Biology subjects

Arya, A.

Publications and source records attributed to Arya, A..

6 recordsLinked to original sources

bioRxiv2026

ABCP_finder: A Transformer Embedding-Based Prediction of Anti-Breast Cancer Peptides

Breast cancer remains one of the leading causes of cancer-related deaths among women worldwide. Drug resistance, toxicity, and limited target specificity are the major challenges in the development of effective therapeutics. Anti-breast cancer peptides (ABCPs) have emerged as effective drug candidate due to its low toxicity, high selectivity, and ability to target cancer. However, it is very time consuming and expensive to identify novel ABCPs only through experiment methods. To address this challenge, we developed ABCP_finder, the first dedicated computational framework specifically designed for the prediction of ABCPs using transformer-based protein language model embeddings. Positive and negative datasets were carefully constructed to ensure a biologically meaningful classification task. To prevent the data leakage and realistic evaluation, homology aware train-test split strategy was utilized by using CD-HIT at 30% sequence identity with 80% coverage. Peptide representations were generated using pretrained transformer models, ProtBERT and ESM2, followed by classification using a multilayer perceptron (MLP). Among the tested models, ProtBERT showed superior performance, achieving 93.82% accuracy, 86.88% recall, 90.59% F1-score, 0.8618 MCC, 96.67% AUC, and a Brier Score of 0.0633, demonstrating strong predictive capability under imbalanced conditions. Calibration analysis supported the selection of a 0.7 probability threshold for identifying high confidence ABCPs. Further external validation using xDeep-AcPEP demonstrated that unknown peptide sequences that has been predicted as ABCPs by ABCP_finder are exhibiting favourable IC values. This supports the biological relevance of these unknown peptides. Overall, ABCP_finder provides a reliable and practical platform for large-scale ABCP screening and can significantly accelerate the discovery of novel peptide therapeutics for breast cancer treatment.

bioinformatics↗

bioRxiv2026

Trinucleotide Distribution, Symmetry Elements and Formulation of Mirror Symmetry Index for G4 Motifs

Symmetry elements in nucleic acids are most strongly correlated with sites of biological function; however, their relevance to non-canonical structures remains underexplored. In this study, we demonstrate the presence and significance of trinucleotide symmetry elements within G-quadruplex (G4) motifs. Our central hypothesis is that the intra-strand mirror symmetry of trinucleotides has been evolutionarily selected to facilitate G4 formation builds on the established sequence-structure association of G-quadruplexes and the natural symmetry law governing nucleotide insertion during genome evolution. Using a conserved G4 motif in the first exon of the MTOR gene as a model, we showed remarkable trinucleotide symmetry preservation across primates and broader mammals, with functional G4 regions displaying locally elevated symmetry relative to the codon-biased exonic background. Analysis of experimentally validated oncogenic G4s, including c-MYC, BCL2, VEGF, and KRAS, revealed that mirror and reverse complement symmetries converge around biologically important G4s. To quantify this feature, we formulated two complementary descriptors: the mirror symmetry index (MSI) and its non-palindromic variant (nMSI). Across 14 oncogene-promoter wild-type G4s, the majority scored MSI [≥] 0.80 (mean 0.884), with only the loop-rich ATG7, BCR, and MDM2 motifs falling below this value, and the KRAS promoter G4 reached individual significance against its mononucleotide-preserving null distribution (p = 0.042). Most decisively, each wild-type G4 scored higher on MSI than its experimentally confirmed G4-abolished mutant in 12 of 14 paired comparisons (sign test, p = 0.0065; mean {Delta}MSI = +0.089, mean {Delta}nMSI = +0.192); the two reversals (BCL2 and HIF-1) are attributable to scrambled mutant controls that introduce more balanced trinucleotide compositions rather than to failure of the index. The directional trend was reproduced across three independently published datasets, with nMSI [≥] 0.50 separating G4-forming from non-G4 sequences at 77.8% sensitivity and 100% specificity, although the collective per-sequence signal from mononucleotide-preserving shuffles remained a non-significant trend (Stouffer combined Z = 1.197, p = 0.116). This first report of trinucleotide symmetry in G4 motifs posits that coordinated nucleotide insertion and quadruplet maintenance act as an evolutionary forcing mechanism that pre-organizes single strands for G4 folding.

bioinformatics↗

bioRxiv2026

Disruption of the SYNGAP1 PDZ ligand motif accelerates differentiation of human iPSC-derived GABAergic neurons

SYNGAP1 haploinsufficiency is a leading genetic cause of neurodevelopmental disorders (NDD), including intellectual disability and epileptic encephalopathy. While most studies on SYNGAP1 function have focused on glutamatergic neurons, its role in GABAergic neurons and during early neuronal development is unclear. Using human iPSC-derived GABAergic neurons, we demonstrate that SYNGAP1 haploinsufficiency accelerates neuronal maturation, characterized by increased dendritic length, synaptic density, and maturation of synaptic structures. Disruption of the isoform-specific SYNGAP1 PDZ binding motif reproduces these phenotypes, highlighting the critical role of PDZ-mediated interactions in regulating GABAergic neuronal differentiation. Proteomic and phosphoproteomic analyses reveal significant dysregulation of synaptic proteins, RNA processing, and transcriptional control, with a significant increase in postsynaptic density proteins content. RNA-seq analysis suggest that the acceleration in neuronal differentiation starts few hours after neuronal induction setting a path to a faster neuronal and synapse maturation. These findings establish that SYNGAP1 acts as a key regulator of neuronal differentiation across both excitatory and inhibitory neurons. Our work underscores the importance of the SYNGAP1 PDZ ligand motif for normal neuronal development and suggests translational strategies targeting SYNGAP1 alpha1 isoform levels to mitigate SYNGAP1-related NDD.

neuroscience↗

bioRxiv2025

An image-based CRISPR screen reveals splicing-mediated control of HP1α condensates

Heterochromatin Protein 1 (HP1) is a fundamental component of constitutive heterochromatin, forming subnuclear condensates whose regulation and function remain poorly understood. Here, we present an image-based CRISPR screen targeting nuclear factors that identifies splicing as a pivotal pathway regulating HP1 condensates. We discovered that unspliced intronic RNA modulates HP1 condensates by interacting co-transcriptionally with HP1. By modulating the intron content, RNA processing restricts HP1-RNA interactions at chromatin, thus enabling heterochromatin organization. Disruption of HP1 condensates due to enhanced interactions with unspliced RNA leads to loss of heterochromatin and the activation of stress response protective genes. We propose that RNA is a central component of heterochromatin that modulates HP1 condensates, and that RNA processing enzymes act as a surveillance mechanism for condensates by dynamically regulating the network of multi-valent interactions between RNA and chromatin factors. This model underscores the crosstalk between chromatin organization, transcription, and RNA processing, potentially governing broader nuclear functions.

genetics↗

bioRxiv2024

Twinfilin is a non-processive depolymerase which synergizes with formin to dramatically accelerate actin filament uncapping by 300-fold

Cellular actin networks assemble by actin filament elongation at barbed ends and are thought to disassemble primarily by depolymerization at filament pointed ends. Contrary to this conventional understanding of actin dynamics, twinfilin was recently shown to promote barbed-end depolymerization. Twinfilin has additionally been suggested to sequester monomers and cap as well as uncap filament barbed ends. As a result, the exact mechanisms by which twinfilin affects barbed-end dynamics remain controversial. Using multicolor single-molecule microscopy, we show that both mouse and yeast twinfilin are non-processive depolymerases that interact only transiently with barbed ends ([~]0.2-0.5 s). Each twinfilin binding event, on average, results in the removal of one or two actin subunits. At CP-capped barbed ends, twinfilin synergizes with formin to accelerate uncapping by up to [~]320-fold. We find that uncapping by twinfilin, alone and together with formin, depends on the nucleotide state of the filament, with the two proteins causing a much more modest enhancement of uncapping of newly assembled filaments. Our study thus establishes twinfilin as a multifunctional barbed-end binding protein capable of non-processively depolymerizing, transiently capping, and synergizing with formin to rapidly uncap actin filament barbed ends.

biochemistry↗

bioRxiv2022

High Throughput Chromosome Conformation Capture identifies differential genome organization in virulent and avirulent strains of Mycobacterium tuberculosis

Recent studies have shown that three-dimensional architecture of bacterial chromatin plays an important role in gene expression regulation. However, genome topological organization in Mycobacterium tuberculosis (M. tuberculosis), the etiologic agent of tuberculosis, remains unknown. On the other hand, exact mechanism of differential pathogenesis in the canonical strains of M. tuberculosis H37Rv and H37Ra remains poorly understood in terms of their raw sequences. In this context, a detailed contact map from a Hi-C experiment is a candidate for what bridges the gap. Here we present the first comprehensive report on genome-wide contact maps between regions of H37Rv and H37Ra genomes. We tracked differences between the genome architectures of H37Rv and H37Ra, which could possibly explain the virulence attenuation in H37Ra. We confirm the existence of a differential organization between the two strains most significantly a higher Chromosome Interacting Domain (CID) size in attenuated H37Ra strain. CID boundaries are also found enriched with highly expressed genes and with higher operon density in H37Rv. Furthermore, most of the differentially expressed PE/PPE genes were present near the CID boundaries in H37Rv and not in H37Ra. Collectively our study proposes a differential genomic topological pattern between H37Rv and H37Ra, which could explain the virulence attenuation in H37Ra.

genomics↗