Abstract S1-01: Whole exome and transcriptome sequencing of resistant ER+ metastatic breast cancer

Background: While great strides have been made in the treatment of estrogen receptor-positive (ER+) metastatic breast cancer (MBC), therapeutic resistance invariably occurs. A better understanding of the underlying resistance mechanisms is critical to enable durable control of this disease.

Methods: We performed whole exome sequencing (WES) and transcriptome sequencing (RNA-seq) on metastatic tumor biopsies from 88 patients with ER+ MBC who had developed resistance to one or more ER-directed therapies. For 27 of these patients, we sequenced the treatment-naïve primary tumors for comparison to the resistant specimens. Tumors were analyzed for point mutations, insertions/deletions, copy number alterations, translocations, and gene expression. Detailed clinicopathologic data was collected for each patient and linked to the genomic information.

Results: WES of all metastatic samples demonstrated several recurrently altered genes whose incidence differed significantly from primary, treatment-naïve ER+ breast cancers sequenced in the TCGA study (TCGA). These include ESR1 mutations (n=17, 19.3%; 32.86 fold enrichment, q.value<7.5e-12), CCND1 amplification (n=52, 59.1%; 2.3 fold enrichment, q.value<0.0073), and MAP2K4 biallelic inactivation (n=14, 15.9%; 3.04 fold enrichment, q.value< 0.054).

Comparing to matched primary samples from the same patient, many alterations were found to be acquired in several cases, including for ESR1, ERBB2, PIK3CA, PTEN, RB1, AKT1, and others. Initial analysis of RNA-seq data from metastatic samples (n=59) allowed classification of individual resistance mechanisms into broader resistance modes based on the observed transcriptional state.

Conclusions: We present a genomic landscape of resistant ER+ MBC using WES and RNA-seq. Multiple genes were recurrently altered in these tumors at significantly higher rates than in ER+ primary breast cancer. When compared with matched primary tumors from the same patient, alterations in these and other genes were often found to be acquired after treatment, suggesting a role in resistance to ER-directed therapies and/or metastasis. Potential resistance mechanisms appear to fall into several categories; integrating RNA-seq data may enhance the ability to identify these categories even when genomic alterations are not identified. Multiple clinically relevant genomic and molecular alterations are identified in metastatic biopsies– with implications for choice of next therapy, clinical trial eligibility, and novel drug targets.

Citation Format: Cohen O, Kim D, Oh C, Waks A, Oliver N, Helvie K, Marini L, Rotem A, Lloyd M, Stover D, Adalsteinsson V, Freeman S, Ha G, Cibulskis C, Anderka K, Tamayo P, Johannessen C, Krop I, Garraway L, Winer E, Lin N, Wagle N. Whole exome and transcriptome sequencing of resistant ER+ metastatic breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr S1-01.

Abstract P3-04-08: The role of HER2 mutations in resistance to endocrine therapy in ER+ breast cancer

Resistance to endocrine therapies in estrogen receptor positive (ER+) metastatic breast cancer is widespread, and understanding the mechanisms whereby these tumors acquire resistance is a critical need. Through whole-exome sequencing of metastatic tumor biopsies from patients with endocrine resistant ER+ metastatic breast cancer, we identified 13 different HER2 mutations, including five in the kinase domain, four in the signaling domain, three in the extracellular domain, and one in the transmembrane region of the protein. Two of the kinase domain mutations (L755S and V777L) have been previously described and shown to be activating and resistant to reversible anti-HER2 targeted therapies; the remaining mutations have not been reported. In several of these patients, whole exome sequencing of a pre-treatment primary tumor did not identify the HER2 mutations seen in the corresponding metastatic tumor, suggesting that they were acquired during therapy. To examine the role of HER2 mutations in endocrine resistance, we generated ER+ breast cancer cell lines (MCF7 and T47D) stably expressing the HER2 mutants observed in our clinical data. Several mutants promoted enhanced growth in charcoal dextran-stripped media, which lacks estradiol and mimics treatment with aromatase inhibitor. In addition, several mutants conferred varying degrees of resistance to fulvestrant and tamoxifen. Taken together, these results suggest that HER2 mutations are associated with acquired resistance to endocrine therapies in patients with ER+ breast cancer. The ability of irreversible anti-HER2 agents as well as other agents that target the HER2 pathway to overcome this resistance is being tested for individual HER2 mutations in vitro. The results from these studies may provide a clinical rationale for therapeutic combination strategies in patients with refractory tumors that have acquired endocrine resistance through HER2 mutations.

Citation Format: Nayar U, Cohen O, Oh C, Wagle N. The role of HER2 mutations in resistance to endocrine therapy in ER+ breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-04-08.

Clinical assessment of rosacea severity: oriental score vs. quantitative assessment method with imaging and biomedical tools

BACKGROUND

Rosacea is a common chronic inflammatory disorder affecting facial skin. Currently, no accurate and objective method is available for assessing the severity of rosacea. Most studies use the National Rosacea Society Standard (NRSS) grading method, which lacks objectivity and yields varying results.

METHODS

Eighteen patients with rosacea were included. Clinical severity was assessed on the basis of the NRSS grade, Investigators' Global Assessment, Patients' Global Assessment, and Dermatology Quality of Life Index. A skin color analysis system was used to measure the facial area showing erythema, and biophysical parameters of facial skin (transepidermal water loss and skin surface hydration) were examined. To find statistical significant in classification severity of the rosacea, statistical analysis was performed with all parameters.

RESULTS

A significant correlation (P < 0.05) was found between the NRSS grade, facial area showing erythema, and biophysical parameters. The latter two factors differed significantly among patients with rosacea of different levels of severity (mild, moderate, severe; P < 0.05).

CONCLUSION

Color imaging systems can be useful and reliable for evaluating the severity of rosacea, in addition to biophysical parameter assessment. The combination of these two analytical methods enabled objective and quantitative evaluation of the severity of rosacea.

Abstract OT2-05-03: The metastatic breast cancer project: A national direct-to-patient research initiative to accelerate genomics research

Over the past decade, genomic characterization of tumors has shed enormous light on the molecular underpinnings of cancer. These discoveries have led to the development of novel therapies and preventive measures that have already revolutionized cancer care. Despite this progress, the genomics of metastatic breast cancer (MBC), one of the leading causes of cancer death in the U.S., remains poorly understood.

The challenge in studying tumor samples from patients with MBC has been that the tumors from most patients are not available for research, largely because the vast majority of patients are cared for in community settings where genomics studies are not typically conducted. To address this, we have launched a nationwide study, The Metastatic Breast Cancer Project, which seeks to empower patients to accelerate cancer research through sharing their samples and clinical information. We have developed an outreach program in collaboration with MBC advocacy organizations to connect MBC patients around the country with genomics research performed at the Broad Institute, allowing them to participate regardless of where they live.

Working with MBC patients and advocates, we designed a website (www.mbcproject.org) with an online questionnaire that allows patients with MBC to provide information about themselves and their cancer. Based on their answers, patients are offered an electronic consent form that explains the risks and benefits of the study and asks for permission to obtain a portion of their stored tumor tissue, a saliva sample, and copies of their medical records. For patients who consent, our clinical research team contacts their physicians and obtains copies of their medical records, which are reviewed to confirm eligibility. Enrolled patients are sent a saliva kit and asked to mail back a saliva sample, which is used to extract germline DNA. The clinical research team also contacts the patient's pathology department and requests a portion of the tumor to be sent to the Broad Institute for genomic analysis. Whole exome and transcriptome sequencing is performed on tumor and germline DNA. Sequencing data are linked to de-identified clinical information, and the resulting data are used to identify drivers of tumorigenesis, mechanisms of response and resistance to therapies, and diagnostic, prognostic, and therapeutic biomarkers. The database of clinically annotated genomic information will be shared with the NIH and the cancer research community. Study updates and discoveries are shared at regular intervals with all patients who complete the initial questionnaire.

This direct-to-patient approach should be particularly enabling for the identification of patients with rare phenotypes or clinical behavior. For this reason, the first cohorts being studied are patients with extraordinary responses to therapies and patients who present with de novo MBC. Additional cohorts will be added in the future, including young women with MBC and patients with drug-resistant MBC. This project seeks to establish a patient-researcher partnership to accelerate genomic discoveries and improve outcomes in MBC, and may ultimately serve as a means to build a new clinical and translational research model for all patients with cancer.

Citation Format: Wagle N, Painter CA, Ilzarbe M, Van Allen EM, Frank E, Oh C, Krevalin M, Lloyd M, Anderka K, Kryukov G, Boehm JS, Winer E, Lander ES, Golub TR. The metastatic breast cancer project: A national direct-to-patient research initiative to accelerate genomics research. [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 OT2-05-03.

Physiologic pineal region, choroid plexus, and dural calcifications in the first decade of life

BACKGROUND AND PURPOSE

Calcifications of the pineal, habenula, choroid plexus, and dura are often physiologic. In the modern CT era with thin-section images and multiplanar reformats, intracranial calcifications have become more conspicuous. We aimed to discover the CT prevalence of pineal region, choroid plexus, and dural calcifications in the first decade of life.

MATERIALS AND METHODS

Five hundred head CTs from different patients (age range, 0-9 years) encountered during a consecutive 6-month period at a single academic children's hospital were reviewed retrospectively after excluding examinations with artifacts and pineal region masses/hemorrhage. All studies were performed on a 320-detector CT, with 0.5-mm collimation and a 512 × 512 matrix. Five-millimeter reformatted axial, sagittal, and coronal images were analyzed for location and extent of intracranial calcifications.

RESULTS

The mean age was 3.5 ± 5.7 years (range, 0-9 years). There were 285 males (57%) and 215 females (43%). Pineal calcifications were present in 5% (n = 25; age range, 3.2-8.9 years; median, 7 years). Habenular calcifications were found in 10% (n = 50; age range, 2.8-8.8 years; median, 7 years). Twelve percent (n = 58) had choroid plexus calcifications, (age range, 0.1-8.8 years). Dural calcifications were rare, present in 1% (n = 6; age range, 2.9-8.7 years).

CONCLUSIONS

Physiologic intracranial calcifications may be found in the first decade, principally in children older than 5 years. Most epithalamic calcifications are habenular. Pineal and habenular calcifications were never present in children younger than 3 and 2 years, respectively. Choroid plexus calcifications may be present in the very young. Dural calcifications are rare.

Non-invasive assessment of cutaneous wound healing using fluorescent imaging

BACKGROUND/PURPOSE

Optical imaging is a very important technique in the biomedical sciences. The purpose of this study was to develop an in vivo optical system for fluorescent imaging and molecular imaging applications using quantum dots (QDs).

METHODS

The in vivo optical system was composed of modular parts, including a light source, light guide, excitation filter wheel, excitation filters, emission filter wheel, emission filters, liquid crystal tunable filter (LCTF), macro lens, dark chamber, and a cooled charged-coupled device (CCD) camera for recording images. Filters were selected based on the excitation and absorption spectra of QDs to allow spectral separation and optimization of the acquired image. In contrast with conventional systems, our system allows selection of the emission bandwidth.

RESULTS

The system was tested in an in vivo study using a wound-healing model in nude mice. The healing process was examined after injection of fibroblasts and keratinocytes labeled with two different sets of QDs. The different QD probes were readily detected and distinguished using our system.

CONCLUSION

An in vivo optical system is a very useful tool for the detection of genes, proteins, and small-molecule drugs inside living animals, and this imaging modality can also be adopted for real-time visualization of cancer cell metastasis in live animals.

Peripheral blood telomere content is greater in patients with endometriosis than in controls

The etiology of endometriosis remains poorly understood but circulating stem cells may contribute. Telomeres shorten with cell divisions and age. Stem cells attempt to compensate for telomere attrition through the action of telomerase. Since circulating stem cells may contribute to endometriosis, we compared telomere content in lymphocytes of patients with and without endometriosis.

METHODS

Observational study comparing peripheral lymphocytes telomere content, measured by quantitative polymerase chain reaction, in patients with (n = 86) and without endometriosis (n = 21).

FINDINGS

Patients with endometriosis had longer telomeres than that of matched, endometriosis-free controls (telomere to single copy gene ratio [T/S ratio] of 1.62 vs 1.34, respectively, P = .00002). Patients with endometriosis were 8.1-fold more likely to have long telomeres. (odds ratio = 8.1, 95% confidence interval: 1.28-51.57, P = .0264).

INTERPRETATION

Longer telomeres could be consistent with a stem cell origin of endometriosis.

Health promotion board-ministry of health clinical practice guidelines: treating tobacco use and dependence

The Health Promotion Board (HPB) has updated the clinical practice guidelines on Treating Tobacco Use and Dependence to provide health professionals in Singapore with evidence-based interventions for smoking cessation. This article reproduces the introduction and executive summary of key guideline recommendations (with recommendations from the guidelines) from the HPB-MOH Clinical Practice Guidelines on Treating Tobacco Use and Dependence, for the information of SMJ readers. Chapters and page numbers mentioned in the reproduced extract refer to the full text of the guidelines, which are available from the Health Promotion Board website: http://www.hpb.gov.sg/cpg-smoking-cessation. The recommendations should be used with reference to the full text of the guidelines. Following this article are multiple choice questions based on the full text of the guidelines.