Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106

STAR: ultrafast universal RNA-seq aligner

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Yu, G., Wang, L.-G., Han, Y., & He, Q.-Y. (2012) · OMICS: A Journal of Integrative Biology · doi:10.1089/omi.2011.0118 · Cited by 36,259

PD-1 and PD-L1 Immune Checkpoint Blockade to Treat Breast Cancer

Hartkopf, A. D., Taran, F., Wallwiener, M., Walter, C. B., Krämer, B., Grischke, E., & Brucker, S. Y. (2016) · Breast Care · doi:10.1159/000453569 · Cited by 30,989

Adverse Renal Effects of Immune Checkpoint Inhibitors: A Narrative Review

Wanchoo, R., Karam, S., Uppal, N. N., Barta, V. S., Deray, G., Devoe, C., Launay‐Vacher, V., Jhaveri, K. D., & on behalf of Cancer and Kidney International Network Workgroup on Immune Checkpoint Inhibitors (2017) · American Journal of Nephrology · doi:10.1159/000455014 · Cited by 15,320

Robust enumeration of cell subsets from tissue expression profiles

Newman, A. M., Liu, C. L., Green, M. R., Gentles, A. J., Feng, W., Xu, Y., Hoang, C. D., Diehn, M., & Alizadeh, A. A. (2015) · Nature Methods · doi:10.1038/nmeth.3337 · Cited by 13,224

Safety, activity, and immune correlates of anti–PD-1 antibody in cancer

Topalian, S. L., Hodi, F. S., Brahmer, J. R., Gettinger, S. N., Smith, D. C., McDermott, D. F., Powderly, J. D., Carvajal, R. D., Sosman, J. A., Atkins, M. B., et al. (2012) · New England Journal of Medicine · doi:10.1056/nejmoa1200690 · Cited by 12,628

Inferring tumour purity and stromal and immune cell admixture from expression data

Yoshihara, K., Shahmoradgoli, M., Martínez, E., Vegesna, R., Kim, H., Torres-Garcia, W., Treviño, V., Shen, H., Laird, P. W., Levine, D. A., et al. (2013) · Nature Communications · doi:10.1038/ncomms3612 · Cited by 9,778

Signatures of mutational processes in human cancer

Initiative, A. P. C. G., Alexandrov, L. B., ICGC Breast Cancer Consortium, ICGC MMML-Seq Consortium, PedBrain, I., Nik-Zainal, S., Wedge, D. C., Aparicio, S. A. J. R., Behjati, S., Biankin, A. V., et al. (2013) · Nature · doi:10.1038/nature12477 · Cited by 9,660

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

Le, D. T., Uram, J. N., Wang, H., Bartlett, B. R., Kemberling, H., Eyring, A. D., Skora, A. D., Luber, B. S., Azad, N. S., Laheru, D., et al. (2015) · New England Journal of Medicine · doi:10.1056/nejmoa1500596 · Cited by 9,377

High Response Rate and Durability Driven by HLA Genetic Diversity in Patients with Kidney Cancer Treated with Lenvatinib and Pembrolizumab

Lee, C., DiNatale, R. G., Chowell, D., Krishna, C., Makarov, V., Valero, C., Vuong, L. H., Lee, M., Weiss, K. L., Hoen, D., et al. (2021) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-21-0053 · Cited by 31

Hyperprogression, a challenge of PD-1/PD-L1 inhibitors treatments: potential mechanisms and coping strategies

Zhao, L.-P., Hu, J.-H., Hu, D., Wang, H., Huang, C.-G., Luo, R., Huang, X., Huang, X., Xie, T., & Lou, J.-S. (2022) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2022.112949 · Cited by 34

Favorable immune checkpoint inhibitor outcome of patients with melanoma and NSCLC harboring FAT1 mutations

Zhang, W., Tang, Y., Guo, Y., Kong, Y., Shi, F., Sheng, C., Wang, S., & Wang, Q. (2022) · npj Precision Oncology · doi:10.1038/s41698-022-00292-6 · Cited by 33

Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data

Claeys, A., Staut, J., Merseburger, P., Marchal, K., & den Eynden, J. V. (2023) · BMC Genomics · doi:10.1186/s12864-023-09351-z · Cited by 33

Immunosuppressive Microenvironment Revealed by Immune Cell Landscape in Pre-metastatic Liver of Colorectal Cancer

Zeng, D., Wang, M., Wu, J., Lin, S., Ye, Z., Zhou, R., Wang, G., Wu, J., Sun, H., Bin, J., et al. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.620688 · Cited by 30

Challenges and Future Directions in the Management of Tumor Mutational Burden-High (TMB-H) Advanced Solid Malignancies

Ahmed, J., Das, B., Shin, S. J., & Chen, A. P. (2023) · Cancers · doi:10.3390/cancers15245841 · Cited by 36

TP53 to mediate immune escape in tumor microenvironment: an overview of the research progress

Zhu, K., Su, F., Yang, J., Xiao, R., Wu, R.-Y., Cao, M.-Y., Ling, X., & Zhang, T. (2024) · Molecular Biology Reports · doi:10.1007/s11033-023-09097-7 · Cited by 35

STC1 competitively binding βPIX enhances melanoma progression via YAP nuclear translocation and M2 macrophage recruitment through the YAP/CCL2/VEGFA/AKT feedback loop

Ren, Z., Xu, Z., Chang, X., Liu, J., & Xiao, W. (2024) · Pharmacological Research · doi:10.1016/j.phrs.2024.107218 · Cited by 31

Neoantigen architectures define immunogenicity and drive immune evasion of tumors with heterogenous neoantigen expression

Roerden, M., Castro, A., Cui, Y., Harake, N., Kim, B., Dye, J., Maiorino, L., White, F. M., Irvine, D. J., Litchfield, K., et al. (2024) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2024-010249 · Cited by 30

Emerging application of genomics-guided therapeutics in personalized lung cancer treatment

Zaman, A., & Bivona, T. G. (2018) · Annals of Translational Medicine · doi:10.21037/atm.2018.05.02 · Cited by 29

Elimination of melanoma by sortase A-generated TCR-like antibody-drug conjugates (TL-ADCs) targeting intracellular melanoma antigen MART-1

Lai, J., Wang, Y., Wu, S., Ding, D., Sun, Z., Zhang, Y., Zhou, J., Zhou, Z. M., Xu, Y., Pan, L., et al. (2018) · Biomaterials · doi:10.1016/j.biomaterials.2018.06.017 · Cited by 30

The DNA damage response in immunotherapy and radiation

Samstein, R. M., & Riaz, N. (2018) · Advances in Radiation Oncology · doi:10.1016/j.adro.2018.08.017 · Cited by 30

Ipilimumab or FOLFOX with Nivolumab and Trastuzumab in previously untreated HER2-positive locally advanced or metastatic EsophagoGastric Adenocarcinoma - the randomized phase 2 INTEGA trial (AIO STO 0217)

Tintelnot, J., Goekkurt, E., Binder, M., Thuss-Patience, P. C., Lorenzen, S., Knorrenschild, J. R., Kretzschmar, A., Ettrich, T. J., Lindig, U., Jacobasch, L., et al. (2020) · BMC Cancer · doi:10.1186/s12885-020-06958-3 · Cited by 30

Comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) in Limited DNA Sequencing Based on Tube and Droplet

Zhou, X., Xu, Y., Zhu, L., Su, Z., Han, X., Zhang, Z., Huang, Y., & Liu, Q. (2020) · Micromachines · doi:10.3390/mi11070645 · Cited by 30

Clonal tracing reveals diverse patterns of response to immune checkpoint blockade

Gu, S. S., Wang, X., Hu, X. S., Jiang, P., Li, Z., Traugh, N. C., Bu, X., Tang, Q., Wang, C., Zeng, Z., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02166-1 · Cited by 29

Biomarkers for Diagnosis, Prognosis and Response to Immunotherapy in Melanoma

Puglisi, R., Bellenghi, M., Pontecorvi, G., Pallante, G., Carè, A., & Mattia, G. (2021) · Cancers · doi:10.3390/cancers13122875 · Cited by 36

Sex Disparities of Genomic Determinants in Response to Immune Checkpoint Inhibitors in Melanoma

Shi, F., Zhang, W., Yang, Y., Yang, Y., Zhao, J., Xie, M., Sheng, C., Wang, S., & Wang, Q. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.721409 · Cited by 31

Systemic Immune Dysfunction in Cancer Patients Driven by IL6 Induction of LAG3 in Peripheral CD8+ T Cells

Somasundaram, A., Cillo, A. R., Lampenfeld, C., Workman, C. J., Kunning, S. R., Oliveri, L., Velez, M. A., Joyce, S. C., Calderon, M. J., Dadey, R., et al. (2022) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-20-0736 · Cited by 30

Taming metabolic competition via glycolysis inhibition for safe and potent tumor immunotherapy

Lei, J., Yang, Y., Lu, Z., Pan, H., Fang, J., Jing, B., Chen, Y., & Yin, L. (2022) · Biochemical Pharmacology · doi:10.1016/j.bcp.2022.115153 · Cited by 31

Recurrent somatic mutations as predictors of immunotherapy response

Gajic, Z. Z., Deshpande, A. S., Legut, M., Imielinski, M. B., & Sanjana, N. E. (2022) · Nature Communications · doi:10.1038/s41467-022-31055-3 · Cited by 32

Exosome-transmitted circ IFNGR2 Modulates Ovarian Cancer Metastasis via miR-378/ST5 Axis

Chen, X., Ren, X., Jiaoting, E., Zhou, Y., & Bian, R. (2023) · Molecular and Cellular Biology · doi:10.1080/10985549.2022.2160605 · Cited by 31

B7-H1 maintains the polyclonal T cell response by protecting dendritic cells from cytotoxic T lymphocyte destruction

Chen, L., Azuma, T., Yu, W., Xu, Z., Luo, L., & Chen, L. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1722043115 · Cited by 30

Anti-PD-1 monoclonal antibody MEDI0680 in a phase I study of patients with advanced solid malignancies

Naing, A., Infante, J. R., Goel, S., Burris, H. A., Black, C., Marshall, S. A., Achour, I., Barbee, S. D., May, R., Morehouse, C., et al. (2019) · Journal for ImmunoTherapy of Cancer · doi:10.1186/s40425-019-0665-2 · Cited by 30

Meta-analysis of tumor and T cell intrinsic mechanisms of sensitization to checkpoint inhibitionPreprint

Litchfield, K., Reading, J. L., Puttick, C., Abbosh, C., Bentham, R. B., Watkins, T. B. K., Rosenthal, R., Biswas, D., Lim, E. L., Bakir, M. A., et al. (2020) · doi:10.21203/rs.3.rs-76468/v1 · Cited by 32

Spatially resolved analyses link genomic and immune diversity and reveal unfavorable neutrophil activation in melanoma

Mitra, A., Andrews, M. C., Roh, W., De Macedo, M. P., Hudgens, C. W., Carapeto, F., Singh, S., Reuben, A., Wang, F., Mao, X., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15538-9 · Cited by 27

Comprehensive Characterizations of Immune Receptor Repertoire in Tumors and Cancer Immunotherapy Studies

Song, L., Ouyang, Z., Cohen, D., Cao, Y., Altreuter, J., Bai, G., Hu, X. S., Livak, K. J., Li, H., Tang, M., et al. (2022) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-21-0965 · Cited by 27

Synergistic induction of tertiary lymphoid structures by chemoimmunotherapy in bladder cancer

Zhang, L., Zhang, R., Jin, D., Zhang, T., Shahatiaili, A., Zang, J., Wang, L., Pu, Y., Zhuang, G., Chen, H., et al. (2024) · British Journal of Cancer · doi:10.1038/s41416-024-02598-7 · Cited by 30

Integrative Multiomics Analyses Identify Molecular Subtypes of Head and Neck Squamous Cell Carcinoma with Distinct Therapeutic Vulnerabilities

Diao, P., Dai, Y., Wang, A., Bu, X., Wang, Z., Li, J., Wu, Y., Jiang, H., Wang, Y., & Cheng, J. (2024) · Cancer Research · doi:10.1158/0008-5472.can-23-3594 · Cited by 31

Translation dysregulation in cancer as a source for targetable antigens

Weller, C., Bartok, O., McGinnis, C. S., Palashati, H., Chang, T., Malko, D. B., Shmueli, M. D., Nagao, A., Hayoun, D., Murayama, A., et al. (2025) · Cancer Cell · doi:10.1016/j.ccell.2025.03.003 · Cited by 32

Immune Checkpoint Inhibition is Safe and Effective for Liver Cancer Prevention in a Mouse Model of Hepatocellular Carcinoma

Chung, A. S., Mettlen, M., Ganguly, D., Lu, T., Wang, T., Brekken, R. A., Hsiehchen, D., & Zhu, H. (2020) · Cancer Prevention Research · doi:10.1158/1940-6207.capr-20-0200 · Cited by 29

Distinct immune signatures in chronic lymphocytic leukemia and Richter syndrome

Wang, Y., Sinha, S., Wellik, L. E., Secreto, C. R., Rech, K. L., Call, T. G., Parikh, S. A., Kenderian, S. S., Muchtar, E., Hayman, S. R., et al. (2021) · Blood Cancer Journal · doi:10.1038/s41408-021-00477-5 · Cited by 29

Pinpointing the tumor-specific T cells via TCR clusters

Goncharov, M. M., Bryushkova, E. A., Sharaev, N. I., Skatova, V. D., Baryshnikova, A. M., Sharonov, G. V., Карнаухов, В. К., Vakhitova, M. T., Самойленко, И. В., Demidov, L. V., et al. (2022) · eLife · doi:10.7554/elife.77274 · Cited by 32

Next-generation sequencing: unraveling genetic mechanisms that shape cancer immunotherapy efficacy

Halima, A., Vuong, W., & Chan, T. A.-T. (2022) · Journal of Clinical Investigation · doi:10.1172/jci154945 · Cited by 31

Multi-modal molecular programs regulate melanoma cell state

Andrews, M. C., Oba, J., Wu, C., Zhu, H., Karpinets, T. V., Creasy, C. A., Forget, M., Yu, X., Song, X., Mao, X., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31510-1 · Cited by 35

Evolution of the Targeted Therapy Landscape for Cholangiocarcinoma: Is Cholangiocarcinoma the ‘NSCLC’ of GI Oncology?

Gupta, A., Kurzrock, R., & Adashek, J. J. (2023) · Cancers · doi:10.3390/cancers15051578 · Cited by 29

Tumor-derived semaphorin 4A improves PD-1–blocking antibody efficacy by enhancing CD8 + T cell cytotoxicity and proliferation

Naito, Y., Koyama, S., Masuhiro, K., Hirai, T., Uenami, T., Inoue, T., Osa, A., Machiyama, H., Watanabe, G., Sax, N., et al. (2023) · Science Advances · doi:10.1126/sciadv.ade0718 · Cited by 29

Single-cell histone chaperones patterns guide intercellular communication of tumor microenvironment that contribute to breast cancer metastases

Xie, J., Deng, W., Deng, X., Liang, J., Tang, Y., Huang, J. T., Tang, H., Zou, Y., Zhou, H., & Xie, X. (2023) · Cancer Cell International · doi:10.1186/s12935-023-03166-4 · Cited by 29

Strategies for Predicting Response to Checkpoint Inhibitors

Zappasodi, R., Wolchok, J. D., & Merghoub, T. (2018) · Current Hematologic Malignancy Reports · doi:10.1007/s11899-018-0471-9 · Cited by 29

Harnessing immunotherapy for liver recipients with hepatocellular carcinoma: a review from a transplant oncology perspective

Ho, C., Chen, H., Hu, R., & Lee, P. (2019) · Therapeutic Advances in Medical Oncology · doi:10.1177/1758835919843463 · Cited by 29

Effects of anti-PD-1 immunotherapy on tumor regression: insights from a patient-derived xenograft model

Martín-Ruiz, A., Fiuza‐Luces, C., Martínez-Martínez, E., Arias, C. F., Gutiérrez, L., Ramírez, M. R., Martín, P., Coronado, M. J., Lucía, A., & Provencio, M. (2020) · Scientific Reports · doi:10.1038/s41598-020-63796-w · Cited by 31

Determinants of anti-PD1 response and resistance in clear cell renal cell carcinomaPreprint

Au, L., Hatipoglu, E., de Massy, M. R., Litchfield, K., Rowan, A., Thompson, R. H., Schnidrig, D., Byrne, F., Beattie, G., Horswell, S. D., et al. (2021) · medRxiv · doi:10.1101/2021.03.19.21253661 · Cited by 29

Dual TLR9 and PD-L1 targeting unleashes dendritic cells to induce durable antitumor immunity

Fernandez-Rodriguez, L., Cianciaruso, C., Bill, R., Trefny, M. P., Klar, R., Kirchhammer, N., Buchi, M., Festag, J., Michel, S., Köhler, R. H., et al. (2023) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2023-006714 · Cited by 28

AI Model for Predicting Anti-PD1 Response in Melanoma Using Multi-Omics Biomarkers

Gschwind, A., & Ossowski, S. (2025) · Cancers · doi:10.3390/cancers17050714 · Cited by 30

Tumor Heterogeneity and the Immune Response in Non-Small Cell Lung Cancer: Emerging Insights and Implications for Immunotherapy

Oh, M. S., Abascal, J. W., Rennels, A. K., Salehi‐Rad, R., Dubinett, S. M., & Liu, B. (2025) · Cancers · doi:10.3390/cancers17061027 · Cited by 33

Significance of BRAF Kinase Inhibitors for Melanoma Treatment: From Bench to Bedside

Fujimura, T., Fujisawa, Y., Kambayashi, Y., & Aiba, S. (2019) · Cancers · doi:10.3390/cancers11091342 · Cited by 28

Genomic profiles and tumor immune microenvironment of primary lung carcinoma and brain oligo-metastasis

Song, Z., Yang, L., Zhou, Z., Li, P., Wang, W., Cheng, G., Chen, R., Chang, L., Zhang, Y., Guan, Y., et al. (2021) · Cell Death and Disease · doi:10.1038/s41419-021-03410-7 · Cited by 28

Hypoxia Molecular Characterization in Hepatocellular Carcinoma Identifies One Risk Signature and Two Nomograms for Clinical Management

Liu, Z., Liu, L., Lu, T., Wang, L., Li, Z., Jiao, D., & Han, X. (2021) · Journal of Oncology · doi:10.1155/2021/6664386 · Cited by 28

Genomic Profiling Identified Novel Prognostic Biomarkers in Chinese Midline Glioma Patients

Li, H., Shan, C., Wu, S., Cheng, B., Fan, C., Cai, L., Chen, Y., Shi, Y., Liu, K., Shao, Y. W., et al. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2020.607429 · Cited by 28

Clinical efficacy of T-cell therapy after short-term BRAF-inhibitor priming in patients with checkpoint inhibitor-resistant metastatic melanoma

Borch, T. H., Harbst, K., Rana, A. H., Andersen, R. S., Martinenaite, E., Kongsted, P., Pedersen, M., Nielsen, M., Kjeldsen, J. W., Kverneland, A. H., et al. (2021) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2021-002703 · Cited by 28

Typical tumor immune microenvironment status determine prognosis in lung adenocarcinoma

Ren, C., Li, J., Zhou, Y., Zhang, S., & Wang, Q. (2022) · Translational Oncology · doi:10.1016/j.tranon.2022.101367 · Cited by 28

High IGKC-Expressing Intratumoral Plasma Cells Predict Response to Immune Checkpoint Blockade

Onieva, J. L., Xiao, Q., Berciano‐Guerrero, M., Laborda-Illanes, A., de Andrea, C., Cháves, P., Piñeiro, P., Garrido-Aranda, A., Gallego, E., Sojo, B., et al. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23169124 · Cited by 28

Attenuated Salmonella potentiate PD-L1 blockade immunotherapy in a preclinical model of colorectal cancer

Al-Saafeen, B. H., Al-Sbiei, A., Bashir, G. H., Mohamed, Y. A., Masad, R. J., Fernández-Cabezudo, M. J., & al-Ramadi, B. K. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1017780 · Cited by 30

Antigen presentation by clonally diverse CXCR5+ B cells to CD4 and CD8 T cells is associated with durable response to immune checkpoint inhibitors

Ding, L., Sun, L., Bu, M. T., Zhang, Y., Scott, L. N., Prins, R. M., Su, M. A., Lechner, M. G., & Hugo, W. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1176994 · Cited by 31

Autotaxin suppresses cytotoxic T cells via LPAR5 to promote anti–PD-1 resistance in non–small cell lung cancer

Konen, J. M., Rodriguez, B. L., Wu, H., Fradette, J. J., Gibson, L., Diao, L., Wang, J., Schmidt, S., Wistuba, I. I., Zhang, J. J., et al. (2023) · Journal of Clinical Investigation · doi:10.1172/jci163128 · Cited by 31

Immune Checkpoint Inhibitors in Hepatocellular Carcinoma: Current Strategies and Biomarkers Predicting Response and/or Resistance

Pelizzaro, F., Farinati, F., & Trevisani, F. (2023) · Biomedicines · doi:10.3390/biomedicines11041020 · Cited by 28

Targeted deletion of CD244 on monocytes promotes differentiation into anti-tumorigenic macrophages and potentiates PD-L1 blockade in melanoma

Kim, J., Kim, T., Chae, S., Ha, H., Park, Y., Park, S. H., Yoon, C. J., Lim, S. A., Lee, H., Kim, J., et al. (2024) · Molecular Cancer · doi:10.1186/s12943-024-01936-w · Cited by 27

A Predictive Network‐Based Immune Checkpoint Blockade Immunotherapeutic Signature Optimizing Patient Selection and Treatment Strategies

Zhang, N., Yang, M., Yang, J., Zhang, C., & Guo, A. (2024) · Small Methods · doi:10.1002/smtd.202301685 · Cited by 27

Mannose Enhances Immunotherapy Efficacy in Ovarian Cancer by Modulating Gut Microbial Metabolites

Zhang, C., Wang, Y., He, M., Wang, C., Cao, K., Zhong, Y., Wang, X., Yang, M., Zhang, G., Lu, J., et al. (2025) · Cancer Research · doi:10.1158/0008-5472.can-24-3209 · Cited by 30

Integrative analysis of multi-omics data and gut microbiota composition reveals prognostic subtypes and predicts immunotherapy response in colorectal cancer using machine learning

Wang, J., Yuan, C., Tang, B., Liu, J., & Pu, K. (2025) · Scientific Reports · doi:10.1038/s41598-025-08915-1 · Cited by 29

Analysis of the Tumor Reactivity of Tumor-Infiltrating Lymphocytes in a Metastatic Melanoma Lesion that Lost Major Histocompatibility Complex Class I Expression after Anti–PD-1 Therapy

Inozume, T., Yaguchi, T., Ariyasu, R., Togashi, Y., Ohnuma, T., Honobe‐Tabuchi, A., Nishikawa, H., Kawakami, Y., & Kawamura, T. (2019) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2019.01.007 · Cited by 27

T cell receptor repertoire characteristics both before and following immunotherapy correlate with clinical response in mesothelioma

Vroman, H. H., Balzaretti, G., Belderbos, R. A., Klarenbeek, P. L., van Nimwegen, M., Bezemer, K., Cornelissen, R., Niewold, I. T. G., van Schaik, B. D. C., van Kampen, A. H., et al. (2020) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2019-000251 · Cited by 27

Immunodynamics of explanted human tumors for immuno‐oncology

Dubuisson, A., Fahrner, J., Goubet, A., Terrisse, S. A., Voisin, N., Bayard, C., Lofek, S., Drubay, D., Bredel, D., Mouraud, S., et al. (2020) · EMBO Molecular Medicine · doi:10.15252/emmm.202012850 · Cited by 27

Pan-cancer analyses reveal regulation and clinical outcome association of the shelterin complex in cancer

Luo, Z., Liu, W., Sun, P., Wang, F., & Feng, X. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa441 · Cited by 26

What role for AHR activation in IL4I1-mediated immunosuppression ?

Castellano, F., Prévost‐Blondel, A., Cohen, J. L., & Molinier‐Frenkel, V. (2021) · OncoImmunology · doi:10.1080/2162402x.2021.1924500 · Cited by 29

Negative trade-off between neoantigen repertoire breadth and the specificity of HLA-I molecules shapes antitumor immunity

Manczinger, M., Koncz, B., Balogh, G. M., Papp, B. T., Asztalos, L., Kemény, L. V., Papp, B., & Pál, C. (2021) · Nature Cancer · doi:10.1038/s43018-021-00226-4 · Cited by 27

Immune cytolytic activity is associated with reduced intra-tumoral genetic heterogeneity and with better clinical outcomes in triple negative breast cancer.

Oshi, M., Kawaguchi, T., Yan, L., Peng, X., Qi, Q., Tian, W., Schulze, A. K., McDonald, K.-A., Narayanan, S., Young, J. S., et al. (2021) · PubMed · Cited by 28

Mutational characteristics of bone metastasis of lung cancer

Huang, X., Shi, X., Huang, D., Li, B., Lin, N., Pan, W., Yan, X., Li, H., Hao, Q., & Ye, Z. (2021) · Annals of Palliative Medicine · doi:10.21037/apm-21-1595 · Cited by 27

A Novel Nomogram and Risk Classification System Predicting the Cancer-Specific Mortality of Patients with Initially Diagnosed Metastatic Cutaneous Melanoma

Li, W., Xiao, Y., Xu, X., & Zhang, Y. (2020) · Annals of Surgical Oncology · doi:10.1245/s10434-020-09341-5 · Cited by 27

Predictive Biomarkers for Outcomes of Immune Checkpoint Inhibitors (ICIs) in Melanoma: A Systematic Review

Baltussen, J. C., Welters, M. J. P., Verdegaal, E. M. E., Kapiteijn, E., Schrader, A. M. R., Slingerland, M., Liefers, G., van der Burg, S. H., Portielje, J. E. A., & de Glas, N. A. (2021) · Cancers · doi:10.3390/cancers13246366 · Cited by 28

Novel Molecular Determinants of Response or Resistance to Immune Checkpoint Inhibitor Therapies in Melanoma

Zhang, W., Kong, Y., Li, Y., Shi, F., Lyu, J., Sheng, C., Wang, S., & Wang, Q. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2021.798474 · Cited by 28

Immunoglobulin somatic hypermutation has clinical impact in DLBCL and potential implications for immune checkpoint blockade and neoantigen-based immunotherapies

Xu-Monette, Z. Y., Li, J., Xia, Y., Crossley, B., Bremel, R. D., Miao, Y., Xiao, M., Snyder, T. M., Manyam, G. C., Tan, X., et al. (2019) · Journal for ImmunoTherapy of Cancer · doi:10.1186/s40425-019-0730-x · Cited by 27

Exploring potential molecular resistance and clonal evolution in advanced HER2-positive gastric cancer under trastuzumab therapy

Xu, Q., Xu, X., Tang, H., Yan, J., Li, J., Bao, H., Wu, X., Shao, Y. W., Luo, C., Wen, H., et al. (2023) · Oncogenesis · doi:10.1038/s41389-023-00466-2 · Cited by 26

Cancer stem cell–immune cell crosstalk in breast tumor microenvironment: a determinant of therapeutic facet

Guha, A., Goswami, K. K., Sultana, J., Ganguly, N., Choudhury, P. R., Chakravarti, M., Bhuniya, A., Sarkar, A., Bera, S., Dhar, S., et al. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1245421 · Cited by 28

Current Technologies and Future Perspectives in Immunotherapy towards a Clinical Oncology Approach

Adhikary, S., Pathak, S., Palani, V., Acar, A., Banerjee, A., Al-Dewik, N. I. E., Essa, M. M., Mohammed, S. G. A. A., & Qoronfleh, M. W. (2024) · Biomedicines · doi:10.3390/biomedicines12010217 · Cited by 28

Intratumor Heterogeneity in Breast Cancer: Tracing Its Origins and Translating Findings into Clinical Practice

Gu, T., Xiao, Y.-L., & Shao, Z.-M. (2024) · Precision Medicine and Engineering · doi:10.1016/j.preme.2024.100006 · Cited by 25

Syndecan-1 inhibition promotes antitumor immune response and facilitates the efficacy of anti-PD1 checkpoint immunotherapy

Liu, Y., Xu, C., Zhang, L., Xu, G., Yang, Z., Xiang, L., Jiao, K., Chen, Z., Zhang, X., & Liu, Y. (2024) · Science Advances · doi:10.1126/sciadv.adi7764 · Cited by 27

Stable Cox regression for survival analysis under distribution shifts

Fan, S., Xu, R., Dong, Q., He, Y., Chang, C., & Cui, P. (2024) · Nature Machine Intelligence · doi:10.1038/s42256-024-00932-5 · Cited by 28

NITUMID: Nonnegative matrix factorization-based Immune-TUmor MIcroenvironment Deconvolution

Tang, D., Park, S., & Zhao, H. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz748 · Cited by 26

A four-gene signature predicts survival and anti-CTLA4 immunotherapeutic responses based on immune classification of melanoma

Mei, Y., Chen, M.-J. M., Liang, H., & Ma, L. (2021) · Communications Biology · doi:10.1038/s42003-021-01911-x · Cited by 27

IL-7 coupled with IL-12 increases intratumoral T cell clonality, leading to complete regression of non-immunogenic tumors

Tasaki, M., YAMASHITA, M., Arai, Y., Nakamura, T., & Nakao, S. (2021) · Cancer Immunology Immunotherapy · doi:10.1007/s00262-021-02947-y · Cited by 25

Follicular Helper T-Cell-Based Classification of Endometrial Cancer Promotes Precise Checkpoint Immunotherapy and Provides Prognostic Stratification

Chen, Y., You, S., Li, J., Zhang, Y., Kokaraki, G., Epstein, E., Carlson, J. W., Huang, W., & Haglund, F. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2021.788959 · Cited by 26

Challenges and the Evolving Landscape of Assessing Blood-Based PD-L1 Expression as a Biomarker for Anti-PD-(L)1 Immunotherapy

Wang, T., Denman, D., Bacot, S. M., & Feldman, G. M. (2022) · Biomedicines · doi:10.3390/biomedicines10051181 · Cited by 27

Tissue-resident memory T cells from a metastatic vaginal melanoma patient are tumor-responsive T cells and increase after anti-PD-1 treatment

Pizzolla, A., Keam, S. P., Vergara, I. A., Caramia, F., Thio, N., Wang, M., Kocovski, N., Tantalo, D. G. M., Jabbari, J. S., Au‐Yeung, G., et al. (2022) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2022-004574 · Cited by 26

Paired primary and metastatic lesions of patients with ipilimumab-treated melanoma: high variation in lymphocyte infiltration and HLA-ABC expression whereas tumor mutational load is similar and correlates with clinical outcome

Gorris, M. A. J., van der Woude, L. L., Kroeze, L. I., Bol, K. F., Verrijp, K. N., Amir, A. L., Meek, J., Textor, J. C., Figdor, C. G., & de Vries, I. J. M. (2022) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2021-004329 · Cited by 28

IGFBP7 and the Tumor Immune Landscape: A Novel Target for Immunotherapy in Bladder Cancer

Yi, X., Zheng, X. S., Xu, H., Li, J., Zhang, T., Ge, P., Liao, D., Li, H., Lyu, X., & Ai, J. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.898493 · Cited by 26

The prognostic biological markers of immunotherapy for non-small cell lung cancer: current landscape and future perspective

Liang, S., Wang, H., Tian, H., Xu, Z., Wu, M., Hua, D., & Li, C. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1249980 · Cited by 25

Assessment of human leukocyte antigen-based neoantigen presentation to determine pan-cancer response to immunotherapy

Han, J., Dong, Y., Zhu, X., Reuben, A., Zhang, J. J., Xu, J., Bai, H., Duan, J., Wan, R., Zhao, J., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-45361-5 · Cited by 28

Deciphering lung adenocarcinoma prognosis and immunotherapy response through an AI ‐driven stemness‐related gene signature

Ye, B., Hongting, G., Zhuang, W., Chen, C., Yi, S., Tang, X., Jiang, A., & Zhong, Y. (2024) · Journal of Cellular and Molecular Medicine · doi:10.1111/jcmm.18564 · Cited by 27

Molecular targets and strategies in the development of nucleic acid cancer vaccines: from shared to personalized antigens

Chi, W.-Y., Hu, Y., Huang, H., Kuo, H., Lin, S., Kuo, C.-T. J., Tao, J., Fan, D., Huang, Y.-M., Wu, A. A., et al. (2024) · Journal of Biomedical Science · doi:10.1186/s12929-024-01082-x · Cited by 27

Systemic longitudinal immune profiling identifies proliferating Treg cells as predictors of immunotherapy benefit: biomarker analysis from the phase 3 CONTINUUM and DIPPER trials

Huang, S.-W., Jiang, W., Xu, S., Zhang, Y., Du, J., Wang, Y., Yang, K.-Y., Zhang, N., Liu, F., Zou, G., et al. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01988-w · Cited by 29

Comprehensive genomic profile of cholangiocarcinomas in China

Tian, W., Hu, W., Shi, X., Liu, P., Ma, X., Zhao, W., Qu, L., Zhang, S., Shi, W., Liu, A., et al. (2020) · Oncology Letters · doi:10.3892/ol.2020.11429 · Cited by 25

Immunotherapy in the Treatment of Urothelial Bladder Cancer: Insights From Single-Cell Analysis

Zang, J., Ye, K., Yang, F., Zhang, R., Chen, H., & Zhuang, G. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.696716 · Cited by 25

PD-1 preferentially inhibits the activation of low-affinity T cells

Shimizu, K., Sugiura, D., Okazaki, I., Maruhashi, T., Takemoto, T., & Okazaki, T. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2107141118 · Cited by 27

Time-spatial analysis of T cell receptor repertoire in esophageal squamous cell carcinoma patients treated with combined radiotherapy and PD-1 blockade

Yan, C., Ma, X., Guo, Z., Wei, X., Han, D., Zhang, T., Chen, X., Cao, F., Dong, J., Zhao, G., et al. (2022) · OncoImmunology · doi:10.1080/2162402x.2022.2025668 · Cited by 25

Association of KDR Mutation With Better Clinical Outcomes in Pan-Cancer for Immune Checkpoint InhibitorsPreprint

Cui, Y., Zhang, P., Liang, X., Xu, J., Liu, X., Wu, Y., Zhang, J., Wang, W. T., Zhang, F., & Guo, R. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3991639 · Cited by 26

Construction of a predictive model for immunotherapy efficacy in lung squamous cell carcinoma based on the degree of tumor-infiltrating immune cells and molecular typing

Yang, L., Wei, S., Zhang, J., Hu, Q., Hu, W., Cao, M., Zhang, L., Wang, Y., Wang, P., & Wang, K. (2022) · Journal of Translational Medicine · doi:10.1186/s12967-022-03565-7 · Cited by 27

A score of DNA damage repair pathway with the predictive ability for chemotherapy and immunotherapy is strongly associated with immune signaling pathway in pan-cancer

Ding, K., He, Y., Wei, J., Fu, S., Wang, J., Chen, Z., Zhang, H., Qu, Y., Liang, K., Gong, X., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.943090 · Cited by 23

Targeting Driver Oncogenes and Other Public Neoantigens Using T Cell Receptor–Based Cellular Therapy

Martinov, T., & Greenberg, P. D. (2023) · Annual Review of Cancer Biology · doi:10.1146/annurev-cancerbio-061521-082114 · Cited by 27

PD-L1 Tumor Expression as a Predictive Biomarker of Immune Checkpoint Inhibitors’ Response and Survival in Advanced Melanoma Patients in Brazil

Sorroche, B. P., Teixeira, R. D. J., Pereira, C. A., Santana, I. V. V., Vujanovic, L. N., Vazquez, V. D. L., & Arantes, L. M. R. B. (2023) · Diagnostics · doi:10.3390/diagnostics13061041 · Cited by 26

Evolution of PD-1 and PD-L1 Gene and Protein Expression in Primary Tumors and Corresponding Liver Metastases of Metastatic Bladder Cancer

Eckstein, M., Sikic, D., Strissel, P. L., & Erlmeier, F. (2018) · European Urology · doi:10.1016/j.eururo.2018.06.028 · Cited by 25

Abstract 2988: Immunogenomic analyses of tumor cells and microenvironment in patients with advanced melanoma before and after treatment with nivolumab

Chan, T. A.-T., Riaz, N., Havel, J. J., Makarov, V., Desrichard, A., Sims, J. S., Hodi, F. S., Martín‐Algarra, S., Sharfman, W. H., Bhatia, S., et al. (2017) · Cancer Research · doi:10.1158/1538-7445.am2017-2988

Abstract 1125: Neoantigen immunogenicity landscapes and evolution of tumor ecosystems during immunotherapy with nivolumab

Alban, T. J., Riaz, N., Parthasarathy, P. B., Makarov, V., Kendall, S., Yoo, S., Shah, R., Weinhold, N., Srivastava, R. M., Ma, X., et al. (2023) · Cancer Research · doi:10.1158/1538-7445.am2023-1125 · Cited by 1

Tumor control

Visan, I. (2017) · Nature Immunology · doi:10.1038/ni.3878

Association of Tumor Microenvironment T-cell Repertoire and Mutational Load with Clinical Outcome after Sequential Checkpoint Blockade in Melanoma

Yusko, E. C., Vignali, M., Wilson, R. K., Mardis, E. R., Hodi, F. S., Horak, C. E., Chang, H., Woods, D. M., Robins, H. S., & Weber, J. S. (2019) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-18-0226 · Cited by 59

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