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Vasanthakumar, A.

Publications and source records attributed to Vasanthakumar, A..

4 recordsLinked to original sources

ICOS blockade alleviates immune suppression in breast tumor microenvironment

Immune checkpoint blockade has become a standard of care for triple-negative breast cancer, yet only around half of patients benefit. Compensatory immunoregulatory pathways may limit the efficacy of PD-1/PD-L1 blockade. ICOS, an inducible co-stimulatory receptor enriched on activated regulatory T cells (Tregs), represents a potential route of such immune regulation, but its role in breast cancer immunotherapy remains unclear. Here, we identify ICOS as selectively upregulated on tumor-infiltrating Tregs and show that ICOS Tregs localize within a tumor niche enriched for exhausted CD8 T cells. We confirmed this cellular and spatial association across 1,359 tumor regions from 279 triple-negative breast cancer patients profiled by imaging mass cytometry, and single-cell transcriptomic data from 129 breast cancer donors. Genetic ablation or pharmacological blockade of ICOS disrupted this intratumoral Treg niche, reducing Treg activation and tissue-residency programs while expanding cytotoxic CD8 T cells with a tissue-resident memory phenotype. In syngeneic orthotopic breast cancer models, ICOS blockade restricted primary tumor growth, reduced spontaneous metastasis and prolonged survival without disrupting systemic immune homeostasis. Therapeutic activity was observed with both neoadjuvant and adjuvant treatment, while combined ICOS and PD-1 blockade further enhanced tumor control. These findings support ICOS blockade as a therapeutic strategy to improve checkpoint immunotherapy.

cancer biology↗

The long non-coding RNA Dreg1 is required for optimal ILC2 development

Gata3 is an essential transcription factor for the development of several distinct immune cell lineages such as T cells, natural killer (NK) cells and innate lymphoid cells (ILC). As such, the levels and timing of Gata3 expression are critical for directing lineage fate decisions. The Gata3 locus has a complex and dynamic distal regulatory enhancer landscape. Recently we identified a non-coding RNA, Dreg1, located immediately upstream of the classic +280kb T/NK cell enhancer (Tce1). To test its function, we excised the Dreg1 locus in mice and observed a selective reduction of group 2 ILCs (ILC2) across multiple tissues, but mature T, NK and other ILC lineages remained unchanged. In bone marrow, common innate lymphoid cell progenitors (ILCP) increased while ILC2 progenitors (ILC2P) decreased, with a modest reduction of Gata3 in upstream progenitors consistent with an early developmental bottleneck. Chromatin profiling showed the Dreg1 locus is accessible in early lymphoid progenitors and became decorated with H3K27ac in ILCP in a Tcf1-dependent manner. Furthermore, Tcf1-deficient cells did not express Dreg1 and showed alterations in the epigenetic landscape of the Dreg1 locus. Finally, we discovered that potential homologues of Dreg1 harboured in a syntenic enhancer of GATA3 are also highly expressed in human ILC2. Taken together we conclude that Dreg1 is a Tcf1-dependent non-coding RNA critical for fine tuning the high level of Gata3 required for the optimal development of the ILC2 lineage.

immunology↗

Validation and pre-analytical considerations for processing cerebrospinal fluid samples on a high-throughput proximity extension assay platform

BackgroundAnalysis of cerebrospinal fluid (CSF) facilitates the understanding of brain-specific molecular changes that may associate with disease progression. Proximity extension assays (PEA) have been deployed in several CSF studies, however the validation of the assay and impact of freeze-thaw cycles on the protein signal has not been documented. We sought to (1) validate the assay on the PEA platform and (2) evaluate the effect of freeze-thaw cycles on the detectability of analytes on the PEA platform. ResultsWe have validated the PEA with Next Generation Sequencing (NGS) readout assay and report on the detectability and coefficient of variation observed in CSF samples. We have also evaluated proteomic signals with a minimum of 3 and a maximum of 9 freeze thaw cycles and detected very minimal change in signal with increasing cycle number. ConclusionOur study is the first to validate PEA using NGS readout platform with CSF samples. We report lower protein detection rates and higher variability in the expansion panels compared to the original 4 panels, with acceptable variation above detectability threshold. In addition, our work demonstrates that the proteomic signal is robust and continues to be stable across multiple freeze thaw cycles. This is highly impactful to the processing and analysis of clinical samples and facilitates the investigation of samples with variable pre-analytical conditions.

neuroscience↗

New Insights on Bridging Integrator 1 Protein Isoforms as a Risk Increasing Gene in Alzheimer's Disease

INTRODUCTIONGenome-wide association studies (GWAS) have identified Bridging Integrator 1 (BIN1) as the second-most significant genetic risk factor for Alzheimers disease (AD). We performed GWAS by proxy (GWAX) using UKBiobank and replicated this finding. However, the mechanism by which BIN1 impacts AD risk is largely unknown. METHODSTo address this, we first measured the expression of BIN1 isoforms in a human induced pluripotent stem cells (hiPSC) model and further evaluated whether the BIN1 risk loci associated with the expression of BIN1 isoforms in a Phase 2 AD clinical trial. RESULTSOur data indicated BIN1 isoform expression patterns associated with the differentiation of hiPSC into neurons or microglia and found the variant rs35103166 impacts the expression of the BIN1 microglia-specific isoforms. DISCUSSIONGiven the strong association with susceptibility to AD, exploring the mechanisms of BIN1 genetic variants and their impacts on cell-type specific expression could serve as a valuable resource for novel drug discovery. HighlightsO_LIBIN1 variants are significantly associated with AD risk in GWAX analysis from UKBB. C_LIO_LIBIN1 isoforms show a cell-type-specific expression pattern during hiPSC differentiation into neurons or microglia. C_LIO_LIBIN1 risk alleles associate with BIN1 isoform expression in a Phase 2 AD trial (NCT02880956). C_LI

neuroscience↗