Biology subjects

Patel, N. D.

Publications and source records attributed to Patel, N. D..

4 recordsLinked to original sources

bioRxiv2026

A rhinovirus vaccine evokes T cell mediated cross-reactive immunity in a preclinical model of rhinovirus infection

Rhinovirus (RV) infection is the most common cause of acute exacerbations of respiratory diseases such as asthma and chronic obstructive pulmonary disease. Vaccines are available for two less common respiratory viruses (influenza and respiratory syncytial viruses), but development of a RV vaccine to protect patients with chronic respiratory disease has been hampered by the large number of serologically distinct RV strains ([~]180, grouped genetically into [~]80 A, [~]30 B and [~]70 C strains). We have explored the potential of the RV-A16 VP0 subunit vaccine in both CpG-adjuvanted protein subunit and mRNA formats. We demonstrate that both vaccine formats induce strong effector CD4 and CD8 T cell responses in the airways and lungs of immunized mice that rapidly expand following infection with a heterotypic RV strain and are associated with enhanced virus clearance. Adjuvanted VP0 protein subunit vaccination evoked strong germinal center reactions in the lymph nodes and markedly accelerated the production of neutralizing antibodies following heterotypic RV infection. In contrast, VP0 mRNA vaccination evoked limited germinal center responses and neutralizing antibody production. Th1 polarized immune responses were induced against a large panel of 20 heterologous RV strains representative of all RV-A, -B and -C strains. This study confirms the potential of RV VP0 vaccination as an approach to overcome the serological diversity of RV and describes the immune response evoked, including cross-strain cellular immunity and protection against heterotypic RV infection.

immunology↗

bioRxiv2023

Increasing Signal Intensity of Fluorescent Oligo-Labeled Antibodies

Full-spectrum flow cytometry has increased antibody-based multiplexing, yet further increases remain potentially impactful. We recently proposed how fluorescence Multiplexing using Spectral Imaging and Combinatorics (MuSIC) could do so using tandem dyes and an oligo-based antibody labeling method. In this work, we found that such labeled antibodies had significantly lower signal intensity than conventionally-labeled antibodies in human cell experiments. To improve signal intensity, we tested moving the fluorophores from the original external (ext.) 5 or 3 end-labeled orientation to internal (int.) fluorophore modifications. Cell-free spectrophotometer measurements showed a [~]6-fold signal intensity increase of the new int. configuration compared to the previous ext. configuration. Time-resolved fluorescence and fluorescence correlation spectroscopy showed that [~]3-fold brightness difference is due to static quenching most likely by the oligo or solution in the ext. configuration. Spectral flow cytometry experiments using peripheral blood mononuclear cells show int. MuSIC probe-labeled antibodies (i) retained increased signal intensity while having no significant difference in the estimated % of CD8+ lymphocytes and (ii) labeled with Atto488, Atto647, and Atto488/647 combinations can be demultiplexed in triple-stained samples. The antibody labeling approach is general and can be broadly applied to many biological and diagnostic applications where spectral detection is available.

molecular biology↗

bioRxiv2022

A Theory for High-Throughput Genetic Interaction Screening

Systematic, genome-scale genetic screens have been instrumental for elucidating genotype-phenotype relationships, but approaches for probing genetic interactions have been limited to at most [~]100 pre-selected gene combinations in mammalian cells. Here, we introduce a theory for high-throughput genetic interaction screens. The theory extends our recently developed Multiplexing using Spectral Imaging and Combinatorics (MuSIC) approach to propose [~]105 spectrally unique, genetically-encoded MuSIC barcodes from 18 currently available fluorescent proteins. Simulation studies based on constraints imposed by spectral flow cytometry equipment suggest that genetic interaction screens at the human genome-scale may be possible if MuSIC barcodes can be paired to guide RNAs. While experimental testing of this theory awaits, it offers transformative potential for genetic perturbation technology and knowledge of genetic function. More broadly, the availability of a genome-scale spectral barcode library for non-destructive identification of single-cells could find more widespread applications such as traditional genetic screening and high-dimensional lineage tracing.

biochemistry↗

bioRxiv2020

Enhancers regulate polyadenylation site cleavage and control 3'UTR isoform expression

Multi-UTR genes are widely transcribed but show cell type-specific 3'UTR isoform expression. As transcriptional enhancers regulate mRNA expression, we investigated if they also regulate mRNA isoform expression. Deletion of an endogenous enhancer of a multi-UTR gene did not impair transcript production but prevented a switch in 3'UTR isoform expression. Also, the same enhancers are able to increase transcript production in the context of single-UTR gene promoters, but they increase 3' end processing activity when paired with multi-UTR gene promoters. We show that transcription factors regulate processing activity of weak polyadenylation sites to control cell type-specific alternative 3'UTR isoform expression of widely expressed genes.

biochemistry↗