Biology subjects

Naqvi, A.

Publications and source records attributed to Naqvi, A..

13 recordsLinked to original sources

bioRxiv2026

Longitudinal Salivary Immunophenotyping Reveals Distinct Cellular Signatures of Periodontal Disease Activity and Resolution

AimTo investigate whether salivary immune cell profiling can serve as a non-invasive approach to monitor periodontal disease activity and therapeutic response by characterizing innate and adaptive immune cell dynamics in periodontitis. Materials and MethodsThis longitudinal study included systemically healthy adults with periodontitis and healthy controls. Periodontal parameters (PPD, BOP, plaque/calculus, and radiographic bone loss) were recorded by calibrated examiners ({kappa}=0.85) following established criteria. Stimulated saliva and gingival biopsies were collected before and 4-6 weeks after non-surgical periodontal therapy (NSPT), and from healthy controls. Multiparametric flow cytometry was used to characterize myeloid and lymphoid cell populations and polarization markers. Bacterial transcripts and host inflammatory markers were assessed by qRT-PCR. Statistical analyses were performed using one-way ANOVA. ResultsPeriodontitis subjects exhibited significantly elevated salivary bacterial transcripts, which decreased but did not normalize following NSPT. Both myeloid and lymphoid immune cell populations increased in periodontitis compared with healthy controls and declined after therapy. This was accompanied by a pronounced pro-inflammatory shift with elevated IFN-{gamma}-producing macrophages, dendritic cells, Th1/Th17 cells, and B cells, including the novel identification of IFN-{gamma}-producing B cells in saliva and mirrors the gingival immune cell profiles. In contrast, anti-inflammatory populations (IL-10-producing myeloid cells, Tr1 cells, and regulatory B cells) were reduced in disease and partially restored following NSPT. ConclusionsSalivary immunophenotyping non-invasively monitors PD activity and therapeutic response by capturing dynamic immune changes that reflect gingival signatures and track post-therapy resolution. Clinical RelevanceO_ST_ABSScientific rationaleC_ST_ABSSalivary immune profiling offers a real-time, non-invasive tool for assessing periodontal disease status and treatment outcomes, with potential applications in precision diagnostics and personalized periodontal care. Principle findingsPeriodontitis was associated with increased salivary bacterial burden and a marked pro-inflammatory immune profile involving both innate and adaptive immune cells, including newly identified IFN-{gamma}-producing B cells. Non-surgical periodontal therapy partially restored anti-inflammatory immune responses and reduced inflammatory cell populations, supporting salivary immunophenotyping as a promising non-invasive biomarker approach for monitoring disease activity and treatment response. Practical implicationsSalivary immune cell profiling could serve as a simple, non-invasive tool to monitor periodontal disease activity and response to therapy in clinical practice. Identification of specific inflammatory cell subsets may also aid in developing personalized diagnostic and therapeutic strategies for periodontitis.

immunology↗

bioRxiv2026

Mapping kinase-dependent tumor immune adaptation with multiplexed single-cell CRISPR screens

Immune dysfunction in cancer is enacted by multiple programs, including tumor cell-intrinsic responses to distinct immune subpopulations. A subset of these immune evasion programs can be systematically recapitulated through direct tumor-immune interactions in vitro. Here, we present an integrated, high-throughput single-cell CRISPR screening framework focused on the protein kinome for mapping the tumor-intrinsic regulation of T cell-driven immune pressure in glioblastoma (GBM). We combine pooled CRISPR interference and activation (CRISPRi/a) with immune-matched NY-ESO-1 antigen-specific allogeneic GBM-T cell co-culture and massively multiplexed single-cell transcriptomics to systematically quantify how genetic perturbation reshapes baseline tumor state and adaptive responses across graded effector-to-target ratios. We further leverage deep generative models for analyzing pooled CRISPR screens to decipher the effects of genetic perturbations on the mechanisms of tumor resistance. This framework resolves distinct modules of immune evasion and survival, including the regulation of the antigen-presentation machinery, interferon/NF-{kappa}B signaling, oxidative stress resilience, and checkpoint/cytokine programs, while identifying perturbations that reroute the continuous tumor transcriptional trajectory induced by T cell engagement. A secondary chemical screen in patient-derived GBM cultures identified putative kinase targets of immune evasion phenotypes (e.g., EPHA2 and PDGFRA), whose inhibition leads to the blockade of evasive programs and enhances T cell-mediated GBM killing. Together, this workflow provides a scalable blueprint for comprehensive charting of the genetic control of tumor-immune interactions.

genomics↗

bioRxiv2025

Oral Cavity Serves as Long-Term COVID-19 Reservoir with Increased Periodontal and Viral Disease Risk

BackgroundSARS-CoV-2 infection can lead to long-term health problems affecting multiple body systems termed long COVID. Currently, limited information exists about long-term oral health manifestations in COVID-19 patients with limited healthcare access. MethodsWe conducted a sequential, cross-sectional study (December 2020-March 2024) to assess how racial/ethnic differences (Black/Hispanic vs White/Asian) and health disparities affect oral and non-oral long COVID symptoms and their relationship with COVID-19 vaccination. We retrospectively reviewed patients oral health record from University of Illinois Chicago dental clinics before vaccination (December 2020; N=1150; Covid+/- N=575/group) and after vaccination (December 2021; N=592; Covid+/- N=292/group). Participants were recruited in two separate prospective groups of COVID-19 positive subjects (February-April 2021; pre-vaccination: N=158; January-March 2024; post-vaccination: N=171), we examined clinical indicators of oral (periodontal and salivary glands) and non-oral (neurologic) sequalae 3-6 months after initial exposure. We measured viral S protein by flow cytometry and quantified inflammatory markers, viral entry receptors, and oral viral load to correlate molecular, and cellular changes in COVID-19 positive subjects before and after vaccination. ResultsOur results identified racial disparity indicating oral associated post-acute sequelae (PASC) primarily manifested as periodontal (gum) disease (COVID-19 positive: 73.1{+/-}18.9% vs COVID-19 negative: 33.1{+/-}14.3%) and correlated with higher rates of dry mouth (57.5%), taste disturbance (47%), and smell loss (20%). Vaccination reduced oral PASC in COVID-19 positive subjects; however, periodontal disease indicators persisted compared to the COVID-19 negative group. Notably, 3-6 months post-infection, while SARS-CoV-2 Spike (S) transcript was rarely detected in saliva ([~]6%), its protein was commonly detected ([~]70%) in the COVID-19 positive subjects indicating incomplete viral clearance. This correlates with significantly higher salivary expression of viral entry receptors (ACE2, and TRMPSS2), and inflammatory mediators (IL-6, IL-8 and MMP-8), in COVID-19 positive subjects. This finding was further supported by higher prevalence of other oral viruses including Epstein-Barr Virus (70.5%), Herpes Simplex Virus (8.1%), and Human Papillomavirus (17.5%) in COVID-19 positive subjects. InterpretationCOVID-19 history significantly correlates with severe oral health complications in predominantly Black communities, while vaccination reduced but did not eliminate these issues. The oral cavity serves as a long-term viral reservoir, and periodontal inflammation with increased oral viral presence in COVID-positive patients may increase susceptibility to oral and non-oral viral diseases and identify risk for long COVID.

microbiology↗

bioRxiv2024

Myeloid-derived Suppressor Cells Mitigate Inflammation in Periodontal Disease

Myeloid derived suppressor cells (MDSCs) are a heterogeneous population of immature, immune suppressive myeloid cells. However, their role in periodontal disease (PD), a microbially induced inflammatory oral disease, remains understudied. Here we show that gingiva (gums) from PD patients exhibit significantly higher levels of MDSC markers including Granulocytic (G)-MDSC and Monocytic (M)-MDSC subsets as well as CD4+ T cells and CD19+ B cells. Gingival MDSC subsets exhibit potent immunoregulatory activity as marked by attenuated autologous CD4+ T cells proliferation and IFN{gamma} production. In a murine model of ligature-induced periodontitis (LIP), we noticed time-dependent gingival MDSC infiltration, which correlates with CD4+ T cell and CD19+ B cell infiltration. To test whether MDSC confer immunoregulatory function in vivo, we adoptively transferred G-MDSCs and M-MDSCs in mice. Interestingly, we observed significant reduction in inflammatory marker expression (IL6, TNF-, and IL-1{beta}), infiltration of CD4+ T cells, and concomitant increase in MDSC-derived immune suppressive molecules, ARG1 and IL-10, and CD4+CD25+FoxP3+ Tregs compared to mock. Conversely, depletion of MDSC using anti-Gr1 antibody resulted in marked induction of periodontal inflammation, reduced Treg population, and significantly higher alveolar bone loss. These findings, for the first time, suggest an anti-inflammatory and osteoprotective function of MDSCs in PD and offer a promising target to treat unresolved periodontal inflammation.

immunology↗

bioRxiv2023

Global Profiling of Differentiating Macrophages Identifies Novel Functional Long Non-coding RNAs Regulating Polarization and Innate Immune Responses

Macrophages (M{varphi}) are functionally dynamic immune cells that bridge innate and adaptive immune responses. However, the underlying epigenetic mechanisms that control the macrophage plasticity and innate immune functions are not well-elucidated. Here we performed transcriptome profiling of differentiating M1M{varphi} and M2M{varphi} and identified thousands of previously known and novel lncRNAs. We characterized three M{varphi}-enriched lncRNAs (LRRC75A-As1, GAPLINC and AL139099.5) with novel functions in M{varphi} differentiation, polarization and innate immunity. Knockdown of LRRC75A-As1, and GAPLINC downregulated M{varphi} differentiation markers CDw93 and CD68, and skewed macrophage polarization by decreasing M1 markers but had no significant impact on M2 markers. LRRC75A-As1, and GAPLINC RNAi in M{varphi} attenuated bacterial phagocytosis, antigen processing and inflammatory cytokine secretion supporting their functional role in potentiating innate immune functions. Mechanistically, lncRNA knockdown perturbed the expression of multiple cytoskeleton signaling thereby impairing M{varphi} migration suggesting their critical role in regulating macrophage polarity and motility. Together, our results show that M{varphi} acquire a unique repertoire of lncRNAs to shape differentiation, polarization and innate immune functions.

immunology↗

bioRxiv2023

Long noncoding RNA AL109754.1 Regulates Myeloid Dendritic Cell Differentiation and Potentiates TLR signaling

Dendritic cells (DCs) are key antigen presentation cells (APC) that bridge innate and adaptive immune functions to contain the pathogenic threats. Long noncoding RNAs (lncRNAs) are implicated in functional regulation of various biological processes including inflammation and immunity. However, the knowledge on myeloid DC expressed lncRNA repertoire and their regulatory functions is limited. In this study, we have reconnoitered the time-kinetics of lncRNA expression profiles during monocyte-to-DC differentiation and their roles in shaping DC functions. Our RNA-seq data identified thousands of differentially expressed lncRNAs associated with primary human monocyte-to-DC differentiation in vitro. We selected two lncRNAs viz., AL109754.1 and AC093278.2 that were enriched during DC differentiation. Knockdown of AL109754.1 but not AC093278 affects DCs differentiation as observed by marked reduction of surface markers CD1a, CD93 and CD209. These DCs also exhibit significant reduction in the expression of TLR 2, 4, 5, 7 and 9, suggesting that AL109754.1 expression is critical in maintaining TLR expression in DCs. Furthermore, reduced phosphorylation of NF-{kappa}B, IRF3 and IRF7 in AL109754.1 knockdown DCs treated with TLR agonists further substantiate their role in potentiating TLR signaling. Mechanistically, AL109754.1 knockdown DC showed significant downregulation of multiple NF-{kappa}B-induced genes and time-dependent inhibition of pro-inflammatory cytokine (IL-1{beta}, IL-6, IL-8 and TNF) secretion upon challenge with TLR 4, 5, or 7 agonists. Overall, this study characterized novel functions of AL109754.1 that regulates DC differentiation, and TLR-dependent innate immune activation.

immunology↗

bioRxiv2023

Dynamic Changes in Macrophage Polarization during the Resolution Phase of Periodontal Disease

Periodontal inflammation is largely governed by infiltration of myeloid cells, in particular macrophages. Polarization of M{varphi} within the gingival tissues is a well-controlled axis and has considerable consequences for how M{varphi} participate in inflammatory and resolution (tissue repair) phases. We hypothesize that periodontal therapy may instigate a pro-resolution environment favoring M2 M{varphi} polarization and contribute towards resolution of inflammation post-therapy. We aimed to evaluate the markers of macrophage polarization before and after periodontal therapy. Gingival biopsies were excised from human subjects with generalized severe periodontitis, undergoing routine non-surgical therapy. A second set of biopsies were excised after 4-6 weeks to assess the impact of therapeutic resolution at the molecular level. As controls, gingival biopsies were excised from periodontally healthy subjects, undergoing crown lengthening. Total RNA was isolated from gingival biopsies to evaluate pro- and anti-inflammatory markers associated with macrophage polarization by RT-qPCR. Mean periodontal probing depths, CAL and BOP reduced significantly after therapy and corroborated with the reduced levels of periopathic bacterial transcripts after therapy. Compared to heathy and treated biopsies, higher load of Aa and Pg transcripts were observed in disease. Lower expression of M1M{varphi} markers (TNF-, STAT1) were observed after therapy as compared to diseased samples. Conversely, M2M{varphi} markers (STAT6, IL-10) were highly expressed in post-therapy as opposed to pre-therapy, which correlated with clinical improvement. These findings corroborated with murine ligature-induced periodontitis and resolution model, comparing the respective murine M{varphi} polarization markers (M1 M{varphi}: cox2, iNOS2 and M2 M{varphi}: tgm2 and arg1). Our findings suggest that imbalance in M1 and M2 polarized macrophages by assessment of their markers can provide relevant clinical information on the successful response of periodontal therapy and can be used to target non-responders with exaggerated immune responses.

immunology↗

bioRxiv2023

LncRNA MALAT1/microRNA-30b axis regulate macrophage polarization and function

IntroductionMacrophages (M{varphi}) can polarize towards the proinflammatory M1 or proresolving M2 phenotype to control diverse biological processes such as inflammation, and tissue regeneration. Noncoding RNAs play critical roles in numerous biological pathways; however, their functional interaction in the regulation of M{varphi} polarization and immune responses remain unclear. ObjectivesTo examine relationship between lncRNA (MALAT1) and microRNA (miR-30b) in shaping macrophage polarization and immune functions. MethodsExpression of MALAT1 and miR-30b was examined in differentiating M1/M2 M{varphi}, human and murine inflamed gingival biopsies by RT-qPCR. MALAT1 and miR-30b direct interaction was examined by dual luciferase assays. Impact of MALAT1 knockdown and miR-30b overexpression was examined on macrophage polarization markers, bacterial phagocytosis, antigen uptake/processing and cytokine profiles. ResultsMALAT1 expression displays a time-dependent induction during M{varphi} differentiation and, upon challenge with TLR4 agonist (E. coli LPS). Knockdown of MALAT1 enhanced the expression of M2M{varphi} markers without affecting the M1M{varphi} markers, suggesting that MALAT1 favors the M1 phenotype by suppressing M2 polarization. MALAT1 knockdown M{varphi} exhibit reduced antigen uptake and processing, bacterial phagocytosis, and bactericidal activity, strongly supporting its critical role in regulating innate immune functions. Consistent with this, MALAT1 knockdown showed impaired cytokine secretion upon challenge with LPS. Importantly, MALAT1 exhibit an antagonistic expression pattern with all five members of the miR-30 family during M2M{varphi} differentiation. Dual-luciferase assays validated a novel sequence on MALAT1 that interacts with miR-30b, a microRNA that promotes the M2 phenotype. Phagocytosis and antigen processing assays unequivocally demonstrated that MALAT1 and miR-30b are functionally antagonistic. In human subjects with periodontal disease and murine model of ligature-induced periodontitis, we observed higher levels of MALAT1, and downregulation of miR-30b that correlates with higher M1M{varphi} markers expression in gingival tissues suggesting a pro-inflammatory function of MALAT1. ConclusionMALAT1/miR-30b antagonistic interaction shapes M{varphi} polarization in vitro and in inflamed gingival biopsies.

immunology↗

bioRxiv2023

Co-transplantation with mesenchymal stem cells and endothelial cells improvise islet engraftment and survival in STZ treated hyperglycemic mice

Though intra-portal islet transplantation demonstrated as best suited strategy for the reversal of hyperglycemia without the threat of iatrogenic hyperglycemia in type 1 diabetes (T1D) in patients, the inferior quality of post-transplantation (tx) vascularization needs to be addressed for the maximization of post-tx islet survival. Therefore, in this study, we have first generated MSCs and endothelial progenitor cells (EPC) from mice bone marrow by in house optimized protocol and then 3-D co-cultured them with mice islets. Secretion of in the culture supernatant suggested the pro-angiogenic nature of 3D cultured mice islets. After 5 days post-tx of these pro-angiogenic islets in the omental pouch of syngeneic mice led to: 1) restoration of normoglycemia, 2) secretion of mouse C-peptide and 3) induction of angiogenic factors after 3 days of post-tx. The induction of angiogenic factors was done by RT-qPCR of omental biopsies. Importantly, pro-angiogenic islet recipient mice also demonstrated the clearance of glucose within 75 min, reflecting their efficient function and engraftment. Our results highlights needs of 3-D co-culture islets for superior quality post-tx islet vasculature and better engraftment - crux to improvise the challenges associated with post-tx islet vascularization and functions.

biochemistry↗

bioRxiv2022

Direct conversion of somatic cells into insulin-producing-cells by user-defined multiplex-epigenetic-engineering vector (MEEV-b)

We demonstrate here a single-step and user-friendly approach to generate insulin producing cells by gRNA driven specific-activation of PDX1, NKX6.1, MAFA, Insulin and Glut2 genes in somatic cells via multiplex-epigenetic-engineering-vector (MEEV-{beta}) containing dCas9.P300core developed by us. Sorted Glut2+ cells could secrete insulin in response to glucose challenge and showed expression of {beta}-cell specific transcription factors: NKX2.2, and aforementioned genes. Expression of Cav1.3, GSK3{beta},, KJNC11, and SLC30A8 genes substantiated the functional insulin secreting machinery genes in these Glut2+ cells. Also, absence of ARX and GCG expression in these cells highlighted the specificity of the conversion.

synthetic biology↗

bioRxiv2020

PRAK-03202: A triple antigen VLP vaccine candidate against SARS CoV-2

The rapid development of safe and effective vaccines against SARS CoV-2 is the need of the hour for the coronavirus outbreak. Here, we have developed PRAK-03202, the worlds first triple antigen VLP vaccine candidate in a highly characterized S. cerevisiae-based D-CryptTM platform, which induced SARS CoV-2 specific neutralizing antibodies in BALB/c mice. Immunizations using three different doses of PRAK-03202 induces antigen specific (Spike, envelope and membrane proteins) humoral response and neutralizing potential. PBMCs from convalescent patients, when exposed to PRAK-03202, showed lymphocyte proliferation and elevated IFN-{gamma} levels suggestive of conservation of epitopes and induction of T helper 1 (Th1)-biased cellular immune responses. These data support the clinical development and testing of PRAK-03202 for use in humans.

immunology↗

bioRxiv2020

Multi-Antigenic Virus-like Particle of SARS CoV-2 produced in Saccharomyces cerevisiae as a vaccine candidate

Spike, Envelope and Membrane proteins from the SARS CoV-2 virus surface coat are important vaccine targets. We hereby report recombinant co-expression of the three proteins (Spike, Envelope and Membrane) in a engineered Saccharomyces cerevisiae platform (D-Crypt) and their self-assembly as Virus-like particle (VLP). This design as a multi-antigenic VLP for SARS CoV-2 has the potential to be a scalable vaccine candidate. The VLP is confirmed by transmission electron microscopy (TEM) images of the SARS CoV-2, along with supportive HPLC, Dynamic Light Scattering (DLS) and allied analytical data. The images clearly outline the presence of a "Corona" like morphology, and uniform size distribution.

biochemistry↗

bioRxiv2019

FK506-binding protein 13 expression is upregulated in interstitial lung disease and correlated with clinical severity: a potentially protective role.

Pulmonary fibrosis is a progressive lung disease characterized by myofibroblast accumulation and excessive extracellular matrix deposition. Endoplasmic reticulum (ER) stress initiates the unfolded protein response (UPR), a cellular stress response pathway that has been implicated in both inflammatory and fibrotic processes. Here, we sought to investigate the role of the 13 kDa FK506-binding protein (FKBP13), an ER stress-inducible molecular chaperone, in various forms of pulmonary fibrosis. We first characterized the gene and protein expression of FKBP13 in lung biopsy samples from 24 patients with idiopathic pulmonary fibrosis (IPF) and 17 control subjects. FKBP13 expression was found to be elevated in the fibrotic regions of IPF lung tissues, and within this cohort, was correlated with declining forced vital capacity and dyspnea severity. FKBP13 expression was also increased in lung biopsies of patients with hypersensitivity pneumonitis, rheumatoid arthritis, and sarcoidosis-associated interstitial lung disease. We next evaluated the role of this protein using FKBP13-/- mice in a bleomycin model of pulmonary fibrosis. Animals were assessed for lung function and histopathology at different stages of lung injury including the inflammatory (Day 7), fibrotic (Day 21) and resolution (Day 50) phase. FKBP13-/- mice showed increased infiltration of inflammatory cells and cytokines at Day 7, increased lung elastance and fibrosis at Day 21, and impaired resolution of fibrosis at Day 50. These changes were associated with an increased number of cells that stained positive for TUNEL and cleaved caspase 3 in the FKBP13-/- lungs, indicating a heightened cellular sensitivity to bleomycin. Our findings suggest that FKBP13 is a potential biomarker for severity or progression of interstitial lung diseases, and that it has a biologically relevant role in protecting mice against bleomycin-induced injury, inflammation and fibrosis.

pathology↗