Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab

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STAR: ultrafast universal RNA-seq aligner

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

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Robust enumeration of cell subsets from tissue expression profiles

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

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Signatures of mutational processes in human cancer

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PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

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IMPRES does not reproducibly predict response to immune checkpoint blockade therapy in metastatic melanoma

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Predictive and Prognostic Implications of Circulating CX3CR1+ CD8+ T Cells in Non–Small Cell Lung Cancer Patients Treated with Chemo-Immunotherapy

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Machine learning-based investigation of regulated cell death for predicting prognosis and immunotherapy response in glioma patients

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S100A9+CD14+ monocytes contribute to anti-PD-1 immunotherapy resistance in advanced hepatocellular carcinoma by attenuating T cell-mediated antitumor function

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A method for predicting drugs that can boost the efficacy of immune checkpoint blockade

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Investigating the impact of regulatory B cells and regulatory B cell-related genes on bladder cancer progression and immunotherapeutic sensitivity

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INHBA promotes tumor growth and induces resistance to PD-L1 blockade by suppressing IFN-γ signaling

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Hallmarks of a genomically distinct subclass of head and neck cancer

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Beyond tumor mutational burden: potential and limitations in using exosomes to predict response to immunotherapy

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Targeted next generation sequencing ( NGS ) to classify melanocytic neoplasms

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KALRN mutations promote antitumor immunity and immunotherapy response in cancer

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Improved T-cell Receptor Diversity Estimates Associate with Survival and Response to Anti–PD-1 Therapy

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Blood Cell Count Biomarkers Predicting Efficacy of Pembrolizumab as Second-line Therapy for Advanced Urothelial Carcinoma

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Weighting tumor-specific TCR repertoires as a classifier to stratify the immunotherapy delivery in non–small cell lung cancers

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Phased differentiation of γδ T and T CD8 tumor-infiltrating lymphocytes revealed by single-cell transcriptomics of human cancers

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Characterization of gastric cancer stem-like molecular features, immune and pharmacogenomic landscapes

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Pan-Cancer Analysis Reveals the Signature of TMC Family of Genes as a Promising Biomarker for Prognosis and Immunotherapeutic Response

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Targeting the NANOG/HDAC1 axis reverses resistance to PD-1 blockade by reinvigorating the antitumor immunity cycle

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A Cancer Associated Fibroblasts-Related Six-Gene Panel for Anti-PD-1 Therapy in Melanoma Driven by Weighted Correlation Network Analysis and Supervised Machine Learning

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Noncoding RNAs and their therapeutics in paclitaxel chemotherapy: Mechanisms of initiation, progression, and drug sensitivity

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Machine learning on syngeneic mouse tumor profiles to model clinical immunotherapy response

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Immunotherapy for Melanoma: The Significance of Immune Checkpoint Inhibitors for the Treatment of Advanced Melanoma

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Pervasiveness of HLA allele-specific expression loss across tumor types

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An Economical, Quantitative, and Robust Protocol for High-Throughput T Cell Receptor Sequencing from Tumor or Blood

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TNF and IFNγ-induced cell death requires IRF1 and ELAVL1 to promote CASP8 expression

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PD-L1 peptides in cancer immunoimaging and immunotherapy

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Macrophage-Derived Itaconate Suppresses Dendritic Cell Function to Promote Acquired Resistance to Anti–PD-1 Immunotherapy

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Integrative multi-omics and machine learning reveal critical functions of proliferating cells in prognosis and personalized treatment of lung adenocarcinoma

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In situ Vaccination by Direct Dendritic Cell Inoculation: The Coming of Age of an Old Idea?

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Unveiling the immune infiltrate modulation in cancer and response to immunotherapy by MIXTURE—an enhanced deconvolution method

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Identification and validation of a prognostic signature and combination drug therapy for immunotherapy of head and neck squamous cell carcinoma

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Identification of subtypes correlated with tumor immunity and immunotherapy in cutaneous melanoma

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Immunotherapy in liver transplantation for hepatocellular carcinoma: Pros and cons

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Biological knowledge graph-guided investigation of immune therapy response in cancer with graph neural network

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Supporting Biomarker-Driven Therapies in Oncology: A Genomic Testing Cost Calculator

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Biomarker-Driven Personalization of Neoadjuvant Immunotherapy in Melanoma

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The tertiary lymphoid structure-related signature identified PTGDS in regulating PD-L1 and promoting the proliferation and migration of glioblastoma

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Toward Systems Biomarkers of Response to Immune Checkpoint Blockers

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Robust immunoscore model to predict the response to anti-PD1 therapy in melanoma

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Comprehensive analysis of single cell and bulk RNA sequencing reveals the heterogeneity of melanoma tumor microenvironment and predicts the response of immunotherapy

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Identification of Hypoxia‐ALCAMhigh Macrophage‐ Exhausted T Cell Axis in Tumor Microenvironment Remodeling for Immunotherapy Resistance

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Network Medicine‐Based Strategy Identifies Maprotiline as a Repurposable Drug by Inhibiting PD‐L1 Expression via Targeting SPOP in Cancer

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CMV serostatus is associated with improved survival and delayed toxicity onset following anti-PD-1 checkpoint blockade

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Generalizable AI predicts immunotherapy outcomes across cancers and treatments

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Engineering Multidimensional Evolutionary Forces to Combat Cancer

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Integration of the Tumor Mutational Burden and Tumor Heterogeneity Identify an Immunological Subtype of Melanoma With Favorable Survival

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Molecular and Immune Biomarkers for Cutaneous Melanoma: Current Status and Future Prospects

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Predicting Toxicity and Response to Pembrolizumab Through Germline Genomic HLA Class 1 Analysis

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Myeloid cell heterogeneity in lung cancer: implication for immunotherapy

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Role of Tumor-Infiltrating B Cells in Clinical Outcome of Patients with Melanoma Treated With Dabrafenib Plus Trametinib

Brase, J. C., Walter, R. F. H., Savchenko, A., Gusenleitner, D., Garrett, J., Schimming, T. T., Váraljai, R., Castelletti, D., Kim, J., Dakappagari, N. K., et al. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-3586 · Cited by 22

Heterogeneity of programmed death-ligand 1 expression and infiltrating lymphocytes in paired resected primary and metastatic non-small cell lung cancer

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A 12-chemokine gene signature is associated with the enhanced immunogram scores and is relevant for precision immunotherapy

Li, X., Wan, Z., Liu, X., Ou, K., & Yang, L. (2022) · Medical Oncology · doi:10.1007/s12032-021-01635-2 · Cited by 24

Mesenchymal stromal cells equipped by IFNα empower T cells with potent anti-tumor immunity

Zhang, T., Wang, Y., Li, Q., Lin, L., Xu, C., Xue, Y., Hu, M., Shi, Y., & Wang, Y. (2022) · Oncogene · doi:10.1038/s41388-022-02201-4 · Cited by 22

Systematic evaluation of the predictive gene expression signatures of immune checkpoint inhibitors in metastatic melanoma

Coleman, S. S., Xie, M., Tarhini, A. A., & Tan, A. C. (2022) · Molecular Carcinogenesis · doi:10.1002/mc.23442 · Cited by 22

Multi-omics analysis of N6-methyladenosine reader IGF2BP3 as a promising biomarker in pan-cancer

Chen, P., Xu, J., Cui, Z., Wu, S., Xie, T., & Zhang, X. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1071675 · Cited by 22

Identifying biomarkers associated with immunotherapy response in melanoma by multi-omics analysis

He, Y., & Wang, X. (2023) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2023.107591 · Cited by 23

Single-cell RNA sequencing integrated with bulk RNA sequencing analysis identifies a tumor immune microenvironment-related lncRNA signature in lung adenocarcinoma

Ren, Y., Wu, R., Li, C., Liu, L., Li, L., Weng, S., Xu, H., Xing, Z., Zhang, Y., Wang, L., et al. (2024) · BMC Biology · doi:10.1186/s12915-024-01866-5 · Cited by 21

Identification and Validation of the Immune Subtypes of Lung Adenocarcinoma: Implications for Immunotherapy

Song, Y., Yan, S., Fan, W., Zhang, M., Liu, W., Lu, H., Cao, M., Hao, C., Chen, L., Tian, F., et al. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.00550 · Cited by 23

Comprehensive Analysis of the Tumor Immune Microenvironment Landscape in Glioblastoma Reveals Tumor Heterogeneity and Implications for Prognosis and Immunotherapy

Zhao, R., Pan, Z., Li, B., Zhao, S., Zhang, S., Qi, Y., Qiu, J., Gao, Z., Yang, F., Guo, Q., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.820673 · Cited by 21

Genome-wide gain-of-function screening characterized lncRNA regulators for tumor immune response

Wang, Y., Zhao, Y., Guo, W., Yadav, G. S., Bhaskarla, C., Wang, X., Wang, X., Li, S., Wang, Y., Chen, Y., et al. (2022) · Science Advances · doi:10.1126/sciadv.add0005 · Cited by 21

Cross-Talks between RKIP and YY1 through a Multilevel Bioinformatics Pan-Cancer Analysis

Baritaki, S., & Zaravinos, A. (2023) · Cancers · doi:10.3390/cancers15204932 · Cited by 22

Unraveling Th subsets: insights into their role in immune checkpoint inhibitor therapy

Ryba-Stanisławowska, M. E. (2024) · Cellular Oncology · doi:10.1007/s13402-024-00992-0 · Cited by 23

Pan-cancer γδ TCR analysis uncovers clonotype diversity and prognostic potential

Yu, X., Song, L., Cen, L., Cao, B., Tao, R., Shen, Y., Abate‐Daga, D., Rodrı́guez, P. C., Conejo-Garcia, J. R., & Wang, X. (2024) · Cell Reports Medicine · doi:10.1016/j.xcrm.2024.101764 · Cited by 23

A dendritic cell vaccine for both vaccination and neoantigen-reactive T cell preparation for cancer immunotherapy in mice

Li, Q., Zeng, H., Liu, T., Wang, P., Zhang, R., Zhao, B., Feng, T., Yang, Y., Wu, J., Zheng, Y., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-54650-y · Cited by 25

Re-challenging immune checkpoint inhibitor in a patient with advanced non-small cell lung cancer: a case report

Hakozaki, T., Okuma, Y., & Kashima, J. (2018) · BMC Cancer · doi:10.1186/s12885-018-4212-1 · Cited by 21

Predictive Biomarkers for PD-1 and PD-L1 Immune Checkpoint Blockade Therapy

Song, Y., Li, Z., Xue, W., & Zhang, M. (2019) · Immunotherapy · doi:10.2217/imt-2018-0173 · Cited by 21

TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures

Xie, M., Lee, K., Lockhart, J. H., Cukras, S., Carvajal, R., Beg, A. A., Flores, E. R., Teng, M., Chung, C. H., & Tan, A. C. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab244 · Cited by 21

Open the Technical Black Box of Tumor Mutational Burden (TMB): Factors Affecting Harmonization and Standardization of Panel-Based TMB

Sung, M., Wang, Y., & Li, C. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23095097 · Cited by 21

CXCR2 expression during melanoma tumorigenesis controls transcriptional programs that facilitate tumor growth

Yang, J., Bergdorf, K. N., Yan, C., Luo, W., Chen, S. C., Ayers, G. D., Liu, Q., Liu, X., Boothby, M. R., Weiss, V. L., et al. (2023) · Molecular Cancer · doi:10.1186/s12943-023-01789-9 · Cited by 21

Microbial biomarkers for immune checkpoint blockade therapy against cancer

Adachi, K., & Tamada, K. (2018) · Journal of Gastroenterology · doi:10.1007/s00535-018-1492-9 · Cited by 21

Biomarkers of response to ibrutinib plus nivolumab in relapsed diffuse large B-cell lymphoma, follicular lymphoma, or Richter's transformation

Hodkinson, B. P., Schäffer, M., Brody, J., Jurczak, W. J., Carpio, C. D. C., Ben‐Yehuda, D., Avivi, I. M., Forslund, A., Özcan, M., Alvarez, J. D., et al. (2020) · Translational Oncology · doi:10.1016/j.tranon.2020.100977 · Cited by 24

Clinical and Molecular Heterogeneity in Patients with Innate Resistance to Anti-PD-1 +/− Anti-CTLA-4 Immunotherapy in Metastatic Melanoma Reveals Distinct Therapeutic Targets

Gide, T. N., da Silva, I. P., Quek, C. Y. J., Ferguson, P. M., Batten, M., Shang, P., Ahmed, T., Menzies, A. M., Carlino, M. S., Saw, R. P. M., et al. (2021) · Cancers · doi:10.3390/cancers13133186 · Cited by 21

Identification of three immune subtypes characterized by distinct tumor immune microenvironment and therapeutic response in stomach adenocarcinoma

Zhu, Y., Zhao, Y., Cao, Z., Chen, Z., & Pan, W. (2022) · Gene · doi:10.1016/j.gene.2021.146177 · Cited by 21

Spatial omics technologies for understanding molecular status associated with cancer progression

Nagasawa, S., Zenkoh, J., Suzuki, Y., & Suzuki, A. (2024) · Cancer Science · doi:10.1111/cas.16283 · Cited by 22

Systemic rewiring of dendritic cells by melanoma-secreted midkine impairs immune surveillance and response to immune checkpoint blockade

Catena, X., Contreras-Alcalde, M., Juan-Larrea, N., Cerezo‐Wallis, D., Calvo, T. G., Mucientes, C., Olmeda, D., Suárez, J., Oterino-Sogo, S., Martínez, L., et al. (2025) · Nature Cancer · doi:10.1038/s43018-025-00929-y · Cited by 19

Identification of Potential Biomarkers for Anti-PD-1 Therapy in Melanoma by Weighted Correlation Network Analysis

Wang, X., Chai, Z., Li, Y., Long, F., Hao, Y., Pan, G., Liu, M., & Li, B. (2020) · Genes · doi:10.3390/genes11040435 · Cited by 20

Diversity of Dominant Peripheral T Cell Receptor Clone and Soluble Immune Checkpoint Proteins Associated With Clinical Outcomes Following Immune Checkpoint Inhibitor Treatment in Advanced Cancers

Li, Y., Wang, J., Wu, L., Li, X., Zhang, X., Zhang, G., Xu, S., Sun, S., & Jiao, S. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.649343 · Cited by 20

Immunotherapy for Head and Neck Cancer

Trivedi, S., Sun, L., & Aggarwal, C. (2021) · Hematology/Oncology Clinics of North America · doi:10.1016/j.hoc.2021.05.010 · Cited by 20

Tumor-Infiltrating PD-1hiCD8+-T-Cell Signature as an Effective Biomarker for Immune Checkpoint Inhibitor Therapy Response Across Multiple Cancers

Yang, Z., Deng, Y., Cheng, J., Wei, S., Luo, H., & Liu, L. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.695006 · Cited by 20

Tumor evolution selectively inactivates the core microRNA machinery for immune evasion

Song, T., Long, M., Zhao, H., Zou, M.-W., Fan, H., Liu, Y., Geng, C., Song, M., Liu, Y.-F., Chen, J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27331-3 · Cited by 20

Various Subtypes of EGFR Mutations in Patients With NSCLC Define Genetic, Immunologic Diversity and Possess Different Prognostic Biomarkers

Lei, Y., Wang, K., Liu, Y., Wang, X., Xiang, X., Ning, X., Ding, W., Duan, J., Li, D., Wei, Z., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.811601 · Cited by 20

Multimodal predictors for precision immunotherapy

Roelofsen, L. M., Kaptein, P., & Thommen, D. S. (2022) · Immuno-Oncology Technology · doi:10.1016/j.iotech.2022.100071 · Cited by 19

Establishment of a lncRNA-Based Prognostic Gene Signature Associated With Altered Immune Responses in HCC

Li, X., Zhang, Z., Liu, M.-C., Fu, X., Jun, A., Chen, G., Wu, S., & Dong, J. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.880288 · Cited by 19

Case Report: PTEN Mutation Induced by anti-PD-1 Therapy in Stage IV Lung Adenocarcinoma

Teng, J., Zhou, K., Lv, D., Wu, C., & Feng, H. (2022) · Frontiers in Pharmacology · doi:10.3389/fphar.2022.714408 · Cited by 20

PD1hi CD200hi CD4+ exhausted T cell increase immunotherapy resistance and tumour progression by promoting epithelial–mesenchymal transition in bladder cancer

Wu, C. J., Duan, L., Li, H., Liu, X., Cai, T., Yang, Y., Yin, Y., Chang, W., Zhong, L., Zhang, L., et al. (2023) · Clinical and Translational Medicine · doi:10.1002/ctm2.1303 · Cited by 20

Decoupled neoantigen cross-presentation by dendritic cells limits anti-tumor immunity against tumors with heterogeneous neoantigen expression

Nguyen, K. B., Roerden, M., Copeland, C., Backlund, C. M., Klop-Packel, N. G., Remba, T. K., Kim, B., Singh, N. K., Birnbaum, M. E., Irvine, D. J., et al. (2023) · eLife · doi:10.7554/elife.85263 · Cited by 20

Multimodal molecular landscape of response to Y90-resin microsphere radioembolization followed by nivolumab for advanced hepatocellular carcinoma

Kaya, N. A., Tai, D. W.-M., Lim, X., Lim, J. Q., Lau, M. C., Goh, D. L. M., Phua, C. Z. J., Wee, F. Y. T., Joseph, C. R., Lim, J. C. T., et al. (2023) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2023-007106 · Cited by 21

A cancer-associated fibroblast subtypes-based signature enables the evaluation of immunotherapy response and prognosis in bladder cancer

Qin, Y., Zu, X., Li, Y., Han, Y. M., Tan, J., Cai, C., Shen, E., Liu, P., Deng, G., Feng, Z., et al. (2023) · iScience · doi:10.1016/j.isci.2023.107722 · Cited by 20

Interleukin‐4 induced 1 ‐mediated resistance to an immune checkpoint inhibitor through suppression of CD8 + T cell infiltration in melanoma

Hirose, S., Mashima, T., Yuan, X., Yamashita, M., Kitano, S., Torii, S., Migita, T., & Seimiya, H. (2024) · Cancer Science · doi:10.1111/cas.16073 · Cited by 20

Systematic investigation of chemo-immunotherapy synergism to shift anti-PD-1 resistance in cancer

Wang, Y., Pattarayan, D., Huang, H., Zhao, Y., Li, S., Wang, Y., Zhang, M., Li, S., & Yang, D. (2024) · Nature Communications · doi:10.1038/s41467-024-47433-y · Cited by 20

MDK promotes M2 macrophage polarization to remodel the tumour microenvironment in clear cell renal cell carcinoma

Shi, N., Chen, S., Wang, D., Wu, T., Zhang, N., Chen, M., & Ding, X. (2024) · Scientific Reports · doi:10.1038/s41598-024-69183-z · Cited by 22

Landscape of the Peripheral Immune Response Induced by Intraoperative Radiotherapy Combined with Surgery in Early Breast Cancer Patients

Dai, D., Li, X.-R., Zhuang, H.-K., Ling, Y., Chen, L.-Z., Long, C., Zhang, J., Wang, Y.-J., Li, Y.-H., Tang, H., et al. (2024) · Advancement of science · doi:10.1002/advs.202308174 · Cited by 21

Cancer research in the era of immunogenomics

Wolf, Y., & Samuels, Y. (2018) · ESMO Open · doi:10.1136/esmoopen-2018-000475 · Cited by 20

Transcriptional Activity and Stability of CD39+CD103+CD8+ T Cells in Human High-Grade Endometrial Cancer

Workel, H. H., van Rooij, N., Plat, A., Spierings, D. C. J., Fehrmann, R. S. N., Nijman, H. W., & de Bruyn, M. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21113770 · Cited by 20

The Association of MUC16 Mutation with Tumor Mutation Burden and Its Prognostic Implications in Cutaneous Melanoma

Wang, X., Yu, X., Krauthammer, M. O., Hugo, W., Duan, C., Kanetsky, P. A., Teer, J. K., Thompson, Z., Kalos, D., Tsai, K. Y., et al. (2020) · Cancer Epidemiology Biomarkers & Prevention · doi:10.1158/1055-9965.epi-20-0307 · Cited by 20

Transient Depletion of CD4+ Cells Induces Remodeling of the TCR Repertoire in Gastrointestinal Cancer

Aoki, H., Ueha, S., Shichino, S., Ogiwara, H., Shitara, K., Shimomura, M., Suzuki, T., Nakatsura, T., Yamashita, M., Kitano, S., et al. (2021) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-20-0989 · Cited by 20

Transcriptional Reprogramming and Constitutive PD-L1 Expression in Melanoma Are Associated with Dedifferentiation and Activation of Interferon and Tumour Necrosis Factor Signalling Pathways

Ahn, A., Rodger, E. J., Motwani, J., Gimenez, G., Stockwell, P. A., Parry, M. F., Hersey, P., Chatterjee, A., & Eccles, M. R. (2021) · Cancers · doi:10.3390/cancers13174250 · Cited by 21

Integrated Profiling Identifies PLOD3 as a Potential Prognostic and Immunotherapy Relevant Biomarker in Colorectal Cancer

Shi, J., Bao, M., Wang, W.-F., Wu, X., Li, Y., Changdong, Z., & Liu, W. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.722807 · Cited by 20

Nanotechnology Addressing Cutaneous Melanoma: The Italian Landscape

Battaglia, L., Scomparin, A., Dianzani, C., Milla, P., Muntoni, E., Arpicco, S., & Cavalli, R. (2021) · Pharmaceutics · doi:10.3390/pharmaceutics13101617 · Cited by 21

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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