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      Genetic Variation in CCL5 Signaling Genes and Triple Negative Breast Cancer: Susceptibility and Prognosis Implications

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          Abstract

          Triple-negative breast cancer (TNBC) accounts for ~15–20% of breast cancer (BC) and has a higher rate of early relapse and mortality compared to other subtypes. The Chemokine (C-C motif) ligand 5 (CCL5) and its signaling pathway have been linked to TNBC. We aimed to investigate the susceptibility and prognostic implications of genetic variation in CCL5 signaling genes in TNBC in the present study. We characterized variants in CCL5 and that of six other CCL5 signaling genes ( CCND1, ZMIZ1, CASP8, NOTCH2, MAP3K21, and HS6ST3) among 1,082 unrelated Tunisian subjects (544 BC patients, including 196 TNBC, and 538 healthy controls), assessed the association of the variants with BC-specific overall survival (OVS) and progression-free survival (PFS), and correlated CCL5 mRNA and serum levels with CCL5 genotypes. We found a highly significant association between the CCND1 rs614367-TT genotype (OR = 5.14; P = 0.004) and TNBC risk, and identified a significant association between the rs614367-T allele and decreased PFS in TNBC. A decreased risk of lymph node metastasis was associated with the MAP3K21 rs1294255-C allele, particularly in rs1294255-GC (OR = 0.47; P = 0.001). CCL5 variants ( rs2107538 and rs2280789) were linked to CCL5 serum and mRNA levels. In the TCGA TNBC/Basal-like cohort the MAP3K21 rs1294255-G allele was associated with a decreased OVS. High expression of CCL5 in breast tumors was significantly associated with an increased OVS in all BC patients, but particularly in TNBC/Basal-like patients. In conclusion, genetic variation in CCL5 signaling genes may predict not only TNBC risk but also disease aggressiveness.

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          Most cited references48

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          Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

          Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel stemness indices for assessing the degree of oncogenic dedifferentiation. We used an innovative one-class logistic regression (OCLR) machine-learning algorithm to extract transcriptomic and epigenetic feature sets derived from non-transformed pluripotent stem cells and their differentiated progeny. Using OCLR, we were able to identify previously undiscovered biological mechanisms associated with the dedifferentiated oncogenic state. Analyses of the tumor microenvironment revealed unanticipated correlation of cancer stemness with immune checkpoint expression and infiltrating immune cells. We found that the dedifferentiated oncogenic phenotype was generally most prominent in metastatic tumors. Application of our stemness indices to single-cell data revealed patterns of intra-tumor molecular heterogeneity. Finally, the indices allowed for the identification of novel targets and possible targeted therapies aimed at tumor differentiation.
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            Prognostic value of tumor-infiltrating lymphocytes in triple-negative breast cancers from two phase III randomized adjuvant breast cancer trials: ECOG 2197 and ECOG 1199.

            Recent studies suggest that tumor-infiltrating lymphocytes (TILs) are associated with disease-free (DFS) and overall survival (OS) in operable triple-negative breast cancer (TNBC). We seek to validate the prognostic impact of TILs in primary TNBCs in two adjuvant phase III trials conducted by the Eastern Cooperative Oncology Group (ECOG). Full-face hematoxylin and eosin–stained sections of 506 tumors from ECOG trials E2197 and E1199 were evaluated for density of TILs in intraepithelial (iTILs) and stromal compartments (sTILs). Patient cases of TNBC from E2197 and E1199 were randomly selected based on availability of sections. For the primary end point of DFS, association with TIL scores was determined by fitting proportional hazards models stratified on study. Secondary end points were OS and distant recurrence–free interval (DRFI). Reporting recommendations for tumor marker prognostic studies criteria were followed, and all analyses were prespecified. The majority of 481 evaluable cancers had TILs (sTILs, 80%; iTILs, 15%). With a median follow-up of 10.6 years, higher sTIL scores were associated with better prognosis; for every 10% increase in sTILs, a 14% reduction of risk of recurrence or death (P = .02), 18% reduction of risk of distant recurrence (P = .04), and 19% reduction of risk of death (P = .01) were observed. Multivariable analysis confirmed sTILs to be an independent prognostic marker of DFS, DRFI, and OS. In two national randomized clinical trials using contemporary adjuvant chemotherapy, we confirm that stromal lymphocytic infiltration constitutes a robust prognostic factor in TNBCs. Studies assessing outcomes and therapeutic efficacies should consider stratification for this parameter.
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              Pathogenic Germline Variants in 10,389 Adult Cancers

              We conducted the largest investigation of predisposition variants in cancer to date, discovering 853 pathogenic or likely pathogenic variants in 8% of 10,389 cases from 33 cancer types. Twenty-one genes showed single or cross-cancer associations, including novel associations of SDHA in melanoma and PALB2 in stomach adenocarcinoma. The 659 predisposition variants and 18 additional large deletions in tumor suppressors, including ATM, BRCA1, and NF1, showed low gene expression and frequent (43%) loss of heterozygosity or biallelic two-hit events. We also discovered 33 such variants in oncogenes, including missenses in MET, RET, and PTPN11 associated with high gene expression. We nominated 47 additional predisposition variants from prioritized VUSs supported by multiple evidences involving case-control frequency, loss of heterozygosity, expression effect, and co-localization with mutations and modified residues. Our integrative approach links rare predisposition variants to functional consequences, informing future guidelines of variant classification and germline genetic testing in cancer.
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                Author and article information

                Contributors
                Journal
                Front Oncol
                Front Oncol
                Front. Oncol.
                Frontiers in Oncology
                Frontiers Media S.A.
                2234-943X
                06 December 2019
                2019
                : 9
                : 1328
                Affiliations
                [1] 1Department of Genetic Medicine, Weill Cornell Medicine , New York, NY, United States
                [2] 2Department of Microbiology and Immunology, Weill Cornell Medicine , New York, NY, United States
                [3] 3Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar , Doha, Qatar
                [4] 4Faculta di Medicina e Chirurgia, Universita Cattolica del Sacro Cuero , Rome, Italy
                [5] 5Translational Genetics and Bioinformatics Section, Research Division, Sidra Medicine , Doha, Qatar
                [6] 6Qatar Computing Research Institute, Hamad Bin Khalifa University , Doha, Qatar
                [7] 7Department of Medical Oncology, National Center for Cancer Care and Research, Hamad Medical Corporation , Doha, Qatar
                [8] 8Department of Population Sciences, City of Hope , Duarte, CA, United States
                [9] 9Department of Laboratory Medicine at UCSF , San Francisco, CA, United States
                [10] 10Helen Diller Family Comprehensive Cancer Center at UCSF , San Francisco, CA, United States
                [11] 11Division of General Internal Medicine, Department of Medicine, Institute for Human Genetics at UCSF , San Francisco, CA, United States
                [12] 12Service de Cancérologie Radiothérapie, CHU Farhat Hached , Sousse, Tunisia
                [13] 13Laboratoire d'Immuno-Oncologie Moléculaire, Faculté de Médecine de Monastir, Université de Monastir , Monastir, Tunisia
                [14] 14Tumor Biology Section, Research Division, Sidra Medicine , Doha, Qatar
                Author notes

                Edited by: Laura Cerchia, Italian National Research Council, Italy

                Reviewed by: Nella Prevete, University of Naples Federico II, Italy; Paola Ungaro, Italian National Research Council, Italy

                *Correspondence: Lotfi Chouchane loc2008@ 123456med.cornell.edu

                This article was submitted to Women's Cancer, a section of the journal Frontiers in Oncology

                Article
                10.3389/fonc.2019.01328
                6915105
                31921621
                a6f7c8e4-e5c3-4ac7-b501-a2529130b460
                Copyright © 2019 Shan, Chouchane, Mokrab, Saad, Boujassoum, Sayaman, Ziv, Bouaouina, Remadi, Gabbouj, Roelands, Ma, Bedognetti and Chouchane.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 29 July 2019
                : 13 November 2019
                Page count
                Figures: 3, Tables: 3, Equations: 0, References: 57, Pages: 13, Words: 8923
                Funding
                Funded by: Qatar National Research Fund 10.13039/100008982
                Award ID: NPRP10-0126-170262
                Award ID: NPRP7-136-3-031
                Categories
                Oncology
                Original Research

                Oncology & Radiotherapy
                ccl5,ccl5 signaling genes,triple negative breast cancer,prognosis,susceptibility

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