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STARTRAC analyses of scRNAseq data from tumor models reveal T cell dynamics and therapeutic targets.

ABSTRACT: Single-cell RNA sequencing is a powerful tool to examine cellular heterogeneity, novel markers and target genes, and therapeutic mechanisms in human cancers and animal models. Here, we analyzed single-cell RNA sequencing data of T cells obtained from multiple mouse tumor models by PCA-based subclustering coupled with TCR tracking using the STARTRAC algorithm. This approach revealed various differentiated T cell subsets and activation states, and a correspondence of T cell subsets between human and mouse tumors. STARTRAC analyses demonstrated peripheral T cell subsets that were developmentally connected with tumor-infiltrating CD8+ cells, CD4+ Th1 cells, and T reg cells. In addition, large amounts of paired TCRα/β sequences enabled us to identify a specific enrichment of paired public TCR clones in tumor. Finally, we identified CCR8 as a tumor-associated T reg cell marker that could preferentially deplete tumor-associated T reg cells. We showed that CCR8-depleting antibody treatment provided therapeutic benefit in CT26 tumors and synergized with anti-PD-1 treatment in MC38 and B16F10 tumor models.

SUBMITTER: Bhatt D

PROVIDER: S-EPMC8077174 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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STARTRAC analyses of scRNAseq data from tumor models reveal T cell dynamics and therapeutic targets.

Bhatt Dev D Kang Boxi B Sawant Deepali D Zheng Liangtao L Perez Kristy K Huang Zhiyu Z Sekirov Laura L Wolak Dan D Huang Julie Y JY Liu Xian X DeVoss Jason J Manzanillo Paolo S PS Pierce Nathan N Zhang Zemin Z Symons Antony A Ouyang Wenjun W

The Journal of experimental medicine 20210601 6

Single-cell RNA sequencing is a powerful tool to examine cellular heterogeneity, novel markers and target genes, and therapeutic mechanisms in human cancers and animal models. Here, we analyzed single-cell RNA sequencing data of T cells obtained from multiple mouse tumor models by PCA-based subclustering coupled with TCR tracking using the STARTRAC algorithm. This approach revealed various differentiated T cell subsets and activation states, and a correspondence of T cell subsets between human a ...[more]

PMID: 33900375

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Project description:BackgroundAndrogen deprivation therapy is a first-line treatment for disseminated prostate cancer (PCa). However, virtually all tumors become resistant and recur as castration-resistant PCa, which has no durable cure. One major hurdle in the development of more effective therapies is the lack of preclinical models that adequately recapitulate the heterogeneity of PCa, significantly hindering the ability to accurately predict therapeutic response.ObjectiveTo leverage the ex vivo culture method termed patient-derived explant (PDE) to examine the impact of PCa therapeutics on a patient-by-patient basis.Design setting and participantsFresh PCa tissue from patients who underwent radical prostatectomy was cultured as PDEs to examine therapeutic response.Outcome measurements and statistical analysisThe impact of genomic and chemical perturbations in PDEs was assessed using various parameters (eg, AR levels, Ki67 staining, and desmoplastic indices).Results and limitationsPDE maintained the integrity of the native tumor microenvironment (TME), tumor tissue morphology, viability, and endogenous hormone signaling. Tumor cells in this model system exhibited de novo proliferative capacity. Examination of the native TME in the PDE revealed a first-in-field insight into patient-specific desmoplastic stromal indices and predicted responsiveness to AR-directed therapeutics.ConclusionsThe PDE model allows for a comprehensive evaluation of individual tumors in their native TME to ultimately develop more effective therapeutic regimens tailored to individuals. Discernment of novel stromal markers may provide a basis for applying precision medicine in treating advanced PCa, which would have a transformative effect on patient outcomes.Patient summaryIn this study, an innovative model system was used to more effectively mimic human disease. The patient-derived explant (PDE) system can be used to predict therapeutic response and identify novel targets in advanced disease. Thus, the PDE will be an asset for the development of novel metrics for the implementation of precision medicine in prostate cancer.The patient-derived explant (PDE) model allows for a comprehensive evaluation of individual human tumors in their native tumor microenvironment (TME). TME analysis revealed first-in-field insight into predicted tumor responsiveness to AR-directed therapeutics through evaluation of patient-specific desmoplastic stromal indices.

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STARTRAC analyses of scRNAseq data from tumor models reveal T cell dynamics and therapeutic targets.

Publications

STARTRAC analyses of scRNAseq data from tumor models reveal T cell dynamics and therapeutic targets.

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