Biology subjects

Shukla, P. C.

Publications and source records attributed to Shukla, P. C..

3 recordsLinked to original sources

bioRxiv2025

UCA1 lncRNA represses γ-globin expression by sequestering miR-148b, a key post-transcriptional regulator of BCL11A

Fetal hemoglobin (HbF; 2{gamma}2) reactivation is a promising strategy to ameliorate {beta}-hemoglobinopathies. However, limited understanding of {gamma}-globin (HBG1/2) regulation constrains development of therapeutic interventions. BCL11A, a key transcriptional repressor of {gamma}-globin, is central to HbF silencing during adult erythropoiesis. Here, we identify a new post-transcriptional regulatory mechanism involving the lncRNA-UCA1 and miR-148b that modulates BCL11A expression. Using UCA1 knockdown and overexpression strategies, combined with in vivo crosslinking and transcriptomic analyses, we demonstrate that UCA1 functions as a competing endogenous RNA (ceRNA), sequestering miR-148b and thereby attenuating its repressive effect on BCL11A. In the present study, we have elucidated the physiological significance of this interaction in adult erythroid cells, including CD34 HSPCs and HUDEP-2 cells, in which UCA1 depletion led to robust {gamma}-globin induction, a phenotype recapitulated by miR-148b overexpression. These findings uncover a previously unrecognized lncRNA-miRNA-mRNA regulatory axis and highlight the UCA1/miR-148b axis as a potential therapeutic target for HbF reactivation in {beta}-hemoglobinopathies.

genetics↗

bioRxiv2025

Apolipoprotein E reduces the number and activation of non-invariant Natural Killer T cells

Natural Killer T (NKT) cells, which modulate atherosclerosis, include two groups - invariant (iNKT) and variant (vNKT). These subsets differentially regulate the disease progression. Yet, the role of vNKTs in atherosclerosis remains unclear. We induced atherosclerosis by feeding high-fat diet (HFD) to Apoe-/- and analyzed the vNKTs in the liver and spleen. The vNKTs were termed non-iNKTs since they were negatively selected within the NKT population. Available literature suggests NKTs as lipid-recognizing cells; however, to our surprise, the non-iNKT numbers and phenotype remained unchanged between HFD-fed and chow-fed Apoe-/-. This was a blindsiding and unexpected outcome of the non-iNKTs being unaltered and unaffected with or without HFD, indicating no observable impact of atherosclerosis on these subsets. Albeit remaining unperturbed by atherosclerosis, these non-iNKTs demonstrated an identical but unique increase and upregulated activation in both the chow and HFD-fed Apoe-/-. These results instigated an investigation of the baseline correlation of the non-iNKTs between young C57BL/6 (WT) and Apoe-/-. Previously unknown and confounding results revealed upregulated activation and increased non-iNKT numbers but decreased IL-4+ non-iNKTs in the Apoe-/- compared to WT. Furthermore, HFD-fed WT that developed dyslipidemia, elucidated increased hepatic non-iNKTs and splenic IFN-{gamma}+ non-iNKTs compared to chow-fed WT controls. These results were not perceived in chow and HFD-fed Apoe-/-. Although lipid-responsive, non-iNKTs in Apoe-/- mice failed to respond to lipid stress, unlike those in dyslipidemic WT mice. These findings reveal that loss of Apoe, rather than atherosclerosis itself, drives altered non-iNKT biology. Thus, Apoe deficiency intrinsically dysregulates non-iNKTs, masking disease-associated immune changes. Apoe loss alters non-iNKT number and function, independent of atherosclerosis, and challenges the interpretation of immune responses by NKT subsets in Apoe-/- models. Therefore, this study warrants the use of Apoe null mice in studying NKT cells.

immunology↗

bioRxiv2021

Debunking the "junk": Unraveling the role of lncRNA-miRNA-mRNA networks in fetal hemoglobin regulation

Fetal hemoglobin (HbF) induction is considered to be a promising therapeutic strategy to ameliorate the clinical severity of {beta}-hemoglobin disorders, and has gained a significant amount of attention in recent times. Despite the enormous efforts towards the pharmacological intervention of HbF reactivation, progress has been stymied due to limited understanding of {gamma}-globin gene regulation. In this study, we intended to investigate the implications of lncRNA-associated competing endogenous RNA (ceRNA) interactions in HbF regulation. Probe repurposing strategies for extraction of lncRNA signatures and subsequent in silico analysis on publicly available datasets (GSE13284, GSE71935 and GSE7874) enabled us to identify 46 differentially expressed lncRNAs (DElncRNAs). Further, an optimum set of 11 lncRNAs that could distinguish between high HbF and normal conditions were predicted from these DElncRNAs using supervised machine learning and a stepwise selection model. The candidate lncRNAs were then linked with differentially expressed miRNAs and mRNAs to identify lncRNA-miRNA-mRNA ceRNA networks. The network revealed that 2 lncRNAs (UCA1 and ZEB1-AS1) and 4 miRNAs (hsa-miR-19b-3p,hsa-miR-3646,hsa-miR-937 and hsa-miR-548j) sequentially mediate cross-talk among different signaling pathways which provide novel insights into the lncRNA-mediated regulatory mechanisms, and thus lay the foundation of future studies to identify lncRNA-mediated therapeutic targets for HbF reactivation.

bioinformatics↗