Biology subjects

Patel, C.

Publications and source records attributed to Patel, C..

13 recordsLinked to original sources

bioRxiv2026

CD19 CAR Engineered T Regulatory Cells Promote Durable Immune Tolerance in Experimental Systemic Lupus Erythematosus

While the immune reset induced by CD19 CAR T therapies has shown striking promise in systemic lupus erythematosus (SLE), the nature and duration of benefit mediated by B cell depletion remains unclear. Loss of tolerance in SLE is driven by extrafollicular and germinal center interactions between dendritic cells and self-reactive T and B cells. We hypothesized that CD19 CAR-engineered regulatory T cells (CAR19 EngTreg), capable of suppressing multiple autoimmune effector cell types, might promote long-term tolerance without producing high-levels of inflammatory mediators. To generate CAR19 EngTreg, we combined CD19 CAR delivery with homology directed repair at the FOXP3 locus to drive constitutive, stable FOXP3 expression in CD4 T cells. CAR19 EngTreg expressed canonical Treg markers; exhibited minimal inflammatory cytokine production; and blocked human B cell differentiation into antibody secreting plasma cells. In humanized mouse models, transfer of CAR19 EngTreg led to a reduction in B cell numbers with low inflammatory cytokine production relative to CD19 CAR Teff, and reduced tissue inflammation. In a short-term, in vivo imiquimod-induced inflammatory model, murine CAR19 EngTreg reduced skin pathology, spleen size, and inflammatory cytokines. Finally, in two distinct mouse models of lupus, CAR19 EngTreg persisted for >4 months leading to reduced autoimmune T and B effector populations, sustained reduction in multiple autoantibodies and improved renal function and histopathology. Thus, CAR19 EngTreg may offer a promising and durable therapeutic avenue for B cell-mediated autoimmune disorders capable of long-term regulation of both autoreactive B and T cells.

immunology↗

bioRxiv2026

MicroRNA-223 Enhances Microglia-Dependent Clearance of Amyloid Beta Plaques and Ameliorates Behavioral Deficits in a Mouse Model of Alzheimer's Disease

The Alzheimers disease (AD) brain is characterized by dysregulated expression of multiple microRNAs (miRNA), positioning them as promising diagnostic and therapeutic targets. The levels of glia-enriched miR-223 are abnormal in the brains and plasma of AD patients and miR-223 is neuroprotective in models of stroke. However, whether miR-223 can be beneficial in AD is not known. Here, we report that intracerebroventricular (ICV) injection of miR-223 oligonucleotide mimic alleviated cognitive impairment, reduced amyloid beta (A{beta}) pathology, and ameliorated the defects in synaptic marker expression in AppNL-G-F AD model mice. Mechanistically, miR-223 induced microglial clustering around A{beta} plaques with a concomitant upregulation of microglial phagocytic receptors AXL, TREM2 and CD11c, while pharmacological microglial depletion abolished the plaque-clearance phenotype. Moreover, in human iPSC-derived microglia miR-223 directly targeted multiple genes in the endo-lysosomal pathway, including AD risk gene SPPL2A, indicating that it acts as a major regulator of microglial phenotype. Lastly, long-term AAV-mediated overexpression of miR-223 recapitulates its beneficial effects on cognition, pathology, and synaptic marker expression. Our study demonstrates a novel approach for the treatment of AD using miR-223 and highlights the potential of RNAi-based therapeutics in neurodegenerative disease.

neuroscience↗

bioRxiv2026

ER-associated protein degradation initiates by retrotranslocation from the ER quality control compartment

Misfolded proteins are eliminated from the endoplasmic reticulum (ER) by ER-associated degradation (ERAD), a process requiring their exit from the ER and delivery to cytosolic proteasomes via the key retrotranslocation step. Conventional assays detect fully extracted substrates, overlooking early initiation events. Here, we use an Escherichia coli-derived Biotin Acceptor Peptide (BAP)-biotin ligase BirA system to detect ERAD substrates upon cytosolic exposure. Using the model ERAD substrate H2a, we show that cytosolic BirA selectively biotinylates luminal BAP tags during early cytosolic exposure, enabling detection of substrates engaging the mammalian retrotranslocation machinery independently of subsequent extraction. Combined with high-resolution expansion fluorescence microscopy, this approach reveals active initiation of ERAD at the specialized ER-derived quality control compartment (ERQC). Substrates become transiently exposed to the cytosol while remaining membrane-associated, followed by tight coupling of polyubiquitination, transmembrane segment extraction, deglycosylation and degradation. Functional perturbations indicate that mannose trimming enables initiation, whereas p97 and HRD1 support later extraction and ubiquitination.

cell biology↗

bioRxiv2024

Oligosaccharyltransferase is involved in targeting to ER-associated degradation

Most membrane and secretory proteins undergo N-glycosylation, catalyzed by oligosaccharyltransferase (OST), a membrane-bound complex in the endoplasmic reticulum (ER). Proteins failing quality control are degraded via ER-associated degradation (ERAD), involving retrotranslocation to cytosolic proteasomes. Using SILAC proteomics, we identified OST subunits as key interactors with a misfolded ER protein bait, suggesting unexpected involvement in ERAD. Previous reports implied additional roles for OST subunits beyond N-glycosylation, such as quality control by ribophorin I. We tested OST engagement in glycoprotein and non-glycosylated protein ERAD; overexpression or partial knockdown of OST subunits interfered with ERAD in conditions that did not affect glycosylation. Effects were studied on misfolded membrane proteins, BACE476 and asialoglycoprotein receptor H2a, and the luminal 1-antitrypsin NHK variant. OST appears to participate in late ERAD stages, interacting with the E3 ligase HRD1 and facilitating retrotranslocation. Molecular dynamics simulations suggest membrane thinning by OST transmembrane domains, possibly assisting retrotranslocation via membrane distortion.

cell biology↗

bioRxiv2023

Maternal IL-10 restricts fetal emergency myelopoiesis

Neonates, in contrast to adults, are highly susceptible to inflammation and infection. Here we investigate how late fetal liver (FL) mouse hematopoietic stem and progenitor cells (HSPC) respond to inflammation, testing the hypothesis that deficits in engagement of emergency myelopoiesis (EM) pathways limit neutrophil output and contribute to perinatal neutropenia. We show that despite similar molecular wiring as adults, fetal HSPCs have limited production of myeloid cells at steady state and fail to activate a classical EM transcriptional program. Moreover, we find that fetal HSPCs are capable of responding to EM-inducing inflammatory stimuli in vitro, but are restricted by maternal anti-inflammatory factors, primarily interleukin-10 (IL-10), from activating EM pathways in utero. Accordingly, we demonstrate that loss of maternal IL-10 restores EM activation in fetal HSPCs but at the cost of premature parturition. These results reveal the evolutionary trade-off inherent in maternal anti-inflammatory responses that maintain pregnancy but render the fetus unresponsive to EM activation signals and susceptible to infection. HIGHLIGHTSO_LIThe structure of the HSPC compartment is conserved from late fetal to adult life. C_LIO_LIFetal HSPCs have diminished steady-state myeloid cell production compared to adult. C_LIO_LIFetal HSPCs are restricted from engaging in emergency myelopoiesis by maternal IL-10. C_LIO_LIRestriction of emergency myelopoiesis may explain neutropenia in septic neonates. C_LI eTOC BLURBFetal hematopoietic stem and progenitor cells are restricted from activating emergency myelopoiesis pathways by maternal IL-10, resulting in inadequate myeloid cell production in response to inflammatory challenges and contributing to neonatal neutropenia.

developmental biology↗

bioRxiv2022

Signaling Node at TSC2 S1365 Potently Regulates T-Cell Differentiation and Improves Adoptive Cellular Cancer Therapy

MTORC1 integrates signaling from the immune microenvironment to regulate T-cell activation, differentiation, and function. TSC2 in the tuberous sclerosis complex potently regulates mTORC1 activation. CD8+ T-cells lacking TSC2 have constitutively enhanced mTORC1 activity and generate potent effector T cells; however sustained mTORC1 activation prevents generation of long-lived memory CD8+ T-cells. Here we show manipulating TSC2 at Ser1365 potently regulates activated but not basal mTORC1 signaling in T cells. Unlike non-stimulated TSC2 knockout cells, CD8+ T-cells expressing mutant TSC2-S1365A (SA) have normal basal mTORC1 activity. PKC and T-cell Receptor (TCR) stimulation induces TSC2 S1365 phosphorylation and preventing this with the SA mutation markedly increases mTORC1 activation and T-cell effector function. Consequently, CD8+ SA T-cells display greater effector responses while retaining their capacity to become long-lived memory T-cells. CD8+ SA T-cells also display enhanced effector function under hypoxic and acidic conditions. In murine and human solid-tumor models, CD8+ SA T-cells used as adoptive cell therapy have greater anti-tumor immunity than WT CD8+ T-cells. These findings reveal an upstream mechanism to regulate mTORC1 activity in T-cells. The TSC2-SA mutation enhances both T-cell effector function and long-term persistence/memory formation, supporting a novel approach to engineer better CAR-T cells to treat cancer.

immunology↗

bioRxiv2022

COP I and II dependent trafficking controls ER-associated degradation

Misfolded proteins and components of the endoplasmic reticulum (ER) quality control and ER associated degradation (ERAD) machineries concentrate in mammalian cells in the pericentriolar ER-derived quality control compartment (ERQC), suggesting it as a staging ground for ERAD. By tracking the chaperone calreticulin and an established ERAD substrate, asialoglycoprotein receptor H2a, we have now determined that the trafficking to the ERQC is reversible and recycling back to the ER is slower than the movement in the ER periphery. The dynamics suggest vesicular trafficking rather than diffusion. Indeed, using dominant negative mutants of ARF1 and Sar1 or the drugs Brefeldin A and H89, we observed that COPI inhibition causes accumulation in the ERQC and increased retrotranslocation and ERAD, whereas COPII inhibition has the opposite effect. Our results suggest that targeting of misfolded proteins to ERAD involves COPII-dependent transport to the ERQC and that they can be retrieved to the peripheral ER in a COPI-dependent manner.

cell biology↗

bioRxiv2022

Engineering functional membrane-membrane interface by InterSpy

Engineering synthetic interfaces between membranes has potential applications in designing non-native cellular communication pathways and creating synthetic tissues. Here, InterSpy is introduced as a synthetic biology tool consisting of a heterodimeric protein engineered to form and maintain membrane-membrane interfaces between apposing synthetic as well as cell membranes through SpyTag/SpyCatcher interaction. Inclusion of split fluorescent protein fragments in the designed InterSpy toolkit allows tracking the formation of membrane-membrane interface and reconstitution of functional fluorescent protein in the space between apposing membranes. We first demonstrate InterSpy by testing split protein designs using a mammalian cell-free expression system. By utilizing co-translational helix insertion, cell-free synthesized InterSpy fragments are incorporated into the membrane of liposomes and supported lipid bilayers with a desired topology. Functional reconstitution of split fluorescent protein between the membranes is strictly dependent on SpyTag/SpyCatcher. Finally, since InterSpy is fully genetically encoded, the engineered system is adapted to cells and showcased. InterSpy demonstrates the power of cell-free expression systems in functional reconstitution of synthetic membrane interfaces via proximity-inducing proteins. This technology may also prove useful for synthetic biology where cell-cell contacts and communication are recreated in a controlled manner using minimal components.

synthetic biology↗

bioRxiv2021

Gene-teratogen interactions influence the penetrance of birth defects by altering Hedgehog signaling strength

Birth defects result from interactions between genetic and environmental factors, but the mechanisms remain poorly understood. We find that mutations and teratogens interact in predictable ways to cause birth defects by changing target cell sensitivity to Hedgehog (Hh) ligands. These interactions converge on a membrane protein complex, the MMM complex, that promotes degradation of the Hh transducer Smoothened (SMO). Deficiency of the MMM component MOSMO results in elevated SMO and increased Hh signaling, causing multiple birth defects. In utero exposure to a teratogen that directly inhibits SMO reduces the penetrance and expressivity of birth defects in Mosmo-/- embryos. Additionally, tissues that develop normally in Mosmo-/- embryos are refractory to the teratogen. Thus, changes in the abundance of the protein target of a teratogen can change birth defect outcomes by quantitative shifts in Hh signaling. Consequently, small molecules that re-calibrate signaling strength could be harnessed to rescue structural birth defects.

developmental biology↗

bioRxiv2020

In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1

Novel severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has claimed more than 1.5 million lives worldwide and counting. As per the GISAID database, the genomics of SARS-CoV2 is extensively studied with more than 500 genome submissions per day. Out of several hotspot mutations within the SARS-CoV-2 genome, researchers have focused a lot on missense variants but the least work is done on the UTRs. One of the most frequent 5 UTR variants in the SARS-CoV-2 genome is the C241T with a global frequency of more than 0.9. In the present study, the effect of the C241T mutation has been studied with respect to change in RNA structure and its interaction with the host replication factors MADP1 Zinc finger CCHC-type and RNA-binding motif 1 (hnRNP1). The results obtained from molecular docking and molecular dynamics simulation indicated weaker interaction of C241T mutant stem loops with host transcription factor MADP1 indicating reduced replication efficiency. The results are also correlated with increased recovery rates and decreased death rates of global SARS-CoV-2 cases.

bioinformatics↗

bioRxiv2018

Behavioral evolution drives hindbrain diversification among Lake Malawi cichlid fish

The evolutionary diversification of animal behavior is often associated with changes in the structure and function of nervous systems. Such evolutionary changes arise either through alterations of individual neural components (\"mosaically\") or through scaling of the whole brain (\"conceitedly\"). Here we show that the evolution of a specific courtship behavior in Malawi cichlid fish, the construction of mating nests known as bowers, is associated with rapid, extensive, and specific diversification of orosensory, gustatory centers in the hindbrain. We find that hindbrain volume varies significantly between species that build pit (depression) compared to castle (mound) type bowers and that hindbrain features evolve rapidly and independently of phylogeny among castle-building species. Using immediate early gene expression, we confirmed a functional role for hindbrain structures during bower building. Comparisons of bower building species in neighboring Lake Tanganyika show patterns of neural diversification parallel to those in Lake Malawi. Our results suggest that mosaic brain evolution via alterations to individual brain structures is more extensive and predictable than previously appreciated.

evolutionary biology↗

bioRxiv2017

Integrated Analysis of Gene Expression Differences in Twins Discordant for Disease and Binary Phenotypes

While both genes and environment contribute to phenotype, deciphering environmental contributions to phenotype is a challenge. Furthermore, elucidating how different phenotypes may share similar environmental etiologies also is challenging. One way to identify environmental influences is through a discordant monozygotic (MZ) twin study design. Here, we assessed differential gene expression in MZ discordant twin pairs (affected vs. non-affected) for seven phenotypes, including chronic fatigue syndrome, obesity, ulcerative colitis, major depressive disorder, intermittent allergic rhinitis, physical activity, and intelligence quotient, comparing the spectrum of genes differentially expressed across seven phenotypes individually. Second, we performed meta-analysis for each gene to identify commonalities and differences in gene expression signatures between the seven phenotypes. In our integrative analyses, we found that there may be a common gene expression signature (with small effect sizes) across the phenotypes; however, differences between phenotypes with respect to differentially expressed genes were more prominently featured. Therefore, defining common environmentally induced pathways in phenotypes remains elusive. We make our work accessible by providing a new database (DiscTwinExprDB: http://apps.chiragjpgroup.org/disctwinexprdb/) for investigators to study non-genotypic influence on gene expression.

genomics↗

bioRxiv2017

Systematic Identification of Correlates of HIV-1 Infection: An X-Wide Association Study in Zambia

BackgroundHIV-1 remains the leading cause of death among adults in Sub-Saharan Africa, and over 1 million people are infected annually. Better identification of at-risk groups could benefit prevention and treatment programmes. We systematically identified factors related to HIV-1 infection in two nationally representative cohorts of women that participated in Zambias Demographic and Health Surveys (DHS).\n\nMethodsWe conducted a comprehensive analysis to identify and replicate the association of 1,415 social, economic, environmental, and behavioral indicators with HIV-1 status. We used the 2007 and 2013-2014 DHS surveys conducted among 5,715 and 15,433 Zambian women, respectively (727 indicators in 2007; 688 in 2013-2014; 688 in both). We used false discovery rate criteria to identify indicators that are strongly associated with HIV-1 in univariate and multivariate models in the entire population, as well as in subgroups stratified by wealth, residence, age, and history of HIV-1 testing.\n\nFindingsIn the univariate analysis we identified 102 and 182 variables that are associated with HIV-1 in the 2007 and 2013-2014 surveys, respectively, among which 79 were associated in both. Variables that were associated with HIV-1 status in all full-sample models (unadjusted and adjusted) as well as in at least 17 out of 18 subgroups include being formerly in a union (adjusted OR 2007 2.8, p<10-16; 2013-2014 2.8, p<10-29), widowhood (adjusted OR 2007 3.7, p<10-12; 2013-2014 4.2, p<10-30), history of genital ulcers in the last 12 months (adjusted 2007 OR 2.4, p<10-5; 2013-2014 2.2, p<10-6), and having a woman for the head of the household (2007 OR 1.7, p<10-7; 2013-2014 OR 2.1, p<10-26), while owning a bicycle (adjusted 2007 OR 0.6, p<10-6; 2013-2014 0.6, p<10-8) and currently breastfeeding (adjusted 2007 OR 0.5, p<10-9; 2013-2014 0.4, p<10-26) were associated with decreased risk. Using the identified variables, area under the curve for HIV-1 positivity ranged from 0.76 to 0.82.\n\nInterpretationOur X-wide association study in Zambian women identifies multiple under-recognized factors correlated with HIV-1 infection in 2007 and 2013-2014, including widowhood, breastfeeding, and being the head of the household. These variables could be used to improve HIV-1 testing and identification programs.

epidemiology↗