Spatial proteomic characterization of HER2-positive breast tumors through neoadjuvant therapy predicts response

The addition of HER2-targeted agents to neoadjuvant chemotherapy has dramatically improved pathological complete response (pCR) rates in early-stage, HER2-positive breast cancer. Nonetheless, up to 50% of patients have residual disease after treatment, while others are likely overtreated. Here, we performed multiplex spatial proteomic characterization of 122 samples from 57 HER2-positive breast tumors from the neoadjuvant TRIO-US B07 clinical trial sampled pre-treatment, after 14-21 d of HER2-targeted therapy and at surgery. We demonstrated that proteomic changes after a single cycle of HER2-targeted therapy aids the identification of tumors that ultimately undergo pCR, outperforming pre-treatment measures or transcriptomic changes. We further developed and validated a classifier that robustly predicted pCR using a single marker, CD45, measured on treatment, and showed that CD45-positive cell counts measured via conventional immunohistochemistry perform comparably. These results demonstrate robust biomarkers that can be used to enable the stratification of sensitive tumors early during neoadjuvant HER2-targeted therapy, with implications for tailoring subsequent therapy.

Pathologic and molecular responses to neoadjuvant trastuzumab and/or lapatinib from a phase II randomized trial in HER2-positive breast cancer (TRIO-US B07)

In this multicenter, open-label, randomized phase II investigator-sponsored neoadjuvant trial with funding provided by Sanofi and GlaxoSmithKline (TRIO-US B07, Clinical Trials NCT00769470), participants with early-stage HER2-positive breast cancer (N = 128) were recruited from 13 United States oncology centers throughout the Translational Research in Oncology network. Participants were randomized to receive trastuzumab (T; N = 34), lapatinib (L; N = 36), or both (TL; N = 58) as HER2-targeted therapy, with each participant given one cycle of this designated anti-HER2 therapy alone followed by six cycles of standard combination chemotherapy with the same anti-HER2 therapy. The primary objective was to estimate the rate of pathologic complete response (pCR) at the time of surgery in each of the three arms. In the intent-to-treat population, we observed similar pCR rates between T (47%, 95% confidence interval [CI] 30-65%) and TL (52%, 95% CI 38-65%), and a lower pCR rate with L (25%, 95% CI 13-43%). In the T arm, 100% of participants completed all protocol-specified treatment prior to surgery, as compared to 69% in the L arm and 74% in the TL arm. Tumor or tumor bed tissue was collected whenever possible pre-treatment (N = 110), after one cycle of HER2-targeted therapy alone (N = 89), and at time of surgery (N = 59). Higher-level amplification of HER2 and hormone receptor (HR)-negative status were associated with a higher pCR rate. Large shifts in the tumor, immune, and stromal gene expression occurred after one cycle of HER2-targeted therapy. In contrast to pCR rates, the L-containing arms exhibited greater proliferation reduction than T at this timepoint. Immune expression signatures increased in all arms after one cycle of HER2-targeted therapy, decreasing again by the time of surgery. Our results inform approaches to early assessment of sensitivity to anti-HER2 therapy and shed light on the role of the immune microenvironment in response to HER2-targeted agents.

Abstract P4-07-01: Tumor expression and microenvironment in HER2-positive breast cancer before and on HER2-targeted therapy: Analysis of microarray expression data from the TRIO-US B07 trial

Background: Neoadjuvant HER2-targeted therapy in combination with chemotherapy is a standard treatment approach for early-stage HER2-positive breast cancer. Proposed biomarkers to predict pathologic complete response (pCR), and thereby inform which patients may benefit from de-escalation of therapy, include expression-based subtyping and immune enrichment scores. Little is known about how tumors and their microenvironment may change with HER2-targeted therapy alone, and whether these changes may predict outcome.

Methods: The TRIO-US B07 phase II trial randomized 128 participants with stage I-III HER2-positive breast cancer to trastuzumab (N=34), lapatinib (N=36), or the combination (N=58) for three weeks, followed by six cycles of docetaxel and carboplatin with continued HER2-targeted therapy. Fresh-frozen core biopsies of the tumor prior to therapy (N=110) and after 14-21 days of HER2-targeted therapy alone (N=89) were collected, and RNA was extracted and subjected to Agilent Whole Human Genome 44K 2-color chip. The pre-treatment tumor RNA was normalized against a mixed breast tumor reference, and the on-treatment tumor RNA against the matched pre-treatment sample. Absolute intrinsic molecular subtyping was used to determine intrinsic subtype, the iC10 expression-based classifier to determine integrative subtype, gene set enrichment analysis (GSEA) to assess signature changes across treatment, single-sample GSEA to compare individual gene signature scores between tumors, and CIBERSORT to quantify immune cell populations before and on treatment.

Results: Primary trial results have been reported previously and showed a pCR rate of 47% with trastuzumab, 25% with lapatinib, and 52% with the combination. Prior to treatment, 56% of tumors classified as the HER2-enriched intrinsic subtype and 78% as the iC5 integrative subtype. HER2-enriched tumors trended toward a higher rate of pCR relative to other intrinsic subtypes (50% vs 33%, P=0.12), as did iC5 tumors relative to other integrative subtypes (48% vs 25%, P=0.08). However, in multivariate analysis, HER2 FISH ratio (P=0.04) and hormone receptor status (P=0.02), each associated themselves with intrinsic and integrative subtype, proved the most valuable in predicting pCR, with little information added by expression-based subtyping. Immune cell signatures correlated with pCR in the trastuzumab-containing arms only. Of 65 gene signatures tested, 47 changed across HER2-targeted therapy with false discovery rate < 0.1, driven by decreasing tumor proliferation, increasing immune cell signatures, and increasing stromal cell/epithelial mesenchymal transition signatures. Quantification of immune cell populations suggested the immune changes were both anti-tumor (CD8+ T cells) and pro-tumor (M2 macrophages). Intrinsic subtype changed in 54% of tumors (79% of these converting to normal-like) and integrative subtype changed in 26%. Change in subtype, proliferation, or immune infiltration with targeted therapy did not correlate with pCR. A higher proportion of tumors treated with trastuzumab alone maintained their proliferation (42%), compared with lapatinib alone (20%; P=0.16) or the combination (16%; P=0.04).

Conclusions: In the TRIO-US B07 study, the biomarkers most predictive of response to neoadjuvant HER2-targeted therapy were hormone receptor status in combination with HER2 FISH ratio. Multiple changes in the tumor and its microenvironment occurred with HER2-targeted therapy, but these changes did not predict pCR. Tumors treated with lapatinib tended to decrease proliferation more than tumors treated with trastuzumab, despite trastuzumab being more effective in preventing recurrence, an observation with implications for window of opportunity studies.

Citation Format: Jennifer L. Caswell-Jin, Katherine L. McNamara, Judy Dering, Hsiao-Wang Chen, Robert Dichmann, Alejandra Perez, Ravindranath Patel, Eran Kotler, Jason J. Zoeller, Joan S. Brugge, Michael F. Press, Dennis J. Slamon, Christina Curtis, Sara A. Hurvitz. Tumor expression and microenvironment in HER2-positive breast cancer before and on HER2-targeted therapy: Analysis of microarray expression data from the TRIO-US B07 trial [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-07-01.

Clonal replacement of tumor-specific T cells following PD-1 blockade

Immunotherapies that block inhibitory checkpoint receptors on T cells have transformed the clinical care of patients with cancer1. However, whether the T cell response to checkpoint blockade relies on reinvigoration of pre-existing tumor-infiltrating lymphocytes or on recruitment of novel T cells remains unclear2-4. Here we performed paired single-cell RNA and T cell receptor sequencing on 79,046 cells from site-matched tumors from patients with basal or squamous cell carcinoma before and after anti-PD-1 therapy. Tracking T cell receptor clones and transcriptional phenotypes revealed coupling of tumor recognition, clonal expansion and T cell dysfunction marked by clonal expansion of CD8+CD39+ T cells, which co-expressed markers of chronic T cell activation and exhaustion. However, the expansion of T cell clones did not derive from pre-existing tumor-infiltrating T lymphocytes; instead, the expanded clones consisted of novel clonotypes that had not previously been observed in the same tumor. Clonal replacement of T cells was preferentially observed in exhausted CD8+ T cells and evident in patients with basal or squamous cell carcinoma. These results demonstrate that pre-existing tumor-specific T cells may have limited reinvigoration capacity, and that the T cell response to checkpoint blockade derives from a distinct repertoire of T cell clones that may have just recently entered the tumor.