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Yaacov A, Ben Cohen G, Landau J, Hope T, Simon I, Rosenberg S. Cancer mutational signatures identification in clinical assays using neural embedding-based representations. Cell Rep Med 2024; 5:101608. [PMID: 38866015 PMCID: PMC11228799 DOI: 10.1016/j.xcrm.2024.101608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/28/2024] [Accepted: 05/16/2024] [Indexed: 06/14/2024]
Abstract
While mutational signatures provide a plethora of prognostic and therapeutic insights, their application in clinical-setting, targeted gene panels is extremely limited. We develop a mutational representation model (which learns and embeds specific mutation signature connections) that enables prediction of dominant signatures with only a few mutations. We predict the dominant signatures across more than 60,000 tumors with gene panels, delineating their landscape across different cancers. Dominant signature predictions in gene panels are of clinical importance. These included UV, tobacco, and apolipoprotein B mRNA editing enzyme, catalytic polypeptide (APOBEC) signatures that are associated with better survival, independently from mutational burden. Further analyses reveal gene and mutation associations with signatures, such as SBS5 with TP53 and APOBEC with FGFR3S249C. In a clinical use case, APOBEC signature is a robust and specific predictor for resistance to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs). Our model provides an easy-to-use way to detect signatures in clinical setting assays with many possible clinical implications for an unprecedented number of cancer patients.
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Affiliation(s)
- Adar Yaacov
- Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel; The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel; Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Gil Ben Cohen
- Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel; The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jakob Landau
- Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel; The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tom Hope
- School of Computer Science and Engineering, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shai Rosenberg
- Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel; The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
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Subramanian A, Nemat-Gorgani N, Ellis-Caleo TJ, van IJzendoorn DGP, Sears TJ, Somani A, Luca BA, Zhou MY, Bradic M, Torres IA, Oladipo E, New C, Kenney DE, Avedian RS, Steffner RJ, Binkley MS, Mohler DG, Tap WD, D'Angelo SP, van de Rijn M, Ganjoo KN, Bui NQ, Charville GW, Newman AM, Moding EJ. Sarcoma microenvironment cell states and ecosystems are associated with prognosis and predict response to immunotherapy. NATURE CANCER 2024; 5:642-658. [PMID: 38429415 PMCID: PMC11058033 DOI: 10.1038/s43018-024-00743-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 02/08/2024] [Indexed: 03/03/2024]
Abstract
Characterization of the diverse malignant and stromal cell states that make up soft tissue sarcomas and their correlation with patient outcomes has proven difficult using fixed clinical specimens. Here, we employed EcoTyper, a machine-learning framework, to identify the fundamental cell states and cellular ecosystems that make up sarcomas on a large scale using bulk transcriptomes with clinical annotations. We identified and validated 23 sarcoma-specific, transcriptionally defined cell states, many of which were highly prognostic of patient outcomes across independent datasets. We discovered three conserved cellular communities or ecotypes associated with underlying genomic alterations and distinct clinical outcomes. We show that one ecotype defined by tumor-associated macrophages and epithelial-like malignant cells predicts response to immune-checkpoint inhibition but not chemotherapy and validate our findings in an independent cohort. Our results may enable identification of patients with soft tissue sarcomas who could benefit from immunotherapy and help develop new therapeutic strategies.
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Affiliation(s)
- Ajay Subramanian
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Neda Nemat-Gorgani
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | | | | | - Timothy J Sears
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Anish Somani
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Bogdan A Luca
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Maggie Y Zhou
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Martina Bradic
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ileana A Torres
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Eniola Oladipo
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Christin New
- Department of Orthopedic Surgery, Stanford University, Stanford, CA, USA
| | - Deborah E Kenney
- Department of Orthopedic Surgery, Stanford University, Stanford, CA, USA
| | - Raffi S Avedian
- Department of Orthopedic Surgery, Stanford University, Stanford, CA, USA
| | - Robert J Steffner
- Department of Orthopedic Surgery, Stanford University, Stanford, CA, USA
| | - Michael S Binkley
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - David G Mohler
- Department of Orthopedic Surgery, Stanford University, Stanford, CA, USA
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical Center, New York, NY, USA
| | - Sandra P D'Angelo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical Center, New York, NY, USA
| | | | - Kristen N Ganjoo
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Nam Q Bui
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | | | - Aaron M Newman
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Everett J Moding
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
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3
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Li Q, Zhu G, Zhang L, Zeng B, Cai T, Wu J, Wei B, Xie Z, He L, Tang W, Lin X, Lu H, Wu F, Huang J, Hu H, Liu N, Fan S. Mutational landscape of head and neck cancer and cervical cancer in Chinese and Western population. Head Neck 2024; 46:528-540. [PMID: 38111234 DOI: 10.1002/hed.27603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 11/12/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND We aimed to unbiasedly map the genetic mutation profile of HNSC and CESC associated with HPV status in the Chinese population (SYSU-cohort) and compare them with Western population (TCGA-cohort). METHODS Fifty-one HNSC patients (SYSU-HNSC) and 38 CESC patients (SYSU-CESC) were enrolled in this study. Genomic alterations were examined, and the profile was produced using the YuanSuTM450 gene panel (OrigiMed, Shanghai, China). The altered genes were inferred and compared to Western patients from TCGA cohorts. RESULTS Compared to the TCGA-HNSC cohort, FGFR3 mutation was identified as a novel target in SYSU-HNSC with therapeutic potential. Compared to the TCGA-CESC cohort, some epigenetic regulation-associated genes were frequently mutated in SYSU-CESC cohort (KMT2C, KMT2D, KDM5C, KMT2A). CONCLUSION In summary, our study provides unbiased insights into the genetic landscape of HNSC and CESC in the Chinese population and highlights potential novel therapeutic targets that may benefit Chinese patients.
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Affiliation(s)
- Qunxing Li
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Genhai Zhu
- Department of Gynecology, Hainan General Hospital, Haikou, China
| | - Lizao Zhang
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | - Binghui Zeng
- Guanghua School of Stomatology, Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Tingting Cai
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiaying Wu
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bin Wei
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhijun Xie
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lile He
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wenbing Tang
- Department of Stomatology, Guangdong Agriculture and Reclamation Central Hospital, Zhanjiang, China
| | - Xinyu Lin
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huaiwu Lu
- Department of Gynecologic Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Fan Wu
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
| | | | - Huijun Hu
- Department of Radiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Niu Liu
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Song Fan
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Guangzhou, China
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McGuinness CF, Black MA, Dunbier AK. Restriction site associated DNA sequencing for tumour mutation burden estimation and mutation signature analysis. Cancer Med 2023; 12:21545-21560. [PMID: 37974533 PMCID: PMC10726921 DOI: 10.1002/cam4.6711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Genome-wide measures of genetic disruption such as tumour mutation burden (TMB) and mutation signatures are emerging as useful biomarkers to stratify patients for treatment. Clinicians commonly use cancer gene panels for tumour mutation burden estimation, and whole genome sequencing is the gold standard for mutation signature analysis. However, the accuracy and cost associated with these assays limits their utility at scale. METHODS WGS data from 560 breast cancer patients was used for in silico library simulations to evaluate the accuracy of an FDA approved cancer gene panel as well as restriction enzyme associated DNA sequencing (RADseq) libraries for TMB estimation and mutation signature analysis. We also transfected a mouse mammary cell line with APOBEC enzymes and sequenced resulting clones to evaluate the efficacy of RADseq in an experimental setting. RESULTS RADseq had improved accuracy of TMB estimation and derivation of mutation profiles when compared to the FDA approved cancer panel. Using simulated immune checkpoint blockade (ICB) trials, we show that inaccurate TMB estimation leads to a reduction in power for deriving an optimal TMB cutoff to stratify patients for immune checkpoint blockade treatment. Additionally, prioritisation of APOBEC hypermutated tumours in these trials optimises TMB cutoff determination for breast cancer. The utility of RADseq in an experimental setting was also demonstrated, based on characterisation of an APOBEC mutation signature in an APOBEC3A transfected mouse cell line. CONCLUSION In conclusion, our work demonstrates that RADseq has the potential to be used as a cost-effective, accurate solution for TMB estimation and mutation signature analysis by both clinicians and basic researchers.
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Affiliation(s)
- Conor F. McGuinness
- Department of BiochemistryUniversity of OtagoDunedinNew Zealand
- Peter MacCallum Cancer CentreMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyThe University of MelbourneMelbourneVictoriaAustralia
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Secrier M, McGrath L, Ng F, Gulati S, Raymond A, Nuttall BRB, Berthe J, Jones EV, Sidders BS, Galon J, Barrett JC, Angell HK. Immune Cell Abundance and T-cell Receptor Landscapes Suggest New Patient Stratification Strategies in Head and Neck Squamous Cell Carcinoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:2133-2145. [PMID: 37819239 PMCID: PMC10588680 DOI: 10.1158/2767-9764.crc-23-0155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/04/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a molecularly and spatially heterogeneous disease frequently characterized by impairment of immunosurveillance mechanisms. Despite recent success with immunotherapy treatment, disease progression still occurs quickly after treatment in the majority of cases, suggesting the need to improve patient selection strategies. In the quest for biomarkers that may help inform response to checkpoint blockade, we characterized the tumor microenvironment (TME) of 162 HNSCC primary tumors of diverse etiologic and spatial origin, through gene expression and IHC profiling of relevant immune proteins, T-cell receptor (TCR) repertoire analysis, and whole-exome sequencing. We identified five HNSCC TME categories based on immune/stromal composition: (i) cytotoxic, (ii) plasma cell rich, (iii) dendritic cell rich, (iv) macrophage rich, and (v) immune-excluded. Remarkably, the cytotoxic and plasma cell rich subgroups exhibited a phenotype similar to tertiary lymphoid structures (TLS), which have been previously linked to immunotherapy response. We also found an increased richness of the TCR repertoire in these two subgroups and in never smokers. Mutational patterns evidencing APOBEC activity were enriched in the plasma cell high subgroup. Furthermore, specific signal propagation patterns within the Ras/ERK and PI3K/AKT pathways associated with distinct immune phenotypes. While traditionally CD8/CD3 T-cell infiltration and immune checkpoint expression (e.g., PD-L1) have been used in the patient selection process for checkpoint blockade treatment, we suggest that additional biomarkers, such as TCR productive clonality, smoking history, and TLS index, may have the ability to pull out potential responders to benefit from immunotherapeutic agents. SIGNIFICANCE Here we present our findings on the genomic and immune landscape of primary disease in a cohort of 162 patients with HNSCC, benefitting from detailed molecular and clinical characterization. By employing whole-exome sequencing and gene expression analysis of relevant immune markers, TCR profiling, and staining of relevant proteins involved in immune response, we highlight how distinct etiologies, cell intrinsic, and environmental factors combine to shape the landscape of HNSCC primary disease.
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Affiliation(s)
- Maria Secrier
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Lara McGrath
- Translational Medicine, Oncology R&D, AstraZeneca, Boston, Massachusetts
| | - Felicia Ng
- Oncology Data Science, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Sakshi Gulati
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Amelia Raymond
- Translational Medicine, Oncology R&D, AstraZeneca, Boston, Massachusetts
| | | | - Julie Berthe
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Emma V. Jones
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Ben S. Sidders
- Oncology Data Science, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Jérôme Galon
- INSERM, Laboratory of Integrative Cancer Immunology, Paris, France
- Sorbonne Université, Université Paris Cité, Centre de Recherche des Cordeliers, Paris, France
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - J. Carl Barrett
- Translational Medicine, Oncology R&D, AstraZeneca, Boston, Massachusetts
| | - Helen K. Angell
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
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Valero C, Golkaram M, Vos JL, Xu B, Fitzgerald C, Lee M, Kaplan S, Han CY, Pei X, Sarkar R, Boe LA, Pandey A, Koh ES, Zuur CL, Solit DB, Pawlowski T, Liu L, Ho AL, Chowell D, Riaz N, Chan TA, Morris LG. Clinical-genomic determinants of immune checkpoint blockade response in head and neck squamous cell carcinoma. J Clin Invest 2023; 133:e169823. [PMID: 37561583 PMCID: PMC10541199 DOI: 10.1172/jci169823] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUNDRecurrent and/or metastatic (R/M) head and neck squamous cell carcinoma (HNSCC) is generally an incurable disease, with patients experiencing median survival of under 10 months and significant morbidity. While immune checkpoint blockade (ICB) drugs are effective in approximately 20% of patients, the remaining experience limited clinical benefit and are exposed to potential adverse effects and financial costs. Clinically approved biomarkers, such as tumor mutational burden (TMB), have a modest predictive value in HNSCC.METHODSWe analyzed clinical and genomic features, generated using whole-exome sequencing, in 133 ICB-treated patients with R/M HNSCC, of whom 69 had virus-associated and 64 had non-virus-associated tumors.RESULTSHierarchical clustering of genomic data revealed 6 molecular subtypes characterized by a wide range of objective response rates and survival after ICB therapy. The prognostic importance of these 6 subtypes was validated in an external cohort. A random forest-based predictive model, using several clinical and genomic features, predicted progression-free survival (PFS), overall survival (OS), and response with greater accuracy than did a model based on TMB alone. Recursive partitioning analysis identified 3 features (systemic inflammatory response index, TMB, and smoking signature) that classified patients into risk groups with accurate discrimination of PFS and OS.CONCLUSIONThese findings shed light on the immunogenomic characteristics of HNSCC tumors that drive differential responses to ICB and identify a clinical-genomic classifier that outperformed the current clinically approved biomarker of TMB. This validated predictive tool may help with clinical risk stratification in patients with R/M HNSCC for whom ICB is being considered.FUNDINGFundación Alfonso Martín Escudero, NIH R01 DE027738, US Department of Defense CA210784, The Geoffrey Beene Cancer Research Center, The MSKCC Population Science Research Program, the Jayme Flowers Fund, the Sebastian Nativo Fund, and the NIH/NCI Cancer Center Support Grant P30 CA008748.
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Affiliation(s)
- Cristina Valero
- Head and Neck Service, Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | | | - Joris L. Vos
- Head and Neck Service, Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Bin Xu
- Department of Pathology and Laboratory Medicine
| | - Conall Fitzgerald
- Head and Neck Service, Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Mark Lee
- Head and Neck Service, Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | | | - Catherine Y. Han
- Head and Neck Service, Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Xin Pei
- Department of Radiation Oncology, and
| | | | - Lillian A. Boe
- Department of Biostatistics and Epidemiology, MSKCC, New York, New York, USA
| | - Abhinav Pandey
- Head and Neck Service, Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Elizabeth S. Koh
- Head and Neck Service, Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Charlotte L. Zuur
- Department of Head and Neck Oncology and Surgery, Antoni van Leeuwenhoek Hospital–Netherlands Cancer Institute, Amsterdam, Netherlands
- Department of Otorhinolaryngology and Head and Neck Surgery, Leiden University Medical Center, Leiden, Netherlands
| | | | | | - Li Liu
- Illumina Inc., San Diego, California, USA
| | - Alan L. Ho
- Department of Medicine, MSKCC, New York, New York, USA
| | - Diego Chowell
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Timothy A. Chan
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Luc G.T. Morris
- Head and Neck Service, Immunogenomic Oncology Platform, Department of Surgery, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
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Ostroverkhova D, Przytycka TM, Panchenko AR. Cancer driver mutations: predictions and reality. Trends Mol Med 2023:S1471-4914(23)00067-9. [PMID: 37076339 DOI: 10.1016/j.molmed.2023.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
Cancer cells accumulate many genetic alterations throughout their lifetime, but only a few of them drive cancer progression, termed driver mutations. Driver mutations may vary between cancer types and patients, can remain latent for a long time and become drivers at particular cancer stages, or may drive oncogenesis only in conjunction with other mutations. The high mutational, biochemical, and histological tumor heterogeneity makes driver mutation identification very challenging. In this review we summarize recent efforts to identify driver mutations in cancer and annotate their effects. We underline the success of computational methods to predict driver mutations in finding novel cancer biomarkers, including in circulating tumor DNA (ctDNA). We also report on the boundaries of their applicability in clinical research.
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Affiliation(s)
- Daria Ostroverkhova
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Teresa M Przytycka
- National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada; Department of Biology and Molecular Sciences, Queen's University, Kingston, ON, Canada; School of Computing, Queen's University, Kingston, ON, Canada; Ontario Institute of Cancer Research, Toronto, ON, Canada.
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Amgalan B, Wojtowicz D, Kim YA, Przytycka TM. Influence network model uncovers relations between biological processes and mutational signatures. Genome Med 2023; 15:15. [PMID: 36879282 PMCID: PMC9987115 DOI: 10.1186/s13073-023-01162-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/08/2023] [Indexed: 03/08/2023] Open
Abstract
BACKGROUND There has been a growing appreciation recently that mutagenic processes can be studied through the lenses of mutational signatures, which represent characteristic mutation patterns attributed to individual mutagens. However, the causal links between mutagens and observed mutation patterns as well as other types of interactions between mutagenic processes and molecular pathways are not fully understood, limiting the utility of mutational signatures. METHODS To gain insights into these relationships, we developed a network-based method, named GENESIGNET that constructs an influence network among genes and mutational signatures. The approach leverages sparse partial correlation among other statistical techniques to uncover dominant influence relations between the activities of network nodes. RESULTS Applying GENESIGNET to cancer data sets, we uncovered important relations between mutational signatures and several cellular processes that can shed light on cancer-related processes. Our results are consistent with previous findings, such as the impact of homologous recombination deficiency on clustered APOBEC mutations in breast cancer. The network identified by GENESIGNET also suggest an interaction between APOBEC hypermutation and activation of regulatory T Cells (Tregs), as well as a relation between APOBEC mutations and changes in DNA conformation. GENESIGNET also exposed a possible link between the SBS8 signature of unknown etiology and the Nucleotide Excision Repair (NER) pathway. CONCLUSIONS GENESIGNET provides a new and powerful method to reveal the relation between mutational signatures and gene expression. The GENESIGNET method was implemented in python, and installable package, source codes and the data sets used for and generated during this study are available at the Github site https://github.com/ncbi/GeneSigNet.
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Affiliation(s)
- Bayarbaatar Amgalan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, 20894, Bethesda, USA
| | - Damian Wojtowicz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, 20894, Bethesda, USA.,Current address: Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, ul. Banacha 2, 02-097, Warszawa, Poland
| | - Yoo-Ah Kim
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, 20894, Bethesda, USA
| | - Teresa M Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, 20894, Bethesda, USA.
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Campo F, Iocca O, De Virgilio A, Mazzola F, Mercante G, Pichi B, Holsinger FC, Di Maio P, Ramella S, Pellini R. Treatment of oropharyngeal squamous cell carcinoma: Is swallowing quality better after TORS or RT? Radiother Oncol 2023; 183:109547. [PMID: 36813176 DOI: 10.1016/j.radonc.2023.109547] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/30/2023] [Accepted: 02/05/2023] [Indexed: 02/22/2023]
Abstract
BACKGROUND AND PURPOSE To answer an important question regarding the long-term morbidity of two oncological equivalent treatment for oropharyngeal squamous cell carcinoma (OPSCC), namely a comparison of swallowing function results between patients treated with trans-oral robotic surgery (TORS) versus patients treated with radiotherapy (RT). MATERIALS AND METHODS Studies included patients with OPSCC treated with TORS or RT. Articles reporting complete data on MD Anderson Dysphagia Inventory (MDADI) and comparing the two treatments (TORS vs RT) were included in the meta-analysis. Swallowing assessed with MDADI was the primary outcome, the evaluation with instrumental methods was the secondary aim. RESULTS Included studies provided a total of 196 OPSCC primarily treated with TORS vs 283 OPSCC primarily treated with RT. The mean difference in MDADI score at the longest follow-up was not significantly different between TORS and RT group (mean difference [MD] -0.52; 95% CI -4.53-3.48; p = 0.80). After treatment, mean composite MDADI scores demonstrated a slight impairment in both groups without reaching a statistical difference compared to the baseline status. DIGEST score and Yale score showed a significantly worse function in both treatment groups at 12-month follow-up compared to baseline status. CONCLUSION The meta-analysis demonstrates that up-front TORS (+- adjuvant therapy) and up-front RT (+- CT) appear to be equivalent treatments in functional outcomes in T1-T2, N0-2 OPSCC, however, both treatments cause impaired swallowing ability. Clinicians should have a holistic approach and work with patients to develop an individualized nutrition plan and swallowing rehabilitation protocol from diagnosis to post-treatment surveillance.
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Affiliation(s)
- Flaminia Campo
- Department of Otolaryngology-Head and Neck Surgery, IRCCS Regina Elena National Cancer Institute, Rome, Italy; Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico 155, 00186 Rome, Italy.
| | - Oreste Iocca
- Division of Maxillofacial Surgery, Surgical Science Department, University of Torino, Torino, Italy
| | - Armando De Virgilio
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; Otorhinolaryngology Unit, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Francesco Mazzola
- Department of Otolaryngology-Head and Neck Surgery, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giuseppe Mercante
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; Otorhinolaryngology Unit, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Barbara Pichi
- Department of Otolaryngology-Head and Neck Surgery, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Floyd Christopher Holsinger
- Department of Otolaryngology - Head and Neck Surgery, Stanford University Medical Center, Palo Alto, CA, USA
| | - Pasquale Di Maio
- Department of Otoralyngology-head and Neck Surgery, Giuseppe Fornaroli Hospital, ASST Ovest Milanese, Magenta-Milan, Italy
| | - Sara Ramella
- Radiation Oncology, Campus Bio-Medico University Hospital Foundation, Rome, Italy
| | - Raul Pellini
- Department of Otolaryngology-Head and Neck Surgery, IRCCS Regina Elena National Cancer Institute, Rome, Italy
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10
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Lactobacillus for ribosome peptide editing cancer. Clin Transl Oncol 2023; 25:1522-1544. [PMID: 36694080 PMCID: PMC9873400 DOI: 10.1007/s12094-022-03066-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/24/2022] [Indexed: 01/25/2023]
Abstract
This study reviews newly discovered insect peptide point mutations as new possible cancer research targets. To interpret newly discovered peptide point mutations in insects as new possible cancer research targets, we focused on the numerous peptide changes found in the 'CSP' family on the sex pheromone gland of the female silkworm moth Bombyx mori. We predict that the Bombyx peptide modifications will have a significant effect on cancer CUP (cancers of unknown primary) therapy and that bacterial peptide editing techniques, specifically Lactobacillus combined to CRISPR, will be used to regulate ribosomes and treat cancer in humans.
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11
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Research on the influence of APOBEC family on the occurrence, diagnosis, and treatment of various tumors. J Cancer Res Clin Oncol 2023; 149:357-366. [PMID: 36222899 DOI: 10.1007/s00432-022-04395-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/05/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Apolipoprotein B mRNA-editing catalytic polypeptide (APOBEC) is a family of highly efficient cytidine deaminase enzymes. APOBECs have been proven to deaminate cytidine on single-stranded DNA or RNA. Inducing the deamination of cytosine on the target gene into uracil, which exerts a variety of physiological functions, plays an important role in innate immunity, adaptive immunity, and antiviral. As the research progresses, APOBECs have been confirmed to be highly expressed in a variety of tumors, causing abnormal mutations in host genes, leading to inactivation of tumor suppressor genes or activation of proto-oncogenes, and their role in tumor development and as diagnostic and treatment markers gradually be found. CONCLUSION This article will review the mechanism of APOBECs and their impact on tumor occurrence, development, diagnosis, and treatment, and provide a theoretical basis for future tumor treatment.
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12
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Xu Q, Chen Y, Jin Y, Wang Z, Dong H, Kaufmann AM, Albers AE, Qian X. Advanced Nanomedicine for High-Risk HPV-Driven Head and Neck Cancer. Viruses 2022; 14:v14122824. [PMID: 36560828 PMCID: PMC9788019 DOI: 10.3390/v14122824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The incidence of high-risk Human Papillomavirus (HR-HPV)-driven head and neck squamous cell carcinoma (HNSCC) is on the rise globally. HR-HPV-driven HNSCC displays molecular and clinical characteristics distinct from HPV-uninvolved cases. Therapeutic strategies for HR-HPV-driven HNSCC are under investigation. HR-HPVs encode the oncogenes E6 and E7, which are essential in tumorigenesis. Meanwhile, involvement of E6 and E7 provides attractive targets for developing new therapeutic regimen. Here we will review some of the recent advancements observed in preclinical studies and clinical trials on HR-HPV-driven HNSCC, focusing on nanotechnology related methods. Materials science innovation leads to great improvement for cancer therapeutics including HNSCC. This article discusses HPV-E6 or -E7- based vaccines, based on plasmid, messenger RNA or peptide, at their current stage of development and testing as well as how nanoparticles can be designed to target and access cancer cells and activate certain immunology pathways besides serving as a delivery vehicle. Nanotechnology was also used for chemotherapy and photothermal treatment. Short interference RNA targeting E6/E7 showed some potential in animal models. Gene editing by CRISPR-CAS9 combined with other treatments has also been assessed. These advancements have the potential to improve the outcome in HR-HPV-driven HNSCC, however breakthroughs are still to be awaited with nanomedicine playing an important role.
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Affiliation(s)
- Qiang Xu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Ye Chen
- Department of Clinical Laboratory, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, No. 1 East Banshan Road, Gongshu District, Hangzhou 310022, China
| | - Yuan Jin
- Department of Clinical Laboratory, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, No. 1 East Banshan Road, Gongshu District, Hangzhou 310022, China
| | - Zhiyu Wang
- Department of Clinical Laboratory, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, No. 1 East Banshan Road, Gongshu District, Hangzhou 310022, China
- Wenzhou Medical University, Wenzhou 325000, China
| | - Haoru Dong
- Department of Clinical Laboratory, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, No. 1 East Banshan Road, Gongshu District, Hangzhou 310022, China
- Wenzhou Medical University, Wenzhou 325000, China
| | - Andreas M. Kaufmann
- Clinic for Gynecology, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, 12203 Berlin, Germany
| | - Andreas E. Albers
- Department of Clinical Medicine, Oto-Rhino-Laryngology, Medical School Berlin, 14197 Berlin, Germany
| | - Xu Qian
- Department of Clinical Laboratory, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, No. 1 East Banshan Road, Gongshu District, Hangzhou 310022, China
- Correspondence:
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13
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Reduced MHC Class I and II Expression in HPV-Negative vs. HPV-Positive Cervical Cancers. Cells 2022; 11:cells11233911. [PMID: 36497170 PMCID: PMC9741043 DOI: 10.3390/cells11233911] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Cervical cancer (CC) is the second most common cancer in women worldwide and the fourth leading cause of cancer-associated death in women. Although human papillomavirus (HPV) infection is associated with nearly all CC, it has recently become clear that HPV-negative (HPV-) CC represents a distinct disease phenotype with increased mortality. HPV-positive (HPV+) and HPV- CC demonstrate different molecular pathology, prognosis, and response to treatment. Furthermore, CC caused by HPV α9 types (HPV16-like) often have better outcomes than those caused by HPV α7 types (HPV18-like). This study systematically and comprehensively compared the expression of genes involved in major histocompatibility complex (MHC) class I and II presentation within CC caused by HPV α9 types, HPV α7 types, and HPV- CC. We observed increased expression of MHC class I and II classical and non-classical genes in HPV+ CC and overall higher expression of genes involved in their antigen loading and presentation apparatus as well as transcriptional regulation. Increased expression of MHC I-related genes differs from previous studies using cell culture models. These findings identify crucial differences between antigen presentation within the tumor immune microenvironments of HPV+ and HPV- CC, as well as modest differences between HPV α9 and α7 CC. These differences may contribute to the altered patient outcomes and responses to immunotherapy observed between these distinct cancers.
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14
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Lin M, Sade-Feldman M, Wirth L, Lawrence MS, Faden DL. Single-cell transcriptomic profiling for inferring tumor origin and mechanisms of therapeutic resistance. NPJ Precis Oncol 2022; 6:71. [PMID: 36210388 PMCID: PMC9548500 DOI: 10.1038/s41698-022-00314-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/23/2022] [Indexed: 02/02/2023] Open
Abstract
Head and Neck Squamous Cell Carcinoma (HNSCC) is an aggressive epithelial cancer with poor overall response rates to checkpoint inhibitor therapy (CPI) despite CPI being the recommended treatment for recurrent or metastatic HNSCC. Mechanisms of resistance to CPI in HNSCC are poorly understood. To identify drivers of response and resistance to CPI in a unique patient who was believed to have developed three separate HNSCCs, we performed single-cell RNA-seq (scRNA-seq) profiling of two responding lesions and one progressive lesion that developed during CPI. Our results not only suggest interferon-induced APOBEC3-mediated acquired resistance as a mechanism of CPI resistance in the progressing lesion but further, that the lesion in question was actually a metastasis as opposed to a new primary tumor, highlighting the immense power of scRNA-seq as a clinical tool for inferring tumor origin and mechanisms of therapeutic resistance.
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Affiliation(s)
- Maoxuan Lin
- grid.39479.300000 0000 8800 3003Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA 02118 USA ,grid.32224.350000 0004 0386 9924Massachusetts General Hospital Cancer Center, Boston, MA 02118 USA
| | - Moshe Sade-Feldman
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital Cancer Center, Boston, MA 02118 USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA 02115 USA
| | - Lori Wirth
- grid.32224.350000 0004 0386 9924Department of Medicine, Massachusetts General Hospital, Boston, MA 02118 USA
| | - Michael S. Lawrence
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital Cancer Center, Boston, MA 02118 USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA 02115 USA
| | - Daniel L. Faden
- grid.39479.300000 0000 8800 3003Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA 02118 USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA 02115 USA
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15
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Warren CJ, Santiago ML, Pyeon D. APOBEC3: Friend or Foe in Human Papillomavirus Infection and Oncogenesis? Annu Rev Virol 2022; 9:375-395. [PMID: 35671565 PMCID: PMC9637027 DOI: 10.1146/annurev-virology-092920-030354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human papillomavirus (HPV) infection is a causative agent of multiple human cancers, including cervical and head and neck cancers. In these HPV-positive tumors, somatic mutations are caused by aberrant activation of DNA mutators such as members of the apolipoprotein B messenger RNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of cytidine deaminases. APOBEC3 proteins are most notable for their restriction of various viruses, including anti-HPV activity. However, the potential role of APOBEC3 proteins in HPV-induced cancer progression has recently garnered significant attention. Ongoing research stems from the observations that elevated APOBEC3 expression is driven by HPV oncogene expression and that APOBEC3 activity is likely a significant contributor to somatic mutagenesis in HPV-positive cancers. This review focuses on recent advances in the study of APOBEC3 proteins and their roles in HPV infection and HPV-driven oncogenesis. Further, we discuss critical gaps and unanswered questions in our understanding of APOBEC3 in virus-associated cancers.
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Affiliation(s)
- Cody J Warren
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
| | - Mario L Santiago
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA;
| | - Dohun Pyeon
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA;
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16
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Pan-Cancer Analysis for Immune Cell Infiltration and Mutational Signatures Using Non-Negative Canonical Correlation Analysis. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12136596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mutational signatures indicate the mutational processes and substitution patterns in cancer cell genomes. However, the functional consequences of mutational signatures remain unclear, and there have been no comprehensive systematic studies to examine the relationships between the mutational signatures and the immune cell infiltration. Here, the relationship between mutational signatures and immune cell infiltration using non-negative canonical correlation analysis based on 8927 patients across 25 tumor types was investigated. By inspecting mutational signatures with the maximal coefficients determined by the non-negative canonical correlation analysis, the study identified mutational signatures related to immune cell infiltration composed of tumor microenvironments. The analysis was validated by showing that the genes associated with the identified mutational signatures were linked to overall survival by a Kaplan–Meier curve and a log-rank test and were mainly related to immunity by gene set enrichment analysis. These results will help expand our knowledge of tumor biology and recognize the functional roles and associations of immune systems with mutational signatures.
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17
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Halima A, Vuong W, Chan TA. Next-generation sequencing: unraveling genetic mechanisms that shape cancer immunotherapy efficacy. J Clin Invest 2022; 132:154945. [PMID: 35703181 PMCID: PMC9197511 DOI: 10.1172/jci154945] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Immunity is governed by fundamental genetic processes. These processes shape the nature of immune cells and set the rules that dictate the myriad complex cellular interactions that power immune systems. Everything from the generation of T cell receptors and antibodies, control of epitope presentation, and recognition of pathogens by the immunoediting of cancer cells is, in large part, made possible by core genetic mechanisms and the cellular machinery that they encode. In the last decade, next-generation sequencing has been used to dissect the complexities of cancer immunity with potent effect. Sequencing of exomes and genomes has begun to reveal how the immune system recognizes “foreign” entities and distinguishes self from non-self, especially in the setting of cancer. High-throughput analyses of transcriptomes have revealed deep insights into how the tumor microenvironment affects immunotherapy efficacy. In this Review, we discuss how high-throughput sequencing has added to our understanding of how immune systems interact with cancer cells and how cancer immunotherapies work.
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Affiliation(s)
- Ahmed Halima
- Department of Radiation Oncology, Taussig Cancer Institute, and
| | - Winston Vuong
- Department of Radiation Oncology, Taussig Cancer Institute, and
| | - Timothy A Chan
- Department of Radiation Oncology, Taussig Cancer Institute, and.,Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, Ohio, USA.,National Center for Regenerative Medicine, Cleveland, Ohio, USA
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18
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Crane J, Shi Q, Xi Y, Lai J, Pham K, Wang H. Emerging Trends in the Pathological Research of Human Papillomavirus-positive Oropharyngeal Squamous Cell Carcinoma. JOURNAL OF CLINICAL AND TRANSLATIONAL PATHOLOGY 2022; 2:31-36. [PMID: 36275841 PMCID: PMC9585478 DOI: 10.14218/jctp.2022.00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Oropharyngeal squamous cell carcinomas (OPSCCs) have shown an alarming rate of increase in incidence over the past several decades, markedly in men. In the United States, transcriptionally-active human papillomavirus (HPV), particularly HPV 16, has become the highest contributive agent of OPSCCs, affecting approximately 16,000 people a year. Compared to patients with HPV-negative OPSCCs, patients with HPV-positive OPSCCs exhibit better health responses to chemoradiotherapy and an overall increase in long-term survival. Despite promising treatment options, many OPSCCs are discovered at an advanced stage, and ~20% of cases will recur after definitive treatment. Therefore, extensive research is ongoing to identify new targets for precision treatment and to stratify tumor prognosis. The aim of this review is to capture the most updated research on HPV-positive OPSCCs, emphasizing their relevance as potential new targets for precision medicine and survival prognosis.
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Affiliation(s)
- Joshua Crane
- Department of Laboratory Medicine and Pathology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Yibo Xi
- Department of Laboratory Medicine and Pathology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Kien Pham
- Department of Laboratory Medicine and Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - He Wang
- Department of Laboratory Medicine and Pathology, Yale University School of Medicine, New Haven, CT, USA
- Correspondence to: He Wang, Department of Laboratory Medicine and Pathology, Yale University School of Medicine, 310 Cedar Street, New Haven, CT 06510, USA. Tel: +1-203-214-2786, Fax: +1-203-214-2764,
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19
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Neoadjuvant immunotherapy with nivolumab and ipilimumab induces major pathological responses in patients with head and neck squamous cell carcinoma. Nat Commun 2021; 12:7348. [PMID: 34937871 PMCID: PMC8695578 DOI: 10.1038/s41467-021-26472-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 10/04/2021] [Indexed: 01/29/2023] Open
Abstract
Surgery for locoregionally advanced head and neck squamous cell carcinoma (HNSCC) results in 30‒50% five-year overall survival. In IMCISION (NCT03003637), a non-randomized phase Ib/IIa trial, 32 HNSCC patients are treated with 2 doses (in weeks 1 and 3) of immune checkpoint blockade (ICB) using nivolumab (NIVO MONO, n = 6, phase Ib arm A) or nivolumab plus a single dose of ipilimumab (COMBO, n = 26, 6 in phase Ib arm B, and 20 in phase IIa) prior to surgery. Primary endpoints are feasibility to resect no later than week 6 (phase Ib) and primary tumor pathological response (phase IIa). Surgery is not delayed or suspended for any patient in phase Ib, meeting the primary endpoint. Grade 3‒4 immune-related adverse events are seen in 2 of 6 (33%) NIVO MONO and 10 of 26 (38%) total COMBO patients. Pathological response, defined as the %-change in primary tumor viable tumor cell percentage from baseline biopsy to on-treatment resection, is evaluable in 17/20 phase IIa patients and 29/32 total trial patients (6/6 NIVO MONO, 23/26 COMBO). We observe a major pathological response (MPR, 90‒100% response) in 35% of patients after COMBO ICB, both in phase IIa (6/17) and in the whole trial (8/23), meeting the phase IIa primary endpoint threshold of 10%. NIVO MONO’s MPR rate is 17% (1/6). None of the MPR patients develop recurrent HSNCC during 24.0 months median postsurgical follow-up. FDG-PET-based total lesion glycolysis identifies MPR patients prior to surgery. A baseline AID/APOBEC-associated mutational profile and an on-treatment decrease in hypoxia RNA signature are observed in MPR patients. Our data indicate that neoadjuvant COMBO ICB is feasible and encouragingly efficacious in HNSCC. Immune checkpoint blockade has become standard care for patients with recurrent metastatic head and neck squamous cell carcinoma (HNSCC). Here the authors present the results of a non-randomized phase Ib/IIa trial, reporting safety and efficacy of neoadjuvant nivolumab monotherapy and nivolumab plus ipilimumab prior to standard-of-care surgery in patients with HNSCC. .
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20
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A Novel Ferroptosis-Related Gene Signature to Predict Prognosis in Patients with Head and Neck Squamous Cell Carcinoma. DISEASE MARKERS 2021; 2021:5759927. [PMID: 34853622 PMCID: PMC8629675 DOI: 10.1155/2021/5759927] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 09/13/2021] [Accepted: 10/28/2021] [Indexed: 12/24/2022]
Abstract
The clinical TNM staging system is currently used to evaluate the prognosis of head and neck squamous cell carcinoma (HNSCC). The 5-year survival rate for patients with HNSCC is less than 50%, which is attributed to the lack of reliable prognostic biomarkers. Ferroptosis-related genes (FRGs) regulate cancer initiation and progression. Therefore, we analyzed the correlation between FRGs and the clinical outcomes of patients with HNSCC. A typical prognostic model of FRGs for HNSCC was constructed using bioinformatics tools and data from public databases, including The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and GeneCards. The model was generated based on the following six FRGs: ATG5, PRDX6, OTUB1, FTH1, SOCS1, and MAP3K5. The accuracy of model prediction was analyzed systematically. The overall survival (OS) of the high-risk group was significantly lower than that of the low-risk group. The AUC for 1-year, 3-year, and 5-year survival were 0.645, 0.721, and 0.737, respectively, in the training set (TCGA cohort) and 0.726, 0.620, and 0.584, respectively, in the validation set (GSE65858). The multivariate Cox regression analysis revealed that the risk score was an independent prognostic factor for HNSCC. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that six FRGs were enriched in the ferroptosis pathway. A novel FRG prognostic signature model was established for HNSCC. The findings of this study reveal that FRGs are potential biomarkers for HNSCC.
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21
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Fenton TR. Accumulation of host cell genetic errors following high-risk HPV infection. Curr Opin Virol 2021; 51:1-8. [PMID: 34543805 DOI: 10.1016/j.coviro.2021.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 12/19/2022]
Affiliation(s)
- Tim R Fenton
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, UK; School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.
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22
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Zhu Z, Ji X, Zhu W, Cai T, Xu C, Huang C, He S, Gong Y, Li X, Lin J, Zhou L. Comprehensive bioinformatics analyses of APOBECs family and identification of APOBEC3D as the unfavorable prognostic biomarker in clear cell renal cell carcinoma. J Cancer 2021; 12:7101-7110. [PMID: 34729111 PMCID: PMC8558646 DOI: 10.7150/jca.61972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 10/03/2021] [Indexed: 01/22/2023] Open
Abstract
Purpose: At present, how early screening for ccRCC is still a thorny issue for urologists. Probing the mechanisms underlying the development of ccRCC and finding relevant prognostic biomarkers remains crucial. Therefore, we systematically analyzed the APOBEC family in this study and identified APOBEC3D as a prognostic biomarker. Methods: In this study, based on the TCGA database, we systematically assessed the expression and prognosis of the APOBEC family and analyzed potential bioinformatic pathways. We then constructed nomograms to predict the prognosis of ccRCC patients better. Afterward, we further focused on APOBEC3D in our data on ccRCC specimens. The APOBEC3D should be extensively studied in ccRCC in the future. Results: The results showed that the APOBEC family showed the most significant changes in expression in ccRCC. The pathway enrichment analysis showed that APOBEC3 family members mainly regulated cytidine and cytosine-related processes. Subsequently, the Cox regression was used to construct prognostic signature, and validated in ICGC and GEO databases. Next, a nomogram was created integrating clinical parameters showing good predictive performance. Finally, we screened for APOBEC3D and found in our clinical sample that patients with high expression of APOBEC3D had a worse prognosis. Conclusion: Based on these results, APOBEC family members play important roles in the development of ccRCC, and APOBEC3D could serve as the biomarker for predicting patient prognosis.
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Affiliation(s)
- Zhenpeng Zhu
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Xing Ji
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Weijie Zhu
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Tianyu Cai
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Chunru Xu
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Cong Huang
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Shiming He
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Jian Lin
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing 100034, China.,Institution of Urology, Peking University, Beijing 100034, China.,National Urological Cancer Center, Beijing 100034, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Beijing 100034, China
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Powell SF, Vu L, Spanos WC, Pyeon D. The Key Differences between Human Papillomavirus-Positive and -Negative Head and Neck Cancers: Biological and Clinical Implications. Cancers (Basel) 2021; 13:5206. [PMID: 34680354 PMCID: PMC8533896 DOI: 10.3390/cancers13205206] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/08/2021] [Accepted: 10/13/2021] [Indexed: 12/17/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a unique malignancy associated with two distinct risk factors: exposure to typical carcinogens and infection of human papillomavirus (HPV). HPV encodes the potent oncoproteins E6 and E7, which bypass many important oncogenic processes and result in cancer development. In contrast, HPV-negative HNSCC is developed through multiple mutations in diverse oncogenic driver genes. While the risk factors associated with HPV-positive and HPV-negative HNSCCs are discrete, HNSCC patients still show highly complex molecular signatures, immune infiltrations, and treatment responses even within the same anatomical subtypes. Here, we summarize the current understanding of biological mechanisms, treatment approaches, and clinical outcomes in comparison between HPV-positive and -negative HNSCCs.
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Affiliation(s)
- Steven F. Powell
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, SD 57104, USA;
| | - Lexi Vu
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA;
| | - William C. Spanos
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, SD 57104, USA;
| | - Dohun Pyeon
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA;
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24
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Rocha ML, Schmid KW, Czapiewski P. The prevalence of DNA microsatellite instability in anaplastic thyroid carcinoma - systematic review and discussion of current therapeutic options. Contemp Oncol (Pozn) 2021; 25:213-223. [PMID: 34729042 PMCID: PMC8547184 DOI: 10.5114/wo.2021.110052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 09/25/2021] [Indexed: 01/02/2023] Open
Abstract
INTRODUCTION Anaplastic thyroid carcinoma is a rare, rapidly progressing, highly aggressive thyroid malignancy. Responses to immune checkpoint inhibitors in mismatch repair-deficient/microsatellite instability-high tumours of other locations have shown promising results, and with the extended approval of the PD-1 receptor inhibitor pembrolizumab by the Food and Drug Administration, also anaplastic thyroid cancer (ATC) requires analysis for microsatellite instability (MSI) status. MATERIAL AND METHODS Systematic research for relevant literature was conducted in different databases. Prevalence, detection methods, and the potential prognostic/predictive value of MSI in view of the available targeted therapies were of special focus. RESULTS Selected citations revealed the prevalence of MSI in 7.4%, with mutations in the MSH2 gene (33%) being the most frequent, followed by MSH6 (25%) and MLH1 (16.7%) occurring in the following combinations: MLH1-MSH2 (8.3%), MSH2-MSH6 (8.3%), and MLH3-MSH5 (8.3%). No mutations in the PMS2 gene were reported. Sixty-six co-mutations in 9 cases were found, with TP53 (88.9%), NF1 (44.4 %), ATM (33.3%), and RB1 (33.3%) being the most frequent. No RAS mutations were noted. Survival ranged between 2.8 and 48 months, and patient age varied between 49 and 84 years. There are insufficient and heterogenous data concerning the predictive or prognostic value of mismatch repair-deficient/microsatellite instability status. CONCLUSIONS Tumour molecular profiling is fundamental in ATC for predictive, prognostic, as well as therapeutic reasons, and analysis of MSI status is strongly suggested because a small subgroup show the MSI signature and might profit from recently approved targeted therapies.
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Affiliation(s)
- Maria Linda Rocha
- Institute of Pathology Königs Wusterhausen, Königs Wusterhausen, Germany
| | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Piotr Czapiewski
- Institute of Pathology, Dessau Medical Centre, Dessau, Germany
- Institute of Pathology, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
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25
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APOBEC Mutagenesis Is Concordant between Tumor and Viral Genomes in HPV-Positive Head and Neck Squamous Cell Carcinoma. Viruses 2021; 13:v13081666. [PMID: 34452530 PMCID: PMC8402723 DOI: 10.3390/v13081666] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 02/06/2023] Open
Abstract
APOBEC is a mutagenic source in human papillomavirus (HPV)-mediated malignancies, including HPV+ oropharyngeal squamous cell carcinoma (HPV + OPSCC), and in HPV genomes. It is unknown why APOBEC mutations predominate in HPV + OPSCC, or if the APOBEC-induced mutations observed in both human cancers and HPV genomes are directly linked. We performed sequencing of host somatic exomes, transcriptomes, and HPV16 genomes from 79 HPV + OPSCC samples, quantifying APOBEC mutational burden and activity in both host and virus. APOBEC was the dominant mutational signature in somatic exomes. In viral genomes, there was a mean of five (range 0-29) mutations per genome. The mean of APOBEC mutations in viral genomes was one (range 0-5). Viral APOBEC mutations, compared to non-APOBEC mutations, were more likely to be low-variant allele fraction mutations, suggesting that APOBEC mutagenesis actively occurrs in viral genomes during infection. HPV16 APOBEC-induced mutation patterns in OPSCC were similar to those previously observed in cervical samples. Paired host and viral analyses revealed that APOBEC-enriched tumor samples had higher viral APOBEC mutation rates (p = 0.028), and APOBEC-associated RNA editing (p = 0.008), supporting the concept that APOBEC mutagenesis in host and viral genomes is directly linked and occurrs during infection. Using paired sequencing of host somatic exomes, transcriptomes, and viral genomes, we demonstrated for the first-time definitive evidence of concordance between tumor and viral APOBEC mutagenesis. This finding provides a missing link connecting APOBEC mutagenesis in host and virus and supports a common mechanism driving APOBEC dysregulation.
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26
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Wiecek AJ, Jacobson DH, Lason W, Secrier M. Pan-Cancer Survey of Tumor Mass Dormancy and Underlying Mutational Processes. Front Cell Dev Biol 2021; 9:698659. [PMID: 34307377 PMCID: PMC8299471 DOI: 10.3389/fcell.2021.698659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/17/2021] [Indexed: 11/13/2022] Open
Abstract
Tumor mass dormancy is the key intermediate step between immune surveillance and cancer progression, yet due to its transitory nature it has been difficult to capture and characterize. Little is understood of its prevalence across cancer types and of the mutational background that may favor such a state. While this balance is finely tuned internally by the equilibrium between cell proliferation and cell death, the main external factors contributing to tumor mass dormancy are immunological and angiogenic. To understand the genomic and cellular context in which tumor mass dormancy may develop, we comprehensively profiled signals of immune and angiogenic dormancy in 9,631 cancers from the Cancer Genome Atlas and linked them to tumor mutagenesis. We find evidence for immunological and angiogenic dormancy-like signals in 16.5% of bulk sequenced tumors, with a frequency of up to 33% in certain tissues. Mutations in the CASP8 and HRAS oncogenes were positively selected in dormant tumors, suggesting an evolutionary pressure for controlling cell growth/apoptosis signals. By surveying the mutational damage patterns left in the genome by known cancer risk factors, we found that aging-induced mutations were relatively depleted in these tumors, while patterns of smoking and defective base excision repair were linked with increased tumor mass dormancy. Furthermore, we identified a link between APOBEC mutagenesis and dormancy, which comes in conjunction with immune exhaustion and may partly depend on the expression of the angiogenesis regulator PLG as well as interferon and chemokine signals. Tumor mass dormancy also appeared to be impaired in hypoxic conditions in the majority of cancers. The microenvironment of dormant cancers was enriched in cytotoxic and regulatory T cells, as expected, but also in macrophages and showed a reduction in inflammatory Th17 signals. Finally, tumor mass dormancy was linked with improved patient survival outcomes. Our analysis sheds light onto the complex interplay between dormancy, exhaustion, APOBEC activity and hypoxia, and sets directions for future mechanistic explorations.
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Affiliation(s)
- Anna Julia Wiecek
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom
| | - Daniel Hadar Jacobson
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom.,UCL Cancer Institute, Paul O'Gorman Building, University College London, London, United Kingdom
| | - Wojciech Lason
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom
| | - Maria Secrier
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom
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27
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Yuan X, Yi M, Zhang W, Xu L, Chu Q, Luo S, Wu K. The biology of combination immunotherapy in recurrent metastatic head and neck cancer. Int J Biochem Cell Biol 2021; 136:106002. [PMID: 33962022 DOI: 10.1016/j.biocel.2021.106002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 04/21/2021] [Accepted: 04/30/2021] [Indexed: 02/08/2023]
Abstract
Preclinical data suggest that head and neck cancer is an intrinsically immunosuppressive disease with abnormal inflammatory components in the tumor microenvironment. The development of immune checkpoint inhibitors, which are monoclonal antibodies capable of inhibiting immune suppressive signals to prime anticancer immunity, has revolutionized the therapeutic landscape in recurrent/metastatic head and neck cancer. However, patients with head and neck cancer present primary resistance to immunotherapy. Many ongoing trials include combinations of immunotherapy with different therapeutic interventions, aiming to improve response rates and overall survival. As novel therapy strategies are leveraged, the significance of immunotherapy in recurrent/metastatic head and neck cancer continues to be revealed. This review aims to summarize combinational immunotherapy in head and neck cancer.
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Affiliation(s)
- Xun Yuan
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Ming Yi
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Wei Zhang
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Linping Xu
- Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
| | - Qian Chu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Suxia Luo
- Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
| | - Kongming Wu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
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28
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Feng B, Hess J. Immune-Related Mutational Landscape and Gene Signatures: Prognostic Value and Therapeutic Impact for Head and Neck Cancer. Cancers (Basel) 2021; 13:cancers13051162. [PMID: 33800421 PMCID: PMC7962834 DOI: 10.3390/cancers13051162] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/28/2021] [Accepted: 03/03/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Immunotherapy has emerged as a standard-of-care for most human malignancies, including head and neck cancer, but only a limited number of patients exhibit a durable clinical benefit. An urgent medical need is the establishment of accurate response predictors, which is handicapped by the growing body of molecular, cellular and clinical variables that modify the complex nature of an effective anti-tumor immune response. This review summarizes more recent efforts to elucidate immune-related mutational landscapes and gene expression signatures by integrative analysis of multi-omics data, and highlights their potential therapeutic impact for head and neck cancer. A better knowledge of the underlying principles and relevant interactions could pave the way for rational therapeutic combinations to improve the efficacy of immunotherapy, in particular for those cancer patients at a higher risk for treatment failure. Abstract Immunotherapy by immune checkpoint inhibition has become a main pillar in the armamentarium to treat head and neck cancer and is based on the premise that the host immune system can be reactivated to successfully eliminate cancer cells. However, the response rate remains low and only a small subset of head and neck cancer patients achieves a durable clinical benefit. The availability of multi-omics data and emerging computational technologies facilitate not only a deeper understanding of the cellular composition in the tumor immune microenvironment but also enables the study of molecular principles in the complex regulation of immune surveillance versus tolerance. These knowledges will pave the way to apply immunotherapy more precisely and effectively. This review aims to provide a holistic view on how the immune landscape dictates the tumor fate and vice versa, and how integrative analysis of multi-omics data contribute to our current knowledge on the accuracy of predictive biomarkers and on a broad range of factors influencing the response to immunotherapy in head and neck cancer.
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Affiliation(s)
- Bohai Feng
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany;
- Department of Otorhinolaryngology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Jochen Hess
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany;
- Research Group Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Correspondence:
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29
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Riva G, Albano C, Gugliesi F, Pasquero S, Pacheco SFC, Pecorari G, Landolfo S, Biolatti M, Dell’Oste V. HPV Meets APOBEC: New Players in Head and Neck Cancer. Int J Mol Sci 2021; 22:1402. [PMID: 33573337 PMCID: PMC7866819 DOI: 10.3390/ijms22031402] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 12/13/2022] Open
Abstract
Besides smoking and alcohol, human papillomavirus (HPV) is a factor promoting head and neck squamous cell carcinoma (HNSCC). In some human tumors, including HNSCC, a number of mutations are caused by aberrantly activated DNA-modifying enzymes, such as the apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC) family of cytidine deaminases. As the enzymatic activity of APOBEC proteins contributes to the innate immune response to viruses, including HPV, the role of APOBEC proteins in HPV-driven head and neck carcinogenesis has recently gained increasing attention. Ongoing research efforts take the cue from two key observations: (1) APOBEC expression depends on HPV infection status in HNSCC; and (2) APOBEC activity plays a major role in HPV-positive HNSCC mutagenesis. This review focuses on recent advances on the role of APOBEC proteins in HPV-positive vs. HPV-negative HNSCC.
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Affiliation(s)
- Giuseppe Riva
- Otorhinolaryngology Division, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy; (G.R.); (G.P.)
| | - Camilla Albano
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; (C.A.); (F.G.); (S.P.); (S.F.C.P.); (S.L.)
| | - Francesca Gugliesi
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; (C.A.); (F.G.); (S.P.); (S.F.C.P.); (S.L.)
| | - Selina Pasquero
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; (C.A.); (F.G.); (S.P.); (S.F.C.P.); (S.L.)
| | - Sergio Fernando Castillo Pacheco
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; (C.A.); (F.G.); (S.P.); (S.F.C.P.); (S.L.)
| | - Giancarlo Pecorari
- Otorhinolaryngology Division, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy; (G.R.); (G.P.)
| | - Santo Landolfo
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; (C.A.); (F.G.); (S.P.); (S.F.C.P.); (S.L.)
| | - Matteo Biolatti
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; (C.A.); (F.G.); (S.P.); (S.F.C.P.); (S.L.)
| | - Valentina Dell’Oste
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; (C.A.); (F.G.); (S.P.); (S.F.C.P.); (S.L.)
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30
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Human Papillomavirus in Sinonasal Squamous Cell Carcinoma: A Systematic Review and Meta-Analysis. Cancers (Basel) 2020; 13:cancers13010045. [PMID: 33561073 PMCID: PMC7796014 DOI: 10.3390/cancers13010045] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
Simple Summary The causative role of human papillomavirus (HPV) in sinonasal squamous cell carcinoma (SNSCC) remains unclear and is hindered by small studies using variable HPV detection techniques. This meta-analysis aims to provide an updated overview of HPV prevalence in SNSCC stratified by detection method, anatomic subsite, and geographic region. From 60 eligible studies, an overall HPV prevalence was estimated at 26%. When stratified by detection method, HPV prevalence was lower when using multiple substrate testing compared to single substrate testing. Anatomic subsite HPV prevalence was higher in subsites with high exposure to secretion flow compared to low exposure subsites. HPV prevalence in SNSCC followed the global distribution of HPV+ oropharyngeal squamous cell carcinoma. Taken together, this meta-analysis further supports a role for HPV in a subset of SNSCCs. Abstract Human papillomavirus (HPV) drives tumorigenesis in a subset of oropharyngeal squamous cell carcinomas (OPSCC) and is increasing in prevalence across the world. Mounting evidence suggests HPV is also involved in a subset of sinonasal squamous cell carcinomas (SNSCC), yet small sample sizes and variability of HPV detection techniques in existing literature hinder definitive conclusions. A systematic review was performed by searching literature through March 29th 2020 using PubMed, Embase, and Web of Science Core Collection databases. Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed by two authors independently. A meta-analysis was performed using the random-effects model. Sixty studies (n = 1449) were eligible for statistical analysis estimating an overall HPV prevalence of 25.5% (95% CI 20.7–31.0). When stratified by HPV detection method, prevalence with multiple substrate testing (20.5%, 95% CI 14.5–28.2) was lower than with single substrate testing (31.7%, 95% CI 23.6–41.1), highest in high-exposure anatomic subsites (nasal cavity and ethmoids) (37.6%, 95% CI 26.5–50.2) vs. low-exposure (15.1%, 95% CI 7.3–28.6) and highest in high HPV+ OPSCC prevalence geographic regions (North America) (30.9%, 95% CI 21.9–41.5) vs. low (Africa) (13.1, 95% CI 6.5–24.5)). While small sample sizes and variability in data cloud firm conclusions, here, we provide a new reference point prevalence for HPV in SNSCC along with orthogonal data supporting a causative role for virally driven tumorigenesis, including that HPV is more commonly found in sinonasal subsites with increased exposure to refluxed oropharyngeal secretions and in geographic regions where HPV+ OPSCC is more prevalent.
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31
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[Tumor biology of oropharyngeal carcinoma]. HNO 2020; 69:249-255. [PMID: 33215226 DOI: 10.1007/s00106-020-00964-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Etiologically, oropharyngeal squamous cell carcinoma (OPSCC) can be divided into OPSCC caused by noxious agents and human papillomavirus (HPV)-driven carcinoma. These types differ with regard to clinical features and prognosis-differences which are rooted in the underlying molecular biology of the tumor. OBJECTIVE The aim of this work is to provide an overview of the molecular biological characteristics of the genetics, epigenetics, and immunology of OPSCC. MATERIALS AND METHODS A literature review was performed on a selection of genetic, epigenetic, and immunological factors characterizing OPSCC. RESULTS The understanding of genetic aberrations and their consequences for cancerogenesis and tumor biology is increasing. Epigenetic phenomena are complementing functional relationships. However, epigenetic mechanisms of gene regulation are complex and much research is still required in this field. Immunological aspects of cancer molecular biology have moved into the focus in light of recent advances in the field of immunotherapy. CONCLUSION The tumor biology of OPSCC is primarily defined by its HPV status. Additionally, HPV-independent genetic, epigenetic, and immunological signatures are being defined. From these advances, rationales for new treatment concepts may evolve.
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Faden DL, Langenbucher A, Kuhs K, Lewis JS, Mirabello L, Yeager M, Boland JF, Bass S, Steinberg M, Cullen M, Lawrence MS, Ferris RL. HPV+ oropharyngeal squamous cell carcinomas from patients with two tumors display synchrony of viral genomes yet discordant mutational profiles and signatures. Carcinogenesis 2020; 42:14-20. [PMID: 33075810 PMCID: PMC8014522 DOI: 10.1093/carcin/bgaa111] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/09/2020] [Accepted: 10/15/2020] [Indexed: 12/22/2022] Open
Abstract
Human papillomavirus (HPV) positive oropharyngeal squamous cell carcinoma (HPV + OPSCC) is increasing in prevalence in the USA, as are cases of patients with multiple HPV + OPSCCs (mHPV + OPSCC). mHPV + OPSCCs present a unique opportunity to examine HPV + OPSCC mutation acquisition and evolution. We performed sequencing of the viral genome, somatic exome and somatic transcriptome from 8 patients each with 2 spatially distinct HPV + OPSCCs, and 37 'traditional' HPV + OPSCCs to first address if paired tumors are caused by the same viral isolate and next, if acquired alterations, and the underlying processes driving mutagenesis, are shared within pairs. All tumor pairs contained viral genomes from the same HPV type 16 sublineage and differed by 0-2 clonal single nucleotide polymorphisms (SNPs), suggesting infection with the same viral isolate. Despite this, there was significant discordance in expression profiles, mutational burden and mutational profiles between tumors in a pair, with only two pairs sharing any overlapping mutations (3/3343 variants). Within tumor pairs there was a striking discrepancy of mutational signatures, exemplified by no paired tumors sharing high APOBEC mutational burden. Here, leveraging mHPV + OPSCCs as a model system to study mutation acquisition in virally mediated tumors, in which the germline, environmental exposures, immune surveillance and tissue/organ type were internally controlled, we demonstrate that despite infection by the same viral isolate, paired mHPV + OPSCCs develop drastically different somatic alterations and even more strikingly, appear to be driven by disparate underlying mutational processes. Thus, despite a common starting point, HPV + OPSCCs evolve through variable mutational processes with resultant stochastic mutational profiles.
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Affiliation(s)
- Daniel L Faden
- Department of Otolaryngology—Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA,Massachusetts General Hospital, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,To whom correspondence should be addressed. 243 Charles Street, Boston, MA 02114, USA. Tel: +1 617 807 7882; Fax: +1 587 206 7220;
| | | | - Krystle Kuhs
- Department of Medicine, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James S Lewis
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA,Department of Otolaryngology—Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Joseph F Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Sara Bass
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Mia Steinberg
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Michael Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Michael S Lawrence
- Massachusetts General Hospital, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robert L Ferris
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA,Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA,UPMC Hillman Cancer Center, Pittsburgh, PA, USA
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33
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Wang HC, Yeh TJ, Chan LP, Hsu CM, Cho SF. Exploration of Feasible Immune Biomarkers for Immune Checkpoint Inhibitors in Head and Neck Squamous Cell Carcinoma Treatment in Real World Clinical Practice. Int J Mol Sci 2020; 21:E7621. [PMID: 33076306 PMCID: PMC7589088 DOI: 10.3390/ijms21207621] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023] Open
Abstract
Recurrent locally advanced or metastatic head and neck squamous cell carcinoma (HNSCC) is associated with dismal prognosis because of its highly invasive behavior and resistance to conventional intensive chemotherapy. The combination of targeted therapy and conventional chemotherapy has significantly improved clinical outcomes. In recent years, the development of immunotherapies, such as immune checkpoint inhibitors (ICIs), has further increased treatment responses and prolonged survival. However, the limited response rate, risk of immunotherapy-related adverse effects and high cost of immunotherapy make the identification of predictive markers to optimize treatment efficacy a critical issue. Biomarkers are biological molecules that have been widely utilized to predict treatment response to certain treatments and clinical outcomes or to detect disease. An ideal biomarker should exhibit good predictive ability, which can guide healthcare professionals to achieve optimal treatment goals and bring clinical benefit to patients. In this review, we summarized the results of recent and important studies focused on HNSCC ICI immunotherapy and discussed potential biomarkers including their strengths and limitations, aiming to gain more insight into HNSCC immunotherapy in real world clinical practice.
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Affiliation(s)
- Hui-Ching Wang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.W.); (T.-J.Y.); (L.-P.C.)
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Tsung-Jang Yeh
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.W.); (T.-J.Y.); (L.-P.C.)
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Leong-Perng Chan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.W.); (T.-J.Y.); (L.-P.C.)
- Department of Otolaryngology-Head and Neck Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chin-Mu Hsu
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Shih-Feng Cho
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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34
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Xu L, Jin Y, Qin X. Comprehensive analysis of significant genes and immune cell infiltration in HPV-related head and neck squamous cell carcinoma. Int Immunopharmacol 2020; 87:106844. [DOI: 10.1016/j.intimp.2020.106844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/28/2020] [Accepted: 07/25/2020] [Indexed: 12/21/2022]
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35
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Fialová A, Koucký V, Hajdušková M, Hladíková K, Špíšek R. Immunological Network in Head and Neck Squamous Cell Carcinoma-A Prognostic Tool Beyond HPV Status. Front Oncol 2020; 10:1701. [PMID: 33042814 PMCID: PMC7522596 DOI: 10.3389/fonc.2020.01701] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/30/2020] [Indexed: 12/31/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a highly heterogeneous disease that affects more than 800,000 patients worldwide each year. The variability of HNSCC is associated with differences in the carcinogenesis processes that are caused by two major etiological agents, namely, alcohol/tobacco, and human papillomavirus (HPV). Compared to non-virally induced carcinomas, the oropharyngeal tumors associated with HPV infection show markedly better clinical outcomes and are characterized by an immunologically “hot” landscape with high levels of tumor-infiltrating lymphocytes. However, the standard of care remains the same for both HPV-positive and HPV-negative HNSCC. Surprisingly, treatment de-escalation trials have not shown any clinical benefit in patients with HPV-positive tumors to date, most likely due to insufficient patient stratification. The in-depth analysis of the immune response, which places an emphasis on tumor-infiltrating immune cells, is a widely accepted prognostic tool that might significantly improve both the stratification of HNSCC patients in de-escalation trials and the development of novel immunotherapeutic approaches.
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Affiliation(s)
| | - Vladimír Koucký
- Sotio, Prague, Czechia.,Department of Otorhinolaryngology and Head and Neck Surgery, First Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czechia
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36
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Association between APOBEC3H-Mediated Demethylation and Immune Landscape in Head and Neck Squamous Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4612375. [PMID: 32775421 PMCID: PMC7397441 DOI: 10.1155/2020/4612375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/31/2020] [Accepted: 06/25/2020] [Indexed: 12/18/2022]
Abstract
Immunotherapy has been demonstrated as a promising strategy in controlling head and neck squamous cell carcinoma (HNSC). The AID/APOBEC family is well characterized as DNA mutator and considered to play critical roles in immune responses in HNSC. However, the expression pattern and deamination-dependent demethylation roles of AID/APOBECs in HNSC are unclear. In this study, the RNA-seq and DNA methylation profiles of HNSC from TCGA database and cell-based experiments were applied to analyze the relationships between AID/APOBEC expression levels, patients' clinical outcomes, methylation alterations, and immune responses. Here, we found that APOBEC3H was abnormally upregulated in HNSC patients. HPV+ patients tended to have higher APOBEC3H levels than HPV- patients. Remarkably, patients with high APOBEC3H levels showed a favorable overall survival. Furthermore, tumors with high APOBEC3H levels exhibited a genome-wide DNA hypomethylation pattern. APOBEC3H was identified to demethylate and upregulate CXCL10 and improve CD8+ T cell tumor infiltration in the tumor microenvironment. Collectively, APOBEC3H plays critical roles in CD8+ T cell immune infiltration and activation in HNSC, which may be a potential biomarker for oncoimmunotherapy in HNSC.
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37
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Messerschmidt C, Obermayer B, Klinghammer K, Ochsenreither S, Treue D, Stenzinger A, Glimm H, Fröhling S, Kindler T, Brandts CH, Schulze-Osthoff K, Weichert W, Tinhofer I, Klauschen F, Keilholz U, Beule D, Rieke DT. Distinct immune evasion in APOBEC-enriched, HPV-negative HNSCC. Int J Cancer 2020; 147:2293-2302. [PMID: 32468570 DOI: 10.1002/ijc.33123] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/06/2020] [Accepted: 05/11/2020] [Indexed: 12/20/2022]
Abstract
Immune checkpoint inhibition leads to response in some patients with head and neck squamous cell carcinoma (HNSCC). Robust biomarkers are lacking to date. We analyzed viral status, gene expression signatures, mutational load and mutational signatures in whole exome and RNA-sequencing data of the HNSCC TCGA dataset (n = 496) and a validation set (DKTK MASTER cohort, n = 10). Public single-cell gene expression data from 17 HPV-negative HNSCC were separately reanalyzed. APOBEC3-associated TCW motif mutations but not total single nucleotide variant burden were significantly associated with inflammation. This association was restricted to HPV-negative HNSCC samples. An APOBEC-enriched, HPV-negative subgroup was identified, that showed higher T-cell inflammation and immune checkpoint expression, as well as expression of APOBEC3 genes. Mutations in immune-evasion pathways were also enriched in these tumors. Analysis of single-cell sequencing data identified expression of APOBEC3B and 3C genes in malignant cells. We identified an APOBEC-enriched subgroup of HPV-negative HNSCC with a distinct immunogenic phenotype, potentially mediating response to immunotherapy.
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Affiliation(s)
- Clemens Messerschmidt
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Berlin, Germany.,Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Benedikt Obermayer
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Berlin, Germany.,Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Konrad Klinghammer
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Hindenburgdamm 30, Berlin, 12203, Germany
| | - Sebastian Ochsenreither
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Hindenburgdamm 30, Berlin, 12203, Germany.,Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Denise Treue
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Albrecht Stenzinger
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hanno Glimm
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), Dresden, Germany.,University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Kindler
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Hematology, Medical Oncology & Pneumology, University Medical Center, Mainz, Germany.,University Cancer Center Mainz (UCT), Johannes Gutenberg-University, Mainz, Germany
| | - Christian H Brandts
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,University Cancer Center Frankfurt (UCT), Goethe University Frankfurt, Frankfurt, Germany.,Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Klaus Schulze-Osthoff
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Interfaculty Institute of Biochemistry, Tübingen University, Tübingen, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, Technical University Munich, Munich, Germany
| | - Ingeborg Tinhofer
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Radiooncology and Radiotherapy, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Frederick Klauschen
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ulrich Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), Berlin, Germany.,Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Damian T Rieke
- Department of Hematology and Oncology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Hindenburgdamm 30, Berlin, 12203, Germany.,Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
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38
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Yoo SK, Song YS, Park YJ, Seo JS. Recent Improvements in Genomic and Transcriptomic Understanding of Anaplastic and Poorly Differentiated Thyroid Cancers. Endocrinol Metab (Seoul) 2020; 35:44-54. [PMID: 32207263 PMCID: PMC7090308 DOI: 10.3803/enm.2020.35.1.44] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 02/21/2020] [Accepted: 02/26/2020] [Indexed: 12/12/2022] Open
Abstract
Anaplastic thyroid cancer (ATC) is a lethal human cancer with a 5-year survival rate of less than 10%. Recently, its genomic and transcriptomic characteristics have been extensively elucidated over 5 years owing to advance in high throughput sequencing. These efforts have extended molecular understandings into the progression mechanisms and therapeutic vulnerabilities of aggressive thyroid cancers. In this review, we provide an overview of genomic and transcriptomic alterations in ATC and poorly-differentiated thyroid cancer, which are distinguished from differentiated thyroid cancers. Clinically relevant genomic alterations and deregulated signaling pathways will be able to shed light on more effective prevention and stratified therapeutic interventions for affected patients.
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Affiliation(s)
- Seong Keun Yoo
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Young Shin Song
- Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Young Joo Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea.
| | - Jeong Sun Seo
- Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam, Korea
- Gong-Wu Genomic Medicine Institute, Seoul National University Bundang Hospital, Seongnam, Korea
- Macrogen Inc., Seoul, Korea.
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39
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Karpathiou G, Dumollard JM, Peoc'h M. Laryngeal Tumor Microenvironment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1296:79-101. [PMID: 34185287 DOI: 10.1007/978-3-030-59038-3_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tumor microenvironment has been extensively studied in various forms of cancer, like head and neck squamous cell carcinoma. Progress in the field revealed the prognostic significance of the various components of the tumor's ecosystem and led to changes in treatment strategies, like including immunotherapy as an important tool. In this chapter, the microenvironment of tumors with a special interest in laryngeal cancer will be described. The issues assessed include innate immune response factors, like neutrophils, neutrophil extracellular traps (NET), platelets, macrophages M1 or M2, dendritic cells, natural killer cells, as well as adaptive immunity aspects, like cytotoxic, exhausted and regulatory T cells, and immune checkpoints (PD-1/PD-L1, CTLA4). Also, stroma-associated factors, like fibroblasts, fibrosis, extracellular matrix, vessels and perineural invasion, hypoxia and cancer metabolism aspects, as well as the pre-metastatic niche, exosomes and cGAS-STING, are reviewed.
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Affiliation(s)
- Georgia Karpathiou
- Pathology Department, North Hospital, University Hospital of Saint-Etienne, Saint-Priest-en-Jarez, France
| | - Jean Marc Dumollard
- Pathology Department, North Hospital, University Hospital of Saint-Etienne, Saint-Priest-en-Jarez, France
| | - Michel Peoc'h
- Pathology Department, North Hospital, University Hospital of Saint-Etienne, Saint-Priest-en-Jarez, France
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40
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Kok VC. Current Understanding of the Mechanisms Underlying Immune Evasion From PD-1/PD-L1 Immune Checkpoint Blockade in Head and Neck Cancer. Front Oncol 2020; 10:268. [PMID: 32185135 PMCID: PMC7058818 DOI: 10.3389/fonc.2020.00268] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/17/2020] [Indexed: 02/05/2023] Open
Abstract
Starting in 2014, large phase III clinical trials began to disclose the study results of using programmed death (PD)-1 immune checkpoint inhibitors (ICIs) (pembrolizumab, nivolumab) and PD-ligand (L)1 (atezolizumab, durvalumab, avelumab) ICIs immunotherapy in patients with advanced head and neck squamous cell carcinoma (HNSCC). In the recurrent and metastatic (R/M), cisplatin-refractory setting, nivolumab achieved a 2.2-fold increase of the median 1-year overall survival as compared with investigators' choice of salvage chemotherapy (36.0 vs. 16.6%). A paradigm shift to the winning regimen, pembrolizumab combined with platinum and infusional fluorouracil, has outperformed the past gold standard of cetuximab-based platinum and fluorouracil combination in terms of overall survival (median, 13.6 vs. 10.1 mo) when administered as the first-line treatment for R/M HNSCC. Nevertheless, many patients still did not respond to the PD-1/PD-L1 checkpoint inhibitor treatment, indicating innate, adapted, or quickly acquired resistance to the immunotherapy. The mechanisms of resistance to ICIs targeting the PD-1/PD-L1 signaling pathway in the context of HNSCC are the focus of this review. The past 5 years have seen improved understanding of the mechanisms underlying checkpoint inhibition resistance in tumor cells, such as: tumor cell adaption with malfunction of the antigen-presenting machinery via class I human leukocyte antigen (HLA), reintroduction of cyclin D-cyclin-dependent kinase (CDK) 4 complex to cell cycles, enrichment of CD44+ cancer stem-like cells, or development of inactivating mutation in IKZF1 gene; impairment of T-cell functions and proliferation through mutations in the interferon-γ-regulating genes, suppression of the stimulator of interferon genes (STING) pathway, or resulted from constitutional nutritional iron deficiency state; metabolic reprogramming by cancer cells with changes in metabolites such as GTP cyclohydrolase 1, tetrahydrobiopterin, kynurenine, indoleamine 2,3-dioxygenase, and arginase 1; defective dendritic cells, CD-69 sufficient state; and the upregulation or activation of the alternative immune checkpoints, including lymphocyte activation gene-3 (LAG3), T-cell immunoglobulin and ITIM domain (TIGIT)/CD155 pathway, T-cell immunoglobulin mucin-3 (TIM-3), and V domain-containing Ig suppressor of T-cell activation (VISTA). Several potential biomarkers or biosignatures, which could predict the response or resistance to the PD-1/PD-L1 checkpoint immunotherapy, are also discussed.
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Affiliation(s)
- Victor C. Kok
- Department of Medical Oncology, Kuang Tien General Hospital Cancer Center, Taichung, Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University Taiwan, Taichung, Taiwan
- *Correspondence: Victor C. Kok
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