scholarly journals Characterization of alternative splicing events and prognostic signatures in breast cancer

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Pihua Han ◽  
Jingjun Zhu ◽  
Guang Feng ◽  
Zizhang Wang ◽  
Yanni Ding
Keyword(s):  
Breast Cancer ◽  
Alternative Splicing ◽  
Proportional Hazards ◽  
Pearson Correlation ◽  
Original Data ◽  
Cox Proportional Hazards ◽  
Prognostic Indicators ◽  
Splicing Factors ◽  
Rna Seq

Abstract Background Breast cancer (BRCA) is one of the most common cancers worldwide. Abnormal alternative splicing (AS) frequently observed in cancers. This study aims to demonstrate AS events and signatures that might serve as prognostic indicators for BRCA. Methods Original data for all seven types of splice events were obtained from TCGA SpliceSeq database. RNA-seq and clinical data of BRCA cohorts were downloaded from TCGA database. Survival-associated AS events in BRCA were analyzed by univariate COX proportional hazards regression model. Prognostic signatures were constructed for prognosis prediction in patients with BRCA based on survival-associated AS events. Pearson correlation analysis was performed to measure the correlation between the expression of splicing factors (SFs) and the percent spliced in (PSI) values of AS events. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted to demonstrate pathways in which survival-associated AS event is enriched. Results A total of 45,421 AS events in 21,232 genes were identified. Among them, 1121 AS events in 931 genes significantly correlated with survival for BRCA. The established AS prognostic signatures of seven types could accurately predict BRCA prognosis. The comprehensive AS signature could serve as independent prognostic factor for BRCA. A SF-AS regulatory network was therefore established based on the correlation between the expression levels of SFs and PSI values of AS events. Conclusions This study revealed survival-associated AS events and signatures that may help predict the survival outcomes of patients with BRCA. Additionally, the constructed SF-AS networks in BRCA can reveal the underlying regulatory mechanisms in BRCA.

Identification of Prognostic Alternative Splicing Signature in Gastric Cancer

2021 ◽  
Author(s):  
Zhiwu Wang ◽  
Qiong Wu ◽  
Yankun Liu ◽  
Jingwu Li
Keyword(s):  
Gastric Cancer ◽  
Alternative Splicing ◽  
Clinical Information ◽  
The Cancer Genome Atlas ◽  
Prognostic Indicators ◽  
Splicing Factors ◽  
Rna Seq ◽  
Oncogenic Pathways ◽  
Splicing Variants ◽  
Cancer Genome Atlas

Abstract Aberrant alternative splicing (AS) events serve as prognostic indicators in a large number of malignancies, whereas comprehensive analysis of prognostic AS in gastric cancer (GC) has not yet been understood. To identify prognostic AS events and clarify the function of the splicing variants in GC. RNA-Seq data, clinical information and percent spliced in (PSI) values were available in the cancer genome atlas (TCGA) and TCGA SpliceSeq data portal. A three-step regression method was conducted to screen prognostic AS events and construct multi-AS-based signatures. The associations between prognostic AS events and splicing factors were also investigated. We identified a total of 1318 survival related AS events in GC, Parent genes of which were implicated in numerous oncogenic pathways. The final prognostic signatures stratified by seven types of AS events or not stratified performed well in risk prediction for GC patients. Moreover, five signatures base on AA, AD, AT, ES and RI events function as independent prognostic indicators after multivariate adjustment of clinicalpathological variables. Splicing network also showed marked correlation between the expression of splicing factors and PSI value of AS events in GC patients. The AS derived signatures allow to predict GC prognosis and might serve as potential therapeutic target for GC.

scholarly journals Changes in Metabolic Syndrome Status and Breast Cancer Risk: A Nationwide Cohort Study

Cancers ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 1177
Author(s):  
In Young Choi ◽  
Sohyun Chun ◽  
Dong Wook Shin ◽  
Kyungdo Han ◽  
Keun Hye Jeon ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Metabolic Syndrome ◽  
Proportional Hazards ◽  
Screening Program ◽  
Cox Proportional Hazards ◽  
Cox Proportional Hazards Models ◽  
Hazard Ratios ◽  
Increased Risk ◽  
Health Screening Program ◽  
Design And Methods

Objective: To our knowledge, no studies have yet looked at how the risk of developing breast cancer (BC) varies with changes in metabolic syndrome (MetS) status. This study aimed to investigate the association between changes in MetS and subsequent BC occurrence. Research Design and Methods: We enrolled 930,055 postmenopausal women aged 40–74 years who participated in a biennial National Health Screening Program in 2009–2010 and 2011–2012. Participants were categorized into four groups according to change in MetS status during the two-year interval screening: sustained non-MetS, transition to MetS, transition to non-MetS, and sustained MetS. We calculated multivariable-adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs) for BC incidence using the Cox proportional hazards models. Results: At baseline, MetS was associated with a significantly increased risk of BC (aHR 1.11, 95% CI 1.06–1.17) and so were all of its components. The risk of BC increased as the number of the components increased (aHR 1.46, 95% CI 1.26–1.61 for women with all five components). Compared to the sustained non-MetS group, the aHR (95% CI) for BC was 1.11 (1.04–1.19) in the transition to MetS group, 1.05 (0.96–1.14) in the transition to non-MetS group, and 1.18 (1.12–1.25) in the sustained MetS group. Conclusions: Significantly increased BC risk was observed in the sustained MetS and transition to MetS groups. These findings are clinically meaningful in that efforts to recover from MetS may lead to reduced risk of BC.

scholarly journals Association between overall diet quality and postmenopausal breast cancer risk in five Finnish cohort studies

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Satu Männistö ◽  
Kennet Harald ◽  
Tommi Härkänen ◽  
Mirkka Maukonen ◽  
Johan G. Eriksson ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Diet Quality ◽  
Proportional Hazards ◽  
Postmenopausal Breast Cancer ◽  
Healthy Eating Index ◽  
Cox Proportional Hazards ◽  
Healthy Diet ◽  
Food Culture ◽  
Alternative Healthy Eating Index

AbstractThere is limited evidence for any dietary factor, except alcohol, in breast cancer (BC) risk. Therefore, studies on a whole diet, using diet quality indices, can broaden our insight. We examined associations of the Nordic Diet (mNDI), Mediterranean diet (mMEDI) and Alternative Healthy Eating Index (mAHEI) with postmenopausal BC risk. Five Finnish cohorts were combined including 6374 postmenopausal women with dietary information. In all, 8–9 dietary components were aggregated in each index, higher total score indicating higher adherence to a healthy diet. Cox proportional hazards regression was used to estimate the combined hazard ratio (HR) and 95% confidence interval (CI) for BC risk. During an average 10-year follow-up period, 274 incident postmenopausal BC cases were diagnosed. In multivariable models, the HR for highest vs. lowest quintile of index was 0.67 (95 %CI 0.48–1.01) for mNDI, 0.88 (0.59–1.30) for mMEDI and 0.89 (0.60–1.32) for mAHEI. In this combined dataset, a borderline preventive finding of high adherence to mNDI on postmenopausal BC risk was found. Of the indices, mNDI was more based on the local food culture than the others. Although a healthy diet has beneficially been related to several chronic diseases, the link with the etiology of postmenopausal BC does not seem to be that obvious.

A Motion of No Confidence: Leadership and Rebel Fragmentation

2020 ◽  
Vol 5 (4) ◽  
pp. 598-616 ◽  
Author(s):  
Austin C Doctor
Keyword(s):  
Civil War ◽  
Proportional Hazards ◽  
Original Data ◽  
Cox Proportional Hazards ◽  
Stage I ◽  
Logistic Regression Models ◽  
Structure And Agency ◽  
Rebel Groups ◽  
Cox Proportional Hazards Models ◽  
War Experiences

Abstract Why do rebel organizations splinter into competing factions during civil war? To explain this outcome, I leverage variation in rebel leadership. I argue that rebel leaders draw on their pre-war experiences—i.e., their military and political experiences—to manage their organizations during conflict. These experiences bear unique patterns of rebel management and, thus, corresponding risks of fragmentation. Empirical evidence comes from a two-stage research design and original data featuring over 200 rebel leaders from 1989 to 2014. In the first stage, I estimate the probability of group fragmentation with a series of logistic regression models. In the second stage, I use Cox proportional-hazards models to estimate leadership effects on the rate of group fragmentation. Results indicate that variation in rebel leadership corresponds with unique risks of fragmentation. In particular, the results suggest that leaders with real military experience are best equipped to maintain group cohesion. This study offers insight into the processes by which rebel groups splinter into armed factions. In addition, it makes an important contribution to the broader discussion on the roles of structure and agency in shaping the dynamics of civil war.

Impact of race and socioeconomic status on breast cancer outcomes within the AJCC staging system.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e18565-e18565
Author(s):  
Olga Kantor ◽  
Monica L. Wang ◽  
Kimberly Bertrand ◽  
Mariana Chavez-MacGregor ◽  
Rachel A. Freedman ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Socioeconomic Status ◽  
Proportional Hazards ◽  
Census Data ◽  
Tumor Biology ◽  
Staging System ◽  
Cox Proportional Hazards ◽  
Cancer Outcomes ◽  
Black Race ◽  
Breast Cancer Outcomes

e18565 Background: The persistent racial and socioeconomic status (SES) disparities in breast cancer outcomes are partially attributed to propensity towards more aggressive cancers or presentation at higher stages among these groups. Chronic stressors related to race and SES are another major mechanism underlying these inequities. This study aims to examine the effect of race and SES within the AJCC 8th-edition staging system, which incorporates anatomic extent of disease and tumor biology. Methods: The SEER breast cancer database linked with county-level census data was used to identify patients with invasive breast cancer from 2010-2015. The database includes a composite SES-index which was analyzed in quintiles. Cox proportional-hazards regression was used to estimate disease-specific survival (DSS). Results: 259,852 patients were included: 176,369 (67.9%) non-Hispanic white, 28,510 (11.0%) Black, 29,737 (11.4%) Hispanic, and 22,887 (8.8%) Asian. Black race, lower SES, public insurance, lower education, and increased poverty were associated with decreased DSS. Adjusted survival analysis for patient, SES, tumor, and treatment characteristics demonstrated that patients of black race had inferior DSS within each stage. Fully adjusted models also showed patients residing in lower SES counties had inferior DSS [Table]. Conclusions: Racial and SES disparities in breast cancer-specific mortality were evident across all stages of disease. Future efforts to improve breast cancer outcomes should systematically assess and address racial and socioeconomic factors as fundamental drivers of inequitable outcomes. Adjusted 5-year DSS Estimates, Stratified by Race and SES.[Table: see text]

scholarly journals Milk Consumption Decreases Risk for Breast Cancer in Korean Women under 50 Years of Age: Results from the Health Examinees Study

Nutrients ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 32 ◽  
Author(s):  
Woo-Kyoung Shin ◽  
Hwi-Won Lee ◽  
Aesun Shin ◽  
Jong-koo Lee ◽  
Daehee Kang
Keyword(s):  
Breast Cancer ◽  
Breast Cancer Risk ◽  
Cancer Risk ◽  
Proportional Hazards ◽  
Proportional Hazards Model ◽  
Epidemiologic Studies ◽  
Cox Proportional Hazards ◽  
Cox Proportional Hazards Model ◽  
Milk Consumption ◽  
Korean Women

Epidemiologic studies regarding breast cancer risk related to milk consumption remain controversial. The aim of this study was to evaluate the association between milk consumption and the risk for breast cancer. A total of 93,306 participants, aged 40–69 years, were included in the prospective cohort study in the Health Examinees-Gem (HEXA-G) study between 2004 and 2013. Dietary intake was assessed using a validated food frequency questionnaire. Information on cancer diagnosis in the eligible cohort was retrieved from the Korea Central Cancer Registry through 31 December 2014. The Cox proportional hazards model was used to estimate multivariate hazard ratios (HRs) and 95% confidence intervals (CIs). A total of 359 breast cancer cases were observed over a median follow-up period of 6.3 years. Milk consumption was not associated with decreased risk for breast cancer in the total population (p for trend = 0.0687). In women under 50 years of age, however, milk consumption was inversely associated with breast cancer risk. In the comparison between highest (≥1 serving/day) and lowest (<1 serving/week) intake categories of milk, the multivariate HR (95% CI) was 0.58 (0.35–0.97, p for trend = 0.0195)) among women under 50 years of age. In conclusion, our findings show that milk consumption in Korean women aged 50 or younger is associated with a decreased risk for breast cancer, when compared to those who never or rarely consumed milk. Further studies need to be conducted to assess this relationship and confirm these results.

Effect of Pregnancy on Overall Survival After the Diagnosis of Early-Stage Breast Cancer

2001 ◽  
Vol 19 (6) ◽  
pp. 1671-1675 ◽  
Author(s):  
Shari Gelber ◽  
Alan S. Coates ◽  
Aron Goldhirsch ◽  
Monica Castiglione-Gertsch ◽  
Gianluigi Marini ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Proportional Hazards ◽  
Comparison Group ◽  
Early Stage ◽  
Pregnant Patient ◽  
Subsequent Pregnancy ◽  
Cox Proportional Hazards ◽  
Early Stage Breast Cancer ◽  
Study Group ◽  
The Impact

PURPOSE: To evaluate the impact of subsequent pregnancy on the prognosis of patients with early breast cancer. PATIENTS AND METHODS: One hundred eight patients who became pregnant after diagnosis of early-stage breast cancer were identified in institutions participating in International Breast Cancer Study Group (IBCSG) studies. Fourteen had relapse of breast cancer before their first subsequent pregnancy. The remaining 94 patients (including eight who relapsed during pregnancy) formed the study group reported here. A comparison group of 188 was obtained by randomly selecting two patients, matched for nodal status, tumor size, age, and year of diagnosis from the IBCSG database, who were free of relapse for at least as long as the time between breast cancer diagnosis and completion of pregnancy for each pregnant patient. Survival comparison used Cox proportional hazards regression models. RESULTS: Overall 5- and 10-year survival percentages (± SE) measured from the diagnosis of early-stage breast cancer among the 94 study group patients were 92% ± 3% and 86% ± 4%, respectively. For the matched comparison group survival was 85% ± 3% at 5 years and 74% ± 4% at 10 years (risk ratio, 0.44; 95% confidence interval, 0.21 to 0.96; P = .04). CONCLUSION: Subsequent pregnancy does not adversely affect the prognosis of early-stage breast cancer. The superior survival seen in this and other controlled series may merely reflect a healthy patient selection bias, but is also consistent with an antitumor effect of the pregnancy.

scholarly journals Urinary Estrogen Metabolites and Long-Term Mortality Following Breast Cancer

2020 ◽  
Vol 4 (3) ◽  
Author(s):  
Tengteng Wang ◽  
Hazel B Nichols ◽  
Sarah J Nyante ◽  
Patrick T Bradshaw ◽  
Patricia G Moorman ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Confidence Intervals ◽  
Proportional Hazards ◽  
Statistical Tests ◽  
Breast Cancer Mortality ◽  
Cox Proportional Hazards ◽  
Urine Collection ◽  
Estrogen Metabolites ◽  
All Cause Mortality

Abstract Background Estrogen metabolite concentrations of 2-hydroxyestrone (2-OHE1) and 16-hydroxyestrone (16-OHE1) may be associated with breast carcinogenesis. However, no study has investigated their possible impact on mortality after breast cancer. Methods This population-based study was initiated in 1996–1997 with spot urine samples obtained shortly after diagnosis (mean = 96 days) from 683 women newly diagnosed with first primary breast cancer and 434 age-matched women without breast cancer. We measured urinary concentrations of 2-OHE1 and 16-OHE1 using an enzyme-linked immunoassay. Vital status was determined via the National Death Index (n = 244 deaths after a median of 17.7 years of follow-up). We used multivariable-adjusted Cox proportional hazards to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for the estrogen metabolites-mortality association. We evaluated effect modification using likelihood ratio tests. All statistical tests were two-sided. Results Urinary concentrations of the 2-OHE1 to 16-OHE1 ratio (&gt;median of 1.8 vs ≤median) were inversely associated with all-cause mortality (HR = 0.74, 95% CI = 0.56 to 0.98) among women with breast cancer. Reduced hazard was also observed for breast cancer mortality (HR = 0.73, 95% CI = 0.45 to 1.17) and cardiovascular diseases mortality (HR = 0.76, 95% CI = 0.47 to 1.23), although the 95% confidence intervals included the null. Similar findings were also observed for women without breast cancer. The association with all-cause mortality was more pronounced among breast cancer participants who began chemotherapy before urine collection (n = 118, HR = 0.42, 95% CI = 0.22 to 0.81) than among those who had not (n = 559, HR = 0.98, 95% CI = 0.72 to 1.34; Pinteraction = .008). Conclusions The urinary 2-OHE1 to 16-OHE1 ratio may be inversely associated with long-term all-cause mortality, which may depend on cancer treatment status at the time of urine collection.

Specific Adverse Events Predict Survival Benefit in Patients Treated With Tamoxifen or Aromatase Inhibitors: An International Tamoxifen Exemestane Adjuvant Multinational Trial Analysis

2013 ◽  
Vol 31 (18) ◽  
pp. 2257-2264 ◽  
Author(s):  
Duveken B.Y. Fontein ◽  
Caroline Seynaeve ◽  
Peyman Hadji ◽  
Elysée T.M. Hille ◽  
Willemien van de Water ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Adverse Events ◽  
Endocrine Therapy ◽  
Proportional Hazards ◽  
Disease Free Survival ◽  
Distant Metastases ◽  
Cox Proportional Hazards ◽  
Endocrine Treatment ◽  
Survival Outcomes ◽  
Cox Proportional Hazards Models

Purpose Specific adverse events (AEs) associated with endocrine therapy and related to depletion or blocking of circulating estrogens may be related to treatment efficacy. We investigated the relationship between survival outcomes and specific AEs including vasomotor symptoms (VMSs), musculoskeletal adverse events (MSAEs), and vulvovaginal symptoms (VVSs) in postmenopausal patients with breast cancer participating in the international Tamoxifen Exemestane Adjuvant Multinational (TEAM) trial. Patients and Methods Primary efficacy end points were disease-free survival (DFS), overall survival (OS), and distant metastases (DM). VMSs, MSAEs, and VVSs arising in the first year of endocrine treatment were considered. Patients who did not start or who discontinued their allocated therapy and/or had an event (recurrence/death) within 1 year after randomization were excluded. Landmark analyses and time-dependent multivariate Cox proportional hazards models assessed survival differences up to 5 years from the start of treatment. Results A total of 9,325 patients were included. Patients with specific AEs (v nonspecific or no AEs) had better DFS and OS (multivariate hazard ratio [HR] for DFS: VMSs, 0.731 [95% CI, 0.618 to 0.866]; MSAEs, 0.826 [95% CI, 0.694 to 0.982]; VVSs, 0.769 [95% CI, 0.585 to 1.01]; multivariate HR for OS: VMSs, 0.583 [95% CI, 0.424 to 0.803]; MSAEs, 0.811 [95% CI, 0.654 to 1.005]; VVSs, 0.570 [95% CI, 0.391 to 0.831]) and fewer DM (VMSs, 0.813 [95% CI, 0.664 to 0.996]; MSAEs, 0.749 [95% CI, 0.601 to 0.934]; VVSs, 0.687 [95% CI, 0.436 to 1.085]) than patients not reporting these symptoms. Increasing numbers of specific AEs were also associated with better survival outcomes. Outcomes were unrelated to treatment allocation. Conclusion Certain specific AEs are associated with superior survival outcomes and may therefore be useful in predicting treatment responses in patients with breast cancer treated with endocrine therapy.

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