Fine scale diversity in the lava: genetic and phenotypic diversity in small populations of Arctic charr Salvelinus alpinus

BACKGROUND

A major goal in evolutionary biology is to understand the processes underlying phenotypic variation in nature. Commonly, studies have focused on large interconnected populations or populations found along strong environmental gradients. However, studies on small fragmented populations can give strong insight into evolutionary processes in relation to discrete ecological factors. Evolution in small populations is believed to be dominated by stochastic processes, but recent work shows that small populations can also display adaptive phenotypic variation, through for example plasticity and rapid adaptive evolution. Such evolution takes place even though there are strong signs of historical bottlenecks and genetic drift. Here we studied 24 small populations of the freshwater fish Arctic charr (Salvelinus alpinus) found in groundwater filled lava caves. Those populations were found within a few km2-area with no apparent water connections between them. We studied the relative contribution of neutral versus non-neutral evolutionary processes in shaping phenotypic divergence, by contrasting patterns of phenotypic and neutral genetic divergence across populations in relation to environmental measurements. This allowed us to model the proportion of phenotypic variance explained by the environment, taking in to account the observed neutral genetic structure.

RESULTS

These populations originated from the nearby Lake Mývatn, and showed small population sizes with low genetic diversity. Phenotypic variation was mostly correlated with neutral genetic diversity with only a small environmental effect.

CONCLUSIONS

Phenotypic diversity in these cave populations appears to be largely the product of neutral processes, fitting the classical evolutionary expectations. However, the fact that neutral processes did not explain fully the phenotypic patterns suggests that further studies can increase our understanding on how neutral evolutionary processes can interact with other forces of selection at early stages of divergence. The accessibility of these populations has provided the opportunity for long-term monitoring of individual fish, allowing tracking how the environment can influence phenotypic and genetic divergence for shaping and maintaining diversity in small populations. Such studies are important, especially in freshwater, as habitat alteration is commonly breaking populations into smaller units, which may or may not be viable.

Transcriptomic Determinants of Response to Pembrolizumab Monotherapy across Solid Tumor Types

PURPOSE

To explore relationships between biological gene expression signatures and pembrolizumab response.

EXPERIMENTAL DESIGN

RNA-sequencing data on baseline tumor tissue from 1,188 patients across seven tumor types treated with pembrolizumab monotherapy in nine clinical trials were used. A total of 11 prespecified gene expression signatures [18-gene T-cell-inflamed gene expression profile (TcellinfGEP), angiogenesis, hypoxia, glycolysis, proliferation, MYC, RAS, granulocytic myeloid-derived suppressor cell (gMDSC), monocytic myeloid-derived suppressor cell (mMDSC), stroma/epithelial-to-mesenchymal transition (EMT)/TGFβ, and WNT] were evaluated for their relationship to objective response rate (per RECIST, version 1.1). Logistic regression analysis of response for consensus signatures was adjusted for tumor type, Eastern Cooperative Oncology Group performance status, and TcellinfGEP, an approach equivalent to evaluating the association between response and the residuals of consensus signatures after detrending them for their relationship with the TcellinfGEP (previously identified as a determinant of pembrolizumab response) and tumor type. Testing of the 10 prespecified non-TcellinfGEP consensus signatures for negative association [except proliferation (hypothesized positive association)] with response was adjusted for multiplicity.

RESULTS

Covariance patterns of the 11 signatures (including TcellinfGEP) identified in Merck-Moffitt and The Cancer Genome Atlas datasets showed highly concordant coexpression patterns in the RNA-sequencing data from pembrolizumab trials. TcellinfGEP was positively associated with response; signatures for angiogenesis, mMDSC, and stroma/EMT/TGFβ were negatively associated with response to pembrolizumab monotherapy.

CONCLUSIONS

These findings suggest that features beyond IFNγ-related T-cell inflammation may be relevant to anti-programmed death 1 monotherapy response and may define other axes of tumor biology as candidates for pembrolizumab combinations. See related commentary by Cho et al., p. 1479.

Usability and applicability of research knowledge translation models in a national health service

Background

The Health Service Executive in Ireland aims to facilitate the translation of research and innovation into policy and practice and increase dissemination of research. Previous HSE surveys showed that a high volume of research was undertaken but the impact on practice and policy was unclear. Researchers reported sharing their research in publications, conferences, and through education and training but identified problems in engaging with practice and policy stakeholders. Survey respondents requested help with dissemination and getting research into practice. An organisation-wide project to identify frameworks to support knowledge translation (KT), dissemination, and impact identified a recommended methodology, created guidance, and training for knowledge creators and users.

Objectives

Provide a series of six guides, tools and templates, to support knowledge creators and users across the organisation Provide online training to support translation and dissemination of research knowledge Underline the importance of planning KT and impact at research commencement and identify the planned outcomes Develop user-friendly training to explain the elements of KT and dissemination.

Results

Two pilot studies were undertaken to test the guidance which, although positively received, resulted in changes to the format, design, and language to increase useability. An explainer video and six online training modules were developed, based on the guidance and pilot feedback to be rolled out from July 2021. Learning was enhanced through transfer of complex information and models into short training modules to be accessed by researchers with a range of experience and understanding.

Conclusions

KT is a complex area and developing education and training for it requires understanding the different learning needs of knowledge creators and users. Education and training should focus on the need for KT and impact from the start of a project.

Key messages

Practical guidance to assist researchers in translation of their research findings into practice and improving dissemination enhances service user impact. Education and training should focus on the need to plan for KT from the start of a project.

Evaluation of blood TMB (bTMB) in KEYNOTE-189: Pembrolizumab (pembro) plus chemotherapy (chemo) with pemetrexed and platinum versus placebo plus chemo as first-line therapy for metastatic nonsquamous NSCLC

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Background: In a previous analysis of KEYNOTE-189 (NCT02578680), we showed that tissue TMB (tTMB) assessed by whole-exome sequencing was not significantly associated with efficacy in either arm and that pembro + chemo improved outcomes vs placebo + chemo in both the tTMB ≥175 and tTMB < 175 mut/exome subgroups. Here, we explored the association of bTMB with efficacy in KEYNOTE-189. Methods: 616 patients (pts) were randomized 2:1 to pembro + chemo or placebo + chemo. bTMB was assessed in cfDNA using the Guardant Health Omni assay. Association of bTMB (continuous square root transformed) with outcomes in each arm was assessed using Cox proportional hazards models (OS, PFS) and logistic regression (ORR) adjusted for ECOG PS; statistical significance was determined at the 0.05 level without multiplicity adjustment. The clinical utility of bTMB on outcomes was assessed using the cutoff that most closely approximated the 175 mut/exome tTMB cutoff as determined by AUROC analysis. Data cutoff was 21 Sep 2018. Results: 235 (38%) treated pts had evaluable tTMB and bTMB: 160 in the pembro + chemo arm and 75 in the placebo + chemo arm. bTMB as a continuous variable was not significantly associated with OS or ORR for pembro + chemo (one-sided P = .229 and .051) or placebo + chemo (two-sided P = .641 and .069); bTMB was significantly associated with PFS in the pembro + chemo arm (one-sided P = .015) but not the placebo + chemo arm (two-sided P = .058). bTMB and tTMB scores were moderately correlated (r = .61). The bTMB cutoff that most closely approximated tTMB 175 mut/exome was 15 mut/Mb (AUROC 0.81, 95% CI 0.75-0.86). 178 (76%) pts had concordant bTMB and tTMB results—101 low and 77 high by both—whereas 57 (24%) had discordant results—21 high bTMB but low tTMB, 36 low bTMB but high tTMB. Pembro + chemo improved OS, PFS, and ORR vs placebo + chemo for bTMB ≥15 and < 15 mut/exome (Table). Conclusions: Similar to previous findings based on tTMB, bTMB has limited clinical utility in the setting of pembro with pemetrexed and platinum given as first-line therapy for metastatic nonsquamous NSCLC. Clinical trial information: NCT02578680 . [Table: see text]

Abstract 2483: An integrated bioinformatics pipeline for profiling cancer-immune interaction from whole exome sequencing of pembrolizumab clinical samples

Purpose We built an integrated analytic pipeline to robustly and comprehensively profile molecular features of pembrolizumab-treated tumors using whole exome sequencing (WES) data from clinical trials across different indications.

Experimental design We implemented a computational framework for analysis of WES data generated by different sequencing vendors for 1467 samples from 8 major tumor types. Reads were first processed by BWA-MEM, Picard, and GATK (v2) to generate analysis-ready BAM files. Quality controls (QC) before downstream analysis included Y/X reads ratio for matched normal sample as patient sex prediction and tumor/normal concordance and contamination estimation by Conpair. Key molecular features were evaluated, including tumor mutation burden (TMB) by MuTect (v1) and VEP; HLA-I typing by OptiType; neoantigen burden by NetMHC (v3.4); mutation signature by deconstructSigs; allele-specific copy number by VarScan2 and Sequenza; clonality by PyClone; presence of oncogenic viruses (eg, EBV, HBV, HPV); and LOH score indicating homologous recombination deficiency (HRD-LOH).

Results Concordance rate between predicted and clinical sex was 1446/1464 (98.8%), and 1420/1467 (96.8%) samples passed tumor-normal alignment QC. Highest TMB (median [range]) was detected in melanoma (245 [2-6246]) and urothelial carcinoma (UC) (124 [4-1579]), with lowest TMB in metastatic castration-resistant prostate cancer (52 [1-6143]) and ovarian cancer (OvCa) (49.5 [8-272]). The correlation of median TMB across 7 cancer types in our data and TCGA was Spearman R = 0.957. Within indications, there was no difference in TMB distribution for sequencing data originating from different sequencing vendors and TCGA data, which demonstrated concordance across data sets and robust TMB calling by our integrated pipeline. Neoantigen burden strongly correlated with TMB (N = 1420; Spearman R = 0.890). HPV was detected in 20/129 (15.5%) head and neck squamous cell carcinomas (HNSCC) and 4/6 (66.7%) anal cancers; EBV was detected in 8/129 (6.2%) HNSCC and 18/318 (5.7%) gastric cancers (GC). The dominant mutation signatures by disease included APOBEC for UC (135/236) and HNSCC (22/122), alcohol for HCC (19/35), HRD for OvCa (12/64) and triple-negative breast cancer (51/175), UV exposure for melanoma (145/176), and dMMR for GC (84/287) and CRPC (16/155). Samples with deleterious BRCA mutations showed significantly higher HRD-LOH score (N = 1420; AUROC = 0.61 [95% CI, 0.53-0.69]) and HRD mutational signature (N = 1316; DOR = 6.4 [95% CI, 3.7-11.1]).

Conclusion We assembled heterogeneous computational modules into an integrated pipeline to reliably profile diverse molecular features from WES data of nearly 1500 clinical samples across different tumor types. These data serve as a foundation for translational research efforts supporting pembrolizumab development.

Citation Format: Xiaoqiao Liu, Xinwei Sher, Hongchao Lu, Jun Zhuang, Weilong Zhao, Andrew Albright, Cinthia Umemoto, Christen Wudarski, Maureen Lane, Mark Ayers, Andrea L. Webber, Sandra C. Souza, Ping Qiu, Diane Levitan, Jennifer Cho, Deepti Aurora-Garg, Matthew Marton, Alexandra Snyder, Michael Morrissey, Andrey Loboda, Ronghua Chen, Razvan Cristescu. An integrated bioinformatics pipeline for profiling cancer-immune interaction from whole exome sequencing of pembrolizumab clinical samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2483.

Genomic profiling of NETs: a comprehensive analysis of the RADIANT trials

Neuroendocrine tumors (NETs) have historically been subcategorized according to histologic features and the site of anatomic origin. Here, we characterize the genomic alterations in patients enrolled in 3 phase 3 clinical trials of NET of different anatomic origins and assessed the potential correlation with clinical outcomes. Whole-exome and targeted panel sequencing was used to characterize 225 NET samples collected in the RADIANT series of clinical trials. Genomic profiling of NET was analyzed along with nongenomic biomarker data on tumor grade and circulating chromogranin A (CgA) and neuron specific enolase (NSE) levels from these patients enrolled in clinical trials. Our results highlight recurrent large-scale chromosomal alterations as a common theme among NET. Although the specific pattern of chromosomal alterations differed between tumor subtypes, the evidence for generalized chromosomal instability (CIN) was observed across all primary sites of NET. In pancreatic NET, although the P-value was not significant, higher CIN suggests a trend towards longer survival (HR, 0.55, P=0.077); whereas in the gastrointestinal NET, lower CIN was associated with longer survival (HR, 0.44, P=0.0006). Our multivariate analyses demonstrated that when combined with other clinical data among patients with progressive advanced NETs, chromosomal level alteration adds important prognostic information. Large-scale CIN is a common feature of NET, and specific patterns of chromosomal gain and loss appeared to have independent prognostic value in NET subtypes. However, whether CIN in general has clinical significance in NET requires validation in larger patient cohort and warrants further mechanistic studies.

Association of MTOR Mutations With Developmental Brain Disorders, Including Megalencephaly, Focal Cortical Dysplasia, and Pigmentary Mosaicism

IMPORTANCE

Focal cortical dysplasia (FCD), hemimegalencephaly, and megalencephaly constitute a spectrum of malformations of cortical development with shared neuropathologic features. These disorders are associated with significant childhood morbidity and mortality.

OBJECTIVE

To identify the underlying molecular cause of FCD, hemimegalencephaly, and diffuse megalencephaly.

DESIGN, SETTING, AND PARTICIPANTS

Patients with FCD, hemimegalencephaly, or megalencephaly (mean age, 11.7 years; range, 2-32 years) were recruited from Pediatric Hospital A. Meyer, the University of Hong Kong, and Seattle Children's Research Institute from June 2012 to June 2014. Whole-exome sequencing (WES) was performed on 8 children with FCD or hemimegalencephaly using standard-depth (50-60X) sequencing in peripheral samples (blood, saliva, or skin) from the affected child and their parents and deep (150-180X) sequencing in affected brain tissue. Targeted sequencing and WES were used to screen 93 children with molecularly unexplained diffuse or focal brain overgrowth. Histopathologic and functional assays of phosphatidylinositol 3-kinase-AKT (serine/threonine kinase)-mammalian target of rapamycin (mTOR) pathway activity in resected brain tissue and cultured neurons were performed to validate mutations.

MAIN OUTCOMES AND MEASURES

Whole-exome sequencing and targeted sequencing identified variants associated with this spectrum of developmental brain disorders.

RESULTS

Low-level mosaic mutations of MTOR were identified in brain tissue in 4 children with FCD type 2a with alternative allele fractions ranging from 0.012 to 0.086. Intermediate-level mosaic mutation of MTOR (p.Thr1977Ile) was also identified in 3 unrelated children with diffuse megalencephaly and pigmentary mosaicism in skin. Finally, a constitutional de novo mutation of MTOR (p.Glu1799Lys) was identified in 3 unrelated children with diffuse megalencephaly and intellectual disability. Molecular and functional analysis in 2 children with FCD2a from whom multiple affected brain tissue samples were available revealed a mutation gradient with an epicenter in the most epileptogenic area. When expressed in cultured neurons, all MTOR mutations identified here drive constitutive activation of mTOR complex 1 and enlarged neuronal size.

CONCLUSIONS AND RELEVANCE

In this study, mutations of MTOR were associated with a spectrum of brain overgrowth phenotypes extending from FCD type 2a to diffuse megalencephaly, distinguished by different mutations and levels of mosaicism. These mutations may be sufficient to cause cellular hypertrophy in cultured neurons and may provide a demonstration of the pattern of mosaicism in brain and substantiate the link between mosaic mutations of MTOR and pigmentary mosaicism in skin.

Gene expression signatures of response to anti-CD19 chimeric antigen receptor (CAR) T-cell therapy in patients with CLL and ALL

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Background: The adoptive transfer of autologous T cells genetically modified to express a CD19-specific, 4-1BB/CD3ζ-signaling CAR (CTL019) has shown remarkable activity and induces long-term remissions in a subset of patients with relapsed/refractory chronic lymphocytic leukemia (CLL) and acute lymphoblastic leukemia (ALL). In ALL, CTL019 induces a complete response (CR) in over 90% of patients while in CLL 25% of patients obtain a CR. It is not fully understood why only certain patients respond to therapy. Methods: We employed next generation sequencing of RNA (RNAseq) to identify predictive indicators of response to CTL019. We performed RNAseq on leukapheresis and manufactured product T cells prior to re-infusion from 35 CLL and 7 pediatric ALL patients with heavily pre-treated and high-risk disease. To characterize potency, we performed RNAseq on the infusion product after stimulation with the CAR. Results: We find that durable remission in CLL is associated with gene expression signatures of early memory and T-effector cells, while T cells from non-responding patients are enriched in signatures of T-regulatory cells, terminal differentiation, and exhaustion. In following the results from CLL, we find that pediatric ALL manufactured T cells are significantly enriched for an early memory, naïve T cell state and all achieved a CR. In parallel in vitro experiments, stimulation of the infusion product further demonstrated that CTL019 cells from CRs have an increased capacity for activation upon stimulation. We tested if we could extend these observations to identify a phenotype of T cells that is predictive of response prior to CTL019 manufacturing and find that the signatures predictive of response at the pre-infusion stage are also observed at the earlier leukapheresis time point. Conclusions: These findings suggest that intrinsic T cell fitness dictates response to CAR T cells. These gene expression signatures, along with additional immunological biomarkers, may be used to identify which patients are most likely to respond to adoptive transfer strategies and suggest manufacturing modifications that might potentiate the generation of maximally efficacious infusion products. Clinical trial information: NCT01029366, NCT01747486, NCT01626495.

Abstract PD8-05: Comparative analysis of the genomic landscape of breast cancers from women of African and European ancestry

Objectives: Paucity of data on populations of African Ancestry in clinical trials continues to limit our ability to design and implement innovative solutions to narrow the breast cancer survival gap amongst Africans, African Americans, and European Americans. We have developed a cross-continent research infrastructure to examine the spectrum of genomic alterations in breast tumors from West Africa and subsequently, to compare them to tumors from African American women and women of European Ancestry in The Cancer Genome Atlas (TCGA) database.

Methods: Consecutive women with breast cancer presenting for treatment at the University College Hospital, Ibadan and at Lagos State University Teaching Hospital, Lagos, Nigeria gave informed consent and were recruited to the West African Breast Cancer Study (WABCS) between 2013-2016. Tumor-normal pairs were subjected to exome and/or high-depth (90x) genome sequencing. High confidence somatic mutations (substitutions, insertions/deletions and structural variants) were obtained by using multiple variant callers. Furthermore, 1,089 exomic and 80 genomic breast tumor-normal pairs from TCGA were harmonized with WABCS samples, resulting in a cohort of 147 West Africans (147 exome; 40 genome), 154 African Americans (154 exome; 31 genome), and 776 Caucasians (776 exome; 43 genome).

Results: Across the exomes, genes commonly altered in breast cancer in TCGA are also altered in women of African ancestry, but the mutational spectrum is quite different, demonstrating overrepresentation of tumors with aggressive phenotypes. Overall, TP53 (65%), ERBB2 (27%), and GATA3 (17%) showed statistically significant higher alteration frequencies in West Africans and African Americans. In contrast, PIK3CA (24%) was less frequently mutated. Of note, GATA3 mutation was statistically significantly more frequent in Nigerians (39%) and African Americans (16.7%) compared to Caucasians (10.5%), in ER-positive cancers. Analysis on Structural Variants (SV), on the other hand, has shown that the genome-wide SV counts among three populations are comparable in ER-negative cancers, while Nigerians have significantly more SV counts compared to African Americans (P=0.0013) or European Americans (P=2.9x10-5) in ER-positive cancers. Similarly, genome-wide substitution patterns in ER+ and ER- cancers varied widely by race/ethnicity. In ER- cases, West Africans carried the highest proportion of canonical APOBEC-associated substitutions, particularly C&gt;T transitions. Conversely, European Americans with ER+ disease showed a higher proportion of C&gt;T than both West Africans (Welch t-test P = 0.044) and African Americans (Welch t-test P = 0.011). Mutation signature analyses highlighted multiple APOBEC signatures, with notable contribution differences across ancestry and ER status. A signature likely corresponding to DNA damage repair correlated with the proportion of genetic ancestry, being most prevalent in European Americans and least common in Nigerians, particularly in ER-negative cancers, with African Americans showing a degree of this signature's contribution in between the two populations (linear model adjusted for age, P=1.0x10-10).

Conclusions: Overall, our data suggests mutation spectra differences in across race/ethnicity and geography. Identification of molecular characteristics such as higher rates of HER2 enriched tumors and higher rates of GATA3 mutations in ER positive tumors are beginning to reveal the genomic basis of race-associated phenotypes and outcomes in breast cancer. Population differences in frequency and spectrum of mutations should now inform the design of innovative clinical trials that improve health equity and accelerate Precision Oncology care in diverse populations.

Citation Format: Olopade OI, Pitt JJ, Riester M, Odetunde A, Yoshimatsu T, Labrot E, Ademola A, Sanni A, Okedere B, Mahan S, Nwosu I, Leary R, Ajani M, Johnson RS, Sveen E, Zheng Y, Wang S, Fitzgerald DJ, Grundstad J, Tuteja J, Clayton W, Khramtsova G, Oludara M, Omodele F, Benson O, Adeoye A, Morhason-Bello O, Ogundiran T, Babalola C, Popoola A, Morrissey M, Chen L, Huo D, Falusi A, Winckler W, Obafunwa J, Papoutsakis D, Ojengbede O, White KP, Ibrahim N, Oluwasola O, Barretina J. Comparative analysis of the genomic landscape of breast cancers from women of African and European ancestry [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 PD8-05.

Abstract P6-03-17: Genomic landscape of breast cancers from women of African ancestry across the diaspora

Objectives: Of all ethnic/racial groups, age-standardized mortality rate from breast cancer is highest for African American women in the US for reasons that remain understudied. The paucity of genomic studies of breast tumors across the African Diaspora further restricts our understanding of the biology of breast cancer in underserved populations. To gain a better understanding of the genomic landscape of breast cancer in women of African Ancestry, we have developed a cross continent translational research infrastructure to examine the spectrum of genetic alterations in breast tumors from West Africa compared to the spectrum of alterations observed in tumors from African-American and other women who are predominantly white in The Cancer Genome Atlas (TCGA) dataset.

Methods: Peripheral blood and breast cancer biopsy tissues were collected from 214 patients enrolled in the West Africa Breast Cancer Study (WABCS) at the University of Ibadan/University College Hospital (UI/UCH) and at Lagos State University Teaching Hospital (LASUTH). Blood DNA as well as breast cancer tissue DNA and RNA were extracted at the Novartis Institutes for Biomedical Research (NIBR), UI/UCH, and LASUTH using a modified protocol of PAXgene Tissue DNA and RNA extraction method. Whole-exome (WES) and transcriptome (RNA-seq) sequencing were performed on the Illumina HiSeq2000 platform at NIBR. Single Nucleotide Variants (SNVs) and insertions/deletions (indels) were called using MuTect and Pindel, while Copy Number Alterations (CNAs) were called using an in-house implementation of the ABSOLUTE method. Observed mutations were compared against those reported in the TCGA dataset. ER, PR and HER2 status were determined by immunohistochemistry (IHC) at UI/UCH, LASUTH and UChicago.

Results: WES data for 95 tumors have been analyzed thus far. Genes commonly mutated in breast cancer in TCGA are also mutated in WABCS but the mutational spectrum is vastly different. TP53 (64%), MYC (31%), and GATA3 (26%), showed significantly higher alteration frequencies in WABCS and African Americans. In contrast, PIK3CA (20%), CDH1 (2%), and MAP3K1 (2%) were less frequently mutated in women of African ancestry. In addition to the high proportion with TP53 mutations, the proportion with HER2 positive subtype of 42.1% and triple-negative subtype of 37.9% suggest that tumors with the most aggressive features are overrepresented in breast cancer patients in West Africa.

Conclusions: In the first study of its kind, high throughput genomic analysis of the largest cohort of women of African ancestry has uncovered alterations in cancer genes, some of which may be amenable to treatment with targeted therapies. Furthermore, we provide evidence that population differences in frequency and spectrum of mutations should drive the design and deployment of precision medicine initiatives. Only then can we develop innovative interventions to reduce the unacceptably high rates of mortality from breast cancer in underserved and under resourced populations.

Citation Format: Olopade OI, Odetunde A, Riester M, Yoshimatsu T, Labrot E, Ademola A, Sanni A, Okedere B, Mahan S, Nwosu I, Leary R, Ajani M, Johnson RS, Sveen E, Zheng Y, Clayton W, Khramtsova G, Oludara M, Omodele F, Benson O, Adeoye A, Morhason-Bello O, Ogundiran T, Babalola C, Popoola A, Morrissey M, Huo D, Falusi A, Winckler W, Obafunwa J, Papoutsakis D, Ojengbede O, Ibrahim N, Oluwasola O, Barretina J. Genomic landscape of breast cancers from women of African ancestry across the diaspora. [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 P6-03-17.

Abstract 26: Biomarker analysis of a male breast cancer patient with prolonged stable disease under mTOR/PI3K inhibitors BEZ235/RAD001

The mTORC1 inhibitor RAD001 (everolimus) has been approved for multiple cancer indications, including ER+/HER2- metastatic breast cancer. The combination of RAD001 with a dual PI3K/mTOR inhibitor BEZ235 was shown to be even more efficacious than RAD001 alone in preclinical models and was evaluated in clinical trials. We identified a male breast cancer patient who experienced a prolonged stable disease with the RAD001/BEZ235 combination as 3rd line treatment for his metastatic disease and investigated molecular mechanisms to explain the extraordinary benefit and subsequent drug resistance.

The 66-year old Caucasian male had stage IIIA invasive ductal carcinoma at initial surgery. He then received two sequential adjuvant therapies: a chemo-radiotherapy and letrozole. When the patient developed multiple metastases, he was treated with chemotherapy and then fulvestrant, before received a 200 mg twice daily BEZ235 and 2.5 mg weekly RAD001 combination regimen, when a left axillary nodal metastasis was developed on fulvestrant. The patient sustained a prolonged stable disease of 18 months while under the therapy before his tumor progressed again.

Tumor biopsy samples (formalin fixed, paraffin embedded) were taken from the patient at diagnosis and after progression and analyzed by immunohistochemistry (IHC) and whole exome sequencing. Blood samples were collected for germline DNA pharmacokinetic (PK) analysis.

PK profile of BEZ235 was collected with Cmax, AUC, and T1/2 of 766 ng/mL, 6308 ng.h/mL, and 5.53 h, respectively. The observed BEZ235 Cmin values ranged from 75.5 to 504 ng/mL over the study. The 2.5 mg weekly RAD001 dose is substantially lower than the standard 10 mg daily dose and the Cmin could not be reliably determined.

IHC assays showed low ER/PR expression (ER 30% 1+; PR 20% 1+, 10% 3+) in the diagnosis sample, but an increase of their expression (60% 1+) in the post progression sample. HER2 expression was negative in both samples. Analysis the same tumor samples using more quantitative AQUA platform demonstrated a drastic 10-fold score increase of ER from 31 to 312 and a 5-fold increase of PR from 271 to 1305. All other examined signaling pathway biomarkers (e.g. pS6, pAKT, pMAPK, pMEK and pEGFR) were expressed in both tumor samples but showed minimal expression changes between the time points.

Whole exome sequencing of the diagnosis and post-progression specimens provided average coverage at 142X and 179X, respectively . No functional somatic alterations resulting in hyperactive PI3K/mTOR pathway was detected in genes such as PIK3CA, PTEN, MTOR, TSC1/2 in either tumor samples. In both specimens, a somatic deletion of 16 bp was detected in SPEN, which encodes a potential negative regulator of the estrogen signaling pathway1 .

In conclusion, no PI3K/mTOR pathway hyperactivity marker was identified in the diagnostic samples. However, the increased ER/PR expression in the post-progression sample suggests that the effect of PI3K/mTOR pathway blockade by RAD001/BEZ235 might have diminished when the tumor gained further dependence on the hormonal receptor signaling. This hypothesis was supported by the observation that the patient's tumor achieved another prolonged disease control of about 13 months by exemestane, after progression from BEZ235/RAD001 treatment.

1Légaré S, et al. SPEN is a novel candidate tumor suppressor gene that regulates response to tamoxifen in estrogen receptor positive breast cancers. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013.

Citation Format: A. Rose Brannron, Davide Melisi, Jennifer Hummel, Carmine Carbone, Melissa Frizziero, Wing Cheung, Parul Patel, Jorge Gallo, Giampaolo Tortora, Michael Morrissey, David Chen. Biomarker analysis of a male breast cancer patient with prolonged stable disease under mTOR/PI3K inhibitors BEZ235/RAD001. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr 26.

Abstract LB-A05: Profiling cell free DNA in breast cancer and non-small cell lung cancer using broad NGS assessment

Introduction: Cell free DNA (cfDNA) has become a promising approach for non-invasive assessment of the tumor genome. Many cfDNA assays target hotspot alterations in a focused set of genes, but do not provide a broad characterization of the cancer. We have developed and optimized a large next generation sequencing (NGS) panel covering the coding regions of over 500 genes. Using this panel, we sequenced cell free DNA from plasma and matched tumor DNA in patients with early stage breast cancer, late stage breast cancer and late stage lung cancer.

Methods: Plasma was collected from patients with cancer using a double spin protocol and, when available, matched archival tumor tissue (representing different time interval with blood collection) was obtained. Next generation sequencing libraries were generated from cell free DNA isolated from 70 plasma samples and genomic DNA from 58 matched tumor samples. The NGS libraries were enriched for the gene panel of interest and were sequenced to a targeted depth of 1,000X for plasma and 300X for matched tumors. We optimized parameters of standard bioinformatics tools to robustly call low allelic fraction events, detecting single nucleotide variants down to 1%, as well as indels and copy number alterations.

Results: We identified 8 PIK3CA hotspot alterations in plasma from late stage breast and lung cancers, in addition to many alterations across driver genes such as AKT1, EGFR, IDH2, NRAS, PTEN and TP53. In plasma samples from patients with late stage breast cancer, we found 4 ESR1 mutations exclusive to the plasma samples, of which 3 are known resistance mutations to endocrine therapy. Copy number alterations in EGFR, CCND1 and KRAS were also identified in patient plasma. When comparing the number of alterations across tumor stages, we found that late stage breast (mean = 12.5 variants) and lung cancers (mean = 12.5 variants) had a larger number of alterations present in plasma than early stage breast cancers (mean = 4.5 variants). We compared somatic mutations calls in plasma and matched tumor samples and found a concordance of 53%-67% at the variant level across patients with late stage cancers (N = 37 pairs). Higher variant level concordance was observed among plasma-tumor pairs collected less than a year apart (N = 11 pairs; 76%-84%) versus more than 5 years apart (N = 8 pairs; 41%-50%).

Conclusion: We have developed and optimized a 500+ gene panel for direct sequencing of cfDNA, and we demonstrate that this broad assessment of circulating tumor DNA can be used for non-invasive characterization of the cancer genome landscape. The number of alterations identified in patient plasma is consistent with higher levels of ctDNA being present in late stage disease than in early stage disease. The time dependent degree of concordance between plasma and tumor collection suggests that cell free DNA assays may provide a more accurate characterization of the current tumor mutational landscape than an archival tumor sample. The identification of plasma specific ESR1 alterations highlights the importance of cfDNA in the context of identifying mechanisms of resistance, particularly for metastatic disease when tumor tissue collection may not be feasible. In addition, a broad NGS panel provides the opportunity to identify lesions unevaluated by targeted assays and to discover resistance mutations.

Citation Format: Nadia Solovieff, Matt Hims, Rebecca Leary, Derek Chiang, Caroline Germa, Cristian Massacesi, Samit Hirawat, Stefan J. Scherer, Michael Morrissey, Wendy Winckler, Emmanuelle di Tomaso. Profiling cell free DNA in breast cancer and non-small cell lung cancer using broad NGS assessment. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr LB-A05.

The identification and characterization of a STAT5 gene signature in hematologic malignancies

BACKGROUND

The JAK-STAT pathway is an important signaling pathway downstream of multiple cytokine and growth factor receptors. Dysregulated JAK-STAT signaling has been implicated in the pathogenesis of multiple human malignancies.

OBJECTIVE

Given this pivotal role of JAK-STAT dysregulation, it is important to identify patients with an overactive JAK-STAT pathway for possible treatment with JAK inhibitors.

METHODS

We developed a gene signature assay to detect overactive JAK-STAT signaling. The cancer cell line encyclopedia and associated gene-expression data were used to correlate the activation status of STAT5 with the induction of a set of STAT5 target genes.

RESULTS

Four target genes were identified (PIM1, CISH, SOCS2, and ID1), the expression of which correlated significantly with pSTAT5 status in 40 hematologic tumor cell lines. In pSTAT5-positive models, the expression of the gene signature genes decreased following ruxolitinib treatment, which corresponded to pSTAT5 downmodulation. In pSTAT5-negative cell lines, neither pSTAT5 modulation nor a change in signature gene expression was observed following ruxolitinib treatment.

CONCLUSIONS

The gene signature can potentially be used to stratify or enrich for patient populations with activated JAK-STAT5 signaling that might benefit from treatments targeting JAK-STAT signaling. Furthermore, the 4-gene signature is a predictor of the pharmacodynamic effects of ruxolitinib.

High Affinity Antibodies against Influenza Characterize the Plasmablast Response in SLE Patients After Vaccination

Breakdown of B cell tolerance is a cardinal feature of systemic lupus erythematosus (SLE). Increased numbers of autoreactive mature naïve B cells have been described in SLE patients and autoantibodies have been shown to arise from autoreactive and non-autoreactive precursors. How these defects, in the regulation of B cell tolerance and selection, influence germinal center (GC) reactions that are directed towards foreign antigens has yet to be investigated. Here, we examined the characteristics of post-GC foreign antigen-specific B cells from SLE patients and healthy controls by analyzing monoclonal antibodies generated from plasmablasts induced specifically by influenza vaccination. We report that many of the SLE patients had anti-influenza antibodies with higher binding affinity and neutralization capacity than those from controls. Although overall frequencies of autoreactivity in the influenza-specific plasmablasts were similar for SLE patients and controls, the variable gene repertoire of influenza-specific plasmablasts from SLE patients was altered, with increased usage of JH6 and long heavy chain CDR3 segments. We found that high affinity anti-influenza antibodies generally characterize the plasmablast responses of SLE patients with low levels of autoreactivity; however, certain exceptions were noted. The high-avidity antibody responses in SLE patients may also be correlated with cytokines that are abnormally expressed in lupus. These findings provide insights into the effects of dysregulated immunity on the quality of antibody responses following influenza vaccination and further our understanding of the underlying abnormalities of lupus.

Newborn screening for X-linked adrenoleukodystrophy in New York State: diagnostic protocol, surveillance protocol and treatment guidelines

PURPOSE

To describe a diagnostic protocol, surveillance and treatment guidelines, genetic counseling considerations and long-term follow-up data elements developed in preparation for X-linked adrenoleukodystrophy (X-ALD) newborn screening in New York State.

METHODS

A group including the director from each regional NYS inherited metabolic disorder center, personnel from the NYS Newborn Screening Program, and others prepared a follow-up plan for X-ALD NBS. Over the months preceding the start of screening, a series of conference calls took place to develop and refine a complete newborn screening system from initial positive screen results to long-term follow-up.

RESULTS

A diagnostic protocol was developed to determine for each newborn with a positive screen whether the final diagnosis is X-ALD, carrier of X-ALD, Zellweger spectrum disorder, acyl CoA oxidase deficiency or D-bifunctional protein deficiency. For asymptomatic males with X-ALD, surveillance protocols were developed for use at the time of diagnosis, during childhood and during adulthood. Considerations for timing of treatment of adrenal and cerebral disease were developed.

CONCLUSION

Because New York was the first newborn screening laboratory to include X-ALD on its panel, and symptoms may not develop for years, long-term follow-up is needed to evaluate the presented guidelines.

Abstract B36: Modeling genetic mechanisms of resistance in melanoma primary tumor xenografts

Melanoma is the most lethal skin cancer and approximately 50% of the cases harbor mutations in the BRAF oncogene, with the mutation V600E representing 80-90% of all BRAF mutations in this indication. BRAF inhibitors as Vemurafenib and Dabrafenib have shown improved overall and progression free survival; however, the long term efficacy of these compounds is limited by the emergence of resistance. Several mechanisms of resistance to BRAF inhibitors have been already described, such as BRAF overexpression, increased ERBB3 signaling, expression of BRAF alternative isoforms, secondary mutations in BRAF or MEK1 and recently BRAF amplifications, among others. A fundamental aspect on devising optimal therapeutic regimes that overcome resistance is to develop preclinical models that resemble the genetic makeup of clinical patients who become resistance during the course of treatment to BRAF inhibitors. To this end, melanoma primary tumor xenografts (PTX) harboring BRAF V600E mutations were subject to treatment with BRAF inhibitors and response data was collected for a maximum of 180 days. Vehicle and treated samples were then sequenced using a targeted next generation sequencing approach in order to characterize their mutational landscape. Raw sequencing data was aligned to the human genome and potential mouse contamination was filter out before downstream analysis. Comparing SNV and copy number calls between treated and control samples revealed that focal amplifications of BRAF and de-novo mutations in the MEK1 gene were frequent genetic aberrations found in the PTX models that developed resistance. In summary, our results indicate that the genetic mechanisms of resistance observed in primary tumor xenograft models closely resemble what is observed in the clinical setting, making these models a valuable research tool for designing optimal therapeutic strategies.

Citation Format: Alejandro Balbin, Angad Singh, Joshua Korn, Hui Gao, Darrin Stuart, John Green, Andrew Crenshaw, Scott Mahan, Nathan Houde, Alina Raza, Rebecca Leary, Derek Chiang, Michael Morrissey, Wendy Winckler, Sellers William. Modeling genetic mechanisms of resistance in melanoma primary tumor xenografts. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr B36.

Identification of pSTAT5 gene signature in hematologic malignancy

7111

Background: The JAK/STAT pathway is an important signaling pathway downstream of multiple cytokine and growth factor receptors. Receptor-associated JAKs are activated following receptor-ligand binding. Activated JAKs phosphorylate STAT proteins, which then dimerize and translocate to the nucleus where they modulate the expression of target genes. Dysregulated JAK/STAT signaling has been implicated in the pathogenesis of multiple human malignancies. Activating mutations in JAK2 and the associated activation of STAT5 in myeloproliferative neoplasia is one example of the involvement of this pathway in human cancer. Additionally, overactivated JAK/STAT signaling has been suggested as a survival mechanism in several human cancers. Given the importance of JAK/STAT dysregulation in human diseases, it is important to identify patients with an overactivated JAK/STAT pathway for possible treatment with JAK inhibitors. Thus, we developed a gene signature assay to detect overactivated JAK/STAT5 signaling. Methods: The cancer cell line encyclopedia (CCLE) and associated gene-expression data were used to correlate the activation status of STAT5 with the induction of a set of STAT5 target genes. First, we used 27 tumor cell lines of hematologic lineage, with predetermined phosphorylated STAT5 (pSTAT5) status, to derive STAT5 activation gene signatures. Next, the putative gene signatures were validated against a different set of 13 hematologic tumor cell lines. Results: With this approach, a collection of 7 target genes were identified (PIM1, CISH, SOCS2, ID1, LCN2, EPOR, and EGR1) whose expression significantly correlated with pSTAT5 status in the 40 hematologic tumor cell lines (P < .0001), either together or in specific subsets of 4 and 6 genes (Table). Conclusions: These 4-, 6-, and 7-gene signatures can be used to stratify or select for a patient population with activated JAK/STAT5 signaling that could potentially benefit from treatments targeting the JAK/STAT5 signaling pathway. [Table: see text]

Abstract 5114: Integrative analysis of the Cancer Cell Line Encyclopedia reveals genetic and transcriptional predictors of compound sensitivity

The Cancer Cell Line Encyclopedia (CCLE) represents a collaborative effort to assemble a comprehensive resource of human cancer models for basic and translational research. It contains a detailed genetic profiling of approximately 1,000 human cancer cell lines spanning many tumor types. Thus far, high-density SNP array data, gene expression microarray data and mutation data from hybrid capture sequencing of 1,650 cancer genes has been obtained. Additionally, we have assessed the sensitivity of these same cell lines using a series of pharmacological compounds that represent both conventional cytotoxic and targeted agents. On major goal of the CCLE effort involves systematic integration of the genomic and pharmacologic datasets in order to identify putative targets of prevalent genetic alterations as well as predictors and modifiers of pharmacologic sensitivity and resistance. The availability of high-quality data generated by uniform criteria across hundreds of cell lines markedly enhances the statistical power to discover genetic alterations involved in carcinogenesis and molecular predictors of pharmacologic vulnerability. We developed a framework based on an elastic net machine-learning regression algorithm, and combined with a bootstrapping procedure, to derive predictive models of the sensitivity to each compound, using all genetic features of the cell lines in the collection. Through this computational prediction approach, we have both rediscovered molecular features predicting response to most drugs in our set but also uncovered novel potential biomarkers of sensitivity and resistance to targeted agents and chemotherapy drugs. For instance, we have found that response to topoisomerase 1 inhibitors seems to be linked to the expression of a single gene. We have also observed that tissue lineage is a key predictor for sensitivity to certain compounds, providing rationale for clinical trials of these drugs in particular cancer types and we identified potential stratifiers for existing EGFR targeted therapies. Finally, we have found an additional target for a certain chemotype of MEK inhibitors, and shown that this interaction was responsible for growth suppression, which might be a new indication for this kind of drug. Our cell line-based platform provides a valuable tool for the development of personalized cancer medicine, revealing critical tumor dependencies and helping to stratify patients for clinical trials.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5114. doi:1538-7445.AM2012-5114

High abundance of plasma cells secreting transglutaminase 2-specific IgA autoantibodies with limited somatic hypermutation in celiac disease intestinal lesions

Celiac disease is an immune-mediated disorder in which mucosal autoantibodies to the enzyme transglutaminase 2 (TG2) are generated in response to the exogenous antigen gluten in individuals who express human leukocyte antigen HLA-DQ2 or HLA-DQ8 (ref. 3). We assessed in a comprehensive and nonbiased manner the IgA anti-TG2 response by expression cloning of the antibody repertoire of ex vivo-isolated intestinal antibody-secreting cells (ASCs). We found that TG2-specific plasma cells are markedly expanded within the duodenal mucosa in individuals with active celiac disease. TG2-specific antibodies were of high affinity yet showed little adaptation by somatic mutations. Unlike infection-induced peripheral blood plasmablasts, the TG2-specific ASCs had not recently proliferated and were not short-lived ex vivo. Altogether, these observations demonstrate that there is a germline repertoire with high affinity for TG2 that may favor massive generation of autoreactive B cells. TG2-specific antibodies did not block enzymatic activity and served as substrates for TG2-mediated crosslinking when expressed as IgD or IgM but not as IgA1 or IgG1. This could result in preferential recruitment of plasma cells from naive IgD- and IgM-expressing B cells, thus possibly explaining why the antibody response to TG2 bears signs of a primary immune response despite the disease chronicity.

Abstract 923: Separating the wheat from the chaff: A first look at the Cancer Cell Lines Encyclopedia sequencing data

Comprehensive characterization of cancer genomic alterations and understanding their functional roles are important steps in the development of personalized cancer treatments. The Cancer Cell Lines Encyclopedia project aims to relate genomic alterations to drug sensitivity of cancer cells. Cancer cell lines are indispensable resource for researchers because of their convenience for high-throughput profiling and availability for follow-up experiments.

We sequenced the coding regions of 1645 genes in over 800 cancer cell lines representing 32 different tumor types. Genes were selected on their likelihood to be cancer-related and sequenced using next-generation Illumina technology after hybrid selection of exonic regions. Although, the absence of matched normal cell lines precludes direct distinction of somatic from germline mutations, we were able to select a subset of mutations highly enriched in somatic events combining the following three approaches: subtraction of known polymorphisms, prediction of strongly detrimental mutations (including computational predictions of amino acid substitutions’ effects on protein function) and detection of abnormal linkage disequilibrium patterns for recurring mutations.

We then searched for the three independent indicators of the potential involvement of mutated genes in cancer: the presence of an unusually high fraction of strongly damaging mutations within a gene, statistically significant deviation of distribution of mutations between cancer types from random expectation and clustering of mutations within a gene. Combined analysis of these lines of evidence revealed both known and novel potential tumor suppressors and oncogenes.

These data should become an import resource for cancer researchers in their search for personalized cancer therapies.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 923. doi:10.1158/1538-7445.AM2011-923

Interfering with resistance to smoothened antagonists by inhibition of the PI3K pathway in medulloblastoma

The malignant brain cancer medulloblastoma is characterized by mutations in Hedgehog (Hh) signaling pathway genes, which lead to constitutive activation of the G protein (heterotrimeric guanosine triphosphate-binding protein)-coupled receptor Smoothened (Smo). The Smo antagonist NVP-LDE225 inhibits Hh signaling and induces tumor regression in animal models of medulloblastoma. However, evidence of resistance was observed during the course of treatment. Molecular analysis of resistant tumors revealed several resistance mechanisms. We noted chromosomal amplification of Gli2, a downstream effector of Hh signaling, and, more rarely, point mutations in Smo that led to reactivated Hh signaling and restored tumor growth. Analysis of pathway gene expression signatures also, unexpectedly, identified up-regulation of phosphatidylinositol 3-kinase (PI3K) signaling in resistant tumors as another potential mechanism of resistance. Probing the relevance of increased PI3K signaling, we demonstrated that addition of the PI3K inhibitor NVP-BKM120 or the dual PI3K-mTOR (mammalian target of rapamycin) inhibitor NVP-BEZ235 to the initial treatment with the Smo antagonist markedly delayed the development of resistance. Our findings may be useful in informing treatment strategies for medulloblastoma.

Broadly cross-reactive antibodies dominate the human B cell response against 2009 pandemic H1N1 influenza virus infection

Although scarce after annual influenza vaccination, B cells producing antibodies capable of neutralizing multiple influenza strains are abundant in humans infected with pandemic 2009 H1N1 influenza.

The 2009 pandemic H1N1 influenza pandemic demonstrated the global health threat of reassortant influenza strains. Herein, we report a detailed analysis of plasmablast and monoclonal antibody responses induced by pandemic H1N1 infection in humans. Unlike antibodies elicited by annual influenza vaccinations, most neutralizing antibodies induced by pandemic H1N1 infection were broadly cross-reactive against epitopes in the hemagglutinin (HA) stalk and head domain of multiple influenza strains. The antibodies were from cells that had undergone extensive affinity maturation. Based on these observations, we postulate that the plasmablasts producing these broadly neutralizing antibodies were predominantly derived from activated memory B cells specific for epitopes conserved in several influenza strains. Consequently, most neutralizing antibodies were broadly reactive against divergent H1N1 and H5N1 influenza strains. This suggests that a pan-influenza vaccine may be possible, given the right immunogen. Antibodies generated potently protected and rescued mice from lethal challenge with pandemic H1N1 or antigenically distinct influenza strains, making them excellent therapeutic candidates.

HeartBeat--improving heart attack care

We aimed to save lives by assuring best practice in ST elevation myocardial infarction (STEMI) through initiating the Institute for Healthcare Improvement (IHI) methodology nationally. Following collection of a minimum dataset, annual change in indicators in the five initiating hospitals for the period Oct 2006 - Sept 2009 was assessed by analysing the percentage of patients receiving the eight components of evidenced based care on admission and discharge and in-hospital mortality rate. For 635 patients, performance on seven of the eight indicators of care exceeded 90% annually. Timely reperfusion therapy (thrombolysis, primary percutaneous coronary intervention (PPCI)) improved non-significantly from 68.2% (107 patients) in year 1 to 77.1% (118 patients) in year 3. In-hospital mortality declined significantly from 12.4% (24 deaths) in year 1 to 5% (9 deaths) in year 3. Evidence based STEMI care is followed to a high degree but timely reperfusion and PPCI provision remain a challenge nationally.

The Polycomb group protein Bmi-1 is essential for the growth of multiple myeloma cells

Bmi-1 is a member of the Polycomb group family of proteins that function in the epigenetic silencing of genes governing self-renewal, differentiation, and proliferation. Bmi-1 was first identified through its ability to accelerate c-Myc-induced lymphomagenesis. Subsequent studies have further supported an oncogenic role for Bmi-1 in several cancers including those of the breast, lung, prostate, and brain. Using a stable and inducible shRNA system to silence Bmi-1 gene expression, we show a novel role for Bmi-1 in regulating the growth and clonogenic capacity of multiple myeloma cells both in vitro and in vivo. Moreover, to elucidate novel gene targets controlled by Bmi-1, global transcriptional profiling studies were performed in the setting of induced loss of Bmi-1 function. We found that the expression of the proapoptotic gene Bim is negatively regulated by Bmi-1 and that Bim knockdown functionally rescues the apoptotic phenotype induced upon loss of Bmi-1. Therefore, these studies not only highlight Bmi-1 as a cancer-dependent factor in multiple myeloma, but also elucidate a novel antiapoptotic mechanism for Bmi-1 function involving the suppression of Bim.

Abstract 1976: The discovery of mechanisms of resistance to SMO antagonists and the therapeutic implications

Smoothened (Smo) is a G-protein coupled receptor (GPCR)-like molecule that activates the Hedgehog (Hh) signal transduction pathway. In the resting state, the 12-pass transmembrane protein Patched (Ptch) inhibits Smo activity. When Ptch inhibition is attenuated, Smo signals via a cytosolic complex of proteins leading to activation of the Gli family of transcription factors. Genetic activation of the Hh pathway at or upstream of Smo is linked to tumorigenesis in several cancers. In particular, somatic mutations in Ptch and Smo leading to constitutive pathway activation are found in sporadic medulloblastoma (MB) and basal cell carcinoma (BCC). Evidence suggests that antagonists of Smo may abrogate the tumorigenic phenotype engendered by Ptch inactivation.

NVP-LDE225 is a potent and selective orally available Smo antagonist that robustly inhibits Smo-dependent signaling in vitro and in vivo. NVP-LDE225 exerted dose-related anti-tumor activity in vivo in several genetically defined MB models that are driven by mutations in Ptch leading to near complete tumor regression and Hh pathway inhibition. However, following long-term continuous dosing of NVP-LDE225 in medulloblastoma allograft models, evidence of resistance to NVP-LDE225 was observed. Here, we describe our efforts to proactively identify mechanisms of resistance to targeted therapy of Smo. Genome-wide DNA- and RNA-profiling of resistant tumors revealed distinct resistance mechanisms allowing tumors to evade the inhibitory effects of Smo antagonists. Chromosomal amplification of Gli2, a downstream effector of Hh signaling, was identified as one mechanism leading to restoration of pathway signaling despite adequate drug exposure. Additional mining of the gene expression data for pathway signatures that are selectively deregulated in resistant tumors identified increased phosphatidylinositol-3-kinase (PI3K) signaling as another potential resistance mechanism. Probing the functional relevance of increased PI3K signaling, we showed that the combination of NVP-LDE225 with the dual PI3K/mTor inhibitor NVP-BEZ235 markedly delayed the development of resistance. Our findings have important clinical implications for future treatment strategies in medulloblastoma.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1976.

Abstract 2620: The Cancer Cell Line Encyclopedia project: From integrative cancer genomics to personalized cancer therapy

Cancer genome characterization efforts such as The Cancer Genome Atlas project are rapidly improving our knowledge of tumor genetic alterations. With the expanded use of massively parallel sequencing, the catalogue of known genetic alterations in cancer is expected to expand at an accelerating rate. In this context, the emphasis is shifting towards systematic identification of the genes and pathways targeted by recurrent genetic alterations, their functional impact in tumor biology, and the resulting cellular dependencies that might be exploited therapeutically. Anticipating the need for a companion resource to systematically probe tumor biology armed with cancer genomics knowledge, we have assembled a compendium of experimentally tractable cancer model systems consisting of ∼1000 human cancer cell lines and performed extensive genomic analysis (at the level of gene expression, DNA copy number and mutations) coupled with pharmacological profiling. This resource, which we call the Cancer Cell Line Encyclopedia (CCLE), is being used not only to identify the putative targets of prevalent genetic alterations, but also to systematically link the presence or absence of certain genetic alterations to drug sensitivity or resistance.

To date, we have identified several previously unappreciated genomic predictors of response or intrinsic resistance to targeted anticancer agents. For instance, through integrative analysis, we have discovered additional mechanisms that may underlie sensitivity to MET inhibitors, beyond amplification of the MET receptor, highlighting the fact that response prediction in the clinic may require assessment of multiple variables. We have also broadened the potential relevance of known predictive biomarkers that might provide a rationale for future genotype-driven clinical trials. As an example, we have expanded on existing knowledge of resistance to receptor tyrosine kinase (RTK) inhibitors, showing that the presence of RAS mutations may predict lack of response to a broad spectrum of RTK inhibitors in addition to EGFR inhibitors. This work demonstrates that pharmacological profiling of large, genomically-annotated cancer model systems may uncover new tumor dependencies as well as positive and negative predictors of drug response. The results of this study are being made publicly available at a CCLE online portal, with the hope they will become a valuable resource for the cancer community to propel translation of the knowledge generated through in vitro integrative genomics into personalized cancer medicine.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2620.

The genetic basis of early-life morphological traits and their relation to alternative male reproductive tactics in Atlantic salmon

Although heritability estimates for traits potentially under natural selection are increasingly being reported, their estimation remains a challenge if we are to understand the patterns of adaptive phenotypic change in nature. Given the potentially important role of selection on the early life phenotype, and thereby on future life history events in many fish species, we conducted a common garden experiment, using the Atlantic salmon (Salmo salar L.), with two major aims. The first objective is to determine how the site of origin, the paternal sexual tactic and additive genetic effects influence phenotypic variation of several morphological traits at hatching and emergence. The second aim is to test whether a link exists between phenotypic characteristics early in life and the incidence of male alternative tactics later in life. We found no evidence of a site or paternal effect on any morphological trait at hatching or emergence, suggesting that the spatial phenotypic differences observed in the natural river system from which these fish originated are mainly environmentally driven. However, we do find significant heritabilities and maternal effects for several traits, including body size. No direct evidence was found correlating the incidence of precocious maturation with early life characteristics. We suggest that under good growing conditions, body size and other traits at early developmental stages are not reliable cues for the surpassing of the threshold values associated with male sexual development.

GP perceptions of workforce shortage in a rural setting

INTRODUCTION

Currently Australia is experiencing a rural medical workforce shortage, especially among GPs. Strategies aimed at improving this shortage have generally been directed at small and remote rural communities (RRMA 4-7); however, longstanding GP shortages also continue in large (RRMA 3) rural communities. The key to the understanding the rural workforce is the perceptions of GPs themselves. This article compared GP perceptions of workforce shortages in Tamworth, New South Wales, Australia (an RRMA 3 town) with actual levels of workforce participation.

METHODS

A survey of 31/33 GPs working in the New South Wales town of Tamworth was conducted in 2005. Participating GPs were individually interviewed and were asked to estimate local GP workforce needs, calculate their weekly consulting time sessions and advise if they were accepting new patients. The survey was repeated 12 months later with the same cohort to track workforce change.

RESULTS

In May 2005 there were 27.8 full time equivalent (FTE) GPs working in Tamworth (population 42 000). In May 2006 this had risen to 31.5 FTE practitioners. Initially, all practitioners surveyed believed there was a workforce shortage, with no practice accepting new patients. This shortage was perceived to be >10 FTE GPs (6.5%), between 5-9 GPs (64.5%) and between 1-4 GPs by 29% of surveyed GPs. In June 2006 there were 31.5 FTE GPs working in Tamworth. The follow-up survey of 29 GPs revealed a significant shift in their perceptions with only 41.4% of GPs perceiving the shortage as 1-4 FTE GPs (p = 0.2), 17.2% between 5-9 GPs and 41.4% nil. No GPs in the follow-up survey perceived the shortage as >10. At the end of the 12 month study period, 8 of 17 practices were accepting new patients.

CONCLUSION

GP perceptions of shortage largely reflected concurrent workforce changes that occurred during the study period where there was a 12% improvement after a prolonged period of workforce stagnation. This change drove improvements in patient access and in many GPs' minds ameliorated much of the perceived shortage. Many factors may be involved, including the increased use of practice nurses, private billing and start-up capacity. General practitioner perceptions appear to be sensitive to workforce changes, with sampled GPs working with higher patient ratios than those seen as acceptable in metropolitan areas.

Contribution of polycomb homologues Bmi-1 and Mel-18 to medulloblastoma pathogenesis

Bmi-1 and Mel-18 are structural homologues that belong to the Polycomb group of transcriptional regulators and are believed to stably maintain repression of gene expression by altering the state of chromatin at specific promoters. While a number of clinical and experimental observations have implicated Bmi-1 in human tumorigenesis, the role of Mel-18 in cancer cell growth has not been investigated. We report here that short hairpin RNA-mediated knockdown of either Bmi-1 or Mel-18 in human medulloblastoma DAOY cells results in the inhibition of proliferation, loss of clonogenic survival, anchorage-independent growth, and suppression of tumor formation in nude mice. Furthermore, overexpression of both Bmi-1 and Mel-18 significantly increases the clonogenic survival of Rat1 fibroblasts. In contrast, stable downregulation of Bmi-1 or Mel-18 alone does not affect the growth of normal human WI38 fibroblasts. Proteomics-based characterization of Bmi-1 and Mel-18 protein complexes isolated from cancer cells revealed substantial similarities in their respective compositions. Finally, gene expression analysis identified a number of cancer-relevant pathways that may be controlled by Bmi-1 and Mel-18 and also showed that these Polycomb proteins regulate a set of common gene targets. Taken together, these results suggest that Bmi-1 and Mel-18 may have overlapping functions in cancer cell growth.

Characterization and comparison of health-related utility in people with diabetes with various single and multiple vascular complications

AIMS

To characterize and compare health-related utility in a large cohort of patients treated in hospital with diabetes and with single and multiple comorbidities.

METHODS

The study was conducted in Cardiff and the Vale of Glamorgan, UK. Health-related utility was measured using the EQ5D(index), a standardized instrument for measuring health outcome. Patients from the Health Outcomes Data Repository (HODaR) were surveyed by postal questionnaire 6 weeks post discharge for in-patients and during clinics for patients attending as out-patients between January 2002 and July 2005. Patients with diabetes were identified by a previous history of in-patient admission with diabetes or as an out-patient with diabetes recorded as a coexisting diagnosis.

RESULTS

We identified 4502 patients with diabetes. Mean ages were 65.4 and 64.2 years for males and females, respectively. Of these, 2003 (45%) had no recorded vascular complication. Overall, the EQ5D(index) was 0.584 (sd 0.325) for males and 0.533 (sd 0.351) for females. For those without any vascular complications the mean EQ5D(index) was 0.735 (sd 0.288). In a general linear model, the presence of single and multiple complications had a detrimental impact on the EQ5D(index).

CONCLUSION

The results of this study provide an indication of the true impact of diabetes in terms of health-related utility. There was a decrease in the mean EQ5D(index) for those with vascular complications. Economic models of diabetes that have used additive or multiplicative methods to assess utility in individuals with several complications may be unreliable, and direct measurements, such as this, are recommended.

Community, social capital and Indigenous health in the Northern Territory

OBJECTIVE

The objective of this paper is to explore the discourse of 'community' and its offshoots, 'social capital' and 'community capacity building', in the contexts of health service delivery to, and the health status of, Indigenous people in the Northern Territory of Australia, and to link this discourse to the wider context of social control and the management of diversity in a multicultural society.

DESIGN

The discourse is subjected to critical theoretical and historical analysis and comparisons are drawn between this and similar discourses in the immigration and settlement area.

RESULTS/CONCLUSIONS

The constitution of Indigenous society as a series of 'communities' and the orientation of primary health care policy towards 'capacity building' has the effect, if not the intention, of depoliticising Indigenous health, whilst reproducing, legitimising and mystifying relations of white dominance and permitting the maintenance of a health service delivery system for Indigenous people which, in relation to need, is grotesquely underfunded and incapable of making serious inroads into the appalling health problems of the Indigenous population.

Evaluation of the association between the EQ-5D (health-related utility) and body mass index (obesity) in hospital-treated people with Type 1 diabetes, Type 2 diabetes and with no diagnosed diabetes

AIMS

The purpose of this study was to characterize the impact of body mass index (BMI) on health-related utility for patients with Type 1 and Type 2 diabetes and those without diabetes.

METHODS

The study was conducted in Cardiff and the Vale of Glamorgan, Wales, UK. Health-related utility was measured using the EQ-5D(index). Patients from the Health Outcomes Data Repository (HODaR) were surveyed by postal questionnaire either 6 weeks post discharge for in-patients or at out-patient clinics between January 2002 and July 2003. BMI was calculated from self-reported data within the survey. Patients with diabetes were identified by a previous history of an in-patient admission with diabetes or as an out-patient with diabetes recorded as a coexisting diagnosis.

RESULTS

Questionnaires were returned from 27 924 patients of whom 2575 had diabetes. Increasing BMI was found to reduce utility in all three groups. BMI was significantly greater for those with Type 2 diabetes compared with those with Type 1, and those without diabetes (P < 0.001). Multiple regression analysis demonstrated that both BMI and diabetes status had a significant effect on utility. However, the rate of change of utility attributable to BMI was not found to be significantly different between the various groups.

CONCLUSIONS

Obesity negatively impacts upon health-related utility and thus quality of life for all patient groups. There was no significant difference in the effect of obesity on utility between those with and without diabetes.

It's good to talk: children's views on food and nutrition

OBJECTIVE

To gain an insight into children's views about food and nutrition.

DESIGN

Data were collected in focus group discussions; two focus group sessions were undertaken with each school group.

SETTING

A total of 11 postprimary schools in Northern Ireland and England.

SUBJECTS

In all, 106 children aged 11-12-y-old (n = 52 boys, n = 54 girls).

RESULTS

Focus group transcripts were analysed using qualitative research methodology. Major barriers to healthy eating were taste, appearance of food, filling power, time/effort, cost, choice/availability, risk, rebellion, and body image/weight concerns. The main difference between sexes was in terms of motivating factors for eating well; girls tended to focus primarily on their appearance whereas boys appeared to be more influenced by sport. There was some mention of balance and variety within the focus group discussions, however, in practice, the children had a tendency to categorise foods as either 'good' or 'bad', 'healthy' or 'unhealthy'.

CONCLUSIONS

This study has revealed a number of barriers to, and motivations for, healthy eating, which should be taken into account when planning nutrition intervention strategies aimed at children moving into adolescence. While it may be possible to immediately attempt to address some of the barriers identified in this study, for example, in nutrition education initiatives, other barriers (such as the lack of available, attractive and affordable healthy foods in the school canteen) will prove more difficult to tackle without changes at the policy level. Overall, it appears that health promotion specialists have a major challenge ahead in order to encourage this age group to view healthy eating as an attractive and achievable behaviour.

SPONSORSHIP

Food Standards Agency, London, UK.

An analysis of acute changes in interleukin-6 levels after treatment of hepatitis C with consensus interferon

Cytokine production has been implicated in the antiviral response to interferon-alpha (IFN-alpha) in hepatitis C and in the development of IFN-alpha-related side effects. We characterized acute changes in serum cytokine levels following administration of a single dose of consensus IFN (IFN-con1) and during continuous treatment of chronic hepatitis C patients. Serum samples were collected at baseline, at multiple times early after IFN administration, and weekly thereafter. Viral RNA titers were assessed by RT-PCR, and viral kinetics were followed. ELISA assays were used to measure IFN-gamma, tumor necrosis factor-alpha (TNF-alpha), interleukin-2 (IL-2), IL-4, IL-6, and IL-16. Serum cytokine levels were low at baseline. IL-6 was detected in patients with hepatitis C but not in healthy control subjects by either ELISA or RT-PCR, indicating that low levels of circulating IL-6 were associated with hepatitis C infection. None of the cytokines measured increased significantly after IFN administration except for IL-6. IL-6 levels rose rapidly, peaked at 6-15 h in a dose-dependent manner, and returned to baseline by 48 h in both patients receiving a single dose of IFN and those receiving continuous treatment. This was confirmed by RT-PCR. Pretreatment IL-6 levels were directly correlated with area under the curve (AUC) for IL-6 during the 24 h after IFN dosing (r = 0.611, p = 0.007). Viral titers decreased within 24-48 h after a single dose of IFN-con1. Changes in hepatitis C RNA titers were not significantly associated with pretreatment IL-6 levels or with changes in IL-6 levels. In conclusion, (1) baseline serum cytokine levels, except for IL-6, were low or within the normal range in patients with hepatitis C, (2) IL-6 levels were detected in some patients with hepatitis C before treatment but not in healthy controls, (3) IL-6 levels increased acutely after a single dose of IFN-alpha, and IL-6 induction was related to baseline IL-6 level, and (4) changes in IL-6 levels did not correlate with the early virologic response to IFN.