Assessment of variation in immunosuppressive pathway genes reveals TGFBR2 to be associated with risk of clear cell ovarian cancer

BACKGROUND

Regulatory T (Treg) cells, a subset of CD4+ T lymphocytes, are mediators of immunosuppression in cancer, and, thus, variants in genes encoding Treg cell immune molecules could be associated with ovarian cancer.

METHODS

In a population of 15,596 epithelial ovarian cancer (EOC) cases and 23,236 controls, we measured genetic associations of 1,351 SNPs in Treg cell pathway genes with odds of ovarian cancer and tested pathway and gene-level associations, overall and by histotype, for the 25 genes, using the admixture likelihood (AML) method. The most significant single SNP associations were tested for correlation with expression levels in 44 ovarian cancer patients.

RESULTS

The most significant global associations for all genes in the pathway were seen in endometrioid ( p = 0.082) and clear cell ( p = 0.083), with the most significant gene level association seen with TGFBR2 ( p = 0.001) and clear cell EOC. Gene associations with histotypes at p < 0.05 included: IL12 ( p = 0.005 and p = 0.008, serous and high-grade serous, respectively), IL8RA ( p = 0.035, endometrioid and mucinous), LGALS1 ( p = 0.03, mucinous), STAT5B ( p = 0.022, clear cell), TGFBR1 ( p = 0.021 endometrioid) and TGFBR2 ( p = 0.017 and p = 0.025, endometrioid and mucinous, respectively).

CONCLUSIONS

Common inherited gene variation in Treg cell pathways shows some evidence of germline genetic contribution to odds of EOC that varies by histologic subtype and may be associated with mRNA expression of immune-complex receptor in EOC patients.

Abstract 5489: A genome-wide association study identifies novel loci associated with taxane-related sensory neuropathy in breast cancer patients enrolled in a cooperative group clinical trial (SWOG S0221)

Introduction: The use of multi-drug regimens, including taxanes (T), has increased survival for breast cancer patients. However, T-induced neuropathy, one of the most common side effects, cannot be predicted, prevented or effectively treated. Using genome wide analyses (GWA), we sought to identify common genetic variants that infer susceptibility to clinical and self-reported neuropathy.

Methods: Women with high risk breast cancer were enrolled in SWOG 0221, a trial of dosing schedules for AC and T. Genotyping was performed using the Illumina 1M chip and SNPs examined in relation to CTCAE grade 3 and 4 neurotoxicity and self-reported symptoms (FACT-TAXANE) among women providing blood samples. Significant associations were tested for replication in CALGB40101.

Results: Among 1269 European Americans (EA) and 139 African Americans (AA) in S0221, there were 147 and 31 grade 3+ neuropathies, respectively. In CALGB40101, grade 3 toxicity was less frequent (59/855 EA and 15/117 AA).  In S0221 EA patients, loci on chromosomes 7, 10, 16 and 17 showed associations with grades 3 and 4 neuropathy at p&lt;5×10e-06, with the most significant genetic association on chromosome 17, rs910920, p = 6.8×10e-08, odds ratio (OR) = 0.44 (95% confidence interval (CI), 0.32-0.61); this SNP is a cis eQTL, thought likely to affect transcription factor binding and linked to expression of VPS53 in lymphoblastoid cell lines. While the rs910920 association was specific to EA, the A allele in rs1858826 on chromosome 7 was associated with reduced odds of neuropathy in both EA (p = 7×10e-07) and AA (p = .02) groups. The S0221 associations at p&lt;5×10e-06 did not replicate in CALGB40101.

A subset of patients (n = 677 EA and n = 42 AA) completed the FACT-TAXANE. The most significant associations with this neuropathy phenotype (p&lt;5×10e-07) were on chromosomes 2 (rs4267555 and rs4443044) and 3 (rs2421468). Of the 168 SNPs tested for association with neuropathy in previous studies, rs1695 in GSTP1 (p = 0.0009) and rs228591 in ATM (p = 0.0006), showed some evidence of association with FACT-TAXANE scores; the latter SNP was significant at p = .005 in ordinal regression analysis of neuropathy grades 0-4 in CALGB40101. None of these SNPs were significantly associated with grade 3 CTCAE neuropathy at p&lt;.05, nor were the top CTCAE associations in relation to FACT-TAXANE scores. Replication of the most significant S0221 FACT-TAXANE findings in CALGB40101 is ongoing.

Conclusions: Failure to replicate S0221 in CALGB40101, and the lack of coherence between self-report and clinical grade in S0221 could be attributable to differences in trial designs as well as differences in defining a complex phenotype. Larger homogeneous trials with similar dosing and criteria for defining neuropathy are needed to assess the relationship of genetics and the neuropathy symptom spectrum.

Citation Format: Lara Sucheston-Campbell, Alyssa Clay, William E. Barlow, G Thomas Budd, Dan Stram, Chris Haiman, Li Yan, Gary Zirpoli, Song Yao, Dawn Hershman, Kathy S. Albain, Daniel F. Hayes, Halle Moore, Timothy J. Hobday, James A. Stewart, Claudine Isaacs, Muhammad Salim, Julie R. Gralow, Gabriel N. Hortobagyi, Robert B. Livingston, Xin Sheng, Deanna L. Kroetz, Christine B. Ambrosone. A genome-wide association study identifies novel loci associated with taxane-related sensory neuropathy in breast cancer patients enrolled in a cooperative group clinical trial (SWOG S0221). [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5489. doi:10.1158/1538-7445.AM2015-5489

Establishment of Definitions and Review Process for Consistent Adjudication of Cause-specific Mortality after Allogeneic Unrelated-donor Hematopoietic Cell Transplantation

Clinical trials commonly use adjudication committees to refine endpoints, but observational research or genome-wide association studies rarely do. Our goals were to establish definitions of cause-specific death after unrelated-donor allogeneic hematopoietic cell transplantation (URD-HCT), to estimate discordance between reported and adjudicated cause-specific death, and to identify factors contributing to inconsistency in cause-specific death determination. A consensus panel adjudicated cause-specific death in 1484 patients who died within 1 year after HCT, derived from 3532 acute leukemia or myelodysplasia patients after URD-HCT from 2000 to 2011 reported by 151 US transplant centers to the Center for International Blood and Marrow Transplant Research. Deaths were classified as disease-related or transplant-related. The panel agreed with >99% of deaths reported by centers as disease-related and 80% reported as transplant-related. Year of transplant (cohort effect) and disease status significantly influenced agreement between the panel and centers. Sensitivity analysis of deaths < 100 days post-transplant yielded the lowest agreement between the panel and centers for myelodysplastic syndrome patients. Standard predefined criteria for adjudicating cause-specific death led to consistent application to similar clinical scenarios and clearer delineation of cause-specific death categories. Other studies of competing events such as cancer-specific versus treatment-related mortality would benefit from our results. Our detailed algorithm should result in more consistent reporting of cause-specific death by centers.

Population-Based Analysis of Hematologic Malignancy Referrals to a Comprehensive Cancer Center, Referrals for Blood and Marrow Transplantation, and Participation in Clinical Trial, Survey, and Biospecimen Research by Race

Racial and ethnic disparities have been reported in clinical trial/research participation, utilization of autologous and allogeneic blood and marrow transplantation (BMT), and availability of allogeneic donors. We performed a population-based cohort study to investigate adult hematologic malignancy referrals to a US tertiary cancer center, utilization of BMT, and participation in clinical trial, survey, and biospecimen research by race. US Census Data and the New York State Public Access Cancer Epidemiology Database identified the racial distribution of the general population and new hematologic malignancy cases in the primary catchment area. From 2005 to 2011, 1106 patients aged 18 to 75 years were referred for BMT consultation; although the rate of BMT among hematologic malignancy referrals did not differ by race, the reasons for not receiving a BMT did. Participation in biospecimen research did not vary by race; however, African Americans and other minorities were significantly less likely to participate in survey research than European Americans. Although rates of hematologic malignancy referrals and use of BMT for minorities appear to be low (<10%), they closely reflect the race distribution of all hematologic malignancy cases and the western New York population. African Americans are equally likely as other races to participate in biospecimen banking, but further study is needed to understand reasons for lower participation in survey research.

Abstract 5079: Adjudicating complex phenotypes for use in GWAS: A study of transplant-related mortality (TRM) after unrelated donor hematopoietic cell transplantation (URD-HCT)

As a first step in a 2-phase GWAS of TRM in patients with acute lymphoblastic leukemia (ALL), acute myelogenous leukemia (AML) and myelodysplastic syndrome (MDS) after URD-HCT, a consensus panel (CP), composed of BMT physicians and epidemiologists, reviewed all cause-specific deaths (CSDs) reported by 151 US transplant centers (TC) from 2000-11. Agreement measures, statistics and models were used to compared CP and TC CSD and the factors impacting the determination of CSDs.

Less affected by prevalence and marginal probabilities than Cohen's K, Gwet's Agreement Coefficient (AC1) measured the agreement between TC and CP CSD and the 95% confidence intervals were generated by bootstrapping the conditional distributions of the CSDs. For each CSD (disease, graft versus host (GvHD), infection, organ failure, other) we determined the proportion of agreement (PA) between the TC and CP and the Bias Index (BI, the proportion of cases the CP moved into or out of a CSD category). Logistic and log-linear models identified factors significantly associated with TC/CP odds of agreement and dependencies between covariates and TC/CP CSD, respectively. The discovery cohort (c1) includes 2609 10/10 HLA matched URD-HCT patients from 2000-8, reported to the Center for International Blood and Marrow Transplant Research (CIBMTR) by TCs. The validation cohort (c2) includes 920 10/10 or 8/8 HLA matched URD-HCT patients from 2000-11. The CP adjudicated CSDs in c1 using in-person meetings and teleconferences over 1 year; c2 cases were reviewed during a 2-day in-person meeting.

A total of 1116 (c1) and 388 patients (c2) died ≤1-yr post-URD-HCT. External and internal validity showed &gt;96% agreement. The AC1 statistic was .751 (.726, .801) and .658 (.567, .682), for c1 and c2 respectively. The PA for GvHD was 12% lower in c2 than c1 but the proportion of GvHD cases was higher in c2; these same differences were also seen for organ failure CSD. BI showed the rate of movement between CSDs was almost identical in both cohorts. In c1, TC and CP were &gt;2 fold less likely to agree on CSD for both ALL and MDS (p&lt;.05) when URD-HCT was in the early 2000s. The log-linear models also showed c1 cohort effects, as well as dependencies in both cohorts between age and TC CSD and CP CSD and disease status (early/advanced).

The cohort effect and age dependencies with TC CSD in c1 were not present when a systematic review of cases by the CP was performed. In c2 the TC CSD did not show evidence of a cohort effect; however a greater understanding of the lower AC1 in c2 vs. c1 was gained through use of PA. In both cohorts the BI and log-linear models show consistency in CSDs as determined by the CP. Our work illustrates that CPs are a worthwhile part of genomic studies of complex multi-factorial phenotypes, and the use of agreement statistics and dependency models is imperative to monitor CP phenotype reliability and understand data structure for subsequent analyses.

Citation Format: Lara Sucheston-Campbell, Theresa Hahn, Leah Preus, Kenan Onel, Xiaochun Zhu, Song Liu, Li Yan, Alyssa Clay, David Tritchler, Marcelo Pasquini, Philip McCarthy. Adjudicating complex phenotypes for use in GWAS: A study of transplant-related mortality (TRM) after unrelated donor hematopoietic cell transplantation (URD-HCT). [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5079. doi:10.1158/1538-7445.AM2014-5079

Differential development of cholinergic-like neurons in the superior olive: a light microscopic study

To better understand the development of cholinergic-like neurons within the superior olivary complex, we investigated the onset and distribution of two well-known markers of cholinergic-like neurons in hamsters: choline acetyltransferase (ChAT) and acetylcholinesterase (AChE). From embryonic day (E) 14 through postnatal day (P) 0, olivary cells immunopositive for ChAT were restricted to the rostral periolivary (RPO) area. Between P0 and P3, ChAT-positive cells are found in progressively more caudal and ventral periolivary locations. Although rostral and ventral periolivary cells exhibited an early onset of ChAT expression, stable numbers were not reached until P4. In contrast, ChAT expression within the lateral superior olive (LSO) is not visible until after P0 and higher numbers of ChAT-positive cells are obtained by P5. The AChE expression lags several days but follows roughly the same pattern of onset as for ChAT. Additionally in rostral and ventral periolivary regions as well as in the LSO, there were fewer AChE-labeled cells than ChAT-labeled cells. The observed temporal relationships in cholinergic-like expression within olivary cells suggest that different cholinergic-like populations may be defined on the basis of the onset of neurotransmitter-related enzymes: RPO cells are first, cells in ventral periolivary regions are second, and cells associated with the LSO are last. The differences observed in the onset of ChAT and AChE expression may reflect differences in the timing of target innervation as well as differences in synaptogenesis.

Electrophysiological-anatomic correlates of ATP-triggered vagal reflex in the dog. IV. Role of LV vagal afferents

The negative chronotropic action and the time to peak effect (t(p)) of ATP and its related analogs [2-methylthio-ATP (2-MeSATP), alpha,beta-methylene-ATP (alpha,beta-mATP), and beta,gamma-methylene-ATP (beta,gamma-mATP)] as well as ADP, AMP, and adenosine were determined in anesthetized dogs. Intra-right atrium (RA) and intra-left main coronary artery (LM) ATP markedly suppressed sinus node automaticity. ATP induced a much greater response when administered into the LM than into the RA. The t(p) of ATP administered at the former site was much shorter than that at the latter site. Intra-LM adenosine had either no effect or a relatively very small effect, and its t(p) was significantly longer than that of intra-LM ATP. Bilateral cervical vagotomy either abolished or markedly attenuated the effect of intra-RA and intra-LM ATP; under these conditions, the actions of ATP and adenosine and their t(p) values became similar. The structure-function cascade of intra-LM ATP and its analogs was alpha,beta-mATP > 2-MeSATP > ATP > or = beta,gamma-mATP > ADP >> AMP = 0. The P2X-purinoceptor antagonist pyridoxal-phosphate-6-azophenyl-2',4'-disulfonic acid markedly attenuated the negative chronotropic action of all purine nucleotides. It was concluded that 1) ATP triggers a cardiocardiac vagal depressor reflex by stimulating vagal afferent nerve terminals in the LV myocardium and 2) this action is mediated by P2X-purinoceptors.

The training of visual acuity in myopia

Seventeen myopes were trained with a computerized optometer to increase their far-point visual acuity from up to 20/800 to 20/25 for limited durations under conditions where "squinting" and pupil size were controlled. No associated changes in refraction were found. The results are best explained by the formation of an artificial contact lens resulting from tear-film changes. Measuring contrast sensitivity across a range of spatial frequencies is suggested to investigate the possibility that a learned perceptual process may also be involved.

The effect of quadruple chemotherapy on the peripheral blood lymphocyte populations in Hodgkin's disease

1 Quadruple chemotherapy with cytotoxic drugs in advanced (Stage IIIB) Hodgkin's disease causes a fall in the blood lymphocyte count with recovery 1 month after stopping treatment. 2 No selective effect on the T or B lymphocyte populations was shown.