Isolation of tumor-infiltrating lymphocytes from preserved human tumor tissue specimens for downstream characterization

Kobayashi, Tamiyo; Kumagai, Shogo; Doi, Rieko; Afonina, Elena; Koyama, Shohei; Nishikawa, Hiroyoshi

doi:10.1016/j.xpro.2022.101557

Cited by 5 publications

(3 citation statements)

References 5 publications

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“…This study aimed at clarifying the differentiation/activation mechanism of tumor-infiltrating T reg cells with multiple sequencing technologies. With the development of our method to gain sufficient immune cells from tiny tumor specimens (27)(28)(29), the chromatin accessibility and gene expression of T reg cells in the TME of non-small cell lung cancer (NSCLC) were comprehensively profiled using assay for transposase-accessible chromatin using sequencing (ATAC-seq), RNA sequencing (RNA-seq), single-cell ATAC sequencing (scATAC-seq), and single-cell RNA sequencing (scRNA-seq) (30,31). These analyses enabled the detection of putative DNA regulatory elements of tumor-infiltrating T reg cells and transcription factor networks that promoted T reg cell differentiation/activation into their unique phenotypes in the TME, resulting in the identification of targetable molecules for T reg cell-targeted therapies.…”

Section: Introductionmentioning

confidence: 99%

BATF epigenetically and transcriptionally controls the activation program of regulatory T cells in human tumors

Itahashi¹,

Irie²,

Yuda

et al. 2022

Sci. Immunol.

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Regulatory T (T reg ) cells suppress effective antitumor immunity in tumor-bearing hosts, thereby becoming promising targets in cancer immunotherapy. Despite the importance of T reg cells in tumor immunity, little is known about their differentiation process and epigenetic profiles in the tumor microenvironment (TME). Here, we showed that T reg cells in the TME of human lung cancers harbored a completely different open chromatin profile compared with CD8 + T cells, conventional CD4 + T cells in the TME, and peripheral T reg cells. The integrative sequencing analyses including ATAC, single-cell RNA, and single-cell ATAC sequencing revealed that BATF, IRF4, NF-κB, and NR4A were important transcription factors for T reg cell differentiation in the TME. In particular, BATF was identified as a key regulator, which leveraged T reg cell differentiation through epigenetically controlling activation-associated gene expression, resulting in the robustness of T reg cells in the TME. The single-cell sequencing approaches also revealed that tissue-resident and tumor-infiltrating T reg cells followed a common pathway for differentiation and activation in a BATF-dependent manner heading toward T reg cells with the most differentiated and activated phenotypes in tissues and tumors. BATF deficiency in T reg cells remarkably inhibited tumor growth, and high BATF expression was associated with poor prognosis in lung cancer, kidney cancer, and melanoma. These findings indicate one of the specific chromatin remodeling and differentiation programs of T reg cells in the TME, which can be applied in the development of T reg cell–targeted therapies.

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Section: Introductionmentioning

confidence: 99%

BATF epigenetically and transcriptionally controls the activation program of regulatory T cells in human tumors

Itahashi¹,

Irie²,

Yuda

et al. 2022

Sci. Immunol.

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“…In 1994, expanded TILs derived from non-small-cell lung cancer (NSCLC) were used in adoptive immunotherapy, following surgery with promising results [32]. Flow cytometric immunophenotypic analysis of TIL immunophenotypes could predict both the clinical effectiveness of immunotherapy [40] and early relapse in localized clear-cell RCC [41].…”

Section: • Analysis Of Tils By Flow Cytometry or Immunohistochemistrymentioning

confidence: 99%

Immune Cytolytic Activity and Strategies for Therapeutic Treatment

Agioti,

Zaravinos

2024

IJMS

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Intratumoral immune cytolytic activity (CYT), calculated as the geometric mean of granzyme-A (GZMA) and perforin-1 (PRF1) expression, has emerged as a critical factor in cancer immunotherapy, with significant implications for patient prognosis and treatment outcomes. Immune checkpoint pathways, the composition of the tumor microenvironment (TME), antigen presentation, and metabolic pathways regulate CYT. Here, we describe the various methods with which we can assess CYT. The detection and analysis of tumor-infiltrating lymphocytes (TILs) using flow cytometry or immunohistochemistry provide important information about immune cell populations within the TME. Gene expression profiling and spatial analysis techniques, such as multiplex immunofluorescence and imaging mass cytometry allow the study of CYT in the context of the TME. We discuss the significant clinical implications that CYT has, as its increased levels are associated with positive clinical outcomes and a favorable prognosis. Moreover, CYT can be used as a prognostic biomarker and aid in patient stratification. Altering CYT through the different methods targeting it, offers promising paths for improving treatment responses. Overall, understanding and modulating CYT is critical for improving cancer immunotherapy. Research into CYT and the factors that influence it has the potential to transform cancer treatment and improve patient outcomes.

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“…Traditionally, PBMCs are used as the source of T lymphocytes in tissue chips (231,257,258), although others have incorporated immortalized Jurkat T cells (Table 4) (232,256). In addition, a number of approaches have been utilized for isolation of tumor infiltrating lymphocytes from human tissues utilizing enzymatic digestion, mechanical digestion, or both (267)(268)(269). Depending on the downstream application, negative selection of T cells can be utilized to prevent activation (270).…”

Section: T Cellsmentioning

confidence: 99%

Sourcing cells for in vitro models of human vascular barriers of inflammation

McCloskey

Zhang²,

Ahmad³

et al. 2022

Front. Med. Technol.

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The vascular system plays a critical role in the progression and resolution of inflammation. The contributions of the vascular endothelium to these processes, however, vary with tissue and disease state. Recently, tissue chip models have emerged as promising tools to understand human disease and for the development of personalized medicine approaches. Inclusion of a vascular component within these platforms is critical for properly evaluating most diseases, but many models to date use “generic” endothelial cells, which can preclude the identification of biomedically meaningful pathways and mechanisms. As the knowledge of vascular heterogeneity and immune cell trafficking throughout the body advances, tissue chip models should also advance to incorporate tissue-specific cells where possible. Here, we discuss the known heterogeneity of leukocyte trafficking in vascular beds of some commonly modeled tissues. We comment on the availability of different tissue-specific cell sources for endothelial cells and pericytes, with a focus on stem cell sources for the full realization of personalized medicine. We discuss sources available for the immune cells needed to model inflammatory processes and the findings of tissue chip models that have used the cells to studying transmigration.

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Isolation of tumor-infiltrating lymphocytes from preserved human tumor tissue specimens for downstream characterization

Cited by 5 publications

References 5 publications

BATF epigenetically and transcriptionally controls the activation program of regulatory T cells in human tumors

BATF epigenetically and transcriptionally controls the activation program of regulatory T cells in human tumors

Immune Cytolytic Activity and Strategies for Therapeutic Treatment

Sourcing cells for in vitro models of human vascular barriers of inflammation

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