Biology subjects

Sahoo, S. S.

Publications and source records attributed to Sahoo, S. S..

7 recordsLinked to original sources

bioRxiv2026

Cryo-EM structures of SAMD9L reveal the arrangement and coordination of multi-domains

Human sterile alpha motif domain-containing 9 (hSAMD9L) is a large ([~]185 kDa) multi-domain interferon-stimulated antiviral effector with strong translation-inhibitory activity. Inherited heterozygous gain-of-function (GoF) mutations in SAMD9L directly associated with severe bone marrow failure syndromes. Using single-particle cryo-electron microscopy (cryo-EM), we determined the first structures of both full-length wild-type hSAMD9L and an N-terminal-truncated mutant at resolutions ranging from 2.8 to 3.7 [A]. Both proteins exist in monomeric and dimeric states, providing clear evidence that the sterile alpha motif (SAM) and AlbA domains are not essential for dimerization. Our cryo-EM analysis reveals a tightly packed, closed architecture defined by interlocking multi-domains. We precisely mapped the extensive dimer interface mediated by Sir2-like and an oligonucleotide/oligosaccharide-binding (OB) domains. Biochemical analyses show that hSAMD9L binds double-stranded DNA in vitro but has no detectable NTP hydrolysis activity under our assay conditions. Accordingly, in our cryo-EM map we observed a clear density for a non-hydrolyzed NTP in the pocket, suggesting nucleotide binding without turnover like in STAND (Signal Transduction ATPases with Numerous Domains) proteins. Together, these results provide a structural framework for hSAMD9L and also providing key insights into its organization, domain packing and dimerization and offer a basis for understanding how GoF variants may alter hSAMD9L regulation thus impacting cell proliferation.

biochemistry↗

bioRxiv2025

Large Language Models Can Extract Metadata for Annotation of Human Neuroimaging Publications

We show that recent (mid-to-late 2024) commercial large language models (LLMs) are capable of good quality metadata extraction and annotation with very little work on the part of investigators for several exemplar real-world annotation tasks in the neuroimaging literature. We investigated the GPT-4o LLM from OpenAI which performed comparably with several groups of specially trained and supervised human annotators. The LLM achieves similar performance to humans, between 0.91 and 0.97 on zero-shot prompts without feedback to the LLM. Reviewing the disagreements between LLM and gold standard human annotations we note that actual LLM errors are comparable to human errors in most cases, and in many cases these disagreements are not errors. Based on the specific types of annotations we tested, with exceptionally reviewed gold-standard correct values, the LLM performance is usable for metadata annotation at scale. We encourage other research groups to develop and make available more specialized "micro-benchmarks," like the ones we provide here, for testing both LLMs, and more complex agent systems annotation performance in real-world metadata annotation tasks.

bioinformatics↗

bioRxiv2024

PAX2 is Transcriptionally Silenced by a Distinct Mechanism of Epigenetic Reprogramming to Initiate Endometrial Carcinogenesis

In most cancers, including endometrial cancer, tumor suppressor genes harboring inactivating mutations have been systematically cataloged. However, locus-specific epigenetic alterations contributing to cancer initiation and progression remain only partly described, creating knowledge gaps about functionally significant tumor suppressors and underlying mechanisms associated with their inactivation. Here, we show that PAX2 is an endometrial tumor suppressor recurrently inactivated by a distinct epigenetic reprogramming event not associated with promoter hypermethylation. PAX2 is expressed throughout normal endometrial glands; however, microscopic clones with PAX2 protein loss arise spontaneously in adulthood and progress to endometrial precancers and cancers. Here we show that PAX2 protein loss occurs via transcriptional silencing in 80% of endometrial cancers. Mechanistically, transcriptomic, epigenomic, 3D genomic, and machine learning analyses showed that silencing is associated with replacement of open/active chromatin features (H3K27ac/H3K4me3) with inaccessible/repressive features (H3K27me3). The spread of the H3K27me3 signal is restrained by cohesin loops, preventing transcriptional dysregulation of neighboring genes. Functionally, PAX2 loss promoted endometrial carcinogenesis by rewiring the transcriptional landscape via global enhancer reprogramming. Genetically engineered mouse models together with organoid and human cell line studies established Pax2 as an in vivo endometrial tumor suppressor that cooperates with Pten to produce lethal cancers. Our discovery of a specific and recurring epigenetic alteration that transcriptionally silences PAX2 to initiate most endometrial cancers opens new lines of investigation into the origins of endometrial cancer with diverse implications for its diagnosis and treatment. One Sentence SummaryWe demonstrate that PAX2 is silenced by a highly recurrent epigenetic mechanism to initiate most endometrial cancers, establishing a novel mechanism of tumor suppressor inactivation.

cancer biology↗

bioRxiv2023

Senescent cells inhibit muscle differentiation via the lipid- SASP 15d-PGJ2 mediated modification and control of HRas

Senescent cells, which are characterized by multiple features such as increased expression of Senescence-Associated {beta}-galactosidase activity (SA {beta}-gal) and cell cycle inhibitors such as p21 or p16, accumulate with tissue damage and dysregulate tissue homeostasis. In the context of skeletal muscle, it is known that agents used for chemotherapy such as Doxorubicin cause buildup of senescent cells, leading to the inhibition of tissue regeneration. Senescent cells influence the neighboring cells via numerous secreted factors which form the senescence-associated secreted phenotype (SASP). Lipids are emerging as a key component of SASP that can control tissue homeostasis. Arachidonic acid-derived lipids have been shown to accumulate within senescent cells, specifically 15d-PGJ2, which is an electrophilic lipid produced by the non-enzymatic dehydration of the prostaglandin PGD2. In this study, we show that 15d-PGJ2 is also released by Doxorubicin-induced senescent cells as a SASP factor. Treatment of skeletal muscle myoblasts with the conditioned medium from these senescent cells inhibits myoblast fusion during differentiation. Inhibition of L-PTGDS, the enzyme that synthesizes PGD2, diminishes the release of 15d-PGJ2 by senescent cells and restores muscle differentiation. We further show that this lipid post-translationally modifies Cys184 of HRas in skeletal muscle cells, causing a reduction in the localization of HRas to the Golgi, increased HRas binding to RAF RBD, and activation of cellular MAPK-Erk signaling (but not the Akt signaling). Mutating C184 of HRas prevents the ability of 15d- PGJ2 to inhibit the differentiation of muscle cells and control the activity of HRas. This work shows that 15d-PGJ2 released from senescent cells could be targeted to restore muscle homeostasis after chemotherapy.

biochemistry↗

bioRxiv2023

C-terminal cysteines of HRas control Erk signaling and 15-deoxy-Δ12,14-prostaglandin J2 (15d-PGJ2) mediated inhibition of myoblast differentiation.

HRas is an important node that controls cellular signaling, proliferation, and differentiation. Mutants of HRas (e.g., the constitutively active HRas V12) can be oncogenic, and can also inhibit myoblast differentiation. The C-terminal cysteines of HRas (Cys181 and Cys184) serve as substrates for intra-cellular reversible palmitoylation and de-palmitoylation reactions, which control its subcellular distribution. The relationship between the C-terminal cysteines of HRas, its intracellular distribution, and its cellular activity has remained unclear. Understanding this relationship has important implications for targeting HRas in pathogenic states where it is activated. In this study, we show that a mutation in the C-terminal of HRas, C181S, is sufficient to cause increased levels of HRas V12 in the Golgi, decreased HRas V12-driven Akt and Erk signaling and reverse the ability of HRas V12 to inhibit myoblast differentiation. This demonstrates the importance of C-terminal cysteines in controlling HRas V12. It has been previously shown that Cys184 can also be irreversibly modified by an electrophilic prostaglandin lipid 15d-PGJ2. This lipid is released by senescent cells as a part of senescence-associated secretory phenotype (SASP). In this study, we show that 15d-PGJ2 is secreted by senescent myoblasts formed by treatment with Doxorubicin. We also show that 15d-PGJ2 causes decreased levels of HRas within Golgi, activates Erk signaling (but not Akt signaling), and inhibits differentiation of C2C12 myoblasts in an HRas Cys184-dependent fashion. Chemotherapeutics such as Doxorubicin drive senescence and loss of skeletal muscle homeostasis in cancer patients. This study suggests that targeting the senescence-derived synthesis of 15-PGJ2 might be a target to promote muscle homeostasis after chemotherapy.

cell biology↗

bioRxiv2021

Elevation of TRPV1 expression on T cells during experimental immunosuppression

An intracellular rise in calcium (Ca2+) is an essential requisite underlying T cell activation and its associated pro-inflammatory cytokine production. Transient receptor potential vanilloid channel (TRPV1) is a thermo-sensitive, polymodal gated and permeable to cations such as Ca2+. It has been reported that TRPV1 expression increases during T cell activation. However, the possible involvement of TRPV1 during immunosuppression of T cells has not been studied yet. Here, we investigated the possible role of TRPV1 in FK506 or B16F10-culture supernatant (B16F10-CS) driven experimental immunosuppression in T cells. Intriguingly, it was found that TRPV1 expression is further elevated during immunosuppression compared to ConA or TCR activated T cells. Similarly, in B16F10 tumor-bearing mice, the TRPV1 expression was upregulated in T cells as compared to control mice, in vivo. Moreover, we observed an immediate rise in intracellular Ca2+ levels in FK506 and B16F10-CS treated T cells as compared to ConA or TCR treated T cells. Likewise, in B16F10 tumor-bearing mice, the basal intracellular calcium level was upregulated in T cells as compared to control mice, in vivo. To further investigate the possible mechanism of such rise in intracellular Ca2+ levels, TRPV1 specific functional inhibitor, 5 -iodoresiniferatoxin (5 -IRTX) was used in calcium influx studies. It was observed that the total intracellular Ca2+ levels decreased significantly in presence of 5 -IRTX for either the FK506 or B16F10-CS as well as with ConA or TCR stimulated T cells, indicating the functional role of TRPV1 channels in FK506 or B16F10-CS mediated increase in intracellular Ca2+ levels. The current findings highlight an essential role of the TRPV1 channel in upregulating intracellular calcium levels during both immune-activation and immunosuppression. This study might also have broad implications in the context of other immune-suppressive diseases as well.

immunology↗

bioRxiv2019

Transient Receptor Potential Ankyrin1 channel is endogenously expressed in T cells and regulates immune functions

Transient Receptor Potential channel subfamily A member 1 (TRPA1) is a non selective cationic channel, identified initially as a cold sensory receptor. TRPA1 responds to diverse exogenous and endogenous stimuli associated with pain and inflammation. However, the role of TRPA1 towards T cell responses remains scanty. In this work, we explored the endogenous expression of TRPA1 in T cells. By RT-PCR we confirmed the expression of TRPA1 in T cell at RNA level. Using confocal microscopy as well as flow cytometry, we demonstrated that TRPA1 is endogenously expressed in primary murine splenic T cells as well as in primary human T cells. The endogenous expression of TRPA1 is confirmed by using another antibody. TRPA1 was primarily located at the cell surface. TRPA1-specific activator namely AITC increases intracellular Ca2+-levels while two different inhibitors namely A-967079 as well as HC-030031 reduce intracellular Ca2+-levels in T cells. Such Ca2+-influx can also be influenced by chelation of intracellular Ca2+ as well as extracellular Ca2+. TRPA1 expression was found to be increased during CD3/CD28 (TCR) or ConA driven stimulation in T cells. TRPA1-specific inhibitor treatment prevented induction of CD25, CD69 in ConA/TCR stimulated T cells and secretion of cytokines like TNF, IFN-{gamma} and IL-2 suggesting that endogenous activity of TRPA1 may be involved in T cell activation. Collectively these results may have implication in T cell-mediated responses and possible role of TRPA1 in immunological disorders.

immunology↗