Jessica Klein

A metastatic colon adenocarcinoma harboring BRAF V600E has a durable major response to dabrafenib/trametinib and chemotherapy.

The subset of metastatic colorectal adenocarcinomas that harbor BRAF V600E mutations are aggressive tumors with significantly shortened survival and limited treatment options. Here we present a colorectal cancer patient whose disease progressed through standard chemotherapy and who developed liver metastasis. Comprehensive genomic profiling (FoundationOne®) identified a BRAF V600E mutation in the liver lesion, as well as other genomic alterations consistent with colorectal cancers. Combination therapy of dabrafenib and trametinib with standard cytotoxic chemotherapy resulted in a durable major ongoing response for the patient. This report illustrates the utility of comprehensive genomic profiling with personalized targeted therapy for aggressive metastatic colorectal adenocarcinomas.

Utilizing Tumor and Plasma Liquid Biopsy in Treatment Decision Making for an Estrogen Receptor-Positive Advanced Breast Cancer Patient

Breast cancer affects 12% of females in the United States and is the leading cause of cancer death in the female population. Personalized therapy is being used in clinical practice to treat breast cancer based on tumor molecular profiling, which can be obtained from tissue biopsy or plasma liquid biopsy as circulating tumor deoxyribonucleic acid (ctDNA). The available ctDNA tests provide a non-invasive way to monitor the cancer genome in a real-time manner. In this case report, a 38-year-old female with recurrent estrogen receptor (ER) positive breast cancer is treated with letrozole, everolimus, and palbociclib. The drugs target the hormonal signaling pathway, phosphoinositide 3-kinase (PI3K)-RAC-alpha serine/threonine-protein kinase (AKT) pathway, and cyclin D1 (CCND1)-CDK4/6 pathway, based on the patient’s estrogen-receptor-positive (ER+) disease and phosphatidylinositol -4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) mutation, as well as PIK3CA and CCND1 amplification. After 11 months of treatment, retinoblastoma protein transcriptional corepressor 1 (RB1) mutation was caught in ctDNA, which suggests an acquired resistance to palbociclib. Pazopanib was then used instead of palbociclib, targeting the fibroblast growth factor 3/4/19 (FGF3/4/19) amplification that was initially observed in her molecular profiling. Trametinib was also suggested recently due to the increasing allele frequency of B-Raf proto-oncogene, serine/threonine kinase (BRAF) mutation in ctDNA, following the treatment of letrozole + everolimus + pazopanib. The patient has no evidence of disease after five months of treatment initiation and has remained disease-free for over 16 months. In conclusion, the analysis of ctDNA is an effective way to monitor the real-time changes in a patients tumor genome, which is a great supplement to the molecular profile from the tissue biopsy. The combination of these two tests provides an efficient strategy to make more informed treatment decisions, which greatly adapt along disease development.

Down’s Syndrome and Triple Negative Breast Cancer: A Rare Occurrence of Distinctive Clinical Relationship

Down’s syndrome (DS), the most common genetic cause of significant intellectual disability in children and adults is caused by the trisomy of either all or a part of human chromosome 21 (HSA21). Patients with DS mostly suffer from characteristic tumor types. Although individual patients of DS are at a higher risk for acute leukemia and testicular cancers, other types of solid tumors including breast cancers are mostly uncommon and have significantly lower-than-expected age-adjusted incidence rates. Except for an increased risk of retinoblastomas, and lymphomas, the risk of developing solid tumors has been found to be lower in both children and adults, and breast cancer was found to be almost absent (Hasle H., The Lancet Oncology, 2001). A study conducted in the United States found only one death when 11.65 were expected (Scholl T et al., Dev Med Child Neurol. 1982). A recent study examined mammogram reports of women with DS treated in the largest medical facility specifically serving adults with DS in the United States. It was found that only 0.7% women with DS had been diagnosed with breast cancers (Chicoine B et al., Intellect Dev Disabil. 2015). Here we describe a case of breast cancer in a 25-year-old patient with DS. The disease was presented as lymph node positive carcinoma with alterations of tumor suppressor genes characteristic to the triple negative breast cancer subtype. Comprehensive Genomic Profiling (CGP) revealed a wild-type status for BRCA1. The CGP report showed a frameshift mutation, A359fs*10 of the tumor suppressor gene INPP4B and another frameshift mutation, R282fs*63 of tumor suppressor gene TP53 in the tumor biopsy as characteristically found in triple-negative breast cancers. The VUS (Variance of Unknown Significance) alteration(s) were identified in ASXL1 (L1395V), NTRK1 (G18E), DDR2 (I159T), RUNX1 (amplification), ERG (amplification), SOX2 (T26A), FAM123B (G1031D), and HNF1A (A301T). Bonafide cancer-related genes of chromosome 21 amplified in the patient’s tumor are RUNX1 and ERG genes. After the completion of the radiation, the patient was placed on everolimus which was based on the result of her CGP report. Thus, post-mastectomy radiation therapy was completed with a recommendation for everolimus for one year. During the time of writing of this report, no metastatic lesions were identified. The patient currently has no evidence of disease.

Abstract P4-08-04: Navigating genomic landscape to find a PI3K-signaling algorithm for a rational combinatin in precision medicine

Background: Treatment of BC is conventionally based on the presence/absence of ER/PR or HER2 status of the primary tumor. We have enriched this approach by including major genetic and proteomic changes in tumors of individual patients in order to develop a better treatment-rationale based on an alteration driven signaling algorithm. Methods: Genomic and proteomic data from 75 BC patients seen in our center were retrospectively analyzed. Patients were re-biopsied after consultation and samples were characterized (IHC for ER, PR, and HER2; FFPE samples for genomic [Foundation Medicine] and proteomic analyses [Theranostics]). In vivo studies were conducted using xenograft models. Results: Although alterations of PIK3CA, PIK3R1, AKT, PTEN, MDM2, MDM4, TSC1, mTOR and RICTOR are most frequently observed in our patients, there is a distinct pattern of alteration(s) of the PI3K pathway genes in different subtypes of BC. A total of 76 genes were altered in 48 ER+BC patients. In 79% of ER+BC patients the above mentioned PI3K pathway genes were altered. Analyzing the set of alterations of genes in individual patients, we observed that within these 48 patients 25% exhibited alterations in more than one node of the pathway; the most common combination (alterations) being the amplification/mutation of PIK3CA with the amplification of MDM2/4 genes. The percentage of patients belonging to HER2+ & TNBC exhibiting similar alterations in the PI3K pathway genes were significantly lower (∼40%). Our previous in vivo studies demonstrated that GDC-0980 and BEZ235 enhanced the antitumor activity of ABT888 plus carboplatin in TNBC or trastuzumab in HER2+ BC respectively and blocked the growth of established xenograft tumors by 80% to 90% with a concomitant decrease in tumor Ki67, pS6RP and CD31. Mechanistically the action of the PI3K-mTOR pathway targeted drug(s) was tested using cell line based models of BC subtypes pertaining to their respective genomic alterations. A combination of a pan-PI3K pathway inhibitor, GDC-0941 or isoform-specific inhibitors along with AI, trastuzumab, or HRD inhibitors (PARP) blocked proliferative signals and enhanced apoptosis (cleaved caspase3) in ER+/PIK3CA mutated, HER2+/PIK3CA mutated or PTEN-null TNBC cells respectively as demonstrated by WB, flow cytometry, cell proliferation, viability and cytotoxicity assays. A recent study demonstrated that exposure to chemotherapy induced a phenotypic shift or cell state transition towards a transient CD44Hi/CD24Hi chemotherapy-tolerant state, leading to the activation of downstream non-receptor tyrosine kinase signaling towards an emerging adaptive resistance (Goldman et al., Nature Comm. 2015). Hence drug combination(s) are being tested for their effect on CD44/CD24 expression levels, results of which will be presented in the meeting. Conclusion: Plotting the genetic alterations from the patient on the signaling landscape will be useful in cracking the code leading to improved treatment options. Patient specific in-depth plotting of genetic alterations of the PI3K-mTOR pathway and the relevance of these alterations in the context of (1) mechanisms of PI3K-mTOR pathway targeted drugs and (2) cell signaling are critical in determining choice of drugs in BC subtypes. Citation Format: Carlson JH, Krie A, Williams C, Sun Y, Lin X, Williams K, Klein J, Friedman L, De P, Dey N, Leyland-Jones B. Navigating genomic landscape to find a PI3K-signaling algorithm for a rational combinatin in precision medicine. [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 P4-08-04.

Abstract 4591: Estrogen receptor-positive breast cancer: from genomic landscape to treatment approach

Background: Estrogen receptor (ER)-positive or luminal breast tumors represent around two-thirds of all breast cancers. Luminal breast cancer is a highly heterogeneous disease comprising different histologies, gene-expression profiles and mutational patterns, with very diverse clinical courses and responses to systemic treatment. Despite adjuvant endocrine therapy and chemotherapy treatment for patients at high risk of relapse, both early and late relapses still occur, a fact that highlights the unmet medical needs of these patients. A catalogue of molecular aberrations in ER+ breast cancer (BC) is critical for developing and deploying therapies that will improve patients’ lives. Methods: Comprehensive genomic profiling from 128 BC patients (February 2014 through October, 2015) were analyzed. Patients were biopsied after consultation and samples were characterized (ER, PR, and HER2 by IHC; FFPE samples for genomic [Foundation One] and proteomic analyses [Theranostics]). We also evaluated mutation distribution in cell free DNA via digital NGS using Guardant 360 panel. Results: Total 97 genes were altered in 83 ER+BC patients and most frequent genetic alterations are PIK3CA (40%), p53 (27.7%) and CCND1 (24%). The PI3K-AKT pathway specific genes (AK1, AKT2, PIK3CA, PIK3CB, PIK3R1, PTEN, MTOR, RICTOR, RAPTOR, TSC2, STK11, MDM2 and MDM4) were altered in 80% of patients. Analyzing the composite alterations in individual ER+BC patients, we observed that 20% of patients had alterations in two or more nodes of the PI3K pathway while alterations of cell cycle pathway genes (CCND1, CCNE1, CDK4, CDKN1B, CDKN2A/B and RB1) were observed in 36% of patients. Interestingly, concurrent alterations of both PI3K and cell cycle pathways were 24%. Hence we tested the anti-tumor efficacy of the combination of isoform-specific PI3K inhibitor (alpha or beta) and LEE011 using ER+ BC cell lines (PIK3CA mutated MCF7, T47D, & PTEN-null MDA-MB415 cells) based model. Data show a synergistic effect of PI3K alpha or beta inhibitor and CDK4/6 inhibitor as determined from the changes in proliferative and apoptotic signals as well as cell cycle arrest. Conclusion: Since a persistent expression of the CDK4-Cyclin D1 pathway activation enables tumor cells survival even in the presence of PI3K inhibitor (Cancer Cell 2014), results of our study demonstrated that the anti-tumor effect of isoform-specific PI3Ki and CDK4/6i be beneficial in RB wt ER+BC patients with a concurrent genetic alterations of these pathways. Citation Format: Pradip De, Casey Williams, Amy Krie, Kirstin Williams, Jessica Klein, Jennifer H. Carlson, Nandini Dey, Brian Leyland-Jones. Estrogen receptor-positive breast cancer: from genomic landscape to treatment approach. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4591.

Abstract B106: Algorithmic basis for combination of PI3K pathway isoform-specific inhibitors: Navigating the genomic landscape in ER+ breast cancers

Introduction: Breast cancers are characterized by diverse genetic alterations. However, genetic alterations often affect a common oncogenic signal transduction pathway. Thus in tumor cells a specific molecular aberration(s) can have characteristic functional consequences which in turn can determine the therapeutic sensitivity of a particular drug. Methods: We retrospectively analyzed data from nearly 150 consecutive BC patients (neoadjuvant, adjuvant and metastatic) which were seen in our center from February 2014 through August 2015. Patients were re-biopsied after consultation and samples were characterized (IHC for ER, PR, and HER2; FFPE samples for genomic [FoundationOne Medicine] and proteomic analyses [Theranostics]). Results: A total of 100 genes were altered in 83 ER+ BC patients. PI3K pathway genes (PIK3CA, PIK3CAR1, PIK3C2B, AKT, PTEN, MDM2, MDM4, TSC2, mTOR, RPTOR) were altered in 77% of ER+ BC patients. The predominant alterations observed in this subtype were the amplification/mutation of PIK3CA gene (41%) followed by the loss of PTEN gene (12%) and the amplification of MDM2/4 genes (14%). The rarest alterations of genes observed in this subtype were the alterations of PIK3CAR1, PIK3C2B, mTOR and RPTOR genes (>1%). Analyzing the composite alterations in individual patients within ER+ BC, we observed that 40% of patients had alterations in more than one node of the pathway. The most common combination (alterations) being the amplification/mutation of PIK3CA with the amplification of MDM2/4 genes. In contrast the percentage of patients belonging to other two subtypes of BC (HER2+ & TNBC) exhibiting a similar alterations in the PI3K pathway genes were significantly lower (∼ 40%). Among these patients only a negligible% exhibited alterations of more than one node of the pathway. In cell line based models, a combination of the pan-PI3K pathway inhibitor, GDC-0941 or isoform-specific inhibitors, GDC-0032 / AZD6482 were tested with AI which blocked proliferative signals and enhanced apoptosis in ER+/PIK3CA mutated and ER+/PTEN mutated cells. In PIK3CA helical domain mutated MCF7 and T47D cells GDC-0941 and GDC-0032 alone or in combination with AI were effective in blocking the direct proliferative signals of PI3K enzyme, including pAKT S473 and pAKT T308 as well as downstream signals of mTOR including pS6RP and p4EBP1 while treatment with AI alone was ineffective. In contrast, p110beta isoform specific inhibitor AZD6482 was effective in blocking the proliferative signals while GDC-0032 failed to abrogate any of proliferative signals in PTEN mutated MDA-MB415 cells. These mechanistic results were confirmed by apoptosis and 3D ON-TOP colony formation assays. Significance: Genomic landscape forms the basis of the algorithm for the combination of PI3K pathway isoform-specific inhibitor(s) and anti-estrogen drug(s) towards precision medicine in ER+ BC. Applying cutting edge knowledge about how tumor cells signal to bring a particular phenotype on the landscape of genetic alterations from an individual patient is the best approach towards achieving success in precision medicine. Citation Format: Nandini Dey, Casey Williams, Jennifer H. Carlson, Kirstin Williams, Jessica Klein, Amy Krie, Pradip De, Brian Leyland-Jones. Algorithmic basis for combination of PI3K pathway isoform-specific inhibitors: Navigating the genomic landscape in ER+ breast cancers. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B106.

Abstract P2-05-14: New treatment options for metastatic breast cancer revealed by reverse-phase protein microarray and genomic profiling

Background: The optimal treatment strategy for patients with metastatic breast cancer (MBC) is currently unknown. Resistance to standard therapies like anthracyclines and taxanes limit the number of treatment options in many patients to a small number of non-cross-resistant regimens. We hypothesized that genomic and proteomic profiling of clinical MBC samples would identify genomic alterations that are linked to targeted therapies, and that this could facilitate a personalized approach to therapy for our patients. Methods: We retrospectively analyzed 31 consecutive metastatic breast cancer patients that had genomic and/or proteomic studies sent over a 4 month period from February to May 2014. All patients were seen in our Genomic Oncology Clinic and subsequently underwent a rebiopsy of a metastatic site. Formalin-fixed, paraffin-embedded (FFPE) tissue was sent to either Foundation Medicine for genomic profiling, Theranostics for reverse-phase protein microarray, or both. Standard immunohistochemistry for ER, PR, and HER2 was also performed on all patients. Results: Genomic or proteomic alterations were identified in all 31 patients. All patients harbored at least one actionable target and a treatment recommendation for a currently available FDA approved drug or drug combination was able to be suggested in all but one patient. The most commonly observed genomic alterations were within PIK3CA (26%), TP53 (23%), CCND1 (19%), and MYC (16%). Over 30 distinct genomic alterations were identified. Proteomic results were available from 16 patients. Activation of the AKT/mTOR pathway was evident in a majority of patients. A change in HER2 status was also found in 26% of patients. 16% of cases underwent a negative to positive conversion in HER2 status while 10% of cases underwent a positive to negative conversion. It is notable that all 5 patients that underwent a negative to positive conversion in HER2 status had biopsies taken from metastatic disease in the liver. Conclusions: All patients in this retrospective study harbored genomic or proteomic alterations that are associated with targeted therapies. Treatment recommendations were suggested in all but one patient and a majority of patients are receiving the suggested therapy. Our data demonstrate that routine genomic and proteomic analysis in a clinical setting makes a significant positive impact for patients. Citation Format: Casey B Williams, Pradip De, Nandini Dey, Kirstin A Williams, Jessica Klein, Michelle King, Misty Small, Brigitte Cyr, Scooter Willis, Yuliang Sun, Jennifer Carlson, Brandon M Young, Amy Krie, Brian Leyland-Jones. New treatment options for metastatic breast cancer revealed by reverse-phase protein microarray and genomic profiling [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-05-14.

HER2 amplification and overexpression between primary and liver metastatic breast cancer: Significance and implication.

150 Background: The systemic management of metastatic breast cancer (MBC) is mostly based on the ER or HER2 status of the primary tumor. However, the hormonal status or the amplificaction/overexpression HER2 may change in every metastatic site because of the effects of the long-term treatment of metastatic cancer with endocrine therapy, chemotherapy, or targeted agents. The purpose of this study was to investigate the frequency of change in HER2 expression in primary and distant metastatic tumors (especially in liver) in HER2+ breast cancer patients. METHODS We retrospectively analyzed the results of 31 consecutive metastatic breast cancer patients that were seen in our center over 4 months from February 2014 through May 2014. All patients were rebiopsied after consultation and samples were sent for standard immunohistochemistry (IHC) for ER, PR, and HER2 and formalin-fixed, paraffin-embedded (FFPE) samples were sent for genomic (Foundation Medicine) and proteomic analysis (Theranostics). All results from the metastatic samples were compared to the baseline IHC and/or FISH results for HER2. RESULTS A change in HER2 status was observed in 26% of the cases. 16% of cases underwent a negative to positive conversion in HER2 status while 10% of cases underwent a positive to negative conversion. It is notable that all 5 patients that underwent a negative to positive conversion in HER2 status had biopsies taken from metastatic disease in the liver. Overall, 45% of patients with metastatic disease in the liver had a negative to positive conversion in HER2 status. CONCLUSIONS The results of this study emphasize the significance of confirming HER2 expression in a recurrence lesion. This discordance may be due to the increasing level of genetic instability occurring throughout disease progression that can significantly influence the alterations of the HER2 gene. If feasible, HER2 reassessment in metastatic lesions should be carefully taken into account, especially for metastases coming from non-HER2 amplified breast cancer. Although HER2 status is usually appraised in primary tumor, knowledge of the HER2 status in metastases may be of potential value for therapeutic decision making.