Biology subjects

Pasupuleti, S.

Publications and source records attributed to Pasupuleti, S..

4 recordsLinked to original sources

bioRxiv2025

Structural variants are enriched in deleterious visible phenotypes in Drosophila

Genome structural variants (SVs) comprise a sizable portion of functionally important genetic variation in all organisms; yet, many SVs evade discovery using short reads. While long-read sequencing can find the hidden SVs, the role of SVs in variation in organismal traits remains largely unclear. To address this gap, we investigate the molecular basis of 50 classical phenotypes in 11 Drosophila melanogaster strains using highly contiguous de novo genome assemblies generated with Oxford Nanopore long reads. These assemblies enabled the creation of a pangenome graph containing comprehensive, nucleotide-resolution maps of SVs, including complex rearrangements such as the interchromosomal inverted duplication Dp(2;4)eyD and large tandem duplications at the Bar locus. We uncovered new candidate causal mutations for 15 phenotypes and new molecular alleles for 2 mutations comprising tandem duplications, transposable element (TE) insertions, and indels. For example, we mapped the tarsal joint defect AblpeyD to an 8 kb Roo retrotransposon insertion into an intergenic enhancer, a finding validated via CRISPR-Cas9. The wing vein phenotype plexus (px1) was linked to a 1.5 kb partial tandem gene duplication, and the century-old Curved (c1) wing phenotype was linked to a 7.5 kb DM412 retrotransposon inserted into the coding sequence of the muscle protein gene Strn-Mlck. We also unveiled 8 SV alleles of previously identified causal genes, including previously uncharacterized SVs underlying the extensively studied white and yellow phenotypes. Overall, 67.4% of the genes causing phenotypic changes harbored candidate SVs over 100 bp, whereas only 28% is expected based on euchromatic SVs. Our data, based on the 50 Drosophila phenotypes, 44 of which are strongly deleterious, suggests a disproportionately larger contribution of SVs to deleterious changes in visible phenotypes in Drosophila.

genomics↗

bioRxiv2025

Hemoglobin alpha regulates T-lymphocyte activation and mitochondrial function

We have recently discovered hemoglobin alpha a1 (Hb-a1 mRNA and Hb protein) in T-lymphocytes and previously reported that its expression was sensitive to mitochondrial redox perturbations. However, outside of its occurrence and basic characterization, the functional role of Hb in T-lymphocytes remained unknown. Herein, we identify Hb in both CD4+ and CD8+ T-lymphocyte subsets, and found its expression is highly dynamic, differs between the two subtypes, and is dependent upon activation stage. Further, the loss of Hb by use of a novel T-lymphocyte-specific Hb knock-out mouse impairs mitochondrial function, dysregulates cytokine production, and lowers the activation threshold primarily in CD4+ T-lymphocytes, indicating a critical role for Hb within this subset. While these data suggested the loss of Hb in T-lymphocytes may promote aberrant activation of autoreactive T-lymphocytes, surprisingly, we discovered that mice lacking Hb in T-lymphocytes exhibited reduced severity of experimental autoimmune encephalomyelitis (EAE) compared to wild-type control animals. Interestingly, T-lymphocytes lacking Hb in vivo appeared to function identically to wild-type controls, which did not explain the protection against EAE. In contrast, T-lymphocyte Hb knock-out mice displayed significantly reduced levels of circulating immunoglobulins and CD40L expression compared to their wild-type counterparts during EAE, suggesting possible impaired intercellular communication. These data elucidate a previously unrecognized role for Hb in T-lymphocyte function, which may have implications for hemoglobin-related diseases (i.e., hemoglobinopathies).

immunology↗

bioRxiv2025

Revealing the nervous system requirements of Alzheimer disease risk genes in Drosophila

Most Alzheimers disease (AD) susceptibility genes have poorly understood roles in the central nervous system (CNS). To address this gap, we systematically characterized 100 conserved candidate AD risk genes using a cross-species strategy in the fruit fly, Drosophila melanogaster. Genes were prioritized based primarily on human functional genomic evidence. We generated custom, loss-of-function alleles for each of the conserved fly orthologs. Most of the genes (80%) are expressed in the adult brain, including 24 neuron- and 13 glia-specific expression patterns. Overall, we identify 50 candidate AD risk gene homologs with requirements for CNS structure or function, including 18 whose loss of function causes neurodegeneration (e.g., Snx6/SNX32 and ClC-a/CLCN1), 35 required for neurophysiology (e.g., Arr1/ARRB2, stai/STMN4), and 8 with diminished CNS resilience following a thermal or mechanical stress (e.g., cindr/CD2AP, Amph/BIN1). In a parallel screen, we found 28 AD risk gene homologs (e.g, Ets98B/SPI1, Yod1/YOD1) that modify the neurotoxicity of either amyloid-{beta} peptide or tau protein, which aggregate to form AD pathology. To translate our findings back to human AD, we developed and deployed oligogenic risk scores based on gene clusters with shared nervous system phenotypes in flies, pinpointing functional pathways that differentially drive AD risk. Our results--available online via the Alzheimers Locus Integrative Cross-species Explorer (alice.nrihub.org)--reveal novel nervous system requirements for dozens of AD risk genes and may enable dissection of causal heterogeneity in AD.

genetics↗

bioRxiv2025

Lemur: A Single-Cell Foundation Model with Fine-Tuning-Free Hierarchical Cell-Type Generation for Drosophila melanogaster

Single-cell genomics has revolutionized our understanding of cellular heterogeneity, but automating its analysis remains an open challenge. Cell-type annotation represents a critical bottleneck, particularly as datasets grow in size and complexity. While foundation models have shown promise in addressing this challenge, existing approaches require extensive fine-tuning for effective cell-type annotation. Here, we present Lemur (Large Expression Model for Understanding scRNA-seq), a single-cell foundation model specifically designed for Drosophila melanogaster. Lemur achieves fine-tuning-free cell-type annotation through comprehensive pre-training on an integrated whole-organism atlas with a unified cell-type annotation schema. To leverage this unified schema, we developed a dedicated hierarchical cell-type decoder architecture. This approach enables Lemur to generate consistent cell-type predictions across multiple levels of granularity without requiring additional training on new datasets. The model demonstrates strong performance across diverse tissue types, experimental conditions, and sequencing technologies. It also achieves batch-effect correction without explicitly training for this task. This automated analysis capability positions Lemur as an effective tool for the fly research community. Beyond its immediate applications, Lemur establishes a framework for accelerating biological discovery. It enables rapid iteration between computational predictions and experimental validation in the highly controlled Drosophila melanogaster system, with potential implications for translational research in human biology, particularly in aging and neurodegenerative disease studies.

bioinformatics↗