A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers
MetadataShow full item record
AbstractWe analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and unique molecular features, clinically significant subtypes, and potential therapeutic targets. We found 61 somatic copy-number alterations (SCNAs) and 46 significantly mutated genes (SMGs). Eleven SCNAs and 11 SMGs had not been identified in previous TCGA studies of the individual tumor types. We found functionally significant estrogen receptor-regulated long non-coding RNAs (lncRNAs) and gene/lncRNA interaction networks. Pathway analysis identified subtypes with high leukocyte infiltration, raising potential implications for immunotherapy. Using 16 key molecular features, we identified five prognostic subtypes and developed a decision tree that classified patients into the subtypes based on just six features that are assessable in clinical laboratories. By performing molecular analyses of 2,579 TCGA gynecological (OV, UCEC, CESC, and UCS) and breast tumors, Berger et al. identify five prognostic subtypes using 16 key molecular features and propose a decision tree based on six clinically assessable features that classifies patients into the subtypes. Copyright 2018 Elsevier Inc.
SponsorsThis work was supported by the following NCI grants: U54 HG003273 , U54 HG003067 , U54 HG003079 , U24 CA143799 , U24 CA143835 , U24 CA143840 , U24 CA143843 , U24 CA143845 , U24 CA143848 , U24 CA143858 , U24 CA143866 , U24 CA143867 , U24 CA143882 , U24 CA143883 , U24 CA144025 , U24 CA210949 , U24 CA210950 , P30 CA016672 , P50 CA136393 .
The Cancer Genome Atlas
Identifier to cite or link to this itemhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85044909989&doi=10.1016%2fj.ccell.2018.03.014&partnerID=40&md5=1d2499b2d0ff55b804214c03e41f81c6; http://hdl.handle.net/10713/9810
- Analysis of the miRNA-mRNA-lncRNA network in human estrogen receptor-positive and estrogen receptor-negative breast cancer based on TCGA data.
- Authors: Xiao B, Zhang W, Chen L, Hang J, Wang L, Zhang R, Liao Y, Chen J, Ma Q, Sun Z, Li L
- Issue date: 2018 Jun 5
- Identification three LncRNA prognostic signature of ovarian cancer based on genome-wide copy number variation.
- Authors: Zheng M, Hu Y, Gou R, Nie X, Li X, Liu J, Lin B
- Issue date: 2020 Apr
- Integrative molecular profiling identifies a novel cluster of estrogen receptor-positive breast cancer in very young women.
- Authors: Park C, Yoon KA, Kim J, Park IH, Park SJ, Kim MK, Jang W, Cho SY, Park B, Kong SY, Lee ES
- Issue date: 2019 May
- Pan-Cancer Analyses Reveal Long Intergenic Non-Coding RNAs Relevant to Tumor Diagnosis, Subtyping and Prognosis.
- Authors: Ching T, Peplowska K, Huang S, Zhu X, Shen Y, Molnar J, Yu H, Tiirikainen M, Fogelgren B, Fan R, Garmire LX
- Issue date: 2016 May
- Systematic identification of lncRNA-based prognostic biomarkers for glioblastoma.
- Authors: Li M, Long S, Hu J, Wang Z, Geng C, Ou S
- Issue date: 2019 Nov 6
Showing items related by title, author, creator and subject.
Comparative proteogenomic analysis of right-sided colon cancer, left-sided colon cancer and rectal cancer reveals distinct mutational profilesImperial, R.; Ahmed, Z.; Toor, O.M. (BioMed Central Ltd., 2018)Right-sided colon cancer (RCC) has worse prognosis compared to left-sided colon cancer (LCC) and rectal cancer. The reason for this difference in outcomes is not well understood. We performed comparative somatic and proteomic analyses of RCC, LCC and rectal cancers to understand the unique molecular features of each tumor sub-types. Utilizing a novel in silico clonal evolution algorithm, we identified common tumor-initiating events involving APC, KRAS and TP53 genes in RCC, LCC and rectal cancers. However, the individual role-played by each event, their order in tumor development and selection of downstream somatic alterations were distinct in all three anatomical locations. Some similarities were noted between LCC and rectal cancer. Hotspot mutation analysis identified a nonsense mutation, APC R1450* specific to RCC. In addition, we discovered new significantly mutated genes at each tumor location, Further in silico proteomic analysis, developed by our group, found distinct central or hub proteins with unique interactomes among each location. Our study revealed significant differences between RCC, LCC and rectal cancers not only at somatic but also at proteomic level that may have therapeutic relevance in these highly complex and heterogeneous tumors. Copyright 2018 The Author(s).
Cancer-work management: Hourly and salaried wage women's experiences managing the cancer-work interface following new breast cancer diagnosis.Tracy, J Kathleen; Adetunji, Fiyinfolu; Al Kibria, Gulam M; Swanberg, Jennifer E (Public Library of Science, 2020-11-05)OBJECTIVE: The purpose of this paper is to report the baseline characteristics of EMPOWER participants-a group of newly diagnosed breast cancer survivors-and describe differences in hourly and salaried wage women's experiences regarding cancer and work management in the three months following breast cancer diagnosis. DESIGN AND SETTING: The EMployment and Potential Outcomes of Working through canceER (EMPOWER) project is a prospective longitudinal, mixed methods pilot study designed to evaluate how employment influences treatment decisions among women diagnosed with breast cancer. Participants were women diagnosed with new breast cancer and treated at one of two clinical sites of the University of Maryland Medical System. Women were enrolled in the study within three months of first breast cancer diagnosis. Study visits occurred every three months for one year. This paper reports data from for the baseline and three-month visit which had been completed by all enrollees. METHODS: Trained research personnel collected demographic information, medical history and health status, social history, employment data, cancer-related data, psychosocial adjustment, and financial wellbeing at the baseline enrollment visit. A semi-structured qualitative interview was administered at the three-month study visit to assess employment decisions and the impact of job demands, cancer care, and cancer-work fit during the three months following diagnosis. RESULT: Fifty women with new, primary diagnosis of breast cancer were enrolled in the study. Mean age of participants was 51 years, and 46% identified their race as Black or other. The majority of women disclosed their diagnosis to their employer and nearly all maintained some level of employment during the first three to six months of treatment. Women with hourly wage jobs were similar to those with salaried wage jobs with respect to demographic and social characteristics. Women with hourly wage jobs were more likely to report working in physically demanding jobs and taking unpaid leave. They were also more likely to experience side effects that required physical restrictions at work, to leave their jobs due to demands of treatment, and to report managing cancer and work concurrently as very difficult. Women in salaried wage jobs were more likely to report falling behind or missing work and working remotely as a cancer-management strategy. Women in hourly jobs more often reported difficulty managing the competing demands of cancer and work. CONCLUSION: While further study is needed, these results suggest that women in hourly and salaried workers reported similar experiences managing cancer and work, with a few key exceptions. These exceptions pertain to the nature of hourly-wage work. Cancer survivors employed in hourly jobs may be more vulnerable to poor employment outcomes due to limited access to paid time off and workplace flexibility, and challenges related to managing physical aspects of cancer and employment.
Gastric microbiota features associated with cancer risk factors and clinical outcomes: A pilot study in gastric cardia cancer patients from Shanxi, ChinaYu, G.; Hu, N.; Wang, L. (Wiley-Liss Inc., 2017)Little is known about the link between gastric microbiota and the epidemiology of gastric cancer. In order to determine the epidemiologic and clinical relevance of gastric microbiota, we used 16 S ribosomal RNA gene sequencing analysis to characterize the composition and structure of the gastric microbial community of 80 paired samples (non-malignant and matched tumor tissues) from gastric cardia adenocarcinoma (GCA) patients in Shanxi, China. We also used PICRUSt to predict microbial functional profiles. Compared to patients without family history of upper gastrointestinal (UGI) cancer in the non-malignant gastric tissue microbiota, patients with family history of UGI cancer had higher Helicobacter pylori (Hp) relative abundance (median: 0.83 vs. 0.38, p = 0.01) and lower alpha diversity (median observed species: 51 vs. 85, p = 0.01). Patients with higher (vs. lower) tumor grade had higher Hp relative abundance (0.73 vs. 0.18, p = 0.03), lower alpha diversity (observed species, 66 vs. 89, p = 0.01), altered beta diversity (weighted UniFrac, p = 0.002) and significant alterations in relative abundance of five KEGG functional modules in non-malignant gastric tissue microbiota. Patients without metastases had higher relative abundance of Lactobacillales than patients with metastases (0.05 vs. 0.01, p = 0.04) in non-malignant gastric tissue microbiota. These associations were observed in non-malignant tissues but not in tumor tissues. In conclusion, this study showed a link of gastric microbiota to a major gastric cancer risk factor and clinical features in GCA patients from Shanxi, China. Studies with both healthy controls and gastric cardia and noncardia cancer cases across different populations are needed to further examine the association between gastric cancer and the microbiota. Copyright 2017 UICC