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Cancer Discov DOI:10.1158/2159-8290.CD-22-0200

Proteogenomic Markers of Chemotherapy Resistance and Response in Triple-Negative Breast Cancer.

Publication TypeJournal Article
Year of Publication2022
AuthorsAnurag, M, Jaehnig, EJ, Krug, K, Lei, JT, Bergstrom, EJ, Kim, B-J, Vashist, TD, Huynh, AMinh Tran, Dou, Y, Gou, X, Huang, C, Shi, Z, Wen, B, Korchina, V, Gibbs, RA, Muzny, DM, Doddapaneni, HV, Dobrolecki, LE, Rodriguez, H, Robles, AI, Hiltke, T, Lewis, MT, Nangia, JR, Shafaee, MNemati, Li, S, Hagemann, IS, Hoog, J, Lim, B, C Osborne, K, Mani, DR, Gillette, MA, Zhang, B, Echeverria, GV, Miles, G, Rimawi, MF, Carr, SA, Ademuyiwa, FO, Satpathy, S, Ellis, MJ
JournalCancer Discov
Date Published2022 Nov 02
KeywordsAntineoplastic Combined Chemotherapy Protocols, Carboplatin, Humans, Neoadjuvant Therapy, Proteogenomics, Proteomics, Triple Negative Breast Neoplasms, X-ray Repair Cross Complementing Protein 1

UNLABELLED: Microscaled proteogenomics was deployed to probe the molecular basis for differential response to neoadjuvant carboplatin and docetaxel combination chemotherapy for triple-negative breast cancer (TNBC). Proteomic analyses of pretreatment patient biopsies uniquely revealed metabolic pathways, including oxidative phosphorylation, adipogenesis, and fatty acid metabolism, that were associated with resistance. Both proteomics and transcriptomics revealed that sensitivity was marked by elevation of DNA repair, E2F targets, G2-M checkpoint, interferon-gamma signaling, and immune-checkpoint components. Proteogenomic analyses of somatic copy-number aberrations identified a resistance-associated 19q13.31-33 deletion where LIG1, POLD1, and XRCC1 are located. In orthogonal datasets, LIG1 (DNA ligase I) gene deletion and/or low mRNA expression levels were associated with lack of pathologic complete response, higher chromosomal instability index (CIN), and poor prognosis in TNBC, as well as carboplatin-selective resistance in TNBC preclinical models. Hemizygous loss of LIG1 was also associated with higher CIN and poor prognosis in other cancer types, demonstrating broader clinical implications.

SIGNIFICANCE: Proteogenomic analysis of triple-negative breast tumors revealed a complex landscape of chemotherapy response associations, including a 19q13.31-33 somatic deletion encoding genes serving lagging-strand DNA synthesis (LIG1, POLD1, and XRCC1), that correlate with lack of pathologic response, carboplatin-selective resistance, and, in pan-cancer studies, poor prognosis and CIN. This article is highlighted in the In This Issue feature, p. 2483.


Alternate JournalCancer Discov
PubMed ID36001024
PubMed Central IDPMC9627136
Grant ListU54 CA224076 / CA / NCI NIH HHS / United States
U24 CA210986 / CA / NCI NIH HHS / United States
U01 CA214125 / CA / NCI NIH HHS / United States
P50 CA186784 / CA / NCI NIH HHS / United States
U24 CA210954 / CA / NCI NIH HHS / United States
U24 CA160034 / CA / NCI NIH HHS / United States
U24 CA226110 / CA / NCI NIH HHS / United States
U54 CA224083 / CA / NCI NIH HHS / United States
T32 CA203690 / CA / NCI NIH HHS / United States