Biology subjects

Saini, D.

Publications and source records attributed to Saini, D..

7 recordsLinked to original sources

bioRxiv2026

Computational drug repurposing identified Artemisinin and Mebendazole as potential inhibitors of virulence-associated proteins SKSR and essential kinases CpCDPK1 of Cryptosporidium parvum

Cryptosporidium parvum is a protozoan parasite responsible for cryptosporidiosis, significantly threatening immunocompromised individuals, particularly HIV/AIDS patients, by causing severe diarrhea and potential mortality. Current treatments are largely ineffective, prompting investigations into new therapeutic options. This study evaluated two antiparasitic drugs: Mebendazole, used for helminth infections, and Artemisinin, used for malaria. The SKSR gene family encodes virulence factors in C. parvum, and Calcium-dependent protein kinase1 (CpCDPK1) regulates the life cycle of C. parvum; targeting these proteins may reduce growth and infection in hosts. In the current study, molecular docking was conducted taking Mebendazole and Artemisinin drugs as ligands, SKSR gene family and CpCDPK1 proteins as drug targets. Results with SKSR showed binding energy of -4.9 kcal/mol, -6.72 kcal/mol for Mebendazole and Artemisinin, respectively. Whereas, with CpCDPK1, the binding energies were -6.44 kcal/mol, -9.18 kcal/mol for Mebendazole and Artemisinin, respectively. Docking of Nitazoxanide (an in-use drug for C. parvum) with SKSR and CpCDPK1 revealed binding energies -4.2 kcal/mol, -4.81 kcal/mol, respectively. The stability of the proteins (targets) upon binding to the ligands was assessed by performing all-atom MD simulations for 100ns using the GROMACS package. No major variations were observed upon binding of Artemisinin and Mebendazole to SKSR and CpCDPK1. The findings of MD simulations imply that both proteins maintain their stability upon binding of Artemisinin and Mebendazole. Molecular Docking and MD simulation studies suggest that Artemisinin and Mebendazole are potential candidates for repurposing in the treatment of C. parvum infections, with recommendations for in vitro studies to validate these findings.

molecular biology↗

bioRxiv2025

Divergent roles of DNA methylation, TRIM28, and p53 surveillance in human embryonic and trophoblast stem cells

Transcriptional regulation of transposons and genes by TRIM28 and 5mC is critical for proper mammalian embryonic development, but the specific roles for these mediators in human embryonic and placental lineage remain unclear. We find that loss of TRIM28 has a limited effect on global transposon expression and instead results in upregulation of genes proximal to TRIM28-bound Long Terminal Repeats (LTRs) in both human trophoblast stem cells (hTSCs) and human embryonic stem cells (hESCs). MER11A elements show especially strong regulatory importance in hTSCs: these elements are bound by both TRIM28 and placental transcription factors and show both heterochromatic and euchromatic features. Some genes are positively regulated by MER11A elements in hTSC basal state, while other MER11A-proximal genes show upregulation only upon TRIM28 deletion. By contrast, loss of DNA methylation in hESCs or hTSCs leads to a global increase in transposon expression. While many genic 5mC targets are shared in hESCs and hTSCs, we also observe evidence that a handful of genes important for somatic development are repressed by 5mC in trophoblast, while a small parallel set of placental genes are repressed by methylation in embryonic tissue. Interestingly, loss of DNMT1 causes hESCs to be rapidly lost from culture in a TP53 and mitotic surveillance checkpoint-dependent manner, while hTSCs show little p53 response to DNMT1 loss or DNA damage generally, instead showing gradual mitotic defects and aneuploidy and slow loss from culture. This discrepancy may explain the higher frequency of karyotypic abnormality found in human placental cells. Together, this study charts the role of TRIM28 and DNA methylation in regulating embryonic and placental transcription and demonstrates divergent p53-dependent responses to genomic instability.

molecular biology↗

bioRxiv2025

Engulfing to Adapt: Efferocytosis by Epithelial Cells Triggers Cell State Transitions During Tissue Remodeling

Hormone deprivation treatments are a leading approach in prostate cancer treatment. Following deprivation, the organ regresses from a fully differentiated secretory organ to one less than 50% of the original size, that has been reprogrammed to a state primed for regeneration. Despite widespread use of hormone treatments, the events linking cellular apoptotic responses following prostate hormone deprivation and cell state reprogramming are not fully understood. We report that the absence of hormones creates a microenvironment rich in apoptotic cells that are engulfed by neighboring prostate epithelial cells. Mechanistically, we found that epithelial cells alter their metabolism and gene expression during efferocytosis. Efferocytic epithelial cells adopt a more glycolytic metabolism, resulting in elevated levels of lactate production. This correlates with increased histone Lactylation over gene regulatory elements for genes regulating autophagy and catabolism. To further demonstrate that efferocytosis is necessary to remodel tissue during regression, we expressed a mutant of the receptor protein MFGE8, MFGE8-D89E to "mask" PtdSer in the prostate epithelium and reduce efferocytosis. This effectively prevented the cell and lumen size changes hormone-deprived prostates usually go through. Our findings suggest new perspectives on how epithelial cell efferocytosis can impact tissue remodeling and altered cellular states.

developmental biology↗

bioRxiv2025

Adaptation of the Chlorella photosynthetic electron transport chain to environmental light conditions

In photosynthetic organisms, the process of photosystem II-cyclic electron flow (PSII-CEF) protects against degradation of the active D1 protein subunit of photosystem II in high light environments. By comparing the photophysiology of the extreme-light (2000 {micro}Ein/m2/s) desert alga Chlorella ohadii to the low-light (20 {micro}Ein/m2/s) aquatic alga Chlorella sp. NIES 642, we can monitor how natural adaptations resulting in differing levels of PSII-CEF affect the photosynthetic electron transport chain. Modeling of chlorophyll fast repetition rate fluorometry shows distinct backward transitions of the Kok cycle in C. ohadii, which are absent in NIES 642. Increase in PSII-CEF also has a positive effect on the occurrence of miss parameters in the water oxidizing complex. Fluorescent Q A- reoxidation kinetics detail that the majority of reaction centers in C. ohadii are performing electron transfer to oxidized QB under saturating light conditions. A combination of kinetic observations excludes plastocyanin as a potential external electron carrier in the mechanistic path of PSII-CEF and suggests that photosystem I-cyclic electron flow works in tandem with PSII-CEF. The combination of these two alternative flow mechanisms expedite electron transfer downstream of PSII and optimize ATP production, respectively. Utilizing 77K spectrofluorometry, congruent photosystem stoichiometry is found between both Chlorella species, despite a 100-fold growth light intensity difference. Electrochromic shift measurements show that C. ohadii has diminished changes to both trans-membrane potential and {Delta}pH during operation of photosynthesis compared to NIES 642, and that excess addition of N,N-dicyclohexylcarbodiimide to Chlorella cells has an inhibitory effect on the photosynthetic electron transport chain.

biochemistry↗

bioRxiv2024

Hypoxia and loss of GCM1 expression prevents differentiation and contact inhibition in human trophoblast stem cells

The placenta develops alongside the embryo and nurtures fetal development to term. During the first stages of embryonic development, due to low blood circulation, the blood and ambient oxygen supply is very low ([~]1-2% O2) and gradually increases upon placental invasion. While a hypoxic environment is associated with stem cell self-renewal and proliferation, persistent hypoxia may have severe effects on differentiating cells and could be the underlying cause of placental disorders. We find that human trophoblast stem cells (hTSC) thrive in low oxygen, whereas differentiation of hTSC to trophoblast to syncytiotrophoblast (STB) and extravillous trophoblast (EVT) is negatively affected by hypoxic conditions. The pro-differentiation factor GCM1 (human Glial Cell Missing-1) is downregulated in low oxygen, and concordantly there is substantial reduction of GCM1-regulated genes in hypoxic conditions. Knockout of GCM1 in hTSC caused impaired EVT and STB formation and function, reduced expression of differentiation-responsive genes, and resulted in maintenance of self-renewal genes. Treatment with a PI3K inhibitor reported to reduce GCM1 protein levels likewise counteracts spontaneous or directed differentiation. Additionally, chromatin immunoprecipitation of GCM1 showed enrichment of GCM1-specific binding near key transcription factors upregulated upon differentiation including the contact inhibition factor CDKN1C. Loss of GCM1 resulted in downregulation of CDKN1C and corresponding loss of contact inhibition, implicating GCM1 in regulation of this critical process.

cell biology↗

bioRxiv2022

ZMYM2 is essential for methylation of germline genes and active transposons in embryogenesis

ZMYM2 is a transcriptional repressor whose role in development is largely unexplored. We found that Zmym2-/- mice show embryonic lethality by E10.5. Molecular characterization of Zmym2-/- embryos revealed two distinct defects. First, they fail to undergo DNA methylation and silencing of germline gene promoters, resulting in widespread upregulation of germline genes. Second, they fail to methylate and silence the evolutionarily youngest and most active LINE element subclasses in mice. Zmym2-/- embryos show ubiquitous overexpression of LINE-1 protein as well as aberrant expression of transposon-gene fusion transcripts. Interaction and colocalization data indicate that ZMYM2 homes to germline genes via binding to the non-canonical polycomb complex PRC1.6 and to transposons via the TRIM28 complex. In the absence of ZMYM2, hypermethylation of histone 3 lysine 4 occurs at target sites, creating a chromatin landscape unfavourable for establishment of DNA methylation. ZMYM2-/- human embryonic stem cells also show aberrant upregulation and demethylation of young LINE elements, indicating a conserved role in repression of active transposons. ZMYM2 is thus an important new factor in DNA methylation patterning in early embryonic development.

molecular biology↗

bioRxiv2021

The DNMT1 inhibitor GSK-3484862 mediates global demethylation in murine embryonic stem cells

BackgroundDNA methylation plays an important role in regulating gene expression in mammals. The covalent DNMT1 inhibitors 5-azacytidine and decitabine are widely used in research to reduce DNA methylation levels, but they impart severe cytotoxicity which limits their demethylation capability and confounds interpretation of experiments. Recently, a non-covalent inhibitor of DNMT1 called GSK-3484862 was developed by GlaxoSmithKline. We sought to determine whether GSK-3484862 can induce demethylation more effectively than 5-azanucleosides. Murine embryonic stem cells (mESC) are an ideal cell type in which to conduct such experiments, as they have a high degree of DNA methylation but tolerate dramatic methylation loss. ResultsWe determined the cytotoxicity and optimal concentration of GSK-3484862 by treating wild-type (WT) or Dnmt1/3a/3b triple knockout (TKO) mESC with different concentrations of the compound, which was obtained from two commercial sources. Concentrations of 10 {micro}M or below were readily tolerated for 14 days of culture. Known DNA methylation targets such as germline genes and GLN-family transposons were upregulated within two days of the start of GSK-3484862 treatment. By contrast, 5-azacytidine and decitabine induced weaker upregulation of methylated genes and extensive cell death. Whole genome bisulfite sequencing (WGBS) showed that treatment with GSK-3484862 induced dramatic DNA methylation loss, with global CpG methylation levels falling from near 70% in WT mESC to less than 18% after 6 days of treatment with GSK-3484862, similar to the methylation level observed in Dnmt1 deficient mESCs. ConclusionsGSK-3484862 mediates striking demethylation in mESCs with minimal non-specific toxicity.

molecular biology↗