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The Landscape of Somatic Genetic Alterations in Breast Cancers From ATM Germline Mutation Carriers
Open accessAbstract
Pathogenic germline variants in ataxia-telangiectasia mutated (ATM), a gene that plays a role in DNA damage response and cell cycle checkpoints, confer an increased breast cancer (BC) risk. Here, we investigated the phenotypic characteristics and landscape of somatic genetic alterations in 24 BCs from ATM germline mutation carriers by whole-exome and targeted sequencing. ATM-associated BCs were consistently hormone receptor positive and largely displayed minimal immune infiltrate. Although 79.2% of these tumors exhibited loss of heterozygosity of the ATM wild-type allele, none displayed high activity of mutational signature 3 associated with defective homologous recombination DNA (HRD) repair. No TP53 mutations were found in the ATM-associated BCs. Analysis of an independent data set confirmed that germline ATM variants and TP53 somatic mutations are mutually exclusive. Our findings indicate that ATM-associated BCs often harbor bi-allelic inactivation of ATM, are phenotypically distinct from BRCA1/2-associated BCs, lack HRD-related mutational signatures, and that TP53 and ATM genetic alterations are likely epistatic.
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“Despite the role of TP53, ATM and CHEK2 in DNA-damage signalling and double-strand breaks detection, these tumours do not show evidence of BRCA-deficient signatures, as previously described [9, 13, 19], but instead they harbour highly complex clustered chromosomal rearrangements.”
From Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers (2019) · cites this paper as [19]
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Pathogenesis of Triple-Negative Breast Cancer
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“The apparent lower sensitivity to PARP inhibitors of tumors harboring an ATM alteration may be due to ATM's role as a sensor of DNA damage rather than a mediator of homologous recombination repair (15).”
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Self-citationSynthetic Lethality in Cancer Therapeutics: The Next Generation
Setton, J. S., Zinda, M. J., Riaz, N., Durocher, D., Zimmermann, M., Koehler, M. T., Reis-Filho, J. S., & Powell, S. N. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-20-1503 · Cited by 214
“In addition to its role in DNA damage signaling, ATM has a key gatekeeper role via regulation of p53 stabilization in response to cellular stress (104); inactivation of ATM appears to suppress p53 signaling to a degree that is sufficient for tumorigenesis, evidenced by the observation that LOF alterations in ATM and T…”
BackgroundSelf-citationSuwinski, P., Ong, C. K., Ling, M. H., Poh, Y. M., Khan, A. M., & Ong, H. S. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00049 · Cited by 218
“…actionable areas of the genome to determine the variations in the exon regions and identify causal variants of a disease or disease-causing mutations (Gorski et al., 2016; LaHaye et al., 2016; Gambin et al., 2017; Gupta et al., 2017; Hixson et al., 2017; Mueller et al., 2018; Weigelt et al., 2018).”
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“However, because ATM functions as a sensor of DNA damage rather than a mediator of DNA repair [8], we hypothesized that patients harboring ATM mutations might not show the same responses to PARP inhibitor therapy as those harboring BRCA1/2 mutations (which are bona fide homologous recombination genes) [9].”
BackgroundGolan, T., O'Kane, G. M., Denroche, R. E., Raitses‐Gurevich, M., Grant, R. C., Holter, S., Wang, Y., Zhang, A. X. W., Jang, G. H., Stossel, C., et al. (2021) · Gastroenterology · doi:10.1053/j.gastro.2021.01.220 · Cited by 157
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“Instead, the main relevance of the pathway to tumor cells may be cell cycle arrest and p53-mediated apoptosis, explaining the mutual exclusivity of ATM and TP53 inactivation in breast cancer [47].”
BackgroundResultda Silva, E. M., Fix, D. J., Sebastião, A. P. M., Selenica, P., Ferrando, L., Kim, S. H., Stylianou, A. A., Paula, A. D. C., Pareja, F. G., Smith, E. S., et al. (2021) · Modern Pathology · doi:10.1038/s41379-021-00799-6 · Cited by 124
Self-citationCamonsertib in DNA damage response-deficient advanced solid tumors: phase 1 trial results
Yap, T. A., Fontana, E., Lee, E. K., Spigel, D. R., Højgaard, M., Lheureux, S., Mettu, N. B., Carneiro, B. A., Carter, L., Plummer, R., et al. (2023) · Nature Medicine · doi:10.1038/s41591-023-02399-0 · Cited by 123
Self-citationLotan, T. L., Kaur, H. B., Salles, D. C., Murali, S., Schaeffer, E. M., Lanchbury, J. S. S., Isaacs, W. B., Brown, R. E., Richardson, A. L., Cussenot, O., et al. (2021) · Modern Pathology · doi:10.1038/s41379-020-00731-4 · Cited by 113
Targeting ATR in patients with cancer
Ngoi, N. Y. L., Pilie, P. G., McGrail, D. J., Zimmermann, M., Schlacher, K., & Yap, T. A. (2024) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-024-00863-5 · Cited by 119
“Few data have also been published regarding the correlation of IHC-determined ATM loss with specific mutational signatures that could help to identify a true ATM loss of function 125 .”
Nones, K., Johnson, J., Newell, F., Patch, A. M., Thorne, H., Kazakoff, S. H., de Luca, X. M., Parsons, M. T., Ferguson, K., Reid, L. E., et al. (2019) · Annals of Oncology · doi:10.1093/annonc/mdz132 · Cited by 93
“Despite the role of TP53, ATM and CHEK2 in DNA-damage signalling and double-strand breaks detection, these tumours do not show evidence of BRCA-deficient signatures, as previously described [9, 13, 19], but instead they harbour highly complex clustered chromosomal rearrangements.”
BackgroundSelf-citationMolecular profiling and molecular classification of endometrioid ovarian carcinomas
Cybulska, P., Paula, A. D. C., Tseng, J. H., Leitão, M. M., Bashashati, A., Huntsman, D. D., Nazeran, T. M., Aghajanian, C. A., Abu‐Rustum, N. R., DeLair, D. F., et al. (2019) · Gynecologic Oncology · doi:10.1016/j.ygyno.2019.07.012 · Cited by 101
“15)[17], and sequencing data analysis was performed as previously described [18,19].”
MethodSelf-citationGenomic Signatures Predict the Immunogenicity of BRCA-Deficient Breast Cancer
Kraya, A., Maxwell, K. N., Wubbenhorst, B. S., Wenz, B. M., Pluta, J. B., Rech, A. J., Dorfman, L. M., Lunceford, N., Barrett, A., Mitra, N., et al. (2019) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-0468 · Cited by 101
Ashley, C. W., Paula, A. D. C., Kumar, R., Mandelker, D. L., Pei, X., Riaz, N., Reis-Filho, J. S., & Weigelt, B. (2018) · Gynecologic Oncology · doi:10.1016/j.ygyno.2018.10.032 · Cited by 94
“Somatic copy number alterations and loss of heterozygosity (LOH) were defined using FACETS[25], as previously described[18].”
MethodInfluentialSelf-citationWarner, E. W., Herberts, C., Fu, S. Y. F., Yip, S., Wong, A., Wang, G., Ritch, E. J., Murtha, A. J., Vandekerkhove, G. R., Fonseca, N. M., et al. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-3708 · Cited by 90
“Conversely, ATM is a kinase that mediates phosphorylation of TP53 in response to DNA damage, and mutations in these two genes appear to be epistatic in breast cancer (28).”
BackgroundFasching, P. A., Yadav, S., Hu, C., Wunderle, M., Häberle, L., Hart, S. N., Rübner, M., Polley, E. C., Lee, K. Y., Gnanaolivu, R. D., et al. (2021) · Journal of Clinical Oncology · doi:10.1200/jco.20.01200 · Cited by 86
“Prior studies have demonstrated that BRCA1-associated breast tumors frequently exhibit HRD, but ATM tumors do not.(27) These differences need to be investigated further to identify whether carriers of mutations in different genes can be studied together in clinical trials.”
BackgroundSelf-citationHereditary breast cancer: syndromes, tumour pathology and molecular testing
Sokolova, A., Johnstone, K. J., Reed, A. E. M., Simpson, P. T., & Lakhani, S. R. (2022) · Histopathology · doi:10.1111/his.14808 · Cited by 95
“ATM variants are most commonly associated with ER-/PRpositive, HER2-negative (luminal B) subtype.(5,138,156,157) CHEK2 variants are associated with all intrinsic breast cancer subtypes except for triplenegative breast cancer.”
BackgroundSehdev, A., Gbolahan, O. B., Hancock, B. A., Stanley, M., Shahda, S., Wan, J., Wu, H. H., Radovich, M., & O’Neil, B. H. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-1472 · Cited by 82
“Of note, we excluded ATM gene mutations (seen in 2 patients) in our analysis as the emerging data suggests that ATM gene mutations does not contribute to homologous recombination DNA repair (34).”
BackgroundPareja, F. G., Brown, D. N., Lee, J. Y., Paula, A. D. C., Selenica, P., Bi, R., Geyer, F. C., Gazzo, A. M., da Silva, E. M., Vahdatinia, M., et al. (2020) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-19-2563 · Cited by 79
“Whole-exome and targeted sequencing analyses WES and MSK-IMPACT targeted sequencing analyses were performed as described in Weigelt and colleagues (21) and Pareja and colleagues (ref.”
MethodSelf-citationATM Dysfunction in Pancreatic Adenocarcinoma and Associated Therapeutic Implications
Armstrong, S. A., Schultz, C. W., Azimi-Sadjadi, A., Brody, J. R., & Pishvaian, M. J. (2019) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-19-0208 · Cited by 78
Pathogenic ATM Mutations in Cancer and a Genetic Basis for Radiotherapeutic Efficacy
Pitter, K. L., Casey, D. L., Lu, Y. C., Hannum, M., Zhang, Z., Song, X., Pecorari, I. L., McMillan, B., Ma, J., Samstein, R. M., et al. (2020) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djaa095 · Cited by 70
“tion of TP53, which we have previously described (30).”
BackgroundSelf-citationGenomic profiling of primary and recurrent adult granulosa cell tumors of the ovary
Paula, A. D. C., da Silva, E. M., Segura, S. E., Pareja, F. G., Bi, R., Selenica, P., Kim, S. H., Ferrando, L., Vahdatinia, M., Soslow, R. A., et al. (2020) · Modern Pathology · doi:10.1038/s41379-020-0514-3 · Cited by 64
Self-citationGermline Genetic Testing for Breast Cancer Risk: The Past, Present, and Future
Yadav, S., & Couch, F. J. (2019) · American Society of Clinical Oncology Educational Book · doi:10.1200/edbk_238987 · Cited by 61
Self-citationLee, J. Y., Schizas, M., Geyer, F. C., Selenica, P., Piscuoglio, S., Sakr, R. A., Ng, C. K. Y., Carniello, J. V. S., Towers, R., Giri, D. D., et al. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-1103 · Cited by 60
“Previous studies have demonstrated the equivalence between the TCGA pipeline and the pipeline employed in this study for mutation detection (19, 32).”
MethodSelf-citationHomologous recombination DNA repair defects in PALB2-associated breast cancers
Li, A., Geyer, F. C., Blecua, P., Lee, J. Y., Selenica, P., Brown, D. N., Pareja, F. G., Lee, S., Kumar, R., Rivera, B., et al. (2019) · npj Breast Cancer · doi:10.1038/s41523-019-0115-9 · Cited by 56
“Mutational signatures(40) were inferred from non-synonymous and silent somatic exonic SNVs (i) using deconstructSigs(41) based on the set of 30 mutational signatures represented in COSMIC(27) or (ii) on the 12 mutational signatures known to occur in breast cancers(27) and (iii) using a non-negative matrix factorizatio…”
MethodSelf-citationSelenica, P., Conlon, N., Gonzalez, C., Frosina, D., Jungbluth, A. A., Beets‐Tan, R. G. H., Rao, M., Zhang, Y., Benayed, R., Ladanyi, M., et al. (2020) · The American Journal of Surgical Pathology · doi:10.1097/pas.0000000000001572 · Cited by 56
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Self-citationLiu, Y. L., Selenica, P., Zhou, Q. C., Iasonos, A. E., Callahan, M. K., Feit, N. Z., Boland, J. L., Vázquez-Garćıa, I., Mandelker, D. L., Zehir, A., et al. (2020) · JCO Precision Oncology · doi:10.1200/po.20.00069 · Cited by 50
“LST scores, defined as a chromosomal breakpoint resulting in allelic imbalance between adjacent regions of at least 10 Mb, were determined, and a cutoff score ≥ 15 was used for LST-high cases, as previously described.(21,22,36,37)”
MethodResultInfluentialSelf-citationThe genomic landscape of metastatic histologic special types of invasive breast cancer
Pareja, F. G., Ferrando, L., Lee, S., de Beça, F. F., Selenica, P., Brown, D. N., Farmanbar, A., Paula, A. D. C., Vahdatinia, M., Zhang, H., et al. (2020) · npj Breast Cancer · doi:10.1038/s41523-020-00195-4 · Cited by 47
Self-citationSolid pseudopapillary neoplasms of the pancreas are dependent on the Wnt pathway
Selenica, P., Raj, N. P., Kumar, R., Brown, D. N., Arqués, O., Reidy‐Lagunes, D. L., Klimstra, D. S., Snuderl, M., Serrano, J., Pálmer, H. G., et al. (2019) · Molecular Oncology · doi:10.1002/1878-0261.12490 · Cited by 46
Self-citationMoukarzel, L. A., Paula, A. D. C., Ferrando, L., Hoang, T. J., Sebastião, A. P. M., Pareja, F. G., Park, K. J., Jungbluth, A. A., Capellá, G., Pineda, M., et al. (2020) · Modern Pathology · doi:10.1038/s41379-020-00721-6 · Cited by 49
Self-citationYadav, S., Kasi, P. M., Bamlet, W. R., Ho, T. P., Polley, E. C., Hu, C., Hart, S. N., Rabe, K. G., Boddicker, N. J., Gnanaolivu, R. D., et al. (2020) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-1788 · Cited by 44
“In a small study of 24 breast cancer tumors from germlineATM carriers, none of the tumors displayed high activity of mutational signature 3 associated with HRR defect (45).”
BackgroundSelf-citationInherited Rare, Deleterious Variants in ATM Increase Lung Adenocarcinoma Risk
Selvan, M. E., Zauderer, M. G., Rudin, C. M., Jones, S., Mukherjee, S., Offit, K., Onel, K., Rennert, G., Velculescu, V. E., Lipkin, S. M., et al. (2020) · Journal of Thoracic Oncology · doi:10.1016/j.jtho.2020.08.017 · Cited by 38
The Landscape of Somatic Genetic Alterations in Breast Cancers from CHEK2 Germline Mutation Carriers
Mandelker, D. L., Kumar, R., Pei, X., Selenica, P., Setton, J. S., Arunachalam, S., Ceyhan‐Birsoy, O., Brown, D. N., Norton, L., Robson, M. E., et al. (2019) · JNCI Cancer Spectrum · doi:10.1093/jncics/pkz027 · Cited by 36
“Akin to ATM -associated BCs (11), either the mechanism by which CHEK2 loss of function contributes to BC development may be independent of the HR pathway or the genomics signatures may differ from those caused by the loss of function of canonical HR-related genes.”
InfluentialSelf-citationA P53-Independent DNA Damage Response Suppresses Oncogenic Proliferation and Genome Instability
Fagan‐Solis, K. D., Simpson, D. A., Kumar, R. J., Martelotto, L. G., Mose, L. E., Rashid, N. U., Ho, A. Y., Powell, S. N., Wen, Y., Parker, J. S., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.01.020 · Cited by 37
Self-citationClinico-genomic Characterization of ATM and HRD in Pancreas Cancer: Application for Practice
Park, W., O'Connor, C. A., Bandlamudi, C., Forman, D., Chou, J. F., Umeda, S., Reyngold, M., Varghese, A. M., Keane, F., Balogun, F., et al. (2022) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-22-1483 · Cited by 34
Combined Tumor Sequencing and Case-Control Analyses of RAD51C in Breast Cancer
Li, N., McInerny, S., Zethoven, M., Cheasley, D. A., Lim, B. W. X., Rowley, S. M., Devereux, L., Grewal, N., Ahmadloo, S., Byrne, D. J., et al. (2019) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djz045 · Cited by 34
“tions, augmentation of case-control and family history data with information about the somatic landscape of the tumors occurring in carriers of rare pathogenic variants has recently been used to provide a detailed understanding of the role of ATM and PALB2 in breast cancer predisposition (10,11).”
BackgroundMethodInfluentialSelf-citationHomologous recombination deficiency: how genomic signatures are generated
Setton, J. S., Reis-Filho, J. S., & Powell, S. N. (2021) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2021.01.002 · Cited by 29
“This signature was first identified in tumors with biallelic BRCA1/2 inactivation [10], but has since been associated with BRCA1, RAD51C promoter methylation, and biallelic inactivation of downstream HR genes, including PALB2, RAD51C, and RAD51D, but not mutations in ATM or CHEK2 [5,11–13].”
BackgroundInfluentialSelf-citationDNA Repair Deficiency in Breast Cancer: Opportunities for Immunotherapy
Gilmore, E. S., McCabe, N., Kennedy, R. D., & Parkes, E. E. (2019) · Journal of Oncology · doi:10.1155/2019/4325105 · Cited by 32
“Whereas BRCA1/2 mutant breast tumors have been recognised to be associated with increased lymphocytic infiltrate [87], early data suggests that loss of other DNA repair response proteins (for example, ATM) results in a markedly altered immune response and tumor microenvironment, with low levels of tumor infiltrating l…”
BackgroundClinical patterns and genomic profiling of recurrent ‘ultra-low risk’ endometrial cancer
Stasenko, M., Feit, N. Z., Lee, S., Shepherd, C., Soslow, R. A., Cadoo, K. A., Alektiar, K. M., da Silva, E. M., Sebastião, A. P. M., Leitão, M. M., et al. (2020) · International Journal of Gynecological Cancer · doi:10.1136/ijgc-2020-001241 · Cited by 32
Self-citationTERT promoter hotspot mutations and gene amplification in metaplastic breast cancer
da Silva, E. M., Selenica, P., Vahdatinia, M., Pareja, F. G., Paula, A. D. C., Ferrando, L., Gazzo, A. M., Dopeso, H., Ross, D. S., Bakhteri, A., et al. (2021) · npj Breast Cancer · doi:10.1038/s41523-021-00250-8 · Cited by 31
Self-citationIntratumor genetic heterogeneity and clonal evolution to decode endometrial cancer progression
Mota, A., Oltra, S. S., Selenica, P., Moiola, C. P., Casas‐Arozamena, C., López-Gil, C., Díaz, E., Gatius, S., Ruiz-Miró, M., Calvo, A., et al. (2022) · Oncogene · doi:10.1038/s41388-022-02221-0 · Cited by 30
“Consistent with previous observations demonstrating that ATM and TP53 loss of function mutations are mutually exclusive [87], this high-grade AEC lacked TP53 mutations, yet it harbored bi-allelic ATM inactivation.”
Self-citationGenomic Alterations as Potential Therapeutic Targets in Extramammary Paget’s Disease of the Vulva
Stasenko, M., Jayakumaran, G., Cowan, R. A., Broach, V. A., Dennis, S., Rossi, A., Hollman, T. J., Zehir, A., Abu‐Rustum, N. R., & Leitão, M. M. (2020) · JCO Precision Oncology · doi:10.1200/po.20.00073 · Cited by 29
“Sequencing data analyses were performed, and mutations, copy number variations, and structural rearrangements were identified and annotated using validated bioinformatics approaches, as previously described.(14,15) These molecular alterations were further curated using OncoKB (Memorial Sloan Kettering Cancer Center, N…”
MethodSelf-citationBlom, M., Schoenaker, M. H. D., Hulst, M., de Vries, M. C., Weemaes, C. M. R., Willemsen, M. A. A. P., Henneman, L., & van der Burg, M. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.02438 · Cited by 26
“, the parents of the newborn that underwent NBS, have a slightly decreased life expectancy and increased risk of developing cancer, especially breast cancer (11, 12).”
BackgroundMassively parallel sequencing analysis of benign melanocytic naevi
Lozada, J. R., Geyer, F. C., Selenica, P., Brown, D. N., Alemar, B., Merghoub, T., Berger, M. F., BUSAM, K. J., Halpern, A. C., Weigelt, B., et al. (2019) · Histopathology · doi:10.1111/his.13843 · Cited by 27
“We further excluded SNVs and indels for which the tumour mutant allele fraction (MAF) was less than five times that of the paired normal MAF, and SNVs and indels found at >5% global minor allele frequency of dbSNP (build 137), as previously described.(30,31) FACETS(32) was used to calculate log2 ratios and B allele fr…”
BackgroundMethodInfluentialSelf-citationMultiple Primary Cancers in Patients Undergoing Tumor-Normal Sequencing Define Novel Associations
Liu, Y. L., Cadoo, K. A., Mukherjee, S., Khurram, A., Tkachuk, K., Kemel, Y. M., Maio, A., Belhadj, S., Carlo, M. I., Latham, A. J., et al. (2021) · Cancer Epidemiology Biomarkers & Prevention · doi:10.1158/1055-9965.epi-21-0820 · Cited by 23
“Further studies are needed to evaluate the contribution of moderate/low penetrance genes (31, 32) in the broad spectrum of tumor types observed, as well as gene–gene and gene–environment interactions (4), and the role of genetic modifiers (33, 34), and further work building on this study is ongoing.”
BackgroundSelf-citationWeigelt, B., Vargas, H. A., Selenica, P., Geyer, F. C., Mazaheri, Y., Blecua, P., Conlon, N., Hoang, L. N., Jungbluth, A. A., Snyder, A., et al. (2019) · JCO Precision Oncology · doi:10.1200/po.18.00410 · Cited by 23
“Whole-exome sequencing (WES) of the microdissected tumor and matched normal DNA samples was performed as described.(15,16) One hundred nine ASSOCIATED CONTENT Appendix Author affiliations and support information (if applicable) appear at the end of this article.”
MethodSelf-citationMorphologic and Genomic Heterogeneity in the Evolution and Progression of Breast Cancer
Kutasovic, J. R., Reed, A. E. M., Sokolova, A., Lakhani, S. R., & Simpson, P. T. (2020) · Cancers · doi:10.3390/cancers12040848 · Cited by 24
Converging and evolving immuno-genomic routes toward immune escape in breast cancer
Blanco-Heredia, J., Souza, C. A., Trincado, J. L., González‐Cao, M., Gonçalves-Ribeiro, S., Gil, S. R., Pravdyvets, D., Cedeño, S., Callari, M., Marra, A., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-45292-1 · Cited by 22
“0.6) 45 , as previously reported 46,47 .”
InfluentialSelf-citationPal, T., Schon, K. R., Astiazarán-Symonds, E., Balmañà, J., Foulkes, W. D., James, P. A., Klugman, S. D., Livinski, A. A., Mak, J. S., Ngeow, J. Y. Y., et al. (2024) · Genetics in Medicine · doi:10.1016/j.gim.2024.101243 · Cited by 22
Self-citationFirst international workshop of the ATM and cancer risk group (4-5 December 2019)
Lesueur, F., Easton, D. F., Renault, A., Tavtigian, S. V., Bernstein, J. L., Kote‐Jarai, Z., Eeles, R. A., Plaseska-Karanfia, D., Feliubadaló, L., Spanish ATM working group, et al. (2021) · Familial Cancer · doi:10.1007/s10689-021-00248-y · Cited by 21
Self-citationLi, N., Lim, B. W. X., Thompson, E. R., McInerny, S., Zethoven, M., Cheasley, D. A., Rowley, S. M., Wong‐Brown, M. W., Devereux, L., Gorringe, K. L., et al. (2021) · npj Breast Cancer · doi:10.1038/s41523-021-00279-9 · Cited by 21
Self-citationRichardson, E. T., Selenica, P., Pareja, F. G., Cin, P. D., Hanlon, E., Weigelt, B., Reis-Filho, J. S., Hornick, J. L., Jo, V. Y., & Schnitt, S. J. (2023) · Modern Pathology · doi:10.1016/j.modpat.2023.100144 · Cited by 21
Self-citationMcGee, R. B., Oak, N., Harrison, L. H., Xu, K., Nuccio, R., Blake, A. K., Mostafavi, R. M., Lewis, S., Taylor, L. M., Kubal, M., et al. (2023) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-22-2482 · Cited by 20
Barakeh, D. H., Aljelaify, R. F., Bashawri, Y., Almutairi, A., Alqubaishi, F., Alnamnakani, M., AlMubarak, L., Naeem, A. A., AlMushawah, F., Alrashed, M. M., et al. (2021) · Oncotarget · doi:10.18632/oncotarget.27909 · Cited by 19
“The majority of Arab BCa cases are not caused by inherited genetic factors but are associated with somatic mutations in breast cells that accumulate over time [44].”
BackgroundPilie, P. G., Giuliani, V., Wang, W., McGrail, D. J., Bristow, C. A., Ngoi, N. Y. L., Kyewalabye, K., Wani, K., Le, H., Campbell, E., et al. (2024) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-23-1763 · Cited by 20
“Mutations in ATM and TP53 genes have been previously shown to be relatively mutually exclusive in certain cancers, which is consistent with our fi ndings herein with tissue-speci fi c differences (4, 41, 46).”
Pareja, F. G., Vahdatinia, M., Marchiò, C., Lee, S., Paula, A. D. C., Derakhshan, F. N., da Silva, E. M., Selenica, P., Dopeso, H., Chandarlapaty, S., et al. (2020) · Journal of Clinical Pathology · doi:10.1136/jclinpath-2020-207052 · Cited by 18
Self-citationKahn, R. M., Selenica, P., Boerner, T., Roche, K. L., Xiao, Y., Sia, T., Maio, A., Kemel, Y. M., Sheehan, M. R., Salo‐Mullen, E. E., et al. (2023) · Gynecologic Oncology · doi:10.1016/j.ygyno.2023.11.019 · Cited by 18
Self-citationRadosevic‐Robin, N., Selenica, P., Zhu, Y., Won, H. H., Berger, M. F., Ferrando, L., Cocco, E., Privat, M., Ponelle‐Chachuat, F., Abrial, C., et al. (2021) · npj Breast Cancer · doi:10.1038/s41523-021-00334-5 · Cited by 17
Self-citationNew Therapeutic Options for BRCA Mutant Patients
Ghanem, A., & Domchek, S. M. (2024) · Annual Review of Medicine · doi:10.1146/annurev-med-082523-083843 · Cited by 17
To indel or not to indel: Factors influencing mutagenesis during chromosomal break end joining
Cisneros‐Aguirre, M., Ping, X., & Stark, J. M. (2022) · DNA repair · doi:10.1016/j.dnarep.2022.103380 · Cited by 18
“In contrast, ATM is not obviously important for HR repair of DSBs [85,86], and breast cancers associated with ATM-deficiency show mutation/rearrangement signatures distinct from those of HRdeficient tumors [87].”
BackgroundSclerosing epithelioid mesenchymal neoplasm of the pancreas – a proposed new entity
Baştürk, O., Weigelt, B., Adsay, V. N., Benhamida, J. K., Aşkan, G., Wang, L., Arcila, M. E., Zamboni, G., Fukushima, N., Gularte‐Mérida, R., et al. (2019) · Modern Pathology · doi:10.1038/s41379-019-0334-5 · Cited by 15
Self-citationVeeraraghavan, J., Gutiérrez, C., Angelis, C. D., Davis, R., Wang, T., Pascual, T., Selenica, P., Sanchez, K., Nitta, H., Kapadia, M. J., et al. (2023) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-22-3753 · Cited by 14
Self-citationMeijer, T. G., Martens, J. W. M., der Smissen, W. J. C. P., Verkaik, N. S., Beaufort, C. M., van Herk, S., Robert-Finestra, T., Hoogenboezem, R. M., Ruigrok-Ritstier, K., Paul, M. W., et al. (2024) · Cancers · doi:10.3390/cancers16040741 · Cited by 13
“However, ATM promoter methylation is unlikely to be causal for the HRD phenotype of HCC2218, since pathogenic germline mutations of ATM also do not cause HRD [46,47].”
BackgroundAdvances in the Understanding of the Pathogenesis of Triple‐Negative Breast Cancer
Liu, Y., Zou, Y., Ye, Y., & Chen, Y. (2024) · Cancer Medicine · doi:10.1002/cam4.70410 · Cited by 15
Lim, B. W. X., Li, N., Mahale, S., McInerny, S., Zethoven, M., Rowley, S. M., Huynh, J., Wang, T., Lee, J. E. A., Friedman, M., et al. (2022) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djac196 · Cited by 13
“It is interesting to note that most of the established HBC genes that have been shown to undergo frequent biallelic inactivation in breast tumors, such as BRCA1, BRCA2, PALB2, and RAD51C, are highly penetrant and/or predispose selectively to TNBC, currently the sole exception being ATM, which is a moderate penetrance…”
MethodInfluentialSelf-citationMolecular characterization of high-grade serous ovarian cancers occurring in younger and older women
Filippova, O. T., Selenica, P., Pareja, F. G., Vahdatinia, M., Zhu, Y., Pei, X., Riaz, N., Roche, K. L., Dennis, S., Abu‐Rustum, N. R., et al. (2021) · Gynecologic Oncology · doi:10.1016/j.ygyno.2021.02.028 · Cited by 13
Self-citationThe utility of homologous recombination deficiency biomarkers across cancer typesPreprint
Takamatsu, S., Brown, J. B., Yamaguchi, K. D., Hamanishi, J., Yamanoi, K., Takaya, H., Kaneyasu, T., Mori, S., Mandai, M., & Matsumura, N. (2021) · medRxiv · doi:10.1101/2021.02.18.21251882 · Cited by 13
Jabbour, T. E., Misyura, M., Cowzer, D., Zimmermann, M., Rimkunas, V. M., Marra, A., Derakhshan, F. N., Selenica, P., Parilla, M., Setton, J. S., et al. (2022) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djac024 · Cited by 13
Self-citationHomologous recombination deficiency and hemizygosity drive resistance in breast cancer
Safonov, A. M., Lee, M. K., Brown, D. N., Bielo, L. B., Mehine, M. M., Bandlamudi, C., O’Leary, B., Shao, H., Vicente, L., Muldoon, D. M., et al. (2026) · Nature · doi:10.1038/s41586-026-10197-0 · Cited by 13
“This analysis robustly validated previously reported enrichment of TP53 alterations in g BRCA1 carriers and mutual exclusivity of g ATM and TP53 alterations 30,31 (Fig.”
Self-citationZammarrelli, W. A., Kim, S. H., Paula, A. D. C., Rios‐Doria, E., Ehmann, S., Yeoshoua, E., Hanlon, E., Zhou, Q. C., Iasonos, A. E., Alektiar, K. M., et al. (2022) · JCO Precision Oncology · doi:10.1200/po.22.00194 · Cited by 11
Self-citationAnalysis, identification and visualization of subgroups in genomics
Völkel, G., Laban, S. A., Fürstberger, A., Werle, S. D., Ikonomi, N., Hoffmann, T. K., Brunner, C., Neuberg, D. S., Gaidzik, V. I., Döhner, H., et al. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa217 · Cited by 11
“In these sets,AVAtar identified crucial genes for breast cancer as ATM [26, 33, 36, 66, 69, 112] and BRCA2 [42, 63, 72, 93, 102, 104] that were not found by the Multi-Dendrix approach.”
Performance of a RAD51-based functional HRD test on paraffin-embedded breast cancer tissue
van Wijk, L. M., Vermeulen, S., ter Haar, N. T., Kramer, C. J. H., Terlouw, D., Vrieling, H., Cohen, D., & Vreeswijk, M. P. G. (2023) · Breast Cancer Research and Treatment · doi:10.1007/s10549-023-07102-y · Cited by 11
“Similarly, breast tumors with ATM PVs lack HRD-related mutational signatures, in line with our functional classification of sample BC-26 with an ATM PV as HRP [41].”
BackgroundNonrepair functions of DNA mismatch repair proteins: new avenues for precision oncology
DeWitt, J. T., Raghunathan, M., & Haricharan, S. (2024) · Trends in cancer · doi:10.1016/j.trecan.2024.10.001 · Cited by 10
Germline ATM Mutations Detected by Somatic DNA Sequencing in Lethal Prostate Cancer
Grochot, R. M., Carreira, S., Miranda, S., Figueiredo, I., Bertan, C. M., Rekowski, J., Yuan, W., Ferreira, A., Riisnaes, R., Neeb, A., et al. (2023) · European Urology Open Science · doi:10.1016/j.euros.2023.04.003 · Cited by 11
“Preservation of protein expression by IHC, in the setting of biallelic loss, is not uncommon, for example, depending on the assay used, abnormal truncated protein may still be detectable by antibody binding its epitope on expressed nonfunctional protein [23].”
BackgroundSmid, M., Schmidt, M. K., der Smissen, W. J. C. P., Ruigrok-Ritstier, K., Schreurs, M. A. C., Cornelissen, S., Garcia, A. M., Broeks, A., Timmermans, A. M., Trapman-Jansen, A., et al. (2023) · Breast Cancer Research · doi:10.1186/s13058-023-01653-0 · Cited by 10
The cold immunological landscape of ATM-deficient cancers
Sinha, S., Ng, V., Novaj, A., Zhu, Y., Yazaki, S., Pei, X., Derakhshan, F. N., Pareja, F. G., Setton, J. S., Naulin, F., et al. (2025) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2024-010548 · Cited by 8
“35 Further, in both human tumors and our isogenic models, we did not observe evidence of increased T-cell infiltrate on ATM loss.”
Self-citationDavidson, A. L., Michailidou, K., Parsons, M. T., Fortuño, C., Bolla, M. K., Wang, Q., Dennis, J., Naven, M., Abubakar, M., Ahearn, T. U., et al. (2024) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2024.07.004 · Cited by 7
Self-citationPARP inhibition in prostate cancer
Nientiedt, C., Duensing, A. U., Zschäbitz, S., Jäger, D., Hohenfellner, M., Stenzinger, A., & Duensing, S. M. (2020) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22903 · Cited by 10
“Analyses of ATM mutated breast cancers have shown that these tumors lack characteristic genomic features commonly found in the presence of HRR deficiency and also exhibit distinct immune infiltrates compared to BRCA1/2 mutated tumors.(57) CDK12 is a cyclin-dependent kinase, which is indirectly involved in HRR through…”
BackgroundWhole‐exome sequencing analysis of juvenile papillomatosis and coexisting breast carcinoma
D’Alfonso, T. M., Pareja, F. G., Paula, A. D. C., Vahdatinia, M., Gazzo, A. M., Ferrando, L., da Silva, E. M., Cheng, E., Sclafani, L. M., Chandarlapaty, S., et al. (2020) · The Journal of Pathology Clinical Research · doi:10.1002/cjp2.190 · Cited by 8
Self-citationGarg, T., Weiss, C. R., & Sheth, R. A. (2022) · Cancers · doi:10.3390/cancers14153628 · Cited by 7
Molecular Basis of Breast Tumor Heterogeneity
Dikoglu, E., & Pareja, F. G. (2025) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-70875-6_13 · Cited by 6
Self-citationExtended gene panel testing in lobular breast cancer
van Veen, E. M., Evans, D. G., Harkness, E. F., Byers, H., Ellingford, J. M., Woodward, E. R., Bowers, N. L., Wallace, A. J., Howell, S. J., Howell, A., et al. (2021) · Familial Cancer · doi:10.1007/s10689-021-00241-5 · Cited by 6
Prasad, A., Bhargava, H., Gupta, A., Shukla, N., Rajagopal, S. P., Gupta, S., Sharma, A., Valadi, J. K., Nigam, V. K., & Suravajhala, P. (2021) · Springer eBooks · doi:10.1007/978-981-33-6191-1_14 · Cited by 6
Ashley, C. W., Paula, A. D. C., Ferrando, L., Gularte‐Mérida, R., Sebastião, A. P. M., Brown, D. N., Gazzo, A. M., Pareja, F. G., Stylianou, A. A., Abu‐Rustum, N. R., et al. (2021) · Histopathology · doi:10.1111/his.14346 · Cited by 6
Self-citationPham, A. T., Yuan, F., Nagathihalli, N. S., & Dosch, A. R. (2026) · Neoplasia · doi:10.1016/j.neo.2026.101309 · Cited by 5
“However, significant variability exists across platforms and thresholds used to define ATM loss, making cross-study comparison difficult[227].”
Oyouni, A. A. A. (2022) · Journal of King Saud University - Science · doi:10.1016/j.jksus.2022.101961 · Cited by 5
Genomic landscape of breast cancer in elderly patients
Selenica, P., Dopeso, H., Repetto, M., Basili, T., Gazzo, A. M., Schwartz, C. J., Derakhshan, F. N., Marra, A., Ferrando, L., Beets‐Tan, R. G. H., et al. (2025) · npj Breast Cancer · doi:10.1038/s41523-025-00781-4 · Cited by 6
“The raw MSK-IMPACT sequencing data (i.e., BAM fi les) were reprocessed using our validated bioinformatics pipeline, as previously described 19,62,63 , for the inference of genome-wide copy number gains and losses, loss of heterozygosity (LOH) of genes targeted by somatic mutations and mutational…”
Self-citationJiang, X., O'Neill, A., Smith, K. R., Lai, Z., Carss, K., Wang, Q., & Petrovski, S. (2022) · Genes Chromosomes and Cancer · doi:10.1002/gcc.23042 · Cited by 4
“Although A-T is a rare disorder with an estimated global prevalence between 1 in 40 000 and 1 in 100 000 live births, heterozygous germline variants in ATM are estimated to occur in 1% of the population and can increase risk of cancer.(2) Small studies using gene-level burden tests and/or variant-level association ana…”
BackgroundMolecular diagnosis in breast cancer
Pareja, F. G., Marchiò, C., & Reis-Filho, J. S. (2018) · Diagnostic histopathology · doi:10.1016/j.mpdhp.2018.01.001 · Cited by 4
Self-citationGawade, P., Nandi, S., Meena, C., & Sarkar, R. R. (2022) · Springer eBooks · doi:10.1007/978-981-19-1953-4_2 · Cited by 4
Comprehensive profiling of pathogenic germline large genomic rearrangements in a pan‐cancer analysis
Sun, Z., Bai, C., Su, M., Tang, H., Wu, X., Wang, Y., Bao, H., Liu, X., Wu, X., Shao, Y., et al. (2023) · Molecular Oncology · doi:10.1002/1878-0261.13430 · Cited by 3
Cursano, M. C., Giunta, E. F., Scarpi, E., Casadei, C., Virga, A., Ulivi, P., Bleve, S., Brighi, N., Ravaglia, G., Pantano, F., et al. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241512436 · Cited by 3
Subramanian, D., Zethoven, M., Pishas, K. I., Marinović, E. R., McInerny, S., Rowley, S. M., Allan, P. E., Devereux, L., Cheasley, D. A., James, P. A., et al. (2025) · npj Genomic Medicine · doi:10.1038/s41525-024-00447-3 · Cited by 3
“Inearlier work, we and others demonstrated the utility of integrating tumour sequencing data from germline variant carriers as a means of providingstrongorthogonalevidencefororagainsttheroleofanewgenein cancer predisposition through identi fi cation of biallelic inactivation 9,16,41 – 43 .”
Self-citationViart, N. M., Renault, A., Eon, S., Jiao, Y., Fuhrmann, L., Houdigui, S. M. E., Gal, D. L., Cavaciuti, E., Dondon, M., Beauvallet, J., et al. (2025) · Breast Cancer Research · doi:10.1186/s13058-025-01988-w · Cited by 3
“We showed that breast tumors developed by ATM PV carriers are more frequently estrogen receptor-positive (ER+; in 97% of the cases) [18], consistent with other studies [11, 12, 19–21], and of histological subtype luminal B or luminal B/HER2 + in 60.7% of the cases.”
InfluentialXu, P., Sun, Y., Song, Y., Jiao, J., Shen, B., Li, W., Jiang, C., Li, Y., Zhang, X., Yu, J., et al. (2020) · Medical Molecular Morphology · doi:10.1007/s00795-020-00247-5 · Cited by 4
AlphaMissense for Identifying Pathogenic Missense Mutations in DNA Damage Repair Genes in Cancer
Yazaki, S., Pei, X., Powell, S. N., Khan, A. J., Setton, J. S., & Riaz, N. (2025) · JCO Precision Oncology · doi:10.1200/po-24-00908 · Cited by 4
Self-citationGatz, S. A., Bender, J. G., Pearson, A. D. J., Ortiz, M. V., Bernardi, R. J., Chesler, L., Clifford, S., Cohen‐Gogo, S., Cuesta, E. A. D. L., de Rojas, T., et al. (2026) · JCO Precision Oncology · doi:10.1200/po-25-00642 · Cited by 2
“…to determine 37,45 because of (1) the dif fi culty in predicting whether a speci fi c mutation is deleterious or a variant of uncertain signi fi - cance, 56 (2) the zygosity of the alteration which may affect the loss of protein function, 57 and (3) nonharmonized immunohistochemistry protocols.”
Metadata
- Authors
- Weigelt, B., Bi, R., Kumar, R., Blecua, P., Mandelker, D. L., Geyer, F. C., Pareja, F., James, P. A., kConFab Investigators, Couch, F. J., Eccles, D. M., Blows, F., Pharoah, P., Li, A., Selenica, P., Lim, R. S., Jayakumaran, G., Waddell, N., Shen, R., Norton, L., Wen, H. Y., Powell, S. N., Riaz, N., Robson, M. E., Reis-Filho, J. S., & Chenevix-Trench, G.
- Affiliations
- Memorial Sloan Kettering Cancer Center (US)
- Peter MacCallum Cancer Centre (AU)
- Mayo Clinic (US)
- University of Cambridge (GB)
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia (NW, GCT)
- Corresponding author
- Reis-Filho, Jorge S
- ORCID
- Weigelt, Britta
- Bi, Rui
- Kumar, Rahul
- Blecua, Pedro
- Mandelker, Diana L
- Geyer, Felipe C
- Pareja, Fresia
- James, Paul A
- Couch, Fergus J
- Eccles, Diana M
- Pharoah, Paul
- Li, Anqi
- Selenica, Pier
- Lim, Raymond S
- Jayakumaran, Gowtham
- Shen, Ronglai
- Norton, Larry
- Wen, Hannah Y
- Powell, Simon N
- Riaz, Nadeem
- Robson, Mark E
- Reis-Filho, Jorge S
- Venue
- JNCI: Journal of the National Cancer Institute
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-02-28
- Volume
- 110
- Issue
- 9
- Pages
- 1030-1034
- ISSN
- 0027-8874 (ISSN-L)
- 1460-2105
- PMC
- PMC6136925
- OpenAlex
- W2792571019
- Cited by
- 128
- References
- 22
- Citations by year
- 2026: 9 · 2025: 11 · 2024: 13 · 2023: 17 · 2022: 16 · 2021: 19 · 2020: 21 · 2019: 18 · 2018: 4
- FWCI
- 9.49
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- JNCI Journal of the National Cancer Institute (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- ePrints Soton (University of Southampton) (acceptedVersion)
- Apollo (University of Cambridge) (submittedVersion)
- Apollo
- Funders
- Meredith Israel Thomas Fund
- Breast Cancer Research Foundation
- National Institutes of Health
- National Cancer Institute (P30CA008748)
- NIH (CA192393, CA176785)
- National Health and Medical Research Council of Australia
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › BRCA gene mutations in cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Keywords
- breast cancer, somatic alterations, loss of heterozygosity, TP53 mutation, epistasis, hormone receptor-positive breast cancer, tumor immune infiltrate, DNA damage response
- MeSH terms
- Exome Sequencing, Adult, Aged, Breast Neoplasms, Female, Heterozygote, Humans, Middle Aged, Mutation, Biomarkers, Tumor, Germ-Line Mutation, Genetic Predisposition to Disease, Genomics, Genetic Association Studies, Ataxia Telangiectasia Mutated Proteins
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