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1. The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer

Author

Alexandra Arias, Edith M. Ross, Oscar M. Rueda, Regina Mayor, Vicente Peg, Carlos Caldas, Dan Reshef, Tania Contente-Cuomo, Stephen John Sammut, Joan Seoane, Elena Martínez-Sáez, Tauanne Dias Amarante, Daniel Guimarães Tiezzi, Nikaoly Ciriaco, Wei Cope, Aliakbar Dariush, Bernard Pereira, H. Raza Ali, Havell Markus, Erez Greenstein, Muhammed Murtaza, Serena Nik-Zainal, Santiago Ramón y Cajal, Yosef E. Maruvka, Nir Friedman, Javier Cortes, Florian Markowetz, Gad Getz, Suet-Feung Chin, Yvonne Hui-Fang Teng, George S. Vassiliou, Leticia De Mattos-Arruda, Rachael Bashford-Rogers, Sandro Morganella, Sammut, Stephen [0000-0003-4472-904X], Bashford-Rogers, Rachael [0000-0002-6838-0711], Chin, Suet-Feung [0000-0001-5697-1082], Ali, Raza [0000-0001-7587-0906], Cope, Wei [0000-0002-5661-3522], Dias Amarante, Tauanne [0000-0002-1999-9753], Vassiliou, George [0000-0003-4337-8022], Nik-Zainal, Serena [0000-0001-5054-1727], Markowetz, Florian [0000-0002-2784-5308], Caldas, Carlos [0000-0003-3547-1489], Apollo - University of Cambridge Repository, Institut Català de la Salut, [De Mattos-Arruda L] Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK. University of Cambridge, Cambridge, UK. Vall d'Hebron Institut d'Oncologia, Barcelona, Spain. Hospital Universitari Vall d'Hebron, Barcelona, Spain. [Sammut SJ, Ross EM] Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK. University of Cambridge, Cambridge, UK. [Bashford-Rogers R] Department of Medicine, University of Cambridge, Cambridge, UK. [Greenstein E] Department of Immunology, Weizmann Institute of Science, Rehovot, Israel. [Markus H] Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, USA. Mayo Clinic Center for Individualized Medicine, Scottsdale, USA. [Mayor R, Arias A] Vall d'Hebron Institut d'Oncologia, Barcelona, Spain. Hospital Universitari Vall d'Hebron, Barcelona, Spain. Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain. [Ciriaco N] Servei d’Anatomia Patològica, Hospital Universitari Vall d'Hebron, Barcelona, Spain. [Martinez-Saez E] Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain. Servei d’Anatomia Patològica, Hospital Universitari Vall d'Hebron, Barcelona, Spain. [Peg V, Ramon Y Cajal S] Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain. Servei d’Anatomia Patològica, Hospital Universitari Vall d'Hebron, Barcelona, Spain. Vall d’Hebron Institut de Recerca, Barcelona, Spain. Universitat Autònoma de Barcelona, Barcelona, Spain. [Cortes J] Vall d'Hebron Institut d'Oncologia, Barcelona, Spain. Hospital Universitari Vall d'Hebron, Barcelona, Spain. Ramon y Cajal Hospital, Madrid, Spain. [Seoane J] Vall d'Hebron Institut d'Oncologia, Barcelona, Spain. Hospital Universitari Vall d'Hebron, Barcelona, Spain. Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain, Hospital Universitari Vall d'Hebron, and Vall d'Hebron Barcelona Hospital Campus

Subjects
0301 basic medicine, Neoplasms::Neoplasms by Site::Breast Neoplasms [DISEASES], metastatic phylogenies, neoplasias::neoplasias por localización::neoplasias de la mama [ENFERMEDADES], Loss of Heterozygosity, Metastases, immunoediting, Loss of heterozygosity, 0302 clinical medicine, Tumor Microenvironment, Otros calificadores::Otros calificadores::/inmunología [Otros calificadores], Neoplasm Metastasis, lcsh:QH301-705.5, immune landscapes, Otros calificadores::Otros calificadores::/genética [Otros calificadores], Neoplasms::Neoplastic Processes::Neoplasm Metastasis [DISEASES], Genomics, Nreast cancer, Genomic landscapes, Metastatic breast cancer, 3. Good health, Gene Expression Regulation, Neoplastic, Female, Mama - Càncer - Aspectes immunològics, Immune landscapes, clade mutations, Clade mutations, genomic landscapes, Breast Neoplasms, Human leukocyte antigen, Biology, Stem mutations, Article, General Biochemistry, Genetics and Molecular Biology, private mutations, 03 medical and health sciences, breast cancer, Breast cancer, Immune system, Metàstasi, Immunoediting, Other subheadings::Other subheadings::/immunology [Other subheadings], Exome Sequencing, Other subheadings::Other subheadings::/genetics [Other subheadings], Biomarkers, Tumor, medicine, Humans, metastases, Tumor microenvironment, Gene Expression Profiling, Neoplasias::Neoplasias por Localización::Neoplasias de la Mama [ENFERMEDADES], stem mutations, medicine.disease, Metastatic phylogenies, Gene expression profiling, TCR repertoire, 030104 developmental biology, lcsh:Biology (General), neoplasias::procesos neoplásicos::metástasis neoplásica [ENFERMEDADES], Mutation, Cancer research, Mama - Càncer - Aspectes genètics, Private mutations, 030217 neurology & neurosurgery
Abstract

Summary The detailed molecular characterization of lethal cancers is a prerequisite to understanding resistance to therapy and escape from cancer immunoediting. We performed extensive multi-platform profiling of multi-regional metastases in autopsies from 10 patients with therapy-resistant breast cancer. The integrated genomic and immune landscapes show that metastases propagate and evolve as communities of clones, reveal their predicted neo-antigen landscapes, and show that they can accumulate HLA loss of heterozygosity (LOH). The data further identify variable tumor microenvironments and reveal, through analyses of T cell receptor repertoires, that adaptive immune responses appear to co-evolve with the metastatic genomes. These findings reveal in fine detail the landscapes of lethal metastatic breast cancer., Graphical Abstract, Highlights • Genomic and transcriptomic landscapes for 10 lethal breast cancers • Within a patient, metastases group in limited clades with shared genomic ancestry • Tumor immune microenvironments across metastases are not uniform • Phylogenetic trees are correlated with TIL-TCR trees across metastases, De Mattos-Arruda et al. profiled multiple metastases from autopsies of patients with therapy-resistant breast cancer, showing that multi-clonal spreading occurs in a small number of founder events. The analysis characterizes predicted neo-antigen landscapes, tumor microenvironments, and accumulation of HLA LOH. T cell immune responses appear to co-evolve with metastatic cancer genomes.

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2. Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma.

Author

Rosenberg MI, Greenstein E, Buchkovich M, Peres A, Santoni-Rugiu E, Yang L, Mikl M, Vaksman Z, Gibbs DL, Reshef D, Salovin A, Irwin MS, Naranjo A, Ulitsky I, de Alarcon PA, Matthay KK, Weigman V, Yaari G, Panzer JA, Friedman N, and Maris JM

Subjects
Child, Humans, Autoimmunity, Autoantibodies, Genes, MHC Class II, Ataxia, Neuroblastoma complications, Neuroblastoma metabolism, Opsoclonus-Myoclonus Syndrome complications, Opsoclonus-Myoclonus Syndrome pathology
Abstract

Neuroblastoma is a lethal childhood solid tumor of developing peripheral nerves. Two percent of children with neuroblastoma develop opsoclonus myoclonus ataxia syndrome (OMAS), a paraneoplastic disease characterized by cerebellar and brainstem-directed autoimmunity but typically with outstanding cancer-related outcomes. We compared tumor transcriptomes and tumor-infiltrating T and B cell repertoires from 38 OMAS subjects with neuroblastoma to 26 non-OMAS-associated neuroblastomas. We found greater B and T cell infiltration in OMAS-associated tumors compared to controls and showed that both were polyclonal expansions. Tertiary lymphoid structures (TLSs) were enriched in OMAS-associated tumors. We identified significant enrichment of the major histocompatibility complex (MHC) class II allele HLA-DOB ∗ 01:01 in OMAS patients. OMAS severity scores were associated with the expression of several candidate autoimmune genes. We propose a model in which polyclonal auto-reactive B lymphocytes act as antigen-presenting cells and drive TLS formation, thereby supporting both sustained polyclonal T cell-mediated anti-tumor immunity and paraneoplastic OMAS neuropathology., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Published
2023
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3. The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer.

Author

De Mattos-Arruda L, Sammut SJ, Ross EM, Bashford-Rogers R, Greenstein E, Markus H, Morganella S, Teng Y, Maruvka Y, Pereira B, Rueda OM, Chin SF, Contente-Cuomo T, Mayor R, Arias A, Ali HR, Cope W, Tiezzi D, Dariush A, Dias Amarante T, Reshef D, Ciriaco N, Martinez-Saez E, Peg V, Ramon Y Cajal S, Cortes J, Vassiliou G, Getz G, Nik-Zainal S, Murtaza M, Friedman N, Markowetz F, Seoane J, and Caldas C

Subjects
Breast Neoplasms secondary, Female, Gene Expression Profiling, Humans, Loss of Heterozygosity, Neoplasm Metastasis, Tumor Microenvironment genetics, Tumor Microenvironment immunology, Exome Sequencing, Biomarkers, Tumor genetics, Breast Neoplasms genetics, Breast Neoplasms immunology, Gene Expression Regulation, Neoplastic, Genomics methods, Mutation
Abstract

The detailed molecular characterization of lethal cancers is a prerequisite to understanding resistance to therapy and escape from cancer immunoediting. We performed extensive multi-platform profiling of multi-regional metastases in autopsies from 10 patients with therapy-resistant breast cancer. The integrated genomic and immune landscapes show that metastases propagate and evolve as communities of clones, reveal their predicted neo-antigen landscapes, and show that they can accumulate HLA loss of heterozygosity (LOH). The data further identify variable tumor microenvironments and reveal, through analyses of T cell receptor repertoires, that adaptive immune responses appear to co-evolve with the metastatic genomes. These findings reveal in fine detail the landscapes of lethal metastatic breast cancer., (Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.)

Published
2019
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