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Zhu M, Li P, Wu W, Zheng W, Huang J, Tulafu H, Lin C, Tao W, Aladaer Q. The genetic characterization of germplasm and identification of the litter size trait associated candidate genes in Dexin mutton and fine-wool sheep. Front Genet 2024; 15:1457634. [PMID: 39211736 PMCID: PMC11359847 DOI: 10.3389/fgene.2024.1457634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024] Open
Abstract
Xinjiang is a major province of sheep breeding in China, which plays an important role in meeting people's needs for meat products, increasing farmers' income and sustainable development of animal husbandry. However, the genetic differentiation relationship between breeds was not clear, and most sheep had low fecundity, which seriously restricted the efficient development of sheep industry. Therefore, this study used the whole genome resequencing to detect the genetic variation of Dexin mutton and fine-wool sheep, explored the selected regions and important genes of the litter size traits, analyzed the genetic mechanism of reproductive traits, and provided new insights for the high fecundity breeding of sheep. A total of 5,236.338 G genome data and 35,884,037 SNPs were obtained. Furthermore, we identified 39 selection signals spanning candidate genes, 99 genes were significantly associated related to growth, reproduction and immunity, among which, BRIP1, BMPR1B, BMP4, NGF, etc. genes, and MAKP signaling pathway, Fanconi anemia pathway and Thyroid hormone signaling pathway and other signaling pathways were significantly correlated with litter size trait. Among them, we identified NGF, TrKA and BRIP1 genes was the important genes for sheep litter size traits and the mutation frequencies of 9 SNPs in BRIP1 gene were significantly different in domestic sheep in the world. The research provided new insights for the breeding of self-cultivated meat fine-wool sheep.
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Affiliation(s)
- Mengting Zhu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Pengfei Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Weiwei Wu
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Wenxin Zheng
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Juncheng Huang
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Hanikzi Tulafu
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Changchun Lin
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Weikun Tao
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Qi Aladaer
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
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Al-Shamsi HO, Abdelwahed N, Abyad A, Abu-Gheida I, Afrit M, Abu ElFuol T, Alasas R, Lababidi B, Dash P, Ahmad M, Dreier NW, ul Haq U, Joshua TLA, Otsmane S, Al-Nouri A, Al-Awadhi A, Tirmazy SH, Alterkait F, Elsabae S, Khan N, Albastaki NK, Sonawane Y, Jouda M, Perdawood F, Iqbal F, Jaafar H. Breast Cancer in the Arabian Gulf Countries. Cancers (Basel) 2023; 15:5398. [PMID: 38001658 PMCID: PMC10670541 DOI: 10.3390/cancers15225398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Breast cancer stands as the prevailing malignancy across all six Gulf Cooperation Council (GCC) nations. In this literature review, we highlighted the incidence and trend of breast cancer in the GCC. Most of the studies reported a consistent increase in breast cancer incidence over the past decades, which was particularly attributed to the adoption of a Westernized lifestyle in the region and the implications of emerging risk factors and other environmental and societal factors, the increase in screening uptake, as well as the improvement in data collection and reporting in the GCC. The data on breast cancer risk factors in the GCC were limited. In this geographic region, breast cancer frequently manifests with distinctive characteristics, including an early onset, typically occurring before the age of 50; an advanced stage at presentation; and a higher pathological grade. Additionally, it often exhibits more aggressive features such as human epidermal growth factor receptor 2 (HER2) positivity or the presence of triple-negative (TN) attributes, particularly among younger patients. Despite the growing body of literature on breast cancer in the GCC, data pertaining to survival rates are, regrettably, meager. Reports on breast cancer survival rates emanating from the GCC region are largely confined to Saudi Arabia and the United Arab Emirates (UAE). In the UAE, predictive modeling reveals 2-year and 5-year survival rates of 97% and 89%, respectively, for the same period under scrutiny. These rates, when compared to Western counterparts such as Australia (89.5%) and Canada (88.2%), fall within the expected range. Conversely, Saudi Arabia reports a notably lower 5-year survival rate, standing at 72%. This disparity in survival rates underscores the need for further research directed toward elucidating risk factors and barriers that hinder early detection and screening. Additionally, there is a pressing need for expanded data reporting on survival outcomes within the GCC. In sum, a more comprehensive and nuanced understanding of breast cancer dynamics in this region is imperative to inform effective strategies for prevention, early detection, and improved patient outcomes.
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Affiliation(s)
- Humaid O. Al-Shamsi
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
- Emirates Oncology Society, Dubai P.O. Box 6600, United Arab Emirates;
- Department of Clinical Sciences, College of Medicine, Gulf Medical University, Ajman P.O. Box 4184, United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Nadia Abdelwahed
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
- Emirates Oncology Society, Dubai P.O. Box 6600, United Arab Emirates;
| | - Amin Abyad
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
- Emirates Oncology Society, Dubai P.O. Box 6600, United Arab Emirates;
| | - Ibrahim Abu-Gheida
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
- Emirates Oncology Society, Dubai P.O. Box 6600, United Arab Emirates;
| | - Mehdi Afrit
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
- Emirates Oncology Society, Dubai P.O. Box 6600, United Arab Emirates;
| | - Tasneem Abu ElFuol
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
| | - Ryad Alasas
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
- Emirates Oncology Society, Dubai P.O. Box 6600, United Arab Emirates;
| | - Bilal Lababidi
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
- Emirates Oncology Society, Dubai P.O. Box 6600, United Arab Emirates;
| | - Prasanta Dash
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
- Emirates Oncology Society, Dubai P.O. Box 6600, United Arab Emirates;
| | - Mudhasir Ahmad
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
- Emirates Oncology Society, Dubai P.O. Box 6600, United Arab Emirates;
| | - Norbert W. Dreier
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
- Emirates Oncology Society, Dubai P.O. Box 6600, United Arab Emirates;
| | - Urfan ul Haq
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
- Emirates Oncology Society, Dubai P.O. Box 6600, United Arab Emirates;
| | - Thanda Lucy Ann Joshua
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
- Emirates Oncology Society, Dubai P.O. Box 6600, United Arab Emirates;
| | - Sonia Otsmane
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
- Emirates Oncology Society, Dubai P.O. Box 6600, United Arab Emirates;
| | - Anwar Al-Nouri
- Kuwait Cancer Control Center, Kuwait City, Kuwait; (A.A.-N.); (F.A.)
| | - Aydah Al-Awadhi
- Emirates Oncology Society, Dubai P.O. Box 6600, United Arab Emirates;
| | | | - Faisal Alterkait
- Kuwait Cancer Control Center, Kuwait City, Kuwait; (A.A.-N.); (F.A.)
| | - Shimaa Elsabae
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
| | - Nyla Khan
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
| | - Nehad Kazim Albastaki
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
| | - Yoginee Sonawane
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
- Emirates Oncology Society, Dubai P.O. Box 6600, United Arab Emirates;
| | - Mohammed Jouda
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
| | - Frea Perdawood
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
| | - Faryal Iqbal
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
| | - Hassan Jaafar
- Burjeel Medical City, Abu Dhabi P.O. Box 92510, United Arab Emirates; (N.A.); (A.A.); (I.A.-G.); (M.A.); (T.A.E.); (R.A.); (B.L.); (P.D.); (M.A.); (N.W.D.); (U.u.H.); (T.L.A.J.); (S.O.); (S.E.); (N.K.); (N.K.A.); (Y.S.); (M.J.); (F.P.); (F.I.); (H.J.)
- Emirates Oncology Society, Dubai P.O. Box 6600, United Arab Emirates;
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Long G, Hu K, Zhang X, Zhou L, Li J. Spectrum of BRCA1 interacting helicase 1 aberrations and potential prognostic and therapeutic implication: a pan cancer analysis. Sci Rep 2023; 13:4435. [PMID: 36932143 PMCID: PMC10023799 DOI: 10.1038/s41598-023-31109-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
BRCA1 interacting helicase 1 (BRIP1) alteration was crucial in tumors and it was a potential therapeutic target in ovarian serous cystadenocarcinoma (OV). Although a small number of studies had focused on BRIP1, an extensive study of BRIP1 genetic mutation and its clinical application in different cancer types had not been analyzed. In the current study, we analyzed BRIP1 abnormal expression, methylation, mutation, and their clinical application via several extensive datasets, which covered over 10,000 tumor samples across more than 30 cancer types. The total mutation rate of BRIP1 was rare in pan cancer. Its alteration frequency, oncogenic effects, mutation, and therapeutic implications were different in each cancer. 242 BRIP1 mutations were found across 32 cancer types. UCEC had the highest alteration (mutation and CNV) frequency. In addition, BRIP1 was a crucial oncogenic factor in OV and BRCA. BRIP1 mutation in PRAD was targetable, and FDA had approved a new drug. Moreover, Kaplan-Meier curve analysis showed that BRIP1 expression and genetic aberrations were closely related to patient survival in several cancers, indicating their potential for application as new tumor markers and therapeutic targets. The current study profiled the total BRIP1 mutation spectrum and offered an extensive molecular outlook of BRIP1 in a pan cancer analysis. And it suggested a brand-new perspective for clinical cancer therapy.
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Affiliation(s)
- Guo Long
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Kuan Hu
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xiaofang Zhang
- Departments of Burn and Plastic, Ningxiang People's Hospital, Hunan University of Chinese Medicine, Changsha, 410600, Hunan, China
| | - Ledu Zhou
- Department of Hepatobiliary Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Juanni Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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Sucularli C. Identification of BRIP1, NSMCE2, ANAPC7, RAD18 and TTL from chromosome segregation gene set associated with hepatocellular carcinoma. Cancer Genet 2022; 268-269:28-36. [PMID: 36126360 DOI: 10.1016/j.cancergen.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 07/12/2022] [Accepted: 09/06/2022] [Indexed: 01/25/2023]
Abstract
INTRODUCTION Hepatocellular carcinoma is one of the most frequent cancers with high mortality rate worldwide. METHODS TCGA LIHC HTseq counts were analyzed. GSEA was performed with GO BP gene sets. GO analysis was performed with differentially expressed genes. The subset of genes contributing most of the enrichment result of GO_BP_CHROMOSOME_SEGREGATION of GSEA were identified. Five genes have been selected in this subset of genes for further analysis. A microarray data set, GSE112790, was analyzed as a validation data set. Survival analysis was performed. RESULTS According to GSEA and GO analysis several gene sets and processes related to chromosome segregation were enriched in LIHC. GO_BP_CHROMOSOME_SEGREGATION gene set from GSEA had the highest size of the genes contributing most of the enrichment. Five genes in this gene set; BRIP1, NSMCE2, ANAPC7, RAD18 and TTL, whose expressions and prognostic values have not been studied in hepatocellular carcinoma in detail, have been selected for further analyses. Expression of these five genes were identified as significantly upregulated in LIHC RNA-seq and HCC microarray data set. Survival analysis showed that high expression of the five genes was associated with poor overall survival in HCC patients. CONCLUSION Selected genes were upregulated and had prognostic value in HCC.
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Affiliation(s)
- Ceren Sucularli
- Department of Bioinformatics, Institute of Health Sciences, Hacettepe University, Ankara, Turkey.
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Ehnes DD, Alghadeer A, Hanson-Drury S, Zhao YT, Tilmes G, Mathieu J, Ruohola-Baker H. Sci-Seq of Human Fetal Salivary Tissue Introduces Human Transcriptional Paradigms and a Novel Cell Population. FRONTIERS IN DENTAL MEDICINE 2022; 3:887057. [PMID: 36540608 PMCID: PMC9762771 DOI: 10.3389/fdmed.2022.887057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023] Open
Abstract
Multiple pathologies and non-pathological factors can disrupt the function of the non-regenerative human salivary gland including cancer and cancer therapeutics, autoimmune diseases, infections, pharmaceutical side effects, and traumatic injury. Despite the wide range of pathologies, no therapeutic or regenerative approaches exist to address salivary gland loss, likely due to significant gaps in our understanding of salivary gland development. Moreover, identifying the tissue of origin when diagnosing salivary carcinomas requires an understanding of human fetal development. Using computational tools, we identify developmental branchpoints, a novel stem cell-like population, and key signaling pathways in the human developing salivary glands by analyzing our human fetal single-cell sequencing data. Trajectory and transcriptional analysis suggest that the earliest progenitors yield excretory duct and myoepithelial cells and a transitional population that will yield later ductal cell types. Importantly, this single-cell analysis revealed a previously undescribed population of stem cell-like cells that are derived from SD and expresses high levels of genes associated with stem cell-like function. We have observed these rare cells, not in a single niche location but dispersed within the developing duct at later developmental stages. Our studies introduce new human-specific developmental paradigms for the salivary gland and lay the groundwork for the development of translational human therapeutics.
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Affiliation(s)
- Devon Duron Ehnes
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | - Ammar Alghadeer
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Biomedical Dental Sciences, College of Dentistry, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Sesha Hanson-Drury
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, United States
| | - Yan Ting Zhao
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA, United States
| | - Gwen Tilmes
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
| | - Julie Mathieu
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Comparative Medicine, University of Washington, Seattle, WA, United States
| | - Hannele Ruohola-Baker
- Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA, United States
- Institute for Stem Cells and Regenerative Medicine, School of Medicine, University of Washington, Seattle, WA, United States
- Department of Biomedical Dental Sciences, College of Dentistry, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
- Department of Bioengineering, University of Washington, Seattle, WA, United States
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Feng A, Yang N, Yu R, Liu J, Pang J, Wu X, Shao Y, Yang Z, Dai H. Prognostic Implications of Six Altered Genes in Asian Non-Surgical Esophageal Carcinoma Patients Treated with Chemoradiotherapy. Onco Targets Ther 2022; 15:41-51. [PMID: 35046666 PMCID: PMC8763582 DOI: 10.2147/ott.s334580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/26/2021] [Indexed: 12/24/2022] Open
Abstract
Background Esophageal cancer (EC), especially esophageal squamous cell carcinoma, remained as one of the most aggressive tumors in China with a five-year survival rate of around 40%. Molecular characteristics through next-generation sequencing are becoming an emerging method in identifying prognostic biomarkers for better treatment management for EC patients. Methods Targeted next-generation sequencing using a 422-gene pan-cancer panel was performed with tumor tissue samples from a total of 69 Asian non-surgical esophageal carcinoma patients (AEC) treated with chemoradiotherapy. A TCGA cohort of 143 EC patients and another Asian ESCC cohort of 47 patients were employed for validation. Results In the AEC cohort, alterations in TP53 (94.2%) and NOTCH1 (55.1%) were the two most frequently observed alterations, whereas in the TCGA cohort, only TP53 alterations were observed at a high ratio (85.3%). Co-amplifications of FGF19 and CCND1 were found at a similar ratio in both cohorts. Multiple alterations in the DNA damage pathway were identified but not associated with overall survival in AEC. Using univariate and multivariate Cox regression analyses, six gene alterations including YAP1 amplification, RB1 alteration, BAP1 mutation, MYC amplification, WRN mutation, and BRIP1 mutation were identified as adverse prognostic factors in the AEC cohort. A Cox proportional hazard model based on the six prognosis-related genes was constructed and showed the ability in distinguishing EC patients with poorer disease outcomes in AEC and two validation cohorts. Conclusion Six gene alterations were found to be potential unfavorable prognostic markers that might provide guidance in the treatment management for EC patients.
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Affiliation(s)
- Alei Feng
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, People's Republic of China.,Shandong Qidu Pharmaceutical Co. Ltd., Shandong Provincial Key Laboratory of Neuroprotective Drugs, Zibo, 255400, People's Republic of China
| | - Ning Yang
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, People's Republic of China
| | - Ruoying Yu
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, People's Republic of China
| | - Jingwen Liu
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, People's Republic of China
| | - Jiaohui Pang
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, People's Republic of China
| | - Xue Wu
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, People's Republic of China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, People's Republic of China.,School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Zhe Yang
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, People's Republic of China
| | - Honghai Dai
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, People's Republic of China
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7
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Khan U, Khan MS. Prognostic Value Estimation of BRIP1 in Breast Cancer by Exploiting Transcriptomics Data Through Bioinformatics Approaches. Bioinform Biol Insights 2021; 15:11779322211055892. [PMID: 34840500 PMCID: PMC8619737 DOI: 10.1177/11779322211055892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/09/2021] [Indexed: 01/04/2023] Open
Abstract
BRIP1 (Breast Cancer 1 Interacting Helicase 1) is a tumor suppressor gene that has vital function in preserving the genetic stability by repairing DNA damage though have significant associations with the onset of breast cancer (BC) if mutated or overexpressed. In this study, the prognostic value of BRIP1 gene was evaluated and validated through bioinformatics approaches utilizing transcriptomic (mRNA expression) data from several BC databases. To determine the prognostic value, the expression level of mRNA transcript was analyzed in context of comparison between breast tumor and normal tissues regarding clinical features, breast tumor subtypes, promoter methylation status, correlation level, mutation frequency, and survival of BC patients. BRIP1 expression was found to be significantly overexpressed in various BC molecular subtypes (e.g. PAM50, Sorlie’s) and clinical status (estrogen and progesterone receptor) than associated normal tissues which correlated with prognosis. Also, in promoter methylation level, its expression was observed as upregulated-hypomethylated regarding various clinicopathological features. Multiple data mining exhibited positive correlation between BRIP1 and INTS2 (Integrator Complex Subunit 2) expressions in BC. Further, mutation analysis revealed that BRIP1 gene was altered by acquiring both somatic and germline mutations. In addition, a total of 42 mutations; 24 missense, 8 fusion, 7 truncating, and 3 inframe mutations in BC patients was detected in BRIP1 protein. Moreover, higher BRIP1 expression was found to be correlated with poor disease-specific, disease metastasis-free, relapse-free, and overall survivals of BC patients. Since, overexpression of BRIP1 was identified to be associated with different clinical features, breast tumor subtypes, promoter methylation status, and survival of BC patients that may provide a risk of ensuing malignant transformation. Thus, lower expression of BRIP1 might hinder BC prognosis. We consider that this analysis will present a proof for BRIP1 gene to be a noteworthy molecular biomarker for BC prognosis.
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Affiliation(s)
- Umama Khan
- Biotechnology & Genetic Engineering Discipline, Khulna University, Khulna, Bangladesh
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8
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Muhseena N K, Mathukkada S, Das SP, Laha S. The repair gene BACH1 - a potential oncogene. Oncol Rev 2021; 15:519. [PMID: 34322202 PMCID: PMC8273628 DOI: 10.4081/oncol.2021.519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 03/02/2021] [Indexed: 12/12/2022] Open
Abstract
BACH1 encodes for a protein that belongs to RecQ DEAH helicase family and interacts with the BRCT repeats of BRCA1. The N-terminus of BACH1 functions in DNA metabolism as DNA-dependent ATPase and helicase. The C-terminus consists of BRCT domain, which interacts with BRCA1 and this interaction is one of the major regulator of BACH1 function. BACH1 plays important roles both in phosphorylated as well as dephosphorylated state and functions in coordination with multiple signaling molecules. The active helicase property of BACH1 is maintained by its dephosphorylated state. Imbalance between these two states enhances the development and progression of the diseased condition. Currently BACH1 is known as a tumor suppressor gene based on the presence of its clinically relevant mutations in different cancers. Through this review we have justified it to be named as an oncogene. In this review, we have explained the mechanism of how BACH1 in collaboration with BRCA1 or independently regulates various pathways like cell cycle progression, DNA replication during both normal and stressed situation, recombination and repair of damaged DNA, chromatin remodeling and epigenetic modifications. Mutation and overexpression of BACH1 are significantly found in different cancer types. This review enlists the molecular players which interact with BACH1 to regulate DNA metabolic functions, thereby revealing its potential for cancer therapeutics. We have identified the most mutated functional domain of BACH1, the hot spot for tumorigenesis, justifying it as a target molecule in different cancer types for therapeutics. BACH1 has high potentials of transforming a normal cell into a tumor cell if compromised under certain circumstances. Thus, through this review, we justify BACH1 as an oncogene along with the existing role of being a tumor suppressant.
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Affiliation(s)
- Katheeja Muhseena N
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Sooraj Mathukkada
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Shankar Prasad Das
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Suparna Laha
- Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
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9
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Mohamed RI, Bargal SA, Mekawy AS, El-Shiekh I, Tuncbag N, Ahmed AS, Badr E, Elserafy M. The overexpression of DNA repair genes in invasive ductal and lobular breast carcinomas: Insights on individual variations and precision medicine. PLoS One 2021; 16:e0247837. [PMID: 33662042 PMCID: PMC7932549 DOI: 10.1371/journal.pone.0247837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/14/2021] [Indexed: 12/22/2022] Open
Abstract
In the era of precision medicine, analyzing the transcriptomic profile of patients is essential to tailor the appropriate therapy. In this study, we explored transcriptional differences between two invasive breast cancer subtypes; infiltrating ductal carcinoma (IDC) and lobular carcinoma (LC) using RNA-Seq data deposited in the TCGA-BRCA project. We revealed 3854 differentially expressed genes between normal ductal tissues and IDC. In addition, IDC to LC comparison resulted in 663 differentially expressed genes. We then focused on DNA repair genes because of their known effects on patients' response to therapy and resistance. We here report that 36 DNA repair genes are overexpressed in a significant number of both IDC and LC patients' samples. Despite the upregulation in a significant number of samples, we observed a noticeable variation in the expression levels of the repair genes across patients of the same cancer subtype. The same trend is valid for the expression of miRNAs, where remarkable variations between patients' samples of the same cancer subtype are also observed. These individual variations could lie behind the differential response of patients to treatment. The future of cancer diagnostics and therapy will inevitably depend on high-throughput genomic and transcriptomic data analysis. However, we propose that performing analysis on individual patients rather than a big set of patients' samples will be necessary to ensure that the best treatment is determined, and therapy resistance is reduced.
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Affiliation(s)
- Ruwaa I. Mohamed
- Center for Informatics Sciences (CIS), Nile University, Giza, Egypt
| | - Salma A. Bargal
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Asmaa S. Mekawy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Iman El-Shiekh
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Nurcan Tuncbag
- Graduate School of Informatics, Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Alaa S. Ahmed
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Eman Badr
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Faculty of Computers and Artificial Intelligence, Cairo University, Giza, Egypt
- * E-mail: (EB); (ME)
| | - Menattallah Elserafy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- * E-mail: (EB); (ME)
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10
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Calvo JA, Fritchman B, Hernandez D, Persky NS, Johannessen CM, Piccioni F, Kelch BA, Cantor SB. Comprehensive Mutational Analysis of the BRCA1-Associated DNA Helicase and Tumor-Suppressor FANCJ/BACH1/BRIP1. Mol Cancer Res 2021; 19:1015-1025. [PMID: 33619228 DOI: 10.1158/1541-7786.mcr-20-0828] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/27/2021] [Accepted: 02/18/2021] [Indexed: 12/15/2022]
Abstract
FANCJ (BRIP1/BACH1) is a hereditary breast and ovarian cancer (HBOC) gene encoding a DNA helicase. Similar to HBOC genes, BRCA1 and BRCA2, FANCJ is critical for processing DNA inter-strand crosslinks (ICL) induced by chemotherapeutics, such as cisplatin. Consequently, cells deficient in FANCJ or its catalytic activity are sensitive to ICL-inducing agents. Unfortunately, the majority of FANCJ clinical mutations remain uncharacterized, limiting therapeutic opportunities to effectively use cisplatin to treat tumors with mutated FANCJ. Here, we sought to perform a comprehensive screen to identify FANCJ loss-of-function (LOF) mutations. We developed a FANCJ lentivirus mutation library representing approximately 450 patient-derived FANCJ nonsense and missense mutations to introduce FANCJ mutants into FANCJ knockout (K/O) HeLa cells. We performed a high-throughput screen to identify FANCJ LOF mutants that, as compared with wild-type FANCJ, fail to robustly restore resistance to ICL-inducing agents, cisplatin or mitomycin C (MMC). On the basis of the failure to confer resistance to either cisplatin or MMC, we identified 26 missense and 25 nonsense LOF mutations. Nonsense mutations elucidated a relationship between location of truncation and ICL sensitivity, as the majority of nonsense mutations before amino acid 860 confer ICL sensitivity. Further validation of a subset of LOF mutations confirmed the ability of the screen to identify FANCJ mutations unable to confer ICL resistance. Finally, mapping the location of LOF mutations to a new homology model provides additional functional information. IMPLICATIONS: We identify 51 FANCJ LOF mutations, providing important classification of FANCJ mutations that will afford additional therapeutic strategies for affected patients.
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Affiliation(s)
- Jennifer A Calvo
- Department of Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Briana Fritchman
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Nicole S Persky
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | - Brian A Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Sharon B Cantor
- Department of Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts.
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11
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Rizeq B, Sif S, Nasrallah GK, Ouhtit A. Novel role of BRCA1 interacting C-terminal helicase 1 (BRIP1) in breast tumour cell invasion. J Cell Mol Med 2020; 24:11477-11488. [PMID: 32888398 PMCID: PMC7576304 DOI: 10.1111/jcmm.15761] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/21/2020] [Accepted: 08/05/2020] [Indexed: 12/14/2022] Open
Abstract
Breast cancer (BC) is the most common malignancy and the leading cause of death in women worldwide. Only 5%‐10% of mutations in BRCA genes are associated with familial breast tumours in Eastern countries, suggesting the contribution of other genes. Using a microarray gene expression profiling study of BC, we have recently identified BRIP1 (fivefold up‐regulation) as a potential gene associated with BC progression in the Omani population. Although BRIP1 regulates DNA repair and cell proliferation, the precise role of BRIP1 in BC cell invasion/metastasis has not been explored yet; this prompted us to test the hypothesis that BRIP1 promotes BC cell proliferation and invasion. Using a combination of cellular and molecular approaches, our results revealed differential overexpression of BRIP1 in different BC cell lines. Functional assays validated further the physiological relevance of BRIP1 in tumour malignancy, and siRNA‐mediated BRIP1 knockdown significantly reduced BC cell motility by targeting key motility‐associated genes. Moreover, down‐regulation of BRIP1 expression significantly attenuated cell proliferation via cell cycle arrest. Our study is the first to show the novel function of BRIP1 in promoting BC cell invasion by regulating expression of various downstream target genes. Furthermore, these findings provide us with a unique opportunity to identify BRIP1‐induced pro‐invasive genes that could serve as biomarkers and/or targets to guide the design of appropriate BC targeted therapies.
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Affiliation(s)
- Balsam Rizeq
- Department of Biological and Environmental Sciences, College of Arts & Sciences, Qatar University, Doha, Qatar.,Biomedical Research Center, Qatar University, Doha, Qatar
| | - Saïd Sif
- Department of Biological and Environmental Sciences, College of Arts & Sciences, Qatar University, Doha, Qatar
| | - Gheyath K Nasrallah
- Biomedical Research Center, Qatar University, Doha, Qatar.,Biomedical Science Department, College of Health Sciences, Qatar University, Doha, Qatar
| | - Allal Ouhtit
- Department of Biological and Environmental Sciences, College of Arts & Sciences, Qatar University, Doha, Qatar
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12
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Min A, Kim K, Jeong K, Choi S, Kim S, Suh KJ, Lee KH, Kim S, Im SA. Homologous repair deficiency score for identifying breast cancers with defective DNA damage response. Sci Rep 2020; 10:12506. [PMID: 32719318 PMCID: PMC7385153 DOI: 10.1038/s41598-020-68176-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/09/2020] [Indexed: 12/13/2022] Open
Abstract
Breast cancer (BC) in patients with germline mutations of BRCA1/BRCA2 are associated with benefit from drugs targeting DNA damage response (DDR), but they account for only 5-7% of overall breast cancer. To define the characteristics of these tumors and also to identify tumors without BRCA mutation but with homologous recombination deficiency (HRD) is clinically relevant. To define characteristic features of HRD tumors and analyze the correlations between BRCA1/BRCA2 and BC subtypes, we analyzed 981 breast tumors from the TCGA database using the signature analyzer. The BRCA signature was strongly associated with the HRD score top 10% (score ≥ 57) population. This population showed a high level of mutations in DDR genes, including BRCA1/BRCA2. HRD tumors were associated with high expression levels of BARD1 and BRIP1. Besides, BRCA1/2 mutations were dominantly observed in basal and luminal subtypes, respectively. A comparison of HRD features in BC revealed that BRCA1 exerts a stronger influence inducing HRD features than BRCA2 does. It reveals genetic differences between BRCA1 and BRCA2 and provides a basis for the identification of HRD and other BRCA-associated tumors.
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Affiliation(s)
- Ahrum Min
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Kwangsoo Kim
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kyeonghun Jeong
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seongmin Choi
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seongyeong Kim
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Koung Jin Suh
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Kyung-Hun Lee
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea.
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Sun Kim
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea
| | - Seock-Ah Im
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea.
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
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13
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Nayak S, Calvo JA, Cong K, Peng M, Berthiaume E, Jackson J, Zaino AM, Vindigni A, Hadden MK, Cantor SB. Inhibition of the translesion synthesis polymerase REV1 exploits replication gaps as a cancer vulnerability. SCIENCE ADVANCES 2020; 6:eaaz7808. [PMID: 32577513 PMCID: PMC7286678 DOI: 10.1126/sciadv.aaz7808] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 04/06/2020] [Indexed: 05/04/2023]
Abstract
The replication stress response, which serves as an anticancer barrier, is activated not only by DNA damage and replication obstacles but also oncogenes, thus obscuring how cancer evolves. Here, we identify that oncogene expression, similar to other replication stress-inducing agents, induces single-stranded DNA (ssDNA) gaps that reduce cell fitness. DNA fiber analysis and electron microscopy reveal that activation of translesion synthesis (TLS) polymerases restricts replication fork slowing, reversal, and fork degradation without inducing replication gaps despite the continuation of replication during stress. Consistent with gap suppression (GS) being fundamental to cancer, we demonstrate that a small-molecule inhibitor targeting the TLS factor REV1 not only disrupts DNA replication and cancer cell fitness but also synergizes with gap-inducing therapies such as inhibitors of ATR or Wee1. Our work illuminates that GS during replication is critical for cancer cell fitness and therefore a targetable vulnerability.
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Affiliation(s)
- Sumeet Nayak
- Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jennifer A. Calvo
- Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ke Cong
- Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Min Peng
- Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Emily Berthiaume
- Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jessica Jackson
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Angela M. Zaino
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, CT 06269, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - M. Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Unit 3092, Storrs, CT 06269, USA
| | - Sharon B. Cantor
- Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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14
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15
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Rahman S, Zayed H. Breast cancer in the GCC countries: A focus on BRCA1/2 and non-BRCA1/2 genes. Gene 2018; 668:73-76. [DOI: 10.1016/j.gene.2018.05.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 05/13/2018] [Indexed: 10/16/2022]
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16
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Drukker K, Li H, Antropova N, Edwards A, Papaioannou J, Giger ML. Most-enhancing tumor volume by MRI radiomics predicts recurrence-free survival "early on" in neoadjuvant treatment of breast cancer. Cancer Imaging 2018; 18:12. [PMID: 29653585 PMCID: PMC5899353 DOI: 10.1186/s40644-018-0145-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/27/2018] [Indexed: 01/09/2023] Open
Abstract
Background The hypothesis of this study was that MRI-based radiomics has the ability to predict recurrence-free survival “early on” in breast cancer neoadjuvant chemotherapy. Methods A subset, based on availability, of the ACRIN 6657 dynamic contrast-enhanced MR images was used in which we analyzed images of all women imaged at pre-treatment baseline (141 women: 40 with a recurrence, 101 without) and all those imaged after completion of the first cycle of chemotherapy, i.e., at early treatment (143 women: 37 with a recurrence vs. 105 without). Our method was completely automated apart from manual localization of the approximate tumor center. The most enhancing tumor volume (METV) was automatically calculated for the pre-treatment and early treatment exams. Performance of METV in the task of predicting a recurrence was evaluated using ROC analysis. The association of recurrence-free survival with METV was assessed using a Cox regression model controlling for patient age, race, and hormone receptor status and evaluated by C-statistics. Kaplan-Meier analysis was used to estimate survival functions. Results The C-statistics for the association of METV with recurrence-free survival were 0.69 with 95% confidence interval of [0.58; 0.80] at pre-treatment and 0.72 [0.60; 0.84] at early treatment. The hazard ratios calculated from Kaplan-Meier curves were 2.28 [1.08; 4.61], 3.43 [1.83; 6.75], and 4.81 [2.16; 10.72] for the lowest quartile, median quartile, and upper quartile cut-points for METV at early treatment, respectively. Conclusion The performance of the automatically-calculated METV rivaled that of a semi-manual model described for the ACRIN 6657 study (published C-statistic 0.72 [0.60; 0.84]), which involved the same dataset but required semi-manual delineation of the functional tumor volume (FTV) and knowledge of the pre-surgical residual cancer burden.
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Affiliation(s)
- Karen Drukker
- Department of Radiology, MC2026, 5841 S Maryland Ave, Chicago, IL, USA.
| | - Hui Li
- Department of Radiology, MC2026, 5841 S Maryland Ave, Chicago, IL, USA
| | - Natalia Antropova
- Department of Radiology, MC2026, 5841 S Maryland Ave, Chicago, IL, USA
| | - Alexandra Edwards
- Department of Radiology, MC2026, 5841 S Maryland Ave, Chicago, IL, USA
| | - John Papaioannou
- Department of Radiology, MC2026, 5841 S Maryland Ave, Chicago, IL, USA
| | - Maryellen L Giger
- Department of Radiology, MC2026, 5841 S Maryland Ave, Chicago, IL, USA
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