Wang Y, Wang M, Wu H, Xu R. Advancing to the era of cancer immunotherapy. Cancer Commun. 2021:cac2.12178. https://doi.org/10.1002/cac2.12178.
Sharma P, Siddiqui BA, Anandhan S, Yadav SS, Subudhi SK, Gao J, et al. The Next Decade of Immune Checkpoint Therapy. Cancer Discov. 2021;11:838–57. https://doi.org/10.1158/2159-8290.CD-20-1680.
Article
CAS
PubMed
Google Scholar
Davoli T, Uno H, Wooten EC, Elledge SJ. Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy. Science. 2017;355:eaaf8399. https://doi.org/10.1126/science.aaf8399.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hakimi AA, Voss MH, Kuo F, Sanchez A, Liu M, Nixon BG, et al. Transcriptomic Profiling of the Tumor Microenvironment Reveals Distinct Subgroups of Clear Cell Renal Cell Cancer: Data from a Randomized Phase III Trial. Cancer Discov. 2019;9:510–25. https://doi.org/10.1158/2159-8290.CD-18-0957.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ott PA, Bang Y-J, Piha-Paul SA, Razak ARA, Bennouna J, Soria J-C, et al. T-Cell–Inflamed Gene-Expression Profile, Programmed Death Ligand 1 Expression, and Tumor Mutational Burden Predict Efficacy in Patients Treated With Pembrolizumab Across 20 Cancers: KEYNOTE-028. J Clin Oncol. 2019;37:318–27. https://doi.org/10.1200/JCO.2018.78.2276.
Article
PubMed
Google Scholar
Zhang Z, Wu H, Lin W, Wang Z, Yang L, Zeng Z, et al. EPHA7 mutation as a predictive biomarker for immune checkpoint inhibitors in multiple cancers. BMC Med. 2021;19:26. https://doi.org/10.1186/s12916-020-01899-x.
Article
CAS
PubMed
PubMed Central
Google Scholar
Auslander N, Zhang G, Lee JS, Frederick DT, Miao B, Moll T, et al. Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma. Nat Med. 2018;24:1545–9. https://doi.org/10.1038/s41591-018-0157-9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fu J, Li K, Zhang W, Wan C, Zhang J, Jiang P, et al. Large-scale public data reuse to model immunotherapy response and resistance. Genome Med. 2020;12:21. https://doi.org/10.1186/s13073-020-0721-z.
Article
PubMed
PubMed Central
Google Scholar
Hwang B, Lee JH, Bang D. Single-cell RNA sequencing technologies and bioinformatics pipelines. Exp Mol Med. 2018;50:1–14. https://doi.org/10.1038/s12276-018-0071-8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen P, Hsu W, Han J, Xia Y, Depinho RA. Cancer stemness meets immunity: from mechanism to therapy. CellReports. 2021;34:108597. https://doi.org/10.1016/j.celrep.2020.108597.
Article
CAS
Google Scholar
Bayik D, Lathia JD. Cancer stem cell-immune cell crosstalk in tumour progression. Nat Rev Cancer. 2021. https://doi.org/10.1038/s41568-021-00366-w.
Miranda A, Hamilton PT, Zhang AW, Pattnaik S, Becht E, Mezheyeuski A, et al. Cancer stemness, intratumoral heterogeneity, and immune response across cancers. Proc Natl Acad Sci. 2019;116:9020–9. https://doi.org/10.1073/pnas.1818210116.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gulati GS, Sikandar SS, Wesche DJ, Manjunath A, Bharadwaj A, Berger MJ, et al. Single-cell transcriptional diversity is a hallmark of developmental potential. Science. 2020;367:405–11. https://doi.org/10.1126/science.aax0249.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su M-J, Melms JC, et al. A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. Cell. 2018;175:984–97.e24. https://doi.org/10.1016/j.cell.2018.09.006.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yost KE, Satpathy AT, Wells DK, Qi Y, Wang C, Kageyama R, et al. Clonal replacement of tumor-specific T cells following PD-1 blockade. Nat Med. 2019;25:1251–9. https://doi.org/10.1038/s41591-019-0522-3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang L, Dai J, Han R-R, Dong L, Feng D, Zhu G, et al. Single-cell map of diverse immune phenotypes in the metastatic brain tumor microenvironment of non small cell lung cancer. bioRxiv. 2019. https://doi.org/10.1101/2019.12.30.890517.
Venteicher AS, Tirosh I, Hebert C, Yizhak K, Neftel C, Filbin MG, et al. Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. Science. 2017;355. https://doi.org/10.1126/science.aai8478.
Tirosh I, Venteicher AS, Hebert C, Escalante LE, Patel AP, Yizhak K, et al. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature. 2016;539:309–13. https://doi.org/10.1038/nature20123.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tirosh I, Izar B, Prakadan SM, Wadsworth MH, Treacy D, Trombetta JJ, et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016;352:189–96. https://doi.org/10.1126/science.aad0501.
Article
CAS
PubMed
PubMed Central
Google Scholar
Song Q, Hawkins GA, Wudel L, Chou PC, Forbes E, Pullikuth AK, et al. Dissecting intratumoral myeloid cell plasticity by single cell RNA-seq. Cancer Med. 2019;8:3072–85. https://doi.org/10.1002/cam4.2113.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shih AJ, Menzin A, Whyte J, Lovecchio J, Liew A, Khalili H, et al. Correction: Identification of grade and origin specific cell populations in serous epithelial ovarian cancer by single cell RNA-seq. PLoS One. 2018;13:1–17. https://doi.org/10.1371/journal.pone.0208778.
Article
Google Scholar
Rao M, Oh K, Moffitt R, Thompson P, Li J, Liu J, et al. Comparative single-cell RNA sequencing (scRNA-seq) reveals liver metastasis–specific targets in a patient with small intestinal neuroendocrine cancer. Mol Case Stud. 2020;6:a004978. https://doi.org/10.1101/mcs.a004978.
Article
CAS
Google Scholar
Puram SV, Tirosh I, Parikh AS, Patel AP, Yizhak K, Gillespie S, et al. Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer. Cell. 2017;171:1611–24.e24. https://doi.org/10.1016/j.cell.2017.10.044.
Article
CAS
PubMed
PubMed Central
Google Scholar
Peng J, Sun BF, Chen CY, Zhou JY, Chen YS, Chen H, et al. Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma. Cell Res. 2019;29:725–38. https://doi.org/10.1038/s41422-019-0195-y.
Article
CAS
PubMed
PubMed Central
Google Scholar
Paulson KG, Voillet V, McAfee MS, Hunter DS, Wagener FD, Perdicchio M, et al. Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA. Nat Commun. 2018;9. https://doi.org/10.1038/s41467-018-06300-3.
Zilionis R, Engblom C, Pfirschke C, Savova V, Zemmour D, Saatcioglu HD, et al. Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species. Immunity. 2019;50:1317–34.e10. https://doi.org/10.1016/j.immuni.2019.03.009.
Article
CAS
PubMed
PubMed Central
Google Scholar
Neftel C, Laffy J, Filbin MG, Hara T, Shore ME, Rahme GJ, et al. An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma. Cell. 2019;178:835–49.e21. https://doi.org/10.1016/j.cell.2019.06.024.
Article
CAS
PubMed
PubMed Central
Google Scholar
Moncada R, Barkley D, Wagner F, Chiodin M, Devlin JC, Baron M, et al. Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas. Nat Biotechnol. 2020;38:333–42. https://doi.org/10.1038/s41587-019-0392-8.
Article
CAS
PubMed
Google Scholar
Ma L, Hernandez MO, Zhao Y, Mehta M, Tran B, Kelly M, et al. Tumor cell biodiversity drives microenvironmental reprogramming in liver cancer. Cancer Cell. 2019;36:418–430.e6. https://doi.org/10.1016/j.ccell.2019.08.007.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ledergor G, Weiner A, Zada M, Wang S-Y, Cohen YC, Gatt ME, et al. Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma. Nat Med. 2018;24:1867–76. https://doi.org/10.1038/s41591-018-0269-2.
Article
CAS
PubMed
Google Scholar
Lambrechts D, Wauters E, Boeckx B, Aibar S, Nittner D, Burton O, et al. Phenotype molding of stromal cells in the lung tumor microenvironment. Nat Med. 2018;24:1277–89. https://doi.org/10.1038/s41591-018-0096-5.
Article
CAS
PubMed
Google Scholar
Kim C, Gao R, Sei E, Brandt R, Hartman J, Hatschek T, et al. Chemoresistance evolution in triple-negative breast cancer delineated by single-cell sequencing. Cell. 2018;173:879–93.e13. https://doi.org/10.1016/j.cell.2018.03.041.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hovestadt V, Smith KS, Bihannic L, Filbin MG, Shaw MKL, Baumgartner A, et al. Resolving medulloblastoma cellular architecture by single-cell genomics. Nature. 2019;572:74–9. https://doi.org/10.1038/s41586-019-1434-6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Filbin MG, Tirosh I, Hovestadt V, Shaw ML, Escalante LE, Mathewson ND, et al. Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. Science. 2018;360:331–5. https://doi.org/10.1126/science.aao4750.
Article
CAS
PubMed
PubMed Central
Google Scholar
Durante MA, Rodriguez DA, Kurtenbach S, Kuznetsov JN, Sanchez MI, Decatur CL, et al. Single-cell analysis reveals new evolutionary complexity in uveal melanoma. Nat Commun. 2020;11. https://doi.org/10.1038/s41467-019-14256-1.
Darmanis S, Sloan SA, Croote D, Mignardi M, Chernikova S, Samghababi P, et al. Single-Cell RNA-Seq analysis of infiltrating neoplastic cells at the migrating front of human glioblastoma. Cell Rep. 2017;21:1399–410. https://doi.org/10.1016/j.celrep.2017.10.030.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao W, Dovas A, Spinazzi EF, Levitin HM, Banu MA, Upadhyayula P, et al. Deconvolution of cell type-specific drug responses in human tumor tissue with single-cell RNA-seq. Genome Med. 2021;13. https://doi.org/10.1186/s13073-021-00894-y.
Zhang P, Yang M, Zhang Y, Xiao S, Lai X, Tan A, et al. Dissecting the single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer. Cell Rep. 2019;27:1934–47.e5. https://doi.org/10.1016/j.celrep.2019.04.052.
Article
CAS
PubMed
Google Scholar
Zhang L, Li Z, Skrzypczynska KM, Fang Q, Zhang W, O’Brien SA, et al. Single-cell analyses inform mechanisms of myeloid-targeted therapies in colon cancer. Cell. 2020;181:442–59.e29. https://doi.org/10.1016/j.cell.2020.03.048.
Article
CAS
PubMed
Google Scholar
Yuan J, Levitin HM, Frattini V, Bush EC, Boyett DM, Samanamud J, et al. Single-cell transcriptome analysis of lineage diversity in high-grade glioma. Genome Med. 2018;10:1–15. https://doi.org/10.1186/s13073-018-0567-9.
Article
CAS
Google Scholar
Wang R, Sharma R, Shen X, Laughney AM, Funato K, Clark PJ, et al. Adult human glioblastomas harbor radial glia-like cells. Stem Cell Rep. 2020;14:338–50. https://doi.org/10.1016/j.stemcr.2020.01.007.
Article
CAS
Google Scholar
Wang L, Catalan F, Shamardani K, Babikir H, Diaz A. Ensemble learning for classifying single-cell data and projection across reference atlases. Bioinformatics. 2020;36:3585–7. https://doi.org/10.1093/bioinformatics/btaa137.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang L, Babikir H, Müller S, Yagnik G, Shamardani K, Catalan F, et al. The phenotypes of proliferating glioblastoma cells reside on a single axis of variation. Cancer Discov. 2019;9:1708–19. https://doi.org/10.1158/2159-8290.CD-19-0329.
Article
CAS
PubMed
PubMed Central
Google Scholar
Goldman MJ, Craft B, Hastie M, Repečka K, McDade F, Kamath A, et al. Visualizing and interpreting cancer genomics data via the Xena platform. Nat Biotechnol. 2020;38:675–8. https://doi.org/10.1038/s41587-020-0546-8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lawson KA, Sousa CM, Zhang X, Kim E, Akthar R, Caumanns JJ, et al. Functional genomic landscape of cancer-intrinsic evasion of killing by T cells. Nature. 2020;586:120–6. https://doi.org/10.1038/s41586-020-2746-2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kearney CJ, Vervoort SJ, Hogg SJ, Ramsbottom KM, Freeman AJ, Lalaoui N, et al. Tumor immune evasion arises through loss of TNF sensitivity. Sci Immunol. 2018;3:eaar3451. https://doi.org/10.1126/sciimmunol.aar3451.
Article
PubMed
Google Scholar
Freeman AJ, Vervoort SJ, Ramsbottom KM, Kelly MJ, Michie J, Pijpers L, et al. Natural killer cells suppress T cell-associated tumor immune evasion. Cell Rep. 2019;28:2784–94.e5. https://doi.org/10.1016/j.celrep.2019.08.017.
Article
CAS
PubMed
Google Scholar
Vredevoogd DW, Kuilman T, Ligtenberg MA, Boshuizen J, Stecker KE, de Bruijn B, et al. augmenting immunotherapy impact by lowering tumor TNF cytotoxicity threshold. Cell. 2019;178:585–99.e15. https://doi.org/10.1016/j.cell.2019.06.014.
Article
CAS
PubMed
Google Scholar
Patel SJ, Sanjana NE, Kishton RJ, Eidizadeh A, Vodnala SK, Cam M, et al. Identification of essential genes for cancer immunotherapy. Nature. 2017;548:537–42. https://doi.org/10.1038/nature23477.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pan D, Kobayashi A, Jiang P, Ferrari de Andrade L, Tay RE, Luoma AM, et al. A major chromatin regulator determines resistance of tumor cells to T cell–mediated killing. Science. 2018;359:770–5. https://doi.org/10.1126/science.aao1710.
Article
CAS
PubMed
PubMed Central
Google Scholar
Manguso RT, Pope HW, Zimmer MD, Brown FD, Yates KB, Miller BC, et al. In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target. Nature. 2017;547:413–8. https://doi.org/10.1038/nature23270.
Article
CAS
PubMed
PubMed Central
Google Scholar
Braun DA, Hou Y, Bakouny Z, Ficial M, Sant’ Angelo M, Forman J, et al. Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma. Nat Med. 2020;26:909–18. https://doi.org/10.1038/s41591-020-0839-y.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mariathasan S, Turley SJ, Nickles D, Castiglioni A, Yuen K, Wang Y, et al. TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells. Nature. 2018;554:544–8. https://doi.org/10.1038/nature25501.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu D, Schilling B, Liu D, Sucker A, Livingstone E, Jerby-amon L, et al. Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma. Nat Med. 2019;25. https://doi.org/10.1038/s41591-019-0654-5.
Gide TN, Quek C, Menzies AM, Tasker AT, Shang P, Holst J, et al. Distinct immune cell populations define response to Anti-PD-1 monotherapy and anti-PD-1/Anti-CTLA-4 combined therapy. Cancer Cell. 2019;35:238–55.e6. https://doi.org/10.1016/j.ccell.2019.01.003.
Article
CAS
PubMed
Google Scholar
Riaz N, Havel JJ, Makarov V, Desrichard A, Urba WJ, Sims JS, et al. Tumor and microenvironment evolution during immunotherapy with nivolumab. Cell. 2017;171:934–49.e16. https://doi.org/10.1016/j.cell.2017.09.028.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao J, Chen AX, Gartrell RD, Silverman AM, Aparicio L, Chu T, et al. Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma. Nat Med. 2019;25:462–9. https://doi.org/10.1038/s41591-019-0349-y.
Article
CAS
PubMed
PubMed Central
Google Scholar
Snyder A, Nathanson T, Funt SA, Ahuja A, Buros Novik J, Hellmann MD, et al. Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: an exploratory multi-omic analysis. PLoS Med. 2017;14:e1002309. https://doi.org/10.1371/journal.pmed.1002309 Minna JD, editor.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hugo W, Zaretsky JM, Sun L, Song C, Moreno BH, Hu-Lieskovan S, et al. Genomic and transcriptomic features of response to anti-PD-1 therapy in metastatic melanoma. Cell. 2016;165:35–44. https://doi.org/10.1016/j.cell.2016.02.065.
Article
CAS
PubMed
PubMed Central
Google Scholar
Van Allen EM, Miao D, Schilling B, Shukla SA, Blank C, Zimmer L, et al. Erratum for the Report “Genomic correlates of response to CTLA-4 blockade in metastatic melanoma”. Science. 2016;352:aaf8264. https://doi.org/10.1126/science.aaf8264 by E. M. Van Allen, D. Miao, B. Schilling, S. A. Shukla, C. Blank, L. Zimmer, A. Sucker, U. Hillen, M. H. Geukes Foppen, S. M. Goldinger, J. Utikal, J. C. Ha.
Article
Google Scholar
Kim ST, Cristescu R, Bass AJ, Kim K-M, Odegaard JI, Kim K, et al. Comprehensive molecular characterization of clinical responses to PD-1 inhibition in metastatic gastric cancer. Nat Med. 2018;24:1449–58. https://doi.org/10.1038/s41591-018-0101-z.
Article
CAS
PubMed
Google Scholar
Sun D, Wang J, Han Y, Dong X, Ge J, Zheng R, et al. TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment. Nucleic Acids Res. 2021;49:D1420–30. https://doi.org/10.1093/nar/gkaa1020.
Article
CAS
PubMed
Google Scholar
Chen Y-T, Shen J-Y, Chen D-P, Wu C-F, Guo R, Zhang P-P, et al. Identification of cross-talk between m6A and 5mC regulators associated with onco-immunogenic features and prognosis across 33 cancer types. J Hematol Oncol. 2020;13:22. https://doi.org/10.1186/s13045-020-00854-w.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, et al. Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal. Sci Signal. 2013;6:pl1. https://doi.org/10.1126/scisignal.2004088.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, et al. The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1. Cancer Discov. 2012;2:401–4. https://doi.org/10.1158/2159-8290.CD-12-0095.
Article
PubMed
Google Scholar
Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang T-H, et al. The Immune Landscape of Cancer. Immunity. 2018;48:812–30.e14. https://doi.org/10.1016/j.immuni.2018.03.023.
Article
CAS
PubMed
PubMed Central
Google Scholar
Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, et al. GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics. 2004;20:3710–5. https://doi.org/10.1093/bioinformatics/bth456.
Article
CAS
PubMed
Google Scholar
Yu G, Wang L-G, Han Y, He Q-Y. clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters. Omi A J Integr Biol. 2012;16:284–7. https://doi.org/10.1089/omi.2011.0118.
Article
CAS
Google Scholar
Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics. 2013;14:7. https://doi.org/10.1186/1471-2105-14-7.
Article
PubMed
PubMed Central
Google Scholar
Becht E, Giraldo NA, Lacroix L, Buttard B, Elarouci N, Petitprez F, et al. Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. Genome Biol. 2016;17:1–20. https://doi.org/10.1186/s13059-016-1070-5.
Article
CAS
Google Scholar
Eisenhauer EA, Therasse P, Bogaerts J, Schwartz LH, Sargent D, Ford R, et al. New response evaluation criteria in solid tumours: Revised RECIST guideline (version 1.1). Eur J Cancer. 2009;45:228–47. https://doi.org/10.1016/j.ejca.2008.10.026.
Article
CAS
PubMed
Google Scholar
Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007;8:118–27. https://doi.org/10.1093/biostatistics/kxj037.
Article
PubMed
Google Scholar
Vougas K, Sakellaropoulos T, Kotsinas A, Foukas G-RP, Ntargaras A, Koinis F, et al. Machine learning and data mining frameworks for predicting drug response in cancer: An overview and a novel in silico screening process based on association rule mining. Pharmacol Ther. 2019;203:107395. https://doi.org/10.1016/j.pharmthera.2019.107395.
Article
CAS
PubMed
Google Scholar
Budczies J, Kosztyla D, von Törne C, Stenzinger A, Drab-Esfahani S, Dietel M, et al. cancerclass: An R Package for development and validation of diagnostic tests from high-dimensional molecular data. J Stat Softw. 2014;59:1–8. https://doi.org/10.18637/jss.v059.i01.
Article
Google Scholar
Sammut S, Crispin-Ortuzar M, Chin S, Provenzano E, Bardwell HA, Ma W, et al. Multi-omic machine learning predictor of breast cancer therapy response. Nature. 2021. https://doi.org/10.1038/s41586-021-04278-5.
Ayers M, Lunceford J, Nebozhyn M, Murphy E, Loboda A, Kaufman DR, et al. IFN-γ–related mRNA profile predicts clinical response to PD-1 blockade. J Clin Invest. 2017;127:2930–40. https://doi.org/10.1172/JCI91190.
Article
PubMed
PubMed Central
Google Scholar
Topalian SL, Hodi FS, Brahmer JR, Gettinger SN, Smith DC, McDermott DF, et al. Safety, activity, and immune correlates of Anti–PD-1 antibody in cancer. N Engl J Med. 2012;366:2443–54. https://doi.org/10.1056/nejmoa1200690.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dominguez CX, Müller S, Keerthivasan S, Koeppen H, Hung J, Gierke S, et al. Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15 + Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy. Cancer Discov. 2020;10:232–53. https://doi.org/10.1158/2159-8290.CD-19-0644.
Article
CAS
PubMed
Google Scholar
Ju M, Bi J, Wei Q, Jiang L, Guan Q, Zhang M, et al. Pan-cancer analysis of NLRP3 inflammasome with potential implications in prognosis and immunotherapy in human cancer. Brief Bioinform. 2020;00:1–16. https://doi.org/10.1093/bib/bbaa345.
Article
CAS
Google Scholar
Rooney MS, Shukla SA, Wu CJ, Getz G, Hacohen N. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell. 2015;160:48–61. https://doi.org/10.1016/j.cell.2014.12.033.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shukla SA, Bachireddy P, Schilling B, Galonska C, Zhan Q, Bango C, et al. Cancer-germline antigen expression discriminates clinical outcome to CTLA-4 Blockade. Cell. 2018;173:624–33.e8. https://doi.org/10.1016/j.cell.2018.03.026.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hugo W, Zaretsky JM, Sun L, Johnson DB, Ribas A, Lo RS, et al. Genomic and transcriptomic features of response to Anti-PD-1 therapy in metastatic melanoma article genomic and transcriptomic features of response to Anti-PD-1 therapy in metastatic melanoma. Cell. 2016:1–10. https://doi.org/10.1016/j.cell.2016.02.065.
Xiong D, Wang Y, You M. A gene expression signature of TREM2hi macrophages and γδ T cells predicts immunotherapy response. Nat Commun. 2020;11:1–12. https://doi.org/10.1038/s41467-020-18546-x.
Article
CAS
Google Scholar
Cui C, Xu C, Yang W, Chi Z, Sheng X, Si L, et al. Ratio of the interferon-γ signature to the immunosuppression signature predicts anti-PD-1 therapy response in melanoma. npj. Genomic Med. 2021;6:7. https://doi.org/10.1038/s41525-021-00169-w.
Article
CAS
Google Scholar
Yan M, Hu J, Ping Y, Xu L, Liao G, Jiang Z, et al. Single-cell transcriptomic analysis reveals a tumor-reactive T Cell signature associated with clinical outcome and immunotherapy response in melanoma. Front Immunol. 2021;12:1–14. https://doi.org/10.3389/fimmu.2021.758288.
Article
Google Scholar
Fluss R, Faraggi D, Reiser B. Estimation of the youden index and its associated cutoff point. Biom J. 2005;47:458–72. https://doi.org/10.1002/bimj.200410135.
Article
PubMed
Google Scholar
Akoglu H. User’s guide to correlation coefficients. Turkish J Emerg Med. 2018;18:91–3. https://doi.org/10.1016/j.tjem.2018.08.001.
Article
Google Scholar
Xiao Q, Wu J, Wang WJ, Chen S, Zheng Y, Yu X, et al. DKK2 imparts tumor immunity evasion through β-catenin-independent suppression of cytotoxic immune-cell activation. Nat Med. 2018;24:262–70. https://doi.org/10.1038/nm.4496.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rosenbaum M, Gewies A, Pechloff K, Heuser C, Engleitner T, Gehring T, et al. Bcl10-controlled Malt1 paracaspase activity is key for the immune suppressive function of regulatory T cells. Nat Commun. 2019;10. https://doi.org/10.1038/s41467-019-10203-2.
Richter C, Mayhew D, Rennhack JP, So J, Stover EH, Hwang JH, et al. Genomic amplification and functional dependency of the gamma actin gene ACTG1 in uterine cancer. Int J Mol Sci. 2020;21:8690. https://doi.org/10.3390/ijms21228690.
Article
CAS
PubMed Central
Google Scholar
Mandili G, Curcio C, Bulfamante S, Follia L, Ferrero G, Mazza E, et al. In pancreatic cancer, chemotherapy increases antitumor responses to tumor-associated antigens and potentiates DNA vaccination. J Immunother Cancer. 2020;8:e001071. https://doi.org/10.1136/jitc-2020-001071.
Article
PubMed
PubMed Central
Google Scholar
Qin G, Wang X, Ye S, Li Y, Chen M, Wang S, et al. NPM1 upregulates the transcription of PD-L1 and suppresses T cell activity in triple-negative breast cancer. Nat Commun. 2020;11. https://doi.org/10.1038/s41467-020-15364-z.
Maugeri-Saccà M, Bartucci M, De Maria R. DNA damage repair pathways in cancer stem cells. Mol Cancer Ther. 2012;11:1627–36. https://doi.org/10.1158/1535-7163.MCT-11-1040.
Article
CAS
PubMed
Google Scholar
Jaiswal AR, Liu AJ, Pudakalakatti S, Dutta P, Jayaprakash P, Bartkowiak T, et al. Melanoma evolves complete immunotherapy resistance through the acquisition of a hypermetabolic phenotype. Cancer Immunol Res. 2020;8:1365–80. https://doi.org/10.1158/2326-6066.CIR-19-0005.
Article
PubMed
PubMed Central
Google Scholar
Casey SC, Tong L, Li Y, Do R, Walz S, Fitzgerald KN, et al. MYC regulates the antitumor immune response through CD47 and PD-L1. Science. 2016;352:227–31. https://doi.org/10.1126/science.aac9935.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Z, Wang Y, Yang T, Xing H, Wang Y, Gao L, et al. Machine learning revealed stemness features and a novel stemness-based classification with appealing implications in discriminating the prognosis, immunotherapy and temozolomide responses of 906 glioblastoma patients. Brief Bioinform. 2021;00:1–20. https://doi.org/10.1093/bib/bbab032.
Article
CAS
Google Scholar
Maccalli C, Rasul KI, Elawad M, Ferrone S. The role of cancer stem cells in the modulation of anti-tumor immune responses. Semin Cancer Biol. 2018;53:189–200. https://doi.org/10.1016/j.semcancer.2018.09.006.
Article
CAS
PubMed
PubMed Central
Google Scholar
Clara JA, Monge C, Yang Y, Takebe N. Targeting signalling pathways and the immune microenvironment of cancer stem cells — a clinical update. Nat Rev Clin Oncol. 2020;17:204–32. https://doi.org/10.1038/s41571-019-0293-2.
Article
PubMed
Google Scholar
Abou Khouzam R, Goutham HV, Zaarour RF, Chamseddine AN, Francis A, Buart S, et al. Integrating tumor hypoxic stress in novel and more adaptable strategies for cancer immunotherapy. Semin Cancer Biol. 2020;65:140–54. https://doi.org/10.1016/j.semcancer.2020.01.003.
Article
CAS
PubMed
Google Scholar
Wei P, Dove KK, Bensard C, Schell JC, Rutter J. The force is strong with this one: metabolism (Over)powers stem cell fate. Trends Cell Biol. 2018;28:551–9. https://doi.org/10.1016/j.tcb.2018.02.007.
Article
CAS
PubMed
PubMed Central
Google Scholar
Deng L, Meng T, Chen L, Wei W, Wang P. The role of ubiquitination in tumorigenesis and targeted drug discovery. Signal Transduct Target Ther. 2020;5. https://doi.org/10.1038/s41392-020-0107-0.
Chen J, Song W, Amato K. Eph receptor tyrosine kinases in cancer stem cells. Cytokine Growth Factor Rev. 2015;26:1–6. https://doi.org/10.1016/j.cytogfr.2014.05.001.
Article
CAS
PubMed
Google Scholar
Helmink BA, Reddy SM, Gao J, Zhang S, Basar R, Thakur R, et al. B cells and tertiary lymphoid structures promote immunotherapy response. Nature. 2020;577:549–55. https://doi.org/10.1038/s41586-019-1922-8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ready N, Hellmann MD, Awad MM, Otterson GA, Gutierrez M, Gainor JF, et al. First-line nivolumab plus ipilimumab in advanced non–small-cell lung cancer (CheckMate 568): outcomes by programmed death ligand 1 and tumor mutational burden as biomarkers. J Clin Oncol. 2019;37:992–1000. https://doi.org/10.1200/JCO.18.01042.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pan H, Cai N, Li M, Liu GH, Izpisua Belmonte JC. Autophagic control of cell “stemness”. EMBO Mol Med. 2013;5:327–31. https://doi.org/10.1002/emmm.201201999.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mgrditchian T, Arakelian T, Paggetti J, Noman MZ, Viry E, Moussay E, et al. Targeting autophagy inhibits melanoma growth by enhancing NK cells infiltration in a CCL5-dependent manner. Proc Natl Acad Sci. 2017;114:E9271–9. https://doi.org/10.1073/pnas.1703921114.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhen Z, Zi-Xian W, Yan-Xing C, Hao-Xiang W, Ling Y, Qi Z, et al. Integrated analysis of single-cell and bulk RNA sequencing data reveals a pan-cancer stemness signature predicting immunotherapy response. Figshare. 2022. https://doi.org/10.6084/m9.figshare.17654633.