Biology subjects

Dutta, I.

Publications and source records attributed to Dutta, I..

7 recordsLinked to original sources

bioRxiv2026

Engineering antigen-driven co-stimulation and T helper cell activity into TCR-T cells with CD8-41BB fusion receptors enhances anti-tumor activity

1Adoptive cell therapy using tumor antigen-targeting T cell receptors (TCRs) offers a compelling approach to treat both hematological cancers and solid tumors due to broad antigen accessibility and the ability to target cancer-specific neoantigens. However, unlike clinically validated second generation CAR-T cells bearing built-in co-stimulatory signaling modules (i.e. 41BB or CD28), TCR-T cells receive little to no co-stimulation within most tumor microenvironments leading to attenuated cellular responses. Additionally, CD4+ TCR-T cells engineered to express HLA-Class I restricted TCRs possess minimal T-helper cell activity and thus do not effectively mobilize CD8+ TCR-T cells or host anti-tumor immune responses. To address these limitations, we used CRISPR-Cas9 to engineer TCR-T cells with targeted integration of chimeric CD8 constructs containing intracellular co-stimulatory domains. We found that expression of wild-type CD8{beta}, but not CD8, could promote CD4+ T cell activities in HLA-Class I restricted TCR-T cells. However, this was insufficient to drive durable anti-tumor responses in challenging tumor mouse models when using a high-affinity WT1-directed TCR. To address this, several CD8 co-stimulatory fusion constructs containing CD28 or 41BB intracellular domains were designed and screened, identifying two CD8-41BB based chimeras that substantially increased TCR-T cell activity relative to wild-type CD8{beta}. WT1-TCR-T cells co-expressing the CD8-41BB fusions demonstrated not only enhanced CD4+ activity including strong and polarized Th1-type cytokine secretion, but also enhanced the proliferation, cytokine release, and cytotoxicity of CD8+ CTLs. Remarkably, when combined with TGFBR2 gene disruption, WT1-TCR-T cells co-expressing CD8-41BB receptors were able to completely regress established cell line-derived ovarian tumors, showed robust in vivo expansion and persistence, and provided long-term protection from tumor rechallenge. Importantly, the specificity profile of the WT1-TCR including its HLA-A*02:01 restriction and WT1 peptide recognition motif was preserved upon expression of CD8-41BB. To simplify cell engineering processes for clinical applications, we configured a homology directed repair (HDR) cassette to allow for efficient CRISPR-Cas9-based insertion of both the TCR and CD8-41BB transgenes in the TRAC locus in a single step with >80% efficiency. Lastly, the enhanced activity conferred by CD8-41BB expression was validated with a second clinically relevant TCR targeting PRAME, suggesting this platform can be a universal approach for enhancing the therapeutic potential of TCR-based cell therapies.

synthetic biology↗

bioRxiv2025

Linguistic Rules of Syntax and Sharing in the Complex Songs of a Tropical Passerine

1. Birdsong offers a powerful model to study the evolution of complex communication systems. While most song syntax and sharing research focuses on temperate species with fixed repertoires, we know far less about tropical songbirds with large, open-ended vocal systems. 2. We examined song structure and cultural transmission in the White-bellied Sholakili Sholicola albiventris, a tropical passerine endemic to the Shola Sky Islands of southern India. We studied song complexity and spectro-temporal variation using over 6,000 songs from 17 color-banded males across five years. We analyzed the song syntax using sequence-based metrics, including Levenshtein Distances and N-gram models. 3. Our results reveal high syntactic variability across short and long timescales, with stable note-type cores and structured expansions of combinatorial sequences. Higher-order N-gram turnover was rapid and strongly individual-specific, while broadly sharing the population-level note pool. Song sharing was significantly higher among neighbors than non-neighbors. 4. Using Generalized Additive Models, we explain how social and ecological factors, including neighbor count, territory area, repertoire size, N-gram usage, and the spectro-temporal structure of N-grams, determine consistency across years and sharing across individuals. This study highlights parallels between human linguistics and syntactic organization in the complex songs of a tropical passerine.

animal behavior and cognition↗

bioRxiv2025

A differentiated and durable allogeneic strategy applicable to cell therapies

Autologous T cell therapies have shown profound clinical responses; however, their widespread use has been limited primarily due to their individualized manufacturing requirements. To develop a persistent "off-the-shelf" allogeneic (Allo) approach, a multiplex Nme2Cas9-based cytosine base editor was deployed to knockout select HLA Class I and II alleles (HLA-A, HLA-B, and the class II transactivator (CIITA)), while retaining HLA-C to protect from NK cell rejection. Matching the residual HLA-C allele from homozygous donors to the host prevented rejection of the donor T cells by allogeneic host T and NK cells. Site-specific integration of a tumor-specific CAR or TCR into the TRAC locus using SpyCas9 nuclease and an adeno-associated virus (AAV) template allowed for high localized insertion rate while simultaneously removing the endogenous TCR and preventing GvHD. Using a lipid nanoparticle (LNP)-based delivery system of the editing components enabled a robust cell engineering process, achieving high editing rates and cell expansion. These allogeneic T cells demonstrated comparable functional activity to their autologous counterparts in preclinical assays. Moreover, this gene editing approach generated cells with minimal chromosomal aberrations. The Allo strategy has also been applied to induced pluripotent stem cells (iPSCs), suggesting potential applications in regenerative medicine applications.

bioengineering↗

bioRxiv2021

Blood-based untargeted metabolomics in Relapsing-Remitting Multiple Sclerosis revealed the testable therapeutic target

Metabolic aberrations impact the pathogenesis of multiple sclerosis (MS) and possibly can provide clues for new treatment strategies. Using untargeted metabolomics, we measured serum metabolites from 35 relapsing-remitting patients and 14 healthy age-matched controls. Out of 632 known metabolites detected, 60 were significantly altered in relapsing-remitting MS (RRMS). Bioinformatics analysis identified an altered "metabotype" in RRMS patients, represented by 4 changed metabolic pathways of glycerophospholipid, citrate cycle, sphingolipid, and pyruvate metabolism. Interestingly, the common upstream metabolic pathway feeding these 4 pathways is the glycolysis pathway. Real-time bioenergetic analysis of the patient derived peripheral blood mononuclear cells, showed enhanced glycolysis, supporting the altered metabolic state of immune cells. Experimental autoimmune encephalomyelitis mice treated with the glycolytic inhibitor, 2-deoxy-D-glucose ameliorated the disease progression and inhibited the disease pathology significantly by promoting the anti-inflammatory phenotype of monocytes/macrophage in the central nervous system. Our study suggests that targeting glycolysis offers a potential target for MS.

neuroscience↗

bioRxiv2020

Docosahexaenoic acid significantly reduces tumor cell growth in preclinical models of ovarian cancer

Despite recent advances in diagnosis and treatment, ovarian cancer (OC) is the most lethal gynecological malignancy and improving the efficacy of chemotherapy is of great interest. This study increases our understanding of how dietary intervention with docosahexaenoic acid (DHA)-a supplement proven safe for human consumption - enhances the anti-cancer effects of conventional chemotherapy. Our results demonstrated synergistic cell killing by DHA and carboplatin in OC cell lines. Furthermore, DHA supplementation alone and in combination with carboplatin significantly reduced OC growth in a high-grade serous OC patient-derived xenograft mouse model. Carboplatin administered intraperitoneally significantly reduced tumor growth in DHA-fed mice compared to mice on the control diet. Intravenous carboplatin administration in combination with DHA reduced tumor growth similarly to carboplatin or DHA monotherapies. The DHA-induced reduction in tumor growth in this model was associated with increased tumor necrosis and improved survival. As such, our findings provide a strong rationale to move to clinical trials that will determine whether DHA supplementation enhances the efficacy and tolerance of cytotoxic chemotherapy in patients with OC.

cancer biology↗

bioRxiv2020

ADAM protease inhibition overcomes resistance of breast cancer stem-like cells to γδ T cell immunotherapy

Breast cancer stem cells (BCSC) are highly resistant to current therapies, and are responsible for metastatic burden and relapse. Gamma delta T cells ({gamma}{delta}Tc) are immunosurveillance cells with tremendous anti-tumoral activity, and a growing number of clinical trials have confirmed the safety of {gamma}{delta}Tc immunotherapy for various malignancies. Herein, we demonstrate that {gamma}{delta}Tc can kill BCSC, but to a lesser extent than non-cancer stem cells (NSC). Immune evasion was orchestrated by several mechanisms. The BCSC secretome rendered {gamma}{delta}Tc hypo-responsive by reducing proliferation, cytotoxicity and IFN-{gamma} production, while increasing expression of co-inhibitory receptors on {gamma}{delta}Tc. BCSC and target cells surviving {gamma}{delta}Tc cytotoxicity had higher PD-L1 co-inhibitory ligand expression, and blocking PD-1 on {gamma}{delta}Tc significantly overcame BCSC resistance to {gamma}{delta}Tc killing. Fas/FasL signaling was dysfunctional in BCSC due to upregulation of the anti-apoptotic protein MCL-1, which could be partially overcome using dMCL1-2, an MCL-1 degrader. Moreover, the BCSC fraction shed higher levels of the NKG2D ligand MICA compared to NSC. Inhibiting MICA shedding using the ADAM inhibitor GW280264X overcame BCSC resistance to {gamma}{delta}Tc killing, rendering BCSC as sensitive to {gamma}{delta}Tc cytotoxicity as NSC. Collectively, our data unravel multiple mechanisms exploited by BCSC to evade {gamma}{delta}Tc killing, which may also come into play in BCSC resistance to other cytotoxic lymphocytes. Developing strategies to overcome this resistance will increase the efficacy of cancer immunotherapy and lead to improved outcomes for cancer patients. One Sentence SummaryBreast cancer stem-like cells are resistant to {gamma}{delta} T cell targeting, which can be overcome by inhibiting ADAM proteases that facilitate MICA/B shedding.

immunology↗

bioRxiv2019

Translational control of breast cancer plasticity

Plasticity of neoplasia, whereby cancer cells attain stem-cell-like properties, is required for disease progression and represents a major therapeutic challenge. We report that in breast cancer cells NANOG, SNAIL and NODAL transcripts manifest multiple isoforms characterized by different 5 Untranslated Regions (5UTRs), whereby translation of a subset of these isoforms is stimulated under hypoxia. This leads to accumulation of corresponding proteins which induce plasticity and \"fate-switching\" toward stem-cell like phenotypes. Surprisingly, we observed that mTOR inhibitors and chemotherapeutics induce translational activation of a subset of NANOG, SNAIL and NODAL mRNA isoforms akin to hypoxia, engendering stem cell-like phenotypes. Strikingly, these effects can be overcome with drugs that antagonize translational reprogramming caused by eIF2 phosphorylation (e.g. ISRIB). Collectively, our findings unravel a hitherto unappreciated mechanism of induction of plasticity of breast cancer cells, and provide a molecular basis for therapeutic strategies aimed at overcoming drug resistance and abrogating metastasis.

cancer biology↗