Genomic education for the next generation of health-care providers

Historically, medical geneticists and genetic counselors have provided the majority of genetic services. Advances in technology, reduction in testing costs, and increased public awareness have led to a growing demand for genetic services in both clinical and direct-to-consumer spaces. Recent and anticipated changes in the workforce of genetic counselors and medical geneticists require a reexamination of the way we educate health-care providers and the means by which we provide access to genetic services. The time is ripe for rapid growth of genetic and genomic services, but to capitalize on these opportunities, we need to consider a variety of educational mechanisms to reach providers both within and beyond the traditional genetic counseling and medical genetics sectors, including nurses, physician assistants, and nongenetics physicians. This article summarizes the educational efforts underway in each of these professions.

Large debris dumps in the northern South China Sea

Knowledge of the abundance, source, and fate of marine debris in the deep sea is largely constrained thus far. Here, we report the existence of large deep-sea debris dumps that have not been reported before on the seafloor worldwide. Marine debris remarkably accumulated at ~1700-1800 m in the tributary submarine canyons of the Xisha Trough, northern South China Sea (SCS). Although marine debris in Xisha Trough is patchy, the debris abundance was as high as 36,818 and 51,929 items/km² at locations SY78 and SY82, respectively, which is one order of magnitude higher than that in other submarine canyons. We propose that most of the debris came from fishery and navigation activities, as indicated by the categories of debris collected from the seafloor dumps. Seasonal surface ocean currents of the SCS and geomorphology of submarine canyons possibly influence the movement of the debris from coasts to the deep seafloor.

From helices to health: undergraduate medical education in genetics and genomics

Rapid advances in genomic technologies combined with drastic reductions in cost and a growing number of clinical genomic tests are transforming medical practice. While enthusiasm about applications of precision medicine is high, the existing clinical genetics workforce is insufficient to meet present demands and will fall increasingly short as the use of genetic and genomic testing becomes more routine. To address this shortage, physicians in all areas of medicine will require genomic literacy. Undergraduate medical students, therefore, need a solid foundation in genetics and genomics so they can apply genomic medicine across a range of specialties. Here, we review the current trends and challenges in undergraduate medical genetics education in North America, highlight innovations and offer recommendations.

Abstract P5-05-01: Metabolic enzyme PFKFB4 activates transcriptional coactivator SRC-3 to drive aggressive metastatic breast cancer

Background: Metabolic rewiring is one of the central hallmarks of cancer progression and survival to support anabolic and energetic demands. Tumor cells constantly alter their metabolic state in response to oncogenic stimuli, nutrient availability, and interaction with immune cells however the precise regulation that precedes the metabolic alteration is poorly understood. Here we report a direct interaction of glycolytic enzyme PFKFB4 with transcriptional coregulator SRC-3. PFKFB4 functions as a critical regulator of Warburg effect and our study reveals that upon glucose stimulation PFKFB4 activates SRC-3 driving an invasive-metastatic breast cancer.

Methods: Molecular experiments were performed to understand the transcriptional activation of SRC-3 by PFKFB4 enzyme. Chromatin immunoprecipitation and gene expression studies were performed to investigate the functions of PFKFB4/SRC-3 crosstalk on transcriptional regulation. Metabolomics and isotope tracing studies were performed to identify the metabolic adaptations regulated by PFKFB4/SRC-3 in breast tumors. PFKFB4-knockout was established using CRISPR-Cas9 system and functional studies were carried out to define its role in tumor cell proliferation, invasion-migration, and breast to lung metastasis. Human breast tumor samples were evaluated to identify the clinical importance of PFKFB4/SRC-3 crosstalk in patients.

Results:Molecular studies revealed that PFKFB4 enzyme phosphorylates SRC-3 at serine 857 (S857) enhancing its transcriptional activity, whereas either suppression of PFKFB4 or ectopic expression of a phosphorylation-deficient SRC-3 mutant S857A (SRC-3S857A) significantly abolished SRC-3-mediated transcriptional output (p<0.000001). Functionally, PFKFB4-driven SRC-3 activation drives glucose flux towards the pentose phosphate pathway enabling purine synthesis by transcriptionally upregulating the expression of enzyme transketolase (TKT). Deletion of PFKFB4 by CRISPR-Cas9 system resulted in significantly reduced proliferation (p<0.05) and migration-invasion (p<0.001) compared to wildtype breast tumor cells. Ablation of SRC-3 or PFKFB4 suppressed in vivo breast tumor growth and prevents metastasis to the lung from an orthotopic setting (p<0.0001). PFKFB4 and phosphorylated SRC-3 levels are significantly increased in breast tumors (p=0.02), whereas, in patients with the basal subtype, PFKFB4 and SRC-3 drive a common protein signature that correlates with the poor survival of TNBC patients (p=0.03).

Conclusion:Our data suggest that the Warburg pathway enzyme PFKFB4 acts as a molecular fulcrum that couples sugar metabolism to transcriptional activation by stimulating SRC-3 to promote aggressive metastatic tumors. It also provides first evidence how Warburg pathway drives aggressive breast tumorigenesis by directly activating powerful oncogene SRC-3. Our work suggests that targeting the PFKFB4–SRC-3 axis may be therapeutically valuable in breast tumors that are notably dependent on glucose metabolism.

(This work is funded by grants from Susan G. Komen and NCI to S.D.)

Citation Format: Dasgupta S, Anand V, John H, Sawant Dessai A, Katsuta E, Takabe K, O'Malley B. Metabolic enzyme PFKFB4 activates transcriptional coactivator SRC-3 to drive aggressive metastatic breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-05-01.

Abstract P2-02-04: CD73 expression regulated by estrogen signaling associates with poor prognosis in estrogen receptor (ER)-positive breast cancer

Introduction: CD73, a cell surface enzyme, catalyzes the generation of adenosine from ATP and ADP in the tumor microenvironment along with CD39. Accumulated extracellular adenosine functions as immune-suppressor, and also binds to adenosine receptors which promotes angiogenesis and cell proliferation that results in accelerate cancer progression. However, the clinical significance and molecular function of CD73 expression in breast cancer remains unclear.

Methods: Utilizing publicly available breast cancer cohorts of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), clinical significance as well as underlying mechanisms were investigated. Molecular experiments were carried out in MCF7 cells, ER-positive breast cancer cell line, to investigate the role of estrogen signaling on CD73/CD39 expression.

Results: In treatment naïve TCGA cohort, CD73 expression level was significantly lower in ER-positive breast cancers compared to ER-negative tumors. Higher CD73 expression was associated with worse overall survival in whole cohort (p=0.021) and ER-positive tumors (p=0.003), but not in ER-negative tumors. Gene Set Enrichment Analysis revealed that estrogen response gene sets (Early; NES=-1.57, p=0.043, Late; NES=-1.61, p=0.021) were significantly enriched in CD73 low expressing ER-positive tumors, suggesting estrogen signaling may repress CD73 expression. To test this hypothesis, we analyzed the expression of CD73 and CD39 in MCF7 cells treated with estrogen, tamoxifen or both. Our data revealed that estrogen treatment suppressed CD73 and CD39 expression, whereas tamoxifen treatment enhanced expression of the genes. These findings suggest that CD73 and CD39 gene expression is suppressed by estrogen signaling, whereas binding of ER antagonists such as tamoxifen can remove the repressive effect on gene expression. On the other hand, epithelial-mesenchymal transition (EMT) (Normalized Enrichment Score; NES=2.41, p<0.001) and angiogenesis (NES=2.33, p<0.001) gene sets were significantly enriched in CD73 high expressing ER-positive tumors. CIBERSORT, which is an algorithm to estimate infiltrating immune cells by gene expression, demonstrated that CD73 high expressing ER-positive tumors have less infiltrating CD8-positive T cells, memory B cells and plasma cells, implying that CD73 high expressing tumors have immune suppressive environment, which is in agreement with the notion that CD73 high tumors are immunosuppressive. Finally, we found that CD73 expression was significantly elevated post-chemotherapy compared to tumors prior to the treatment (p=0.007), and CD73 high expression patients showed worse relapse-free survival in neoadjuvant chemotherapy patients cohort (p=0.003).

Conclusion: Molecular studies revealed that CD73 expression is regulated by estrogen signaling. Increased expression of CD73 significantly correlates with worse outcomes in ER-positive breast cancer patients. This may be due to upregulated pro-metastatic gene signatures such as EMT and angiogenesis as well as less infiltration of anti-cancer immune cells by adenosine generated by CD73 in the tumor microenvironment. Our data reveals an intriguing mechanism which may be responsible for recurrence and metastasis of ER-positive breast cancer.

Citation Format: Katsuta E, Anand V, Yan L, Dasgupta S, Takabe K. CD73 expression regulated by estrogen signaling associates with poor prognosis in estrogen receptor (ER)-positive breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-02-04.

Homogeneous reduced moment in a gapful scalar chiral kagome antiferromagnet

We present a quantitative experimental investigation of the scalar chiral magnetic order with in Nd3Sb3Mg2O14. Static magnetization reveals a net ferromagnetic ground state, and inelastic neutron scattering from the hyperfine coupled nuclear spin reveals a local ordered moment of 1.76(6) μ B , just 61(2)% of the saturated moment size. The experiments exclude static disorder as the source of the reduced moment. A 38(1) μ eV gap in the magnetic excitation spectrum inferred from heat capacity rules out thermal fluctuations and suggests a multipolar explanation for the moment reduction. We compare Nd3Sb3Mg2O14 to Nd pyrochlores and show that Nd2Zr2O7 is in a spin fragmented state using nuclear Schottky heat capacity.

The Undergraduate Training in Genomics (UTRIG) Initiative: early & active training for physicians in the genomic medicine era

Genomic medicine is transforming patient care. However, the speed of development has left a knowledge gap between discovery and effective implementation into clinical practice. Since 2010, the Training Residents in Genomics (TRIG) Working Group has found success in building a rigorous genomics curriculum with implementation tools aimed at pathology residents in postgraduate training years 1-4. Based on the TRIG model, the interprofessional Undergraduate Training in Genomics (UTRIG) Working Group was formed. Under the aegis of the Undergraduate Medical Educators Section of the Association of Pathology Chairs and representation from nine additional professional societies, UTRIG's collaborative goal is building medical student genomic literacy through development of a ready-to-use genomics curriculum. Key elements to the UTRIG curriculum are expert consensus-driven objectives, active learning methods, rigorous assessment and integration.

Transpectoral Anterior Approach to the Axilla for Lymph Node Dissection in Association with Mastectomy Preserving Both Pectoral Muscles and Their Neurovascular Bundles

In Patey's mastectomy, which is still the most common operation for breast cancer, axillary node dissection (AND) is performed through the base of the axilla after retracting the pectoralis major muscle and excising the pectoralis minor muscle (some surgeons preserve the latter). This has the disadvantage of inadequate exposure of the axilla and the risk of damage to the neurovascular bundles supplying the pectoral muscles, which in the long run may lead to atrophy of these muscles. A transpectoral anterior approach to the axilla for AND in association with mastectomy was attempted in 115 cases to obviate the above-mentioned disadvantages. The approach included: 1) splitting of the pectoralis major between the clavicular and sternal fibers; 2) mobilization and swinging of the pectoralis minor into different directions by means of a sling to facilitate AND at selected levels. The major advantages of this approach were: 1) total preservation of both pectoral muscles with their neurovascular bundles maintained the normal anatomy and function of the shoulder; 2) the axilla was directly approached through the anterior wall instead of through the base; in this way the axillary contents were exposed almost at surface level; 3) the dissection plane could be limited to anterior to and below the axillary vein and the risk of postoperative lymphedema could thus be minimized; 4) change of position of the ipsilateral arm was not necessary; 5) the duration of surgery was reduced. Monoblock ablation of significant and suspected tissues, maintaining the normal anatomy and function of the shoulder, could be easily accomplished with this approach.

The art and science of selecting graduate students in the biomedical sciences: Performance in doctoral study of the foundational sciences

The goal of this study was to investigate associations between admissions criteria and performance in Ph.D. programs at Boston University School of Medicine. The initial phase of this project examined student performance in the classroom component of a newly established curriculum named "Foundations in Biomedical Sciences (FiBS)". Quantitative measures including undergraduate grade point average (GPA), graduate record examination (GRE; a standardized, computer-based test) scores for the verbal (assessment of test takers' ability to analyze, evaluate, and synthesize information and concepts provided in writing) and quantitative (assessment of test takers' problem-solving ability) components of the examination, previous research experience, and competitiveness of previous research institution were used in the study. These criteria were compared with competencies in the program defined as students who pass the curriculum as well as students categorized as High Performers. These data indicated that there is a significant positive correlation between FiBS performance and undergraduate GPA, GRE scores, and competitiveness of undergraduate institution. No significant correlations were found between FiBS performance and research background. By taking a data-driven approach to examine admissions and performance, we hope to refine our admissions criteria to facilitate an unbiased approach to recruitment of students in the life sciences and to share our strategy to support similar goals at other institutions.

Status of COMPASS RICH-1 Upgrade with MPGD-based Photon Detectors

A Set of new MPGD-based Photon Detectors is being built for the upgrade of COMPASS RICH-1. The detectors cover a total active area of 1.4 m2 and are based on a hybrid architecture consisting of two THGEM layers and a Micromegas. A CsI film on one THGEM acts as a reflective photocathode. The characteristics of the detector, the production of the components and their validation tests are described in detail.

Nano- and microparticles at fluid and biological interfaces

Systems with interfaces are abundant in both technological applications and biology. While a fluid interface separates two fluids, membranes separate the inside of vesicles from the outside, the interior of biological cells from the environment, and compartmentalize cells into organelles. The physical properties of interfaces are characterized by interface tension, those of membranes are characterized by bending and stretching elasticity. Amphiphilic molecules like surfactants that are added to a system with two immiscible fluids decrease the interface tension and induce a bending rigidity. Lipid bilayer membranes of vesicles can be stretched or compressed by osmotic pressure; in biological cells, also the presence of a cytoskeleton can induce membrane tension. If the thickness of the interface or the membrane is small compared with its lateral extension, both can be described using two-dimensional mathematical surfaces embedded in three-dimensional space. We review recent work on the interaction of particles with interfaces and membranes. This can be micrometer-sized particles at interfaces that stabilise emulsions or form colloidosomes, as well as typically nanometer-sized particles at membranes, such as viruses, parasites, and engineered drug delivery systems. In both cases, we first discuss the interaction of single particles with interfaces and membranes, e.g. particles in external fields, non-spherical particles, and particles at curved interfaces, followed by interface-mediated interaction between two particles, many-particle interactions, interface and membrane curvature-induced phenomena, and applications.

First Measurement of Transverse-Spin-Dependent Azimuthal Asymmetries in the Drell-Yan Process

The first measurement of transverse-spin-dependent azimuthal asymmetries in the pion-induced Drell-Yan (DY) process is reported. We use the CERN SPS 190  GeV/c π^{-} beam and a transversely polarized ammonia target. Three azimuthal asymmetries giving access to different transverse-momentum-dependent (TMD) parton distribution functions (PDFs) are extracted using dimuon events with invariant mass between 4.3  GeV/c^{2} and 8.5  GeV/c^{2}. Within the experimental uncertainties, the observed sign of the Sivers asymmetry is found to be consistent with the fundamental prediction of quantum chromodynamics (QCD) that the Sivers TMD PDFs extracted from DY have a sign opposite to the one extracted from semi-inclusive deep-inelastic scattering (SIDIS) data. We present two other asymmetries originating from the pion Boer-Mulders TMD PDFs convoluted with either the nucleon transversity or pretzelosity TMD PDFs. A recent COMPASS SIDIS measurement was obtained at a hard scale comparable to that of these DY results. This opens the way for possible tests of fundamental QCD universality predictions.

Genetics in LGB Assisted Reproduction: Two Flipped Classroom, Progressive Disclosure Cases

INTRODUCTION

There have been several educational reforms calling for increasing lesbian, gay, bisexual, and transgender (LGBT) education materials, application of basic sciences to clinical medicine, and active engagement of students. While the amount of educational materials for LGBT clinical cases is increasing, this session for preclinical medical students uniquely combines basic science population genetics, cisgender lesbian, gay, and bisexual (LGB) cultural issues and reproductive endocrinology in a 1.5-hour flipped classroom session.

METHODS

Students were assigned a prediscussion video and reading. Facilitators attended a 1.5-hour training session prior to discussion. Each classroom of 30 students with small groups of six was led by a third- or fourth-year medical student facilitator who taught from a PowerPoint that included discussion questions. An audience response system was used to show aggregated, real-time anonymous responses to case questions, a pre- and postsurvey was used to analyze changes in student attitudes and knowledge of assisted reproduction services for same-sex couples, and course evaluations captured overarching student impressions.

RESULTS

All first-year students (N = 180) attended this mandatory session. Audience response questions showed a high level of knowledge of population genetics concepts. Voluntary surveys showed a higher number of assisted reproduction recommendations for LGB patients compared to heterosexual patients before discussion, with this difference disappearing after the discussion. This may indicate a shift in student attitudes and knowledge of LGB patient barriers and assisted reproduction. Course evaluations showed appreciation of LGB material integration within the course.

DISCUSSION

Educators will be able to successfully integrate the application of population genetics, assisted reproduction cases, and an examination of cultural barriers in health care for LGB patients with this session.

Medical Genetics Ethics Case Collection: Discussion Materials for Medical Students in the Genomic Era

INTRODUCTION

This collection of cases in medical genetics focuses on ethical dimensions of genetic testing. Given the recent and continuing revolution in genetic testing technologies, understanding the nuances of genetic tests and the implications of their outcomes for patients is a critical learning goal for medical students.

METHODS

This case collection was developed for first-year medical students. The cases fall into two types: discussion cases that lend themselves to both small-group and lecture settings and brief audience-response clicker cases to be used in larger lecture settings. The cases span topics such as direct-to-consumer genetic testing, patient privacy, economic and legal issues of genetic testing, and secondary findings in whole exome/genome sequencing. The clicker cases can be used to punctuate class sessions on the related science, while the discussion cases can be deployed as a single 2-hour session focusing on ethics. The associated materials include teaching notes on the scientific and ethical dimensions of the cases, a slide presentation of the cases, and implementation advice.

RESULTS

Students found that engaging with these cases was very stimulating and eye-opening. Student comments indicated that they appreciated the opportunity to grapple with the ethical dimensions of the genetic testing technologies and that the challenges brought to light highlighted the complexity of medical practice in the genomic era.

DISCUSSION

Although these cases were originally developed for use with medical students, they could easily be adapted for use in postgraduate and CME settings to explore complex ethical scenarios on which even the experts disagree.

Abstract P6-01-15: Novel regulation of breast cancer cell aggressiveness by cancer testis antigen

We recently demonstrated that a vesicular endocytosis associated protein SH3GL2, attenuates spontaneous metastases of breast cancer cells by inducing a mesenchymal to epithelial differentiation and the onset of the intrinsic apoptotic pathway. The present study aims to understand the molecular mechanism behind the SH3Gl2 mediated reduction of spontaneous metastasis of the breast cancer cells.

We employed a cDNA microarray analysis of the SH3GL2-overexpressing breast cancer cells exhibiting reduced pulmonary metastasis and identified a 12.1 fold downregulation of SPANXB1, a cancer-testis antigen that regulates sperm motility. A limited number of studies reported an association between increased SPANXB1 expression and progression of melanoma and hepatocellular carcinoma. Augmented SPANXB1 mRNA and protein expression was evident in primary breast tumors and its upregulation was associated with pulmonary metastasis of breast cancer cells. However, the expression pattern of SPANXB1 and its role in BCa development and progression is unknown. By immunohistochemical analysis, we detected high expression (p=0.002) of SPANXB1 in 78% (18/23) of the primary breast cancer tissues and corresponding lymph node metastases compared to the matched normal breast tissues. A couple of non-tumorigenic human breast epithelial cell lines were stably transformed with SPANXB1 to understand its effect on cellular growth and progression. The SPANXB1-transformed cells exhibited increased invasion (p=0.0001) and epithelial to mesenchymal transition accompanied by an augmented expression ratio of Vimentin/E-Cadherin, molecules regulating differentiation and metastasis. The SPANXB1-transformed cells also exhibited a markedly reduced expression of SH3GL2, implicating a SPANXB1:SH3GL2 crosstalk accompanied by an enhanced production of lactate (p=0.004). Our investigation identifies new breast cancer promoting role of a cancer testis antigen, which bears potential for biomarker and targeted therapeutic development.

Citation Format: Kannan A, Wells RM, Ikebe M, Dasgupta S. Novel regulation of breast cancer cell aggressiveness by cancer testis antigen [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 P6-01-15.

A Single-center Experience of Kidney Transplantation from Donation after Circulatory Death: Challenges and Scope in India

Donation after circulatory death (DCD) has never been attempted in India because of legal constraints and lack of guidelines for the withdrawal of life support in end-of-life situations. The present report describes the initial experience of transplantation of organs from DCD donors in a tertiary care center in India. Between 2011 and 2015, five donors had kidneys retrieved after cardiac arrest. These patients were declared dead after waiting for 5 min with no electrocardiographic signal on monitor following cardiopulmonary resuscitation (CPR), which was restarted in three patients till organ retrieval. All donors received heparin and underwent rapid cannulation of aorta, infusion of preservative cold solution, and immediate surface cooling of organs during retrieval surgery. 9/10 kidneys were utilized. Mean donor age was 29.6 ± 16.3 years, M:F 4:1 and mean age of recipients was 38.7 ± 10.8 years, M:F 7:2. Seven patients required dialysis in postoperative period. Mean postoperative day 0 urine output was 1.9 ± 2.6 L. Baseline creatinine achieved was 1.38 ± 0.35 mg/dl after a mean duration of 26.12 ± 15.4 days. Kidneys from donors where CPR was continued after the declaration of death (n = 3) had better recovery of renal function (time to reach baseline creatinine 21.2 ± 7.2 vs. 34.3 ± 23.7 days, baseline creatinine 1.36 ± 0.25 vs. 1.52 ± 0.45 mg%). In donors without CPR, one kidney never functioned and others had patchy cortical necrosis on protocol biopsy, which was not seen in the kidneys from donors with CPR. Kidneys from DCD donors can serve as a useful adjunct in deceased donor program. Continuing CPR after the declaration of death seems to help in improving outcomes.