A road map for the treatment of pediatric diffuse midline glioma

Recent clinical trials for H3K27-altered diffuse midline gliomas (DMGs) have shown much promise. We present a consensus roadmap and identify three major barriers: (1) refinement of experimental models to include immune and brain-specific components; (2) collaboration among researchers, clinicians, and industry to integrate patient-derived data through sharing, transparency, and regulatory considerations; and (3) streamlining clinical efforts including biopsy, CNS-drug delivery, endpoint determination, and response monitoring. We highlight the importance of comprehensive collaboration to advance the understanding, diagnostics, and therapeutics for DMGs.

Clinical Efficacy of ONC201 in H3K27M-Mutant Diffuse Midline Gliomas Is Driven by Disruption of Integrated Metabolic and Epigenetic Pathways

Patients with H3K27M-mutant diffuse midline glioma (DMG) have no proven effective therapies. ONC201 has recently demonstrated efficacy in these patients, but the mechanism behind this finding remains unknown. We assessed clinical outcomes, tumor sequencing, and tissue/cerebrospinal fluid (CSF) correlate samples from patients treated in two completed multisite clinical studies. Patients treated with ONC201 following initial radiation but prior to recurrence demonstrated a median overall survival of 21.7 months, whereas those treated after recurrence had a median overall survival of 9.3 months. Radiographic response was associated with increased expression of key tricarboxylic acid cycle-related genes in baseline tumor sequencing. ONC201 treatment increased 2-hydroxyglutarate levels in cultured H3K27M-DMG cells and patient CSF samples. This corresponded with increases in repressive H3K27me3 in vitro and in human tumors accompanied by epigenetic downregulation of cell cycle regulation and neuroglial differentiation genes. Overall, ONC201 demonstrates efficacy in H3K27M-DMG by disrupting integrated metabolic and epigenetic pathways and reversing pathognomonic H3K27me3 reduction.

SIGNIFICANCE

The clinical, radiographic, and molecular analyses included in this study demonstrate the efficacy of ONC201 in H3K27M-mutant DMG and support ONC201 as the first monotherapy to improve outcomes in H3K27M-mutant DMG beyond radiation. Mechanistically, ONC201 disrupts integrated metabolic and epigenetic pathways and reverses pathognomonic H3K27me3 reduction. This article is featured in Selected Articles from This Issue, p. 2293.

Analysis of Female Participant Representation in Registered Oncology Clinical Trials in the United States from 2008 to 2020

BACKGROUND

Female underrepresentation in oncology clinical trials can result in outcome disparities. We evaluated female participant representation in US oncology trials by intervention type, cancer site, and funding.

MATERIALS AND METHODS

Data were extracted from the publicly available Aggregate Analysis of ClinicalTrials.gov database. Initially, 270,172 studies were identified. Following the exclusion of trials using Medical Subject Heading terms, manual review, those with incomplete status, non-US location, sex-specific organ cancers, or lacking participant sex data, 1650 trials consisting of 240,776 participants remained. The primary outcome was participation to prevalence ratio (PPR): percent females among trial participants divided by percent females in the disease population per US Surveillance, Epidemiology, and End Results Program data. PPRs of 0.8-1.2 reflect proportional female representation.

RESULTS

Females represented 46.9% of participants (95% CI, 45.4-48.4); mean PPR for all trials was 0.912. Females were underrepresented in surgical (PPR 0.74) and other invasive (PPR 0.69) oncology trials. Among cancer sites, females were underrepresented in bladder (odds ratio [OR] 0.48, 95% CI 0.26-0.91, P = .02), head/neck (OR 0.44, 95% CI 0.29-0.68, P < .01), stomach (OR 0.40, 95% CI 0.23-0.70, P < .01), and esophageal (OR 0.40 95% CI 0.22-0.74, P < .01) trials. Hematologic (OR 1.78, 95% CI 1.09-1.82, P < .01) and pancreatic (OR 2.18, 95% CI 1.46-3.26, P < .01) trials had higher odds of proportional female representation. Industry-funded trials had greater odds of proportional female representation (OR 1.41, 95% CI 1.09-1.82, P = .01) than US government and academic-funded trials.

CONCLUSIONS

Stakeholders should look to hematologic, pancreatic, and industry-funded cancer trials as exemplars of female participant representation and consider female representation when interpreting trial results.

Abstract 3523: A systematic comparison of molecular features shared by H3K27-altered diffuse midline gliomas and posterior fossa A ependymomas

In children, brain tumors account for the highest mortality rates of all malignancies, and in contrast to adult brain cancers, pediatric tumors often arise in infratentorial regions. Two tumors in particular, H3K27-altered diffuse midline gliomas (DMGs) and group-A posterior fossa ependymomas (PFAs) arise from structures around the fourth ventricle, and strikingly, both tumors exhibit a global decrease in the histone mark histone 3, lysine 27 tri-methylation (H3K27me3) that is associated with transcriptional repression. H3K27-altered DMGs primarily are found primarily in the pons and exhibit by lysine-to-methionine mutations at H3K27 (H3K27M). This missense mutation results in inhibition of the catalytic activity of the polycomb repressive complex 2 (PRC2) which mediates H3K27me3 deposition. PFAs are found in the lateral recess of the fourth ventricle and the cerebellum and demonstrate overexpression of EZH inhibitory protein (EZHIP). EZHIP contains a domain with striking resemblance to the mutant H3K27M histone tail and similarly blocks PRC2 activity. Although H3K27me3 levels are dramatically reduced in both areas, select genes retain H3K27me3 in both tumor types. Increasingly, data have emerged demonstrating that cases of PFAs actually harbor H3K27M mutations and cases of H3-wildtype DMGs in fact overexpress EZHIP. The neighboring origins and overlapping recurrent H3K27me3-modulating alterations observed in these two pediatric brain tumors suggest certain populations of cells in the developing hindbrain may be particularly prone to malignant transformation in the setting of PRC2 inhibition. A systematic comparison of genomic, transcriptomic, and epigenomic datasets for both tumors identified key molecular similarities between subsets of DMGs and PFAs and highlighted how developmental signatures may be preserved in tumor expression profiles. Specifically, these analyses identify shared copy-number profiles between PFAs and different subtypes of DMGs and demonstrate that the Activin A Receptor Type 1 (ACVR1), a gene with recurrent activating mutations in H3K27-altered DMGs, is overexpressed in a subset PFAs with worse survival outcomes. Additionally, interrogation of the H3K27me3 and enhancer landscapes identified critical genes with similar chromatin profiles and revealed heterogeneity in repression of H3K27me3-marked genes that correlated with patterns of inferred anatomic origins for each tumor. Moreover, one of these genes, cellular retinoic acid binding partner 1 (CRABP1) showed enrichment in progenitor cell types in single-cell transcriptomic datasets. Together, these analyses characterize the common and unique molecular features of H3K27-altered DMGs and PFAs and shed light on the cellular contexts of the developing hindbrain that lead to development of each tumor.

Citation Format: Matthew Pun, Drew Pratt, Patricia R. Nano, Piyush K. Joshi, Li Jiang, Bernhard Englinger, Arvind Rao, Marcin Cieslik, Arul M. Chinnaiyan, Kenneth Aldape, Stefan Pfister, Mariella G. Filbin, Aparna Bhaduri, Sriram Venneti. A systematic comparison of molecular features shared by H3K27-altered diffuse midline gliomas and posterior fossa A ependymomas. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3523.

Common molecular features of H3K27M DMGs and PFA ependymomas map to hindbrain developmental pathways

Globally decreased histone 3, lysine 27 tri-methylation (H3K27me3) is a hallmark of H3K27-altered diffuse midline gliomas (DMGs) and group-A posterior fossa ependymomas (PFAs). H3K27-altered DMGs are largely characterized by lysine-to-methionine mutations in histone 3 at position 27 (H3K27M). Most PFAs overexpress EZH inhibitory protein (EZHIP), which possesses a region of similarity to the mutant H3K27M. Both H3K27M and EZHIP inhibit the function of the polycomb repressive complex 2 (PRC2) responsible for H3K27me3 deposition. These tumors often arise in neighboring regions of the brainstem and posterior fossa. In rare cases PFAs harbor H3K27M mutations, and DMGs overexpress EZHIP. These findings together raise the possibility that certain cell populations in the developing hindbrain/posterior fossa are especially sensitive to modulation of H3K27me3 states. We identified shared molecular features by comparing genomic, bulk transcriptomic, chromatin-based profiles, and single-cell RNA-sequencing (scRNA-seq) data from the two tumor classes. Our approach demonstrated that 1q gain, a key biomarker in PFAs, is prognostic in H3.1K27M, but not H3.3K27M gliomas. Conversely, Activin A Receptor Type 1 (ACVR1), which is associated with mutations in H3.1K27M gliomas, is overexpressed in a subset of PFAs with poor outcome. Despite diffuse H3K27me3 reduction, previous work shows that both tumors maintain genomic H3K27me3 deposition at select sites. We demonstrate heterogeneity in shared patterns of residual H3K27me3 for both tumors that largely segregated with inferred anatomic tumor origins and progenitor populations of tumor cells. In contrast, analysis of genes linked to H3K27 acetylation (H3K27ac)-marked enhancers showed higher expression in astrocytic-like tumor cells. Finally, common H3K27me3-marked genes mapped closely to expression patterns in the human developing hindbrain. Overall, our data demonstrate developmentally relevant molecular similarities between PFAs and H3K27M DMGs and support the overall hypothesis that deregulated mechanisms of hindbrain development are central to the biology of both tumors.

A Distinct Chromatin State Drives Therapeutic Resistance in Invasive Lobular Breast Cancer

Most invasive lobular breast cancers (ILC) are of the luminal A subtype and are strongly hormone receptor-positive. Yet, ILC is relatively resistant to tamoxifen and associated with inferior long-term outcomes compared with invasive ductal cancers (IDC). In this study, we sought to gain mechanistic insights into these clinical findings that are not explained by the genetic landscape of ILC and to identify strategies to improve patient outcomes. A comprehensive analysis of the epigenome of ILC in preclinical models and clinical samples showed that, compared with IDC, ILC harbored a distinct chromatin state linked to gained recruitment of FOXA1, a lineage-defining pioneer transcription factor. This resulted in an ILC-unique FOXA1-estrogen receptor (ER) axis that promoted the transcription of genes associated with tumor progression and poor outcomes. The ILC-unique FOXA1-ER axis led to retained ER chromatin binding after tamoxifen treatment, which facilitated tamoxifen resistance while remaining strongly dependent on ER signaling. Mechanistically, gained FOXA1 binding was associated with the autoinduction of FOXA1 in ILC through an ILC-unique FOXA1 binding site. Targeted silencing of this regulatory site resulted in the disruption of the feed-forward loop and growth inhibition in ILC. In summary, ILC is characterized by a unique chromatin state and FOXA1-ER axis that is associated with tumor progression, offering a novel mechanism of tamoxifen resistance. These results underscore the importance of conducting clinical trials dedicated to patients with ILC in order to optimize treatments in this breast cancer subtype.

SIGNIFICANCE

A unique FOXA1-ER axis in invasive lobular breast cancer promotes disease progression and tamoxifen resistance, highlighting a potential therapeutic avenue for clinical investigations dedicated to this disease. See related commentary by Blawski and Toska, p. 3668.

Abstract 6049: Identifying shared features of low-H3K27me3 pediatric brain tumors

Brain tumors have the worse survival rates of all childhood malignancies, and a better understanding of their biology is needed for therapeutic development. Two especially devastating subtypes of pediatric brain tumors—diffuse midline gliomas, H3K27M-mutant (DMGs) and posterior fossa ependymomas, group A (PFAs) are both characterized by a hallmark of global reduction of histone 3 lysine 27 trimethylation, a mark associated with transcriptional repression. DMGs primarily harbor mutations of histone 3 (H3K27M) that inhibit the function of the H3 methyltransferase enhancer of zeste homolog 2 (EZH2)-containing polycomb repressive complex (PRC2). Most PFAs overexpress EZH inhibitory protein (EZHIP), resulting in a similar effect on PRC2 activity. Intriguingly, a small subset of DMGs found to be lacking H3K27M mutations express EZHIP, and a fraction of histological PFAs lacking EZHIP expression harbor H3K27M mutations. Given the highly similar putative driving alterations and epigenetic features in these two tumor types, we undertook a systematic evaluation of the clinical and molecular features of each tumor class to elucidate additional shared features and potential targetable vulnerabilities. We performed detailed analyses of genomic aberrations, gene expression, and epigenomic landscapes to identify key similarities and differences in tumor biology. From preliminary studies, our findings demonstrate similar H3K27me3 landscapes with convergence of residual tri-methylated loci between PFA and DMG tumors. We additionally found shared recurrent copy number gain of the long arm of chromosome 1 (1q) and identified several 1q genes whose expression correlated with survival differences in cohorts of both tumors. Together, these findings better define the commonalities and differences of these highly aggressive, low-H3K27me3 pediatric brain tumors and will provide a framework for understanding which therapeutic strategies may translate from one tumor to the other.

Citation Format: Matthew Pun, Drew Pratt, Sriram Venneti. Identifying shared features of low-H3K27me3 pediatric brain tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6049.

Abstract GS2-09: Tamoxifen instigates uterine cancer development by activating PI3K signaling and supersedes PIK3CA driver mutations

Tamoxifen is widely used in the adjuvant treatment of estrogen receptor–positive (ER+) breast cancer and is an important drug for pre-menopausal women and post-menopausal patients who cannot tolerate aromatase inhibitors. Despite the clear clinical benefit in improving relapse-free and overall survival in these patients, an adverse effect of tamoxifen is a 2- to 7-fold increased risk of uterine cancer (UC) after 2-5 years of treatment. To date, the mechanism of tamoxifen-driven tumorigenesis is not well understood, and preventive approaches are lacking. Here, to molecularly characterize tamoxifen-associated uterine cancers (TA-UCs) and gain insights into their unique evolution, we performed whole-exome sequencing of 21 TA-UCs (discovery cohort) and droplet digital PCR (ddPCR) of an additional 40 TA-UCs (validation cohort) obtained from the ‘Tamoxifen Associated Malignancies: Aspects of Risk’ (TAMARISK) study. In addition, we used in vivo mouse models to: (i) further investigate tamoxifen-activated molecular pathways that may be involved in TA-UC tumorigenesis; and (ii) offer mechanistic insights. Overall, we discovered that TA-UCs were genomically similar to non–TA-UCs from The Cancer Genome Atlas (TCGA) project, with one profound exception: TA-UCs are characterized by a lower-than-expected frequency of mutations in two highly prevalent UC driver genes in the PI3K pathway: PIK3CA (14% [3/21] vs 48% [265/554] in non–TA-UC; P=0.003, Fisher’s exact test; Q=0.02, Benjamini-Hochberg FDR) and PIK3R1 (0%, [0/21] vs 31% [174/554]; P=0.001; Q=0.01). We used ddPCR in the independent TA-UC validation cohort and confirmed the low frequency of mutations in PIK3CA (7.5% [3/40] vs 21% [144/685] in control UCs from the Dana-Farber contribution to the AACR GENIE project; P=0.04). We next performed mouse in vivo studies and demonstrated that tamoxifen activated the PI3K pathway and increased cell proliferation in normal mouse uterine tissue through paracrine and autocrine effects, both of which were abrogated by the PI3K inhibitor alpelisib. Taken together, we describe a distinct and novel pathway of carcinogenesis in which tamoxifen acts as a driver event in the uterus and promotes tumor development in a mutation-independent manner. Indeed, tamoxifen may increase the risk of UC by activating the PI3K pathway, which can substitute for the early acquisition of oncogenic PIK3CA or PIK3R1 mutations observed in non–TA-UC tumors. Furthermore, the ability of a PI3K inhibitor to reduce cell proliferation in our mouse model raises the possibility that downregulating the PI3K pathway may prevent or significantly reduce TA-UC development, offering a potential future therapeutic and prevention strategy for specific high-risk patients undergoing tamoxifen therapy.

Citation Format: Kirsten Kubler, Agostina Nardone, Shankara Anand, Daniel Gorvich, Marjolein Droog, Francisco Hermida-Prado, Tara Akshi, Avery S Feit, Gabriella Cohen, Gwen Dackus, Matthew Pun, Yanan Kuang, Justin Cha, Mendy Miller, William J Gibson, Cloud P Paweletz, Eliezer M Van Allen, Flora E van Leeuwen, Petra Nederlof, Harry Hollema, Quang-Dé Nguyen, Marian JE Mourits, Ignaty Leshchiner, Chip Stewart, Ursula A Matulonis, Wilbert Zwart, Yosef E Maruvka, Gad Getz, Rinath Jeselsohn. Tamoxifen instigates uterine cancer development by activating PI3K signaling and supersedes PIK3CA driver mutations [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr GS2-09.

Epigenetically defined therapeutic targeting in H3.3G34R/V high-grade gliomas

High-grade gliomas with arginine or valine substitutions of the histone H3.3 glycine-34 residue (H3.3G34R/V) carry a dismal prognosis, and current treatments, including radiotherapy and chemotherapy, are not curative. Because H3.3G34R/V mutations reprogram epigenetic modifications, we undertook a comprehensive epigenetic approach using ChIP sequencing and ChromHMM computational analysis to define therapeutic dependencies in H3.3G34R/V gliomas. Our analyses revealed a convergence of epigenetic alterations, including (i) activating epigenetic modifications on histone H3 lysine (K) residues such as H3K36 trimethylation (H3K36me3), H3K27 acetylation (H3K27ac), and H3K4 trimethylation (H3K4me3); (ii) DNA promoter hypomethylation; and (iii) redistribution of repressive histone H3K27 trimethylation (H3K27me3) to intergenic regions at the leukemia inhibitory factor (LIF) locus to drive increased LIF abundance and secretion by H3.3G34R/V cells. LIF activated signal transducer and activator of transcription 3 (STAT3) signaling in an autocrine/paracrine manner to promote survival of H3.3G34R/V glioma cells. Moreover, immunohistochemistry and single-cell RNA sequencing from H3.3G34R/V patient tumors revealed high STAT3 protein and RNA expression, respectively, in tumor cells with both inter- and intratumor heterogeneity. We targeted STAT3 using a blood-brain barrier–penetrable small-molecule inhibitor, WP1066, currently in clinical trials for adult gliomas. WP1066 treatment resulted in H3.3G34R/V tumor cell toxicity in vitro and tumor suppression in preclinical mouse models established with KNS42 cells, SJ-HGGx42-c cells, or in utero electroporation techniques. Our studies identify the LIF/STAT3 pathway as a key epigenetically driven and druggable vulnerability in H3.3G34R/V gliomas. This finding could inform development of targeted, combination therapies for these lethal brain tumors.

Targeting integrated epigenetic and metabolic pathways in lethal childhood PFA ependymomas

Childhood posterior fossa group A ependymomas (PFAs) have limited treatment options and bear dismal prognoses compared to group B ependymomas (PFBs). PFAs overexpress the oncohistone-like protein EZHIP (enhancer of Zeste homologs inhibitory protein), causing global reduction of repressive histone H3 lysine 27 trimethylation (H3K27me3), similar to the oncohistone H3K27M. Integrated metabolic analyses in patient-derived cells and tumors, single-cell RNA sequencing of tumors, and noninvasive metabolic imaging in patients demonstrated enhanced glycolysis and tricarboxylic acid (TCA) cycle metabolism in PFAs. Furthermore, high glycolytic gene expression in PFAs was associated with a poor outcome. PFAs demonstrated high EZHIP expression associated with poor prognosis and elevated activating mark histone H3 lysine 27 acetylation (H3K27ac). Genomic H3K27ac was enriched in PFAs at key glycolytic and TCA cycle–related genes including hexokinase-2 and pyruvate dehydrogenase. Similarly, mouse neuronal stem cells (NSCs) expressing wild-type EZHIP (EZHIP-WT) versus catalytically attenuated EZHIP-M406K demonstrated H3K27ac enrichment at hexokinase-2 and pyruvate dehydrogenase, accompanied by enhanced glycolysis and TCA cycle metabolism. AMPKα-2, a key component of the metabolic regulator AMP-activated protein kinase (AMPK), also showed H3K27ac enrichment in PFAs and EZHIP-WT NSCs. The AMPK activator metformin lowered EZHIP protein concentrations, increased H3K27me3, suppressed TCA cycle metabolism, and showed therapeutic efficacy in vitro and in vivo in patient-derived PFA xenografts in mice. Our data indicate that PFAs and EZHIP-WT–expressing NSCs are characterized by enhanced glycolysis and TCA cycle metabolism. Repurposing the antidiabetic drug metformin lowered pathogenic EZHIP, increased H3K27me3, and suppressed tumor growth, suggesting that targeting integrated metabolic/epigenetic pathways is a potential therapeutic strategy for treating childhood ependymomas.

Female participation in U.S. oncology clinical trials registered on ClinicalTrials.gov from 2008 to 2020

85

Background: Females are thought to be underrepresented in clinical trials, which may lead to care disparities. We characterized female enrollment trends in U.S. oncology trials registered on ClinicalTrials.gov and identified features associated with accurate representation. Methods: We employed a cross-sectional study design with descriptive, logistic regression, and cox regression analyses. We downloaded 270,172 studies registered on the Aggregate Analysis of the ClinicalTrials.gov database from October 1, 2008 to March 9, 2020, excluding non-interventional and reproductive organ specific trials. We then applied cancer/oncology specific Medical Subject Heading terms and manually reviewed the remaining 27,521 trials for true oncology content. Prevalence-corrected estimates for female participation were calculated as the percentage of females among trial participants divided by the percentage of females in the disease population per U.S. Surveillance, Epidemiology, and End Results Program (SEER) data (participation to prevalence ratio [PPR]), with a range between 0.8 and 1.2 reflecting accurate female representation in the trial. Results: Of 26,894 trials meeting eligibility criteria, 9,059 trials were completed in the U.S., 2,499 trials reported completed study status, and only 1,256 trials reported sex. Among 1,256 oncology trials and 229,056 participants, overall female representation was 46.9% (95% CI, 45.4-48.4%). 43% of trials were industry funded, 29% academic, and 28% U.S. government. Females were underrepresented compared to their disease burden in anal canal (PPR 0.21), thyroid (PPR 0.57), stomach (PPR 0.68), kidney (PPR 0.77), and bone (PPR 0.79) cancer trials. They were accurately represented in head and neck (PPR 0.80), lung (PPR 0.84), bladder (PPR 0.85), skin (PPR 0.88), pancreas (PPR 0.88), colon (PPR 0.90), hematologic (PPR 0.91), liver (PPR 1.01), CNS (PPR 1.03), soft tissue (PPR 1.05), and esophagus (PPR 1.05) cancer trials. Accurate representation was significantly associated with industry funding and pancreas cancer trial focus, but not associated with trial type (medical, surgical, radiation, other invasive, other) (Table). Conclusions: Females are underrepresented compared to their disease burden in many solid tumor clinical trials. Stakeholders can look to industry funded and pancreas cancer trials as models of improvement, but must increase female representation in clinical trials to improve cancer care. [Table: see text]

Experiential-Learning Opportunities Enhance Engagement in Pipeline Program: A Qualitative Study of the Doctors of Tomorrow Summer Internship Program

PURPOSE

Doctors of Tomorrow (DoT) is a pipeline program between the University of Michigan Medical School and Cass Technical High School in Detroit where the overall mission is to encourage youth from communities that are underrepresented in medicine to pursue their interests in healthcare careers. Students have the opportunity to apply for a summer internship between 9th grade and 10th grade. There is limited literature on the effectiveness of experiential-learning opportunities in pipeline programs to support development of personal and professional skills. The purpose of this study was to examine the experiences of students participating in the DoT summer internship program in order to better understand how their engagement influenced personal and professional development.

METHOD

An exploratory qualitative study was conducted using responses from 27 students who participated in the DoT summer internship program between 2014 and 2018. Students engaged in self-reflective practices prompted by weekly surveys. Data were analyzed through an inductive process by coding and thematic analysis.

RESULTS

Four overarching themes were identified: (1) engagement in authentic experiential-learning opportunities; (2) development of professional skills; (3) self-reflection and actualization; and (4) real world barriers in experiential-learning.

CONCLUSIONS

High school students engaged in a variety of different community internships and shared insights that illustrated depth and diversity of understanding health in their community. Their reflections illustrate the added value of experiential-education in pipeline programs.

Unraveling the clinicopathological features driving the emergence of ESR1 mutations in metastatic breast cancer

ESR1 mutations were recently found to be an important mechanism of endocrine resistance in ER-positive (ER + ) metastatic breast cancer. To determine the clinicopathological features driving the emergence of the ESR1 mutations we studied plasma cfDNA and detailed clinical data collected from patients with metastatic breast cancer. Droplet Digital PCR was performed for the detection of the most common ESR1 mutations and PIK3CA mutations. Among the patients with ER + /HER2- disease, ESR1 mutations were detected in 30% of the patients. There were no associations between the pathological features of the primary disease or time to distant recurrence and the emergence of ESR1 mutations in metastatic disease. The prevalence of the ESR1 mutations was significantly associated with prior treatment with an aromatase inhibitor in the adjuvant or metastatic setting. The prevalence of the ESR1 mutations was also positively associated with prior fulvestrant treatment. Conversely, the prevalence of ESR1 mutations was lower after treatment with a CDK4/6 inhibitor. There were no significant associations between specific systemic treatments and the prevalence of PIK3CA mutations. These results support the evolution of the ESR1 mutations under the selective pressure of treatment with aromatase inhibitors in the adjuvant and metastatic settings and have important implications in the optimization of adjuvant and metastatic treatment in ER + breast cancer.

Treatment with aromatase inhibitors, a class of drugs that suppress the synthesis of estrogen, can drive the evolution of mutations in the estrogen receptor gene ESR1, leading to tumor resistance against hormone therapies. To better understand the emergence of ESR1 mutations, Rinath Jeselsohn from the Dana-Farber Cancer Institute 
in Boston, Massachusetts, USA, and coworkers tested tumor DNA contained within blood samples from 155 women with metastatic breast cancer. They found ESR1 mutations rarely in women with any molecular subtype of cancer other than estrogen receptor-positive disease. Nothing about the primary tumor predicted who would develop ESR1 mutations; however, treatment with an aromatase inhibitor was associated with mutations arising. The findings highlight the need to develop therapeutic regimens that reduce the selective pressure for ESR1 mutations and/or target these mutations directly.

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

Background

RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology has led to the continuous development of new tools for every step of analysis from alignment to downstream pathway analysis. However, effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts.

Results

Using the workflow management system Snakemake we have developed a user friendly, fast, efficient, and comprehensive pipeline for RNA-seq analysis. VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis workflow that combines some of the most popular tools to take RNA-seq analysis from raw sequencing data, through alignment and quality control, into downstream differential expression and pathway analysis. VIPER has been created in a modular fashion to allow for the rapid incorporation of new tools to expand the capabilities. This capacity has already been exploited to include very recently developed tools that explore immune infiltrate and T-cell CDR (Complementarity-Determining Regions) reconstruction abilities. The pipeline has been conveniently packaged such that minimal computational skills are required to download and install the dozens of software packages that VIPER uses.

Conclusions

VIPER is a comprehensive solution that performs most standard RNA-seq analyses quickly and effectively with a built-in capacity for customization and expansion.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2139-9) contains supplementary material, which is available to authorized users.

Allele-Specific Chromatin Recruitment and Therapeutic Vulnerabilities of ESR1 Activating Mutations

Estrogen receptor α (ER) ligand-binding domain (LBD) mutations are found in a substantial number of endocrine treatment-resistant metastatic ER-positive (ER⁺) breast cancers. We investigated the chromatin recruitment, transcriptional network, and genetic vulnerabilities in breast cancer models harboring the clinically relevant ER mutations. These mutants exhibit both ligand-independent functions that mimic estradiol-bound wild-type ER as well as allele-specific neomorphic properties that promote a pro-metastatic phenotype. Analysis of the genome-wide ER binding sites identified mutant ER unique recruitment mediating the allele-specific transcriptional program. Genetic screens identified genes that are essential for the ligand-independent growth driven by the mutants. These studies provide insights into the mechanism of endocrine therapy resistance engendered by ER mutations and potential therapeutic targets.

Embryonic transcription factor SOX9 drives breast cancer endocrine resistance

The estrogen receptor (ER) drives the growth of most luminal breast cancers and is the primary target of endocrine therapy. Although ER blockade with drugs such as tamoxifen is very effective, a major clinical limitation is the development of endocrine resistance especially in the setting of metastatic disease. Preclinical and clinical observations suggest that even following the development of endocrine resistance, ER signaling continues to exert a pivotal role in tumor progression in the majority of cases. Through the analysis of the ER cistrome in tamoxifen-resistant breast cancer cells, we have uncovered a role for an RUNX2-ER complex that stimulates the transcription of a set of genes, including most notably the stem cell factor SOX9, that promote proliferation and a metastatic phenotype. We show that up-regulation of SOX9 is sufficient to cause relative endocrine resistance. The gain of SOX9 as an ER-regulated gene associated with tamoxifen resistance was validated in a unique set of clinical samples supporting the need for the development of improved ER antagonists.

Abstract S5-05: Impact of pre-operative exercise on breast cancer gene expression

Background: Exercise is linked to a lower risk of developing and dying from breast cancer, but the biological mechanisms through which exercise could impact breast cancer are unclear. In animal models, exercise impacts tumor formation and progression, but there are few data regarding direct effects of exercise on tumor tissue in humans. The Pre-Operative Health and Body (PreHAB) Study was a randomized window of opportunity trial designed to explore the impact of exercise on molecular pathways in women with breast cancer.

Methods: Inactive women with Stage I-III breast cancer were enrolled through Dana-Farber Cancer Institute and Yale University prior to surgery. Participants were randomized 1:1 to an aerobic and strength training exercise intervention or mind body control intervention and participated in the interventions between enrollment and the time of surgery. Tumor tissue was collected at enrollment and surgery; samples were reviewed by a breast pathologist and were macrodissected to include sections of tumor with at least 10% cellularity. Capture RNA-sequencing of the transcriptome coding regions was performed using the Illumina Truseq RNA access platform.

Results: 49 women were randomized (27 exercise and 22 control). At baseline, mean age was 52.6, BMI was 30.2kg/m2 and exercise was 49 min/wk. Mean time between enrollment and surgery was 4.2 weeks. Participants in the exercise arm significantly increased exercise vs. controls (increase of 203 vs. 23 min/wk, p&lt;0.0001). Transcriptomic analysis was performed on the tumors from the pre and post intervention biopsies from 32 patients (16 exercise and 16 control). Quality Control analysis of the RNA-sequencing data showed an average read depth of 25 million reads per sample, mapping ∼79% to exonic regions. Principal Component Analysis revealed no read bias or batch effects and unsupervised clustering showed that pre- and post-operative samples clustered together by patient. Differential gene expression analysis by DEseq2 revealed a limited number of individual genes with significant changes after the intervention. KEGG pathway analysis, however, of 214 KEGG pathways using the bioconductor package GAGE (Generally Applicable Gene-Set Enrichment for Pathway Analysis) demonstrated upregulation of 13 unique pathways between the baseline biopsy and surgical excision in exercise participants and none in mind body participants (q&lt;0.1). The top ranked upregulated pathway was cytokine-cytokine receptor interactions (q=6.93E-05, set size=238 genes). Il6, CCL3 and other cytokines are among the genes upregulated in this pathway. Analysis also demonstrated downregulation of 13 unique pathways (q&lt;0.1) including cell cycle, RNA transport and DNA replication pathways, in exercise participants over the intervention period.

Conclusions: A pre-operative exercise intervention led to alterations in gene expression in tumor tissue in women with breast cancer. Validation in additional data sets and an analysis of which cellular compartments within the tumor are responsible for the changes is needed. These findings demonstrate that exercise may have a direct effect on breast tumor tissue in humans, providing new insights into the biologic mechanisms through which exercise could lower the risk of developing and dying from breast cancer.

Citation Format: Ligibel JA, Irwin M, Dillon D, Barry W, Giobbie-Hurder A, Frank E, Winer EP, McTiernan A, Cornwell M, Pun M, Brown M, Jeselsohn R. Impact of pre-operative exercise on breast cancer gene expression [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 S5-05.

Pulmonary Functions are Impaired among Carpet Factory Workers: A Spirometric Evaluation

INTRODUCTION

Carpet factory produces various types of dusts and workers occupationally get exposed to them continuously. It has adverse health effects and most notably to the pulmonary functions. Nepal is one of the carpet exporter developing countries and still does have many factories within Kathmandu valley. However, the health hazards especially the status of pulmonary function of carpet factory workers from Nepal has not been studied.

METHODS

A cross-sectional comparative study was designed to recruit carpet factory workers and healthy controls to assess their pulmonary functions. A total of 118 subjects (59 males and 59 females) were recruited (60 carpet factory workers and 58 controls). Pulmonary function tests were carried out using Medical International Research Spirolab II portable spirometer.

RESULTS

The carpet factory workers had significantly less FEV1 (90.37 ±16.6 % vs. 103.89±9.79%, p<0.001), FVC (87.78 ± 15.48 % vs. 102.81 ± 8.41 %, p < 0.001) and PEFR (66.19 ± 20.29 % vs. 102.81 ± 11.09 %, p < 0.001) as compared to control group. Similarly the carpet factory workers had significantly higher FEV1/FVC ratio (89.96 ± 6.42 % vs. 87.12 ± 4.58 %, p = 0.007) as compared to control.

CONCLUSIONS

Carpet industry dusts exposure adversely affects pulmonary functions among its workers. The findings significant increase in the FEV1/FVC ratio and decrease in FEV1, FVC, and PEFR suggest that the effects are both restrictive and obstructive patterns of lung disease.

Estimation of Physiological Cost Index as an Energy Expenditure Index using MacGregor's Equation

INTRODUCTION

Physical activity and energy expenditure can be quantified by measuring heart rate, oxygen uptake and respiratory quotient. The Physiological Cost Index (PCI) proposed by MacGregor is a simple and straightforward method to estimate the energy expenditure index. Here, we aim to estimate the energy expenditure among young Asian population using MacGregor's equation.

METHODS

A total of 50 young randomly selected healthy females performed 50m, 100m and 150m walking test at their self-selected preferred speed. The physiological cost index values for 100 m walk at speeds slower and faster than the preferred speed were also obtained. The physiological cost index during exercise was calculated using MacGregor's equation considering heart rate and speed of walking over the varying distances.

RESULTS

The PCI values on three different distances are consistent during self selected preferred speed. The PCI estimation on second and third tests for all three distances walked consistently reproducible. However for each distance walked, the first test the PCI was significantly higher than the second and third test values. The PCI values increased significantly when subjects walked either slower (p = 0.02) or faster (p = 0.001) than their normal preferred speed.

CONCLUSION

The physiological cost index values were similar for varying distances walks. The PCI was the least at the preferred speed of walking and increased when the subjects either walked slower or faster than the preferred speed. The first estimation was higher than subsequent estimations.

Snodgrass Tubularized Incised Plate Urethroplasty for Distal and Midpenile Hypospadias

Introduction: Despite hundreds of repair techniques for hypospadias, the introduction of tubularized incised plate urethroplasty (TIP) by Warren T. Snodgrass has become popular because of good functional and cosmetic outcome. The objective of this study was to share our experience of Snodgrass tubularized incised plate (TIP) urethroplasty for the repair of distal and mid-penile hypospadias. Materials and Methods: This prospective study was carried out for a period of 24 months. It included 46 male patients with the mean age of 4.1 years (18 months to 10 years). Proximal hypospadias and those distal with moderate to severe chordee were excluded. All cases underwent TIP urethroplasty as described by Snodgrass and the neourethra was covered by single or double layer of dorsal prepucial layer. The results were analyzed on the basis of duration of surgery, types of postoperative complications like urethrocutaneous fistula, meatal stenosis and wound dehiscence. Functional results assessed with ease of voiding, force and direction of urinary stream and cosmetic with external look of penis. Results: The overall complication rate requiring surgical intervention was 8 (17.3%). Mean duration of surgery was 66 minutes (60-80 minutes). Urethrocutaneous fistula occurred in 5 (10.8%), meatal stenosis in 1 (2.1%) and wound dehiscence in 2 (4.3%) patient. The cosmetic appearance was excellent in all patients involved in this study except 2 cases of wound dehiscence. All of them had vertically oriented slit like meatus with straight urinary stream. Conclusion: Tubularized incised plate urethroplasty gives good functional and excellent cosmetic results with low rate of complications in distal and mid-penile hypospadias. DOI: http://dx.doi.org/10.3126/jnps.v34i1.8692 J Nepal Paediatr Soc 2014;34(1):29-33