Helping Scholars Overcome Socioeconomic Barriers to Medical and Biomedical Careers: Creating a Pipeline Initiative

Problem: To achieve their potential in medical and biomedical careers, students (scholars) from under-resourced backgrounds must build sophisticated skills and develop confidence and professionalism. To flourish in an advanced educational system that may be unfamiliar, these scholars also need networks of mentors and role models. These challenges can affect scholars at multiple stages of their education. Intervention: To meet these challenges, we created a broad and innovative biomedical research-focused pipeline program: the Johns Hopkins Initiative for Careers in Science in Medicine (CSM Initiative). This initiative targets three levels: high school, undergraduate, and post-baccalaureate/pre-doctoral (graduate and medical). We provide training in essential academic, research, professional, and social skills to meet the unique challenges of our scholars from under-resourced backgrounds. Scholars also build relationships with mentors who provide career guidance and support. We present an overview of the training and assessment at each level of this initiative. Context: The initiative took place at an institution located in the greater Baltimore area and that is endowed with exceptional doctoral and postdoctoral trainees, staff, and faculty including clinicians, physician-scientists, and scientists who served as key role models and mentors. Our pipeline program draws from local high school students and a local and national pool of undergraduates and post-baccalaureates preparing for medical or graduate school. Impact: Our goals for the high school scholars are significant improvement in academic skills, increased confidence, and matriculation into higher education systems. Currently, at least 83% of high school scholars have matriculated into four-year college programs and 73% have chosen science, technology, engineering, math, and medicine (STEMM)-related majors. Among undergraduate participants, 42% have matriculated thus far into medical or biomedical graduate programs and this number is expected to rise as more scholars graduate from college and either enter graduate training or pursue STEMM careers. Another 25% have returned to our post-baccalaureate program. Among post-baccalaureate scholars, 71% have now matriculated into doctoral-level graduate biomedical programs (medical or graduate school) and the remaining 29% are pursuing careers in STEMM-related fields such as biomedical research with some still aiming at graduate-level education. Our long-term goal is to see a large majority of our scholars become successful professionals in medicine, biomedical research, allied healthcare, or other STEMM fields. Analysis of the early phases of the CSM initiative demonstrates such outcomes are attainable. Lessons Learned: This program provides experiences in which scholars develop and practice core competencies essential for developing their self-identity as scientists and professionals. The most important lesson learned is that mentorship teams must be highly dynamic, flexible, thoughtful, and personal in responding to the wide range of challenges and obstacles that scholars from under-resourced backgrounds must overcome to achieve career success.

Allosteric coupling between Mn2+ and dsDNA controls the catalytic efficiency and fidelity of cGAS

Cyclic-G/AMP (cGAMP) synthase (cGAS) triggers host innate immune responses against cytosolic double-stranded (ds)DNA arising from genotoxic stress and pathogen invasion. The canonical activation mechanism of cGAS entails dsDNA-binding and dimerization. Here, we report an unexpected activation mechanism of cGAS in which Mn2+ activates monomeric cGAS without dsDNA. Importantly, the Mn2+-mediated activation positively couples with dsDNA-dependent activation in a concerted manner. Moreover, the positive coupling between Mn2+ and dsDNA length-dependent activation requires the cognate ATP/GTP substrate pair, while negative-cooperativity suppresses Mn2+ utilization by either ATP or GTP alone. Additionally, while Mn2+ accelerates the overall catalytic activity, dsDNA length-dependent dimerization specifically accelerates the cyclization of cGAMP. Together, we demonstrate how the intrinsic allostery of cGAS efficiently yet precisely tunes its activity.

Chromatin-bound cGAS is an inhibitor of DNA repair and hence accelerates genome destabilization and cell death

DNA repair via homologous recombination (HR) is indispensable for genome integrity and cell survival but if unrestrained can result in undesired chromosomal rearrangements. The regulatory mechanisms of HR are not fully understood. Cyclic GMP-AMP synthase (cGAS) is best known as a cytosolic innate immune sensor critical for the outcome of infections, inflammatory diseases, and cancer. Here, we report that cGAS is primarily a chromatin-bound protein that inhibits DNA repair by HR, thereby accelerating genome destabilization, micronucleus generation, and cell death under conditions of genomic stress. This function is independent of the canonical STING-dependent innate immune activation and is physiologically relevant for irradiation-induced depletion of bone marrow cells in mice. Mechanistically, we demonstrate that inhibition of HR repair by cGAS is linked to its ability to self-oligomerize, causing compaction of bound template dsDNA into a higher-ordered state less amenable to strand invasion by RAD51-coated ssDNA filaments. This previously unknown role of cGAS has implications for understanding its involvement in genome instability-associated disorders including cancer.

Characterization of DNA bound cyclic GMP-AMP synthase using atomic force microscopy imaging

The protocol described herein allows for acquiring topography images of DNA-protein complexes using Atomic Force Microscopy imaging. Since the very beginning of this method, AFM has been an indispensable tool for characterization of biomolecular complexes with exceptional capability of observing single complexes. This method can visualize structural characteristics of DNA-protein assemblies and evaluate differences between individual complexes. Although this protocol is generally applicable to a large number of various proteins complexed with DNA, we use cyclic G/AMP synthase (cGAS) enzyme as a case study for the protocol description.

Tracking the polymerization of DNA sensors and inflammasomes using FRET

Upon activation, DNA sensors and inflammasomes often polymerize into filamentous oligomers, and transduce the incoming pathogenic signal via inducing the assembly of downstream filaments. Given the complexity of these supramolecular structures, kinetics and thermodynamics that govern their assembly mechanisms remain poorly understood. Here, we present a simple yet robust assay that can track the assembly of these filaments in a quantitative manner. This FRET-based measurement is cost effective and also amenable to high-throughput screening.

A pyrophosphatase-coupled assay to monitor the NTase activity of cGAS

Cyclic GMP-AMP synthase, cGAS, converts ATP and GTP into a cyclic dinucleotide second messenger, cyclic GMP-AMP or cGAMP, through its enzymatic, nucleotidyl transferase (NTase) activity. Although many methods are available to directly measure cGAMP production, these assays often have high cost of implementation and/or experimental limitations. This chapter details how to implement an alternative approach that is relatively inexpensive, accurate and medium-throughput. The assay measures cGAS NTase activity by quantifying pyrophosphate production, a byproduct of the cGAS reaction. A coupling enzyme, pyrophosphatase, catalyzes the hydrolysis of pyrophosphate into inorganic phosphate, which enables facile detection of cGAS activity through conventional phosphomolybdate-malachite green absorbance methodology. This method is amenable for conventional steady-state kinetic measurements as well as high-throughput compound screening.

Preparation of filamentous proteins for electron microscopy visualization and reconstruction

Cryo electron microscopy (cryo-EM) has become a mainstream tool for determining the structures of macromolecular complexes at the atomic resolution. It has many advantages over other techniques such as X-ray crystallography and nuclear magnetic resonance (NMR). However, it also entails several challenges, a major one being preparation of an ideal sample. Recent studies have identified that DNA sensors and inflammasomes often assemble into filamentous oligomers, which poses a unique set of challenges in preparing ideal samples for high-resolution reconstruction using cryo-EM. This chapter will discuss how to overcome several major issues in cryo-EM sample preparation including construct design, screening using negative stain (ns) EM, and tips on working with filamentous proteins.

Abstract OT3-02-02: PATHWAY: Asian, multicenter, phase 3 trial of tamoxifen with or without palbociclib ± goserelin in women with hormone receptor-positive, HER2-negative advanced or metastatic breast cancer

BACKGROUND:

The incidence rates of breast cancer (BC) in Asian counties have been rising rapidly. The age-specific female BC incidence rates peak before menopause (around 40-50 years of age) in Asia, however treatment options for pre/perimenopausal patients are limited. Palbociclib (P) is an oral novel cyclin-dependent kinase 4/6 (CDK4/6) inhibitor. The addition of P to endocrine therapy (ET) such as aromatase inhibitor or fulvestrant has been demonstrated improved progression-free survival (PFS) in phase 3 studies PALOMA-2 and PALOMA-3. This study is designed to evaluate efficacy and safety of P plus tamoxifen (TAM) in patients with hormone receptor (HR)-positive, human epidermal growth factor receptor 2 (HER2)-negative advanced or metastatic BC regardless of menopausal status. This study is conducted as a Clinical Research Collaboration by National Cancer Center Hospital with research funding from Pfizer.

TRIAL DESIGN:

PATHWAY/NCCH1607 is a double-blind, placebo-controlled, randomized, phase 3 study. Patients will be randomized 1:1 to receive either P (125 mg once daily, days1-21 of a 28-day cycle) or placebo in combination with TAM (20 mg once daily, continuously). Pre/perimenopausal women should receive concurrent ovarian function suppression with goserelin. Randomization will be stratified by prior ET for advanced/metastatic BC (1st line ET vs. 2nd line ET) and menopausal status (pre/perimenopausal vs. postmenopausal).

KEY ELIGIBILITY CRITERIA:

Eligible patients include women of any menopausal status with HR-positive, HER2-negative advanced or metastatic BC; candidates to receive TAM as 1st line or 2nd line ET for advanced/metastatic disease; ≥18 years of age; measurable or non-measurable disease (RECIST v.1.1); ECOG performance status 0-1; adequate organ function; have not received treatment with TAM (except for patients who have had more than 12 months from completion of adjuvant therapy with TAM); and have not received any CDK4/6 or phosphoinositide 3-kinase (PI3K) - mammalian target of rapamycin (mTOR) inhibitors.

SPECIFIC AIMS:

The primary endpoint is PFS as assessed by the investigator. Secondary endpoints include overall survival (OS), 1, 2, and 3-year survival probabilities, objective response (OR), duration of response, clinical benefit rate (CBR), pharmacokinetics, safety, and patient-reported outcomes.

STATISTICAL METHODS:

The sample size was determined to detect a 38% reduction in the hazard of disease progression or death in P plus TAM arm with a 1-sided significance level of 2.5% and power of 80%. A stratified log rank test will be used to compare PFS between the 2 treatment arms.

PRESENT ACCRUAL AND TARGET ACCRUAL:

Target accrual of 180 patients will be enrolled within 23 sites among Japan, Korea, Taiwan, and Singapore. As of June 2018, 46 patients have been enrolled.

CONTACT INFORMATION:

This trial is registered at ClinicalTrials.gov NCT03423199 and UMIN000030816. For more information, email NCCH1607_office@ml.res.ncc.go.jp

Citation Format: Noguchi E, Hata T, Nakamura K, Kuchiba A, Hayashi M, Hamada A, Yonemori K, Sohn J, Lu Y-S, Yap Y-S, Fujiwara Y, Tamura K. PATHWAY: Asian, multicenter, phase 3 trial of tamoxifen with or without palbociclib ± goserelin in women with hormone receptor-positive, HER2-negative advanced or 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 OT3-02-02.

Abstract P3-10-09: Relationship between tumor infiltrating lymphocytes (TILs) and response to pembrolizumab (Pembro)+chemotherapy (Chemo) as neoadjuvant treatment (NAT) for triple-negative breast cancer (TNBC): phase Ib KEYNOTE-173 trial

Background:Increasing quantities of stromal TILs (sTILs) are associated with higher pathologic complete response (pCR) rates with conventional chemo in early-stage TNBC. We evaluated the association between sTILs and PD-L1 expression with response to pembro+chemo as NAT for TNBC in the KEYNOTE-173 trial (NCT02622074).

Methods: sTILs were quantified using light microscopy of H&E-stained slides from pretreatment and on-treatment (during first 3 weeks of pembro monotherapy) tumor biopsies by a pathologist blind to response data. Pretreatment PD-L1 expression was assessed using the PD-L1 IHC 22C3 pharmDx assay and reported as combined positive score (CPS). Endpoints were pCR rate by ypT0 ypN0 and ypT0/Tis ypN0 and objective response rate (ORR; RECIST v1.1) after the first 4 cycles of NAT (taxane±carboplatin+pembro) by MRI. sTILs and PD-L1 CPS were evaluated as continuous variables. Association between sTILs and PD-L1 CPS with response was assessed using logistic regression and area under the reciever operating curve (AUROC) analyses, with a 1-sided alpha level of 0.10. Correlation between PD-L1 and sTILs was assessed by Spearman's rank correlation coefficient. Multivariate analysis included sTILs (pretreatment and on-treatment) and PD-L1 CPS. Likelihood ratio tests were used to evaluate the added value of factors in predicting pCR rate.

Results: Of 60 total pts, 34 had tumors evaluated for pretreatment sTILs, 52 for PD-L1 CPS, and 33 for both sTILs and CPS. On-treatment sTILs were evaluated in 31 pts. Overall pCR rates were 56.7% and 60% by ypT0 ypN0 and ypT0/Tis ypN0, respectively; ORR was 78.3%. In pts evaluated for sTILs and CPS (individually), pCR rates and ORR were comparable with overall pCR rates and ORR. There was a significant correlation between pretreatment sTILs and PD-L1 CPS (ρ=0.65, P<0.001).Higher pretreatment sTILs were significantly associated with response: ypT0 ypN0 P= 0.011; ypT0/Tis ypN0 P=0.006; ORR P=0.061. On-treatment sTILs were also significantly associated with response: ypT0 ypN0 P=0.061; ypT0/Tis ypN0 P=0.041; ORR P=0.031. Pretreatment PD-L1 CPS was significantly associated with response: ypT0 ypN0 P=0.073; ypT0/is ypN0 P=0.030; and ORR P=0.021. AUROC of pretreatment sTIL association with pCR was numerically higher than with on-treatment sTILs and PD-L1 CPS (0.69 vs 0.61 vs 0.56 for ypT0ypN0 and 0.72 vs 0.67 vs 0.62 for ypT0/Tis ypN0). Responders had higher median pretreatment sTIL levels vs nonresponders: 45% [10, 75] vs 10% [5, 20] for pCR rate by ypT0 ypN0 and 52.5% [10, 73.8] vs 10% [5, 20] for pCR rate by ypT0/Tis ypN0; 25% [5, 70] vs 10% [6.3, 27.5] for ORR. In multivariate analysis, only pretreatment sTILs were significant for both pCR endpoints (ypT0 ypN0 P=0.031; ypT0/Tis ypN0 P=0.034). Likelihood ratio tests demonstrated that for both pCR endpoints, PD-L1 CPS (P=0.683/P=0.422) and on-treatment sTILs (P=0.984/P=0.568) did not add significantly more value to pretreatment sTILs when predicting pCR.

Conclusions:Higher quantities of pretreatment sTILs and PD-L1 CPS and on-treatment sTILs were significantly associated with higher pCR rates and ORR in primary TNBC treated with pembro and NAT.

Citation Format: Loi S, Schmid P, Cortés J, Park YH, Muñoz-Couselo E, Kim S-B, Sohn J, Im S-A, Holgado E, Foukakis T, Kuemmel S, Dent R, Wang A, Aktan G, Karantza V, Salgado R. Relationship between tumor infiltrating lymphocytes (TILs) and response to pembrolizumab (Pembro)+chemotherapy (Chemo) as neoadjuvant treatment (NAT) for triple-negative breast cancer (TNBC): phase Ib KEYNOTE-173 trial [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 P3-10-09.

Abstract P6-18-06: Ribociclib treatment benefit in patients with advanced breast cancer with ≥1 dose reduction: Data from the MONALEESA-2, -3, and -7 trials

Background: In the MONALEESA (ML) trials, addition of ribociclib (RIB; cyclin-dependent kinase 4/6 inhibitor) to endocrine therapy (ET) prolonged progression-free survival (PFS) in patients (pts) with hormone receptor-positive (HR+), HER2-negative (HER2–) advanced breast cancer (ABC). RIB was generally well tolerated, with adverse events (AEs) managed effectively by dose modifications. Here we present efficacy data for RIB-based regimens of interest for the proposed indication (i.e. with a non-steroidal aromatase inhibitor [NSAI] or fulvestrant [FUL]) from ML-2, -3, and -7 in pts who received no prior ET for ABC and who had ≥1 RIB dose reduction, to explore the efficacy of RIB in pts who need to dose reduce.

Methods: Pts included in this analysis were: postmenopausal women with HR+, HER2– ABC and no prior ET for ABC who received RIB (600 mg; 3-weeks-on/1-week-off) with letrozole (2.5 mg/day; ML-2 [NCT01958021]), or FUL (500 mg per label; ML-3 [NCT02422615]); and premenopausal women with no prior ET and ≤1 line of chemotherapy for ABC who received RIB with an NSAI (anastrozole: 1 mg/day; letrozole: 2.5 mg/day; ML-7 [NCT02278120]) plus goserelin (3.6 mg every 28 days). Dose reductions for RIB (600 to 400 to 200 mg) were permitted. Primary endpoint was PFS. Secondary endpoints included overall response rate (ORR), clinical benefit rate (CBR), and safety.

Results: In ML-2, -3, and -7, ≥1 RIB dose reduction occurred (n/N) in 169/334 (51%), 92/238 (39%), and 91/246 (37%) pts assigned to RIB, respectively. AEs were the main reason for dose reduction, with all-grade neutropenia the most common AE leading to dose reduction (ML-2 69%, ML-3 80%, ML-7 82%). Median PFS (months) was prolonged with RIB vs placebo in pts without a RIB dose reduction (ML-2: 27.7 vs 16.0; ML-3: not reached [NR] vs 18.3; ML-7: 23.8 vs 13.8); median PFS in pts with ≥1 RIB dose reduction was: ML-2 25.3, ML-3 NR, and ML-7 27.5 months. In pts with measurable disease and without a RIB dose reduction, ORR was 46% (ML-2), 43% (ML-3), and 48% (ML-7); CBR was 70%, 68%, and 79%, respectively. In pts with measurable disease and ≥1 RIB dose reduction, ORR was 62% (ML-2), 57% (ML-3), and 55% (ML-7); CBR was 88%, 85%, and 88%, respectively. The most common Grade 3/4 AEs in the RIB vs placebo groups (≥5% of pts in either ML trial, irrespective of causality or dose reduction) were neutropenia (ML-2: 62% vs 1%; ML-3: 55% vs 0; ML-7: 65% vs 4%), leukopenia (ML-2: 21% vs 1%; ML-3: 12% vs 0; ML-7: 16% vs 1%), hypertension (ML-2: 13% vs 13%; ML-3: 5% vs 5%; ML-7: 2% vs 3%), increased alanine aminotransferase (ML-2: 10% vs 1%; ML-3: 10% vs 0; ML-7: 5% vs 1%), and increased aspartate aminotransferase (ML-2: 6% vs 1%; ML-3: 6% vs 0; ML-7: 4% vs 1%).

Conclusions: Results from the ML-2, -3, and -7 trials suggest that pts who start on 600 mg of RIB and require dose reduction for the management of their AEs, or for other reasons, continue to derive clinical benefit.

Citation Format: Beck JT, Neven P, Sohn J, Chan A, Sonke GS, Bachelot T, Campos-Gomez S, Martin M, Bardia A, Alam J, Miller M, Diaz-Padilla I, Kong O, Hart L. Ribociclib treatment benefit in patients with advanced breast cancer with ≥1 dose reduction: Data from the MONALEESA-2, -3, and -7 trials [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 P6-18-06.