An integrated pipeline for comprehensive analysis of immune cells in human brain tumor clinical samples

Roeltje R. Maas, Klara Soukup, Florian Klemm, Mara Kornete, Robert L. Bowman, Romain Bedel, Damien N. Marie, Ángel F. Álvarez-Prado, Danny Labes, Anne Wilson, Jean-Philippe Brouland, Roy T. Daniel, Monika E. Hegi, Johanna A. Joyce

Published: 2021-08-29 DOI: 10.1038/s41596-021-00594-2

tissue processing

RNA sequencing

brain tumor

immune microenvironment

cell populations

AI 解读

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Human tissue samples represent an invaluable source of information for the analysis of disease-specific cellular alterations and their variation between different pathologies. In cancer research, advancing a comprehensive understanding of the unique chara
Introduction
Materials
Procedure
Troubleshooting
Timing
- Steps that need to be performed on the day of tissue reception, as soon as possible post-resection
- Steps that can be performed at a later time point
Anticipated results
- References
References
ACKNOWLEDGMENTS
ACKNOWLEDGMENTS

Achrol, A. S. et al. Brain metastases. Nat. Rev. Dis. Prim. 5, 5 (2019).
Stupp, R. et al. Radiotherapy plus concomitant and adjuvant temozolomide for glioblastoma. N. Engl. J. Med. 352, 987–996 (2005).
Quail, D. F. & Joyce, J. A. The microenvironmental landscape of brain tumors. Cancer Cell 31, 326–341 (2017).
Bejarano, L., Jordao, M. J. C. & Joyce, J. A. Therapeutic targeting of the tumor microenvironment. Cancer Discov. 11, 933–959 (2021).
Klemm, F. et al. Interrogation of the microenvironmental landscape in brain tumors reveals disease-specific alterations of immune cells. Cell 181, 1643–1660 e1617 (2020).
Friebel, E. et al. Single-cell mapping of human brain cancer reveals tumor-specific instruction of tissue-invading leukocytes. Cell 181, 1626–1642 e1620 (2020).
Long, G. V. et al. Combination nivolumab and ipilimumab or nivolumab alone in melanoma brain metastases: a multicentre randomised phase 2 study. Lancet Oncol. 19, 672–681 (2018).
Tawbi, H. A. et al. Combined nivolumab and ipilimumab in melanoma metastatic to the brain. N. Engl. J. Med. 379, 722–730 (2018).
Hendriks, L. E. L. et al. Outcome of patients with non-small cell lung cancer and brain metastases treated with checkpoint inhibitors. J. Thorac. Oncol. 14, 1244–1254 (2019).
Lim, M., Xia, Y., Bettegowda, C. & Weller, M. Current state of immunotherapy for glioblastoma. Nat. Rev. Clin. Oncol. 15, 422–442 (2018).
Schalper, K. A. et al. Neoadjuvant nivolumab modifies the tumor immune microenvironment in resectable glioblastoma. Nat. Med. 25, 470–476 (2019).
Bunevicius, A., Schregel, K., Sinkus, R., Golby, A. & Patz, S. REVIEW: MR elastography of brain tumors. Neuroimage Clin. 25, 102109 (2020).
Gritsenko, P. G. et al. p120-catenin-dependent collective brain infiltration by glioma cell networks. Nat. Cell Biol. 22, 97–107 (2020).
Leelatian, N. et al. Unsupervised machine learning reveals risk stratifying glioblastoma tumor cells. eLife http://doi.org/10.7554/eLife.56879 (2020).
Garofano, L. et al. Pathway-based classification of glioblastoma uncovers a mitochondrial subtype with therapeutic vulnerabilities. Nat. Cancer 2, 141–156 (2021).
Yuan, J. et al. Single-cell transcriptome analysis of lineage diversity in high-grade glioma. Genome Med. 10, 57 (2018).
Sankowski, R. et al. Mapping microglia states in the human brain through the integration of high-dimensional techniques. Nat. Neurosci. 22, 2098–2110 (2019).
Pombo Antunes, A. R. et al. Single-cell profiling of myeloid cells in glioblastoma across species and disease stage reveals macrophage competition and specialization. Nat. Neurosci. http://doi.org/10.1038/s41593-020-00789-y (2021).
Chen, A. X. et al. Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker. Genome Med. 13, 88 (2021).
Castellan, M. et al. Single-cell analyses reveal YAP/TAZ as regulators of stemness and cell plasticity in glioblastoma. Nat. Cancer 2, 174–188 (2021).
Richards, L. M. et al. Gradient of developmental and injury response transcriptional states defines functional vulnerabilities underpinning glioblastoma heterogeneity. Nat. Cancer 2, 157–173 (2021).
Kim, N. et al. Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma. Nat. Commun. 11, 2285 (2020).
Laughney, A. M. et al. Regenerative lineages and immune-mediated pruning in lung cancer metastasis. Nat. Med. 26, 259–269 (2020).
Rubio-Perez, C. et al. Immune cell profiling of the cerebrospinal fluid enables the characterization of the brain metastasis microenvironment. Nat. Commun. 12, 1503 (2021).
Berghoff, A. S. et al. Density of tumor-infiltrating lymphocytes correlates with extent of brain edema and overall survival time in patients with brain metastases. Oncoimmunology 5, e1057388 (2016).
Berghoff, A. S. et al. Correlation of immune phenotype with IDH mutation in diffuse glioma. Neuro Oncol. 19, 1460–1468 (2017).
Kohanbash, G. et al. Isocitrate dehydrogenase mutations suppress STAT1 and CD8+ T cell accumulation in gliomas. J. Clin. Invest. 127, 1425–1437 (2017).
Hodges, T. R. et al. Mutational burden, immune checkpoint expression, and mismatch repair in glioma: implications for immune checkpoint immunotherapy. Neuro Oncol. 19, 1047–1057 (2017).
Shih, D. J. H. et al. Genomic characterization of human brain metastases identifies drivers of metastatic lung adenocarcinoma. Nat. Genet. 52, 371–377 (2020).
Brastianos, P. K. et al. Genomic characterization of brain metastases reveals branched evolution and potential therapeutic targets. Cancer Discov. 5, 1164–1177 (2015).
Gromeier, M. et al. Very low mutation burden is a feature of inflamed recurrent glioblastomas responsive to cancer immunotherapy. Nat. Commun. 12, 352 (2021).
Berghoff, A. S. et al. Invasion patterns in brain metastases of solid cancers. Neuro Oncol. 15, 1664–1672 (2013).
O’Flanagan, C. H. et al. Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses. Genome Biol. 20, 210 (2019).
Hansen, D. M. et al. A holistic analysis of the intestinal stem cell niche network. Preprint at bioRxiv http://doi.org/10.1101/2019.12.12.871756 (2019).
Wenisch, C., Fladerer, P., Patruta, S., Krause, R. & Horl, W. Assessment of neutrophil function in patients with septic shock: comparison of methods. Clin. Diagn. Lab. Immunol. 8, 178–180 (2001).
Van Gassen, S., Gaudilliere, B., Angst, M. S., Saeys, Y. & Aghaeepour, N. CytoNorm: a normalization algorithm for cytometry data. Cytom. Part A 97, 268–278 (2020).
Plouffe, B. D., Murthy, S. K. & Lewis, L. H. Fundamentals and application of magnetic particles in cell isolation and enrichment: a review. Rep. Prog. Phys. 78, 016601 (2015).
Son, K. et al. Improved recovery of functionally active eosinophils and neutrophils using novel immunomagnetic technology. J. Immunol. Methods 449, 44–55 (2017).
Lozano-Ojalvo, D., et al. PBMC-derived T cells. in The Impact of Food Bioactives on Health: In Vitro and Ex Vivo Models (eds Verhoeckx, K. et al.) 169–180 (Springer, 2015).
Chometon, T. Q. et al. A protocol for rapid monocyte isolation and generation of singular human monocyte-derived dendritic cells. PLoS One 15, e0231132 (2020).
Ferrara, F. et al. Rapid purification of billions of circulating CD19+ B cells directly from leukophoresis samples. N. Biotechnol. 46, 14–21 (2018).
Swartzlander, D. B. et al. Concurrent cell type-specific isolation and profiling of mouse brains in inflammation and Alzheimer’s disease. JCI Insight http://doi.org/10.1172/jci.insight.121109 (2018).
National Society for Histotechnology (NSH). Guidelines for Hematoxylin & Eosin Staining. http://nsh.org/sites/default/files/Guidelines_For_Hematoxylin_and_Eosin_Staining.pdf (reviewed July 2001).
Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 9, 171–181 (2014).
Callahan, M. K., Williamson, P. & Schlegel, R. A. Surface expression of phosphatidylserine on macrophages is required for phagocytosis of apoptotic thymocytes. Cell Death Differ. 7, 645–653 (2000).
Macosko, E. Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202–1214 (2015).

An integrated pipeline for comprehensive analysis of immune cells in human brain tumor clinical samples

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