Biology subjects

Chopra, A.

Publications and source records attributed to Chopra, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Enhanced cortical tracking of unfamiliar languages in both monolinguals and bilinguals

Humans routinely encounter speech in languages they have never heard, yet how the brain responds to such input and whether bilingual experience shapes this response remains unknown. Here, we used electroencephalography (EEG) and temporal response function (TRF) modeling to examine cortical tracking of the speech envelope in 24 English-monolingual and 24 English-Mandarin bilingual adults. Participants listened to naturally produced continuous speech in three languages: English (familiar to all), Mandarin (familiar to bilinguals only), and Vietnamese (unfamiliar to all). We report two main findings. First, both monolinguals and bilinguals showed enhanced cortical tracking for unfamiliar relative to familiar languages, evidenced by higher EEG prediction accuracy (PA). Monolinguals showed enhanced tracking for both Mandarin and Vietnamese, whereas bilinguals showed enhancement only for Vietnamese, consistent with Mandarin being a familiar language for this group. This finding suggests that enhanced cortical encoding of unfamiliar speech is a general property of the listening brain, not a signature of listening to a non-native language or reduced language proficiency. Second, bilinguals strikingly showed stronger cortical tracking than monolinguals overall, in both PA and TRF peak weights, with the TRF peak weight advantage present across all three languages, suggesting a difference in how bilingual experience shapes the neural encoding of speech. These findings have implications for understanding how the brain navigates the linguistic diversity of everyday life in an increasingly global, multilingual world.

neuroscience↗

bioRxiv2026

Copper chelation reprograms the tumour microenvironment to enhance immune checkpoint blockade therapy in preclinical mesothelioma

Immune checkpoint blockade provides durable benefit to only a minority of patients with pleural mesothelioma. Here we investigated whether targeting copper homeostasis could enhance anti-tumour immunity and improve responses to immune checkpoint blockade. Copper homeostasis genes were upregulated in human mesothelioma, localised to malignant and stromal cells but downregulated in lymphocytes. In murine mesothelioma, these genes were dynamically regulated during anti-CTLA-4 and anti-PD-1 therapy. Treatment with copper chelator triethylenetetramine reduced intratumoural copper, increased cytotoxic lymphocytes, and enriched inflammatory genes in tumour-infiltrating myeloid and lymphoid compartments. Furthermore, copper chelation enhanced anti-CTLA-4 and anti-PD-1 therapy in immunocompetent mesothelioma mouse models, leading to durable tumour control. Our findings identify copper homeostasis as a therapeutic vulnerability in mesothelioma and support clinical evaluation of copper depletion with first-line immune checkpoint blockade.

immunology↗

bioRxiv2026

SETD6-mediated methylation of PPARγ establishes a transcriptional feedback circuit promoting lipid accumulation in liver-derived cells

Peroxisome proliferator-activated receptor gamma (PPAR{gamma}) is a key transcriptional regulator of genes mediating adipogenesis (fat-cell differentiation) and lipid storage in several cell types like hepatocytes. As such, its regulation is crucial for cell and organismal physiology. Indeed, PPAR{gamma}s activity is regulated by multiple mechanisms, including post-transcriptional modifications, which, when dys-coordinated, may contribute to the pathogenesis of various states, including obesity, insulin resistance, and fatty liver disease. Here, we demonstrate that SETD6 binds to, and methylates PPAR{gamma} at lysine 170 (K170) both in vitro and in liver-derived cells. This methylation event, in turn, is required for PPAR{gamma}-mediated activation of SETD6 transcription via promoter binding, forming a positive feedback regulatory loop. RNA sequencing revealed that both SETD6 and PPAR{gamma} methylation at K170 are required for full induction of lipid metabolism genes expression, manifesting functionally in lipid droplet biogenesis in liver-derived cells. Together, our findings uncover a novel role for lysine methylation of PPAR{gamma} in the regulation of lipid synthesis and lipid droplet biogenesis, thereby identifying putative new therapeutic targets for lipid over-production diseases, including MAFLD (Metabolic dysfunction-associated fatty liver disease) and obesity.

cell biology↗

bioRxiv2025

Proteo-transcriptomic reprogramming and resource reallocation define the aging mammalian brain

Brain aging is a major risk for neurodegeneration, yet the underlying molecular mechanisms remain poorly understood. Here we performed an integrative proteo-transcriptomic analysis of the aging mouse brain, uncovering molecular signatures of aging through the assessment of protein aggregation, mRNA relocalization, and comparative proteomics across eight models of premature aging and neurodegeneration. We identified dynamic changes in physiological aging highlighting differences in synaptic maintenance and energy-allocation. These were linked to changes associated with fundamental protein biochemical properties such as size and net charge. Network analysis highlighted a decrease in mitochondrial complex I proteins not compensated at the mRNA level. Aggregation of 60S ribosome subunits indicated deteriorating translation efficiency and was accompanied by mitochondrial and proteasomal imbalance. The analysis of the nine models revealed key similarities and differences between physiological aging and pathology. Overall, our study provides an extensive resource on molecular aging, and offers insights into mechanisms predisposing to neurodegeneration, easily accessible at our Brain Aging and Molecular Atlas Project (BrainAging-MAP) website.

neuroscience↗

bioRxiv2025

A 3D Human Neuron-on-Chip Platform to Monitor Neuronal Injury Responses

Traumatic brain injury (TBI) is a major cause of neurological dysfunction and long-term neurodegeneration, yet the intrinsic neuronal contributions to TBI pathophysiology remain incompletely defined. Here, we present a novel Neuron-on-Chip microfluidic platform that can be used to mechanically injure mature human prefrontal cortex neurons (hPFCs) embedded in three-dimensional (3D) hydrogels, enabling the study of injury responses in pure neuronal cultures. We assessed real-time calcium dynamics across 13 metrics of single-cell and network activity, revealing a biphasic injury response: an early phase (0.5-24 hr) characterized by excitotoxicity, hyper-synchronized bursting, and network collapse; and a late phase (8 d) marked by sustained depolarization and structural remodeling. Secretome profiling uncovered progressive elevations in extracellular pT181 and total Tau from days 1 to 5 post-injury. Cytokine analyses identified early (24 hr) elevations in IP-10, IL-10, IFN2, and NCAM, and late increases (8 d) in CXCL9 and MPO, linking neuronal activity changes to stage-specific inflammatory signaling. Immunocytochemistry and immunoblotting confirmed temporally ordered upregulation of calpain-1 and active caspase-3 (days 1-3), phosphorylated Tau (AT8+, days 5-8), and neurofibrillary tangle-like Tau aggregates (NFT+, day 8). These findings establish our platform as a scalable microphysiological model for probing the dynamic cellular and molecular sequelae of neuronal response to injury, offering insights into neurodegeneration and opportunities for therapeutic discovery.

neuroscience↗

bioRxiv2025

The HOTAIRM1-miR-222 Axis Regulates Venetoclax Resistance and Defines a High-Risk Subset in Pediatric t(8;21) Acute Myeloid Leukemia

Although acute myeloid leukemia (AML) with the RUNX1::RUNX1T1 fusion [t(8;21)(q22;q22.1)] defines a distinct cytogenetic subtype, differences in treatment response suggest additional molecular contributors beyond chromosomal abnormalities. Deregulated hematopoietic lineage-specific long non-coding RNAs (lncRNAs) contribute to leukemogenesis and therapy resistance. To investigate their role in t(8;21) AML, we performed whole-transcriptome sequencing of pediatric patients and age-matched healthy controls, identifying significant downregulation of lncRNA HOTAIRM1, a regulator of myeloid differentiation (adjusted P < 0.05). This was confirmed in a single-cell RNA-sequencing dataset (GSE116256) and the Leukemia MILE dataset (GSE13159, P=0.03). Validation of expression in our study cohort using qPCR specifically demonstrated significant downregulation of the myeloid specific isoform, HOTAIRM1 - HM1V2 (P<0.0001). Analysis of downstream pathways activated by HM1V2 loss identified miR-222, an oncomiR, as a de-repressed target (P=0.01). Elevated miR-222 expression was observed across AML cell lines (P<0.05), leukemic stem and progenitor cells (GSE117090, P<0.05), AML plasma-derived exosomes (GSE142699, P<0.0001), the current study dataset (P<0.0001), and the TARGET AML dataset (P<0.0001). Restoring HM1V2 expression with epigenetic agents azacytidine and panobinostat induced apoptosis in venetoclax-resistant Kasumi-1 cells (P < 0.01), through suppression of miR-222 (P < 0.01) and downregulation of anti-apoptotic proteins BCL-xL and MCL-1 (P < 0.05), key mediators of the venetoclax resistance mechanism. Machine learning based feature selection and Cox regression analysis showed that high miR-222 expression predicts poor outcome in pediatric t(8;21) AML, validated in both our institutional pediatric AML cohort (P < 0.05) and the multi-institutional TARGET cohort (P < 0.0001). Together, our findings highlight an epigenetic based approach to restore isoform-specific HM1V2 pathway function in venetoclax-resistant AML cells, and identifies miR-222 as a prognostic marker to refine risk stratification within the traditionally favorable-risk t(8;21) AML subgroup. Key PointsO_LILoss of myeloid lineage specific isoform of lncRNA HOTAIRM1 - HOTAIRM1 variant 2, results in de-repression of microRNA miR-222, and contributes to venetoclax resistance in pediatric AML patients harbouring the t(8;21)(q22;q22.1)/RUNX1::RUNX1T1 fusion. C_LIO_LIMicroRNA miR-222 shows potential as a single marker predictor that complements current risk stratification by identifying a subset of pediatric t(8;21) AML patients with poor prognosis. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/663834v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@19a0931org.highwire.dtl.DTLVardef@1d1a51aorg.highwire.dtl.DTLVardef@ae6783org.highwire.dtl.DTLVardef@de78e_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Crystallographic fragment screening of the dengue virus polymerase reveals multiple binding sites for the development of non-nucleoside antiflavivirals

Dengue viruses (DENV) infect approximately 400 million people each year, and there are currently no effective therapeutics available. To explore potential starting points for antiviral drug development, we conducted a large-scale crystallographic fragment screen targeting the RNA-dependent RNA polymerase (RdRp) domain of the non-structural protein 5 (NS5) from DENV serotype 2. Our screening, which involved 1,108 fragments, identified 60 hit compounds across various known binding sites, including the active site, N pocket, and RNA tunnel. Additionally, we discovered a novel binding site and a fragment-binding hotspot in thumb site II. These structural findings open amenable avenues for developing non-nucleoside inhibitors and offer valuable insights for future structure-based drug design aimed at DENV and other flaviviral RdRps.

biophysics↗

bioRxiv2025

BTK-NLRP3-Caspase1 and Gasdermin D-Caspase 11 pathways jointly drive neuroinflammation and functional impairments in a rat model of psychosocial stress

Despite serious health and economic burden, borne more prominently by lower and lower middle-income countries, pharmacotherapy for common psychiatric disorders rely on drugs altering neurotransmission, with partial efficacies. The persistence of a chronic yet sub-threshold inflammation across the periphery and the brain is well documented in the patients and animal models of these disorders and can be investigated for augmenting pharmacotherapy. IL1{beta}, a pleiotropic cytokine and a key regulator of neuroinflammation has been of particular interest in this regard. Previous studies on rodent models of anxiogenic stress show activation of a large multiprotein complex - the NLRP3 inflammasome, which increases IL1{beta} production facilitated by caspase 1, through what is considered a canonical inflammasome activation pathway. However, there exists a second non canonical inflammasome activation pathway whose impact on IL1{beta} release, inflammation and behavioral consequences remain unclear. Using rat models of physical and psychosocial stress, we observed stress-induced sex-specific upregulation of activated caspase 11 and gasdermin D N-terminal fragments, the mediators of the non-canonical inflammasome pathway that facilitates IL1{beta} release through pore formations in the plasma membrane. This is the first report of non-canonical inflammasome pathway being activated in the brain and peripheral immune cells in response to psychosocial stress. Inhibition of caspase 11 with wedelolactone, or Gasdermin D cleavage with Disulfiram reduced stress-induced elevation of IL1{beta} levels, anxiety and fear acquisition, facilitated fear extinction and recall, and improved working memory. Combination treatments targeting both canonical (ibrutinib for pBTK/NLRP3 or MCC950 for NLRP3 inhibition) and non-canonical (wedelolactone for caspase 11 or disulfiram for gasdermin D) pathways proved more efficacious in reducing stress-mediated neuroinflammation, dendritic spine elimination in the CA3 region of the hippocampus and behavioral dysfunction. Furthermore, psychosocial stress drove peripheral inflammation, in peripheral blood mononuclear cells, which was mitigated by the combination treatment. Taken together, this study reveals a novel mechanism underlying psychosocial stress involving both canonical and non-canonical inflammasome signaling to facilitate IL1{beta} induction and behavioral changes. Our finding further suggests that combined targeting of the NLRP3 inflammasome and gasdermin D could contribute to the development of future transdiagnostic therapeutic targets for stress, anxiety, and depression.

neuroscience↗

bioRxiv2024

AuroraB-kinase methylation by SETD6 regulates cytokinesis and protects cells from chromosomal instability

SETD6 is a non-histone lysine methylatransferase, previously shown to participate in several housekeeping signaling pathways such as the NFkB pathway, Wnt signaling pathway, mitosis and more. In the current study we show evidence that SETD6 methylation is involved in the regulation of cytokinesis - the final process that divides cell contents into two daughter cells. SETD6 depleted HeLa cells presented high levels of chromatin bridges and actin patches, which are commonly observed following chromosomal segregation errors. In a proteomic screen we identified Aurora-B as a novel SETD6 substrate. Aurora-B kinase is an essential regulator of cytokinesis, known to actively delay cytokinesis as a response to the presence of chromatin in the midzone. We found that SETD6 binds and methylates Aurora-B on two adjacent lysine residues. Upon replication stress, Aurora-B methylation by SETD6 increases but is abolished when the two lysine methylation targets are substituted. In addition, replication stress led to a high tendency of SETD6 depleted cells to multinucleate, a major chromosomal-instability (CIN) phenotype. We detected a significant reduction in the Aurora-B kinase activity during cytokinesis in SETD6 knockout cells upon replication stress, which could be the mechanism underlying the accumulation of CIN phenotypes in these cells. CIN is a hallmark of cancer and is associated with tumor cell malignancy. Our findings suggest that Aurora-B methylation by SETD6 carries meaningful implications on tumorigenic cellular pathways.

cell biology↗

bioRxiv2024

The epitranscriptomic m6A RNA modification modulates synaptic function in ageing and in a mouse model of synucleinopathy

N6-methyladenosine (m6A) is the most abundant and conserved transcriptional modification in eukaryotic RNA, regulating RNA fate. While the functions of m6A in the development of the mammalian brain have been extensively studied, its roles in synaptic plasticity, cognitive decline, motor function, or other brain circuits remain underexplored. To date, the role of this modification in Parkinsons disease (PD) and other synucleinopathies has been largely unknown. Here, we investigated the m6A epitranscriptome in a mouse model of synucleinopathy. We performed m6A RNA immunoprecipitation sequencing (meRIP-seq) to obtain the m6A epitranscriptome of the midbrain in young (3 mo) and aged (15 mo) A30P-aSyn transgenic mice (aSyn Tg) and C57BL6 control wild type (Wt) mice. We observed hypermethylation of synaptic genes in 3 mo aSyn Tg mice compared to age-matched Wt mice. This methylation was reduced during ageing, with synaptic genes becoming increasingly hypomethylated. Using immunofluorescence imaging alongside biochemical analysis, we further investigated the expression of m6A regulatory enzymes -- writer, N6-Adenosine-Methyltransferase Complex Catalytic Subunit (METTL3); reader, YTH N6-methyladenosine RNA-binding protein (YTHDF1); and eraser, fat mass and obesity-associated protein (FTO) -- in the cortex, striatum, hippocampus, and cerebellum of Wt and aSyn Tg mice, as well as in primary cortical neuronal cultures. We observed that the levels of METTL3, YTHDF1 and FTO were similar between Wt and aSyn Tg mice. Interestingly, the writer protein METTL3 was found in both the nucleus and in the post-synaptic compartment in neuronal cultures. Our findings suggest that alterations in the regulation of m6A RNA methylation may be associated with neurodegeneration and ageing and that this level of epitranscriptomic regulation plays a significant role at the synapse.

neuroscience↗

bioRxiv2024

A pumpless and tubeless microfluidic device enables extended in vitro development of Cryptosporidium parvum

The enteric parasite Cryptosporidium remains a treatment challenge for drinking water utilities globally due to its resistance to chlorine disinfection. However, the lack of an in vitro culture system for Cryptosporidium that is both cost-effective and reliable remains a key bottleneck in Cryptosporidium research. Here we report that the microfluidic culture of HCT-8 cells under fluid shear stress enables the extended development of Cryptosporidium parvum. Specifically, the growth of C. parvum in a user-friendly pumpless microfluidic device was assessed using immunofluorescence assays, scanning electron microscopy and quantitative PCR, which revealed that development peaked at six days post-infection but continued for ten days in total. Oocysts produced within the microfluidic device were infective to fresh HCT-8 monolayers, however these oocysts were only present at low levels. We anticipate that such microfluidic approaches will facilitate a wide range of in vitro studies on Cryptosporidium and may have the potential to be further developed as a routine infectivity assessment tool for the water industry.

microbiology↗

bioRxiv2023

Design of SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model

The emergence of SARS-CoV-2 variants and drug-resistant mutants calls for additional oral antivirals. The SARS-CoV-2 papain-like protease (PLpro) is a promising but challenging drug target. In this study, we designed and synthesized 85 noncovalent PLpro inhibitors that bind to the newly discovered Val70Ub site and the known BL2 groove pocket. Potent compounds inhibited PLpro with inhibitory constant Ki values from 13.2 to 88.2 nM. The co-crystal structures of PLpro with eight leads revealed their interaction modes. The in vivo lead Jun12682 inhibited SARS-CoV-2 and its variants, including nirmatrelvir-resistant strains with EC50 from 0.44 to 2.02 {micro}M. Oral treatment with Jun12682 significantly improved survival and reduced lung viral loads and lesions in a SARS-CoV-2 infection mouse model, suggesting PLpro inhibitors are promising oral SARS-CoV-2 antiviral candidates. One-Sentence SummaryStructure-guided design of SARS-CoV-2 PLpro inhibitors with in vivo antiviral efficacy in a mouse model.

microbiology↗

bioRxiv2023

Multiomic single-cell sequencing defines tissue-specific responses in Stevens-Johnson Syndrome and Toxic epidermal necrolysis.

Stevens-Johnson syndrome and toxic epidermal necrolysis (SJS/TEN) is a rare but life-threatening cutaneous drug reaction mediated by human leukocyte antigen (HLA) class I-restricted CD8+ T-cells. To obtain an unbiased assessment of SJS/TEN cellular immunopathogenesis, we performed single-cell (sc) transcriptome, surface proteome, and TCR sequencing on unaffected skin, affected skin, and blister fluid from 17 SJS/TEN patients. From 119,784 total cells, we identified 16 scRNA-defined subsets, confirmed by subset-defining surface protein expression. Keratinocytes upregulated HLA and IFN-response genes in the affected skin. Cytotoxic CD8+ T-cell subpopulations of expanded and unexpanded TCR{beta} clonotypes were shared in affected skin and blister fluid but absent or unexpanded in SJS/TEN unaffected skin. SJS/TEN blister fluid is a rich reservoir of oligoclonal CD8+ T-cells with an effector phenotype driving SJS/TEN pathogenesis. This multiomic database will act as the basis to define antigen-reactivity, HLA restriction, and signatures of drug-antigen-reactive T-cell clonotypes at a tissue level.

immunology↗

bioRxiv2023

Distinct blood CD3+ CD14+ T Cell-Monocyte complexes harbor HIV and are dynamic, glucose-dependent, and increased in individuals with glucose intolerance

An increased risk of cardiometabolic disease accompanies persistent systemic inflammation. Yet, the innate and adaptive immune system features in persons who develop these conditions remain poorly defined. Doublets, or cell-cell complexes, are routinely eliminated from flow cytometric and other immune phenotyping analyses, which limits our understanding of their relationship to disease states. Using well-characterized clinical cohorts, including participants with controlled HIV as a model for chronic inflammation and increased immune cell interactions, we show that circulating CD14+ monocytes complexed to CD3+ T cells are dynamic, biologically relevant, and increased in individuals with diabetes after adjusting for confounding factors. The complexes form functional immune synapses with increased expression of proinflammatory cytokines and greater glucose utilization. Furthermore, in persons with HIV, the CD3+T-cell: CD14+monocyte complexes had more HIV copies compared to matched CD14+ monocytes or CD4+ T cells alone. Our results demonstrate that circulating CD3+T-cell:CD14+monocyte pairs represent dynamic cellular interactions that may contribute to inflammation and cardiometabolic disease pathogenesis and may originate or be maintained, in part, by chronic viral infections. These findings provide a foundation for future studies investigating mechanisms linking T cell-monocyte cell-cell complexes to developing immune-mediated diseases, including HIV and diabetes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/538020v2_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@fdc324org.highwire.dtl.DTLVardef@168fc4org.highwire.dtl.DTLVardef@138a9a0org.highwire.dtl.DTLVardef@1087108_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LICirculating CD3+ CD14+ T cell-monocyte complexes are higher in individuals with diabetes. C_LIO_LICD3+ CD14+ T cell-monocytes complexes comprise a heterogenous group of functional and dynamic cell-cell interactions. C_LIO_LIThe proportion of CD3+ CD14+ T cell-monocyte complexes is positively associated with fasting blood glucose and negatively with plasma IL-10 levels and CD4+ T regulatory cells. C_LIO_LICD3+ CD14+ T cell-monocyte complexes are metabolically flexible and can utilize both glycolysis and oxidative phosphorylation for their energy requirements. C_LIO_LIIn persons with treated HIV, CD3+ CD14+ T cell-monocytes have more detectable HIV DNA than circulating CD4+ T cells alone. C_LI

immunology↗

bioRxiv2022

The Halo Library, a Tool for Rapid Identification of Ligand Binding Sites on Proteins Using Crystallographic Fragment Screening

X-ray crystallographic fragment screening (XCFS) uses fragment-sized molecules ([~]60 - 300 Da) to access binding sites on proteins that may be inaccessible to larger drug-like molecules (>300 Da). Previous studies from our lab and others have shown that fragments containing halogen atoms have a higher binding occurrence compared to non-halogenated fragments. Specifically, we showed that 4-halopyrazoles hold potential for predicting the likelihood of success of a XCFS campaign. Here, we designed the Halo Library containing 46 halogenated fragments (including the "universal fragment" 4-bromopyrazole). The basis of fragment selection was presence of (at least) one halogen atom, and binding to or inhibitory activity against (at least) two targets in literature. The library was screened against crystals of HIV-1 reverse transcriptase with drug rilpivirine, yielding an overall hit rate of 26%. Two new binding sites were discovered in addition to previously reported sites, and several hot spots were identified (i.e., sites with multiple fragment hits). This small library may thus provide a convenient tool for assessing feasibility of a target for XCFS, mapping hot spots and cryptic sites, as well as finding fragment binders that can be useful for developing drug leads.

biochemistry↗

bioRxiv2022

Multiplexed measurement of binding- and neutralizing antibodies to SARS-CoV-2 variants in 12.000 post-vaccine sera

Diagnostic assays currently used to monitor the efficacy of COVID-19 vaccines measure levels of antibodies to the receptor-binding domain of ancestral SARS-CoV-2 (RBDwt). However, the predictive value for protection against new variants of concern (VOCs) has not been firmly established. Here, we used bead-based arrays and flow cytometry to measure binding of antibodies to spike proteins and receptor-binding domains (RBDs) from VOCs in 12,000 sera. Effects of sera on RBD-ACE2 interactions were measured as a proxy for neutralizing antibodies. The samples were obtained from healthy individuals or patients on immunosuppressive therapy who had received two to four doses of COVID-19 vaccines and from COVID-19 convalescents. The results show that anti-RBDwt titers correlate with the levels of binding- and neutralizing antibodies against the Alpha, Beta, Gamma, Delta, Epsilon and Omicron variants. The benefit of multiplexed analysis lies in the ability to measure a wide range of anti-RBD titers using a single dilution of serum for each assay. The reactivity patterns also yield an internal reference for neutralizing activity and binding antibody units per milliliter (BAU/ml). Results obtained with sera from vaccinated healthy individuals and patients confirmed and extended results from previous studies on time-dependent waning of antibody levels and effects of immunosuppressive agents. We conclude that anti-RBDwt titers correlate with levels of neutralizing antibodies against VOCs and propose that our method may be implemented to enhance the precision and throughput of immunomonitoring.

immunology↗

bioRxiv2022

A Single-Cell Molecular Atlas of White Adipose Tissue Shows Differences in Myeloid and Lymphoid Cell Polarization in Type 2 Diabetes and HIV Infection

Subcutaneous adipose tissue (SAT) is a critical regulator of systemic metabolic homeostasis. Persons with HIV (PWH) have an increased risk of metabolic diseases and significant alterations in the SAT immune environment compared with the general population. We generated a comprehensive SAT atlas to characterize cellular compositional and transcriptional changes in 59 PWH with a spectrum of metabolic health. Glucose intolerance was associated with increased lipid-associated macrophages and CD4+ and CD8+ T effector memory cells, and decreased perivascular macrophages. We observed a coordinated intercellular regulatory program which enriched for genes related to inflammation and lipid-processing across multiple cell types as glucose intolerance increased. Increased CD4+ effector memory tissue resident cells most strongly associated with altered expression of adipocyte genes critical for lipid metabolism and cellular regulation. Many of these findings were present in a separate group of 32 diabetic HIV-negative persons, suggesting these changes are not specific to HIV.

immunology↗

bioRxiv2022

Evaluation of the antimicrobial, anti-adhesion, anti-biofilm and cell proliferation assay of a de-novo goji berry extract against periodontal pathogens: a comparative in-vitro study

Lycium barbarum, commonly known as goji berry, Chinese berry, or Tibetian berry, is emerging as a popular "superfood" with anti-inflammatory and antioxidant properties. Goji berry is being used for the treatment of various cancers, gastrointestional disorders, stroke, diabetes, Alzheimers disease, and glaucoma. However, its use for management of oral inflammatory diseases has not been explored. Therefore, the present study aims to evaluate the antimicrobial, anti-adhesion, and anti-biofilm, and cytotoxic properties of an ethanolic extract of Lycium barbarum (LBE) against oral and periodontal pathogens. The antimicrobial properties of LBE against five microorganisms were tested and compared against Chlorhexidine and doxycycline along with cytotoxicity and cell viability on the gingival fibroblast and modified keratinocyte cell lines. The anti-adhesion and anti-biofilm properties of LBE against Porphyromonas gingivalis, at its minimal bactericidal value, were evaluated. The antimicrobial, anti-adhesion and antibiofilm properties of LBE were found to be comparable to chlorhexidine but less than that of doxycycline. The LBE extract was also compactible to gingival fibroblast tissues and oral keratinocytes at 1 mg/ml. The results proved that goji berry is as effective as chlorhexidine and can be used as a promising natural herb for the management of inflammatory diseases of oral cavity.

microbiology↗