Molecular evaluation of residual disease following neoadjuvant chemotherapy in triple-negative breast cancer CALGB 40603 (Alliance).

Patrick D R&#xe4;dler; Brooke M Felsheim; Aranzazu Fernandez-Martinez; Adam D Pfefferle; Michele C Hayward; Baljit Singh; William Sikov; Lisa A Carey; Charles M Perou

doi:10.1172/jci205962

PubMed · 42550611

Molecular evaluation of residual disease following neoadjuvant chemotherapy in triple-negative breast cancer CALGB 40603 (Alliance).

Patrick D Rädler·Brooke M Felsheim·Aranzazu Fernandez-Martinez·Adam D Pfefferle·Michele C Hayward·Baljit Singh·William Sikov·Lisa A Carey·Charles M Perou

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Abstract

BACKGROUNDDespite therapeutic advances in early-stage triple-negative breast cancer (TNBC), residual disease (RD) following neoadjuvant therapy remains a key predictor of a worse prognosis and obstacle to improving patient outcomes.METHODSTo better characterize RD and identify survival-associated features, we performed comprehensive transcriptomic profiling of 340 pretreatment stage II/III TNBCs and 70 matched posttreatment RD samples from the randomized CALGB 40603 (Alliance) phase II clinical trial. To explore preclinical treatment strategies for RD, patient-derived xenograft (PDX) mouse models mimicking RD were treated with antibody-drug conjugates (ADCs).RESULTSOur study shows prognostic genomic features measured pretreatment may differ from prognostic features measured posttreatment from RD specimens. Patients with a genomic PAM50 subtype of basal-like in RD specimens had a poor survival outcome, and their matching pretreatment tumors were characterized by elevated chromosomal amplifications of oncogenic drivers and significantly reduced B and T cell expression features. Paired analyses of basal-like RD and matched pretreatment tumors revealed further lymphocyte depletion in RD, along with lower expression of MHC class I and interferon signaling, indicating an immune-cold RD microenvironment. Treatment of a basal-like and conventional chemotherapy-resistant PDX model, resembling basal-like RD, with sacituzumab govitecan or trastuzumab deruxtecan produced a marked antitumor response.CONCLUSIONRD biology differs from pretreatment tumors, with basal-like subtype RD following neoadjuvant chemotherapy being immune cold and associated with poor survival. Preclinical modeling suggests this high-risk group may benefit from adjuvant ADC therapy.TRIAL REGISTRATIONClinicalTrials.gov NCT00861705.FUNDINGNIH NCI U10CA180821 (Alliance for Clinical Trials in Oncology), NCI U24CA176171 (Alliance for Clinical Trials in Oncology), NCI UG1CA233373 (Alliance for Clinical Trials in Oncology), NCI Breast SPORE program P50-CA058223; Susan G. Komen SAC-160074; Breast Cancer Research Foundation BCRF-23-127; NIH NCI R01-CA229409; UNC LCCC Triple Negative Breast Cancer Center.

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Humans Female Triple Negative Breast Neoplasms Animals Neoadjuvant Therapy Neoplasm, Residual Mice Immunoconjugates Middle Aged Xenograft Model Antitumor Assays Biomarkers Breast cancer Clinical Research Oncology Transcriptomics Journal Article Clinical Trial, Phase II Randomized Controlled Trial

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Patrick D Rädler, Brooke M Felsheim, Aranzazu Fernandez-Martinez, Adam D Pfefferle, Michele C Hayward, Baljit Singh, William Sikov, Lisa A Carey, Charles M Perou. 2026-08-04. Molecular evaluation of residual disease following neoadjuvant chemotherapy in triple-negative breast cancer CALGB 40603 (Alliance).. https://doi.org/10.1172/jci205962

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Animals subject Biomarkers subject Clinical Trial, Phase II subject Female subject Humans subject Journal Article subject Mice subject Middle Aged subject Oncology subject Randomized controlled trials study

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