Gene-based GWAS analysis for consecutive studies of GEFOS

By integrating the multilevel biological evidence and bioinformatics analyses, the present study represents a systemic endeavor to identify BMD-associated genes and their roles in skeletal metabolism.

INTRODUCTION

Single-nucleotide polymorphism (SNP)-based genome-wide association studies (GWASs) have already identified about 100 loci associated with bone mineral density (BMD), but these loci only explain a small proportion of heritability to osteoporosis risk. In the present study, we performed a gene-based analysis of the largest GWASs in the bone field to identify additional BMD-associated genes.

METHODS

BMD-associated genes were identified by combining the summary statistic P values of SNPs across individual genes in the two consecutive meta-analyses of GWASs from the Genetic Factors for Osteoporosis (GEFOS) studies. The potential functionality of these genes to bone was partially assessed by differential gene expression analysis. Additionally, the consistency of the identification of potential bone mineral density (BMD)-associated variants were evaluated by estimating the correlation of the P values of the same single-nucleotide polymorphisms (SNPs)/genes between the two consecutive Genetic Factors for Osteoporosis Studies (GEFOS) with largely overlapping samples.

RESULTS

Compared to the SNP-based analysis, the gene-based strategy identified additional BMD-associated genes with genome-wide significance and increased their mutual replication between the two GEFOS datasets. Among these BMD-associated genes, three novel genes (UBTF, AAAS, and C11orf58) were partially validated at the gene expression level. The correlation analysis presented a moderately high between-study consistency of potential BMD-associated variants.

CONCLUSIONS

Gene-based analysis as a supplementary strategy to SNP-based genome-wide association studies, when applied here, is shown that it helped identify some novel BMD-associated genes. In addition to its empirically increased statistical power, gene-based analysis also provides a higher testing stability for identification of BMD genes.

Immediate prophylactic vs endoscopic or symptomatic-driven azathioprine treatment to prevent surgical recurrence after intestinal resection for Crohn's disease

AIM

Azathioprine can prevent postoperative recurrences in Crohn's disease. We compared the efficacy of azathioprine in preventing surgical recurrence to explore whether immediate prophylaxis after surgery is better than azathioprine started after endoscopic or clinical recurrence.

METHOD

Data of patients with intestinal resection and ileocolic anastomosis for Crohn's disease between 2006 and 2015 were retrieved from a prospectively maintained database. Patients were grouped according to the strategies of postoperative therapy with azathioprine. Univariate and multivariate proportional hazard Cox regression analyses were conducted to identify independent predictive factors for surgical recurrence.

RESULTS

Only age equal to or less than 16 years at diagnosis was an independent risk factor for surgical recurrence in all 166 patients (P = 0.005). In patients with high risk of recurrence (27 in the symptom-driven group, 39 in the endoscopy-driven group and 69 in the immediate prophylaxis group), both immediate and endoscopy-driven azathioprine delayed and reduced surgical recurrence compared with symptom-driven azathioprine (P = 0.035, 0.019). Their efficacy in reducing surgical recurrence was confirmed by Cox regression analyses (hazard ratio 0.465, P = 0.045; hazard ratio 0.352, P = 0.028). Surgical recurrence was similar between the immediate and endoscopy-driven groups. In addition, age ≤ 16 at diagnosis was still an independent risk factor for surgical recurrence in this subgroup.

CONCLUSIONS

In patients with high risk of recurrence, both immediate prophylactic azathioprine after surgery and azathioprine started after endoscopic recurrence can delay and reduce surgical recurrence compared with azathioprine started after clinical recurrence. In addition, azathioprine started immediately after surgery was not superior to azathioprine started after discovery of endoscopic recurrence.

Flavin monooxygenase 3, the host hepatic enzyme in the metaorganismal trimethylamine N-oxide-generating pathway, modulates platelet responsiveness and thrombosis risk

Essentials Microbe-dependent production of trimethylamine N-oxide (TMAO) contributes to thrombosis risk. The impact of host flavin monooxygenase 3 (FMO3) modulation on platelet function is unknown. Genetic manipulation of FMO3 in mice alters systemic TMAO levels and thrombosis potential. Genetic manipulation of FMO3 is associated with alteration of gut microbial community structure.

SUMMARY

Background Gut microbes play a critical role in the production of trimethylamine N-oxide (TMAO), an atherogenic metabolite that impacts platelet responsiveness and thrombosis potential. Involving both microbe and host enzymatic machinery, TMAO generation utilizes a metaorganismal pathway, beginning with ingestion of trimethylamine (TMA)-containing dietary nutrients such as choline, phosphatidylcholine and carnitine, which are abundant in a Western diet. Gut microbial TMA lyases use these nutrients as substrates to produce TMA, which upon delivery to the liver via the portal circulation, is converted into TMAO by host hepatic flavin monooxygenases (FMOs). Gut microbial production of TMA is rate limiting in the metaorganismal TMAO pathway because hepatic FMO activity is typically in excess. Objectives FMO3 is the major FMO responsible for host generation of TMAO; however, a role for FMO3 in altering platelet responsiveness and thrombosis potential in vivo has not yet been explored. Methods The impact of FMO3 suppression (antisense oligonucleotide-targeting) and overexpression (as transgene) on plasma TMAO levels, platelet responsiveness and thrombosis potential was examined using a murine FeCl3 -induced carotid artery injury model. Cecal microbial composition was examined using 16S analyses. Results Modulation of FMO3 directly impacts systemic TMAO levels, platelet responsiveness and rate of thrombus formation in vivo. Microbial composition analyses reveal taxa whose proportions are associated with both plasma TMAO levels and in vivo thrombosis potential. Conclusions The present studies demonstrate that host hepatic FMO3, the terminal step in the metaorganismal TMAO pathway, participates in diet-dependent and gut microbiota-dependent changes in both platelet responsiveness and thrombosis potential in vivo.

Preoperative breast MRI and mortality in older women with breast cancer

PURPOSE

The survival benefit from detecting additional breast cancers by preoperative magnetic resonance imaging (MRI) continues to be controversial.

METHODS

We followed a cohort of 4454 women diagnosed with non-metastatic breast cancer (stage I-III) from 2/2005-6/2010 in five registries of the breast cancer surveillance consortium (BCSC). BCSC clinical and registry data were linked to Medicare claims and enrollment data. We estimated the cumulative probability of breast cancer-specific and all-cause mortality. We tested the association of preoperative MRI with all-cause mortality using a Cox proportional hazards model.

RESULTS

917 (20.6%) women underwent preoperative MRI. No significant difference in the cumulative probability of breast cancer-specific mortality was found. We observed no significant difference in the hazard of all-cause mortality during the follow-up period after adjusting for sociodemographic and clinical factors among women with MRI (HR 0.90; 95% CI 0.72-1.12) compared to those without MRI.

CONCLUSION

Our findings of no breast cancer-specific or all-cause mortality benefit supplement prior results that indicate a lack of improvement in surgical outcomes associated with use of preoperative MRI. In combination with other reports, the results of this analysis highlight the importance of exploring the benefit of preoperative MRI in patient-reported outcomes such as women's decision quality and confidence levels with decisions involving treatment choices.

Breast Density and Risk of Invasive Breast Cancer among Older Women Undergoing Mammography: The Breast Cancer Surveillance Consortium Cohort Study

This study examined whether breast density is associated with risk of breast cancer in women age ≥65 years undergoing screening mammography in community practice. Methods: We used prospective cohort data between 1996 and 2012 from the Breast Cancer Surveillance Consortium (BCSC). We calculated separate cumulative incidence models for breast cancer incidence according to Breast Imaging Reporting and Data System (BI-RADS) breast density for women ages 65–74 and ages ≥75. Multivariable Cox proportional hazards regression models were fitted to determine the risk of invasive breast cancer adjusted for BCSC registry, race/ethnicity, BMI, hormone therapy use and benign breast disease. Results: Among the 403,268 women included in the study, approximately 40% were ages ≥75. The annual incidence rate of invasive breast cancer increased with increasing breast density among women ages 65–74 [BI- RADS fatty breasts: 2.2% (95% CI, 2.1%–2.4%) vs. heterogeneously or extremely dense breasts: 4.7% (95% CI, 4.6%–4.9%)] and women ages 75+ [BI-RADS fatty breasts: 2.3% (95% CI, 2.1%–2.5%) vs. heterogeneously or extremely dense: 4.3% (95% CI, 4.1%–4.5%)]. Women with BI-RADS fatty breasts had a decreased risk of breast cancer among women ages 65–74 [HR: 0.66 (95% CI: 0.58%–0.78%) and women ages ≥75 [HR: 0.73 (95% CI: 0.62%–0.87%). Women with BI-RADS heterogeneously or extremely dense breasts were found to have increased risk of breast cancer among women ages 65–74 [HR: 1.39 (95% CI: 1.28%–1.51%)] and women ages ≥75 [HR: 1.23 (95% CI: 1.10%–1.37%)]. Conclusions: Older women with higher BI-RADS density had a significantly increased risk of breast cancer. These findings add further evidence that breast density continues to be associated with an increased risk of breast cancer, even among women age ≥75 years.

A combustion method to synthesize nanoporous graphene

In this paper, we introduce a combustion method which is rapid, low cost, mass-producing and environmentally friendly to produce nanoporous graphene. After loading a graphene oxide aerogel (GOA)/paper (GOP) on a preheated hot plate (as the heat source, with a temperature as low as 200 °C) under an ambient environment, in a few seconds, the GOA/GOP would self-combust and change into reduced graphene oxide (RGO) with nanopores mainly concentrated in the 0.4-2.0 nm range and a large specific surface area of 536 m2 g-1. Supercapacitors fabricated with the synthesized porous RGO (P-RGO) showed a high specific capacitance of 245 F g-1 at 0.1 A g-1, and a retention rate of about 96.9% after 12 000 cycle tests with respect to the initial specific capacitance with a scan rate of 10.0 A g-1. The production yield of this method was as high as 77.0%.

Abstract P3-04-09: Integrated analysis of genetic variations in Chinese breast cancer from a single institution

To investigate the characteristics of somatic mutation or copy number variations in Chinese breast cancer, tumor tissues from 105 patients diagnosed at age from 26 to 81 (median age 48) were assessed by next-generation sequencing technology using a customized panel, including 33 genes of putative tumor suppressors or oncogenes. At least one genetic alteration (including mutations, copy number variations and fusion genes) was observed in 99/105 (94%) samples. Similar to the previous report in TCGA dataset, TP53 (49%) and PIK3CA (43%) were the most frequently mutated genes, which occurred in a significant mutual exclusive manner (p<0.05). Three genes including MYC copy number amplification (35%), FGFR1 (19%) and GATA3 mutation (16%) were altered at the frequency of >10% in our dataset, in which the occurrence of MYC amplification was higher than the TCGA cohort (22%, p<0.05). Importantly, we identified four fusion genes of FGFR1 including one previously reported (TACC1-FGFR1) and three novel fusion ones (MIR1268A-FGFR1, LZTS1-AS1-FGFR1, and LINC01605-FGFR1). Unlike the high prevalence of CCND1 amplification (17%) and CDH1 mutations (13%) in TCGA dataset, genetic variations of CCND1 and CDH1 in our study occurred at a low frequency with 2% and 4%, respectively (p<0.05). In addition, we also identified three novel ESR1 mutations (ESR1 G74R, D230H and M250T) in the untreated patients with early breast cancer. Furthermore, nonnegative matrix factorization (NMF) clustering of genetic variations revealed five distinct molecular classes in our dataset. NMF class I was characterized by a high rate of HR+/ERBB2- tumors (80%) and genetic alterations of FGFR1 (100%). A gain of ERBB2 gene was observed in 93% of NMF class II along with TOP2A amplification in 57% of HR+/ERBB2+ tumors. NMF class III was characterized by a high rate of HR+/ERBB2- (95%) and GATA3 mutations (75%) without TP53 mutation. The characteristics of NMF class IV were the high rate of PIK3CA mutations (95%) and HR+/ERBB2- tumors (75%) along with low rate of TP53 mutations. More HR-/ERBB2- tumors (39%) were observed in NMF class V with a high rate of MYC amplification (82%) and TP53 mutation (89%). Further analysis in the TCGA cohort revealed the patients in NMF class V had the shorter survival time than other clusters. Collectively, we identified several novel genetic variations and generated a preliminary profile of somatic genetic aberrations that could classify Chinese breast cancer in this study, and may represent novel therapeutic targets for molecular subsets of breast cancer.

This study was supported in part by National Natural Science Foundation of China (8160111571) and Guangdong Natural Science Foundation (2016A030313768).

Citation Format: Liao N, Zhang G-C, Wang Y, Cao L, Li K, Ren C-Y, Wen L-Z, Shi Y, Zhu W, Chen X. Integrated analysis of genetic variations in Chinese breast cancer from a single institution [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-04-09.

Abstract P6-14-05: Phase 2 study evaluating the efficacy and safety of eribulin mesylate administered biweekly for patients with human epidermal growth factor receptor 2-negative metastatic breast cancer

Background: Eribulin mesylate, a microtubule inhibitor, is approved in the US for the treatment of patients (pts) with metastatic breast cancer (MBC) who have previously received at least 2 chemotherapeutic regimens for the treatment of metastatic disease, including an anthracycline and a taxane. The recommended dose is 1.4 mg/m2 (equivalent to 1.23 mg/m2 eribulin [expressed as free base]) on day (D) 1 and D8 of a 21-D cycle. However, this schedule can result in dose delays and reductions due to myelosuppression. A dosing regimen of eribulin (1.4 mg/m2) administered intravenously (IV) biweekly (Q2W; on D1 and D15) in 28-D cycles was evaluated with the intent of improving eribulin's safety profile without compromising efficacy.

Methods: Female pts with human epidermal growth factor receptor (HER)2-negative MBC, who had received 2-5 prior chemotherapy regimens and had ECOG PS ≤2 were enrolled in 12 sites in the US. Prophylactic granulocyte colony-stimulating factor (G-CSF) was not allowed. If neutropenia occurred, growth factors were used during eribulin treatment at the physician's discretion. Primary endpoints were objective response rate (ORR) and disease control rate (DCR). Secondary endpoints were progression-free survival (PFS), overall survival (OS), dose intensity (measured by feasibility rate), safety and tolerability.

Results: Median age of the 58 enrolled pts was 64 yrs (range: 38-85). The majority of pts (93%) had ECOG PS ≤1, and 12% of pts had triple-negative MBC. Number of prior chemotherapeutic regimens: 2 (17% of patients), 3 (24%), 4 (27%), and 5 (31%). 76% Of pts had visceral disease and 86% had previous taxane therapy. ORR (95% confidence interval [CI]) was 12% (5-24), DCR (CR+PR+SD) was 65% (95% CI: 51-77), and CBR (CR+PR+SD ≥23 weeks) was 30% (95% CI: 18-43) [n=57]. Median PFS (95% CI) was 3.6 mo (2.9-4.1). Median OS (95% CI) was 13.2 mo (10.6-not estimable). 6-Month and 12-month OS rates were 84% and 54%, respectively. Dose intensity measured by the feasibility rate (defined as the percentage of pts completing the first 2 and 4 cycles without a dose delay >5 days or dose reduction due to an adverse event [AE]) was 70% and 46%, respectively.

The most frequent AEs (all grades) were neutropenia (69%), fatigue (48%), alopecia (45%), and constipation (36%). 22% Of pts had grade (G) 1 alopecia and 22% of pts had G2 alopecia. 72% Of pts had G3/4 AEs: neutropenia, 57%, and peripheral neuropathy, 12%. G3 peripheral sensory neuropathy occurred in 9% of pts, with no G4 incidence. There were 2 deaths (1 sepsis, 1 acute respiratory failure), which were considered not related to treatment. 50% (29/58) Of all patients received at least 1 dose of growth factor and 70% (28/40) of patients with neutropenia received growth-factor support.

Conclusions: Tumor response rates and OS of this treatment schedule in a heavily pretreated patient population were similar compared to previously reported phase 3 studies of eribulin. The toxicities associated with biweekly eribulin were manageable.

Citation Format: Smith II J, Irwin A, Jensen L, Tedesco K, Misir S, Zhu W, Almonte A, He Y, Olivo M, O'Shaughnessy J. Phase 2 study evaluating the efficacy and safety of eribulin mesylate administered biweekly for patients with human epidermal growth factor receptor 2-negative metastatic breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P6-14-05.

Abstract P4-04-18: Estrogen receptor α-dependent transcriptional induction of selenium-binding protein 1 increases the sensitivity of tamoxifen treatment in breast cancer

Reduction of selenium-binding protein 1 (SELENBP1) has been frequently observed in various solid tumors, and associated with poor clinical prognosis, implicating SELENBP1 as a potential tumor suppressor. However, the molecular mechanism underlying the transcriptional regulation of SELENBP1 remains poorly understood. In this study, we first analyzed the relationship between SELENBP1 mRNA levels and clinical or pathological features of breast cancer in METABRIC datasets, and found that SELENBP1 mRNA levels were differentially expressed in PAM50 molecular subtypes with highest levels in Luminal A/B subtype and lowest levels in Basal-like/Claudin-low subtype, indicating that SELENBP1 might function as the downstream player of estrogen receptor α (ERα). Following the adjustment of clinicopathological characteristics including the menopausal status, ER/HR/ERBB2 status, TNM stage and histological grade, the Kaplan-Meier survival analysis surprisingly showed that patients with higher levels of SELENBP1 mRNA (n=43) had shorter survival time than those with moderate levels of SELENBP1 expression (n=102) in Luminal A subtype (Hazard Ratio 1.59; 95% CI 0.99-2.54; Logrank p=0.0367), although the patients with lower SELENBP1 levels were consistent the poor prognosis in Basal-like/Claudin-low subtype (Hazard Ratio 1.54; 95% CI 0.97-2.44; Logrank p=0.0356). To elucidate this controversy, we knocked down the expression of ERα in MCF-7 cells using shRNA targeting ERα, and found that knockdown of ERα resulted in the down-regulation of mRNA and protein expression of SELENBP1. In addition, SELENBP1 promoter-driven luciferase reporter assay reveled ERα regulated the expression of SELENBP1 at transcriptional level. Interestingly, we further found that the addition of 4-hydroxytamoxifen (4-OHT) led to a dramatic reduction of SELENBP1 protein expression in MCF-7 cells, while forced expression of SELENBP1 in MCF-7 cells significantly enhanced 4-OHT-mediated inhibition of anchor-independent cancer cell growth. Collectively, these results suggested that the transcriptional induction of SELENBP1 by ERα might function as a downstream tumor suppressor in breast cancer cells, but endocrine therapy led to the down-regulation of SELENBP1 expression due to the blocking of ERα signaling in the patients with Luminal subtype, which was likely to explain the observation of differential predictive value for SELENBP1 mRNA levels in the Luminal and Basal-like/Claudin-low subtypes. Further investigation in vitro and in vivo has been ongoing in our laboratory, and the results from which will help us better understand the clinical relevance for SELENBP1 as a promising therapeutic target in improving the efficacy of endocrine therapy.

This study was supported in part by National Natural Science Foundation of China (8160111571) and Guangdong Natural Science Foundation (2016A030313768).

Citation Format: Liao N, Wang Y, Zhang G, Cao L, Li K, Ren C-Y, Wen L-Z, Shi Y, Zhu W, Chen X. Estrogen receptor α-dependent transcriptional induction of selenium-binding protein 1 increases the sensitivity of tamoxifen treatment in breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-04-18.

Abstract P1-01-17: Characterization of novel ESR1 (c.749T>C; p.Met250Thr) mutation in enhancing cellular invasiveness of breast cancer

Emerging evidence has revealed that the mutations in estrogen receptor alpha (ERα) gene (ESR1) is frequently observed in ER+ metastatic breast cancer, and is associated with the aggressively invasive and metastatic phenotype in advanced breast cancer due to the resistance of endocrine therapy. In our previous study, we have identified three novel mutations of ESR1, including ESR1 G74R, D230H and M250T, in the untreated patients with early breast cancer. However, the functional roles for these novel mutations in the cellular biology of breast cancer remain to be elucidated. In this study, we described the molecular mechanism underlying potential roles for the novel mutation ESR1 p.Met250Thr (c.749T>C) in regulating the cellular invasiveness of breast cancer. Firstly, we found, as compared with wild-type (WT) HA-ESR1, forced expression of HA-ESR1 M250T enhanced the invasive capacity of breast cancer MCF-7 cells by using Transwell assay. Moreover, we found that the levels of miR-190 were significantly up-regulated in the MCF-7 (HA-ESR1 M250T) cells, and further verified that miR-190 played an important role in ESR1 M250T-mediated induction of cellular invasiveness by using specific shRNA to knock down miR-190 levels in MCF-7 (HA-ESR1 M250T) cells. Further bioinformatics analysis showed that there were several half Estrogen Response Elements (EREs) in the promoter region of Talin-2, as the host gene of miR-190. Talin-2-driven luciferase reporter assay indicated ESR1 M250T resulted in a higher increase in the luciferase activity than ESR1 WT. Chromatin-immunoprecipitation (ChIP) assay identified a higher binding ability with Talin-2 promoter for ESR1 M250T than ESR1 WT. Collectively, our mechanistic study revealed that the ESR1 M250T mutation, located in the DNA-binding domain, increased the invasive capacity of breast cancer cells via the transcriptional induction of Talin-2 and miR-190. The potential role for ESR1 M250T in affecting the efficacy of endocrine therapy has been under the investigation in our laboratory, and the result from which will help us better elucidate the clinical relevance for novel ESR1 mutations in affecting the sensitivity of endocrine therapy.

This study was supported in part by National Natural Science Foundation of China (8160111571) and Guangdong Natural Science Foundation (2016A030313768).

Citation Format: Liao N, Zhang G-C, Wang Y, Cao L, Li K, Ren C-Y, Wen L-Z, Shi Y, Zhu W, Chen X. Characterization of novel ESR1 (c.749T>C; p.Met250Thr) mutation in enhancing cellular invasiveness of breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-01-17.

Effects of nutritional support on short-term clinical outcomes and immune response in unresectable locally advanced oesophageal squamous cell carcinoma

This retrospective study investigated the efficiency of nutritional support in unresectable locally advanced oesophageal squamous cell carcinoma (LAOSCC) patients who received concurrent chemoradiotherapy (CCRT) based on 5-fluorouracil and cisplatin. In the routine care group, 63 patients served as historical controls and received nutrition support in a reactive manner. In addition, 57 patients in the nutritional support group received timely diet counselling, oral nutritional supplements, enteral nutrition and/or parenteral nutrition during CCRT. This support was based on scores from nutritional risk screening 2002 (NRS-2002) after June 2014. The nutritional support group had significant advantages over the routine care group with respect to the incidence of neutropenia, the objective response rate, the change in serum albumin and the lengths of hospital stay. In addition, the nutritional support group had significantly higher levels of IgG and IL-2, higher proportions of NK, CD3⁺ and CD4⁺ cells as well as a higher ratio of CD4⁺ /CD8⁺ cells than the routine care group (p < .05). In contrast, the nutritional support group had a significantly lower level of IL-6. In conclusion, the current nutritional care programme could bring benefits of improving treatment compliance, reducing toxicity and lengths of hospital stay and enhancing the immune response.