Case report: 16-yr life history and genomic evolution of an ER+ HER2- breast cancer

Metastatic breast cancer is one of the leading causes of cancer-related death in women. Limited studies have been done on the genomic evolution between primary and metastatic breast cancer. We reconstructed the genomic evolution through the 16-yr history of an ER+ HER2- breast cancer patient to investigate molecular mechanisms of disease relapse and treatment resistance after long-term exposure to hormonal therapy. Genomic and transcriptome profiling was performed on primary breast tumor (2002), initial recurrence (2012), and liver metastasis (2015) samples. Cell-free DNA analysis was performed at 11 time points (2015-2017). Mutational analysis revealed a low mutational burden in the primary tumor that doubled at the time of progression, with driver mutations in PI3K-Akt and RAS-RAF signaling pathways. Phylogenetic analysis showed an early branching off between primary tumor and metastasis. Liquid biopsies, although initially negative, started to detect an ESR1 E380Q mutation in 2016 with increasing allele frequency until the end of 2017. Transcriptome analysis revealed 721 (193 up, 528 down) genes to be differentially expressed between primary tumor and first relapse. The most significantly down-regulated genes were TFF1 and PGR, indicating resistance to aromatase inhibitor (AI) therapy. The most up-regulated genes included PTHLH, S100P, and SOX2, promoting tumor growth and metastasis. This phylogenetic reconstruction of the life history of a single patient's cancer as well as monitoring tumor progression through liquid biopsies allowed for uncovering the molecular mechanisms leading to initial relapse, metastatic spread, and treatment resistance.

Abstract P4-05-20: Case report - 16 year life history and genomic evolution of an ER+ HER2- breast cancer

Introduction

Metastasis is the primary cause of cancer-related death, with genomic evolution between primary and metastatic breast cancer only recently being studied in smaller numbers. We reconstructed the tumor evolution of a female patient originally diagnosed with localized ER+ HER2- disease to investigate the molecular changes that triggered relapse after long term aromatase inhibitor (AI) therapy and tracked them during subsequent treatments. The patient was diagnosed in 2002, relapsed in 2012 (regional lymph node), progressed in 2015 (liver metastasis), and passed away in 2018. We performed DNA- and RNA-sequencing on FFPE tumor samples and multiple liquid biopsies. The patient underwent eight lines of therapy including genome guided targeted therapy.

Materials and Methods

Whole exome and transcriptome sequencing was performed on the patient's primary tumor site at diagnosis (T1) and a metastatic lymph node (M1). Targeted DNA sequencing was performed on a metastatic liver sample (M2, 315 genes) and on liquid biopsies (n=11, 70 genes) every 2-3 months from 2015-2018.

Results

The mutational landscape between timepoints T1, M1 and M2 revealed low mutational burden at diagnosis which ultimately doubled at progression with active mutational processes (APOBEC, POLE) showing concordance between timepoints. DNA-based analysis revealed multiple mutations in the PI3K-Akt signaling pathway. Two mutations were shared between the samples: a clonal PIK3CA Q546R and a TP53 E180K mutation detected as clonal in M1/M2 and subclonal in T1. Individual samples carried private driver mutations, ranging from n=4 in T1, n=7 in M1 to n=16 in M2. While T1 harbored a single clonal driver mutation, with additional driver mutations being subclonal, M1 and M2 harbored multiple clonal driver mutations and a smaller percentage of subclonal driver mutations. A phylogenetic tree showed branching off between T1 and M1/M2. Liquid biopsies, while initially negative, started to detect mutations found among T1, M1 and M2, with increasing allele frequency (AF) throughout time. By the end of 2016, an ESR1 E380Q mutation not previously detected was found at a low AF that had rapidly increased by the end of 2017. RNA-Seq analysis revealed 908 (209 up, 699 down) genes to be differentially expressed between T1 and M1. Most significantly downregulated genes in M1 were TFF1 and PGR indicating loss-of-sensitivity / resistance to AI therapy. Most upregulated genes in M1 included PTHLH, S100P, and SOX2 which have been implicated in promoting tumor growth and metastasis. Pathway analysis between T1 and M1 showed enrichment for the hallmark gene sets ‘Estrogen Response early and late’ and ‘Epithelial mesenchymal transition’.

Conclusions

This phylogenetic reconstruction of the life history of a single patient's cancer revealed an increased mutational rate over time between the patient's primary tumor at diagnosis and samples taken at relapse; and a high level of heterogeneity with metastatic sites sharing only one driver mutation with the primary tumor at diagnosis and having acquired multiple de-novo driver mutations. Transcriptome profiling aided in uncovering the mechanisms that lead to the patient's initial relapse, indicating expression profile changes that promote tumor progression and metastasis as well as reduced sensitivity / resistance to the patients AI based therapy. Monitoring tumor progression through frequent liquid biopsies allowed for the detection of mutations from multiple metastatic sites, in addition to the detection and growth of an AI resistant clone harboring an ESR1 E380Q mutation that was not present in any of the solid tissue samples.

Citation Format: Bing Xu, Anu Amallraja, Padmapriya Swaminathan, Rachel Elsey, Christel Davis, Stephanie Theel, Sarah Viet, Jason Petersen, Amy Krie, Gareth E Davies, Casey B Williams, Erik Ehli, Tobias Meissner. Case report - 16 year life history and genomic evolution of an ER+ HER2- breast cancer [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 P4-05-20.

Exploratory Analysis of Single-Gene Predictive Biomarkers in HERA DASL Cohort Reveals That C8A mRNA Expression Is Prognostic of Outcome and Predictive of Benefit of Trastuzumab

Purpose

The Herceptin Adjuvant study is an international multicenter randomized trial that compared 1 or 2 years of trastuzumab given every 3 weeks with observation in women with human epidermal growth factor 2-positive (HER2+) breast cancer after chemotherapy. Identification of biomarkers predictive of a benefit from trastuzumab will minimize overtreatment and lower health care costs.

Methods

To identify possible single-gene biomarkers, an exploratory analysis of 3,669 gene probes not expected to be expressed in normal breast tissue was conducted. Disease-free survival (DFS) was used as the end point in a Cox regression model, with the interaction term between C8A mRNA and treatment as a categorical variable split on the cohort mean.

Results

A significant interaction between C8A mRNA and treatment was detected (P < .001), indicating a predictive response to trastuzumab treatment. For the C8A-low subgroup (mRNA expression lower than the cohort mean), no significant treatment benefit was observed (P = .73). In the C8A-high subgroup, patients receiving trastuzumab experienced a lower hazard of a DFS event by approximately 75% compared with those in the observation arm (hazard ratio [HR], 0.25; P < .001). A significant prognostic effect of C8A mRNA also was seen (P < .001) in the observation arm, where the C8A-high group hazard of a DFS event was three times the respective hazard of the C8A-low group (HR, 3.27; P < .001). C8A mRNA is highly prognostic in the Hungarian Academy of Science HER2+ gastric cancer cohort (HR, 1.72; P < .001).

Conclusion

C8A as a single-gene biomarker prognostic of DFS and predictive of a benefit from trastuzumab has the potential to improve the standard of care in HER2+ breast cancer if validated by additional studies. Understanding the advantage of overexpression of C8A related to the innate immune response can give insight into the mechanisms that drive cancer.

Abstract P2-05-09: Vascular mimicry in metastatic breast cancer patients: Molecular insight to vascular mimicry using in vitro and in vivo models

Background: Vascular Mimicry (VM) is an endothelium-independent matrix-embedded, blood-perfusion phenomenon exhibited by highly plastic and aggressive tumor cells in patients with solid tumors including breast. VM is characterized by PAS+ de novo formations of micro-vascular networks which are essentially CD31- and CD34-. VM is a micro-circulatory phenomenon which perfuses rapidly growing tumors, transporting fluid from leaky vessels and/or connects with the constituent endothelial-lined vasculature. One of the hallmarks of metastasis in BC is the heterogeneity observed between primary tumors and metastases (&amp; among metastases) (Marino etal., 2013). Recently a model of BC heterogeneity revealed VM as a driver of metastasis which in turn has been associated with disease heterogeneity (Wagenblast etal., 2015). Aim: Since BC is an aggressive and heterogeneous disease and VM is associated with the aggressiveness / poor outcome in BC, we sought to understand the functional relationship of VM with metastasis. Method: Tumors from our BC patients and TMAs were stained for CD31/PAS and CD34/PAS to identify VM. Genomic and proteomic data from these patients were obtained from re-biopsied (after consultation) samples (IHC for ER, PR, and HER2; FFPE samples for genomic [Foundation Medicine] and proteomic [Theralink] analyses). Result: VM was identified in metastatic tumors from ER+ and TNBC patients as CD31-/PAS+ and CD34-/PAS+ structures in contrast to the CD31+/PAS+ and CD34+/PAS+ angiogenic compartment of the individual tumor(s). Metastatic tumors exhibiting VM were characterized by pathological features like metaplastic lesions, positive lympho-vascular invasion and were found to be poorly differentiated. Predominant genetic alterations in these patients included (1) PI3K-mTOR pathway genes, (2) p53 (R273P, D281V), (3) BRCA1 E1683* (for TNBC), (4) MYC amplification, (5) aurora kinase, (6) CCND1 &amp; CDK4 amplifications and (7) loss of CDH1 exons1-3. Amplifications of cell surface TKIs/ligands included EGFR, FGFR and several FGFs. Proteomic data indicated an overexpression/activation of HER family (HER1/HER2/HER3), mTOR activation (p∼S2448), MEK1/2 activation (p∼S217-221) and JAK2 activation. In order study VM, we standardized VM formation both in 2D and 3D configurations in multiple BC cell lines which exhibited VM at differing times. The earliest response was observed around 2-3 hours in BT20, Hs578t and MDA-MB231. By 24 hours BT474, BT474HerR, SUM149, DKAT, MDA-MB231BR, Hs578t and MDA-MB468 cells demonstrated 2D VM. The BT20 cell line showed the most pronounced 3D-VM at 24 hours while MDA-MB468 was least sensitive to VM. Typical cord formation in HUVEC cells stained with hematoxylin and PAS were used for comparison. Using 2D and 3D models of VM we demonstrated the involvement of PI3K and Wnt-beta-catenin pathways in VM. Considering the involvement of VM in mediating the aggressive/metastatic nature of TNBC, we also tested VM in in vivo xenograft models using brain metastasic specific MDA-MB231BR cells, results of which will be presented in the meeting. Significance: To our knowledge this is the first report to identify genetic alterations and proteomic changes associated with VM in metastatic BC.

Citation Format: Dey N, Carlson JH, Lin X, Sun Y, Theel S, Krie A, Sulaiman RA, Williams C, De PK, Leyland-Jones BR. Vascular mimicry in metastatic breast cancer patients: Molecular insight to vascular mimicry using in vitro and in vivo models. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-05-09.

Nitric oxide activation of Erk1/2 regulates the stability and translation of mRNA transcripts containing CU-rich elements

Nitric oxide (NO*) can stabilize mRNA by activating p38 mitogen-activated protein kinase (MAPK). Here, transcript stabilization by NO* was investigated in human THP-1 cells using microarrays. After LPS pre-stimulation, cells were treated with actinomycin D and then exposed to NO* without or with the p38 MAPK inhibitor SB202190 (SB). The decay of 220 mRNAs was affected; most were stabilized by NO*. Unexpectedly, SB often enhanced rather than antagonized transcript stability. NO* activated p38 MAPK and Erk1/2; SB blocked p38 MAPK, but further activated Erk1/2. RT-PCR confirmed that NO* and SB could additively stabilize certain mRNA transcripts, an effect abolished by Erk1/2 inhibition. In affected genes, these responses were associated with CU-rich elements (CURE) in 3'-untranslated regions (3'-UTR). NO* stabilized the mRNA of a CURE-containing reporter gene, while repressing translation. Dominant-negative Mek1, an Erk1/2 inhibitor, abolished this effect. NO* similarly stabilized, but blocked translation of MAP3K7IP2, a natural CURE-containing gene. NO* increased hnRNP translocation to the cytoplasm and binding to CURE. Over-expression of hnRNP K, like NO*, repressed translation of CURE-containing mRNA. These findings define a sequence-specific mechanism of NO*-triggered gene regulation that stabilizes mRNA, but represses translation.