Iyer, R. K. | Search bioRxiv

bioRxiv2025

Modulation of cellular ageing regulates Integrated Stress Response signalling to control blood cell homeostasis

Organismal ageing is associated with a decline in cellular and molecular functions. One of the hallmarks of ageing is stem cell exhaustion which occurs due to dynamic changes in the stem cell - niche microenvironment. Ageing affects stem cell potency impacting self-renewal and differentiation trajectories. Blood cell homeostasis in the hematopoietic system is tightly regulated by a fine balance between stemness and differentiation. Here, we employ the Drosophila hematopoietic organ, the larval lymph gland (LG) to investigate the impact of modulating cellular ageing on organ homeostasis. LG consists of a Posterior Signalling Center (PSC) that acts as a stem cell niche and maintains the prohemocytes housed in the Medullary Zone (MZ). Cortical Zone (CZ) consists of differentiated hemocytes namely plasmatocytes, crystal cells and lamellocytes. Intricate signalling networks active in the PSC and MZ orchestrate and regulate homeostasis. In this study, we characterize the effect of genetic perturbation of the molecular circuitry of ageing locally and systemically to investigate its effect on LG blood cell homeostasis. Genetic modulation of cellular ageing displays traditional hallmarks of ageing validating our model in the LG. Our results indicate that induction of accelerated ageing both locally and systemically leads to a reduction in stem cell niche size, DNA damage accumulation and increased progenitor differentiation whereas decelerated ageing shows an opposite trend. We show that the Integrated Stress Response (ISR) pathway is activated upon inducing accelerated ageing in the LG hemocytes possibly to recoup back to homeostatic conditions. Furthermore, LGs of ISR pathway mutants or upon perturbation of ISR pathway components in prohemocytes show increased blood cell differentiation indicating disruption of homeostasis. Genetic epistasis analysis shows that ectopic over-expression of ISR pathway genes in an accelerated ageing scenario over and above the existing levels can rescue the defects in blood cell homeostasis. Overall, our study explores how modulation of cellular aging locally or systemically can impact tissue homeostasis. Our research paves way to understand the cellular mechanisms underlying an aged versus young stem cell-niche microenvironment and how its abrogation may lead to onset of disease.

developmental biology↗

bioRxiv2021

Exogene: A performant workflow for detecting viral integrations from paired-end next-generation sequencing data

The integration of viruses into the human genome is known to be associated with tumorigenesis in many cancers, but the accurate detection of integration breakpoints from short read sequencing data is made difficult by human-viral homologies, viral genome heterogeneity, coverage limitations, and other factors. To address this, we present Exogene, a sensitive and efficient workflow for detecting viral integrations from paired-end next generation sequencing data. Exogenes read filtering and breakpoint detection strategies yield integration coordinates that are highly concordant with those found in long read validation sets. We demonstrate this concordance across 6 TCGA Hepatocellular carcinoma (HCC) tumor samples, identifying integrations of hepatitis B virus that are validated by long reads. Additionally, we applied Exogene to targeted capture data from 426 previously studied HCC samples, achieving 98.9% concordance with existing methods and identifying 238 high-confidence integrations that were not previously reported. Exogene is applicable to multiple types of paired-end sequence data, including genome, exome, RNA-Seq or targeted capture.

bioinformatics↗

bioRxiv2018

Performance benchmarking of GATK3.8 and GATK4

Use of the Genome Analysis Toolkit (GATK) continues to be the standard practice in genomic variant calling in both research and the clinic. Recently the toolkit has been rapidly evolving. Significant computational performance improvements have been introduced in GATK3.8 through collaboration with Intel in 2017. The first release of GATK4 in early 2018 revealed significant rewrites in the code base, as the stepping stone toward a Spark implementation. As the software continues to be a moving target for optimal deployment in highly productive environments, we present a detailed analysis of these improvements, to help the community stay abreast with changes in performance. We re-evaluated the options previously identified as advantageous, such as threading, parallel garbage collection, I/O options and data-level parallelization. Based on our results, we consider the performance and cost trade-offs of using GATK3.8 and GATK4 for different types of analyses.

bioinformatics↗