Citations

Abstract Integrative genomics has the potential to uncover relevant loci, as clinical outcome and response to chemotherapies are most likely not due to a single gene (or data type) but rather a complex relationship involving genetic variation, mRNA, DNA methylation, and copy number variation. In addition to this complexity, many complex phenotypes are thought to be controlled by the interplay of multiple genes within the same molecular pathway or gene set (GS). To address these two challenges, we propose an integrative gene set analysis approach and apply this strategy to a cisplatin (CDDP) pharmacogenomics study involving lymphoblastoid cell lines for which genome-wide SNP and mRNA expression data was collected. Application of the integrative GS analysis implicated the role of the RNA binding and cytoskeletal part GSs. The genes LMNB1 and CENPF, within the cytoskeletal part GS, were functionally validated with siRNA knockdown experiments, where the knockdown of LMNB1 and CENPF resulted in CDDP resistance in multiple cancer cell lines. This study demonstrates the utility of an integrative GS analysis strategy for detecting novel genes associated with response to cancer therapies, moving closer to tailored therapy decisions for cancer patients.

BACKGROUNDHuman epidermal growth factor receptor 2 (HER2) is a therapeutic target in patients with esophageal adenocarcinoma (EAC), with gene amplification used as a selection criterion for treatment, although to the authors' knowledge the concordance between amplification and HER2 protein expression remains undefined in EAC. Furthermore, the association between HER2 and its interacting partner, human epidermal growth factor receptor 3 (HER3), is unknown yet appears to be of potential therapeutic relevance.METHODSPatients with untreated EACs (N = 673) were analyzed for HER2 amplification and polysomy 17 by fluorescence in situ hybridization in parallel with immunohistochemistry (IHC) (IHC scores of 0‐1+, 2+, and 3+). Amplification was defined as HER2/CEP17 ≥ 2. HER3 expression by IHC was analyzed in randomly selected cases (n = 224). IHC and fluorescence in situ hybridization results were compared using least squares linear regression.RESULTSOverall, 17% of the EACs (116 of 673 EACs) were HER2‐amplified with an amplification frequency that was highest among IHC3+ cases (89%) and declined among IHC2+ cases (13%) and IHC0 to IHC1+ cases (4%). Among HER2‐amplified cases, the level of amplification increased linearly with HER2 membranous expression (HER2/CEP17 ratio: 7.9 in IHC3+ and 5.5 in IHC2+ vs 2.8 in IHC0 to IHC1+ [P < .0001]), with 14% of amplified tumors demonstrating absent/faint expression (IHC0 to IHC1+). Polysomy 17 was not found to be associated with HER2 expression. Cytoplasmic HER3 expression was detected in 87% of tumors (195 of 224 tumors) and was found to be significantly associated with better differentiation (P < .0001). Stepwise increases in HER3 expression were associated with higher HER2 expression levels (P = .0019).CONCLUSIONSLevels of HER2 protein expression and amplification were found to be linearly associated and highly concordant. Among amplified tumors with absent/faint expression, the level of amplification was low. Frequent expression of HER3 suggests its relevance as a therapeutic target, and its significant association with HER2 supports ongoing efforts to inhibit HER2/HER3 in patients with EAC. Cancer 2014;120:415–424. © 2013 American Cancer Society.

AbstractBackgroundBotulinum toxin A (BTX) confers flaccid paralysis and pain modulation when injected into a muscle. We hypothesized that long‐term paralysis of the abdominal wall musculature (i.e., chemical component paralysis, CCP) would benefit incisional hernia repair (IHR) by decreasing postoperative pain, the use of opioid analgesia, and thus opioid‐related side effects.MethodsAdult patients who underwent elective IHR with preoperative CCP (n = 22) were compared to concurrent matched controls (n = 66, 1:3 ratio) based on age (±5 years), sex, body mass index (±5 kg/m2), history of hernia recurrence (0 vs. ≥1), and type of repair (open vs. laparoscopic). BTX was injected under ultrasonographic guidance into the transversus abdominis and internal and external oblique muscles at three sites bilaterally (300 units total).ResultsPatients who underwent IHR with CCP used significantly less opioid analgesia (mean ± SD morphine equivalents) when compared to controls on hospital days (HDs) 2 and 5: HD2, 48 ± 27 versus 87 ± 41; HD5, 17 ± 16 versus 48 ± 45. Likewise, CCP patients reported significantly less pain (visual analogue scale 1–10) when compared to controls on HD2 (5.2 ± 1.5 vs. 6.8 ± 2) and HD4 (3.6 ± 1.2 vs. 5.2 ± 1.9): all p < 0.007 (Bonferroni adjusted). There was no difference in postoperative complications (surgical site, 9 vs. 14 %), opioid‐related adverse events (ileus 5 vs. 5 %), hospital stay (4 ± 3 vs. 3 ± 2 days), or hernia recurrence (18 months mean follow‐up: 9 vs. 9 %).ConclusionsDespite similar multimodality treatment of postoperative pain after IHR, patients who underwent CCP required significantly less opioid analgesia and reported less pain.

Abstract Background: Both shorter and longer telomeres in peripheral blood leukocyte (PBL) DNA have been associated with cancer risk. However, associations remain inconsistent across studies of the same cancer type. This study compares DNA preparation methods to determine telomere length from patients with colorectal cancer. Methods: We examined PBL relative telomere length (RTL) measured by quantitative PCR (qPCR) in 1,033 patients with colorectal cancer and 2,952 healthy controls. DNA was extracted with phenol/chloroform, PureGene, or QIAamp. Results: We observed differences in RTL depending on DNA extraction method (P &lt; 0.001). Phenol/chloroform-extracted DNA had a mean RTL (T/S ratio) of 0.78 (range 0.01–6.54) compared with PureGene-extracted DNA (mean RTL of 0.75; range 0.00–12.33). DNA extracted by QIAamp yielded a mean RTL of 0.38 (range 0.02–3.69). We subsequently compared RTL measured by qPCR from an independent set of 20 colorectal cancer cases and 24 normal controls in PBL DNA extracted by each of the three extraction methods. The range of RTL measured by qPCR from QIAamp-extracted DNA (0.17–0.58) was less than from either PureGene or phenol/chloroform (ranges, 0.04–2.67 and 0.32–2.81, respectively). Conclusions: RTL measured by qPCR from QIAamp-extracted DNA was less than from either PureGene or phenol/chloroform (P &lt; 0.001). Impact: Differences in DNA extraction method may contribute to the discrepancies between studies seeking to find an association between the risk of cancer or other diseases and RTL. Cancer Epidemiol Biomarkers Prev; 22(11); 2047–54. ©2013 AACR.

Abstract Purpose: This study investigated the association between tumor MYC protein expression and disease-free survival (DFS) of patients randomized to receive chemotherapy alone (Arm A) or chemotherapy with sequential (Arm B) or concurrent trastuzumab (Arm C) in the N9831 (Alliance) adjuvant HER2+ trastuzumab breast cancer trial. Experimental Design: This analysis included 1,736 patients randomized to Arms A, B, and C on N9831. Nuclear MYC protein expression was determined in tissue microarray sections containing three biopsies per patient or whole tissue sections using standard immunohistochemistry (clone 9E10). A tumor was considered positive for MYC protein overexpression (MYC+) if the nuclear 3+ staining percentage was more than 30%. Results: Five hundred and seventy-four (33%) tumors were MYC+. MYC+ was associated with hormone receptor positivity (χ2, P = 0.006), tumors 2 cm or more (χ2, P = 0.02), and a higher rate of nodal positivity (χ2, P &lt; 0.001). HRs for DFS (median follow-up: 6.1 years) for Arm C versus A were 0.52 (P = 0.006) and 0.65 (P = 0.006) for patients with MYC+ and MYC− tumors, respectively (Pinteraction = 0.40). For Arm B versus A, HRs for patients with MYC+ and MYC− tumors were 0.79 (P = 0.21) and 0.74 (P = 0.04), respectively (Pinteraction = 0.71). For Arm C versus B, HRs for patients with MYC+ and MYC− tumors were 0.56 (P = 0.02) and 0.89 (P = 0.49), respectively (Pinteraction = 0.17). Conclusions: Our data do not support an impact of tumor MYC protein expression on differential benefit from adjuvant trastuzumab. Clin Cancer Res; 19(20); 5798–807. ©2013 AACR.

Objective Genome-wide association studies have identified a large number of single nucleotide polymorphisms (SNPs) associated with a wide array of cancer sites. Several of these variants demonstrate associations with multiple cancers, suggesting pleiotropic effects and shared biological mechanisms across some cancers. We hypothesised that SNPs previously associated with other cancers may additionally be associated with colorectal cancer. In a large-scale study, we examined 171 SNPs previously associated with 18 different cancers for their associations with colorectal cancer. Design We examined 13 338 colorectal cancer cases and 40 967 controls from three consortia: Population Architecture using Genomics and Epidemiology (PAGE), Genetic Epidemiology of Colorectal Cancer (GECCO), and the Colon Cancer Family Registry (CCFR). Study-specific logistic regression results, adjusted for age, sex, principal components of genetic ancestry, and/or study specific factors (as relevant) were combined using fixed-effect meta-analyses to evaluate the association between each SNP and colorectal cancer risk. A Bonferroni-corrected p value of 2.92×10 −4 was used to determine statistical significance of the associations. Results Two correlated SNPs—rs10090154 and rs4242382—in Region 1 of chromosome 8q24, a prostate cancer susceptibility region, demonstrated statistically significant associations with colorectal cancer risk. The most significant association was observed with rs4242382 (meta-analysis OR=1.12; 95% CI 1.07 to 1.18; p=1.74×10 −5 ), which also demonstrated similar associations across racial/ethnic populations and anatomical sub-sites. Conclusions This is the first study to clearly demonstrate Region 1 of chromosome 8q24 as a susceptibility locus for colorectal cancer; thus, adding colorectal cancer to the list of cancer sites linked to this particular multicancer risk region at 8q24.

Abstract Background: The Colorectal Cancer Family Registry (Colon CFR) has served as an international resource for studies of the genetics and epidemiology of colorectal cancer (CRC) since 1997. It is the largest family-based resource in the world for the study of CRC and other cancers, such as endometrial cancer, that occur in CRC families. The Colon CFR has recruited participants via six institutions: Cancer Care Ontario, Fred Hutchinson Cancer Research Center, Mayo Clinic, University of Hawaii, University of Southern California Consortium, and University of Melbourne. Methods: CRC cases were recruited from both population-based cancer registries and family cancer clinics. Controls were recruited from population-based sources. Relatives were recruited via cases and controls. Participants were asked to: donate a blood sample; give permission to access any tumor tissue; complete a detailed personal and family history of cancer including degree of relationship, site of cancer and age of diagnosis; and complete a detailed baseline lifestyle questionnaire that was administered across all recruitment sites, which included items on established and suspected risk factors for colorectal cancer: personal characteristics including age, sex, height and weight, country of birth, ethnicity, race and religion; history of exercise, alcohol consumption and smoking; medication use including NSAIDs, cholesterol-lowering agents, diabetes medication and post- menopausal hormone use; history of colorectal cancer screening including fecal occult blood test, sigmoidoscopy, colonoscopy; personal history of surgery including polypectomy, other bowel surgery and hysterectomy; frequency of meat consumption and method of cooking; reproductive history (for women). Participants were also asked for detail information on the frequency of food consumption and portion size using a food frequency questionnaire. Follow-up of participants has been conducted every five years, by questionnaire, to update vital status, surgery, cancer screening, polypectomy, and personal and family history of cancer history. Participants have been characterized for major known predisposing CRC gene mutations and have undergone a genome-wide SNP testing and tested for known CRC SNPs. Results: The Colon CFR has enrolled 35,297 participants (11,635 affected with CRC, 3,629 affected with other cancers, and 20,033 unaffected) who have completed baseline questionnaires. We have 5-year follow-up data on 24,692 participants (6,329 affected with CRC, 2,261 affected with other cancers, and 16,102 unaffected) and 10-year follow-up data on 10,467 (3,654 affected with CRC, 1,182 affected with other cancers, and 5,631 unaffected). We have GWAS data on 3,830 participants, candidate SNP data on 18,000 participants, and mismatch repair gene mutation data on 2,697 participants (and observed 1,697 carriers with a deleterious mutation). Conclusion: This largest and best characterized CRC cohort in the world will facilitate post-GWAS research to provide insight into the role of environmental factors, and how they interact with genetic factors on CRC risk. Researchers are encouraged by the National Cancer Institute (USA) and the Colon CFR investigators to apply for access to this unique resource of data and biospecimens for collaborative research. Citation Format: Aung Ko Win, Daniel D. Buchanan, Noralane M. Lindor, Robert W. Haile, Polly A. Newcomb, Loic Le Marchand, Steven Gallinger, Hopper L. John, Casey Graham, Mark A. Jenkins. The Colon Cancer Family Registry: A major resource for post-GWAS gene-environment studies. [abstract]. In: Proceedings of the AACR Special Conference on Post-GWAS Horizons in Molecular Epidemiology: Digging Deeper into the Environment; 2012 Nov 11-14; Hollywood, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2012;21(11 Suppl):Abstract nr 43.

AbstractHigh stress is a prevalent problem in the worksite. To reduce stress, improve productivity, reduce absenteeism, and lower healthcare costs, many companies offer exercise classes or stress management programmes. Although physical activity is an important component of stress management, few worksites have integrated physical activity into their comprehensive stress reduction programmes. The purpose of this single‐arm pilot project was to examine the potential effectiveness of an integrated exercise (studio cycling) and cognitive–behavioural stress management programme. Eighty‐four adults, 75% female, mostly aged 40+ years, participated in an integrated 12‐week cycling studio and cognitive–behavioural stress management programme. Participants experienced a significant and clinically meaningful reduction on the Perceived Stress Scale (p < 0.01), rating of current stress level and confidence to manage stress at the programme's end and at a 1‐month follow‐up. Participants also reported having significantly improved overall health, improved nutritional habits, higher physical activity level, greater confidence in their ability to follow a healthy diet, higher spiritual well‐being, improved sleep, receiving more support for maintaining healthy living and improved quality of life at the completion of the 12‐week programme and 1‐month follow‐up. These findings provide further support for an integrated exercise and stress management programme. Copyright © 2013 John Wiley & Sons, Ltd.

BACKGROUNDPatients diagnosed with primary sclerosing cholangitis (PSC) and dominant strictures often undergo endoscopic retrograde cholangiopancreatography with brush cytology to exclude or confirm the development of malignancy. Equivocal (atypical or suspicious) routine cytologic results may confound patient management decisions, especially in the absence of a mass on imaging. The objective of the current study was to identify independent predictors of malignancy in patients with PSC with an equivocal cytology diagnosis.METHODSPatients with PSC underwent brush cytology for routine cytology and fluorescence in situ hybridization (FISH) during endoscopy as per standard care. FISH slides were classified as polysomy if at least 5 cells displayed a gain of ≥ 2 probes. A retrospective search identified 102 patients without a mass lesion noted on initial imaging studies, an equivocal routine cytology, and ≥ 2 years of follow‐up.RESULTSOf 102 patients, 30 (29%) with an equivocal cytology result developed cancer within 2 years. Serum carbohydrate antigen 19‐9 (CA 19‐9) levels ≥ 129 U/mL (hazard ratio [HR] 3.19; P = .001) and polysomy (HR 8.70; P < .001) were each found to be predictive of cancer. Of 10 patients who had elevated CA 19‐9 levels and polysomy, all went on to develop cancer (9 within 2 years). Although only 10 patients were included in this subset, the combination of elevated CA 19‐9 and polysomy was found to be predictive of cancer (HR 10.92; P < .001).CONCLUSIONSPolysomy by FISH identified those patients most likely to have or develop malignancy in the challenging clinical scenario of PSC with no mass at baseline and equivocal cytology. The combination of an elevated serum CA 19‐9 level with polysomy is highly suspicious for the presence of malignancy. Cancer (Cancer Cytopathol) 2013;121:708–717. © 2013 American Cancer Society.