Biology subjects

Giri, K.

Publications and source records attributed to Giri, K..

5 recordsLinked to original sources

bioRxiv2026

Non-canonical alternate interactors of SARS CoV-2 Spike protein implicated in placental susceptibilty

Vertical transmission of SARS-CoV-2 is controversial. Owing to the low expression of ACE2 along with TMPRSS2 in placenta, role of secondary receptors becomes significant. In our study we predicted twelve interactors of spike protein expressed in placenta through interactome analysis followed by docking and molecular dynamic simulation. Three interactors of SARS-CoV-2 spike protein were found to be CD147, EGFR and LDLR. Expression at transcriptomic and translational level by real-time PCR and immunohistochemistry respectively was observed in placenta samples obtained from women with COVID exposure risk and compared to control. Elevated protein levels of CD147 (OR=14.667), ACE2 (OR=8.25) and LDLR (OR=1.9) was associated with higher exposure risk. However, the variation in mRNA expression was not statistically significant. Computational study showed that CD147/basigin, EGFR and LDLR stably interact with spike protein outside its primary receptor binding domain. In-vitro binding assay confirmed the physical interaction between spike protein and the placental receptors. In-silico site-directed mutagenesis further identified key potential binding hotspots of spike protein- Tyr28 and Trp64 for CD147, Phe643, Val642, Thr632 for LDLR and Leu8, Phe59, Phe32, Tyr28, Trp64, Trwp152, His245, and Val213 for EGFR. Finally, concluded that CD147, EGFR and LDLR might act as secondary non-canonical cofactors for SARS-CoV-2 spike protein in placenta, thereby increasing its susceptibility and tissue tropism. The study overall gives a better insight into potential placental suscpetibility providing targeted therapeutic opportunities.

microbiology↗

bioRxiv2026

Paclitaxel sensitizes TRAIL (tumor necrosis factor-related apoptosis-inducing ligand)-resistant breast cancer cells towards TRAIL-mediated apoptosis

BackgroundThe ability of TRAIL to specifically induce apoptosis in cancer cells makes it a promising candidate to be an effective chemotherapeutic drug. But resistance to TRAIL treatment is a major obstacle. Finding combinatorial therapies that make resistant tumors more susceptible to TRAIL is an effective preclinical approach. In this work, we investigated the possibility that pre-treatment of paclitaxel may promote apoptosis in TRAIL-resistant breast cancer cells. MethodsIn silico analysis was done to investigate the binding affinity between TRAIL receptors (DR5 and DCR2) and paclitaxel via docking and MD simulation. To check whether any non-lethal dose of paclitaxel can modulate the expression of TRAIL receptors, qPCR was done in paclitaxel treated breast cancer cells. Next, paclitaxel was pre-administered to TRAIL-resistant MCF7 and MDA-MB-453 human breast cancer cells followed by rhTRAIL treatment. Cell viability and survival was evaluated using the MTT assay and colony formation assay, respectively. Immunoblot for caspase-3 was performed to study apoptosis. The expression level changes of DR5 and DCR2 were analyzed post-treatment using qPCR and immunoblot assay. ResultsIn silico analysis showed that paclitaxel can bind with higher stability to DCR2 in comparison to DR5 thereby changing the preference of TRAIL molecules towards DR5. Next, in cell line experiments we observed that administering a non-lethal dose of paclitaxel to MDA-MB-231 and MCF7 breast cancer cells resulted in no significant cell death but led to an increase in DR5 and a decrease in DCR2 expression at both the transcript and protein levels. Furthermore, in TRAIL-resistant MCF7 and MDA-MB-453 cells, pre-treatment with paclitaxel followed by rhTRAIL administration induced significant cell death due to paclitaxel induced increase in DR5 as well as decrease in DCR2 expression at both the transcript and protein levels. Moreover, long term survival of MDA-MB-453 cells was significantly lower when pretreated with paclitaxel and exposed to rhTRAIL compared to control, paclitaxel alone or rhTRAIL alone group. ConclusionThus, our study uncovers a novel therapeutic strategy to overcome TRAIL resistance underscoring the clinical potential of using a non-lethal dose of paclitaxel to modulate TRAIL receptor dynamics. Future research should be aimed at exploring the potentiality of using paclitaxel-based combinatorial approaches in crafting effective TRAIL therapies.

cancer biology↗

bioRxiv2026

Development of hybrid alphavirus-influenza A, B, and D pseudovirions for rapid quantification of neutralization antibodies and antiviral drugs

The emergence and spread of highly pathogenic avian influenza H5N1 subtypes have raised global concerns due to their ability to cross species barriers and occasional spillover to humans. The viruses primarily infect wild birds and poultry, which have caused significant, sporadic outbreaks in mammals including dairy cattle. Influenza D virus is a recently identified influenza virus that mainly affects cattle with frequent spillover to other species such as swine. Despite the availability of poultry vaccines, there are no H5N1 and Influenza D vaccines for cattle or other potentially affected livestock. Given a history of frequent influenza pandemics originating from avian and mammalian hosts, there is an urgent need for enhanced surveillance, biosecurity, and the development of antivirals and vaccines. Here we describe the development of a novel hybrid alphavirus-influenza pseudovirion (Ha-IV), which is a non-replicating influenza virus-like particle composed of viral structural proteins and an RNA genome derived from a fast-expressing alphaviral vector. As a proof-of-concept, we assembled Ha-IV pseudoviruses based on influenza D and influenza A and B subtypes, and demonstrated their infectivity. In addition, we validated an influenza A pseudovirus based on the H5N1 clade 2.3.4.4b strain, A/Texas/37/2024, for rapid quantification of neutralization antibodies within 4 to 18 hours. Furthermore, we used the pseudovirus to quantify infected cow sera and performed a correlation study with the classic hemagglutinin inhibition assay (HIA). We demonstrate that the Ha-IAV pseudovirus-based assay is consistent with HIA in identifying protective antibody responses. Our results demonstrate that this new Ha-IV pseudovirus provides a rapid tool for quantifying the infectivity of emerging HA mutants and for assessing neutralizing antibody responses.

microbiology↗

bioRxiv2024

Autoimmunity and clinical pathology amelioration in SLE by Dexamethasone primed Mesenchymal Stem Cell derived conditioned media

This study proposes a novel approach, utilizing cell-free dexamethasone (Dex) primed Whartons jelly mesenchymal stem cells derived conditioned media (DW), offering improved efficacy, simplicity, and alternative medicine for addressing complications associated with systemic lupus erythematosus (SLE). This study explores the immunomodulatory effects of DW treatment on immune cell populations in SLE patients and a pristane-induced lupus (PIL) mouse model. DW induces significant expansion of Tregs, Bregs, suppressing Th17, double-negative T cells, and inflammatory neutrophils through modulating IL-10 and IL-17A production. Comparisons with the standard drug hydroxychloroquine reveal similar effects, suggesting TGF beta; pathway mediation in DWs actions. Compared with the immunosuppressive drug Dex, DW better attenuated autoantibody production, increased anti-inflammatory cytokines and maintained a balanced Th17/Treg ratio. In the preclinical in vivo studies, DW exhibits therapeutic efficacy, reducing mortality, preventing proteinuria, and reversing limb inflammation, seizure and alopecia. Organ specific evaluations using advanced live imaging or histopathological analysis highlighted DWs protective effects on kidneys, liver, lungs, heart, and spleen. This provided insight into the immunomodulatory benefits of DW at various levels and suggested that it could be a potential therapeutic avenue for managing complications related to SLE.

immunology↗

bioRxiv2023

A mechanistic study on the tolerance of PAM distal end mismatch by SpCas9

CRISPR-Cas9 is the newest technology available for targeted genome editing. It is very efficient and cheap compared to other genome editing techniques. However, its therapeutic application is limited due to its off-target activity. To have a better understanding of this off-target effect, we concentrated our efforts on its mismatch-prone PAM distal end. Current off-target prediction algorithms use RNA-DNA complementation derived energy as a major factor in predicting off-target effect. RNA-DNA complementation derived energy drives Cas9 conformational change, which in turn drives its functional activity. In the case of lower RNA-DNA complementarity, a partial conformational change occurs resulting in a slower reaction rate and partial activity. However, extensive mismatches are often tolerated despite lower complementation derived energy available from RNA: DNA duplex formation. Thus, the off-target activity of Cas9 depends directly on the nature of mismatches which in turn result in deviation of the active site of the enzyme due to structural instability in the duplex strand. In order to test the hypothesis, we have designed an array of mismatched target sites and performed in vitro and cell line-based experiments to assess the effects of PAM distal mismatches in Cas9 activity. For further mechanistic validation, Molecular dynamics simulation was performed and it revealed that certain mismatch mutations induced pronounced conformational instability within the RNA-DNA duplex, leading to elevated root mean square deviation (RMSD) values. We found that, target sites having mismatches in the 18th to 16th position upstream of the PAM showed no to little activity.

genomics↗