Biology subjects

Mehrotra, N.

Publications and source records attributed to Mehrotra, N..

3 recordsLinked to original sources

bioRxiv2026

immgenT CD4: a reference landscape of mouse CD4+ T cell

CD4+ T cells are orchestrators of the immune system with diverse effector functions. Their full molecular diversity remains unclear due to the lack of a unified framework. Within the immgenT project, we profiled RNA, surface markers, and TCR clonotypes in conventional CD4+ T cells across >700 samples. Integration with a joint RNA-protein deep generative model revealed an ensemble of 20 CD4 states that account for all cells across tissues and challenges. Small, highly polarized clusters ("tips") that evoke Th1, Th2, Th17, and Tfh states co-exist with a majority of activated cells with mixed programs occupying "midland" states. Unlike CD8+ T cells, memory CD4+ cells largely mapped to the same states as effectors. Resting states proved quite diverse, and we uncovered unexpected similarities between Tfh and chronically stimulated states. Together, immgenT provides a unified molecular reference for CD4+ T cell diversity.

immunology↗

bioRxiv2026

immgenT Treg: A Reference Landscape of Regulatory T Cell States in Mice

CD4+FoxP3+ regulatory T cells (Tregs) are central to immunity, tolerance, and tissue homeostasis, yet their extensive heterogeneity lacks a unifying framework. Within the immgenT project, we profiled gene expression, surface markers and TCR clonotypes of mouse Tregs. Using a joint RNA-protein deep generative model, we define the Treg landscape, organized around eight conserved clusters shared across tissues and conditions, with immune context reshaping their relative abundance rather than generating new states, including a prominent circulating effector Treg population enriched in select non-lymphoid tissues. We validate this framework by integrating external datasets from conditions not represented in immgenT and by defining a flow cytometry panel spanning the Treg landscape. Together, immgenT provides a scalable, reusable reference that unifies Treg heterogeneity across tissues and immune challenges.

immunology↗

bioRxiv2019

Correlation of mRNA delivery timing and protein expression in lipid-based transfection

Non-viral gene delivery is constrained by the dwell time that most synthetic nucleic acid nanocarriers spend inside endosomal compartments. In order to overcome this endosomal-release bottleneck, methods are required that measure nanocarrier uptake kinetics and transfection efficiency simultaneously. Here, we employ live-cell imaging on single-cell arrays (LISCA) to study the delivery-time distribution of lipid-based mRNA complexes under varied serum conditions. By fitting a translation-maturation model to hundreds of individual eGFP reporter fluorescence time courses, the protein expression onset times and the expression rates after transfection are determined. Using this approach, we find that delivery timing and protein expression rates are not intrinsically correlated at the single-cell level, even though population-averaged values of both parameters conjointly change as a function of increasing external serum protein fraction. Lipofectamine mediated delivery showed decreased transfection efficiency and longer delivery times with increasing serum protein concentration. This is in contrast to ionizable lipid nanoparticles (LNPs) mediated transfer, which showed increased efficiency and faster uptake in the presence of serum. In conclusion, the interdependences of single-cell expression rates and onset timing provide additional clues on uptake and release mechanisms, which are useful for improving nucleic acid delivery.

systems biology↗