Biology subjects

Chidambaram, S.

Publications and source records attributed to Chidambaram, S..

8 recordsLinked to original sources

bioRxiv2026

HIWI2 Influences Endosomal Trafficking and Eph Receptor Signaling in Photoreceptor Cells

Photoreceptor integrity depends on the precise coordination of membrane trafficking and signal transmission. Despite their well-known roles in germline biology, the functions of PIWI family proteins in post-mitotic neuronal cells remain unclear. We investigated the role of HIWI2 in photoreceptor-derived 661W cells. Silencing of HIWI2 resulted in a significant decrease in the early endosomal marker, Rab5, and its effector EEA1, and reduced expression of the recycling endosome marker Rab11, indicating poor endosomal sorting and receptor recycling. In contrast, the marker for late endosomes, Rab7, was significantly upregulated, suggesting a shift toward degradative trafficking pathways, in line with increased receptor breakdown. These trafficking shifts led to the degradation of EphA2 and EphB2 receptors, as confirmed by a phospho-proteome receptor tyrosine kinase array and further supported by immunoblotting, and were accompanied by a compensatory increase in Akt phosphorylation. Furthermore, HIWI2 deficiency impaired cell motility in wound-healing assays. These results propose HIWI2 as a critical regulator of endosomal sorting and Eph receptor stability, providing a novel link between the PIWI pathway and photoreceptor integrity.

biochemistry↗

bioRxiv2026

Syntaxin-3 regulates Tight Junction Assembly in Human Retinal Pigment Epithelium

The retinal pigment epithelium (RPE) consists of polarized epithelial cells, serving as a support system for photoreceptor maintenance, where the polarity is contributed by the distribution of syntaxins (STX) within the cell. STX3, a known regulator of apical trafficking in epithelial cells, was previously understood to be absent in human RPE cells, with its functions thought to be compensated by STX1A. However, our results on SNARE mRNA expression profile in RPE detected the presence of 2 splice variants of STX3. Further investigation in donor retina, primary hRPE, and ARPE-19 cells revealed detectable levels of STX3 mRNA and protein. STX3 knockdown in ARPE19 resulted in a significant reduction of tight junction (TJ) proteins, compromising TJ assembly, highlighting the critical role of STX3 in maintaining RPE integrity. In addition, immunoprecipitation followed by LC-MS/MS analysis revealed that STX3 and STX1A have a distinct novel protein interactome in RPE. This study identified unique and shared interactants for STX3 and STX1A, suggesting a broader role for RPE beyond its traditional photoreceptor support function. This further emphasises the biological significance of STX1A and STX3 in maintaining retinal homeostasis, which could facilitate the development of novel therapeutic strategies for retinal disorders. SignificanceThis study identified the presence of STX3 in the human RPE cells, which was previously reported to be absent. Further, we demonstrated that STX3 knockdown in ARPE19 cells disrupted TJ assembly, highlighting its potential role in preserving RPE cell polarity and structural integrity, challenging the notion that STX3 functions were thought to be compensated by STX1A. Moreover, immunoprecipitation followed by LC-MS/MS analysis in RPE identified the protein interaction networks of both STX1A and STX3. Interestingly, unique and shared interactants, including proteins associated with neuronal plasticity, indicated unidentified functions of STX3 and STX1A in RPE. This suggests that they might perform both overlapping and distinct functions for maintaining RPE cell integrity and thus retinal homeostasis. Overall, our preliminary findings challenge the established view that STX3 is non-existent in RPE cells and initiate new directions for exploring the multifaceted and potentially non-redundant functions of STX3 in RPE.

cell biology↗

bioRxiv2022

Taking shortcuts: Great for travel, but not for reproducible methods sections

Methods sections are often missing critical details needed to reproduce an experiment. Methodological shortcut citations, in which authors cite previous papers instead of describing the method in detail, may contribute to this problem. This meta-research study used three approaches to systematically examine the use of shortcut citations in neuroscience, biology and psychiatry. First, we examined papers to determine why authors use citations in the methods section and to assess how often shortcut citations were used. Common reasons for using citations in the methods section included explaining how something was done by citing a previous resource that used the method (methodological shortcut citation), giving credit or specifying what was used (who or what citation), and providing context or a justification (why citation). Next, we reviewed 15 papers to determine what can happen when readers follow shortcut citations to find methodological details. While shortcut citations can be used effectively, problems encountered included difficulty identifying or accessing the cited materials, missing or insufficient descriptions of the cited method, and chains of shortcut citations. Third, we examined journal policies. Fewer than one quarter of journals had policies describing how authors should report methods that have been described previously or asking authors to explain modifications of previously described methods. We propose that methodological shortcut citations should meet three criteria; cited resources should describe a method very similar to the authors method, provide enough detail to allow others to implement the method, and be open access. We outline actions that authors and journals can take to use shortcut citations responsibly, while fostering a culture of open and reproducible methods reporting.

neuroscience↗

bioRxiv2022

A novel maxillofacial technique to deliver drugs to the visual pathway, the optic nerve and the retina using the glymphatic system.

The blood neural barriers are formidable barriers that prevent delivery of drugs into the eye and the brain. Currently, large biologics are used for treating many diseases of the eye and the brain. But the blood retinal barrier and the blood brain barrier prevent entry of these useful drugs into the eye and the brain respectively. Hence, there is a need for a drug delivery technique to bypass these natural barriers. Bevacizumab (Avastin) is a full length humanized monoclonal antibody with a molecular weight of 149kda. It binds to circulating vascular endothelial growth factor A and prevents interaction with vascular endothelial growth receptors. This results in blocking endothelial response and tumor vascularization. Bevacizumab is used to prevent choroidal neovascularization in age related macular degeneration and to prevent retinal neovascularization in diabetic retinopathy. It is also used for treating certain types of brain cancer. But it crosses neither the blood retinal barrier nor the blood brain barrier. This in vivo mouse study assessed the delivery of a commercial formulation of bevacizumab into the retina of mice using different ocular techniques like topical drops, subconjunctival injection, intravitreal injection and a novel maxillofacial technique. The objective was to assess whether the novel maxillofacial drug delivery technique could deliver drugs into the retina and to compare the efficacy of the maxillofacial technique with the mentioned ocular techniques. The distribution of bevacizumab was further compared with retinoschisin which is a small protein with a molecular weight of 24kda. Intravitreal injection and maxillofacial technique were effective in delivering drugs into the retina. In addition, the maxillofacial technique could target the brain including regions involved in the visual pathway and the optic nerve. The glymphatic pathway could also be targeted for drug delivery. Drug was also detected in the contralateral optic nerve and retina. Based on our study findings, we propose a new concept to explain the presence of the drug in the contralateral eye. We propose that after maxillofacial drug delivery, early distribution of the drug can occur in the CSF at the optic chiasma from the brain via the glymphatic system. In the case of the intravitreal injection, the drug from the experimental eye may be cleared through the glymphatic pathway of the ipsilateral optic nerve into the CSF surrounding the nerve. The crossover of the ipsilateral optic nerve fibers at the optic chiasma can result in further distribution of the drug in the CSF at the optic chiasma. From the region of the optic chiasma, the drug can distribute into the CSF surrounding the contralateral optic nerve. The drug can be then distributed into the contralateral optic nerve through the glymphatic pathway and be delivered into the contralateral eye. The drug can be further cleared into the aqueous of the contralateral eye through the anterior clearance pathway.

neuroscience↗

bioRxiv2020

Subventricular zone adult mouse neural stem cells and human glioblastoma stem cells require insulin receptor for self-renewal

The insulin receptor (IR) is an evolutionarily conserved signaling protein that regulates development and cellular metabolism. IR signaling regulates neurogenesis in Drosophila; however, a specific role for the IR in maintaining adult neural stem cells (NSCs) in mammals has not been investigated. We show that conditionally deleting the IR reduces adult NSCs of the subventricular zone by [~]70% accompanied by a corresponding increase in progenitors. IR deletion produced hyposmia due to aberrant olfactory bulb neurogenesis. Interestingly, hippocampal neurogenesis was not perturbed nor were hippocampal dependent behaviors. Highly aggressive proneural and mesenchymal glioblastomas (GBMs) had high IR/insulin-like growth factor (IGF) pathway gene expression, and isolated glioma stem cells had an aberrantly high ratio of IR:IGF1R receptors. Moreover, IR knockdown inhibited proneural and mesenchymal GBM tumorsphere growth. Altogether, these data demonstrate that the IR is essential for a subset of normal NSCs as well as for brain tumor cancer stem cell self-renewal.

neuroscience↗

bioRxiv2019

LncRNA Mrhl orchestrates differentiation programs in mouse embryonic stem cells through chromatin mediated regulation

Long non-coding RNAs (lncRNAs) have been well-established to act as regulators and mediators of development and cell fate specification programs. LncRNA Mrhl (meiotic recombination hotspot locus) has been shown to act in a negative feedback loop with WNT signaling to regulate male germ cell meiotic commitment. In our current study, we have addressed the role of Mrhl in development and differentiation using mouse embryonic stem cells (mESCs) as our model system of study. We found Mrhl to be a nuclear-localized, chromatin-bound lncRNA with moderately stable expression in mESCs. Transcriptome analyses and loss-of-function phenotype studies revealed dysregulation of developmental processes and lineage-specific genes along with aberrance in specification of early lineages during differentiation of mESCs. Genome-wide chromatin occupancy studies suggest regulation of chromatin architecture at key target loci through triplex formation. Our studies thus reveal a role for lncRNA Mrhl in regulating differentiation programs in mESCs in the context of appropriate cues through chromatin-mediated responses.

developmental biology↗

bioRxiv2018

Interaction between Retinoschisin and Norrin: Physical or Functional Relationship?

BackgroundRetinoschisis and Norrie disease are X-linked recessive retinal disorders caused by mutations in RS1 and NDP genes respectively. Both are likely to be monogenic and no locus heterogeneity has been reported. However, there are reports showing overlapping clinical features of Norrie disease and retinoschisis in a NDP knock-out mouse model and also the involvement of both the genes in retinoschisis patients. Yet, the exact molecular mechanism and relationship between the two disorders have still not been understood.\n\nObjectiveIn this study, we aim to investigate the association between retinoschisin (RS1) and norrin (NDP) using in vitro and in silico approaches.\n\nMethodSpecific protein-protein interaction between RS1 and NDP was determined in human retina by co-immunoprecipitation assay and immunoblotting. The immunoprecipitated complexes of RS1 and NDP were analyzed using MALDI-TOF mass spectrometry to validate the findings. STRING database was used to explore the functional relationship.\n\nResultsCo-immunoprecipitation and immunoblotting demonstrated lack of a direct interaction between RS1 and NDP. This was further substantiated by analyzing the immunoprecipitation complexes using MALDI-TOF mass spectrometry. STRING did not reveal any direct functional association between the two proteins.\n\nConclusionWhile literature suggest the existence of digenic involvement of RS1 and NDP in the pathophysiology of retinoschisis and Norrie disease, our data provides evidence for lack of a physical interaction between the two proteins. However, we cannot exclude the possibility of an indirect functional association as our analyses point to MAP kinase signaling pathway, which is presumed to be the link between them.

molecular biology↗

bioRxiv2018

In silico analysis of piRNAs in retina reveals potential targets in intracellular transport and retinal degeneration

Long considered to be active only in germline, PIWI/piRNA pathway is now known to play significant role in somatic cells, especially neurons. Nonetheless, so far there is no evidence for the presence of piRNAs in the neurosensory retina. In this study, we have uncovered 102 piRNAs in human retina and retinal pigment epithelium (RPE) by analysing RNA-seq data. The identified piRNAs were enriched with three motifs predicted to be involved in rRNA processing and sensory perception. Further, expression of piRNAs in donor eyes were assessed by qRT-PCR. Loss of piRNAs in HIWI2 knockdown ARPE19 cells downregulated targets implicated in intracellular transport (SNAREs and Rabs), circadian clock (TIMELESS) and retinal degeneration (LRPAP1 and RPGRIP1). Moreover, piRNAs were dysregulated under oxidative stress indicating their potential role in retinal pathology. Intriguingly, computational analysis revealed complete and partial seed sequence similarity between piR-62011 and sensory organ specific miR-183/96/182 cluster. Furthermore, the expression of retina enriched piR-62011 positively correlated with miR-182 in HIWI2 silenced Y79 cells. Thus, our data provides an evidence for the expression of piRNAs in human retina and RPE. Collectively, our work demonstrates that piRNAs dynamically regulate distinct molecular events in the maintenance of retinal homeostasis.

cell biology↗