Biology subjects

Abhilash, D.

Publications and source records attributed to Abhilash, D..

3 recordsLinked to original sources

bioRxiv2025

Unraveling Genomic Signatures of lncRNA Expression in Zebrafish Caudal Fin Regeneration: Bridging Regenerative Potential and Positional Memory.

Zebrafish (Danio rerio) is an essential model organism for tissue regeneration, but the function of long non-coding RNAs (lncRNAs) in tissue regeneration is not well understood. Identifying important regeneration-associated lncRNAs may allow for cross-species applications, improving tissue repair in other organisms. However, few studies and a lack of functional validation complicate our understanding of their mechanistic functions. This research explores novel lncRNAs associated with caudal fin regeneration and positional memory, aiming to identify those that are evolutionarily important across species and may hold universal significance. RNA-seq data deposited in the NCBI database were compared at various important time points (0h post-amputation (hpa), 12 hpa, 1 day post-amputation (dpa), two dpa, three dpa, and seven dpa) and fin parts (proximal, middle, and distal) to uncover major regulatory lncRNAs. Using HISAT2, StringTie, FEELnc, Conservation Analysis and WGCNA (Weighted Gene Co-expression Network Analysis), we found 107 lncRNAs related to regeneration time points and 229 about positional memory during regeneration. Overlapping analysis identified 13 common genomic regions that are complete or partial lncRNAs, indicating a functional connection between regeneration and positional identity and expressed differently in each time point and each position. Additionally, a comparison with regeneration-associated mRNAs revealed that these 13 regions play critical roles in both processes, providing insights into the molecular mechanisms of regenerative precision. Following validation by RT-PCR, the results further suggest that these overlapping regions are differentially expressed across distinct positions within the same tissue, despite a consistent injury pattern. This positional variation in expression may indicate potential roles in both evolutionary adaptation and the regulation of regenerative processes across multiple tissues.

genomics↗

bioRxiv2024

Discovery of Novel Long Non-Coding RNAs That May Potentially Play a Role in Zebrafish Brain Regeneration Post Traumatic Injury

Understanding brain regeneration mechanisms is vital for treating neurological conditions. Zebrafish (Danio rerio) are an excellent model due to their genetic similarity to humans and strong regenerative abilities. In this study, we identified novel long non-coding RNAs (lncRNAs) in the regenerating zebrafish brain following traumatic brain injury (TBI). RNA sequencing data of the zebrafish telencephalon from the BioStudies database was analyzed for novel long non-coding RNA expression (lncRNA) at control, one day post-lesion (early wound healing), three days post-lesion (cell proliferation), and 14 days post-lesion (differentiation). We identified 689 potential lncRNAs using HISAT2, StringTie, FEELnc, and PhastCon analysis tools. Principal component analysis (PCA) of identified lncRNAs revealed a distinct expression profile at 1-day post-lesion, indicating their significant role in early wound healing. Weighted Gene Co-expression Network Analysis (WGCNA) identified two modules (brown and turquoise) showing unique expression patterns critical to brain regeneration. Pathway enrichment analysis linked brown module lncRNAs to peptide biosynthesis, cellular amide metabolism, and ribosome biogenesis. In contrast, turquoise module lncRNAs were associated with ion transmembrane transport and cell adhesion pathways. qPCR validation confirmed co-expression patterns of selected lncRNAs and correlated genes, emphasizing their regulatory roles. This study demonstrates that lncRNAs play crucial roles in zebrafish brain regeneration by modulating gene expression during the early wound healing stage. These insights offer potential therapeutic applications of lncRNAs in neuroregenerative medicine.

bioinformatics↗

bioRxiv2021

Molecular signature of postmortem lung tissue from COVID-19 patients suggests distinct trajectories driving mortality

The precise molecular mechanisms behind life-threatening lung abnormalities during severe SARS-CoV-2 infections are still unclear. To address this challenge, we performed whole transcriptome sequencing of lung autopsies from 31 patients suffering from severe COVID-19 related complications and 10 uninfected controls. Using a metatranscriptome analysis of lung tissue samples we identified the existence of two distinct molecular signatures of lethal COVID-19. The dominant "classical" signature (n=23) showed upregulation of unfolded protein response, steroid biosynthesis and complement activation supported by massive metabolic reprogramming leading to characteristic lung damage. The rarer signature (n=8) potentially representing "Cytokine Release Syndrome" (CRS) showed upregulation of cytokines such IL1 and CCL19 but absence of complement activation and muted inflammation. Further, dissecting expression of individual genes within enriched pathways for patient signature suggests heterogeneity in host response to the primary infection. We found that the majority of patients cleared the SARS-CoV-2 infection, but all suffered from acute dysbiosis with characteristic enrichment of opportunistic pathogens such as Staphylococcus cohnii in "classical" patients and Pasteurella multocida in CRS patients. Our results suggest two distinct models of lung pathology in severe COVID-19 patients that can be identified through the status of the complement activation, presence of specific cytokines and characteristic microbiome. This information can be used to design personalized therapy to treat COVID-19 related complications corresponding to patient signature such as using the identified drug molecules or mitigating specific secondary infections.

molecular biology↗