1
|
Garcia-Marquez MA, Thelen M, Bauer E, Maas L, Wennhold K, Lehmann J, Keller D, Nikolić M, George J, Zander T, Schröder W, Müller P, Yazbeck AM, Bruns C, Thomas R, Gathof B, Quaas A, Peifer M, Hillmer AM, von Bergwelt-Baildon M, Schlößer HA. Germline homozygosity and allelic imbalance of HLA-I are common in esophagogastric adenocarcinoma and impair the repertoire of immunogenic peptides. J Immunother Cancer 2024; 12:e007268. [PMID: 38631707 PMCID: PMC11029431 DOI: 10.1136/jitc-2023-007268] [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] [Accepted: 03/17/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND The individual HLA-I genotype is associated with cancer, autoimmune diseases and infections. This study elucidates the role of germline homozygosity or allelic imbalance of HLA-I loci in esophago-gastric adenocarcinoma (EGA) and determines the resulting repertoires of potentially immunogenic peptides. METHODS HLA genotypes and sequences of either (1) 10 relevant tumor-associated antigens (TAAs) or (2) patient-specific mutation-associated neoantigens (MANAs) were used to predict good-affinity binders using an in silico approach for MHC-binding (www.iedb.org). Imbalanced or lost expression of HLA-I-A/B/C alleles was analyzed by transcriptome sequencing. FluoroSpot assays and TCR sequencing were used to determine peptide-specific T-cell responses. RESULTS We show that germline homozygosity of HLA-I genes is significantly enriched in EGA patients (n=80) compared with an HLA-matched reference cohort (n=7605). Whereas the overall mutational burden is similar, the repertoire of potentially immunogenic peptides derived from TAAs and MANAs was lower in homozygous patients. Promiscuity of peptides binding to different HLA-I molecules was low for most TAAs and MANAs and in silico modeling of the homozygous to a heterozygous HLA genotype revealed normalized peptide repertoires. Transcriptome sequencing showed imbalanced expression of HLA-I alleles in 75% of heterozygous patients. Out of these, 33% showed complete loss of heterozygosity, whereas 66% had altered expression of only one or two HLA-I molecules. In a FluoroSpot assay, we determined that peptide-specific T-cell responses against NY-ESO-1 are derived from multiple peptides, which often exclusively bind only one HLA-I allele. CONCLUSION The high frequency of germline homozygosity in EGA patients suggests reduced cancer immunosurveillance leading to an increased cancer risk. Therapeutic targeting of allelic imbalance of HLA-I molecules should be considered in EGA.
Collapse
Affiliation(s)
- Maria Alejandra Garcia-Marquez
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Martin Thelen
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Eugen Bauer
- Institute of Transfusion Medicine, University of Cologne, Cologne, Germany
| | - Lukas Maas
- Department of Translational Genomics, University of Cologne, Cologne, Germany
| | - Kerstin Wennhold
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Jonas Lehmann
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Diandra Keller
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Miloš Nikolić
- Department of Translational Genomics, University of Cologne, Cologne, Germany
| | - Julie George
- Department of Translational Genomics, University of Cologne, Cologne, Germany
- Department of Otorhinolaryngology Head and Neck Surgery, University Hospital Cologne, Cologne, Germany
| | - Thomas Zander
- Department I of Internal Medicine and Center for Integrated Oncology (CIO) Aachen Bonn Cologne Duesseldorf, University Hospital Cologne, Cologne, Germany
| | - Wolfgang Schröder
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Philipp Müller
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Ali M Yazbeck
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Christiane Bruns
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| | - Roman Thomas
- Department of Translational Genomics, University of Cologne, Cologne, Germany
- Institute of Pathology, University of Cologne, Cologne, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Birgit Gathof
- Institute of Transfusion Medicine, University of Cologne, Cologne, Germany
| | - Alexander Quaas
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Martin Peifer
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of Translational Genomics, University of Cologne, Cologne, Germany
| | - Axel M Hillmer
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Michael von Bergwelt-Baildon
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Gene Centre, Ludwig Maximilians University Munich, Munchen, Germany
- Department of Medicine III, Ludwig Maximilians University Munich, Munchen, Germany
| | - Hans Anton Schlößer
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Department of General, Visceral, Cancer and Transplantation Surgery, University of Cologne, Cologne, Germany
| |
Collapse
|
2
|
Saigí M, Mate JL, Carcereny E, Martínez-Cardús A, Esteve A, Andreo F, Centeno C, Cucurull M, Mesia R, Pros E, Sanchez-Cespedes M. HLA-I levels correlate with survival outcomes in response to immune checkpoint inhibitors in non-small cell lung cancer. Lung Cancer 2024; 189:107502. [PMID: 38359742 DOI: 10.1016/j.lungcan.2024.107502] [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: 10/03/2023] [Revised: 01/16/2024] [Accepted: 02/04/2024] [Indexed: 02/17/2024]
Abstract
OBJECTIVES Immune checkpoint inhibitors (ICIs) have provided a breakthrough in the treatment of non-small cell lung cancer (NSCLC) patients, but only some patients benefit substantively. Identifying definitive predictive biomarkers could overcome this limitation. MATERIALS AND METHODS We selected 146 metastatic NSCLC patients treated with anti-PD-(L)1. Immunohistochemistry of HLA-I, PD-L1 and CD73 was performed in 122 tumor biopsies at diagnosis. The association with patients, tumor parameters, and the predictive value to ICI treatment were determined. RESULTS In our cohort, 42 %, 25 %, and 21 % of the tumors exhibited high levels of HLA-I, PD-L1, and CD73, respectively. Lung adenocarcinomas displayed elevated CD73 levels, compared with lung squamous cell carcinomas (P = 0.026). High PD-L1 was significantly correlated with high levels of HLA-I (P = 0.005) and of CD73 (P = 0.025). Patients with high-level HLA-I tumors exhibited more favorable clinical outcomes following ICI, with a median overall survival of 30.7 months (95 % confidence interval [CI]: 18.3 months-not reached), compared with 18.2 months (95 % CI: 12.4-25.2 months) in patients with low-level HLA-I tumors (P = 0.016). The median progression-free survival (PFS) for patients with high-level HLA-I tumors was 18.5 months (95 % CI: 11.1-57.1 months), longer than patients with low-level HLA-I tumors, whose median PFS was 9.2 months (95 % CI: 7.2-11.9 months) (P = 0.006). In a multivariable analysis, high-level HLA-I was independently associated with lower risk of progression to ICI (HR = 0.46, 95 % CI 0.24-0.87; P = 0.018). CONCLUSIONS High-level HLA-I were associated with better clinical outcomes to ICI in our cohort of NSCLC patients. Therefore, further investigations are warranted to refine this biomarker and validate its efficacy in prospective and larger set of patients.
Collapse
Affiliation(s)
- Maria Saigí
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Badalona, Barcelona, Spain; Badalona·Applied Research Group in Oncology (B·ARGO), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain.
| | - Jose L Mate
- Department of Pathology, Germans Trias i Pujol University Hospital, Badalona, Barcelona, Spain
| | - Enric Carcereny
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Badalona, Barcelona, Spain; Badalona·Applied Research Group in Oncology (B·ARGO), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Anna Martínez-Cardús
- Badalona·Applied Research Group in Oncology (B·ARGO), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Anna Esteve
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Badalona, Barcelona, Spain; Statistics Department, Catalan Institute of Oncology (ICO)-Badalona, Badalona, Barcelona, Spain
| | - Felipe Andreo
- Pulmonology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Carmen Centeno
- Pulmonology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Marc Cucurull
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Badalona, Barcelona, Spain; Badalona·Applied Research Group in Oncology (B·ARGO), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Ricard Mesia
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Badalona, Barcelona, Spain; Badalona·Applied Research Group in Oncology (B·ARGO), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Eva Pros
- Cancer Genetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Montse Sanchez-Cespedes
- Cancer Genetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain.
| |
Collapse
|
3
|
Marzouka NAD, Alnaqbi H, Al-Aamri A, Tay G, Alsafar H. Investigating the genetic makeup of the major histocompatibility complex (MHC) in the United Arab Emirates population through next-generation sequencing. Sci Rep 2024; 14:3392. [PMID: 38337023 PMCID: PMC10858242 DOI: 10.1038/s41598-024-53986-1] [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: 11/26/2023] [Accepted: 02/07/2024] [Indexed: 02/12/2024] Open
Abstract
The Human leukocyte antigen (HLA) molecules are central to immune response and have associations with the phenotypes of various diseases and induced drug toxicity. Further, the role of HLA molecules in presenting antigens significantly affects the transplantation outcome. The objective of this study was to examine the extent of the diversity of HLA alleles in the population of the United Arab Emirates (UAE) using Next-Generation Sequencing methodologies and encompassing a larger cohort of individuals. A cohort of 570 unrelated healthy citizens of the UAE volunteered to provide samples for Whole Genome Sequencing and Whole Exome Sequencing. The definition of the HLA alleles was achieved through the application of the bioinformatics tools, HLA-LA and xHLA. Subsequently, the findings from this study were compared with other local and international datasets. A broad range of HLA alleles in the UAE population, of which some were previously unreported, was identified. A comparison with other populations confirmed the current population's unique intertwined genetic heritage while highlighting similarities with populations from the Middle East region. Some disease-associated HLA alleles were detected at a frequency of > 5%, such as HLA-B*51:01, HLA-DRB1*03:01, HLA-DRB1*15:01, and HLA-DQB1*02:01. The increase in allele homozygosity, especially for HLA class I genes, was identified in samples with a higher level of genome-wide homozygosity. This highlights a possible effect of consanguinity on the HLA homozygosity. The HLA allele distribution in the UAE population showcases a unique profile, underscoring the need for tailored databases for traditional activities such as unrelated transplant matching and for newer initiatives in precision medicine based on specific populations. This research is part of a concerted effort to improve the knowledge base, particularly in the fields of transplant medicine and investigating disease associations as well as in understanding human migration patterns within the Arabian Peninsula and surrounding regions.
Collapse
Affiliation(s)
- Nour Al Dain Marzouka
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Halima Alnaqbi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Amira Al-Aamri
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan Tay
- Division of Psychiatry, Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
- College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
| |
Collapse
|
4
|
Lim WC, Marques Da Costa ME, Godefroy K, Jacquet E, Gragert L, Rondof W, Marchais A, Nhiri N, Dalfovo D, Viard M, Labaied N, Khan AM, Dessen P, Romanel A, Pasqualini C, Schleiermacher G, Carrington M, Zitvogel L, Scoazec JY, Geoerger B, Salmon J. Divergent HLA variations and heterogeneous expression but recurrent HLA loss-of- heterozygosity and common HLA-B and TAP transcriptional silencing across advanced pediatric solid cancers. Front Immunol 2024; 14:1265469. [PMID: 38318504 PMCID: PMC10839790 DOI: 10.3389/fimmu.2023.1265469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/06/2023] [Indexed: 02/07/2024] Open
Abstract
The human leukocyte antigen (HLA) system is a major factor controlling cancer immunosurveillance and response to immunotherapy, yet its status in pediatric cancers remains fragmentary. We determined high-confidence HLA genotypes in 576 children, adolescents and young adults with recurrent/refractory solid tumors from the MOSCATO-01 and MAPPYACTS trials, using normal and tumor whole exome and RNA sequencing data and benchmarked algorithms. There was no evidence for narrowed HLA allelic diversity but discordant homozygosity and allele frequencies across tumor types and subtypes, such as in embryonal and alveolar rhabdomyosarcoma, neuroblastoma MYCN and 11q subtypes, and high-grade glioma, and several alleles may represent protective or susceptibility factors to specific pediatric solid cancers. There was a paucity of somatic mutations in HLA and antigen processing and presentation (APP) genes in most tumors, except in cases with mismatch repair deficiency or genetic instability. The prevalence of loss-of-heterozygosity (LOH) ranged from 5.9 to 7.7% in HLA class I and 8.0 to 16.7% in HLA class II genes, but was widely increased in osteosarcoma and glioblastoma (~15-25%), and for DRB1-DQA1-DQB1 in Ewing sarcoma (~23-28%) and low-grade glioma (~33-50%). HLA class I and HLA-DR antigen expression was assessed in 194 tumors and 44 patient-derived xenografts (PDXs) by immunochemistry, and class I and APP transcript levels quantified in PDXs by RT-qPCR. We confirmed that HLA class I antigen expression is heterogeneous in advanced pediatric solid tumors, with class I loss commonly associated with the transcriptional downregulation of HLA-B and transporter associated with antigen processing (TAP) genes, whereas class II antigen expression is scarce on tumor cells and occurs on immune infiltrating cells. Patients with tumors expressing sufficient HLA class I and TAP levels such as some glioma, osteosarcoma, Ewing sarcoma and non-rhabdomyosarcoma soft-tissue sarcoma cases may more likely benefit from T cell-based approaches, whereas strategies to upregulate HLA expression, to expand the immunopeptidome, and to target TAP-independent epitopes or possibly LOH might provide novel therapeutic opportunities in others. The consequences of HLA class II expression by immune cells remain to be established. Immunogenetic profiling should be implemented in routine to inform immunotherapy trials for precision medicine of pediatric cancers.
Collapse
Affiliation(s)
- Wan Ching Lim
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia
| | | | - Karine Godefroy
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Loren Gragert
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Windy Rondof
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Antonin Marchais
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Naima Nhiri
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Davide Dalfovo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Mathias Viard
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Nizar Labaied
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Asif M. Khan
- School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia
| | - Philippe Dessen
- Bioinformatics Platform, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Alessandro Romanel
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Claudia Pasqualini
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Gudrun Schleiermacher
- INSERM U830, Recherche Translationnelle en Oncologie Pédiatrique (RTOP), and SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), PSL Research University, Institut Curie, Paris, France
| | - Mary Carrington
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, United States
| | - Laurence Zitvogel
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Jean-Yves Scoazec
- Department of Pathology and Laboratory Medicine, Translational Research Laboratory and Biobank, AMMICA, INSERM US23/CNRS UMS3655, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Birgit Geoerger
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Jerome Salmon
- INSERM U1015, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| |
Collapse
|
5
|
de Joode K, Heersche N, Basak EA, Bins S, van der Veldt AAM, van Schaik RHN, Mathijssen RHJ. Review - The impact of pharmacogenetics on the outcome of immune checkpoint inhibitors. Cancer Treat Rev 2024; 122:102662. [PMID: 38043396 DOI: 10.1016/j.ctrv.2023.102662] [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: 10/04/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/05/2023]
Abstract
The development of immune checkpoint inhibitors (ICIs) has a tremendous effect on the treatment options for multiple types of cancer. Nonetheless, there is a large interpatient variability in response, survival, and the development of immune-related adverse events (irAEs). Pharmacogenetics is the general term for germline genetic variations, which may cause the observed interindividual differences in response or toxicity to treatment. These genetic variations can either be single-nucleotide polymorphisms (SNPs) or structural variants, such as gene deletions, amplifications or rearrangements. For ICIs, pharmacogenetic variation in the human leukocyte antigen molecules has also been studied with regard to treatment outcome. This review presents a summary of the literature regarding the pharmacogenetics of ICI treatment, discusses the most important known genetic variations and offers recommendations on the application of pharmacogenetics for ICI treatment.
Collapse
Affiliation(s)
- Karlijn de Joode
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Niels Heersche
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Department of Clinical Chemistry, Erasmus MC, Erasmus University Hospital, Rotterdam, the Netherlands
| | - Edwin A Basak
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Sander Bins
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Astrid A M van der Veldt
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands; Department of Radiology & Nuclear Medicine, Erasmus MC, Erasmus University Hospital, Rotterdam, the Netherlands
| | - Ron H N van Schaik
- Department of Clinical Chemistry, Erasmus MC, Erasmus University Hospital, Rotterdam, the Netherlands
| | - Ron H J Mathijssen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
| |
Collapse
|
6
|
Lee CK, Lee JB, Park SJ, Che J, Kwon WS, Kim HS, Jung M, Lee S, Park SR, Koo DH, Lee HW, Bae WK, Jeung HC, Hwang IG, Kim H, Nam CM, Chung HC, Rha SY. Second-line chemoimmunotherapy with nivolumab and paclitaxel in immune-related biomarker-enriched advanced gastric cancer: a multicenter phase Ib/II study. Gastric Cancer 2024; 27:118-130. [PMID: 37906316 DOI: 10.1007/s10120-023-01435-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/29/2023] [Indexed: 11/02/2023]
Abstract
BACKGROUND We conducted a trial to evaluate the efficacy and safety of nivolumab and paclitaxel as second-line therapy for immune-related biomarker-enriched advanced gastric cancer (AGC). METHODS This open-label, single-arm, phase Ib/II study was a part of multi-institutional, biomarker-integrated umbrella study conducted in Korea. In phase Ib, patients received nivolumab (3 mg/kg) on Days 1 and 15 and paclitaxel (dose level 1, 70 mg/m2 or dose level 2, 80 mg/m2) on Days 1, 8, 15 every four weeks. In phase II, patients with Epstein-Barr virus-related, deficient mismatch repair or programmed cell death-ligand-1-positive AGC were enrolled. The primary endpoints were recommended phase II dose (RP2D, phase Ib) and progression-free survival (PFS, phase II). Secondary endpoints included objective response rate (ORR), overall survival (OS), safety, and exploratory biomarker analysis. RESULTS Dose level 2 was selected as RP2D. In phase II, 48 patients were enrolled. The median PFS and OS were 3.9 and 11.2 months, respectively. The ORR was 23.3%, and the median response duration was 16.7 months. Grade 3 or higher treatment-related adverse events, mainly neutropenia, occurred in 20 patients (41.7%). Targeted sequencing revealed that patients with RTK/RAS pathway alterations or the HLA-A02 supertype had better survival. Patients with elevated baseline interleukin-1 receptor antagonist levels had worse survival. CONCLUSIONS Although the study did not meet its primary end point, nivolumab and paclitaxel for AGC demonstrated a durable response with manageable toxicity profiles. Genomic analysis or plasma cytokine analysis may provide information for the selection of patients who would benefit more from immunotherapy combined with chemotherapy.
Collapse
Affiliation(s)
- Choong-Kun Lee
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, 50-1 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, South Korea
| | - Jii Bum Lee
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, 50-1 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
| | - Se Jung Park
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, South Korea
| | - Jingmin Che
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, South Korea
| | - Woo Sun Kwon
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, South Korea
| | - Hyo Song Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, 50-1 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, South Korea
| | - Minkyu Jung
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, 50-1 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, South Korea
| | - Seulkee Lee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sook Ryun Park
- Division of Oncology, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Dong-Hoe Koo
- Division of Hematology/Oncology, Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hyun Woo Lee
- Department of Hematology-Oncology, Ajou University School of Medicine, Suwon, South Korea
| | - Woo Kyun Bae
- Division of Hematology and Oncology, Department of Internal Medicine, Chonnam National University Medical School and Hwasun Hospital, Jeonnam, South Korea
| | - Hei-Cheul Jeung
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - In Gyu Hwang
- Department of Internal Medicine, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Hyunki Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, South Korea
| | - Chung Mo Nam
- Department of Preventive Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Hyun Cheol Chung
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, 50-1 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, South Korea
| | - Sun Young Rha
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, 50-1 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, South Korea.
- Sondang Institute for Cancer Research, Yonsei University College of Medicine, Seoul, South Korea.
| |
Collapse
|
7
|
Eng C, Kim A, Yehia L. Genomic diversity in functionally relevant genes modifies neurodevelopmental versus neoplastic risks in individuals with germline PTEN variants. RESEARCH SQUARE 2023:rs.3.rs-3734368. [PMID: 38168271 PMCID: PMC10760312 DOI: 10.21203/rs.3.rs-3734368/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Individuals with germline PTEN variants (PHTS) have increased risks of the seemingly disparate phenotypes of cancer and neurodevelopmental disorders (NDD), including autism spectrum disorder (ASD). Etiology of the phenotypic variability remains elusive. Here, we hypothesized that decreased genomic diversity, manifested by increased homozygosity, may be one etiology. Comprehensive analyses of 376 PHTS patients of European ancestry revealed significant enrichment of homozygous common variants in genes involved in inflammatory processes in the PHTS-NDD group and in genes involved in differentiation and chromatin structure regulation in the PHTS-ASD group. Pathway analysis revealed pathways germane to NDD/ASD, including neuroinflammation and synaptogenesis. Collapsing analysis of the homozygous variants identified suggestive modifier NDD/ASD genes. In contrast, we found enrichment of homozygous ultra-rare variants in genes modulating cell death in the PHTS-cancer group. Finally, homozygosity burden as a predictor of ASD versus cancer outcomes in our validated prediction model for NDD/ASD performed favorably.
Collapse
|
8
|
Otálora-Otálora BA, López-Rivera JJ, Aristizábal-Guzmán C, Isaza-Ruget MA, Álvarez-Moreno CA. Host Transcriptional Regulatory Genes and Microbiome Networks Crosstalk through Immune Receptors Establishing Normal and Tumor Multiomics Metafirm of the Oral-Gut-Lung Axis. Int J Mol Sci 2023; 24:16638. [PMID: 38068961 PMCID: PMC10706695 DOI: 10.3390/ijms242316638] [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: 10/12/2023] [Revised: 11/13/2023] [Accepted: 11/18/2023] [Indexed: 12/18/2023] Open
Abstract
The microbiome has shown a correlation with the diet and lifestyle of each population in health and disease, the ability to communicate at the cellular level with the host through innate and adaptative immune receptors, and therefore an important role in modulating inflammatory process related to the establishment and progression of cancer. The oral cavity is one of the most important interaction windows between the human body and the environment, allowing the entry of an important number of microorganisms and their passage across the gastrointestinal tract and lungs. In this review, the contribution of the microbiome network to the establishment of systemic diseases like cancer is analyzed through their synergistic interactions and bidirectional crosstalk in the oral-gut-lung axis as well as its communication with the host cells. Moreover, the impact of the characteristic microbiota of each population in the formation of the multiomics molecular metafirm of the oral-gut-lung axis is also analyzed through state-of-the-art sequencing techniques, which allow a global study of the molecular processes involved of the flow of the microbiota environmental signals through cancer-related cells and its relationship with the establishment of the transcription factor network responsible for the control of regulatory processes involved with tumorigenesis.
Collapse
Affiliation(s)
| | - Juan Javier López-Rivera
- Grupo de Investigación INPAC, Specialized Laboratory, Clinica Universitaria Colombia, Clínica Colsanitas S.A., Bogotá 111321, Colombia;
| | - Claudia Aristizábal-Guzmán
- Grupo de Investigación INPAC, Unidad de Investigación, Fundación Universitaria Sanitas, Bogotá 110131, Colombia;
| | - Mario Arturo Isaza-Ruget
- Keralty, Sanitas International Organization, Grupo de Investigación INPAC, Fundación Universitaria Sanitas, Bogotá 110131, Colombia;
| | - Carlos Arturo Álvarez-Moreno
- Infectious Diseases Department, Clinica Universitaria Colombia, Clínica Colsanitas S.A., Bogotá 111321, Colombia;
| |
Collapse
|
9
|
Liu M, Li N, Tang H, Chen L, Liu X, Wang Y, Lin Y, Luo Y, Wei S, Wen W, Chen M, Wang J, Zhang N, Chen J. The Mutational, Prognostic, and Therapeutic Landscape of Neuroendocrine Neoplasms. Oncologist 2023; 28:e723-e736. [PMID: 37086484 PMCID: PMC10485279 DOI: 10.1093/oncolo/oyad093] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/11/2023] [Indexed: 04/24/2023] Open
Abstract
BACKGROUND Neuroendocrine neoplasms (NENs) represent clinically and genetically heterogeneous malignancies, thus a comprehensive understanding of underlying molecular characteristics, prognostic signatures, and potential therapeutic targets is urgently needed. METHODS Next-generation sequencing (NGS) and immunohistochemistry were applied to acquire genomic and immune profiles of NENs from 47 patients. RESULTS Difference was distinguished based on differentiation grade and primary localization. Poorly differentiated neuroendocrine carcinomas (NECs) and well-differentiated neuroendocrine tumors (NETs) harbored distinct molecular features; we observed that tumor mutational burden (TMB) and tumor neoantigen burden (TNB) were significantly higher in NECs versus NETs. Notably, we identified a 7-gene panel (MLH3, NACA, NOTCH1, NPAP1, RANBP17, TSC2, and ZFHX4) as a novel prognostic signature in NENs; patients who carried mutations in any of the 7 genes exhibited significantly poorer survival. Furthermore, loss of heterozygosity (LOH) and germline homogeneity in human leukocyte antigen (HLA) are common in NENs, accounting for 39% and 36%, respectively. Notably, HLA LOH was an important prognostic biomarker for a subgroup of NEN patients. Finally, we analyzed clinically actionable targets in NENs, revealing that TMB high (TMB-H) or gene mutations in TP53, KRAS, and HRAS were the most frequently observed therapeutic indicators, which granted eligibility to immune checkpoint blockade (ICB) and targeted therapy. CONCLUSION Our study revealed heterogeneity of NENs, and identified novel prognostic signatures and potential therapeutic targets, which directing improvements of clinical management for NEN patients in the foreseeable future.
Collapse
Affiliation(s)
- Man Liu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Na Li
- Department of Translational Medicine, YuceBio Technology Co., Ltd, Shenzhen, People’s Republic of China
| | - Hongzhen Tang
- Department of Medicine, YuceBio Technology Co., Ltd, Shenzhen, People’s Republic of China
| | - Luohai Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Xuemei Liu
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, People’s Republic of China
| | - Yu Wang
- Department of Interventional Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yuan Lin
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yanji Luo
- Department of Radiology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Shaozhen Wei
- Department of Translational Medicine, YuceBio Technology Co., Ltd, Shenzhen, People’s Republic of China
| | - Wenli Wen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Jiaqian Wang
- Department of Translational Medicine, YuceBio Technology Co., Ltd, Shenzhen, People’s Republic of China
| | - Ning Zhang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Jie Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai, People’s Republic of China
| |
Collapse
|
10
|
Yang K, Halima A, Chan TA. Antigen presentation in cancer - mechanisms and clinical implications for immunotherapy. Nat Rev Clin Oncol 2023; 20:604-623. [PMID: 37328642 DOI: 10.1038/s41571-023-00789-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2023] [Indexed: 06/18/2023]
Abstract
Over the past decade, the emergence of effective immunotherapies has revolutionized the clinical management of many types of cancers. However, long-term durable tumour control is only achieved in a fraction of patients who receive these therapies. Understanding the mechanisms underlying clinical response and resistance to treatment is therefore essential to expanding the level of clinical benefit obtained from immunotherapies. In this Review, we describe the molecular mechanisms of antigen processing and presentation in tumours and their clinical consequences. We examine how various aspects of the antigen-presentation machinery (APM) shape tumour immunity. In particular, we discuss genomic variants in HLA alleles and other APM components, highlighting their influence on the immunopeptidomes of both malignant cells and immune cells. Understanding the APM, how it is regulated and how it changes in tumour cells is crucial for determining which patients will respond to immunotherapy and why some patients develop resistance. We focus on recently discovered molecular and genomic alterations that drive the clinical outcomes of patients receiving immune-checkpoint inhibitors. An improved understanding of how these variables mediate tumour-immune interactions is expected to guide the more precise administration of immunotherapies and reveal potentially promising directions for the development of new immunotherapeutic approaches.
Collapse
Affiliation(s)
- Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA
| | - Ahmed Halima
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA
| | - Timothy A Chan
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA.
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA.
- National Center for Regenerative Medicine, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, Cleveland, OH, USA.
| |
Collapse
|
11
|
Chen G, Zhu W, Liu Y, Zhang L, Xie L, Song X, Song X. The clonal heterogeneity of colon cancer with liver metastases. J Gastroenterol 2023; 58:642-655. [PMID: 37042990 PMCID: PMC10307713 DOI: 10.1007/s00535-023-01989-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 03/29/2023] [Indexed: 04/13/2023]
Abstract
BACKGROUND Colon cancer with liver metastases (CCLM) characterized by genetic heterogeneity is an evolutionary process leading to variations in response to selective pressure, but the underlying evolutionary models still remains unclear. METHODS Total of 30 samples, including primary tumor and two to four matched liver metastases from 8 treatment-naïve patients with CCLM were collected, and subjected to whole-exome DNA sequencing. PyClone was used to calculate intra and inter-tumor heterogeneity, LICHeE was used to reconstruct the cancer phylogeny trees and investigate the subclonal composition. RESULTS The genetic differences were observed between primary and metastatic lesions, as well as among multiple metastases in all patients. The natural history models of colorectal cancer in each case were identified, including parallel, linear, and branching evolution. Liver metastases could originate from primary lesions or other metastases. Pathway and process enrichment analysis also showed obvious heterogeneity and enhancement of several molecular functions. CONCLUSIONS Our data reveal the genetic and heterogeneity between primary and metastatic lesions, as well as among multiple metastases and provide genomic evidence for clonal heterogeneity for CCLM.
Collapse
Affiliation(s)
- Guanxuan Chen
- Department of Intensive Care Unit, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Wanqi Zhu
- Department of Research and Education, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Yang Liu
- Shanghai OrigiMed Co., Ltd, Shanghai, People's Republic of China
| | - Liwen Zhang
- Shanghai OrigiMed Co., Ltd, Shanghai, People's Republic of China
| | - Li Xie
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Xingguo Song
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China.
| | - Xianrang Song
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China.
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China.
| |
Collapse
|
12
|
Wu X, Wang H, Xue F, Jiang T, Chen N, Wang T, Zhang Y, Zhang G, Fu J, Wu Q. Frequency changes in HLA-I alleles: A marker to guide immunotherapy in lung adenocarcinoma patients and its relationship with tumor mutational burden and PD-L1 expression. Thorac Cancer 2023; 14:1932-1940. [PMID: 37246469 PMCID: PMC10344735 DOI: 10.1111/1759-7714.14939] [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: 03/10/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND The aim of the study was to investigate differences in HLA-I alleles between lung adenocarcinoma patients and healthy controls and determine their association with PD-L1 expression and tumor mutational burden (TMB) to understand the mechanism underlying lung adenocarcinoma susceptibility. METHODS Differences in HLA allele frequencies between the two groups were analyzed in a case-control study. PD-L1 expression and TMB in lung adenocarcinoma patients were determined and their relationships with HLA-I were analyzed. RESULTS The lung adenocarcinoma group showed significantly higher HLA-A*30:01 (p = 0.0067, odds ratio [OR], 1.834; 95% confidence interval [CI]: 1.176-2.860), B*13:02 (p = 0.0050, OR, 1.855; 95% CI: 1.217-2.829), and C*06:02 (p = 0.0260, OR, 1.478; 95% CI: 1.060-2.060) and significantly lower B*51:01 (p = 0.0290, OR, 0.6019; 95% CI: 0.3827-0.9467), and C*14:02 (p = 0.0255, OR, 0.5089; 95% CI: 0.2781-0.9312) than the control group. Haplotype analysis results showed that HLA-A*30:01-B*13:02 (p = 0.0100, OR, 1.909; 95% CI: 1.182-3.085), A*11:01-C*01:02 (p = 0.0056, OR, 1.909; 95% CI: 1.182-3.085), A*30:01-C*06:02 (p = 0.0111, OR, 1.846; 95% CI: 1.147-2.969), and B*13:02-C*06:02 (p = 0.0067, OR, 1.846; 95% CI: 1.147-2.969) frequencies significantly increased and B*51:01-C*14:02 (p = 0.0219, OR, 0.490; 95% CI: 0.263-0.914) frequency significantly decreased in lung adenocarcinoma patients. Three-locus haplotype analysis showed that HLA-A*30:01-B*13:02-C*06:02 frequency (p = 0.0100, OR, 1.909; 95% CI: 1.182-3.085) significantly increased in patients. CONCLUSION HLA-A*30:01, B*13:02, and C*06:02 may be the susceptibility genes and HLA-B*51:01 and C*14:01 act as the resistance genes of lung adenocarcinoma. The changes in HLA-I allele frequencies had no association with PD-L1 expression and TMB among these patients.
Collapse
Affiliation(s)
- Xuanpeng Wu
- Department of Thoracic SurgeryThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Hao Wang
- Department of Thoracic SurgeryThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Fei Xue
- Department of Thoracic SurgeryThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Tao Jiang
- Department of Thoracic SurgeryThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Nanzheng Chen
- Department of Thoracic SurgeryThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Tianju Wang
- HLA Typing Laboratory, Blood Center of the Shaanxi ProvinceInstitute of Xi'an Blood BankXi'anChina
| | - Yong Zhang
- Department of Thoracic SurgeryThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Guangjian Zhang
- Department of Thoracic SurgeryThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Junke Fu
- Department of Thoracic SurgeryThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Qifei Wu
- Department of Thoracic SurgeryThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| |
Collapse
|
13
|
Homan EJ, Bremel RD. Determinants of tumor immune evasion: the role of T cell exposed motif frequency and mutant amino acid exposure. Front Immunol 2023; 14:1155679. [PMID: 37215122 PMCID: PMC10196236 DOI: 10.3389/fimmu.2023.1155679] [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: 01/31/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
Few neoepitopes detected in tumor biopsies are immunogenic. Tumor-specific T cell responses require both the presentation of an epitope that differs from wildtype and the presence of T cells with neoepitope-cognate receptors. We show that mutations detected in tumor biopsies result in an increased frequency of rare amino acid combinations compared to the human proteome and gastrointestinal microorganisms. Mutations in a large data set of oncogene and tumor suppressor gene products were compared to wildtype, and to the count of corresponding amino acid motifs in the human proteome and gastrointestinal microbiome. Mutant amino acids in T cell exposed positions of potential neoepitopes consistently generated amino acid motifs that are less common in both proteome reference datasets. Approximately 10% of the mutant amino acid motifs are absent from the human proteome. Motif frequency does not change when mutants were positioned in the MHC anchor positions hidden from T cell receptors. Analysis of neoepitopes in GBM and LUSC cases showed less common T cell exposed motifs, and HLA binding preferentially placing mutant amino acids in an anchor position for both MHC I and MHC II. Cross-presentation of mutant exposed neoepitopes by MHC I and MHC II was particularly uncommon. Review of a tumor mutation dataset known to generate T cell responses showed immunogenic epitopes were those with mutant amino acids exposed to the T cell receptor and with exposed pentamer motifs present in the human and microbiome reference databases. The study illustrates a previously unrecognized mechanism of tumor immune evasion, as rare T cell exposed motifs produced by mutation are less likely to have cognate T cells in the T cell repertoire. The complex interactions of HLA genotype, binding positions, and mutation specific changes in T cell exposed motif underscore the necessity of evaluating potential neoepitopes in each individual patient.
Collapse
|
14
|
Takahashi S, Narita S, Fujiyama N, Hatakeyama S, Kobayashi T, Kato R, Naito S, Sakatani T, Kashima S, Koizumi A, Yamamoto R, Nara T, Kanda S, Numakura K, Saito M, Obara W, Tsuchiya N, Ohyama C, Ogawa O, Habuchi T. Impact of germline HLA genotypes on clinical outcomes in patients with urothelial cancer treated with pembrolizumab. Cancer Sci 2022; 113:4059-4069. [PMID: 35848083 DOI: 10.1111/cas.15488] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 12/15/2022] Open
Abstract
Human leukocyte antigen class I (HLA-I) genotypes are suggested to influence the cancer response to checkpoint blockade immunotherapy. This study assessed the impact of germline HLA genotypes on clinical outcomes in patients with chemoresistant advanced urothelial cancer (UC) treated with pembrolizumab. Zygosity, supertypes, evolutionary divergency, and specific alleles of germline HLA-I and -II were evaluated using the Luminex technique in 108 patients with chemoresistant metastatic or locally advanced UC treated with pembrolizumab. Among the 108 patients, 69 died and 83 showed radiographic progression during follow-up. Homozygous for at least one HLA-I locus, absence of the HLA-A03 supertype, and high HLA-I evolutionary divergence were associated with a radiographic response, but were not associated with survival outcomes. Patients with the HLA-DQB1*03:01 allele had significantly lower disease control rates than patients without the allele (17.4% vs. 53.8%, p = 0.002); its presence was also an independent risk factor for progressive disease (hazard ratio 4.35, 95% confidence interval 1.03-18.46). Furthermore, patients with the HLA-DQB1*03:01 allele had significantly worse progression-free survival than patients without the allele (median progression-free survival 3.1 vs. 4.8 months, p = 0.035). There was no significant relationship between any HLA status and the incidence of severe adverse events. Several germline HLA genotypes, especially HLA-DQB1*03:01, may be associated with radiographic progression. However, their impact on treatment response is limited, and germline HLA genotypes was not independently associated with survival outcomes. Further prospective studies are needed to confirm the relationship between germline HLA genotypes and clinical outcomes in patients with chemoresistant advanced UC treated with pembrolizumab.
Collapse
Affiliation(s)
- Shuhei Takahashi
- Department of Urology, Akita University School of Medicine, Akita, Japan
| | - Shintaro Narita
- Department of Urology, Akita University School of Medicine, Akita, Japan
| | - Nobuhiro Fujiyama
- Clinical Research Support Center, Akita University Hospital, Akita, Japan
| | - Shingo Hatakeyama
- Department of Urology, Hirosaki University School of Medicine, Hirosaki, Japan
| | - Takashi Kobayashi
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Renpei Kato
- Department of Urology, Iwate Medical School of Medicine, Iwate, Japan
| | - Sei Naito
- Department of Urology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Toru Sakatani
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Soki Kashima
- Department of Urology, Akita University School of Medicine, Akita, Japan
| | - Atsushi Koizumi
- Department of Urology, Akita University School of Medicine, Akita, Japan
| | - Ryohei Yamamoto
- Department of Urology, Akita University School of Medicine, Akita, Japan
| | - Taketoshi Nara
- Department of Urology, Akita University School of Medicine, Akita, Japan
| | - Souhei Kanda
- Department of Urology, Akita University School of Medicine, Akita, Japan
| | - Kazuyuki Numakura
- Department of Urology, Akita University School of Medicine, Akita, Japan
| | - Mitsuru Saito
- Department of Urology, Akita University School of Medicine, Akita, Japan
| | - Wataru Obara
- Department of Urology, Iwate Medical School of Medicine, Iwate, Japan
| | - Norihiko Tsuchiya
- Department of Urology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Chikara Ohyama
- Department of Urology, Hirosaki University School of Medicine, Hirosaki, Japan
| | - Osamu Ogawa
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomonori Habuchi
- Department of Urology, Akita University School of Medicine, Akita, Japan
| |
Collapse
|
15
|
Bigelow E, Saria S, Piening B, Curti B, Dowdell A, Weerasinghe R, Bifulco C, Urba W, Finkelstein N, Fertig EJ, Baras A, Zaidi N, Jaffee E, Yarchoan M. A Random Forest Genomic Classifier for Tumor Agnostic Prediction of Response to Anti-PD1 Immunotherapy. Cancer Inform 2022; 21:11769351221136081. [PMID: 36439024 PMCID: PMC9685115 DOI: 10.1177/11769351221136081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
Tumor mutational burden (TMB), a surrogate for tumor neoepitope burden, is used as a pan-tumor biomarker to identify patients who may benefit from anti-program cell death 1 (PD1) immunotherapy, but it is an imperfect biomarker. Multiple additional genomic characteristics are associated with anti-PD1 responses, but the combined predictive value of these features and the added informativeness of each respective feature remains unknown. We evaluated whether machine learning (ML) approaches using proposed determinants of anti-PD1 response derived from whole exome sequencing (WES) could improve prediction of anti-PD1 responders over TMB alone. Random forest classifiers were trained on publicly available anti-PD1 data (n = 104), and subsequently tested on an independent anti-PD1 cohort (n = 69). Both the training and test datasets included a range of cancer types such as non-small cell lung cancer (NSCLC), head and neck squamous cell carcinoma (HNSCC), melanoma, and smaller numbers of patients from other tumor types. Features used include summaries such as TMB and number of frameshift mutations, as well as more gene-level features such as counts of mutations associated with immune checkpoint response and resistance. Both ML algorithms demonstrated area under the receiver-operator curves (AUC) that exceeded TMB alone (AUC 0.63 "human-guided," 0.64 "cluster," and 0.58 TMB alone). Mutations within oncogenes disproportionately modulate anti-PD1 responses relative to their overall contribution to tumor neoepitope burden. The use of a ML algorithm evaluating multiple proposed genomic determinants of anti-PD1 responses modestly improves performance over TMB alone, highlighting the need to integrate other biomarkers to further improve model performance.
Collapse
Affiliation(s)
- Emma Bigelow
- Sidney Kimmel Comprehensive Cancer
Center, Johns Hopkins, Baltimore, MD, USA
| | - Suchi Saria
- Departments of Computer Science and
Statistics, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD,
USA
- Department of Health Policy and
Management, Bloomberg School of Public Health, Johns Hopkins University, Baltimore,
MD, USA
- Bayesian Health, New York, NY,
USA
| | - Brian Piening
- Earle A. Chiles Research Institute,
Providence Portland Medical Center, Portland, OR, USA
| | - Brendan Curti
- Earle A. Chiles Research Institute,
Providence Portland Medical Center, Portland, OR, USA
| | - Alexa Dowdell
- Earle A. Chiles Research Institute,
Providence Portland Medical Center, Portland, OR, USA
| | | | - Carlo Bifulco
- Earle A. Chiles Research Institute,
Providence Portland Medical Center, Portland, OR, USA
| | - Walter Urba
- Earle A. Chiles Research Institute,
Providence Portland Medical Center, Portland, OR, USA
| | - Noam Finkelstein
- Departments of Computer Science and
Statistics, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD,
USA
| | - Elana J Fertig
- Sidney Kimmel Comprehensive Cancer
Center, Johns Hopkins, Baltimore, MD, USA
| | - Alex Baras
- Sidney Kimmel Comprehensive Cancer
Center, Johns Hopkins, Baltimore, MD, USA
| | - Neeha Zaidi
- Sidney Kimmel Comprehensive Cancer
Center, Johns Hopkins, Baltimore, MD, USA
| | - Elizabeth Jaffee
- Sidney Kimmel Comprehensive Cancer
Center, Johns Hopkins, Baltimore, MD, USA
| | - Mark Yarchoan
- Sidney Kimmel Comprehensive Cancer
Center, Johns Hopkins, Baltimore, MD, USA
| |
Collapse
|
16
|
Křížová Ľ, Šafaříková M, Kalousová M, Pfeiferová L, Kuběna AA, Vočka M, Ulrych J, Franková V, Petruželka L, Zima T, Feltl D. New methodology of TMB assessment from tissue and liquid biopsy in NSCLC. PLoS One 2022; 17:e0275121. [PMID: 36155654 PMCID: PMC9512185 DOI: 10.1371/journal.pone.0275121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 09/10/2022] [Indexed: 12/04/2022] Open
Abstract
Immunotherapy has dramatically influenced and changed therapeutical approach in non-small cell lung cancer (NSCLC) in recent five years. Even though we can reach long-term response to this treatment in approximately 20% of patients with NSCLC, we are still not able to identify this cohort of patients based on predictive biomarkers. In our study we have focused on tumor mutation burden (TMB), one of the potential biomarkers which could predict effectiveness of check-point inhibitors, but has several limitations, especially in multiple approaches to TMB quantification and ununiform threshold. We determined the value of TMB in tumor tissue (tTMB) and blood (bTMB) in 20 patients with early stage NSCLC using original custom gene panel LMB_TMB1. We evaluated various possibilities of TMB calculation and concluded that TMB should be counted from both somatic non-synonymous and synonymous mutations. Considering various factors, we established cut-offs of tTMB in/excluding HLA genes as ≥22 mut/Mb and 12 mut/Mb respectively, and cut-offs of bTMB were defined as ≥21 mut/Mb and ≥5 mut/Mb, respectively. We also observed trend in correlation of somatic mutations in HLA genes with overall survival of patients.
Collapse
Affiliation(s)
- Ľudmila Křížová
- Department of Oncology, General University Hospital in Prague and First Faculty of Medicine, Charles University, Prague, Czech Republic
- * E-mail:
| | - Markéta Šafaříková
- Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital in Prague and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marta Kalousová
- Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital in Prague and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lucie Pfeiferová
- Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital in Prague and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Aleš Antonín Kuběna
- Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital in Prague and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Michal Vočka
- Department of Oncology, General University Hospital in Prague and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan Ulrych
- First Department of Surgery, Department of Abdominal, Thoracic Surgery and Traumatology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Věra Franková
- Department of Paediatrics and Inherited Metabolic Disorders, General University Hospital and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Luboš Petruželka
- Department of Oncology, General University Hospital in Prague and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Tomáš Zima
- Institute of Medical Biochemistry and Laboratory Diagnostics, General University Hospital in Prague and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - David Feltl
- Department of Oncology, General University Hospital in Prague and First Faculty of Medicine, Charles University, Prague, Czech Republic
| |
Collapse
|
17
|
Scott SC, Shao XM, Niknafs N, Balan A, Pereira G, Marrone KA, Lam VK, Murray JC, Feliciano JL, Levy BP, Ettinger DS, Hann CL, Brahmer JR, Forde PM, Karchin R, Naidoo J, Anagnostou V. Sex-specific differences in immunogenomic features of response to immune checkpoint blockade. Front Oncol 2022; 12:945798. [PMID: 35992816 PMCID: PMC9382103 DOI: 10.3389/fonc.2022.945798] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/04/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction The magnitude of response to immune checkpoint inhibitor (ICI) therapy may be sex-dependent, as females have lower response rates and decreased survival after ICI monotherapy. The mechanisms underlying this sex dimorphism in ICI response are unknown, and may be related to sex-driven differences in the immunogenomic landscape of tumors that shape anti-tumor immune responses in the context of therapy. Methods To investigate the association of immunogenic mutations with HLA haplotypes, we leveraged whole exome sequence data and HLA genotypes from 482 non-small cell lung cancer (NSCLC) tumors from The Cancer Genome Atlas (TCGA). To explore sex-specific genomic features linked with ICI response, we analyzed whole exome sequence data from patients with NSCLC treated with ICI. Tumor mutational burden (TMB), HLA class I and II restricted immunogenic missense mutation (IMM) load, and mutational smoking signature were defined for each tumor. IMM load was combined with HLA class I and II haplotypes and correlated with therapeutic response and survival following ICI treatment. We examined rates of durable clinical benefit (DCB) for at least six months from ICI treatment initiation. Findings were validated utilizing whole exome sequence data from an independent cohort of ICI treated NSCLC. Results Analysis of whole exome sequence data from NSCLC tumors of females and males revealed that germline HLA class II diversity (≥9 unique HLA alleles) was associated with higher tumor class II IMM load in females (p=0.01) and not in males (p=0.64). Similarly, in tumors of female patients, somatic HLA class II loss of heterozygosity was associated with increased IMM load (p=0.01) while this association was not observed in tumors in males (p=0.20). In females, TMB (p=0.005), class I IMM load (p=0.005), class II IMM load (p=0.004), and mutational smoking signature (p<0.001) were significantly higher in tumors responding to ICI as compared to non-responding tumors. In contrast, among males, there was no significant association between DCB and any of these features. When IMM was considered in the context of HLA zygosity, high MHC-II restricted IMM load and high HLA class II diversity was significantly associated with overall survival in males (p=0.017). Conclusions Inherent sex-driven differences in immune surveillance affect the immunogenomic determinants of response to ICI and likely mediate the dimorphic outcomes with ICI therapy. Deeper understanding of the selective pressures and mechanisms of immune escape in tumors in males and females can inform patient selection strategies and can be utilized to further hone immunotherapy approaches in cancer.
Collapse
Affiliation(s)
- Susan C. Scott
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Xiaoshan M. Shao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Noushin Niknafs
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Archana Balan
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Gavin Pereira
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Kristen A. Marrone
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Vincent K. Lam
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Joseph C. Murray
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Josephine L. Feliciano
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Benjamin P. Levy
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - David S. Ettinger
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Christine L. Hann
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Julie R. Brahmer
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Patrick M. Forde
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Rachel Karchin
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Jarushka Naidoo
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Oncology, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Department of Oncology, Beaumont Hospital, Dublin, Ireland
| | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: Valsamo Anagnostou,
| |
Collapse
|
18
|
Cuppens K, Baas P, Geerdens E, Cruys B, Froyen G, Decoster L, Thomeer M, Maes B. HLA-I diversity and tumor mutational burden by comprehensive next-generation sequencing as predictive biomarkers for the treatment of non-small cell lung cancer with PD-(L)1 inhibitors. Lung Cancer 2022; 170:1-10. [DOI: 10.1016/j.lungcan.2022.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 10/18/2022]
|
19
|
Gunjur A, Manrique‐Rincón AJ, Klein O, Behren A, Lawley TD, Welsh SJ, Adams DJ. 'Know thyself' - host factors influencing cancer response to immune checkpoint inhibitors. J Pathol 2022; 257:513-525. [PMID: 35394069 PMCID: PMC9320825 DOI: 10.1002/path.5907] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 11/30/2022]
Abstract
Immune checkpoint inhibitors (ICIs) have revolutionised oncology and are now standard-of-care for the treatment of a wide variety of solid neoplasms. However, tumour responses remain unpredictable, experienced by only a minority of ICI recipients across malignancy types. Therefore, there is an urgent need for better predictive biomarkers to identify a priori the patients most likely to benefit from these therapies. Despite considerable efforts, only three such biomarkers are FDA-approved for clinical use, and all rely on the availability of tumour tissue for immunohistochemical staining or genomic assays. There is emerging evidence that host factors - for example, genetic, metabolic, and immune factors, as well as the composition of one's gut microbiota - influence the response of a patient's cancer to ICIs. Tantalisingly, some of these factors are modifiable, paving the way for co-therapies that may enhance the therapeutic index of these treatments. Herein, we review key host factors that are of potential biomarker value for response to ICI therapy, with a particular focus on the proposed mechanisms for these influences. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Ashray Gunjur
- Experimental Cancer Genetics, Wellcome Sanger InstituteHinxtonUK,Olivia Newton‐John Cancer Research InstituteLa Trobe University School of Cancer MedicineHeidelbergAustralia
| | - Andrea J Manrique‐Rincón
- Experimental Cancer Genetics, Wellcome Sanger InstituteHinxtonUK,Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of MedicineUniversity of CambridgeCambridgeUK
| | - Oliver Klein
- Olivia Newton‐John Cancer Research InstituteLa Trobe University School of Cancer MedicineHeidelbergAustralia,Department of Medical OncologyAustin HealthHeidelbergAustralia
| | - Andreas Behren
- Olivia Newton‐John Cancer Research InstituteLa Trobe University School of Cancer MedicineHeidelbergAustralia,Department of MedicineUniversity of MelbourneParkvilleAustralia
| | | | - Sarah J Welsh
- Department of SurgeryUniversity of CambridgeCambridgeUK,Cambridge University Hospitals NHS Foundation TrustCambridgeUK
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger InstituteHinxtonUK
| |
Collapse
|
20
|
Abed A, Law N, Calapre L, Lo J, Bhat V, Bowyer S, Millward M, Gray ES. Human leucocyte antigen genotype association with the development of immune-related adverse events in patients with non-small cell lung cancer treated with single agent immunotherapy. Eur J Cancer 2022; 172:98-106. [PMID: 35759816 DOI: 10.1016/j.ejca.2022.05.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/23/2022] [Accepted: 05/17/2022] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Biomarkers that predict the risk of immune-mediated adverse events (irAEs) among patients with non-small cell lung cancer (NSCLC) may reduce morbidity and mortality associated with these treatments. METHODS We carried out high resolution human leucocyte antigen (HLA)-I typing on 179 patients with NSCLC treated with anti-program death (PD)-1/program death ligand (PDL)-1. Toxicity data were collected and graded as per common terminology criteria for adverse event (CTCAE) v5.0. We used 14.8-week for landmark analysis to address lead-time bias to investigate the correlation between HLA-I/II zygosity, supertypes and alleles with irAE. Furthermore, we assessed the association for irAE with clinical benefit rate (CBR), progression-free survival (PFS) and overall survival (OS). RESULTS Homozygosity at one or more HLA-I loci, but not HLA-II, was associated with a reduced risk of irAE (relative risk (RR) = 0.61, 95% CI 0.33-0.95, P = 0.035) especially pneumonitis or any grade 3 toxicity. Patients with HLA-A03 supertype had a higher risk of developing irAE (RR = 1.42, 95% CI 1.02-2.01, P = 0.039). The occurrence of any irAE was significantly associated with improved CBR (RR = 1.48, P < 0.0001), PFS (HR = 0.45, P = 0.0003) and OS (HR = 0.34, P < 0.0001). CONCLUSIONS Homozygosity at one or more HLA-I loci may serve as biomarker to predict patients who are unlikely to experience severe irAEs among patients with NSCLC and treated with anti-PD1/PDL1, but less likely to derive clinical benefit. Patients with HLA-I homozygous might benefit from additional therapy.
Collapse
Affiliation(s)
- Afaf Abed
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia; Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia; Linear Clinical Research, Nedlands, WA, Australia; School of Medicine, University of Western Australia, Nedlands, Australia.
| | - Ngie Law
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia.
| | - Leslie Calapre
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia; Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia.
| | - Johnny Lo
- School of Sciences, Edith Cowan University, Joondalup, WA, Australia; Centre for Artificial Intelligence and Machine Learning, Edith Cowan University, Joondalup, WA, Australia.
| | - Vikas Bhat
- School of Medicine, University of Western Australia, Nedlands, Australia.
| | - Samantha Bowyer
- Linear Clinical Research, Nedlands, WA, Australia; School of Medicine, University of Western Australia, Nedlands, Australia; Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia.
| | - Michael Millward
- Linear Clinical Research, Nedlands, WA, Australia; School of Medicine, University of Western Australia, Nedlands, Australia.
| | - Elin S Gray
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia; Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia.
| |
Collapse
|
21
|
Yan X, Duan H, Ni Y, Zhou Y, Wang X, Qi H, Gong L, Liu H, Tian F, Lu Q, Sun J, Yang E, Zhong D, Wang T, Huang L, Wang J, Chaoyang Wang, Wang Y, Wan Z, Lei J, Zhao J, Jiang T. Tislelizumab combined with chemotherapy as neoadjuvant therapy for surgically resectable esophageal cancer: A prospective, single-arm, phase II study (TD-NICE). Int J Surg 2022; 103:106680. [PMID: 35595021 DOI: 10.1016/j.ijsu.2022.106680] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/18/2022] [Accepted: 05/07/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Clinical benefit of neoadjuvant immunotherapy in resectable esophageal squamous cell carcinoma (ESCC). remains unclear. This study evaluated the efficacy and safety of the programmed death 1 (PD-1) inhibitor tislelizumab combined with chemotherapy as neoadjuvant therapy in patients with resectable ESCC. METHODS Treatment-naïve patients were enrolled and eligible patients received 3 cycles of neoadjuvant therapy with tislelizumab, carboplatin, and nab-paclitaxel. The primary endpoint was surgery patients major pathological response (MPR). Subgroup analysis was stratified by tumor downstaging, circumferential resection margin (CRM), PD-ligand 1 (PD-L1) expression, and tumor mutation burden (TMB). Safety was assessed by adverse events (AEs) and postoperative complications. RESULTS Between September 2020 and March 2021, 45 patients were enrolled. Thirty-six (80.0%) of 45 patients underwent surgery, and 29 (80.5%) underwent successful R0 resection. MPR and pathological complete response (pCR) for surgery patients were 72.0% and 50.0%, respectively. Intention to treatment (ITT) patients MPR and PCR were 57.5% and 40%. Downgrading occurred in 75% of 36 patients. MPR and pCR were identified to be associated with tumor downstaging and CRM but not PD-L1 expression or TMB. TPS levels in MPR and pCR group were significantly higher than that in Non-MPR and Non-pCR group, respectively. Treatment-related AEs of grade 3-4 and immune-related AEs occurred in 42.2% and 22.2% of 45 patients, respectively, and postoperative complications occurred in 77.8% of 36 patients. No treatment-related surgical delay or death occurred. No associations between gene mutation and pathological efficacy were observed. CONCLUSIONS Tislelizumab plus chemotherapy as neoadjuvant therapy demonstrates promising antitumor activity for resectable ESCC with high rates of MPR, pCR, and R0 resection, as well as acceptable tolerability.
Collapse
Affiliation(s)
- Xiaolong Yan
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Hongtao Duan
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Yunfeng Ni
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Yongan Zhou
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Xiaoping Wang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Haini Qi
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Li Gong
- Department of Pathology, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Honggang Liu
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Feng Tian
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Qiang Lu
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Jianyong Sun
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Ende Yang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Daixing Zhong
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Tao Wang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Lijun Huang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Jian Wang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Chaoyang Wang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Yuanyong Wang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Zhiyi Wan
- Genecast Biotechnology Co., Ltd, 88 Danshan Road, Xidong Chuangrong Building, Suite C 1310-1318, Xishan District, Wuxi City, Jiangsu, 214104, China.
| | - Jie Lei
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Jinbo Zhao
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| | - Tao Jiang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military Medical University, No.1. Xinsi Road, Xi'an, Shaanxi, China.
| |
Collapse
|
22
|
Schehr JL, Sethakorn N, Schultz ZD, Hernandez CI, Bade RM, Eyzaguirre D, Singh A, Niles DJ, Henderson L, Warrick JW, Berry SM, Sundling KE, Beebe DJ, Leal TA, Lang JM. Analytical validation and initial clinical testing of quantitative microscopic evaluation for PD-L1 and HLA I expression on circulating tumor cells from patients with non-small cell lung cancer. Biomark Res 2022; 10:26. [PMID: 35468853 PMCID: PMC9040226 DOI: 10.1186/s40364-022-00370-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/25/2022] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION PD-L1 expression in non-small cell lung cancer (NSCLC) predicts response to immune checkpoint blockade, however is an imperfect biomarker given tumor heterogeneity, and the antigen presentation pathway requiring other components including HLA I expression. HLA I downregulation may contribute to resistance, warranting its evaluation in attempts to guide patient selection. In addition, earlier detection of acquired resistance could prompt earlier change in treatment and prolong patient survival. Analysis of circulating tumor cells (CTCs) captures heterogeneity across multiple sites of metastases, enables detection of changes in tumor burden that precede radiographic response, and can be obtained in serial fashion. METHODS To quantify the expression of both PD-L1 and HLA I on CTCs, we developed exclusion-based sample preparation technology, achieving high-yield with gentle magnetic movement of antibody-labeled cells through virtual barriers of surface tension. To achieve clinical-grade quantification of rare cells, we employ high quality fluorescence microscopy image acquisition and automated image analysis together termed quantitative microscopy. RESULTS In preparation for clinical laboratory implementation, we demonstrate high precision and accuracy of these methodologies using a diverse set of control materials. Preliminary testing of CTCs isolated from patients with NSCLC demonstrate heterogeneity in PD-L1 and HLA I expression and promising clinical value in predicting PFS in response to PD-L1 targeted therapies. CONCLUSIONS By confirming high performance, we ensure compatibility for clinical laboratory implementation and future application to better predict and detect resistance to PD-L1 targeted therapy in patients with NSCLC.
Collapse
Affiliation(s)
| | - Nan Sethakorn
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | | | | | - Rory M Bade
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | - Diego Eyzaguirre
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | - Anupama Singh
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | - David J Niles
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, 53705, USA
| | | | - Jay W Warrick
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, 53705, USA
| | - Scott M Berry
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, 53705, USA
| | - Kaitlin E Sundling
- Wisconsin State Lab of Hygiene, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, USA
| | - David J Beebe
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, 53705, USA
| | - Ticiana A Leal
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Joshua M Lang
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA.
- Department of Medicine, University of Wisconsin, Madison, WI, USA.
- Department of Medicine, Carbone Cancer Center, University of Wisconsin, 1111 Highland Avenue, WIMR 7151, Madison, WI, 53705, USA.
| |
Collapse
|
23
|
Wang L, Zhu Y, Zhang B, Wang X, Mo H, Jiao Y, Xu J, Huang J. Prognostic and predictive impact of neutrophil-to-lymphocyte ratio and HLA-I genotyping in advanced esophageal squamous cell carcinoma patients receiving immune checkpoint inhibitor monotherapy. Thorac Cancer 2022; 13:1631-1641. [PMID: 35437954 PMCID: PMC9161342 DOI: 10.1111/1759-7714.14431] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 01/02/2023] Open
Abstract
Background Immune checkpoint inhibitors (ICIs) have become standard‐of‐care in patients with pretreated advanced esophageal squamous cell carcinoma (ESCC). However, reliable biomarkers for clinical outcomes are lacking for ICIs. The exploration of effective biomarkers is therefore needed to optimize patient benefit in the treatment of ESCC. Methods Sixty‐nine patients with advanced ESCC enrolled at one center from two prospective trials were consecutively analyzed. NLR was dynamically collected and high‐resolution HLA‐I genotyping were performed on genomic DNA. Overall response rate (ORR), median progression‐free survival (mPFS) and median overall survival (mOS) were investigated. Results Thirty‐three (47.8%) of 69 patients with baseline NLR ≥4 demonstrated significantly worse clinical outcomes (ORR 9.1% vs. 36.1%, p = 0.018; mPFS 1.8 vs. 3.2 months, hazard ratio [HR] 1.79, p = 0.026; mOS 7.4 vs. 11.0 months, HR 2.28, p = 0.008). An NLR decrease ≥20% at the first radiological evaluation was associated with longer OS (median, 14.0 vs. 7.9 months, p = 0.038). Eleven (15.9%) patients with HLA‐I homozygosity presented poorer clinical outcomes (ORR 0 vs. 27.6%, p = 0.056; mPFS 1.8 vs. 2.4 months, HR 3.37, p = 0.010; mOS 5.6 vs. 10.5 months, HR 3.97, p = 0.004). Patients with baseline NLR ≥4 and HLA‐I homozygosity had the worst outcome (ORR 0; mPFS 1.4 months; mOS 1.8 months) among all. The association between NLR, HLA‐I genotyping and clinical outcomes was independent of programmed death receptor ligand‐1 expression. Conclusions NLR and HLA‐I genotyping could have predictive and prognostic value in patients with advanced ESCC receiving camrelizumab, and the combination of biomarkers may help to identify more patient benefit from immunotherapy.
Collapse
Affiliation(s)
- Lin Wang
- Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yanrong Zhu
- Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bo Zhang
- Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xi Wang
- Daycare Center, Peking University Cancer Hospital & Institute, Beijing, China
| | - Hongnan Mo
- Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yuchen Jiao
- Laboratory of Cell and Molecular Biology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiachen Xu
- Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jing Huang
- Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| |
Collapse
|
24
|
Predictive Markers for Immune Checkpoint Inhibitors in Non-Small Cell Lung Cancer. J Clin Med 2022; 11:jcm11071855. [PMID: 35407463 PMCID: PMC9000007 DOI: 10.3390/jcm11071855] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 12/12/2022] Open
Abstract
Immune checkpoint inhibitors (ICIs) have dramatically improved the outcomes of non-small cell lung cancer patients and have increased the possibility of long-term survival. However, few patients benefit from ICIs, and no predictive biomarkers other than tumor programmed cell death ligand 1 (PD-L1) expression have been established. Hence, the identification of biomarkers is an urgent issue. This review outlines the current understanding of predictive markers for the efficacy of ICIs, including PD-L1, tumor mutation burden, DNA mismatch repair deficiency, microsatellite instability, CD8+ tumor-infiltrating lymphocytes, human leukocyte antigen class I, tumor/specific genotype, and blood biomarkers such as peripheral T-cell phenotype, neutrophil-to-lymphocyte ratio, interferon-gamma, and interleukin-8. A tremendous number of biomarkers are in development, but individual biomarkers are insufficient. Tissue biomarkers have issues in reproducibility and accuracy because of intratumoral heterogeneity and biopsy invasiveness. Furthermore, blood biomarkers have difficulty in reflecting the tumor microenvironment and therefore tend to be less predictive for the efficacy of ICIs than tissue samples. In addition to individual biomarkers, the development of composite markers, including novel technologies such as machine learning and high-throughput analysis, may make it easier to comprehensively analyze multiple biomarkers.
Collapse
|
25
|
Naranbhai V, Viard M, Dean M, Groha S, Braun DA, Labaki C, Shukla SA, Yuki Y, Shah P, Chin K, Wind-Rotolo M, Mu XJ, Robbins PB, Gusev A, Choueiri TK, Gulley JL, Carrington M. HLA-A*03 and response to immune checkpoint blockade in cancer: an epidemiological biomarker study. Lancet Oncol 2022; 23:172-184. [PMID: 34895481 PMCID: PMC8742225 DOI: 10.1016/s1470-2045(21)00582-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND Predictive biomarkers could allow more precise use of immune checkpoint inhibitors (ICIs) in treating advanced cancers. Given the central role of HLA molecules in immunity, variation at the HLA loci could differentially affect the response to ICIs. The aim of this epidemiological study was to determine the effect of HLA-A*03 as a biomarker for predicting response to immunotherapy. METHODS In this epidemiological study, we investigated the clinical outcomes (overall survival, progression free survival, and objective response rate) after treatment for advanced cancer in eight cohorts of patients: three observational cohorts of patients with various types of advanced tumours (the Memorial Sloan Kettering Integrated Mutation Profiling of Actionable Cancer Targets [MSK-IMPACT] cohort, the Dana-Farber Cancer Institute [DFCI] Profile cohort, and The Cancer Genome Atlas) and five clinical trials of patients with advanced bladder cancer (JAVELIN Solid Tumour) or renal cell carcinoma (CheckMate-009, CheckMate-010, CheckMate-025, and JAVELIN Renal 101). In total, these cohorts included 3335 patients treated with various ICI agents (anti-PD-1, anti-PD-L1, and anti-CTLA-4 inhibitors) and 10 917 patients treated with non-ICI cancer-directed therapeutic approaches. We initially modelled the association of HLA amino-acid variation with overall survival in the MSK-IMPACT discovery cohort, followed by a detailed analysis of the association between HLA-A*03 and clinical outcomes in MSK-IMPACT, with replication in the additional cohorts (two further observational cohorts and five clinical trials). FINDINGS HLA-A*03 was associated in an additive manner with reduced overall survival after ICI treatment in the MSK-IMPACT cohort (HR 1·48 per HLA-A*03 allele [95% CI 1·20-1·82], p=0·00022), the validation DFCI Profile cohort (HR 1·22 per HLA-A*03 allele, 1·05-1·42; p=0·0097), and in the JAVELIN Solid Tumour clinical trial for bladder cancer (HR 1·36 per HLA-A*03 allele, 1·01-1·85; p=0·047). The HLA-A*03 effect was observed across ICI agents and tumour types, but not in patients treated with alternative therapies. Patients with HLA-A*03 had shorter progression-free survival in the pooled patient population from the three CheckMate clinical trials of nivolumab for renal cell carcinoma (HR 1·31, 1·01-1·71; p=0·044), but not in those receiving control (everolimus) therapies. Objective responses were observed in none of eight HLA-A*03 homozygotes in the ICI group (compared with 59 [26·6%] of 222 HLA-A*03 non-carriers and 13 (17·1%) of 76 HLA-A*03 heterozygotes). HLA-A*03 was associated with shorter progression-free survival in patients receiving ICI in the JAVELIN Renal 101 randomised clinical trial for renal cell carcinoma (avelumab plus axitinib; HR 1·59 per HLA-A*03 allele, 1·16-2·16; p=0·0036), but not in those receiving control (sunitinib) therapy. Objective responses were recorded in one (12·5%) of eight HLA-A*03 homozygotes in the ICI group (compared with 162 [63·8%] of 254 HLA-A*03 non-carriers and 40 [55·6%] of 72 HLA-A*03 heterozygotes). HLA-A*03 was associated with impaired outcome in meta-analysis of all 3335 patients treated with ICI at genome-wide significance (p=2·01 × 10-8) with no evidence of heterogeneity in effect (I2 0%, 95% CI 0-0·76) INTERPRETATION: HLA-A*03 is a predictive biomarker of poor response to ICI. Further evaluation of HLA-A*03 is warranted in randomised trials. HLA-A*03 carriage could be considered in decisions to initiate ICI in patients with cancer. FUNDING National Institutes of Health, Merck KGaA, and Pfizer.
Collapse
Affiliation(s)
- Vivek Naranbhai
- Massachusetts General Hospital, Boston, MA, USA; Dana-Farber Cancer Institute, Boston, MA, USA; Centre for the AIDS Programme of Research In South Africa, Durban, South Africa
| | - Mathias Viard
- Basic Science Programme, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | | | | | - Yuko Yuki
- Basic Science Programme, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
| | - Parantu Shah
- Bioinformatics, Department of Translational Medicine and Global Clinical Development, EMD Serono Research and Development Institute, Merck KGaA, Darmstadt, Germany
| | - Kevin Chin
- Immunooncology, EMD Serono Research and Development Institute, Merck KGaA, Darmstadt, Germany
| | | | | | | | | | | | - James L Gulley
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mary Carrington
- Basic Science Programme, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
26
|
Zhou YF, Xiao Y, Jin X, Di GH, Jiang YZ, Shao ZM. Integrated analysis reveals prognostic value of HLA-I LOH in triple-negative breast cancer. J Immunother Cancer 2021; 9:jitc-2021-003371. [PMID: 34615706 PMCID: PMC8496394 DOI: 10.1136/jitc-2021-003371] [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] [Accepted: 08/29/2021] [Indexed: 12/20/2022] Open
Abstract
Background Triple-negative breast cancers (TNBCs), especially those non-immune-inflamed tumors, have a poor prognosis and limited therapies. Human leukocyte antigen (HLA)-I not only contributes to antitumor immune response and the phenotype of the tumor microenvironment, but also is a negative predictor of outcomes after immunotherapy. However, the importance of HLA functional status in TNBCs remains poorly understood. Methods Using the largest original multiomics datasets on TNBCs, we systematically characterized the HLA-Ⅰ status of TNBCs from the perspective of HLA-Ⅰ homogeneity and loss of heterozygosity (LOH). The prognostic significance of HLA-I status was measured. To explain the potential mechanism of prognostic value in HLA-Ⅰ status, the mutational signature, copy number alteration, neoantigen and intratumoral heterogeneity were measured. Furthermore, the correlation between HLA-Ⅰ functional status and the tumor immune microenvironment was analyzed. Results LOH and homogeneity in HLA-I accounted for 18% and 21% of TNBCs, respectively. HLA-I LOH instead of HLA-I homogeneity was an independent prognostic biomarker in TNBCs. In particular, for patients with non-immune-inflamed tumors, HLA-I LOH indicated a worse prognosis than HLA-I non-LOH. Furthermore, integrated genomic and transcriptomic analysis showed that HLA-I LOH was accompanied by upregulated scores of mutational signature 3 and homologous recombination deficiency scores, which implied the failure of DNA double-strand break repair. Moreover, HLA-I LOH had higher mutation and neoantigen loads and more subclones than HLA-I non-LOH. These results indicated that although HLA-I LOH tumors with failure of DNA double-strand break repair were prone to produce neoantigens, their limited capacity for antigen presentation finally contributed to poor immune selection pressure. Conclusion Our study illustrates the genomic landscape of HLA-I functional status and stresses the prognostic significance of HLA-I LOH in TNBCs. For “cold” tumors in TNBCs, HLA-I LOH indicated a worse prognosis than HLA-I non-LOH.
Collapse
Affiliation(s)
- Yi-Fan Zhou
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Yi Xiao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Xi Jin
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Gen-Hong Di
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| |
Collapse
|
27
|
Lee D, Park J, Choi H, Gim G, Cho S, Kim L, Oh Y, Kang CY, Kim Y, Tan D, de Viveiros PAH, Chae YK. Association of HLA class I homozygosity with unfavorable clinical outcomes in patients with non-small cell lung cancer treated with chemo-immunotherapy or immunotherapy as first-line therapy. Heliyon 2021; 7:e07916. [PMID: 34568594 PMCID: PMC8449023 DOI: 10.1016/j.heliyon.2021.e07916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/19/2021] [Accepted: 08/31/2021] [Indexed: 11/19/2022] Open
Abstract
Background Homozygosity at HLA-I locus has been reported to be an unfavorable predictive biomarker of second-line or beyond immunotherapy in patients with different types of cancer. The linkage between HLA-I zygosity and survival in NSCLC patients treated with first-line immunotherapy with or without chemotherapy has not been reported. Methods Next generation sequencing with HLA genotyping was performed on patients with advanced NSCLC treated with immune checkpoint inhibitors with or without chemotherapy as first-line (N = 29). Progression free survival was compared between HLA-I homozygous (defined as homozygosity in at least one locus A, B, or C) and heterozygous patients. Kaplan-Meier curves were built, and log-rank test was used. Results Among 29 enrollees, 25 patients (86.2%) were HLA-I heterozygous and four patients (13.8%) were HLA-I homozygous. Treatment response was not available in five patients with HLA-I heterozygosity. Among 20 patients with HLA-I heterozygosity, five patients (20.0%) had partial response, 10 patients (50.0%) had stable disease, two patients (8.0%) had non-complete response/non-progressive disease, and three patients (12.0%) had progressive disease. Among four patients with HLA-I heterozygosity, one patient (25.0%) had partial response, one patient (25.0%) had stable disease, and two patients (50.0%) had progressive disease. The median progression free survival was not reached in heterozygous group and was 2.97 months in homozygous group (Log-rank p = 0.68). Conclusions We observed a trend toward an inverse association between HLA-I homozygosity and survival outcomes in patients with NSCLC treated with first-line therapy in conjunction with immunotherapy. Further prospective studies to validate aforementioned relationship are warranted.
Collapse
Affiliation(s)
- Dongyup Lee
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Geisinger Health System, Danville, PA, USA
| | - Jonghanne Park
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Horyun Choi
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- University of Hawaii, Honolulu, HI, USA
| | - Gahyun Gim
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- St. Elizabeth's Medical Center, Tufts University School of Medicine, Boston, MA, USA
| | - Sukjoo Cho
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- University of South Florida Morsani College of Medicine, Tampa, FL, USA
| | - Leeseul Kim
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Youjin Oh
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Cyra Y. Kang
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- John H. Stroger, Jr. Hospital of Cook County, Chicago, IL, USA
| | - Yeseul Kim
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Dean Tan
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Young Kwang Chae
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
- Corresponding author.
| |
Collapse
|
28
|
Kobayashi M, Fujiyama N, Tanegashima T, Narita S, Yamamoto Y, Fujimoto N, Ueda S, Takeuchi A, Numakura K, Habuchi T, Matsuyama H, Eto M, Shiota M. Effect of HLA genotype on intravesical recurrence after bacillus Calmette-Guérin therapy for non-muscle-invasive bladder cancer. Cancer Immunol Immunother 2021; 71:727-736. [PMID: 34379177 DOI: 10.1007/s00262-021-03032-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/04/2021] [Indexed: 12/19/2022]
Abstract
The intravesical administration of bacillus Calmette-Guérin (BCG) is widely used to control the intravesical recurrence of non-muscle-invasive bladder cancer (NMIBC). This study aimed to reveal the effects of zygosity on human leukocyte antigen (HLA) genes and individual HLA genotypes on intravesical recurrence after intravesical BCG therapy for NMIBC. This study included Japanese patients who had received intravesical BCG for NMIBC. HLA genotyping of HLA-A, B, C, and DRB1 was performed. The effect of HLA zygosity and HLA genotype on intravesical recurrence was evaluated. Among 195 patients, those homozygous for the HLA-B supertype were more likely than those heterozygous for the HLA-B supertype to experience intravesical recurrence by univariate analysis (hazard ratio [HR], 95% confidence interval [CI]; 1.87, 1.14-3.05, P = 0.012) and multivariate analysis (HR, 95% CI; 2.26, 1.02-5.01, P = 0.045). Patients with B07 or B44 had a decreased risk of intravesical recurrence by univariate analysis (HR, 95% CI; 0.43, 0.24-0.78, P = 0.0056) and multivariate analysis (HR, 95% CI; 0.36, 0.16-0.82, P = 0.016). This study suggests the importance of the diversity and specificity of HLA-B loci in the antitumor effect of BCG immunotherapy for NMIBC. These findings may contribute to the delineation of risk strata for BCG therapy and improve the medical management of NMIBC.
Collapse
Affiliation(s)
- Mizuki Kobayashi
- Department of Urology, Graduate School of Medicine, Akita University, Akita, 010-8543, Japan
| | - Nobuhiro Fujiyama
- Center for Kidney Disease and Transplantation, Akita University Hospital, Akita, 010-8543, Japan
| | - Tokiyoshi Tanegashima
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Shintaro Narita
- Department of Urology, Graduate School of Medicine, Akita University, Akita, 010-8543, Japan
| | - Yoshiaki Yamamoto
- Department of Urology, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505, Japan
| | - Naohiro Fujimoto
- Department of Urology, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, 807-8556, Japan
| | - Shohei Ueda
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Ario Takeuchi
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Kazuyuki Numakura
- Department of Urology, Graduate School of Medicine, Akita University, Akita, 010-8543, Japan
| | - Tomonori Habuchi
- Department of Urology, Graduate School of Medicine, Akita University, Akita, 010-8543, Japan
| | - Hideyasu Matsuyama
- Department of Urology, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505, Japan
| | - Masatoshi Eto
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Masaki Shiota
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
| |
Collapse
|