Citations

Abstract The goal of this study is to evaluate the potential use of gene expression profile of peripheral blood mononuclear cells (PBMCs) as a non-invasive biomarker for predicting the response of anti-PD-1 therapy in non-small cell lung cancer (NSCLC) subjects. Peripheral blood of NSCLC stage 4 subjects treated with an anti-PD-1 monoclonal antibody was collected prior to treatment (week 0) and subsequent infusions. Total RNA was extracted, and libraries were prepared using TruSeq Stranded mRNA LT Sample Prep Kit and sequenced by Illumina NextSeq. The paired-end reads were mapped to human reference hg38 using STAR and gene expressions were calculated using RSEM. Preliminary analysis of differential gene expression (DE) was performed among the responders at respectively (T1) weeks 3-4, (T2) weeks 6-9 and (T3) weeks 12-16 after treatment, compared with the baseline at T0. Further DE analysis was performed between the baseline samples of responders and non-responders. Genes with FDR-adjusted p values less than 0.05 were selected for pathway enrichment analysis with DAVID. Altogether 30 RNA-Seq samples of seven subjects were collected at multiple time points before and after treatment. According to standard RECIST 1.1 criteria, five subjects had a partial response to the therapy, whereas two subjects had stable disease or no response. In addition, liquid biopsy results were available for selected samples. Among the responders, there are 203 DE genes for T1 with log2 fold change (LFC) of gene expression from -2.4 to 3.5, 859 DE genes for T2 with LFC from -3.4 to 3.3, and 395 DE genes for T3 with LFC from -3 to 6.8. Among the DE genes for the three time points, 155 genes are common to T1/T2, 250 common to T2/T3, and 104 common to T1/T2/T3. Pathway enrichment test using Gene Ontology Biological Process terms shows that the strongest DE pathways for initial response after treatment at T1 are regulation of immune response (FDR adjusted p = 2.5E-5), oxygen transport (p = 5.5E-3) and T cell costimulation (p = 3.9E-3). Based on the 104 common DE genes, oxygen transport (p = 0.029) is the only pathway consistently perturbed due to an increase in hemoglobin. When comparing the baseline of responders and non-responders, we identified a candidate gene signature, with some of the genes also reported in other studies. However, more samples are required to establish its statistical significance. Systemic immune response after first dose of anti-PD1 treatment is reflected by DE genes in blood samples collected in weeks 3-4. Tumor regression might be indicated by the consistent increase in hemoglobin level. The results of these analyses show promise of developing a predictive signature for the response of anti-PD-1 immunotherapy in NSCLC subjects based on the gene expression profile of PBMCs. While these are preliminary results, we continue to recruit subjects, and will present the up-to-date results at the conference. Citation Format: Yee Him Cheung, Jie Wu, Weihua Huang, Changhong Yin, Katherine Linder, Kaushal Parikh, Ke Tang, Christopher Kasbek, Jun Huang, Zeil Rosenberg, Michael Fanucchi, John Fallon, Nevenka Dimitrova. Differential gene expression analysis reveals pathways involved in anti-pd-1 therapy response prediction [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 4994.

Abstract Background: Understanding the joint effect on breast cancer risk of rare pathogenic variants in cancer predisposition genes and polygenic risk scores (PRS) from common variants can enable a precision approach to breast cancer management. Previous work found that PRS were associated with breast cancer risk in BRCA1 and BRCA2 mutation carriers recruited from cancer genetics clinics (Kuchenbaecker et al. JNCI 2017). The joint effects of pathogenic variants and PRS have not been studied in samples drawn from the general population. There is also no existing study evaluating the effect of PRS in mutation carriers in genes other than BRCA1/2. Here we evaluate the joint effects of PRS and pathogenic mutations in established cancer predisposition genes in a population-based case-control sample. Method: We analyzed 53,199 European-ancestry individuals (20,730 controls and 21,272 cases) drawn from 7 cohorts and 2 population-based case-control studies in the CAnceR RIsk Estimates Related to Susceptibility” (CARRIERS) consortium. Targeted sequencing was performed using dual bar-coded QIAseq. Mutation calling was conducted with Haplotype Caller and Vardict. We sequenced 18 breast cancer predisposition genes: ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CDKN2A, CHECK2, FANCC, MLH1, MSH2, MSH6, NF1, PALB2, PTEN, RAD51C, RAD51D and TP53. The PRS was calculated based on 128 common variants using effect estimates from the largest published breast cancer GWAS. The PRS was standardized to a mean of 0 and standard deviation of 1. Logistic regression was performed to assess the combined effect of identified mutation and common variants (including main and interaction effects for carrier status and PRS). Results: A total of 1,770 pathogenic mutations were observed. About 1% of the study sample had mutations in either BRCA1 (n=209) or BRCA2 gene (n=305), and 2.2% had mutations in other genes (n=1,176). The effect of PRS in BRCA1 carriers was OR= 0.97 (95%CI: 0.62, 1.52); however, this is not statistically significantly different from the PRS in non-carriers [OR=1.23 (95%CI: 1.20, 1.25)] or previous estimates in carriers [OR: 1.14, 95%CI: 1.11-1.17]. The effect of PRS in BRCA2 carriers was OR=1.87 (95%CI: 1.31, 2.78) which was statistically significantly different from that of the non-carriers. Among the mutation carriers in genes other than BRCA, the effect of PRS on breast cancer was OR=1.00 (95%CI: 0.88,1.15). Conclusion: Consistent with previous studies, we did not find evidence that the effect of the PRS among BRCA1 carriers was statistically significantly different than non-carriers. We found some evidence that the PRS effect may be larger among BRCA2 carriers than non-carriers. Our results also suggest that PRS may not have a strong effect on breast cancer risk in mutation carriers of other predisposition genes; further work is needed for verification. Citation Format: Chi Gao, Chunling Hu, Steven N. Hart, Rohan Gnanaolivu, Kun Y. Lee, Jenna Lilyquist, Nicholas J. Boddicker, Bruce Eckloff, Raed Samara, Josh Klebba, Paul Auer, Leslie Bernstein, Mia Gaudet, Hoda Anton-Culver, Amy Trentham-Dietz, Julie R. Palmer, Song Yao, Christopher Haiman, Janet E. Olson, Susan Domchek, Jeffrey Weitzel, David Goldgar, Katherine L. Nathanson, Eric C. Polley, Fergus J. Couch, Peter Kraft. The joint effects of polygenic risk scores and pathogenic variants in cancer predisposition genes on breast cancer risk in the general population: results from the CARRIERS study [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 4177.

Abstract Clinical germline genetic testing of cancer predisposition gene panels is used to identify women at increased risk for breast cancer. Pathogenic mutations in cancer predisposition genes are associated with established risks of breast cancer and are actively used for risk management of breast cancer for women qualifying for genetic testing because of a family history of breast and/or ovarian cancer or young age of diagnosis. However, the risks of breast cancer associated with mutations in these genes have likely been overestimated for many women in the general population. The goal of the “CAnceR RIsk Estimates Related to Susceptibility” (CARRIERS) study was to estimate breast cancer risks associated with mutations in hereditary cancer panel genes. Germline DNA from 32,298 breast cancer patients and 31,869 matched unaffected controls enrolled in cohorts and population-based case-control studies were sequenced to identify pathogenic mutations in 37 cancer predisposition genes.The average age at diagnosis was 61.2 years and the average age of last follow-up was 62.1 years. DNA was subjected to dual bar-coded QIAseq multiplex PCR-based amplification of 1733 target regions in 37 predisposition genes. Products from 768 samples were pooled and sequenced in a single lane of a HiSeq 4000 system. Mutations were called by GATK Haplotype Caller and Vardict.High quality sequence data was obtained for 99.3% of target regions. Pathogenic mutations in 12 known breast cancer predisposition genes were identified in 6.2% of all breast cancer cases and 2.1% of controls; and in 6.7% of African American breast cancer cases and 1.8% of controls. In case-control association analyses adjusted for age at diagnosis or last follow up and family history of breast and ovarian cancer, mutations in BRCA1, BRCA2, and PALB2 were associated with high risks of breast cancer (odds ratio (OR)>4.0). Mutations in CHEK2 and BARD1 were associated with moderate risks of breast cancer (OR>2.0), whereas mutations in ATM had lower clinical relevance (OR=1.6). Stratification by ER, PR, and HER2 status of tumors found that BRCA1, BRCA2, PALB2 and TP53 were associated with high risks of studies of triple negative breast cancer (TNBC), and that BARD1, BRIP1, FANCM, and RAD51C were associated with moderate risks of TNBC. Overall, results from the CARRIERS study establish that mutations in predisposition genes are associated with lower risks of breast cancer in the general population than in high-risk families. The age-related estimates of breast cancer risk for each of the hereditary cancer panel genes in this study may inform on the use of cancer screening and other risk management strategies for women in the general population with mutations in predisposition genes. Citation Format: Fergus J. Couch, Chunling Hu, Steven N. Hart, Rohan Gnanaolivu, Jenna Lilyquist, Kun Y. Lee, Chi Gao, Bruce Eckloff, Hoda Anton-Culver, Paul Auer, Leslie Bernstein, Mia Gaudet, Christopher Haiman, Julie Palmer, Amy Tentham-Dietz, Song Yao, Susan Domchek, Jeffrey N. Weitzel, David E. Goldgar, Katherine L. Nathanson, Peter Kraft, Eric C. Polley. Population-based breast cancer risk estimates associated with cancer predisposition gene mutations from 32,298 breast cancer patients and 31,869 matched unaffected controls from the CARRIERS study [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 4169.

Abstract Background Cardiac troponin (cTn) assays are used for the diagnosis of acute myocardial infarction and frequently require serial measurements. Recollection of unacceptable specimens for hemolysis can delay results and disrupt timing of serial measurements. This study was designed to assess the influence of hemolysis on a high-sensitivity cTnT assay in granular detail at clinically important concentrations. These were used in consultation with the clinical practice to evaluate risk-based thresholds for acceptable amounts of hemolysis. Methods Plasma pools ranging from <10 to >100 ng/L cTnT were spiked with hemolysate to various degrees of hemolysis and measured using the Elecsys Troponin T Gen 5 STAT assay. The impact of accepting expanded hemolysis thresholds was completed using retrospective data of 12225 serial cTnT results and an additional 4651 baseline cTnT results. Results The mean percent change in cTnT was consistent for a given degree of hemolysis regardless of the initial nonhemolyzed cTnT concentration. Tiered hemolysis thresholds were evaluated for low-risk patients (apparent cTnT ≤8 ng/L), intermediate-risk patients (thresholds for 9–37 ng/L, 38–66 ng/L, and 67–99 ng/L cTnT), and high-risk patients (≥100 ng/L cTnT). The influence of tiered hemolysis thresholds was calculated for patients with serial (0 and 2 h) cTnT results, which demonstrated that the majority of 2-h delta interpretations were unchanged. Implementation of tiered thresholds dramatically decreased recollections for hemolyzed cTnT samples. Conclusion Tiered hemolysis cutoffs minimized disruption to patient care for low- and high-risk patients, while maintaining the integrity of serial measurements for those with intermediate cTnT concentrations.

SummaryObjectiveWeight perception and degree of confidence in achieving healthy lifestyle can be determinants of engagement in obesity interventions. This study explored patients' perceived need for weight loss and the degree of self‐confidence in ability to lose weight and sought to identify factors associated with patients' self‐confidence in ability to lose weight.MethodsThe authors analysed data from a survey mailed to primary care patients within five sites of the Learning Health Systems Network that explored participants' prior experience with weight management.ResultsAmong the 2,263 participants who completed the survey section on ‘Patients’ Experience with Weight Management’, perceived need to lose 51 lb or more was statistically significant among those with class III obesity compared with other body mass index (BMI) groups (p value < 0.001). Reported desire to lose weight was also significantly higher among those with the highest BMI than those who were overweight (p value < 0.001). However, this same group had the lowest belief in ability to lose weight (p value < 0.001). In a multiple regression analysis, female gender, higher BMI and need to lose >10 lb were each independently associated with less belief in being able to lose weight.ConclusionsPatients had varying perceptions on weight loss; those with category III obesity had the highest desire to lose weight but had the least confidence in ability to lose weight. Higher BMI, female gender and need to lose >10 lb were associated with decreased self‐confidence in ability to lose weight.

Abstract Background Understanding the relationship between clinical and patient-reported outcomes (PROs) will help support clinical care and future clinical trial design of novel therapies for focal segmental glomerulosclerosis (FSGS). Methods FSGS patients ≥8 years of age enrolled in the Nephrotic Syndrome Study Network completed Patient-Reported Outcomes Measurement Information System PRO measures of health-related quality of life (HRQoL) (children: global health, mobility, fatigue, pain interference, depression, anxiety, stress and peer relationships; adults: physical functioning, fatigue, pain interference, sleep impairment, mental health, depression, anxiety and social satisfaction) at baseline and during longitudinal follow-up for a maximum of 5 years. Linear mixed-effects models were used to determine which demographic, clinical and laboratory features were associated with PROs for each of the eight children and eight adults studied. Results There were 45 children and 114 adult FSGS patients enrolled that had at least one PRO assessment and 519 patient visits. Multivariable analyses among children found that edema was associated with global health (−7.6 points, P = 0.02) and mobility (−4.2, P = 0.02), the number of reported symptoms was associated with worse depression (−2.7 per symptom, P = 0.009) and anxiety (−2.3, P = 0.02) and the number of emergency room (ER) visits in the prior 6 months was associated with worse mobility (−2.8 per visit, P &lt; 0.001) and fatigue (−2.4, P = 0.03). Multivariable analyses among adults found the number of reported symptoms was associated with worse function in all eight PROMIS measures and the number of ER visits was associated with worse fatigue, pain interference, sleep impairment, depression, anxiety and social satisfaction. Laboratory markers of disease severity (i.e. proteinuria, estimated glomerular filtration rate and serum albumin) did not predict PRO in multivariable analyses, with the single exception of complete remission and better pain interference scores among children (+9.3, P = 0.03). Conclusions PROs provide important information about HRQoL for persons with FSGS that is not captured solely by the examination of laboratory-based markers of disease. However, it is critical that instruments capture the patient experience and FSGS clinical trials may benefit from a disease-specific instrument more sensitive to within-patient changes.

Objectives Literature suggests an inconsistent, but largely inverse, association between asthma and risk of glioma, which is primarily due to methodological inconsistency in sampling frame and ascertainment of asthma. The objective of the study was to clarify the association between asthma and risk of glioma by minimising methodological biases (eg, recall and detection bias). Design A population-based case–control study. Setting General population in Olmsted County, Minnesota, USA. Participants All eligible biopsy-proven incident glioma cases (1995–2014) and two sets of controls among residents matched to age and sex (first set: community controls without glioma; second set: MRI-negative controls from the same community). Methods The predetermined asthma criteria via medical record review were applied to ascertain asthma status of cases and controls. History of asthma prior to index date was compared between glioma cases and their matched controls using conditional logistic regression models. Propensity score for asthma status was adjusted for multivariate analysis. Results We enrolled 135 glioma cases (median age at index date: 53 years) and 270 controls. Of the cases, 21 had a history of asthma (16%), compared with 36 of MRI controls (27%) (OR (95% CI) 0.48 (0.26 to 0.91), p=0.03). With MRI controls, an inverse association between asthma and risk of glioma persisted after adjusting for the propensity score for asthma status, but did not reach statistical significance probably due to the lack of statistical power (OR (95% CI) 0.48 (0.21 to 1.09); p=0.08). Based on comparison of characteristics of controls and cases, community controls seem to be more susceptible to a detection bias. Conclusions While differential detection might account for the association between asthma and risk of glioma, asthma may potentially pose a protective effect on risk of glioma. Our study results need to be replicated by a larger study.