and screened subcellular redistribution of proteins, capturing their localization and abundance changes, providing insight into forces determining paralog retention. Paralogs showed dependency, whereby proteins required their paralog to maintain their native abundance or localization, more often than compensation. Network feature analysis suggested the importance of functional redundancy and rewiring of protein and genetic interactions underlying redistribution response of paralogs. Translation of non-canonical protein isoform emerged as a novel compensatory mechanism. This study provides new insights into paralog retention and evolutionary forces that shape genomes.

systems biology↗

bioRxiv2023

The fitness cost of spurious phosphorylation

The fidelity of signal transduction requires the binding of regulatory molecules to their cognate targets. However, the crowded cell interior risks off-target interactions between proteins that are functionally unrelated. How such off-target interactions impact fitness is not generally known, but quantifying this is required to understand the constraints faced by cell systems as they evolve. Here, we use the model organism S. cerevisiae to inducibly express tyrosine kinases. Because yeast lacks bona fide tyrosine kinases, most of the resulting tyrosine phosphorylation is spurious. This provides a suitable system to measure the impact of artificial protein interactions on fitness. We engineered 44 yeast strains each expressing a tyrosine kinase, and quantitatively analysed their phosphoproteomes. This analysis resulted in [~]30,000 phosphosites mapping to [~]3,500 proteins. Examination of the fitness costs in each strain revealed a strong correlation between the number of spurious pY sites and decreased growth. Moreover, the analysis of pY effects on protein structure and on protein function revealed over 1000 pY events that we predict to be deleterious. However, we also find that a large number of the spurious pY sites have a negligible effect on fitness, possibly because of their low stoichiometry. This result is consistent with our evolutionary analyses demonstrating a lack of phosphotyrosine counter-selection in species with bona fide tyrosine kinases. Taken together, our results suggest that, alongside the risk for toxicity, the cell can tolerate a large degree of non-functional crosstalk as interaction networks evolve.

systems biology↗

bioRxiv2020

Frequent assembly of chimeric complexes in the protein interaction network of an interspecies hybrid

Hybrids between species often show extreme phenotypes, including some that take place at the molecular level. In this study, we investigated the phenotypes of an interspecies diploid hybrid in terms of protein-protein interactions inferred from protein correlation profiling. We used two yeast species, Saccharomyces cerevisiae and Saccharomyces uvarum, which are interfertile, but yet have proteins diverged enough to be differentiated using mass spectrometry. Most of the protein-protein interactions are similar between hybrid and parents, and are consistent with the assembly of chimeric complexes, which we validated using an orthogonal approach for prefoldin complex. We also identify instances of altered protein-protein interactions in the hybrid, for instance in complexes related to proteostasis and in mitochondrial protein complexes. Overall, this study uncovers likely frequent occurrence of chimeric protein complexes with few exceptions, which may result from incompatibilities or imbalances between the parental proteins.

evolutionary biology↗

bioRxiv2020

The specificity of SRC Homology 3 (SH3) domain interactions is modulated by their protein context in vivo

Protein-protein interactions (PPIs) between modular binding domains and their target peptide motifs are thought to largely depend on the intrinsic binding specificities of the domains. By combining deletion, mutation, swapping and shuffling of SRC Homology 3 (SH3) domains and measuring their impact on protein interactions, we find that most SH3s do not autonomously dictate PPI specificity in vivo. The identity of the host protein and the position of the SH3 domains within their host are both critical for PPI specificity, for cellular functions and for key biophysical processes such as phase separation. Our work demonstrates the importance of the interplay between a modular PPI domain such as SH3 and its host protein in establishing specificity to wire PPI networks.Competing Interest StatementThe authors have declared no competing interest.View Full Text

systems biology↗

bioRxiv2019

Paralog dependency indirectly affects the robustness of human cells

Gene duplicates provide protection against loss-of-function mutations. This protective redundancy partly relies on the fact that paralogs carry their functions independently, i.e. the inactivation of one gene copy does not impair the function of the other copy. However, a significant fraction of paralogous proteins may form functionally dependent pairs, for instance through heteromerization. As a consequence, one could expect these heteromeric paralogs to be less protective against deleterious mutations. To test this hypothesis, we examined the fitness landscape of gene loss-of-function by CRISPR-Cas9 in more than 450 human cell lines. Our analysis revealed a robustness landscape of human cells showing regions of higher vulnerability to gene inactivation as a function of key paralog properties. We find that heteromerizing paralogs are indeed less protective than non-heteromeric ones, but this association is largely due to their higher abundance and their larger number of protein-protein interaction partners.

evolutionary biology↗

bioRxiv2019

Distinct metabolic states of a cell guide alternate fates of mutational buffering through altered proteostasis

Changes in metabolism can alter the cellular milieu; can this also change intracellular proteostasis? Since proteostasis can modulate mutational buffering, if change in metabolism has the ability to change proteostasis, arguably, it should also alter mutational buffering. Building on this, we find that altered cellular metabolic states in E. coli buffer distinct mutations. Buffered-mutants had folding problems in vivo and were differently chaperoned in different metabolic states. Notably, this assistance was dependent upon the metabolites and not on the increase in canonical chaperone machineries. Additionally, we were able to reconstitute the folding assistance afforded by metabolites in vitro and propose that changes in metabolite concentrations have the potential to alter proteostasis. Collectively, we unravel that the metabolite pools are bona fide members of proteostasis and aid in mutational buffering. Given the plasticity in cellular metabolism, we posit that metabolic alterations may play an important role in the positive or negative regulation of proteostasis.

biochemistry↗

bioRxiv2018

beditor: A computational workflow for designing libraries of guide RNAs for CRISPR base editing

CRISPR-mediated base editors have opened unique avenues for scar-free genome-wide mutagenesis. Here, we describe a comprehensive computational workflow called beditor that can be broadly adapted for designing guide RNA libraries with a range of CRISPR-mediated base editors, PAM recognition sequences and genomes of many species. Additionally, in order to assist users in selecting the best sets of guide RNAs for their experiments, a priori estimates, called beditor scores are calculated. These beditor scores are intended to select guide RNAs that conform to requirements for optimal base editing: editable base falls within maximum activity window of the CRISPR-mediated base editor and produces non-confounding mutational effects with minimal off-target effects. We demonstrate the utility of the software by designing guide RNAs for base-editing mediated edition of thousands of clinically important human disease mutations.

synthetic biology↗

bioRxiv2017

Differential Strengths Of Molecular Determinants Guide Environment Specific Mutational Fates

Under the influence of selection pressures imposed by natural environments, organisms maintain competitive fitness through underlying molecular evolution of individual genes across the genome. For molecular evolution, how multiple interdependent molecular constraints play a role in determination of fitness under different environmental conditions is largely unknown. Here, using Deep Mutational Scanning (DMS), we quantitated empirical fitness of [~]2000 single site mutants of Gentamicin-resistant gene (GmR). This enabled a systematic investigation of effects of different physical and chemical environments on the fitness landscape of the gene. Molecular constraints of the fitness landscapes seem to bear differential strengths in an environment dependent manner. Among them, conformity of the identified directionalities of the environmental selection pressures with known effects of the environments on protein folding proves that along with substrate binding, protein stability is the common strong constraint of the fitness landscape. Our study thus provides mechanistic insights into the molecular constraints that allow accessibility of mutational fates in environment dependent manner.\n\nAuthor SummaryEnvironmental conditions play a central role in both organismal adaptations and underlying molecular evolution. Understanding of environmental effects on evolution of genotype is still lacking a depth of mechanistic insights needed to assist much needed ability to forecast mutational fates. Here, we address this issue by culminating high throughput mutational scanning using deep sequencing. This approach allowed comprehensive mechanistic investigation of environmental effects on molecular evolution. We monitored effects of various physical and chemical environments onto single site mutants of model antibiotic resistant gene. Alongside, to get mechanistic understanding, we identified multiple molecular constraints which contribute to various degrees in determining the resulting survivabilities of mutants. Across all tested environments, we find that along with substrate binding, protein stability stands out as the common strong constraints. Remarkable direct dependence of the environmental fitness effects on the type of environmental alteration of protein folding further proves that protein stability is the major constraint of the gene. So, our findings reveal that under the influence of environmental conditions, mutational fates are channeled by various degrees of strengths of underlying molecular constraints.

evolutionary biology↗