Biology subjects

Khan, S. S.

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

7 recordsLinked to original sources

bioRxiv2026

Glucose-Responsive CD20+ Cytotoxic T Cells: A Novel Pro-inflammatory Mediator in the Immunopathogenesis of Type 2 Diabetes

ObjectiveAlthough T-cell-mediated inflammation is a hallmark of Type 2 Diabetes (T2D), the contribution of CD20-expressing T cells--a highly potent subset recently implicated in various autoimmune conditions--to T2D pathogenesis remains unknown. This study aimed to characterize the frequency, functional profile, and glucose-responsiveness of CD20+ cytotoxic T lymphocytes (CTLs) in patients with T2D. Research Design and MethodsPeripheral blood mononuclear cells (PBMCs) from 25 treatment-naive T2D patients and 20 age-matched healthy controls (HC) were analyzed using multicolor flow cytometry. We assessed the frequency of CD3+CD8+CD20+ cells and their production of cytotoxic molecules (Granzyme B, Perforin, Granzyme K) and pro-inflammatory cytokines (IFN-{gamma}, TNF-, GM-CSF). To further establish the link with hyperglycemia, HC-derived CTLs were exposed to increasing glucose concentrations (100-450 mg/dL) in vitro. Single-cell RNA sequencing (scRNA-seq) data from a public T2D dataset was utilized to validate the molecular signature of MS4A1 (CD20)+ CTLs. ResultsThe frequency of circulating CD20+ CTLs was significantly elevated in T2D patients compared to HCs (p<0.0001) and demonstrated a strong positive correlation with HbA1c, fasting glucose, and triglyceride levels. Notably, CD20+ CTLs from T2D patients exhibited a "hyperfunctional" phenotype, characterized by significantly higher degranulation (CD107a), elevated expression of Granzymes B/K and Perforin, and increased production of IFN-{gamma} and TNF- compared to HCs (p<0.01 for all). In contrast, no such differences were observed in the CD20-CTL compartment. In vitro experiments revealed that escalating glucose levels directly enhanced the proliferation and cytotoxic potential of CD20+ CTLs, suggesting a nutrient-sensing mechanism. scRNA-seq analysis further confirmed the distinct pro-inflammatory and effector transcriptional profile of MS4A1+ T cells in T2D. ConclusionsOur findings identify CD20+ CTLs as a novel, glucose-sensitive, and hyperfunctional immune subset in T2D. The strong correlation between these cells and clinical metabolic parameters suggests that CD20+ CTLs may act as a critical link between chronic hyperglycemia and systemic inflammation, representing a potential new therapeutic target for immunomodulation in T2D.

immunology↗

bioRxiv2025

Soil and water microbial communities: A source of novel antibiotics for sustainable plant disease control

Pathogenic microorganisms pose a significant threat to plant health and agricultural productivity worldwide. Herein, this study explores the potential of natural microbial communities as sources of biopesticides. We analyzed 20 soil and water samples from remote areas, isolating 121 colonies using nutrient agar. Antibacterial activity was assessed through agar diffusion, revealing that 12 colonies exhibited significant inhibitory effects against various pathogenic bacteria. Measurement of inhibition zones indicated that these colonies could produce antibiotics. Subsequently, molecular characterization with 16S rRNA and BLAST searches of 12 unidentified sequences highlighted substantial microbial diversity within the samples. This research underscores the promise of these natural microbial communities in developing biocontrol agents for managing plant diseases in greenhouse and field environments. Extraction and purification techniques could further refine these antibiotics, advancing sustainable agricultural practices.

microbiology↗

bioRxiv2025

Super-compensator alleles rescue diverse deleterious substitutions and buffer the effects of mutations

Compensatory mutations can mitigate the fitness costs of deleterious mutations, yet their distribution, structural contexts, and evolutionary roles remain poorly characterized. Here, we systematically analyzed a public deep mutational scanning (DMS) dataset comprising ~400,000 amino acid variants of imidazole glycerol-phosphate dehydratase (IGPD), with substitutions spanning the entire length of the protein. We found that roughly one-tenth of nonfunctional missense variants can regain function through additional substitutions, predominantly at solvent exposed residues with weak local contacts. Notably, we identified a distinct class of super compensatory substitutions that enhance fitness across diverse genetic backgrounds and buffer mutational effects, resulting in genotypes that occupy locally flatter regions of the fitness landscape. Comparative analyses of additional public DMS datasets across diverse proteins and assays revealed that super compensators recur across different natural sequence-function maps, indicating a broadly represented mode of compensatory effects that sustains mutational persistence and contributes to protein evolutionary robustness.

evolutionary biology↗

bioRxiv2024

Priming Epigenetic Landscape at Gene Promoters through Transcriptional Activation in Mammalian Germ Cells

In mammalian germ cells, a cycle of erasing and resetting epigenetic information is crucial for sex-specific gametogenesis and early embryogenesis. Specific chromatin states at promoters allow genes to be expressed at the appropriate time during germ cell development, however, the mechanism that establishes such characteristic chromatin states remains unclear. Here, we show that, in mouse male embryonic germ cells, promoters of developmental and housekeeping genes are selectively protected from de novo DNA methylation, coinciding with their transient upregulation and genome-wide erasure of H3K27me3. Importantly, a specific level of H3K4me3 density at the promoters serves as a potent probe that distinguishes between hypo- and hyper-DNA methylation states. Subsequent restoration of H3K27me3 contributes to establishing bivalent chromatin states that prime genes for activation at later developmental stages. These findings reveal a molecular framework shaping the epigenetic landscape at promoters with long-term effects beyond germ cell development.

genomics↗

bioRxiv2024

Loss of primary cilia and dopaminergic neuroprotection in pathogenic LRRK2-driven and idiopathic Parkinsons disease

Activating LRRK2 mutations cause Parkinsons disease. Previously, we showed that cholinergic interneurons and astrocytes but not medium spiny neurons of the dorsal striatum lose primary cilia in LRRK2 mutant mice. Single nucleus RNA sequencing shows that cilia loss in cholinergic interneurons correlates with higher LRRK2 expression and decreased glial derived neurotrophic factor transcription. Nevertheless, much higher LRRK2 expression is seen in medium spiny neurons that have normal cilia in mice and humans. In parallel with decreased striatal dopaminergic neurite density, LRRK2 G2019S neurons show increased autism-linked CNTN5 adhesion protein expression; glial cells show significant loss of ferritin heavy chain. Human striatal tissue from LRRK2 pathway mutation carriers and idiopathic Parkinsons disease show similar cilia loss in cholinergic interneurons and astrocytes and overall loss of such neurons. These data strongly suggest that loss of cilia in specific striatal cell types decreases neuroprotection for dopamine neurons in mice and human Parkinsons disease. TeaserCilia loss in Parkinsons disease decreases dopaminergic neuroprotection due to inability to sense Hedgehog signals

neuroscience↗

bioRxiv2022

Zika virus NS4A hijacks host ANKLE2 to promote viral replication

Zika virus (ZIKV) is infamous among flaviviruses for its unique association with congenital birth defects, notably microcephaly. We previously mapped ZIKV-host protein interactions and identified the interaction between ZIKV NS4A and host ANKLE2, which itself has established ties to congenital microcephaly. In fruit flies, NS4A induces microcephaly phenotypes in an ANKLE2-dependent manner. This suggests that NS4A interacts with ANKLE2 to dysregulate cell behavior and contributes to abnormal host neurodevelopment. Here, we explore the role of ANKLE2 in ZIKV replication to understand the biological significance of the interaction from the viral perspective. We show that knockdown of ANKLE2 reduces replication of two ZIKV strains, across multiple MOIs and timepoints. We observe that localization of ANKLE2 is drastically shifted to sites of NS4A accumulation during infection. We investigate which domains of ANKLE2 mediate this behavior and the interaction with NS4A. Using co-immunoprecipitation, we show that deletion of either the transmembrane or LEM domain has little impact on the interaction, but deletion of both significantly reduces interaction with NS4A. We show that the C-terminal transmembrane domains of NS4A stabilize the interaction with ANKLE2. Finally, we explore this interaction in other flaviviruses and observe ANKLE2 interacts with NS4A across four additional mosquito-borne flaviviruses. Together, these results suggest NS4A interacts with ANKLE2 through a combination of its transmembrane and LEM domains, bringing it to sites of ZIKV replication to promote replication through an unknown mechanism. Taken together with our previous results, our findings indicate that, in the process of hijacking ANKLE2 for replication, ZIKV disrupts its physiological function to cause disease. ImportanceThe ZIKV epidemic led to the astonishing revelation that congenital ZIKV infection is associated with devastating birth defects, including microcephaly. Microcephaly is the condition in which head and brain size are severely reduced, and is often accompanied by intellectual disability. The molecular mechanisms by which ZIKV replicates and causes microcephaly are still incompletely understood. We previously identified the protein interaction between ZIKV NS4A and host ANKLE2, which is associated with congenital microcephaly. In flies, NS4A induces microcephaly in an ANKLE2-dependent manner, suggesting this interaction is crucial for ZIKV pathogenesis. Here, we explore the relevance of this physical interaction for virus replication. We find that ANKLE2 promotes ZIKV replication, concentrates at sites of NS4A accumulation during infection, and interacts with NS4A via its N-terminal domain. Thus, this represents a rare example of a ZIKV-host protein interaction that impacts both disease and virus replication.

molecular biology↗

bioRxiv2021

Pathogenic LRRK2 control of primary cilia and Hedgehog signaling in neurons and astrocytes of mouse brain

Previously, we showed that cholinergic interneurons of the dorsal striatum lose cilia in mice harboring the Parkinsons disease associated, kinase activating, R1441C LRRK2 mutation (Dhekne et al., 2018). Here we show that this phenotype is also seen in two mouse strains carrying the most common human G2019S LRRK2 mutation. Heterozygous loss of the PPM1H phosphatase that is specific for LRRK2-phosphorylated Rab GTPases (Berndsen et al., 2019) yields the same cilia loss phenotype, strongly supporting a connection between Rab GTPase phosphorylation and cilia loss. In addition, astrocytes throughout the striatum show a ciliation defect in LRRK2 and PPM1H-/+ mutant models. Hedgehog signaling requires cilia, and loss of cilia correlates here with a loss in induction of Hedgehog signaling as monitored by in situ hybridization of Gli1 transcripts. These data support a model in which LRRK2 and PPM1H mutant mice struggle to receive and respond to critical Hedgehog signals in the nigral-striatal pathway.

cell biology↗