Biology subjects

Shaji, S.

Publications and source records attributed to Shaji, S..

3 recordsLinked to original sources

bioRxiv2026

Distinct trajectories of urbanization shape the human gut microbiome across South Asia

Human gut microbiomes respond to lifestyle transitions, yet the extent to which these responses are conserved across spatio-cultural contexts remains undercharacterized. We present the South Asian MicroBiome ARray (SAMBAR), a population-scale 16S gut microbiome study of 575 adults from ten geographically and socio-culturally diverse South Asian communities. Each community was sampled in ancestral villages and urban centers, enabling controlled comparisons of geography and lifestyle. Relative to global cohorts, SAMBAR microbiomes occupy a distinct compositional space with stronger correlation to geography and community membership than lifestyle. Although urbanization is consistently associated with increased abundance of disease-linked taxa, microbiome responses to lifestyle transitions are largely community-driven, including the acquisition of wheat- and dairying-associated microbial modules in some communities that may facilitate non-genetic adaptation to lactase non-persistence. Microbiome responses to urbanization are heterogeneous even at regional scales, reflecting local culture and geography and underscoring the need for community-specific investigations of health impacts.

microbiology↗

bioRxiv2025

Versatile and efficient non-viral integration of large transgenes in human T cells via CRISPR knock-in and engineered integrases

Current gene transfer methods often lack the precision, versatility, or efficiency when integrating large transgenes, limiting the ability to engineer therapeutic T-cells with more complex payloads. Here, we report one-pot PASTA (Programmable and Site-specific Transgene Addition), a non-viral genome engineering strategy for large gene insertion that combines CRISPR-Cas-mediated homology-directed repair (HDR) and site-specific recombination via serine integrases. Using one-pot PASTA with the Bxb1 integrase, we demonstrate efficient integration of transgenes at multiple genomic loci relevant for T-cell engineering (e.g., TRAC, B2M, CD3E, CD3Z, GAPDH). For constructs > 8 kb, one-pot PASTA outperforms conventional HDR by 19-fold on average and prime-editing-assisted site-specific integrase gene editing (PASSIGE) by 5-fold. This enables the delivery of multi-cistronic cargo to generate dual-antigen targeting CAR T-cells with a safety-switch that overcome antigen escape in lymphoma models. Finally, one-pot PASTA can be further optimized with improved integrase enzymes, such as engineered variants of Pa01 or Bxb1, and plasmids with minimized backbones. In summary, one-pot PASTA represents a versatile and scalable platform for precise, non-viral gene insertion in T-cells.

synthetic biology↗

bioRxiv2025

Injectable Immune-Engineered Hydrogel Niche Remote From The Immune Suppressed Tumor Microenvironment For Cancer Immunotherapy

Immunocompromise is a hallmark of cancer, affecting both the peripheral immune system and local tumor microenvironment (TME). Current immunotherapies like checkpoint inhibitors, CAR-T cells, and neo-antigen vaccines show limited efficacy due to severe immunosuppression in most patients. Here, we report an immunologically engineered injectable nano-hydrogel (iHG) that can: (i) recruit the desired set of immune cells away from the suppressed TME and peripheral organs, (ii) activate them within a protective ambit of engineered immune-stimulatory hydrogel niche, and (iii) release them to target cancer even in distant locations. Biodegradable and injectable iHG compositions were tested and optimized for their ability to attract and activate dendritic cells, macrophages, monocytes, NK cells, B cells, and T cells via STING, TLR, CD86, and Th1-polarized cytokine pathway without requiring exogenously introduced neo-antigens as vaccines. In a mouse melanoma model, optimized iHGs elicited a robust antitumor immune response through innate and adaptive arms. Most importantly, iHGs as a single agent immunomodulator exhibited better tumor control than when combined with anti-PD1 immune checkpoint antibody. These findings highlight the potential of engineering immunologically functional and injectable hydrogel niches as a new type of immunotherapeutics to reprogram immune cells to overcome both local and systemic immunosuppression and combat cancer effectively.

immunology↗