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Cao X, Song Y, Wu H, Ren X, Sun Q, Liang Z. Quantifying spatial CXCL9 distribution with image analysis predicts improved prognosis of triple-negative breast cancer. Front Genet 2024; 15:1421573. [PMID: 38957805 PMCID: PMC11217326 DOI: 10.3389/fgene.2024.1421573] [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: 04/22/2024] [Accepted: 05/29/2024] [Indexed: 07/04/2024] Open
Abstract
Background: The C-X-C motif chemokine ligand 9 (CXCL9) plays a pivotal role in tumor immunity by recruiting and activating immune cells. However, the relationship between CXCL9 expression and prognosis in triple-negative breast cancer (TNBC) is unclear. Methods: We investigated CXCL9 mRNA expression, clinicopathological features, and prognosis in TNBC patients. We also used computational image analysis to quantify and assess the distribution of CXCL9 protein in the tumor core (TC) and invasive margin (IM). Results: CXCL9 mRNA expression was significantly higher in TNBC tumors compared to normal tissue (p < 0.001) and was associated with smaller tumors (p = 0.022) and earlier stages (p = 0.033). High CXCL9 mRNA expression was correlated with improved overall survival (OS) in three independent cohorts (all p < 0.05). In a separate analysis, low CXCL9 protein expression was associated with increased lymph node metastasis (p = 0.018 and p = 0.036). High CXCL9 protein expression in the TC, IM, or both was associated with prolonged OS (all p < 0.001). Conclusion: High CXCL9 expression, at both the mRNA and protein levels, is associated with improved prognosis in TNBC patients. CXCL9 expression in the TC and/or IM may be an independent prognostic factor.
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Affiliation(s)
- Xi Cao
- Department of Breast Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yu Song
- Department of Breast Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xinyu Ren
- Department of Pathology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Qiang Sun
- Department of Breast Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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Jiang X, Dong L, Wang S, Wen Z, Chen M, Xu L, Xiao G, Li Q. Reconstructing Spatial Transcriptomics at the Single-cell Resolution with BayesDeep. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570715. [PMID: 38106214 PMCID: PMC10723442 DOI: 10.1101/2023.12.07.570715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Spatially resolved transcriptomics (SRT) techniques have revolutionized the characterization of molecular profiles while preserving spatial and morphological context. However, most next-generation sequencing-based SRT techniques are limited to measuring gene expression in a confined array of spots, capturing only a fraction of the spatial domain. Typically, these spots encompass gene expression from a few to hundreds of cells, underscoring a critical need for more detailed, single-cell resolution SRT data to enhance our understanding of biological functions within the tissue context. Addressing this challenge, we introduce BayesDeep, a novel Bayesian hierarchical model that leverages cellular morphological data from histology images, commonly paired with SRT data, to reconstruct SRT data at the single-cell resolution. BayesDeep effectively model count data from SRT studies via a negative binomial regression model. This model incorporates explanatory variables such as cell types and nuclei-shape information for each cell extracted from the paired histology image. A feature selection scheme is integrated to examine the association between the morphological and molecular profiles, thereby improving the model robustness. We applied BayesDeep to two real SRT datasets, successfully demonstrating its capability to reconstruct SRT data at the single-cell resolution. This advancement not only yields new biological insights but also significantly enhances various downstream analyses, such as pseudotime and cell-cell communication.
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Affiliation(s)
- Xi Jiang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas, U.S.A
- Department of Statistics and Data Science, Southern Methodist University, Dallas, Texas, U.S.A
| | - Lei Dong
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas, U.S.A
| | - Shidan Wang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas, U.S.A
| | - Zhuoyu Wen
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas, U.S.A
| | - Mingyi Chen
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas, U.S.A
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas, U.S.A
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, U.S.A
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas, U.S.A
| | - Qiwei Li
- Department of Mathematical Sciences, The University of Texas at Dallas, Richardson, Texas, U.S.A
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Zhang W, Wang Y, Deng S, Zhu YC. LncRNA RP11-10E18.7 cooperates with lncRNA RP11-481C4.2 to affect the overall survival of breast cancer patients: a TCGA-based retrospective study. Transl Cancer Res 2023; 12:3156-3165. [PMID: 38130297 PMCID: PMC10731347 DOI: 10.21037/tcr-23-1941] [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: 10/18/2023] [Accepted: 11/07/2023] [Indexed: 12/23/2023]
Abstract
Background As either oncogenes or tumor suppressor genes, long non-coding RNAs (lncRNAs) have a major role in both tumorigenesis and progression of human cancers, including breast cancer (BC). However, the statistical correlation between the lncRNA-lncRNA interaction and prognosis of BC remains unclear. Methods We analyzed the fragments per kilobase per million (FPKM) lncRNA expression data in tumor tissue samples from 890 female patients with BC in The Cancer Genome Atlas (TCGA) between May 2021 and October 2022. The Cox proportional hazards model adjusted for age, race, clinical stage, neoadjuvant therapy, estrogen receptor (ER), and progesterone receptor (PR) was adopted to evaluate the lncRNA-lncRNA interaction regarding overall survival (OS) of BC. The multiple comparison was corrected by Bonferroni method. Results RP11-10E18.7×RP11-481C4.2 was significantly associated with OS of BC patients [hazard ratio (HR)interaction =1.04, 95% confidence interval (CI): 1.03-1.06, P=3.35×10-9]. Then, gene-gene interaction analysis was performed for genes co-expressed with lncRNAs. FOXA1×U2SURP (HRinteraction =1.49, 95% CI: 1.28-1.73, P=2.16×10-7) was found to have a similar interactive pattern to RP11-10E18.7×RP11-481C4.2. after classifying the patients by intersection (3.47), we observed that the effect of FOXA1 opposite in patients with different U2SURP expression level (HRhigh vs. low =0.58, 95% CI: 0.34-0.99, P=0.046 in low expression of U2SURP; HRhigh vs. low =1.56, 95% CI: 1.18-2.87, P=0.029 in high expression of U2SURP). Conclusions Our comprehensive study identified RP11-10E18.7×RP11-481C4.2 as a potential biomarker of BC prognosis. The results play an essential role in the impact of lncRNA-lncRNA interaction on BC survival. Our findings elucidated potential molecular mechanisms of BC progression under complex association patterns and provided potential dynamic and reversible therapeutic targets for BC patients.
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Affiliation(s)
- Wenzhong Zhang
- Department of Surgery, Pudong New Area People’s Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Yueming Wang
- Department of Surgery, Pudong New Area People’s Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Shuhao Deng
- Department of Ultrasound, Pudong New Area People’s Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Yi-Cheng Zhu
- Department of Ultrasound, Pudong New Area People’s Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, China
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4
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Venetis K, Sajjadi E, Ivanova M, Peccatori FA, Fusco N, Guerini-Rocco E. Characterization of the immune environment in pregnancy-associated breast cancer. Future Oncol 2023. [PMID: 37376974 DOI: 10.2217/fon-2022-1321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023] Open
Abstract
Pregnancy-associated breast cancer (PrBC) is a rare and clinically challenging condition. Specific immune mechanisms and pathways are involved in maternal-fetal tolerance and tumor-host immunoediting. The comprehension of the molecular processes underpinning this immune synergy in PrBC is needed to improve patients' clinical management. Only a few studies focused on the immune biology of PrBC and attempted to identify bona fide biomarkers. Therefore, clinically actionable information remains extremely puzzling for these patients. In this review article, we discuss the current knowledge on the immune environment of PrBC, in comparison with pregnancy-unrelated breast cancer and in the context of maternal immune changes during pregnancy. A particular emphasis is given to the actual role of potential immune-related biomarkers for PrBC clinical management.
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Affiliation(s)
- Konstantinos Venetis
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
| | - Elham Sajjadi
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
- Department of Oncology & Hemato-Oncology, University of Milan, Milan, 20122, Italy
| | - Mariia Ivanova
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
| | - Fedro Alessandro Peccatori
- Fertility & Procreation Unit, Division of Gynecologic Oncology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
- Department of Oncology & Hemato-Oncology, University of Milan, Milan, 20122, Italy
| | - Elena Guerini-Rocco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
- Department of Oncology & Hemato-Oncology, University of Milan, Milan, 20122, Italy
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5
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Liu Y, Ouyang W, Huang H, Tan Y, Zhang Z, Yu Y, Yao H. Identification of a tumor immune-inflammation signature predicting prognosis and immune status in breast cancer. Front Oncol 2023; 12:960579. [PMID: 36713514 PMCID: PMC9881411 DOI: 10.3389/fonc.2022.960579] [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: 06/03/2022] [Accepted: 11/24/2022] [Indexed: 01/15/2023] Open
Abstract
Background Breast cancer has become the malignancy with the highest mortality rate in female patients worldwide. The limited efficacy of immunotherapy as a breast cancer treatment has fueled the development of research on the tumor immune microenvironment. Methods In this study, data on breast cancer patients were collected from The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) cohorts. Differential gene expression analysis, univariate Cox regression analysis, and least absolute shrinkage and selection operator (LASSO) Cox regression analysis were performed to select overall survival (OS)-related, tumor tissue highly expressed, and immune- and inflammation-related genes. A tumor immune-inflammation signature (TIIS) consisting of 18 genes was finally screened out in the LASSO Cox regression model. Model performance was assessed by time-dependent receiver operating characteristic (ROC) curves. In addition, the CIBERSORT algorithm and abundant expression of immune checkpoints were utilized to clarify the correlation between the risk signature and immune landscape in breast cancer. Furthermore, the association of IL27 with the immune signature was analyzed in pan-cancer and the effect of IL27 on the migration of breast cancer cells was investigated since the regression coefficient of IL27 was the highest. Results A TIIS based on 18 genes was constructed via LASSO Cox regression analysis. In the TCGA-BRCA training cohort, 10-year AUC reached 0.89, and prediction performance of this signature was also validated in the METABRIC set. The high-risk group was significantly correlated with less infiltration of tumor-killing immune cells and the lower expression level of the immune checkpoint. Furthermore, we recommended some small-molecule drugs as novel targeted drugs for new breast cancer types. Finally, the relationship between IL27, a significant prognostic immune and inflammation cytokine, and immune status was analyzed in pan-cancer. Expression of IL27 was significantly correlated with immune regulatory gene expression and immune cell infiltration in pan-cancer. Furthermore, IL27 treatment improved breast cancer cell migration. Conclusion The TIIS represents a promising prognostic tool for estimating OS in patients with breast cancer and is correlated with immune status.
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Affiliation(s)
- Yajing Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Center, Phase I Clinical Trial Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wenhao Ouyang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Center, Phase I Clinical Trial Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hong Huang
- School of Medicine, Guilin Medical College, Guilin, China
| | - Yujie Tan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Center, Phase I Clinical Trial Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zebang Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Center, Phase I Clinical Trial Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yunfang Yu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Center, Phase I Clinical Trial Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China,Faculty of Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China,*Correspondence: Herui Yao, ; Yunfang Yu,
| | - Herui Yao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Medical Oncology, Breast Tumor Center, Phase I Clinical Trial Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China,*Correspondence: Herui Yao, ; Yunfang Yu,
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6
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Zhu Y, Iwamoto T, Kajiwara Y, Takahashi Y, Kochi M, Shien T, Taira N, Toyooka S, Doihara H. Predictive value of immune genomic signatures from breast cancer cohorts containing data for both response to neoadjuvant chemotherapy and prognosis after surgery. Breast Cancer 2023; 30:56-67. [PMID: 35994199 DOI: 10.1007/s12282-022-01397-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/17/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Previous studies of immune genomic signatures (IGSs) in breast cancer have attempted to predict the response to chemotherapy or prognosis and were performed using different patient cohorts. The purpose of this study was to evaluate the predictive functions of various IGSs using the same patient cohort that included data for response to chemotherapy as well as the prognosis after surgery. METHODS We applied five previously described IGS models in a public dataset of 508 breast cancer patients treated with neoadjuvant chemotherapy. The prognostic and predictive values of each model were evaluated, and their correlations were compared. RESULTS We observed a high proportion of expression concordance among the IGS models (r: 0.56-1). Higher scores of IGSs were detected in aggressive breast cancer subtypes (basal and HER2-enriched) (P < 0.001). Four of the five IGSs could predict chemotherapy responses and two could predict 5-year relapse-free survival in cases with hormone receptor-positive (HR +) tumors. However, the models showed no significant differences in their predictive abilities for hormone receptor-negative (HR-) tumors. CONCLUSIONS IGSs are, to some extent, useful for predicting prognosis and chemotherapy response; moreover, they show substantial agreement for specific breast cancer subtypes. However, it is necessary to identify more compelling biomarkers for both prognosis and response to chemotherapy in HR- and HER2 + cases.
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Affiliation(s)
- Yidan Zhu
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1, Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Takayuki Iwamoto
- Department of Breast and Endocrine Surgery, Okayama University Hospital, Okayama, Japan.
| | - Yukiko Kajiwara
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1, Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
- Department of Breast and Endocrine Surgery, Okayama University Hospital, Okayama, Japan
| | - Yuko Takahashi
- Department of Breast and Endocrine Surgery, Okayama University Hospital, Okayama, Japan
| | - Mariko Kochi
- Department of Breast and Endocrine Surgery, Okayama University Hospital, Okayama, Japan
| | - Tadahiko Shien
- Department of Breast and Endocrine Surgery, Okayama University Hospital, Okayama, Japan
| | - Naruto Taira
- Department of Breast and Endocrine Surgery, Okayama University Hospital, Okayama, Japan
| | - Shinichi Toyooka
- Department of General Thoracic Surgery and Breast and Endocrinological Surgery, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1, Shikata-cho, Kita-ku, Okayama, 700-8558, Japan
| | - Hiroyoshi Doihara
- Department of Breast and Endocrine Surgery, Okayama University Hospital, Okayama, Japan
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Zhang J, Jin H, Pan S, Han C, Sun Q, Han X. Immune checkpoints expression patterns in early-stage triple-negative breast cancer predict prognosis and remodel the tumor immune microenvironment. Front Immunol 2023; 14:1073550. [PMID: 36814908 PMCID: PMC9939840 DOI: 10.3389/fimmu.2023.1073550] [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: 10/18/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023] Open
Abstract
Background Currently, targeting immune checkpoint molecules holds great promise for triple-negative breast cancer (TNBC). However, the expression landscape of immune checkpoint genes (ICGs) in TNBC remains largely unknown. Method Herein, we systematically investigated the ICGs expression patterns in 422 TNBC samples. We evaluated the ICGs molecular typing based on the ICGs expression profile and explored the associations between ICGs molecular subtypes and tumor immune characteristics, clinical significance, and response to immune checkpoint inhibitors (ICIs). Results Two ICGs clusters and two ICGs-related gene clusters were determined, which were involved in different survival outcomes, biological roles and infiltration levels of immune cells. We established a quantification system ICGs riskscore (named IRS) to assess the ICGs expression patterns for individuals. TNBC patients with lower IRS were characterized by increased immune cell infiltration, favorable clinical outcomes and high sensitivity to ICIs therapy. We also developed a nomogram model combining clinicopathological variables to predict overall survival in TNBC. Genomic feature analysis revealed that high IRS group presented an increased tumor mutation burden compared with the low IRS group. Conclusion Collectively, dissecting the ICGs expression patterns not only provides a new insight into TNBC subtypes but also deepens the understanding of ICGs in the tumor immune microenvironment.
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Affiliation(s)
- Jinguo Zhang
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, China.,Department of Medical Oncology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Hongwei Jin
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, China.,Department of Medical Oncology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China.,School of Medical Oncology, Anhui Medical University, Hefei, China
| | - Shuaikang Pan
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, China.,School of Medical Oncology, Wan Nan Medical College, Wuhu, China
| | - Chaoqiang Han
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, China
| | - Qingqing Sun
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, China.,Department of Medical Oncology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China.,School of Medical Oncology, Anhui Medical University, Hefei, China
| | - Xinghua Han
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, China.,Department of Medical Oncology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China.,School of Medical Oncology, Anhui Medical University, Hefei, China
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Development and Validation of Ferroptosis-Related lncRNAs as Prognosis and Diagnosis Biomarkers for Breast Cancer. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2390764. [PMID: 36303582 PMCID: PMC9596248 DOI: 10.1155/2022/2390764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/07/2022] [Accepted: 09/23/2022] [Indexed: 12/01/2022]
Abstract
Breast cancer (BC) is one of the most common malignancies affecting women. Ferroptosis is a novel cancer treatment option. The present study is aimed to identify suitable ferroptosis-related lncRNAs to predict and diagnose BC. Differential expression and Cox regression analyses were used to screen suitable prognostic biomarkers and construct a suitable risk model. We identified four ferroptosis-related differentially expressed lncRNAs (FR-DELs) (LINC01152, AC004585.1, MAPT-IT1, and AC026401.3), which were independently correlated with the overall survival of BC patients. The area under the curve value of the prognostic model using those four biomarkers was over 0.60 in all three groups. The sensitivity and specificity of the diagnostic model using those four biomarkers were 86.89% and 86.73%, respectively. Our present study indicated that these four FR-DELs (LINC01152, AC004585.1, MAPT-IT1, and AC026401.3) could be prognostic biomarkers for BC, although clinical validation studies are required.
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9
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Ribeiro R, Carvalho MJ, Goncalves J, Moreira JN. Immunotherapy in triple-negative breast cancer: Insights into tumor immune landscape and therapeutic opportunities. Front Mol Biosci 2022; 9:903065. [PMID: 36060249 PMCID: PMC9437219 DOI: 10.3389/fmolb.2022.903065] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/13/2022] [Indexed: 12/24/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a clinically aggressive subtype of breast cancer that represents 15-20% of breast tumors and is more prevalent in young pre-menopausal women. It is the subtype of breast cancers with the highest metastatic potential and recurrence at the first 5 years after diagnosis. In addition, mortality increases when a complete pathological response is not achieved. As TNBC cells lack estrogen, progesterone, and HER2 receptors, patients do not respond well to hormone and anti-HER2 therapies, and conventional chemotherapy remains the standard treatment. Despite efforts to develop targeted therapies, this disease continues to have a high unmet medical need, and there is an urgent demand for customized diagnosis and therapeutics. As immunotherapy is changing the paradigm of anticancer treatment, it arises as an alternative treatment for TNBC patients. TNBC is classified as an immunogenic subtype of breast cancer due to its high levels of tumor mutational burden and presence of immune cell infiltrates. This review addresses the implications of these characteristics for the diagnosis, treatment, and prognosis of the disease. Herein, the role of immune gene signatures and tumor-infiltrating lymphocytes as biomarkers in TNBC is reviewed, identifying their application in patient diagnosis and stratification, as well as predictors of efficacy. The expression of PD-L1 expression is already considered to be predictive of response to checkpoint inhibitor therapy, but the challenges regarding its value as biomarker are described. Moreover, the rationales for different formats of immunotherapy against TNBC currently under clinical research are discussed, and major clinical trials are highlighted. Immune checkpoint inhibitors have demonstrated clinical benefit, particularly in early-stage tumors and when administered in combination with chemotherapy, with several regimens approved by the regulatory authorities. The success of antibody-drug conjugates and research on other emerging approaches, such as vaccines and cell therapies, will also be addressed. These advances give hope on the development of personalized, more effective, and safe treatments, which will improve the survival and quality of life of patients with TNBC.
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Affiliation(s)
- Rita Ribeiro
- CNC—Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Faculty of Medicine (Polo 1), Coimbra, Portugal
- iMed.ULisboa—Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
- Univ Coimbra—University of Coimbra, CIBB, Faculty of Pharmacy, Coimbra, Portugal
| | - Maria João Carvalho
- Univ Coimbra—University of Coimbra, CIBB, Faculty of Pharmacy, Coimbra, Portugal
- CHUC—Coimbra Hospital and University Centre, Department of Gynaecology, Coimbra, Portugal
- Univ Coimbra—University Clinic of Gynaecology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- iCBR—Institute for Clinical and Biomedical Research Area of Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- CACC—Clinical Academic Center of Coimbra, Coimbra, Portugal
| | - João Goncalves
- iMed.ULisboa—Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - João Nuno Moreira
- CNC—Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Faculty of Medicine (Polo 1), Coimbra, Portugal
- Univ Coimbra—University of Coimbra, CIBB, Faculty of Pharmacy, Coimbra, Portugal
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10
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Chen P, Mao X, Ma N, Wang C, Yao G, Ye G, Zhou D. Dynamic changes in intrinsic subtype, immunity status, and risk score before and after neoadjuvant chemo- and HER2-targeted therapy without pCR in HER2-positive breast cancers: A cross-sectional analysis. Medicine (Baltimore) 2022; 101:e29877. [PMID: 35945759 PMCID: PMC9351872 DOI: 10.1097/md.0000000000029877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Very few studies have been done in HER2 positive patients without complete pathological response (pCR) after combined neoadjuvant chemo- and HER2-target therapy to investigate changes in intrinsic subtype, risk of recurrence (ROR) score, and immunity status before and after treatment. Patients with nonmetastatic HER2-positive breast cancer failed to achieve pCR after neoadjuvant chemotherapy plus trastuzumab were included in current study. We examined the distribution of PAM50 subtypes, ROR score and immunity score in 25 paired baseline and surgical samples. The Miller-Payne grading system was used to evaluate the efficacy of the neoadjuvant therapy. It was observed that the distribution of intrinsic subtype, ROR category and immunity subgroup varied according to hormone receptor (HR) status. HER2-enriched and basal-like subtypes, median-high ROR categories and immunity-weak subgroup were dominant in baseline tumors. Compared to baseline samples, conversion of intrinsic subtype, ROR categories and immunity subgroups were found in 15 (60.0%), 13(52.0%), and 11(44.0%) surgical samples, respectively. The PAM50 subtype, ROR category, and immunity subgroup were concordant between baseline and surgical samples where nonluminal subtypes, median-high ROR categories and i-weak subgroup were still common. In conclusion, the HER2-positive breast cancer is highly heterogeneous with a distribution of 72-gene expression varying according to HR co-expression. The dynamics of the 72-gene expression pre- and posttreatment may become novel biomarker for guiding adjuvant therapy and hence warrant further investigation.
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Affiliation(s)
- Peixian Chen
- Department of Breast Surgery, The First People’s Hospital of Foshan, Guangdong, China
| | - Xiaofan Mao
- Clinical Research Institute, The First People’s Hospital of Foshan, Guangdong, China
| | - Na Ma
- Department of Pathology, The First People’s Hospital of Foshan, Guangdong, China
| | - Chuan Wang
- The First People’s Hospital of Foshan, Guangdong, China
| | - Guangyu Yao
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Province, hina
| | - Guolin Ye
- Department of Breast Surgery, The First People’s Hospital of Foshan, Guangdong, China
| | - Dan Zhou
- Department of Breast Surgery, The First People’s Hospital of Foshan, Guangdong, China
- * Correspondence: Dan Zhou, MD, Department of Breast Surgery, The First People’s Hospital of Foshan, #81, North Lingnan Avenue, Chancheng, Foshan, Guangdong, China (e-mail: )
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11
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Zhou Y, Tian Q, Gao H, Zhu L, Zhang Y, Zhang C, Yang J, Wang B. Immunity and Extracellular Matrix Characteristics of Breast Cancer Subtypes Based on Identification by T Helper Cells Profiling. Front Immunol 2022; 13:859581. [PMID: 35795662 PMCID: PMC9251002 DOI: 10.3389/fimmu.2022.859581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/19/2022] [Indexed: 01/04/2023] Open
Abstract
Background The therapeutic effect of immune checkpoint inhibitors on tumors is not only related to CD8+ effector T cells but also sufficiently related to CD4+ helper T (TH) cells. The immune characteristics of breast cancer, including gene characteristics and tumor-infiltrating lymphocytes, have become significant biomarkers for predicting prognosis and immunotherapy response in recent years. Methods Breast cancer samples from The Cancer Genome Atlas (TCGA) database and triple-negative breast cancer (TNBC) samples from GSE31519 in the Gene Expression Omnibus (GEO) database were extracted and clustered based on gene sets representing TH cell signatures. CIBERSORT simulations of immune cell components in the tumor microenvironment and gene set enrichment analyses (GSEAs) were performed in the different clusters to verify the classification of the subtypes. The acquisition of differentially expressed genes (DEGs) in the different clusters was further used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The clinical information from different clusters was used for survival analysis. Finally, the surgical tissues of TNBC samples were stained by immunofluorescence staining and Masson’s trichrome staining to explore the correlation of TH cell subtypes with extracellular matrix (ECM). Results The breast cancer samples from the datasets in TCGA database and GEO database were classified into TH-activated and TH-silenced clusters, which was verified by the immune cell components and enriched immune-related pathways. The DEGs of TH-activated and TH-silenced clusters were obtained. In addition to TH cells and other immune-related pathways, ECM-related pathways were found to be enriched by DEGs. Furthermore, the survival data of TCGA samples and GSE31519 samples showed that the 10-year overall survival (p-value < 0.001) and 10-year event-free survival (p-value = 0.162) of the TH-activated cluster were better, respectively. Fluorescent labeling of TH cell subtypes and staining of the collagen area of surgical specimens further illustrated the relationship between TH cell subtypes and ECM in breast cancer, among which high TH1 infiltration was related to low collagen content (p-value < 0.001), while high TH2 and Treg infiltration contained more abundant collagen (p-value < 0.05) in TNBC. With regard to the relationship of TH cell subtypes, TH2 was positively correlated with Treg (p-value < 0.05), while TH1 was negatively correlated with both of them. Conclusions The immune and ECM characteristics of breast cancer subtypes based on TH cell characteristics were revealed, and the relationship between different TH cell subsets and ECM and prognosis was explored in this study. The crosstalk between ECM and TH cell subtypes formed a balanced TME influencing the prognosis and treatment response in breast cancer, which suggests that the correlation between TH cells and ECM needs to be further emphasized in future breast cancer studies.
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Affiliation(s)
- Yan Zhou
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Qi Tian
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Huan Gao
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Lizhe Zhu
- Department of Breast Surgery, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Ying Zhang
- Department of Gastroenterology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Chenchen Zhang
- Department of Clinical Laboratory, the 940th Hospital of Joint Logistics Support Force of Chinese People’s Liberation Army, Key Laboratory of Stem Cells and Gene Drug in Gansu Province, Lanzhou, China
| | - Jiao Yang
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Jiao Yang, ; Bo Wang, ; orcid.org/0000-0001-7633-4435
| | - Bo Wang
- Center for Translational Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Xi’an, China
- *Correspondence: Jiao Yang, ; Bo Wang, ; orcid.org/0000-0001-7633-4435
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12
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Prognostic significance of different molecular typing methods and immune status based on RNA sequencing in HR-positive and HER2-negative early-stage breast cancer. BMC Cancer 2022; 22:548. [PMID: 35568835 PMCID: PMC9107692 DOI: 10.1186/s12885-022-09656-4] [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: 07/06/2021] [Accepted: 05/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND This study was conducted to evaluate the prognostic significance of different molecular typing methods and immune status based on RNA sequencing (RNA-seq) in hormone receptor (HR)-positive and human epidermal growth factor receptor 2 (HER2)-negative (HR + /HER2-) early-stage breast cancer and develop a modified immunohistochemistry (IHC)-based surrogate for intrinsic subtype analysis. METHODS The gene expression profiles of samples from 87 HR + /HER2- early-stage breast cancer patients were evaluated using the RNA-seq of Oncotype Dx recurrence score (RS), PAM50 risk of recurrence (ROR), and immune score. Intrinsic tumor subtypes were determined using both PAM50- and IHC-based detection of estrogen receptor, progesterone receptor, Ki-67, epidermal growth factor receptor, and cytokeratins 14 and 5/6. Prognostic variables were analyzed through Cox regression analysis of disease-free survival (DFS) and distant metastasis-free survival (DMFS). RESULTS Survival analysis showed that ROR better predicted recurrence and distant metastasis compared to RS (for DFS: ROR, P = 0.000; RS, P = 0.027; for DMFS, ROR, P = 0.047; RS, P = 0.621). Patients with HR + /HER2- early-stage breast cancer was classified into the luminal A, luminal B, HER2-enriched, and basal-like subtypes by PAM50. Basal-like subgroups showed the shortest DFS and DMFS. A modified IHC-based surrogate for intrinsic subtype analysis improved the concordance with PAM50 from 66.7% to 73.6%, particularly for basal-like subtype identification. High level of TILs and high expression of immune genes predicted poor prognosis. Multi-factor Cox analysis showed that IHC-based basal-like markers were the only independent factors affecting DMFS. CONCLUSIONS Prognosis is better evaluated by PAM50 ROR in early-stage HR + /HER2- breast cancer and significantly differs among intrinsic subtypes. The modified IHC-based subtype can improve the basal-like subtype identification of PAM50. High immunity status and IHC-based basal-like markers are negative prognostic factors.
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13
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Egelston CA, Guo W, Tan J, Avalos C, Simons DL, Lim MH, Huang YJ, Nelson MS, Chowdhury A, Schmolze DB, Yim JH, Kruper L, Melstrom L, Margolin K, Mortimer JE, Yuan Y, Waisman JR, Lee PP. Tumor-infiltrating exhausted CD8+ T cells dictate reduced survival in premenopausal estrogen receptor-positive breast cancer. JCI Insight 2022; 7:153963. [PMID: 35132960 PMCID: PMC8855819 DOI: 10.1172/jci.insight.153963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/21/2021] [Indexed: 12/31/2022] Open
Abstract
CD8+ tumor-infiltrating lymphocytes (TILs) are associated with improved survival in triple-negative breast cancer (TNBC) yet have no association with survival in estrogen receptor–positive (ER+) BC. The basis for these contrasting findings remains elusive. We identified subsets of BC tumors infiltrated by CD8+ T cells with characteristic features of exhausted T cells (TEX). Tumors with abundant CD8+ TEX exhibited a distinct tumor microenvironment marked by amplified interferon-γ signaling–related pathways and higher programmed death ligand 1 expression. Paradoxically, higher levels of tumor-infiltrating CD8+ TEX associated with decreased overall survival of patients with ER+ BC but not patients with TNBC. Moreover, high tumor expression of a CD8+ TEX signature identified dramatically reduced survival in premenopausal, but not postmenopausal, patients with ER+ BC. Finally, we demonstrated the value of a tumor TEX signature score in identifying high-risk premenopausal ER+ BC patients among those with intermediate Oncotype DX Breast Recurrence Scores. Our data highlight the complex relationship between CD8+ TILs, interferon-γ signaling, and ER status in BC patient survival. This work identifies tumor-infiltrating CD8+ TEX as a key feature of reduced survival outcomes in premenopausal patients with early-stage ER+ BC.
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Affiliation(s)
| | - Weihua Guo
- Department of Immuno-Oncology, Beckman Research Institute
| | - Jiayi Tan
- Department of Immuno-Oncology, Beckman Research Institute
| | | | - Diana L Simons
- Department of Immuno-Oncology, Beckman Research Institute
| | - Min Hui Lim
- Department of Immuno-Oncology, Beckman Research Institute
| | | | - Michael S Nelson
- Light Microscopy Digital Imaging Core, Beckman Research Institute
| | - Arnab Chowdhury
- Division of Biostatistics, Department of Computational and Quantitative Medicine, Beckman Research Institute; and
| | | | | | | | | | - Kim Margolin
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, California, USA
| | - Joanne E Mortimer
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, California, USA
| | - Yuan Yuan
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, California, USA
| | - James R Waisman
- Department of Medical Oncology & Therapeutics Research, City of Hope, Duarte, California, USA
| | - Peter P Lee
- Department of Immuno-Oncology, Beckman Research Institute
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14
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Gene Expression Profiling in Early Breast Cancer-Patient Stratification Based on Molecular and Tumor Microenvironment Features. Biomedicines 2022; 10:biomedicines10020248. [PMID: 35203458 PMCID: PMC8869155 DOI: 10.3390/biomedicines10020248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/12/2022] [Accepted: 01/19/2022] [Indexed: 11/17/2022] Open
Abstract
Patients with early-stage hormone receptor-positive, human epidermal growth factor receptor 2-negative (HER2−) breast cancer (BC) are typically treated with surgery, followed by adjuvant systemic endocrine therapy with or without adjuvant chemotherapy and radiation therapy. Current guidelines regarding the use of adjuvant systemic therapy depend on clinical and pathological factors, such as the morphological assessment of tumor subtype; histological grade; tumor size; lymphovascular invasion; and lymph node status combined with estrogen receptor, progesterone receptor, and HER2 biomarker profiles assessed using immunohistochemistry and in situ hybridization. Additionally, the prognostic and predictive value of tumor-infiltrating lymphocytes and their composition is emerging as a key marker in triple negative (TNBC) and HER2-enriched molecular breast tumor subtypes. However, all these factors do not necessarily reflect the molecular heterogeneity and complexity of breast cancer. In the last two decades, gene expression signatures or profiling (GEP) tests have been developed to predict the risk of disease recurrence and estimate the potential benefit of receiving adjuvant systemic chemotherapy in patients with luminal breast cancer. GEPs have been utilized to help physicians to refine decision-making process, complementing clinicopathological parameters, and can now be used to classify the risk of recurrence and tailoring personalized treatments. Several clinical trials using GEPs validate the increasing value of such assays in different clinical settings, addressing relevant clinical endpoints. Finally, the recent approval of immune checkpoint inhibitors in TNBC and the increasing use of immunotherapy in different molecular BC populations highlight the opportunity to refine current GEPs by including a variety of immune-related genes that may help to improve predicting drug response and finetune prognosis.
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15
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Liao G, Jiang Z, Yang Y, Zhang C, Jiang M, Zhu J, Xu L, Xie A, Yan M, Zhang Y, Xiao Y, Li X. Combined homologous recombination repair deficiency and immune activation analysis for predicting intensified responses of anthracycline, cyclophosphamide and taxane chemotherapy in triple-negative breast cancer. BMC Med 2021; 19:190. [PMID: 34465315 PMCID: PMC8408988 DOI: 10.1186/s12916-021-02068-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/20/2021] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is a clinically aggressive disease with abundant variants that cause homologous recombination repair deficiency (HRD). Whether TNBC patients with HRD are sensitive to anthracycline, cyclophosphamide and taxane (ACT), and whether the combination of HRD and tumour immunity can improve the recognition of ACT responders are still unknown. METHODS Data from 83 TNBC patients in The Cancer Genome Atlas (TCGA) was used as a discovery cohort to analyse the association between HRD and ACT chemotherapy benefits. The combined effects of HRD and immune activation on ACT chemotherapy were explored at both the genome and the transcriptome levels. Independent cohorts from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) and Gene Expression Omnibus (GEO) were adopted to validate our findings. RESULTS HRD was associated with a longer ACT chemotherapy failure-free interval (FFI) with a hazard ratio of 0.16 (P = 0.004) and improved patient prognosis (P = 0.0063). By analysing both HRD status and ACT response, we identified patients with a distinct TNBC subtype (ACT-S&HR-P) that showed higher tumour lymphocyte infiltration, IFN-γ activity and NK cell levels. Patients with ACT-S&HR-P had significantly elevated immune inhibitor levels and presented immune activation associated with the increased activities of both innate immune cells and adaptive immune cells, which suggested treatment with immune checkpoint blockade as an option for this subtype. Our analysis revealed that the combination of HRD and immune activation enhanced the efficiency of identifying responders to ACT chemotherapy (AUC = 0.91, P = 1.06e-04) and synergistically contributed to the clinical benefits of TNBC patients. A transcriptional HRD signature of ACT response-related prognostic factors was identified and independently validated to be significantly associated with improved survival in the GEO cohort (P = 0.0038) and the METABRIC dataset (P < 0.0001). CONCLUSIONS These findings highlight that HR deficiency prolongs FFI and predicts intensified responses in TNBC patients by combining HRD and immune activation, which provides a molecular basis for identifying ACT responders.
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Affiliation(s)
- Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Zedong Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yiran Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Cong Zhang
- Department of Ultrasonic Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, 150010, Heilongjiang, China
| | - Meiting Jiang
- Key Laboratory of University in Heilongjiang Province, Department of Pharmacy, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Jiali Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Aimin Xie
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Min Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China. .,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, 150081, Heilongjiang, China.
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China. .,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, 150081, Heilongjiang, China.
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16
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Iwanowycz S, Ngoi S, Li Y, Hill M, Koivisto C, Parrish M, Guo B, Li Z, Liu B. Type-2 dendritic cells mediate control of cytotoxic T cell-resistant tumors. JCI Insight 2021; 6:e145885. [PMID: 34283809 PMCID: PMC8492342 DOI: 10.1172/jci.insight.145885] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 07/15/2021] [Indexed: 11/17/2022] Open
Abstract
Type 2 DCs (DC2s) comprise the majority of conventional DCs within most tumors; however, little is known about their ability to initiate and sustain antitumor immunity, as most studies have focused on antigen cross-presenting DC1s. Here, we report that DC2 infiltration identified by analysis of multiple human cancer data sets showed a significant correlation with survival across multiple human cancers, with the benefit being seen in tumors resistant to cytotoxic T cell control. Characterization of DC subtype infiltration into an immunotherapy-resistant model of breast cancer revealed that impairment of DC1s through 2 unique models resulted in enhanced DC2 functionality and improved tumor control. BATF3 deficiency depleted intratumoral DC1s, which led to increased DC2 lymph node migration and CD4+ T cell activation. Enhancing DC2 stimulatory potential by genetic deletion of Hsp90b1 (encoding molecular chaperon GP96) led to a similar enhancement of T cell immunity and improved survival in a spontaneous breast cancer model. These data highlight the therapeutic and prognostic potential of DC2s within checkpoint blockade–resistant tumors.
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Affiliation(s)
- Stephen Iwanowycz
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, United States of America
| | - Soo Ngoi
- Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, United States of America
| | - Yingqi Li
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, United States of America
| | - Megan Hill
- Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, United States of America
| | - Christopher Koivisto
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, United States of America
| | - Melodie Parrish
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, United States of America
| | - Beichu Guo
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, United States of America
| | - Zihai Li
- The Pelotonia Institute for Immuno-Oncology, The Ohio State University College of Medicine, Columbus, United States of America
| | - Bei Liu
- Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, United States of America
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17
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Mathias C, Muzzi JCD, Antunes BB, Gradia DF, Castro MAA, Carvalho de Oliveira J. Unraveling Immune-Related lncRNAs in Breast Cancer Molecular Subtypes. Front Oncol 2021; 11:692170. [PMID: 34136413 PMCID: PMC8202402 DOI: 10.3389/fonc.2021.692170] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/06/2021] [Indexed: 12/15/2022] Open
Abstract
Breast cancer (BRCA) is the most leading cause of cancer worldwide. It is a heterogeneous disease with at least five molecular subtypes including luminal A, luminal B, basal-like, HER2-enriched, and normal-like. These five molecular subtypes are usually stratified according to their mRNA profile patterns; however, ncRNAs are increasingly being used for this purpose. Among the ncRNAs class, the long non-coding RNAs (lncRNAs) are molecules with more than 200 nucleotides with versatile regulatory roles; and high tissue-specific expression profiles. The heterogeneity of BRCA can also be reflected regarding tumor microenvironment immune cells composition, which can directly impact a patient's prognosis and therapy response. Using BRCA immunogenomics data from a previous study, we propose here a bioinformatics approach to include lncRNAs complexity in BRCA molecular and immune subtype. RNA-seq data from The Cancer Genome Atlas (TCGA) BRCA cohort was analyzed, and signal-to-noise ratio metrics were applied to create these subtype-specific signatures. Five immune-related signatures were generated with approximately ten specific lncRNAs, which were then functionally analyzed using GSEA enrichment and survival analysis. We highlighted here some lncRNAs in each subtype. LINC01871 is related to immune response activation and favorable overall survival in basal-like samples; EBLN3P is related to immune response suppression and progression in luminal B, MEG3, XXYLT1-AS2, and LINC02613 were related with immune response activation in luminal A, HER2-enriched and normal-like subtypes, respectively. In this way, we emphasize the need to know better the role of lncRNAs as regulators of immune response to provide new perspectives regarding diagnosis, prognosis and therapeutical targets in BRCA molecular subtypes.
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Affiliation(s)
- Carolina Mathias
- Department of Genetics, Federal University of Parana, Post-graduation Program in Genetics, Curitiba, Brazil
| | - João Carlos Degraf Muzzi
- Bioinformatics and Systems Biology Lab, Federal University of Parana (UFPR), Polytechnic Center, Curitiba, Brazil.,Immunochemistry Laboratory (LIMQ), Federal University of Parana, Post-graduation Program in Microbiology, Parasitology and Pathology, Curitiba, Brazil.,Instituto de Pesquisa Pelé Pequeno Príncipe, Oncology Division, Curitiba, Brazil
| | - Bruna Borba Antunes
- Department of Genetics, Federal University of Parana, Post-graduation Program in Genetics, Curitiba, Brazil.,Bioinformatics and Systems Biology Lab, Federal University of Parana (UFPR), Polytechnic Center, Curitiba, Brazil
| | - Daniela F Gradia
- Department of Genetics, Federal University of Parana, Post-graduation Program in Genetics, Curitiba, Brazil
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Lab, Federal University of Parana (UFPR), Polytechnic Center, Curitiba, Brazil
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18
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Wu HJ, Chu PY. Recent Discoveries of Macromolecule- and Cell-Based Biomarkers and Therapeutic Implications in Breast Cancer. Int J Mol Sci 2021; 22:ijms22020636. [PMID: 33435254 PMCID: PMC7827149 DOI: 10.3390/ijms22020636] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/31/2020] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
Breast cancer is the most commonly diagnosed cancer type and the leading cause of cancer-related mortality in women worldwide. Breast cancer is fairly heterogeneous and reveals six molecular subtypes: luminal A, luminal B, HER2+, basal-like subtype (ER−, PR−, and HER2−), normal breast-like, and claudin-low. Breast cancer screening and early diagnosis play critical roles in improving therapeutic outcomes and prognosis. Mammography is currently the main commercially available detection method for breast cancer; however, it has numerous limitations. Therefore, reliable noninvasive diagnostic and prognostic biomarkers are required. Biomarkers used in cancer range from macromolecules, such as DNA, RNA, and proteins, to whole cells. Biomarkers for cancer risk, diagnosis, proliferation, metastasis, drug resistance, and prognosis have been identified in breast cancer. In addition, there is currently a greater demand for personalized or precise treatments; moreover, the identification of novel biomarkers to further the development of new drugs is urgently needed. In this review, we summarize and focus on the recent discoveries of promising macromolecules and cell-based biomarkers for the diagnosis and prognosis of breast cancer and provide implications for therapeutic strategies.
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Affiliation(s)
- Hsing-Ju Wu
- Department of Biology, National Changhua University of Education, Changhua 500, Taiwan;
- Research Assistant Center, Show Chwan Memorial Hospital, Changhua 500, Taiwan
- Department of Medical Research, Chang Bing Show Chwan Memorial Hospital, Lukang Town, Changhua County 505, Taiwan
| | - Pei-Yi Chu
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 231, Taiwan
- Department of Pathology, Show Chwan Memorial Hospital, No. 542, Sec. 1 Chung-Shan Rd., Changhua 500, Taiwan
- Department of Health Food, Chung Chou University of Science and Technology, Changhua 510, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
- Correspondence: ; Tel.: +886-975-611-855; Fax: +886-4-7227-116
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19
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Lee H, Kwon MJ, Koo BM, Park HG, Han J, Shin YK. A novel immune prognostic index for stratification of high-risk patients with early breast cancer. Sci Rep 2021; 11:128. [PMID: 33420250 PMCID: PMC7794340 DOI: 10.1038/s41598-020-80274-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 12/18/2020] [Indexed: 12/22/2022] Open
Abstract
The prognostic value of current multigene assays for breast cancer is limited to hormone receptor-positive, human epidermal growth factor receptor 2-negative early breast cancer. Despite the prognostic significance of immune response-related genes in breast cancer, immune gene signatures have not been incorporated into most multigene assays. Here, using public gene expression microarray datasets, we classified breast cancer patients into three risk groups according to clinical risk and proliferation risk. We then developed the immune prognostic index based on expression of five immune response-related genes (TRAT1, IL2RB, CTLA4, IGHM and IL21R) and lymph node status to predict the risk of recurrence in the clinical and proliferation high-risk (CPH) group. The 10-year probability of disease-free survival (DFS) or distant metastasis-free survival (DMFS) of patients classified as high risk according to the immune prognostic index was significantly lower than those of patients classified as intermediate or low risk. Multivariate analysis revealed that the index is an independent prognostic factor for DFS or DMFS. Moreover, the C-index revealed that it is superior to clinicopathological variables for predicting prognosis. Its prognostic significance was also validated in independent datasets. The immune prognostic index identified low-risk patients among patients classified as CPH, regardless of the molecular subtype of breast cancer, and may overcome the limitations of current multigene assays.
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Affiliation(s)
- Hannah Lee
- Interdisciplinary Program in Bioinformatics, College of Natural Sciences, Seoul National University, Seoul, 41566, Republic of Korea
| | - Mi Jeong Kwon
- College of Pharmacy, Kyungpook National University, Daegu, 41566, Republic of Korea.,Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Beom-Mo Koo
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hee Geon Park
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jinil Han
- Gencurix, Inc., Seoul, 08394, Republic of Korea
| | - Young Kee Shin
- Interdisciplinary Program in Bioinformatics, College of Natural Sciences, Seoul National University, Seoul, 41566, Republic of Korea. .,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, 08826, Republic of Korea. .,Laboratory of Molecular Pathology and Cancer Genomics, Department of Pharmacy, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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20
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Inflammation Is Associated with Worse Outcome in the Whole Cohort but with Better Outcome in Triple-Negative Subtype of Breast Cancer Patients. J Immunol Res 2020; 2020:5618786. [PMID: 33457427 PMCID: PMC7787871 DOI: 10.1155/2020/5618786] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 11/24/2020] [Accepted: 11/28/2020] [Indexed: 02/07/2023] Open
Abstract
Inflammation has been linked with cancer, but whether it is part of the problem or part of the solution remains to be a matter of debate in breast cancer. Our group and others have demonstrated that inflammation aggravates cancer progression; however, some claim that inflammation may support immune cell infiltration and suppress cancer. We defined the gene set variation analysis of the Molecular Signatures Database Hallmark inflammatory response gene set as the inflammatory pathway score and analyzed 3632 tumors in total from 4 breast cancer cohorts (METABRIC, TCGA, GSE25066, and GSE21094). In the whole breast cancer cohort, high-score tumors were associated with aggressive clinical characteristics, such as worse disease specific survival, higher Nottingham histological grade, and younger age. Inflammatory score was significantly higher in triple-negative (TNBC) as well as basal and normal subtypes compared with the other subtypes, which suggest that the detrimental effect of high level of inflammation may be because it includes a more aggressive subtype. On the contrary, high score within TNBC was significantly associated with better survival. TNBC with high score enriched not only IFN-α, IFN-γ response, IL-2/STAT5 signaling, Allograft rejection, Complement, p53 pathway, Reactive Oxygen, and Apoptosis but also TNF-α signaling, IL6-JAK-STAT signaling, TGF-β signaling, Coagulation, Angiogenesis, EMT, KRAS signaling, and PI3K-AKT-MTOR signaling gene sets. High score was associated with mainly favorable anticancerous immune cell infiltration as well as Leukocyte fraction, TIL regional fraction, Lymphocyte infiltration, IFN-γ response, TGF-β response, and cytolytic activity scores. Although the inflammatory pathway score was not associated with neoadjuvant treatment response, it associated with expressions of immune checkpoint molecules. In conclusion, inflammation was associated with worse outcome in the whole breast cancer cohort, but with better outcome in TNBC, which was associated with favorable anticancerous immune response and immune cell infiltrations.
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Pandey K, Park N, Park KS, Hur J, Cho YB, Kang M, An HJ, Kim S, Hwang S, Moon YW. Combined CDK2 and CDK4/6 Inhibition Overcomes Palbociclib Resistance in Breast Cancer by Enhancing Senescence. Cancers (Basel) 2020; 12:E3566. [PMID: 33260316 PMCID: PMC7768442 DOI: 10.3390/cancers12123566] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/19/2022] Open
Abstract
Breast cancer represents the number one global cancer burden in women and the hormone receptor (HR)-positive subtype comprises approximately 70% of breast cancers. Unfortunately, acquired resistance ultimately occurs in almost all cases, even though cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitors are a highly effective therapy for HR-positive/human epidermal growth factor receptor 2-negative subtype. Here, we investigated mechanisms of resistance to CDK4/6 inhibitor and potential therapeutic strategies using our palbociclib-resistant preclinical model. We observed that cyclin E was significantly overexpressed in palbociclib-resistant cells, and similar association was also confirmed in pleural effusion samples collected from HR-positive breast cancer patients. After confirmation of cyclin E-CDK2 interaction by co-immunoprecipitation, we demonstrated CDK2 inhibition combined with palbociclib synergistically suppressed proliferation of palbociclib-resistant cells and growth of palbociclib-resistant xenograft in mice. We also proved that enhancing C-MYC-mediated senescence is a novel mechanism behind the synergism created by targeting both CDK2 and CDK4/6. Furthermore, the clinical relevance of cyclin E as a therapeutic target was supported by significant association between CCNE1 overexpression and poor prognosis based on large-scale public gene expression data sets in HR-positive breast cancer patients. Therefore, we propose cyclin E-CDK2 signaling as a promising therapeutic target for overcoming cyclin E-associated resistance to CDK4/6 inhibitor.
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Affiliation(s)
- Kamal Pandey
- Hematology and Oncology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam 13488, Korea; (K.P.); (N.P.); (J.H.); (Y.B.C.); (M.K.)
- Department of Biomedical Science, CHA University, Seongnam 13488, Korea; (K.-S.P.); (S.H.)
| | - Nahee Park
- Hematology and Oncology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam 13488, Korea; (K.P.); (N.P.); (J.H.); (Y.B.C.); (M.K.)
| | - Kyung-Soon Park
- Department of Biomedical Science, CHA University, Seongnam 13488, Korea; (K.-S.P.); (S.H.)
| | - Jin Hur
- Hematology and Oncology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam 13488, Korea; (K.P.); (N.P.); (J.H.); (Y.B.C.); (M.K.)
- Department of Biomedical Science, CHA University, Seongnam 13488, Korea; (K.-S.P.); (S.H.)
| | - Yong Bin Cho
- Hematology and Oncology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam 13488, Korea; (K.P.); (N.P.); (J.H.); (Y.B.C.); (M.K.)
| | - Minsil Kang
- Hematology and Oncology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam 13488, Korea; (K.P.); (N.P.); (J.H.); (Y.B.C.); (M.K.)
| | - Hee-Jung An
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam 13488, Korea; (H.-J.A.); (S.K.)
| | - Sewha Kim
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam 13488, Korea; (H.-J.A.); (S.K.)
| | - Sohyun Hwang
- Department of Biomedical Science, CHA University, Seongnam 13488, Korea; (K.-S.P.); (S.H.)
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam 13488, Korea; (H.-J.A.); (S.K.)
| | - Yong Wha Moon
- Hematology and Oncology, Department of Internal Medicine, CHA Bundang Medical Center, CHA University, Seongnam 13488, Korea; (K.P.); (N.P.); (J.H.); (Y.B.C.); (M.K.)
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22
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Wang Y, Luo M, Chen Y, Wang Y, Zhang B, Ren Z, Bao L, Wang Y, Wang JE, Fu YX, Luo W, Wang Y. ZMYND8 Expression in Breast Cancer Cells Blocks T-Lymphocyte Surveillance to Promote Tumor Growth. Cancer Res 2020; 81:174-186. [PMID: 33148660 DOI: 10.1158/0008-5472.can-20-1710] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 10/05/2020] [Accepted: 10/30/2020] [Indexed: 11/16/2022]
Abstract
Emerging studies indicate that DNA damage in cancer cells triggers antitumor immunity, but its intrinsic regulatory mechanism in breast cancer cells remains poorly understood. Here, we show that ZMYND8 is upregulated and inhibits micronucleus formation and DNA damage in breast cancer cells. Loss of ZMYND8 triggered activation of the DNA sensor cyclic guanosine monophosphate-adenosine monophosphate synthase in micronuclei, leading to further activation of the downstream signaling effectors stimulator of IFN genes and NF-κB, but not TANK-binding kinase 1 and IFN regulatory factor 3, thereby inducing the expression of IFNβ and IFN-stimulated genes (ISG) in breast cancer cells in vitro and tumors in vivo. ZMYND8 knockout (KO) in breast cancer cells promoted infiltration of CD4+ and CD8+ T cells, leading to tumor inhibition in syngeneic mouse models, which was significantly attenuated by treatment of anti-CD4/CD8-depleting antibodies or anti-IFNAR1 antibody and in immunodeficient Rag1 KO mice. In human breast tumors, ZMYND8 was negatively correlated with ISGs, CD4, CD8A, CD8B, and the tumor-lymphocyte infiltration phenotype. Collectively, these findings demonstrate that maintenance of genome stability by ZMYND8 causes breast cancer cells to evade cytotoxic T-lymphocyte surveillance, which leads to tumor growth. SIGNIFICANCE: These findings show that ZMYND8 is a new negative and intrinsic regulator of the innate immune response in breast tumor cells, and ZMYND8 may be a possible target for antitumor immunotherapy.
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Affiliation(s)
- Yong Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Maowu Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Yan Chen
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Yijie Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Bo Zhang
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Zhenhua Ren
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Lei Bao
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Yanan Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Jennifer E Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Yang-Xin Fu
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | - Weibo Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas. .,Department of Pharmacology, UT Southwestern Medical Center, Dallas, Texas
| | - Yingfei Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas. .,Department of Neurology, UT Southwestern Medical Center, Dallas, Texas
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23
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Porter W, Snowden E, Hahn F, Ferguson M, Tong F, Dillmore WS, Blaesius R. High accuracy gene expression profiling of sorted cell subpopulations from breast cancer PDX model tissue. PLoS One 2020; 15:e0238594. [PMID: 32911489 PMCID: PMC7482927 DOI: 10.1371/journal.pone.0238594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/19/2020] [Indexed: 01/01/2023] Open
Abstract
Intratumor Heterogeneity (ITH) is a functionally important property of tumor tissue and may be involved in drug resistance mechanisms. Although descriptions of ITH can be traced back to very early reports about cancer tissue, mechanistic investigations are still limited by the precision of analysis methods and access to relevant tissue sources. PDX models have provided a reproducible source of tissue with at least a partial representation of naturally occurring ITH. We investigated the properties of phenotypically distinct cell populations by Fluorescence activated cell sorting (FACS) tissue derived cells from multiple tumors from a triple negative breast cancer patient derived xenograft (PDX) model. We subsequently subjected each population to in depth gene expression analysis. Our findings suggest that process related gene expression changes (caused by tissue dissociation and FACS sorting) are restricted to Immediate Early Genes (IEGs). This allowed us to discover highly reproducible gene expression profiles of distinct cellular compartments identifiable by cell surface markers in this particular tumor model. Within the context of data from a previously published model our work suggests that gene expression profiles associated with hypoxia, stemness and drug resistance may reside in tumor subpopulations predictably growing in PDX models. This approach provides a novel opportunity for prospective mechanistic studies of ITH.
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Affiliation(s)
- Warren Porter
- BD Technologies and Innovation, Research Triangle Park, NC, United States of America
| | - Eileen Snowden
- BD Technologies and Innovation, Research Triangle Park, NC, United States of America
| | - Friedrich Hahn
- BD Technologies and Innovation, Research Triangle Park, NC, United States of America
| | - Mitchell Ferguson
- BD Technologies and Innovation, Research Triangle Park, NC, United States of America
| | - Frances Tong
- BD Technologies and Innovation, Research Triangle Park, NC, United States of America
| | - W. Shannon Dillmore
- BD Technologies and Innovation, Research Triangle Park, NC, United States of America
| | - Rainer Blaesius
- BD Technologies and Innovation, Research Triangle Park, NC, United States of America
- * E-mail:
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24
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Zhang Z, Li J, He T, Ding J. Bioinformatics Identified 17 Immune Genes as Prognostic Biomarkers for Breast Cancer: Application Study Based on Artificial Intelligence Algorithms. Front Oncol 2020; 10:330. [PMID: 32296631 PMCID: PMC7137378 DOI: 10.3389/fonc.2020.00330] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/25/2020] [Indexed: 12/16/2022] Open
Abstract
An increasing body of evidence supports the association of immune genes with tumorigenesis and prognosis of breast cancer (BC). This research aims at exploring potential regulatory mechanisms and identifying immunogenic prognostic markers for BC, which were used to construct a prognostic signature for disease-free survival (DFS) of BC based on artificial intelligence algorithms. Differentially expressed immune genes were identified between normal tissues and tumor tissues. Univariate Cox regression identified potential prognostic immune genes. Thirty-four transcription factors and 34 immune genes were used to develop an immune regulatory network. The artificial intelligence survival prediction system was developed based on three artificial intelligence algorithms. Multivariate Cox analyses determined 17 immune genes (ADAMTS8, IFNG, XG, APOA5, SIAH2, C2CD2, STAR, CAMP, CDH19, NTSR1, PCDHA1, AMELX, FREM1, CLEC10A, CD1B, CD6, and LTA) as prognostic biomarkers for BC. A prognostic nomogram was constructed on these prognostic genes. Concordance indexes were 0.782, 0.734, and 0.735 for 1-, 3-, and 5- year DFS. The DFS in high-risk group was significantly worse than that in low-risk group. Artificial intelligence survival prediction system provided three individual mortality risk predictive curves based on three artificial intelligence algorithms. In conclusion, comprehensive bioinformatics identified 17 immune genes as potential prognostic biomarkers, which might be potential candidates of immunotherapy targets in BC patients. The current study depicted regulatory network between transcription factors and immune genes, which was helpful to deepen the understanding of immune regulatory mechanisms for BC cancer. Two artificial intelligence survival predictive systems are available at https://zhangzhiqiao7.shinyapps.io/Smart_Cancer_Survival_Predictive_System_16_BC_C1005/ and https://zhangzhiqiao8.shinyapps.io/Gene_Survival_Subgroup_Analysis_16_BC_C1005/. These novel artificial intelligence survival predictive systems will be helpful to improve individualized treatment decision-making.
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Affiliation(s)
- Zhiqiao Zhang
- Department of Infectious Diseases, Shunde Hospital, Southern Medical University, Shunde, China
| | - Jing Li
- Department of Infectious Diseases, Shunde Hospital, Southern Medical University, Shunde, China
| | - Tingshan He
- Department of Infectious Diseases, Shunde Hospital, Southern Medical University, Shunde, China
| | - Jianqiang Ding
- Department of Infectious Diseases, Shunde Hospital, Southern Medical University, Shunde, China
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25
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A benchmark of hemoglobin blocking during library preparation for mRNA-Sequencing of human blood samples. Sci Rep 2020; 10:5630. [PMID: 32221409 PMCID: PMC7101437 DOI: 10.1038/s41598-020-62637-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/17/2020] [Indexed: 01/03/2023] Open
Abstract
RNA-Sequencing (RNA-Seq) of peripheral blood can be a valuable source of information for investigating the status and mechanism of diseases. However, blood contains 50–80% unwanted hemoglobin (Hb) transcripts. Lexogen’s QuantSeq mRNA-Seq-Kit for Illumina RNA-Seq features a ‘Globin Block’ (GB) module that depletes Hb cDNAs during library preparation. Here, we aimed to assess GB’s effectiveness and checked for technical biases attributable to GB. Using whole blood total RNA samples of 91 healthy individuals, we sequenced 91 pairs of GB and non-blocked samples (noGB) on Illumina HiSeq2500 and 8 pairs of GB/noGB technical replicates on HiSeq4000. GB reduced the fraction of Hb transcripts from 43% (s.d. 14%) to 8.0% (s.d. 4.3%). From GB samples we detected 1,397 more expressed genes at approximately 11 million reads per RNA-isolate. Enrichment and differential expression analyses did not reveal significant differences for GB and noGB samples with respect to molecular function. In contrast to results from studies that have examined the performance of GB during RNA isolation, we were able to assign GB to corresponding noGB samples (from multiple sequencing runs on HiSeq2500) with at least 89.8% accuracy from the complete correlation matrix of all GB/GB, noGB/noGB and GB/noGB pairs. However, the use of different sequencers (HiSeq2500 vs HiSeq4000) impaired assignment of technical replicates, whereas assignment of GB to corresponding noGB samples worked perfectly when sequencing on one lane on HiSeq4000. Lexogen’s GB RNA-Seq module is a valuable addition during mRNA-Seq library preparation which works even with low amounts of input total RNA (50 ng per sample). GB facilitated the detection of low abundant transcripts and yielded more non-hemoglobin reads, while preserving biological information. We observed that differences in sequencing run and platform have a far greater effect on technical variation than the use of GB.
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26
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Xu M, Li Y, Li W, Zhao Q, Zhang Q, Le K, Huang Z, Yi P. Immune and Stroma Related Genes in Breast Cancer: A Comprehensive Analysis of Tumor Microenvironment Based on the Cancer Genome Atlas (TCGA) Database. Front Med (Lausanne) 2020; 7:64. [PMID: 32195260 PMCID: PMC7066229 DOI: 10.3389/fmed.2020.00064] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/12/2020] [Indexed: 01/02/2023] Open
Abstract
Background: Tumor microenvironment is essential for breast cancer progression and metastasis. Our study sets out to examine the genes affecting stromal and immune infiltration in breast cancer progression and prognosis. Materials and Methods: This work provides an approach for quantifying stromal and immune scores by using ESTIMATE algorithm based on gene expression matrix of breast cancer patients in TCGA database. We found differentially expressed genes (DEGs) through limma R package. Functional enrichments were accessed through Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Besides, we constructed a protein-protein network, identified several hub genes in Cytoscape, and discovered functionally similar genes in GeneMANIA. Hub genes were validated with prognostic data by Kaplan-Meier analysis both in The Cancer Genome Atlas (TCGA) database and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) database and a meta-analysis of hub genes prognosis data was utilized in multiple databases. Furthermore, their relationship with infiltrating immune cells was evaluated by Tumor IMmune Estimation Resource (TIMER) web tool. Cox regression was utilized for overall survival (OS) and recurrence-free survival (RFS) in TCGA database and OS in METABRIC database in order to evaluate the impact of stromal and immune scores on patients prognosis. Results: One thousand and eighty-five breast cancer patients were investigated and 480 differentiated expressed genes (DEGs) were found based on the analysis of mRNA expression profiles. Functional analysis of DEGs revealed their potential functions in immune response and extracellular interaction. Protein-protein interaction network gave evidence of 10 hub genes. Some of the hub genes could be used as predictive markers for patients prognosis. In this study, we found that tumor purity and specific immune cells infiltration varied in response to hub genes expression. The multivariate cox regression highlighted the fact that immune score played a detrimental role in overall survival (HR = 0.45, 95% CI: 0.27–0.74, p = 0.002) and recurrence-free survival (HR = 0.41, 95% CI: 0.22–0.77, p = 0.006) in TCGA database. These result was confirmed in METABRIC database that immune score was a protector of OS (HR = 0.88, 95% CI: 0.77–0.99, p = 0.039). Conclusions: Our findings promote a better understanding of the potential genes behind the regulation of tumor microenvironment and cells infiltration. Immune score should be considered as a prognostic factor for patients' survival.
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Affiliation(s)
- Ming Xu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Li
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenhui Li
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiuyang Zhao
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiulei Zhang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kehao Le
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ziwei Huang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pengfei Yi
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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27
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Pennock ND, Jindal S, Horton W, Sun D, Narasimhan J, Carbone L, Fei SS, Searles R, Harrington CA, Burchard J, Weinmann S, Schedin P, Xia Z. RNA-seq from archival FFPE breast cancer samples: molecular pathway fidelity and novel discovery. BMC Med Genomics 2019; 12:195. [PMID: 31856832 PMCID: PMC6924022 DOI: 10.1186/s12920-019-0643-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/08/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Formalin-fixed, paraffin-embedded (FFPE) tissues for RNA-seq have advantages over fresh frozen tissue including abundance and availability, connection to rich clinical data, and association with patient outcomes. However, FFPE-derived RNA is highly degraded and chemically modified, which impacts its utility as a faithful source for biological inquiry. METHODS True archival FFPE breast cancer cases (n = 58), stored at room temperature for 2-23 years, were utilized to identify key steps in tissue selection, RNA isolation, and library choice. Gene expression fidelity was evaluated by comparing FFPE data to public data obtained from fresh tissues, and by employing single-gene, gene set and transcription network-based regulon analyses. RESULTS We report a single 10 μm section of breast tissue yields sufficient RNA for RNA-seq, and a relationship between RNA quality and block age that was not linear. We find single-gene analysis is limiting with FFPE tissues, while targeted gene set approaches effectively distinguish ER+ from ER- breast cancers. Novel utilization of regulon analysis identified the transcription factor KDM4B to associate with ER+ disease, with KDM4B regulon activity and gene expression having prognostic significance in an independent cohort of ER+ cases. CONCLUSION Our results, which outline a robust FFPE-RNA-seq pipeline for broad use, support utilizing FFPE tissues to address key questions in the breast cancer field, including the delineation between indolent and life-threatening disease, biological stratification and molecular mechanisms of treatment resistance.
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Affiliation(s)
- Nathan D Pennock
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA
| | - Sonali Jindal
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA
- Knight Cancer Institute, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA
| | - Wesley Horton
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA
- Computational Biology Program, Oregon Health & Science University, Portland, OR, 97201, USA
| | - Duanchen Sun
- Computational Biology Program, Oregon Health & Science University, Portland, OR, 97201, USA
| | - Jayasri Narasimhan
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA
| | - Lucia Carbone
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, 3303 SW Bond Ave, Portland, OR, 97239, USA
| | - Suzanne S Fei
- Bioinformatics & Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
| | - Robert Searles
- Integrated Genomics Laboratory, Knight Cancer Institute, Oregon Health & Science University Knight Cancer Institute, Portland, OR, 97239, USA
| | - Christina A Harrington
- Integrated Genomics Laboratory, Knight Cancer Institute, Oregon Health & Science University Knight Cancer Institute, Portland, OR, 97239, USA
| | - Julja Burchard
- Computational Biology Program, Oregon Health & Science University, Portland, OR, 97201, USA
| | - Sheila Weinmann
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR, 97278, USA
| | - Pepper Schedin
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA.
- Knight Cancer Institute, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA.
- Young Women's Breast Cancer Translational Program, University of Colorado Anschutz Medical Campus, 1665 Aurora Court, USA, Aurora, CO, 80045, USA.
| | - Zheng Xia
- Computational Biology Program, Oregon Health & Science University, Portland, OR, 97201, USA.
- Department of Molecular Microbiology and Immunology Oregon Health & Science University, Portland, OR, 97273, USA.
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28
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Li H, Gao C, Liu L, Zhuang J, Yang J, Liu C, Zhou C, Feng F, Sun C. 7-lncRNA Assessment Model for Monitoring and Prognosis of Breast Cancer Patients: Based on Cox Regression and Co-expression Analysis. Front Oncol 2019; 9:1348. [PMID: 31850229 PMCID: PMC6901675 DOI: 10.3389/fonc.2019.01348] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 11/15/2019] [Indexed: 01/11/2023] Open
Abstract
Background: Breast cancer is one of the deadliest malignant tumors worldwide. Due to its complex molecular and cellular heterogeneity, the efficacy of existing breast cancer risk prediction models is unsatisfactory. In this study, we developed a new lncRNA model to predict the prognosis of patients with BRCA. Methods: BRCA-related differentially-expressed long non-coding RNA were screened from the Cancer Genome Atlas database. A novel lncRNA model was developed by univariate and multivariate analyses to predict the prognosis of patients with BRCA. The efficacy of the model was verified by TCGA-based breast cancer samples. Identified lncRNA-related mRNA based on the co-expression method. Results: We constructed a 7-lncRNA breast cancer prediction model including LINC00377, LINC00536, LINC01224, LINC00668, LINC01234, LINC02037, and LINC01456. The breast cancer samples were divided into high-risk and low-risk groups based on the model, which verified the specificity and sensitivity of the model. The Area Under Curve (AUC) of the 3- and 5-year Receiver Operating Characteristic curve were 0.711 and 0.734, respectively, indicating that the model has good performance. Conclusion: We constructed a 7-lncRNA model to predict the prognosis of patients with BRCA, and suggest that these lncRNAs may play a specific role in the carcinogenesis of BRCA.
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Affiliation(s)
- Huayao Li
- College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chundi Gao
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Lijuan Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Jing Zhuang
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Jing Yang
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China
| | - Cun Liu
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chao Zhou
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Fubin Feng
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Changgang Sun
- Chinese Medicine Innovation Institute, Shandong University of Traditional Chinese Medicine, Jinan, China
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29
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Emerging immune gene signatures as prognostic or predictive biomarkers in breast cancer. Arch Pharm Res 2019; 42:947-961. [PMID: 31707598 DOI: 10.1007/s12272-019-01189-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/01/2019] [Indexed: 12/20/2022]
Abstract
Several multigene assays have been developed to predict the risk of distant recurrence and response to adjuvant therapy in early breast cancer. However, the prognostic or predictive value of current proliferation gene signature-based assays are limited to hormone receptor-positive, human epidermal growth factor receptor 2-negative (HR+/HER2-) early breast cancer. Considerable discordance between the different assays in classifying patients into risk groups has also been reported, thus raising questions about the clinical utility of these assays for individual patients. Therefore, there still remains a need for better prognostic or predictive biomarkers for breast cancer. The role of immune cells comprising tumor microenvironment in tumor progression has been recognized. Accumulating evidences have shown that immune gene signatures and tumor-infiltrating lymphocytes (TILs) can be prognostic or predictive factors in breast cancer, particularly with regard to HER2+ and triple-negative breast cancer. In this review, I summarize current multigene assays for breast cancer and discuss recent progress in identifying novel breast cancer biomarkers, focusing on the emerging importance of immune gene signatures and TILs as prognostic or predictive biomarkers.
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Vihervuori H, Autere TA, Repo H, Kurki S, Kallio L, Lintunen MM, Talvinen K, Kronqvist P. Tumor-infiltrating lymphocytes and CD8 + T cells predict survival of triple-negative breast cancer. J Cancer Res Clin Oncol 2019; 145:3105-3114. [PMID: 31562550 PMCID: PMC6861359 DOI: 10.1007/s00432-019-03036-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/19/2019] [Indexed: 12/31/2022]
Abstract
PURPOSE Tumor inflammatory response was evaluated as a prognostic feature in triple-negative breast cancer (TNBC) and compared with the clinical prognosticators of breast cancer and selected biomarkers of cancer cell proliferation. METHODS TNBC patients (n = 179) with complete clinical data and up to 18-year follow-up were obtained from Auria biobank, Turku University Hospital, Turku, Finland. Tumor-infiltrating lymphocytes (TILs) and several subtypes of inflammatory cells detected with immunohistochemistry were evaluated in different tumor compartments in full tissue sections and tissue microarrays. RESULTS Deficiency of stromal TILs and low number of CD8+ T cells independently predicted mortality in TNBC (HR 2.4, p 0.02 and HR 2.1, p 0.02, respectively). Each 10% decrease in stromal TILs resulted in 20% increased risk of mortality. An average of 13.2-year survival difference was observed between the majority (> 75%) of patients with low (< 14% of TILs) vs high (≥ 14% of TILs) frequency of CD8+ T cells. The prognostic value of TILs and CD8+ T cells varied when evaluated in different tumor compartments. TILs and CD8+ T cells were significantly associated with Securin and Separase, essential regulators of metaphase-anaphase transition of the cell cycle. DISCUSSION TILs and CD8+ T cells provide additional prognostic value to the established clinical prognostic markers in TNBC. However, possible clinical applications would still benefit from systematic guidelines for evaluating tumor inflammatory response. Increasing understanding on the interactions between the regulation of cancer cell proliferation and inflammatory response may in future advance treatment of TNBC.
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Affiliation(s)
- H Vihervuori
- Department of Pathology, Institute of Biomedicine, University of Turku, Turku, Finland.
| | - T A Autere
- Department of Pathology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - H Repo
- Department of Pathology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - S Kurki
- Auria Biobank, Turku, Finland
| | | | - M M Lintunen
- Department of Pathology, Turku University Hospital, Turku, Finland
| | - K Talvinen
- Department of Pathology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - P Kronqvist
- Department of Pathology, Institute of Biomedicine, University of Turku, Turku, Finland.,Department of Pathology, Turku University Hospital, Turku, Finland
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Wang J, Li Y, Fu W, Zhang Y, Jiang J, Zhang Y, Qi X. Prognostic nomogram based on immune scores for breast cancer patients. Cancer Med 2019; 8:5214-5222. [PMID: 31342666 PMCID: PMC6718583 DOI: 10.1002/cam4.2428] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/29/2019] [Accepted: 07/05/2019] [Indexed: 12/29/2022] Open
Abstract
Background Increased attention has been focused on cancer immunity gene signature. However, the threshold of immune scores to predict disease‐free survival (DFS) and overall survival (OS) in breast cancer has not yet been defined. This study aimed to explore the association of immune scores with prognosis and build a clinical nomogram to predict the survival of patients with breast cancer. Methods A total of 986 subjects were analyzed, and clinicopathological characteristics and immune scores were obtained from the TCGA database. Cox proportional hazards regression model was used to estimate the adjusted hazard ratios (HRs). Based on results of multivariate analysis, nomograms were built. The models were subjected to bootstrap internal validation. The predictive accuracy and discriminative ability were measured by concordance index (C‐index) and the calibration curve. Results The patients were divided into three subgroups according to their immune scores. We found that compared with patients with low immune scores, those with intermediate and high immune scores had significantly improved DFS (HR and 95% confidence interval [CI]: 0.439 [0.242‐0.799], 0.541 [0.343‐0.855], respectively), whereas only intermediate immune scores significantly indicated better OS (HR and 95% CI: 0.385 [0.163‐0.910]). The C‐index for DFS and OS prediction was 0.723 (95% CI, 0.661‐0.785) and 0.800 (95% CI, 0.724‐0.877), respectively. The calibration curves for probability of 3‐ and 5‐year DFS showed significant agreement between nomogram predictions and the actual observations. Conclusions High and/or intermediate immune scores are significantly correlated with better DFS and OS in patients with breast cancer. Moreover, the nomograms for predicting prognosis may help to estimate the survival of patients.
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Affiliation(s)
- Ju Wang
- Department of Epidemiology and Biostatistics, West China School of Public Health, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Yanling Li
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, P.R. China
| | - Wenying Fu
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, P.R. China
| | - Ye Zhang
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, P.R. China
| | - Jun Jiang
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, P.R. China
| | - Yi Zhang
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, P.R. China
| | - Xiaowei Qi
- Department of Breast and Thyroid Surgery, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, P.R. China
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