publication . Article . Other literature type . 2019

The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer

De Mattos-Arruda, Leticia; Sammut, Stephen; Ross, Edith M; Bashford-Rogers, Rachael; Greenstein, Erez; Markus, Havell; Morganella, Sandro; Teng, Yvonne; Maruvka, Yosef; Pereira, Bernard; ...
Open Access
  • Published: 01 May 2019 Journal: Cell Reports, volume 27, pages 2,690-27,080,000,000,000 (issn: 2211-1247, Copyright policy)
  • Publisher: Elsevier BV
  • Country: United Kingdom
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
Subjects
free text keywords: Humans, Breast Neoplasms, Neoplasm Metastasis, Gene Expression Profiling, Genomics, Gene Expression Regulation, Neoplastic, Mutation, Loss of Heterozygosity, Female, Tumor Microenvironment, Biomarkers, Tumor, Whole Exome Sequencing, Mama - Càncer - Aspectes genètics, Mama - Càncer - Aspectes immunològics, Metàstasi, :Neoplasms::Neoplasms by Site::Breast Neoplasms [DISEASES], :Neoplasms::Neoplastic Processes::Neoplasm Metastasis [DISEASES], :Other subheadings::Other subheadings::/genetics [Other subheadings], :Other subheadings::Other subheadings::/immunology [Other subheadings], :Neoplasias::Neoplasias por Localización::Neoplasias de la Mama [ENFERMEDADES], :Neoplasias::Procesos Neoplásicos::Metástasis de la Neoplasia [ENFERMEDADES], :Otros calificadores::Otros calificadores::/genética [Otros calificadores], :Otros calificadores::Otros calificadores::/inmunología [Otros calificadores], Biology (General), QH301-705.5, Article, breast cancer, metastases, stem mutations, clade mutations, private mutations, genomic landscapes, immune landscapes, metastatic phylogenies, immunoediting, TCR repertoire
Funded by
WT
Project
  • Funder: Wellcome Trust (WT)
111 references, page 1 of 8

Aceto, N., Bardia, A., Miyamoto, D.T., Donaldson, M.C., Wittner, B.S., Spencer, J.A., Yu, M., Pely, A., Engstrom, A., Zhu, H., et al. (2014). Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis. Cell 158, 1110-1122. [OpenAIRE]

Alexandrov, L.B., Nik-Zainal, S., Wedge, D.C., Campbell, P.J., and Stratton, M.R. (2013). Deciphering signatures of mutational processes operative in human cancer. Cell Rep. 3, 246-259. [OpenAIRE]

Ali, H.R., Rueda, O.M., Chin, S.F., Curtis, C., Dunning, M.J., Aparicio, S.A., and Caldas, C. (2014). Genome-driven integrated classification of breast cancer validated in over 7,500 samples. Genome Biol. 15, 431.

Ali, H.R., Chlon, L., Pharoah, P.D., Markowetz, F., and Caldas, C. (2016a). Patterns of Immune Infiltration in Breast Cancer and Their Clinical Implications: A Gene-Expression-Based Retrospective Study. PLoS Med. 13, e1002194. [OpenAIRE]

Ali, H.R., Dariush, A., Provenzano, E., Bardwell, H., Abraham, J.E., Iddawela, M., Vallier, A.L., Hiller, L., Dunn, J.A., Bowden, S.J., et al. (2016b). Computational pathology of pre-treatment biopsies identifies lymphocyte density as a predictor of response to neoadjuvant chemotherapy in breast cancer. Breast Cancer Res. 18, 21.

Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410.

Bashford-Rogers, R.J., Palser, A.L., Huntly, B.J., Rance, R., Vassiliou, G.S., Follows, G.A., and Kellam, P. (2013). Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations. [OpenAIRE]

Genome Res. 23, 1874-1884.

Bronner, I.F., Quail, M.A., Turner, D.J., and Swerdlow, H. (2014). Improved Protocols for Illumina Sequencing. Curr. Protoc. Hum. Genet. 80, 18.2.1-42.

Brown, D., Smeets, D., Szekely, B., Larsimont, D., Szasz, A.M., Adnet, P.Y., Rothe, F., Rouas, G., Nagy, Z.I., Farago, Z., et al. (2017). Phylogenetic analysis of metastatic progression in breast cancer using somatic mutations and copy number aberrations. Nat. Commun. 8, 14944.

Brown, S.D., Warren, R.L., Gibb, E.A., Martin, S.D., Spinelli, J.J., Nelson, B.H., and Holt, R.A. (2014). Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival. Genome Res. 24, 743-750.

(2016). A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds. Cell 167, 260-274.e22.

Callari, M., Sammut, S.J., De Mattos-Arruda, L., Bruna, A., Rueda, O.M., Chin, S.F., and Caldas, C. (2017). Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers. Genome Med. 9, 35. [OpenAIRE]

Cancer Genome Atlas, N.; Cancer Genome Atlas Network (2012). Comprehensive molecular portraits of human breast tumours. Nature 490, 61-70.

Charoentong, P., Finotello, F., Angelova, M., Mayer, C., Efremova, M., Rieder, D., Hackl, H., and Trajanoski, Z. (2017). Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade. Cell Rep. 18, 248-262.

111 references, page 1 of 8
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
Subjects
free text keywords: Humans, Breast Neoplasms, Neoplasm Metastasis, Gene Expression Profiling, Genomics, Gene Expression Regulation, Neoplastic, Mutation, Loss of Heterozygosity, Female, Tumor Microenvironment, Biomarkers, Tumor, Whole Exome Sequencing, Mama - Càncer - Aspectes genètics, Mama - Càncer - Aspectes immunològics, Metàstasi, :Neoplasms::Neoplasms by Site::Breast Neoplasms [DISEASES], :Neoplasms::Neoplastic Processes::Neoplasm Metastasis [DISEASES], :Other subheadings::Other subheadings::/genetics [Other subheadings], :Other subheadings::Other subheadings::/immunology [Other subheadings], :Neoplasias::Neoplasias por Localización::Neoplasias de la Mama [ENFERMEDADES], :Neoplasias::Procesos Neoplásicos::Metástasis de la Neoplasia [ENFERMEDADES], :Otros calificadores::Otros calificadores::/genética [Otros calificadores], :Otros calificadores::Otros calificadores::/inmunología [Otros calificadores], Biology (General), QH301-705.5, Article, breast cancer, metastases, stem mutations, clade mutations, private mutations, genomic landscapes, immune landscapes, metastatic phylogenies, immunoediting, TCR repertoire
Funded by
WT
Project
  • Funder: Wellcome Trust (WT)
111 references, page 1 of 8

Aceto, N., Bardia, A., Miyamoto, D.T., Donaldson, M.C., Wittner, B.S., Spencer, J.A., Yu, M., Pely, A., Engstrom, A., Zhu, H., et al. (2014). Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis. Cell 158, 1110-1122. [OpenAIRE]

Alexandrov, L.B., Nik-Zainal, S., Wedge, D.C., Campbell, P.J., and Stratton, M.R. (2013). Deciphering signatures of mutational processes operative in human cancer. Cell Rep. 3, 246-259. [OpenAIRE]

Ali, H.R., Rueda, O.M., Chin, S.F., Curtis, C., Dunning, M.J., Aparicio, S.A., and Caldas, C. (2014). Genome-driven integrated classification of breast cancer validated in over 7,500 samples. Genome Biol. 15, 431.

Ali, H.R., Chlon, L., Pharoah, P.D., Markowetz, F., and Caldas, C. (2016a). Patterns of Immune Infiltration in Breast Cancer and Their Clinical Implications: A Gene-Expression-Based Retrospective Study. PLoS Med. 13, e1002194. [OpenAIRE]

Ali, H.R., Dariush, A., Provenzano, E., Bardwell, H., Abraham, J.E., Iddawela, M., Vallier, A.L., Hiller, L., Dunn, J.A., Bowden, S.J., et al. (2016b). Computational pathology of pre-treatment biopsies identifies lymphocyte density as a predictor of response to neoadjuvant chemotherapy in breast cancer. Breast Cancer Res. 18, 21.

Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410.

Bashford-Rogers, R.J., Palser, A.L., Huntly, B.J., Rance, R., Vassiliou, G.S., Follows, G.A., and Kellam, P. (2013). Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations. [OpenAIRE]

Genome Res. 23, 1874-1884.

Bronner, I.F., Quail, M.A., Turner, D.J., and Swerdlow, H. (2014). Improved Protocols for Illumina Sequencing. Curr. Protoc. Hum. Genet. 80, 18.2.1-42.

Brown, D., Smeets, D., Szekely, B., Larsimont, D., Szasz, A.M., Adnet, P.Y., Rothe, F., Rouas, G., Nagy, Z.I., Farago, Z., et al. (2017). Phylogenetic analysis of metastatic progression in breast cancer using somatic mutations and copy number aberrations. Nat. Commun. 8, 14944.

Brown, S.D., Warren, R.L., Gibb, E.A., Martin, S.D., Spinelli, J.J., Nelson, B.H., and Holt, R.A. (2014). Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival. Genome Res. 24, 743-750.

(2016). A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds. Cell 167, 260-274.e22.

Callari, M., Sammut, S.J., De Mattos-Arruda, L., Bruna, A., Rueda, O.M., Chin, S.F., and Caldas, C. (2017). Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers. Genome Med. 9, 35. [OpenAIRE]

Cancer Genome Atlas, N.; Cancer Genome Atlas Network (2012). Comprehensive molecular portraits of human breast tumours. Nature 490, 61-70.

Charoentong, P., Finotello, F., Angelova, M., Mayer, C., Efremova, M., Rieder, D., Hackl, H., and Trajanoski, Z. (2017). Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade. Cell Rep. 18, 248-262.

111 references, page 1 of 8
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