Biology subjects

Venugopalan, A.

Publications and source records attributed to Venugopalan, A..

5 recordsLinked to original sources

bioRxiv2026

A Duplicate Resolved Paddlefish Genome Provides Insights into the Mechanisms of Rediploidisation and Hox Cluster Evolution

Whole-genome duplication (WGD; or polyploidy) has played a major role in the evolution of many lineages however, our understanding of the processes that shape genome evolution following WGD remains incomplete. While polyploidy duplicates the entire genome sequence, it is rediploidisation that establishes independent duplicated genes. Rediploidisation proceeds through suppression of meiotic recombination across polysomic loci thus restoring disomic inheritance, a process that is not synchronised across the genome. Despite its importance, the mechanisms underlying this process remain poorly understood. The slowly evolving genomes of paleopolyploid Acipenseriformes paddlefish and sturgeon provide an invaluable system for investigating this, as rediploidisation was highly asynchronous in these lineages. In both genomes ohnologs tend to segregate into blocks on the chromosomes according to rediploidisation timing, a pattern that suggests links between chromosomal structure and rediploidisation. Here, we analyse a newly-produced duplicate-resolved paddlefish genome assembly and show a strong concordance between genome rearrangement and rediploidisation timing. We also find that topologically associated domain (TAD) boundaries are associated with rediploidisation block boundaries. Together these results indicate that rediploidisation in acipenseriformes occurred through a process of genome rearrangements that was subject to functional constraints imposed by 3D genome architecture. We investigate the evolution of Hox clusters in these lineages, revealing a previously overlooked duplicate HoxC region in paddlefish, and both ancestral and lineage-specific Hox cluster rediploidisation with substantially different timings. These findings highlight a complex evolutionary history following WGD in Acipenseriformes with implications for understanding short-term adaptations to polyploidy as well as longer-term diversification of lineages.

evolutionary biology↗

bioRxiv2024

Animal-encoded nonribosomal pathway to bursatellin analogs.

The bursatellin-oxazinin family is a series of tyrosine-derived, nitrile-containing marine natural products from gastro-pod and bivalve molluscs. Although the first analogs were identified and associated with toxicity forty years ago, their biosynthetic origins were unknown. During an investigation of published mollusc genomes and transcriptomes, we serendipitously identified a putative bursatellin biosynthetic gene cluster (referred hereafter as the bur-ox pathway). Through biochemical characterization of some bur-ox genes, we provide evidence suggesting that bursatellin-type metabolites are produced by molluscs themselves rather than by their microbial symbionts. We show that the reductive domain from a monomodular nonribosomal peptide synthetase (NRPS) protein FmtATR performs a four-electron reduction to produce tyrosinols from tyrosine derivatives. Moreover, an aminocarboxypro-pyltransferase enzyme, ACT, uses S-adenosylmethionine (SAM) to transform tyrosinols into their phenolic homoserine ethers, which in bursatellin is further modified to the nitrile. Widespread occurrence of bur-ox in molluscs suggests a common biosynthetic origin for bursatellins and oxazinins as well as an important but currently unidentified physiological role for this metabolite family in molluscs inhabiting diverse ecological niches. Further, the presence of bur-ox pathway homologs in many culinary bivalves such as mussels and geoducks suggests that possible impacts on human consumers should be investigated. As one of the few NRPS pathways of animal origin to be characterized, bur-ox sheds light on underappreciated chemical and biochemical diversity in animals.

biochemistry↗

bioRxiv2024

Single-Stranded DNA with Internal Base Modifications Mediates Highly Efficient Gene Insertion in Primary Cells

Single-stranded DNA (ssDNA) templates along with Cas9 have been used for gene insertion but suffer from low efficiency. Here, we show that ssDNA with chemical modifications in 10-17% of internal bases (eDNA) is compatible with the homologous recombination machinery. Moreover, eDNA templates improve gene insertion by 2-3 fold compared to unmodified and end-modified ssDNA in airway basal stem cells (ABCs), hematopoietic stem and progenitor cells (HSPCs), T-cells and endothelial cells. Over 50% of alleles showed gene insertion in three clinically relevant loci (CFTR, HBB, and CCR5) in ABCs using eDNA and up to 70% of alleles showed gene insertion in the HBB locus in HSPCs. This level of correction is therapeutically relevant and is comparable to adeno-associated virus-based templates. Knocking out TREX1 nuclease improved gene insertion using unmodified ssDNA but not eDNA suggesting that chemical modifications inhibit TREX1. This approach can be used for therapeutic applications and biological modeling.

molecular biology↗

bioRxiv2018

Quantitative mass spectrometry to interrogate proteomic heterogeneity in metastatic lung adenocarcinoma and validate a novel somatic mutation CDK12-G879V

Lung cancer is the leading cause of cancer death both in men and women. Tumor heterogeneity is an impediment to targeted treatment of all cancers, including lung cancer. Here, we sought to characterize changes in tumor proteome and phosphoproteome by longitudinal, prospective collection of tumor tissue of an exceptional responder lung adenocarcinoma patient who survived with metastatic lung adenocarcinoma for more than seven years with HER2-directed therapy in combination with chemotherapy. We employed \"Super-SILAC\" and TMT labeling strategies to quantify the proteome and phosphoproteome of a lung metastatic site and ten different metastatic progressive lymph nodes collected across a span of seven years, including five lymph nodes procured at autopsy. We identified specific signaling networks enriched in lung compared to the lymph node metastatic sites. We correlated the changes in protein abundance with changes in copy number alteration (CNA) and transcript expression. To further interrogate the mass spectrometry data, patient-specific database was built incorporating all the somatic variants identified by whole genome sequencing (WGS) of genomic DNA from the lung, one lymph node metastatic site and blood. An extensive validation pipeline was built for confirmation of variant peptides. We validated 360 spectra corresponding to 55 germline and 6 somatic variant peptides. Targeted MRM assays demonstrated expression of two novel variant somatic peptides, CDK12-G879V and FASN-R1439Q, with expression in lung and lymph node metastatic sites, respectively. CDK12 G879V mutation likely results in a nonfunctional CDK12 kinase and chemotherapy susceptibility in lung metastatic sites. Knockdown of CDK12 in lung adenocarcinoma cells results in increased chemotherapy sensitivity, explaining the complete resolution of the lung metastatic sites in this patient.

cancer biology↗

bioRxiv2018

Integrated proteogenomic analysis of metastatic thoracic tumors identifies APOBEC mutagenesis and copy number alterations as drivers of proteogenomic tumor evolution and heterogeneity

Elucidation of the proteogenomic evolution of metastatic tumors may offer insight into the poor prognosis of patients harboring metastatic disease. We performed whole-exome and transcriptome sequencing, copy number alterations (CNA) and mass spectrometry-based quantitative proteomics of 37 lung adenocarcinoma (LUAD) and thymic carcinoma (TC) metastases obtained by rapid autopsy and found evidence of patient-specific, multi-dimensional heterogeneity. Extreme mutational heterogeneity was evident in a subset of patients whose tumors showed increased APOBEC-signature mutations and expression of APOBEC3 region transcripts compared to patients with lesser mutational heterogeneity. TP53 mutation status was associated with APOBEC hypermutators in our cohort and in three independent LUAD datasets. In a thymic carcinoma patient, extreme heterogeneity and increased APOBEC3AB expression was associated with a high-risk germline APOBEC3AB variant allele. Patients with CNA occurring late in tumor evolution had corresponding changes in gene expression and protein abundance indicating genomic instability as a mechanism of downstream transcriptomic and proteomic heterogeneity between metastases. Across all tumors, proteomic heterogeneity was greater than copy number and transcriptomic heterogeneity. Enrichment of interferon pathways was evident both in the transcriptome and proteome of the tumors enriched for APOBEC mutagenesis despite a heterogeneous immune microenvironment across metastases suggesting a role for the immune microenvironment in the expression of APOBEC transcripts and generation of mutational heterogeneity. The evolving, heterogeneous nature of LUAD and TC, through APOBEC-mutagenesis and CNA illustrate the challenges facing treatment outcomes.

cancer biology↗