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Zhou Y, Mo S, Cui H, Sun R, Zhang W, Zhuang X, Xu E, Li H, Cheng Y, Meng Y, Liu M, Yan T, Liu H, Zhang L, Yang B, Xi Y, Wang S, Cheng X, Li S, Liu Z, Zhan Q, Hu Z, Cui Y. Immune-tumor interaction dictates spatially directed evolution of esophageal squamous cell carcinoma. Natl Sci Rev 2024; 11:nwae150. [PMID: 38803565 PMCID: PMC11129594 DOI: 10.1093/nsr/nwae150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/14/2024] [Accepted: 04/08/2024] [Indexed: 05/29/2024] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a poor-prognostic cancer type with extensive intra- and inter-patient heterogeneity in both genomic variations and tumor microenvironment (TME). However, the patterns and drivers of spatial genomic and microenvironmental heterogeneity of ESCC remain largely unknown. Here, we generated a spatial multi-omic atlas by whole-exome, transcriptome, and methylome sequencing of 507 tumor samples from 103 patients. We identified a novel tumor suppressor PREX2, accounting for 22% of ESCCs with frequent somatic mutations or hyper-methylation, which promoted migration and invasion of ESCC cells in vitro. Analysis of the TME and quantification of subclonal expansion indicated that ESCCs undergo spatially directed evolution, where subclones mostly originated from the tumor center but had a biased clonal expansion to the upper direction of the esophagus. Interestingly, we found upper regions of ESCCs often underwent stronger immunoediting with increased selective fitness, suggesting more stringent immune selection. In addition, distinct TMEs were associated with variable genomic and clinical outcomes. Among them, hot TME was associated with high immune evasion and subclonal heterogeneity. We also found that immunoediting, instead of CD8+ T cell abundance, acts as an independent prognostic factor of ESCCs. Importantly, we found significant heterogeneity in previously considered potential therapeutic targets, as well as BRCAness characteristics in a subset of patients, emphasizing the importance of focusing on heterogeneity in ESCC targeted therapy. Collectively, these findings provide novel insights into the mechanisms of the spatial evolution of ESCC and inform precision therapeutic strategies.
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Affiliation(s)
- Yong Zhou
- Cancer Institute, Department of Pathology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518000, China
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan 030001, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen 518000, China
| | - Shanlan Mo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518000, China
| | - Heyang Cui
- Cancer Institute, Department of Pathology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518000, China
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan 030001, China
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Ruifang Sun
- Department of Tumor Biobank, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, China
| | - Weimin Zhang
- Cancer Institute, Department of Pathology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518000, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China; Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaofei Zhuang
- Department of Thoracic Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, China
| | - Enwei Xu
- Department of Pathology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, China
| | - Hongyi Li
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan 030001, China
| | - Yikun Cheng
- Cancer Institute, Department of Pathology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518000, China
- College of Letters & Science, University of California Berkeley, Berkeley, CA 94704, USA
| | - Yongsheng Meng
- Department of Tumor Biobank, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, China
| | - Meilin Liu
- Department of Tumor Biobank, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, China
| | - Ting Yan
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan 030001, China
| | - Huijuan Liu
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan 030001, China
| | - Ling Zhang
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan 030001, China
| | - Bin Yang
- Department of Thoracic Surgery, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, China
| | - Yanfeng Xi
- Department of Pathology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, China
| | - Shubin Wang
- Cancer Institute, Department of Pathology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Xiaolong Cheng
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan 030001, China
| | - ShuaiCheng Li
- City University of Hong Kong Shenzhen Research Institute, Shenzhen 518000, China
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Qimin Zhan
- Cancer Institute, Department of Pathology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518000, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China; Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, China
| | - Zheng Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518000, China
| | - Yongping Cui
- Cancer Institute, Department of Pathology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518000, China
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan 030001, China
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2
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Shiomi K, Ichinoe M, Ushiwata A, Eshima K, Nagashio R, Hayashi S, Sonoda D, Kondo Y, Maruyama R, Mikubo M, Murakumo Y, Satoh Y. Insight into the significance of CD8+ tumor-infiltrating lymphocytes in squamous cell lung cancer. Thorac Cancer 2024; 15:299-306. [PMID: 38124453 PMCID: PMC10834194 DOI: 10.1111/1759-7714.15187] [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: 10/28/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Although there are great expectations regarding the use of tumor-infiltrating lymphocytes (TILs) to predict effects of immunotherapies and prognosis, knowledge about TILs remains insufficient for clinical application. METHODS We objectively investigated the prognostic significance of tumor-infiltrating CD8 + lymphocytes (CD8 + TILs) in squamous cell lung cancer (SQ-LC). Among patients who underwent surgical resection of SQ-LC in 2011-2017, 100 patients with pathological stage IA3-III were immunohistochemically studied to evaluate CD8 + TILs in the tumor stroma and parenchyma. The impact of CD8 + TILs on relapse-free survival was analyzed using a Kaplan-Meier survival analysis and multivariate analyses using Fine-Gray and Cox proportional hazards models. RESULTS The multivariate analysis showed that large and small numbers, but not intermediate numbers, of CD8 + TILs in the tumor stroma may be related to a more favorable prognosis (small vs. intermediate: HR, 0.64; 95% CI: 0.29-1.41, p = 0.27; large vs. intermediate: HR, 0.48; 95% CI: 0.21-1.09, p = 0.08). In contrast, a large number of CD8 + TILs in the tumor parenchyma was associated with a poor prognosis (HR, 2.60; 95% CI: 0.91-7.42, p = 0.075). An exploratory analysis showed a potentially strong association between an extremely large number of CD8 + TILs in the tumor parenchyma and a poor prognosis, even with a large number of CD8 + TILs in the tumor stroma. CONCLUSION Our study provided partial but important information on the significance of CD8 + TILs in SQ-LC. To use CD8 + TILs as biomarkers, a better understanding of CD8 + TILs as well as other important components in the tumor microenvironment and the inflammatory phenotypes they form may be needed.
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Affiliation(s)
- Kazu Shiomi
- Department of Thoracic SurgeryKitasato University School of MedicineSagamihara‐shiJapan
| | - Masaaki Ichinoe
- Department of PathologyKitasato University School of MedicineSagamihara‐shiJapan
| | - Ai Ushiwata
- Department of Clinical Medicine (Biostatistics)Kitasato University School of PharmacyTokyoJapan
| | - Koji Eshima
- Department of BiosciencesKitasato University School of SciencesSagamihara‐shiJapan
| | - Ryo Nagashio
- Department of Applied Tumor Pathology, Graduate School of Medical SciencesKitasato UniversitySagamihara‐shiJapan
| | - Shoko Hayashi
- Department of Thoracic SurgeryKitasato University School of MedicineSagamihara‐shiJapan
| | - Dai Sonoda
- Department of Thoracic SurgeryKitasato University School of MedicineSagamihara‐shiJapan
| | - Yasuto Kondo
- Department of Thoracic SurgeryKitasato University School of MedicineSagamihara‐shiJapan
| | - Raito Maruyama
- Department of Thoracic SurgeryKitasato University School of MedicineSagamihara‐shiJapan
| | - Masashi Mikubo
- Department of Thoracic SurgeryKitasato University School of MedicineSagamihara‐shiJapan
| | - Yoshiki Murakumo
- Department of PathologyKitasato University School of MedicineSagamihara‐shiJapan
| | - Yukitoshi Satoh
- Department of Thoracic SurgeryKitasato University School of MedicineSagamihara‐shiJapan
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Jääskeläinen MM, Tumelius R, Hämäläinen K, Rilla K, Oikari S, Rönkä A, Selander T, Mannermaa A, Tiainen S, Auvinen P. High Numbers of CD163+ Tumor-Associated Macrophages Predict Poor Prognosis in HER2+ Breast Cancer. Cancers (Basel) 2024; 16:634. [PMID: 38339385 PMCID: PMC10854814 DOI: 10.3390/cancers16030634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/22/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Tumor-associated macrophages (TAMs) are associated with a poor outcome in breast cancer (BC), but their prognostic value in different BC subtypes has remained somewhat unclear. Here, we investigated the prognostic value of M2-like TAMs (CD163+) and all TAMs (CD68+) in a patient cohort of 278 non-metastatic BC patients, half of whom were HER2+ (n = 139). The survival endpoints investigated were overall survival (OS), breast cancer-specific survival (BCSS) and disease-free survival (DFS). In the whole patient cohort (n = 278), a high CD163+ TAM count and a high CD68+ TAM count were associated with a worse outcome (p ≤ 0.023). In HER2+ BC, a high CD163+ TAM count was an independent factor for a poor prognosis across all the investigated survival endpoints (p < 0.001). The prognostic effect was evident in both the HER2+/hormone receptor-positive (p < 0.001) and HER2+/hormone receptor-negative (p ≤ 0.012) subgroups and regardless of the provision of adjuvant trastuzumab (p ≤ 0.002). In HER2-negative BC, the CD163+ TAM count was not significantly associated with survival. These results suggest that a high CD163+ TAM count predicts an inferior outcome, especially in HER2+ BC patients, and as adjuvant trastuzumab did not overcome the poor prognostic effect, combination treatments including therapies targeting the macrophage function could represent an effective therapeutic approach in HER2+ BC.
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Affiliation(s)
- Minna M. Jääskeläinen
- Cancer Center, Kuopio University Hospital, Wellbeing Services County of North Savo, 70029 Kuopio, Finland
- Institute of Clinical Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Ritva Tumelius
- Kuopio Center for Gene and Cell Therapy, 70210 Kuopio, Finland
| | - Kirsi Hämäläinen
- Institute of Clinical Medicine, Clinical Pathology and Forensic Medicine, University of Eastern Finland, 70211 Kuopio, Finland
- Imaging Center, Clinical Pathology, Kuopio University Hospital, Wellbeing Services County of North Savo, 70029 Kuopio, Finland
- Biocenter Kuopio and Cancer Center of Eastern Finland, University of Eastern Finland, 70211 Kuopio, Finland
| | - Kirsi Rilla
- Institute of Biomedicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Sanna Oikari
- Institute of Biomedicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Aino Rönkä
- Cancer Center, Kuopio University Hospital, Wellbeing Services County of North Savo, 70029 Kuopio, Finland
- Institute of Clinical Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Tuomas Selander
- Science Services Center, Kuopio University Hospital, Wellbeing Services County of North Savo, 70029 Kuopio, Finland
| | - Arto Mannermaa
- Institute of Clinical Medicine, Clinical Pathology and Forensic Medicine, University of Eastern Finland, 70211 Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Wellbeing Services County of North Savo, 700029 Kuopio, Finland
| | - Satu Tiainen
- Cancer Center, Kuopio University Hospital, Wellbeing Services County of North Savo, 70029 Kuopio, Finland
- Institute of Clinical Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Päivi Auvinen
- Cancer Center, Kuopio University Hospital, Wellbeing Services County of North Savo, 70029 Kuopio, Finland
- Institute of Clinical Medicine, University of Eastern Finland, 70211 Kuopio, Finland
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Li C, Xu Y, Zhang J, Zhang Y, He W, Ju J, Wu Y, Wang Y. The effect of resveratrol, curcumin and quercetin combination on immuno-suppression of tumor microenvironment for breast tumor-bearing mice. Sci Rep 2023; 13:13278. [PMID: 37587146 PMCID: PMC10432483 DOI: 10.1038/s41598-023-39279-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/22/2023] [Indexed: 08/18/2023] Open
Abstract
Resveratrol, curcumin, and quercetin are the secondary metabolites from medicinal food homology plants, that have been proven their potency in cancer treatment. However, the antitumor effect of a single component is weak. So, herein, we designed an antitumor compound named RCQ composed of resveratrol, curcumin, and quercetin. This study examined the effect on tumorigenesis and development of 4T1 breast cancer-bearing mice following administering RCQ by intragastric administration. RCQ increased the recruitment of T cells and reduced the accumulation of neutrophils and macrophages in the tumor microenvironment. Meanwhile, RCQ suppressed the development of tumor-infiltrating lymphocytes into immunosuppressive cell subpopulations, including CD4+ T cells to T helper Type 2 type (Th2), tumor-associated neutrophils (TANs) to the N2 TANs, and tumor-associated macrophages (TAMs) cells to M2 TAMs. RCQ reversed the predominance of immunosuppressive infiltrating cells in the tumor microenvironment and tipped the immune balance toward an immune activation state. In vitro the study showed that RCQ significantly increased reactive oxygen species (ROS), reduce mitochondrial membrane potentials in cancer cells, and modulate pro-apoptotic Bcl-2 family members. In conclusion, RCQ can promote the ROS apoptosis mechanism of tumor cells and alleviate immunosuppression of the tumor microenvironment to enhance the anti-tumor effect.
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Affiliation(s)
- Chenchen Li
- School of Medicine and School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, People's Republic of China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, International Associated Research Center for Intelligent Human Computer Collaboration on Tumor Precision Medicine, School of Pharmacy and The First Affiliated Hospital, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Yajun Xu
- School of Medicine and School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, People's Republic of China
| | - Junfeng Zhang
- School of Medicine and School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, People's Republic of China
| | - Yuxi Zhang
- School of Medicine and School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, People's Republic of China
| | - Wen He
- School of Medicine and School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, People's Republic of China
| | - Jiale Ju
- School of Medicine and School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, People's Republic of China
| | - Yinghua Wu
- School of Medicine and School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, People's Republic of China
| | - Yanli Wang
- School of Medicine and School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, People's Republic of China.
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Sun GY, Zhang J, Wang BZ, Jing H, Fang H, Tang Y, Song YW, Jin J, Liu YP, Tang Y, Qi SN, Chen B, Lu NN, Li N, Li YX, Ying JM, Wang SL. The prognostic value of tumour-infiltrating lymphocytes, programmed cell death protein-1 and programmed cell death ligand-1 in Stage I-III triple-negative breast cancer. Br J Cancer 2023; 128:2044-2053. [PMID: 36966236 PMCID: PMC10205737 DOI: 10.1038/s41416-023-02218-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 02/09/2023] [Accepted: 02/23/2023] [Indexed: 03/27/2023] Open
Abstract
BACKGROUND Tumour-infiltrating lymphocytes (TILs) represent a robust biological prognostic biomarker in triple-negative breast cancer (TNBC); however, the contribution of different subsets of immune cells is unclear. We investigated the prognostic value of immune markers, including stromal TILs (sTILs), CD8+T and FOPX3+T cells, PD-1 and PD-L1 in non-metastatic TNBC. METHODS In total, 259 patients with Stage I-III TNBC were reviewed. The density of sTILs along with the presence of total (t), stromal (s), and intratumoral (i) CD8+T cells and FOPX3+T cells were evaluated by haematoxylin and eosin and immunohistochemical staining. Immunohistochemical staining of PD-1, PD-L1 was also conducted. RESULTS All immune markers were positively correlated with each other (P < 0.05). In the multivariate analysis, sTILs (P = 0.046), tCD8+T cells (P = 0.024), iCD8+T cells (P = 0.050) and PD-1 (P = 0.039) were identified as independent prognostic factors for disease-free survival (DFS). Further analysis showed that tCD8+T cells (P = 0.026), iCD8+T cells (P = 0.017) and PD-1 (P = 0.037) increased the prognostic value for DFS beyond that of the classic clinicopathological factors and sTILs. CONCLUSIONS In addition to sTILs, inclusion of tCD8+T, iCD8+T cells, or PD-1 may further refine the prognostic model for non-metastatic TNBC beyond that including classical factors alone.
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Affiliation(s)
- Guang-Yi Sun
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Jing Zhang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Department of Pathology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, 350014, Fuzhou, China
| | - Bing-Zhi Wang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Hao Jing
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Hui Fang
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yu Tang
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yong-Wen Song
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Jing Jin
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yue-Ping Liu
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yuan Tang
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Shu-Nan Qi
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Bo Chen
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Ning-Ning Lu
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Ning Li
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Ye-Xiong Li
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
| | - Jian-Ming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
| | - Shu-Lian Wang
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
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Huo Q, Ning L, Xie N. Identification of GZMA as a Potential Therapeutic Target Involved in Immune Infiltration in Breast Cancer by Integrated Bioinformatical Analysis. BREAST CANCER (DOVE MEDICAL PRESS) 2023; 15:213-226. [PMID: 36926265 PMCID: PMC10013577 DOI: 10.2147/bctt.s400808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/18/2023] [Indexed: 03/12/2023]
Abstract
Purpose Granzyme A (GZMA) is a potential prognostic target for various cancer types. However, its therapeutic significance in breast cancer with immune infiltration remains controversial. We analyzed GZMA expression and its prognostic value in breast cancer with immune cell infiltration. Patients and methods Data was obtained from patients with breast cancer registered at The Cancer Genome Atlas. A correlation was performed between GZMA expression and patient's clinicopathological features such as age, pathologic stage, metastasis stage, overall survival (OS), disease-specific survival (DSS), and progress free interval (PFI). Kaplan-Meier analyses and Cox proportional hazard regression model were used to examine the predictive significance of GZMA expression for breast cancer. The co-expression pattern of GZMA was assessed by the LinkedOmics web portal. The relationship between GZMA expression and immune cells was analyzed using the TIMER database. The correlation between GZMA and lymphocytes and immunomodulators was established with the TISIDB database. Results There was a lower GZMA expression in breast cancer tissue than in normal tissue. Interestingly, GZMA expression was associated with age, pathologic stage, and the Tumour, Node, and Metastasis stage. Overexpression of GZMA was also associated with better OS, DSS, and PFI. Based on the Cox regression analysis, GZMA was identified as an independent favorable prognostic factor for breast cancer. Our findings demonstrated a strong association between GZMA and T-cell checkpoints (PD-1, PD-L1, and cytotoxic T lymphocyte-associated antigen (CTLA-4)) in breast cancer. Moreover, we evaluated the interactions between GZMA expression and markers of dendritic and CD8+ T cells using quantitative immunofluorescence. We discovered that increased infiltration of dendritic and CD8+ T cells was associated with GZMA expression in breast cancer. Conclusion GZMA expression is associated with a favorable prognosis in breast cancer and is significantly correlated with immune cell infiltration. GZMA may be considered a promising therapeutic target for patients with breast cancer.
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Affiliation(s)
- Qin Huo
- Biobank, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, People's Republic of China
| | - Lvwen Ning
- Biobank, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, People's Republic of China
| | - Ni Xie
- Biobank, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, People's Republic of China
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Qian L, Liu YF, Lu SM, Yang JJ, Miao HJ, He X, Huang H, Zhang JG. Construction of a fatty acid metabolism-related gene signature for predicting prognosis and immune response in breast cancer. Front Genet 2023; 14:1002157. [PMID: 36936412 PMCID: PMC10014556 DOI: 10.3389/fgene.2023.1002157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 02/20/2023] [Indexed: 03/05/2023] Open
Abstract
Background: Breast cancer has the highest incidence among malignant tumors in women, and its prevalence ranks first in global cancer morbidity. Aim: This study aimed to explore the feasibility of a prognostic model for patients with breast cancer based on the differential expression of genes related to fatty acid metabolism. Methods: The mRNA expression matrix of breast cancer and paracancer tissues was downloaded from The Cancer Genome Atlas database. The differentially expressed genes related to fatty acid metabolism were screened in R language. The TRRUST database was used to predict transcriptional regulators related to hub genes and construct an mRNA-transcription factor interaction network. A consensus clustering approach was used to identify different fatty acid regulatory patterns. In combination with patient survival data, Lasso and multivariate Cox proportional risk regression models were used to establish polygenic prognostic models based on fatty acid metabolism. The median risk score was used to categorize patients into high- and low-risk groups. Kaplan-Meier survival curves were used to analyze the survival differences between both groups. The Cox regression analysis included risk score and clinicopathological factors to determine whether risk score was an independent risk factor. Models based on genes associated with fatty acid metabolism were evaluated using receiver operating characteristic curves. A comparison was made between risk score levels and the fatty acid metabolism-associated genes in different subtypes of breast cancer. The differential gene sets of the Kyoto Encyclopedia of Genes and Genomes for screening high- and low-risk populations were compared using a gene set enrichment analysis. Furthermore, we utilized CIBERSORT to examine the abundance of immune cells in breast cancer in different clustering models. Results: High expression levels of ALDH1A1 and UBE2L6 prevented breast cancer, whereas high RDH16 expression levels increased its risk. Our comprehensive assessment of the association between prognostic risk scoring models and tumor microenvironment characteristics showed significant differences in the abundance of various immune cells between high- and low-risk breast cancer patients. Conclusions: By assessing fatty acid metabolism patterns, we gained a better understanding of the infiltration characteristics of the tumor microenvironment. Our findings are valuable for prognosis prediction and treatment of patients with breast cancer based on their clinicopathological characteristics.
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Affiliation(s)
- Li Qian
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Yi-Fei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Shu-Min Lu
- Department of Oncology, Shanghai Jiaotong University School of Medicine Xinhua Hospital, Shanghai, China
| | - Juan-Juan Yang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Hua-Jie Miao
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Xin He
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Hua Huang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
- *Correspondence: Hua Huang, ; Jian-Guo Zhang,
| | - Jian-Guo Zhang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
- *Correspondence: Hua Huang, ; Jian-Guo Zhang,
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8
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Surveying lncRNA-lncRNA cooperations reveals dominant effect on tumor immunity cross cancers. Commun Biol 2022; 5:1324. [PMID: 36463330 PMCID: PMC9719535 DOI: 10.1038/s42003-022-04249-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/11/2022] [Indexed: 12/04/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) can crosstalk with each other by post-transcriptionally co-regulating genes involved in the same or similar functions; however, the regulatory principles and biological insights in tumor-immune are still unclear. Here, we show a multiple-step model to identify lncRNA-lncRNA immune cooperation based on co-regulating functional modules by integrating multi-omics data across 20 cancer types. Moreover, lncRNA immune cooperative networks (LICNs) are constructed, which are likely to modulate tumor-immune microenvironment by regulating immune-related functions. We highlight conserved and rewired network hubs which can regulate interactions between immune cells and tumor cells by targeting ligands and activating or inhibitory receptors such as PDCD1, CTLA4 and CD86. Immune cooperative lncRNAs (IC-lncRNAs) playing central roles in many cancers also tend to target known anticancer drug targets. In addition, these IC-lncRNAs tend to be highly expressed in immune cell populations and are significantly correlated with immune cell infiltration. The similar immune mechanisms cross cancers are revealed by the LICNs. Finally, we identify two subtypes of skin cutaneous melanoma with different immune context and prognosis based on IC-lncRNAs. In summary, this study contributes to a comprehensive understanding of the cooperative behaviours of lncRNAs and accelerating discovery of lncRNA-based biomarkers in cancer.
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9
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Schüler K, Bethmann D, Kaufhold S, Hartung C, Stückrath K, Lantzsch T, Uleer C, Hanf V, Peschel S, John J, Pöhler M, Buchmann J, Bürrig KF, Weigert E, Thomssen C, Kantelhardt EJ, Vetter M. Prognostic Value of Tumour-Infiltrating Lymphocytes in an Unselected Cohort of Breast Cancer Patients. Diagnostics (Basel) 2022; 12:2527. [PMID: 36292215 PMCID: PMC9601161 DOI: 10.3390/diagnostics12102527] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 02/13/2024] Open
Abstract
Tumour-infiltrating lymphocytes (TILs) are considered to have prognostic and predictive value for patients with early breast cancer. We examined 1166 breast cancer patients from a prospective, multicentre cohort (Prognostic Assessment in Routine Application (PiA), n = 1270, NCT01592825) following recommendations from the International TILs Working Group. TIL quantification was performed using predefined groups and as a continuous variable in 10% increments. The primary objective was the distribution of TILs in different breast cancer types. The second objective was the association with the recurrence-free interval (RFI) and overall survival (OS). Stromal infiltration with more than 60% TILs appeared in 2% of hormone receptor (HR)-positive and HER2-negative tumours, in 9.8% of HER2-positive tumours (any HR) and 19.4% of triple-negative breast cancers (TNBCs). Each 10% increment was associated with an improvement in the prognosis in HER2-positive samples (RFI, hazard ratio 0.773, 95% CI 0.587-1.017; OS, hazard ratio 0.700, 95% CI 0.523-0.937). When defining exploratory cut-offs for TILs, the use of a 30% threshold for the HR-positive and HER2-negative group, a 20% threshold for the HER2 group and a 60% threshold for the TNBC group appeared to be the most suitable. TILs bore prognostic value, especially in HER2-positive breast cancer. For clinical use, additional research on the components of immune infiltration might be reasonable.
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Affiliation(s)
- Kathleen Schüler
- Department of Gynaecology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Daniel Bethmann
- Institute of Pathology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Sandy Kaufhold
- Department of Gynaecology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Carolin Hartung
- Department of Gynaecology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Kathrin Stückrath
- Department of Gynaecology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Tilmann Lantzsch
- Department of Gynaecology, Hospital St. Elisabeth and St. Barbara, 06110 Halle (Saale), Germany
| | - Christoph Uleer
- Gynäkologisch-Onkologische Praxis, 31134 Hildesheim, Germany
| | - Volker Hanf
- Department of Gynaecology, Nathanstift, Hospital Fürth, 90766 Fürth, Germany
| | - Susanne Peschel
- Department of Gynaecology, St. Bernward Hospital, 31134 Hildesheim, Germany
| | - Jutta John
- Department of Gynaecology, Helios Hospital Hildesheim, 31135 Hildesheim, Germany
| | - Marleen Pöhler
- Department of Gynaecology, Asklepios Hospital Goslar, 38642 Goslar, Germany
| | - Jörg Buchmann
- Institute of Pathology, Hospital Martha-Maria, 81479 Halle (Saale), Germany
| | | | - Edith Weigert
- Institute of Pathology, Hospital Fürth, 90766 Fürth, Germany
| | - Christoph Thomssen
- Department of Gynaecology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Eva Johanna Kantelhardt
- Department of Gynaecology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
- Institute of Epidemiology, Biometry and Informatics, Martin Luther University Halle-Wittenberg, 06108 Halle (Saale), Germany
| | - Martina Vetter
- Department of Gynaecology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
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10
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Tian C, Wang Y, Song X. Prognostic Characteristics of Immune-Related Genes and the Related Regulatory Axis in Patients With Stage N+M0 Breast Cancer. Front Oncol 2022; 12:878219. [PMID: 35785160 PMCID: PMC9243266 DOI: 10.3389/fonc.2022.878219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Breast cancer (BRCA) has the highest incidence rate among female tumours. The function of the immune system affects treatment efficacy and prognosis in patients with BRCA. However, the exact role of immune-related genes (IRGs) in stage N+M0 BRCA is unknown. We constructed a predictive risk scoring model with five IRGs (CDH1, FGFR3, INHBA, S100B, and SCG2) based on the clinical, mutation, and RNA sequencing data of individuals with stage N+M0 BRCA sourced from The Cancer Genome Atlas. Results from the Shandong Cancer Hospital and Institute validation cohort suggested that regardless of clinical stage, tumour size, or the number of lymph node metastases, this model was able to reliably discriminate low-risk patients from high-risk ones and assess the prognosis of patients with stage N+M0 BRCA, and low-risk patients could benefit more from immunotherapy than high-risk patients. In addition, significant inter-group variations in immunocyte infiltration and the tumour microenvironment were observed. Moreover, risk score and age were found to be independent factors in multivariate COX regression analysis, which influenced the outcome of patients with stage N+M0 BRCA. Based on the above findings, we plotted a prognostic nomogram. Finally, we constructed a lncRNA KCNQ1OT1-LINC00665-TUG1/miR-9-5p/CDH1 regulatory axis of the ceRNA network to explore the mechanism of BRCA progression. In summary, we conducted a systemic and extensive bioinformatics investigation and established an IRG-based prognostic scoring model. Finally, we constructed a ceRNA regulatory axis that might play a significant role in BRCA development. More research is required to confirm this result. Scoring system-based patient grouping can help predict the outcome of patients with stage N+M0 BRCA more effectively and determine their sensitivity to immunotherapies, which will aid the development of personalised therapeutic strategies and inspire the research and development of novel medications.
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Affiliation(s)
- Chonglin Tian
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Burn and Plastic Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Yongsheng Wang
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- *Correspondence: Yongsheng Wang, ; Xianrang Song,
| | - Xianrang Song
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- *Correspondence: Yongsheng Wang, ; Xianrang Song,
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11
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Larsson AM, Nordström O, Johansson A, Rydén L, Leandersson K, Bergenfelz C. Peripheral Blood Mononuclear Cell Populations Correlate with Outcome in Patients with Metastatic Breast Cancer. Cells 2022; 11:1639. [PMID: 35626676 PMCID: PMC9139201 DOI: 10.3390/cells11101639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/04/2022] [Accepted: 05/11/2022] [Indexed: 01/04/2023] Open
Abstract
Local tumor-associated immune cells hold prognostic and predictive value in various forms of malignancy. The role of systemic, circulating leukocytes is, however, not well-characterized. In this prospective and explorative study, we aim to delineate the clinical relevance of a broad panel of circulating immune cells in 32 patients with newly diagnosed metastatic breast cancer (MBC) before the start of systemic treatment. Freshly isolated peripheral blood mononuclear cells (PBMCs) were analyzed by flow cytometry and evaluated for potential associations to clinicopathological variables and patient outcome. We show that the levels of specific circulating leukocyte populations are associated with clinical parameters such as hormone receptor status, histological subtype, number of circulating tumor cells (CTCs) and metastatic burden. Importantly, high levels of CD8+ cytotoxic T lymphocytes (CTLs) are significantly linked to improved overall survival (OS). In patients with estrogen receptor (ER)-positive primary tumors, high levels of circulating CTLs and non-classical (CD14+CD16++) monocytes were associated with improved OS, whereas in patients with ER-negative tumors low levels of circulating natural killer (NK) cells potentially associate with improved OS. We propose that the levels of specific circulating immune cell populations, such as CD8+ CTLs, may be used to predict clinical outcomes in MBC patients. Thus, larger studies are warranted to validate these findings.
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Affiliation(s)
- Anna-Maria Larsson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, SE-223 81 Lund, Sweden; (A.-M.L.); (A.J.); (L.R.)
| | - Olle Nordström
- Experimental Infection Medicine, Department of Translational Medicine, Lund University, SE-214 28 Malmö, Sweden;
| | - Alexandra Johansson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, SE-223 81 Lund, Sweden; (A.-M.L.); (A.J.); (L.R.)
| | - Lisa Rydén
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, SE-223 81 Lund, Sweden; (A.-M.L.); (A.J.); (L.R.)
- Department of Surgery, Skåne University Hospital, SE-223 81 Lund, Sweden
| | - Karin Leandersson
- Cancer Immunology, Department of Translational Medicine, Lund University, SE-214 28 Malmö, Sweden;
| | - Caroline Bergenfelz
- Experimental Infection Medicine, Department of Translational Medicine, Lund University, SE-214 28 Malmö, Sweden;
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12
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Investigating the Prognostic Relevance of Tumor Immune Microenvironment and Immune Gene Assembly in Breast Carcinoma Subtypes. Cancers (Basel) 2022; 14:cancers14081942. [PMID: 35454849 PMCID: PMC9031175 DOI: 10.3390/cancers14081942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/29/2022] [Accepted: 04/06/2022] [Indexed: 02/04/2023] Open
Abstract
We hypothesized that different BC subtypes are characterized by spatially distinct tumor immune microenvironment (TIME) and that immune gene assembly of metastatic (Met) and non-metastatic (Ctrl) BCs vary across subtypes. Peritumoral, stromal and intratumoral TIL was assessed on 309 BC cases. Hot, cold and immune-excluded groups were defined, and the prognostic role of this classification was assessed. CD4+/CD8+ positivity was analyzed in 75 cases in four systematically predefined tumor regions. Immune gene expression of Met and Ctrl HER2-negative BCs was compared by using NanoString nCounter technology. The amount of TIL infiltration varied greatly within all BC subtypes. Two-third of the cases were cold tumors with no significant survival difference compared to hot tumors. A lower CD4+/CD8+ ratio at the stromal internal tumor region was significantly associated with longer distant metastasis-free survival. The differentially expressed immune genes between Met and Ctrl varied across the studied BC subtypes with TNBC showing distinct features from the luminal subtypes. The TIME is characterized by a considerable heterogeneity; however, low level of TILs does not equate to disease progression. The differences in immune gene expression observed between Met and Ctrl breast carcinomas call attention to the important role of altered immune function in BC progression.
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13
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Stoll G, Naldi A, Noël V, Viara E, Barillot E, Kroemer G, Thieffry D, Calzone L. UPMaBoSS: A Novel Framework for Dynamic Cell Population Modeling. Front Mol Biosci 2022; 9:800152. [PMID: 35309516 PMCID: PMC8924294 DOI: 10.3389/fmolb.2022.800152] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
Mathematical modeling aims at understanding the effects of biological perturbations, suggesting ways to intervene and to reestablish proper cell functioning in diseases such as cancer or in autoimmune disorders. This is a difficult task for obvious reasons: the level of details needed to describe the intra-cellular processes involved, the numerous interactions between cells and cell types, and the complex dynamical properties of such populations where cells die, divide and interact constantly, to cite a few. Another important difficulty comes from the spatial distribution of these cells, their diffusion and motility. All of these aspects cannot be easily resolved in a unique mathematical model or with a unique formalism. To cope with some of these issues, we introduce here a novel framework, UPMaBoSS (for Update Population MaBoSS), dedicated to modeling dynamic populations of interacting cells. We rely on the preexisting tool MaBoSS, which enables probabilistic simulations of cellular networks. A novel software layer is added to account for cell interactions and population dynamics, but without considering the spatial dimension. This modeling approach can be seen as an intermediate step towards more complex spatial descriptions. We illustrate our methodology by means of a case study dealing with TNF-induced cell death. Interestingly, the simulation of cell population dynamics with UPMaBoSS reveals a mechanism of resistance triggered by TNF treatment. Relatively easy to encode, UPMaBoSS simulations require only moderate computational power and execution time. To ease the reproduction of simulations, we provide several Jupyter notebooks that can be accessed within the CoLoMoTo Docker image, which contains all software and models used for this study.
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Affiliation(s)
- Gautier Stoll
- Equipe Labellisée Par La Ligue Contre Le Cancer, Université de Paris, Sorbonne Université, INSERM UMR1138, Centre de Recherche des Cordeliers, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Aurélien Naldi
- Institut de Biologie de L’ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Lifeware Group, Inria Saclay-Ile de France, Palaiseau, France
| | - Vincent Noël
- Institut Curie, PSL Research University, Paris, France
- INSERM U900, Paris, France
- MINES ParisTech, CBIO-Centre for Computational Biology, PSL Research University, Paris, France
| | | | - Emmanuel Barillot
- Institut Curie, PSL Research University, Paris, France
- INSERM U900, Paris, France
- MINES ParisTech, CBIO-Centre for Computational Biology, PSL Research University, Paris, France
| | - Guido Kroemer
- Equipe Labellisée Par La Ligue Contre Le Cancer, Université de Paris, Sorbonne Université, INSERM UMR1138, Centre de Recherche des Cordeliers, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
- Pôle de Biologie, Hôpital européen Georges Pompidou, AP-HP, Paris, France
| | - Denis Thieffry
- Institut de Biologie de L’ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Lifeware Group, Inria Saclay-Ile de France, Palaiseau, France
| | - Laurence Calzone
- Institut Curie, PSL Research University, Paris, France
- INSERM U900, Paris, France
- MINES ParisTech, CBIO-Centre for Computational Biology, PSL Research University, Paris, France
- *Correspondence: Laurence Calzone,
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14
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Tan H, Wang L, Liu Z. Role of Suprabasin in the Dedifferentiation of Follicular Epithelial Cell-Derived Thyroid Cancer and Identification of Related Immune Markers. Front Genet 2022; 13:810681. [PMID: 35222534 PMCID: PMC8865917 DOI: 10.3389/fgene.2022.810681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 01/14/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Aberrant regulation of suprabasin (SBSN) is associated with the development of cancer and immune disorders. SBSN influences tumor cell migration, proliferation, angiogenesis, and immune resistance. In this study, we investigated the potential correlation between SBSN expression and immune infiltration in thyroid cancer. Methods: The expression of SBSN in 80 papillary thyroid carcinoma (PTC) specimens was determined using quantitative reverse-transcription polymerase chain reaction, western blotting, and immunohistochemical staining. The expression of SBSN in 9 cases of poorly differentiated thyroid carcinoma (PDTC) and 18 cases of anaplastic thyroid carcinoma (ATC) was evaluated by immunohistochemical staining. Comprehensive bioinformatics analysis of SBSN expression was performed using The Cancer Genome Atlas and Gene Expression Omnibus datasets, and the relationship of SBSN expression with M2 macrophages and T regulatory cells (Tregs) in ATC and PTC was verified by immunohistochemical staining. Results: Compared with those in adjacent normal tissues, the expression levels of SBSN mRNA and protein were significantly higher in PTC tissues. SBSN expression level was correlated with that of cervical lymph node metastasis in PTC patients. Immunohistochemical staining results showed statistically significant differences among high-positive expression rates of SBSN in PTC, PDTC, and ATC. Functional enrichment analysis showed that SBSN expression was associated with pathways related to cancer, cell signaling, and immune response. Furthermore, analysis of the tumor microenvironment (using CIBERSORT-ABS and xCell algorithms) showed that SBSN expression affected immune cell infiltration and the cancer immunity cycle, and immunohistochemistry confirmed a significant increase in M2 macrophage and Treg infiltration in tumor tissues with high-positive SBSN expression. Conclusion: These findings reveal that SBSN may be involved in thyroid carcinogenesis, tumor dedifferentiation progression, and immunosuppression as an important regulator of tumor immune cell infiltration.
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15
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Yan L, He J, Liao X, Liang T, Zhu J, Wei W, He Y, Zhou X, Peng T. A comprehensive analysis of the diagnostic and prognostic value associated with the SLC7A family members in breast cancer. Gland Surg 2022; 11:389-411. [PMID: 35284318 PMCID: PMC8899434 DOI: 10.21037/gs-21-909] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/30/2022] [Indexed: 07/21/2023]
Abstract
BACKGROUND The solute carrier (SLC) 7 family genes play central roles in cancer cell metabolism as glucose and glutamate transporters. However, their expression and prognostic value in breast cancer (BC) remains to be elucidated. METHODS Clinical data from BC patients were downloaded from The Cancer Genome Atlas (TCGA) and the Kaplan-Meier (KM) plotter database. The mechanisms underlying the association between SLC7A expression and overall survival (OS) were explored using Cox regression and log-rank tests. ESTIMATE gives a measure of the immune-cell infiltrates. Single-sample (ss) Gene Set Enrichment Analysis (GSEA) was conducted to quantify immune cell infiltration. RESULTS High SLC7A5 expression was associated with a poorer survival time in BC patients according to the TCGA and KM plotter data. SLC7A4 was associated with good progression-free interval (PFI) and disease-specific survival (DSS) according to the TCGA data. Furthermore, SLC7A4 was correlated with good prognosis of OS, distant metastasis-free survival (DMFS), relapse-free survival (RFS), and post-progression survival (PPS) according to the KM plotter data. SLC7A3 expression was positively associated with OS, but was not strongly associated with PFI nor DSS in the TCGA data. However, SLC7A3 was positively correlated with DMFS and RFS in the KM database analysis. SLC7A had excellent diagnostic value in BC patients and was strongly correlated with tumor infiltration. T helper 2 (Th2) cells, CD56 bright natural killer (NK) cells, and NK cells were the most strongly correlated with the SLC7A family genes, suggesting that these genes play a crucial role in BC partly by modulating immune infiltration. CONCLUSIONS SLC7A4 and SLC7A5 expression levels may be sensitive biomarkers for predicting BC outcomes. SLC7A3 may be a potential diagnostic and prognostic biomarker in BC, but further studies are warranted to verify these results.
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Affiliation(s)
- Liping Yan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Key Laboratory of High-Incidence-Tumor Prevention and Treatment Guangxi Medical University, Nanning, China
| | - Jianxin He
- Department of Ultrasound Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Tianyi Liang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jia Zhu
- Department of Breast Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wensong Wei
- Department of Breast Surgery, The Third Hospital of Nanchang, Nanchang, China
| | - Yongfei He
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xin Zhou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Key Laboratory of High-Incidence-Tumor Prevention and Treatment Guangxi Medical University, Nanning, China
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16
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Maisel BA, Yi M, Peck AR, Sun Y, Hooke JA, Kovatich AJ, Shriver CD, Hu H, Nevalainen MT, Tanaka T, Simone N, Wang LL, Rui H, Chervoneva I. Spatial Metrics of Interaction between CD163-Positive Macrophages and Cancer Cells and Progression-Free Survival in Chemo-Treated Breast Cancer. Cancers (Basel) 2022; 14:308. [PMID: 35053472 PMCID: PMC8773496 DOI: 10.3390/cancers14020308] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 02/07/2023] Open
Abstract
Tumor-associated macrophages (TAMs) promote progression of breast cancer and other solid malignancies via immunosuppressive, pro-angiogenic and pro-metastatic effects. Tumor-promoting TAMs tend to express M2-like macrophage markers, including CD163. Histopathological assessments suggest that the density of CD163-positive TAMs within the tumor microenvironment is associated with reduced efficacy of chemotherapy and unfavorable prognosis. However, previous analyses have required research-oriented pathologists to visually enumerate CD163+ TAMs, which is both laborious and subjective and hampers clinical implementation. Objective, operator-independent image analysis methods to quantify TAM-associated information are needed. In addition, since M2-like TAMs exert local effects on cancer cells through direct juxtacrine cell-to-cell interactions, paracrine signaling, and metabolic factors, we hypothesized that spatial metrics of adjacency of M2-like TAMs to breast cancer cells will have further information value. Immunofluorescence histo-cytometry of CD163+ TAMs was performed retrospectively on tumor microarrays of 443 cases of invasive breast cancer from patients who subsequently received adjuvant chemotherapy. An objective and automated algorithm was developed to phenotype CD163+ TAMs and calculate their density within the tumor stroma and derive several spatial metrics of interaction with cancer cells. Shorter progression-free survival was associated with a high density of CD163+ TAMs, shorter median cancer-to-CD163+ nearest neighbor distance, and a high number of either directly adjacent CD163+ TAMs (within juxtacrine proximity <12 μm to cancer cells) or communicating CD163+ TAMs (within paracrine communication distance <250 μm to cancer cells) after multivariable adjustment for clinical and pathological risk factors and correction for optimistic bias due to dichotomization.
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Affiliation(s)
- Brenton A. Maisel
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA; (B.A.M.); (M.Y.)
| | - Misung Yi
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA; (B.A.M.); (M.Y.)
| | - Amy R. Peck
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA; (A.R.P.); (Y.S.); (M.T.N.)
| | - Yunguang Sun
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA; (A.R.P.); (Y.S.); (M.T.N.)
| | - Jeffrey A. Hooke
- John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (J.A.H.); (A.J.K.); (C.D.S.)
| | - Albert J. Kovatich
- John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (J.A.H.); (A.J.K.); (C.D.S.)
| | - Craig D. Shriver
- John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD 20814, USA; (J.A.H.); (A.J.K.); (C.D.S.)
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA;
| | - Marja T. Nevalainen
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA; (A.R.P.); (Y.S.); (M.T.N.)
| | - Takemi Tanaka
- Department of Pathology, University of Oklahoma Health Sciences Center, Stephenson Cancer Center, Oklahoma City, OK 73104, USA;
| | - Nicole Simone
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA;
| | - Li Lily Wang
- Department of Translational Hematology and Oncology Research, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195, USA;
| | - Hallgeir Rui
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA; (A.R.P.); (Y.S.); (M.T.N.)
| | - Inna Chervoneva
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA; (B.A.M.); (M.Y.)
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17
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Lynch KT, Squeo GC, Kane WJ, Meneveau MO, Petroni G, Olson WC, Chianese-Bullock KA, Slingluff CL, Foley EF, Friel CM. A pilot trial of vaccination with Carcinoembryonic antigen and Her2/neu peptides in advanced colorectal cancer. Int J Cancer 2022; 150:164-173. [PMID: 34480368 DOI: 10.1002/ijc.33793] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/03/2021] [Accepted: 06/23/2021] [Indexed: 12/14/2022]
Abstract
Checkpoint-blockade therapy (CBT) is approved for select colorectal cancer (CRC) patents, but additional immunotherapeutic options are needed. We hypothesized that vaccination with carcinoembryonic antigen (CEA) and Her2/neu (Her2) peptides would be immunogenic and well tolerated by participants with advanced CRC. A pilot clinical trial (NCT00091286) was conducted in HLA-A2+ or -A3+ Stage IIIC-IV CRC patients. Participants were vaccinated weekly with CEA and Her2 peptides plus tetanus peptide and GM-CSF emulsified in Montanide ISA-51 adjuvant for 3 weeks. Adverse events (AEs) were recorded per NIH Common Terminology Criteria for Adverse Events version 3. Immunogenicity was evaluated by interferon-gamma ELISpot assay of in vitro sensitized peripheral blood mononuclear cells and lymphocytes from the sentinel immunized node. Eleven participants were enrolled and treated; one was retrospectively found to be ineligible due to HLA type. All 11 participants were included in AEs and survival analyses, and the 10 eligible participants were evaluated for immunogenicity. All participants reported AEs: 82% were Grade 1-2, most commonly fatigue or injection site reactions. Two participants (18%) experienced treatment-related dose-limiting Grade 3 AEs; both were self-limiting. Immune responses to Her2 or CEA peptides were detected in 70% of participants. Median overall survival (OS) was 16 months; among those enrolled with no evidence of disease (n = 3), median OS was not reached after 10 years of follow-up. These data demonstrate that vaccination with CEA or Her2 peptides is well tolerated and immunogenic. Further study is warranted to assess potential clinical benefits of vaccination in advanced CRC either alone or in combination with CBT.
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Affiliation(s)
- Kevin T Lynch
- Department of Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Gabriella C Squeo
- Department of Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - William J Kane
- Department of Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Max O Meneveau
- Department of Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Gina Petroni
- Department of Public Health Sciences, University of Virginia Cancer Center, Charlottesville, Virginia, USA
| | - Walter C Olson
- Department of Surgery, University of Virginia, Charlottesville, Virginia, USA
| | | | - Craig L Slingluff
- Department of Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Eugene F Foley
- Department of Surgery, University of Wisconsin, Madison, Wisconsin, USA
| | - Charles M Friel
- Department of Surgery, University of Virginia, Charlottesville, Virginia, USA
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18
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Holm JB, Rosendahl AH, Borgquist S. Local Biomarkers Involved in the Interplay between Obesity and Breast Cancer. Cancers (Basel) 2021; 13:cancers13246286. [PMID: 34944905 PMCID: PMC8699696 DOI: 10.3390/cancers13246286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Breast cancer is the second most common cancer in women worldwide. The risk of developing breast cancer depends on various mechanisms, such as age, heredity, reproductive factors, physical inactivity, and obesity. Obesity increases the risk of breast cancer and worsens outcomes for breast cancer patients. The rate of obesity is increasing worldwide, stressing the need for awareness of the association between obesity and breast cancer. In this review, we outline the biomarkers—including cellular and soluble factors—in the breast, associated with obesity, that affect the risk of breast cancer and breast cancer prognosis. Through these biomarkers, we aim to better identify patients with obesity with a higher risk of breast cancer and an inferior prognosis. Abstract Obesity is associated with an increased risk of breast cancer, which is the most common cancer in women worldwide (excluding non-melanoma skin cancer). Furthermore, breast cancer patients with obesity have an impaired prognosis. Adipose tissue is abundant in the breast. Therefore, breast cancer develops in an adipose-rich environment. During obesity, changes in the local environment in the breast occur which are associated with breast cancer. A shift towards a pro-inflammatory state is seen, resulting in altered levels of cytokines and immune cells. Levels of adipokines, such as leptin, adiponectin, and resistin, are changed. Aromatase activity rises, resulting in higher levels of potent estrogen in the breast. Lastly, remodeling of the extracellular matrix takes place. In this review, we address the current knowledge on the changes in the breast adipose tissue in obesity associated with breast cancer initiation and progression. We aim to identify obesity-associated biomarkers in the breast involved in the interplay between obesity and breast cancer. Hereby, we can improve identification of women with obesity with an increased risk of breast cancer and an impaired prognosis. Studies investigating mammary adipocytes and breast adipose tissue in women with obesity versus women without obesity are, however, sparse and further research is needed.
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Affiliation(s)
- Jonas Busk Holm
- Department of Oncology, Aarhus University Hospital, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark
- Correspondence: (J.B.H.); (S.B.)
| | - Ann H. Rosendahl
- Department of Clinical Sciences Lund, Oncology, Lund University, Skåne University Hospital, Barngatan 4, 221 85 Lund, Sweden;
| | - Signe Borgquist
- Department of Oncology, Aarhus University Hospital, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark
- Department of Clinical Sciences Lund, Oncology, Lund University, Skåne University Hospital, Barngatan 4, 221 85 Lund, Sweden;
- Correspondence: (J.B.H.); (S.B.)
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19
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Lv W, Tan Y, Zhao C, Wang Y, Wu M, Wu Y, Ren Y, Zhang Q. Identification of pyroptosis-related lncRNAs for constructing a prognostic model and their correlation with immune infiltration in breast cancer. J Cell Mol Med 2021; 25:10403-10417. [PMID: 34632690 PMCID: PMC8581320 DOI: 10.1111/jcmm.16969] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/28/2021] [Accepted: 09/19/2021] [Indexed: 12/19/2022] Open
Abstract
The inflammasome-dependent cell death, which is denoted as pyroptosis, might be abnormally regulated during oncogenesis and tumour progression. Long non-coding RNAs (LncRNAs) are pivotal orchestrators in breast cancer (BC), which have the potential to be a biomarker for BC diagnosis and therapy. The present study aims to explore the correlation between pyroptosis-related lncRNAs and BC prognosis. In this study, a profile of 8 differentially expressed lncRNAs was screened in the TCGA database and used to construct a prognostic model. The BC patients were divided into high- and low-risk groups dependent on the median cutoff of the risk score in the model. Interestingly, the risk model significantly distinguished the clinical characteristics of BC patients between high- and low-risk groups. Then, the risk score of the model was identified to be an excellent independent prognostic factor. Notably, the GO, KEGG, GSEA and ssGSEA analyses revealed the different immune statuses between the high- and low-risk groups. Particularly, the 8 lncRNAs expressed differentially in BC tissues between two risk subgroups in vitro validation. Collectively, this constructed well-validated model is of high effectiveness to predict the prognosis of BC, which will provide novel means that is applicable for BC prognosis recognition.
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Affiliation(s)
- Wenchang Lv
- Department of Plastic and Cosmetic SurgeryTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yufang Tan
- Department of Plastic and Cosmetic SurgeryTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Chongru Zhao
- Department of Plastic and Cosmetic SurgeryTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yichen Wang
- Department of Plastic and Cosmetic SurgeryTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Min Wu
- Department of Plastic and Cosmetic SurgeryTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yiping Wu
- Department of Plastic and Cosmetic SurgeryTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yuping Ren
- Department of Plastic and Cosmetic SurgeryTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Qi Zhang
- Department of Plastic and Cosmetic SurgeryTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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20
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Fu C, Liu Y, Han X, Pan Y, Wang HQ, Wang H, Dai H, Yang W. An Immune-Associated Genomic Signature Effectively Predicts Pathologic Complete Response to Neoadjuvant Paclitaxel and Anthracycline-Based Chemotherapy in Breast Cancer. Front Immunol 2021; 12:704655. [PMID: 34526986 PMCID: PMC8435784 DOI: 10.3389/fimmu.2021.704655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 08/09/2021] [Indexed: 12/25/2022] Open
Abstract
Breast cancer is now the leading cause of cancer morbidity and mortality among women worldwide. Paclitaxel and anthracycline-based neoadjuvant chemotherapy is widely used for the treatment of breast cancer, but its sensitivity remains difficult to predict for clinical use. In our study, a LASSO logistic regression method was applied to develop a genomic classifier for predicting pathologic complete response (pCR) to neoadjuvant chemotherapy in breast cancer. The predictive accuracy of the signature classifier was further evaluated using four other independent test sets. Also, functional enrichment analysis of genes in the signature was performed, and the correlations between the prediction score of the signature classifier and immune characteristics were explored. We found a 25-gene signature classifier through the modeling, which showed a strong ability to predict pCR to neoadjuvant chemotherapy in breast cancer. For T/FAC-based training and test sets, and a T/AC-based test set, the AUC of the signature classifier is 1.0, 0.9071, 0.9683, 0.9151, and 0.7350, respectively, indicating that it has good predictive ability for both T/FAC and T/AC schemes. The multivariate model showed that 25-gene signature was far superior to other clinical parameters as independent predictor. Functional enrichment analysis indicated that genes in the signature are mainly enriched in immune-related biological processes. The prediction score of the classifier was significantly positively correlated with the immune score. There were also significant differences in immune cell types between pCR and residual disease (RD) samples. Conclusively, we developed a 25-gene signature classifier that can effectively predict pCR to paclitaxel and anthracycline-based neoadjuvant chemotherapy in breast cancer. Our study also suggests that the immune ecosystem is actively involved in modulating clinical response to neoadjuvant chemotherapy and is beneficial to patient outcomes.
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Affiliation(s)
- Changfang Fu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.,Science Island Branch, Graduate School of University of Science and Technology of China, Hefei, China.,Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China.,The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yu Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.,Science Island Branch, Graduate School of University of Science and Technology of China, Hefei, China.,Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Xinghua Han
- The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yueyin Pan
- The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Hong-Qiang Wang
- Biological Molecular Information System Laboratory, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Hongzhi Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.,Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Haiming Dai
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.,Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Wulin Yang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China.,Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
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21
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Jhun I, Shepherd D, Hung YP, Madrigal E, Le LP, Mino-Kenudson M. Digital Image Analysis for Estimating Stromal CD8+ Tumor-Infiltrating Lymphocytes in Lung Adenocarcinoma. J Pathol Inform 2021; 12:28. [PMID: 34447608 PMCID: PMC8359732 DOI: 10.4103/jpi.jpi_36_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 03/03/2021] [Accepted: 03/11/2021] [Indexed: 01/22/2023] Open
Abstract
Background: Stromal CD8+ tumor-infiltrating lymphocytes (TILs) are an important prognostic and predictive indicator in non-small cell lung cancer (NSCLC). In this study, we aimed to develop and test the feasibility of a digital image analysis (DIA) workflow for estimating stromal CD8+ TIL density. Methods: A DIA workflow developed in a software platform (QuPath) was applied to a specified region of interest (ROI) within the stromal compartment of dual PD-L1/CD8 immunostained slides from 50 lung adenocarcinoma patients. A random tree classifier was trained from 25 training cases and applied to 25 test cases. The DIA-estimated CD8+ TIL densities were compared to manual estimates of three pathologists, who independently quantitated the percentage of CD8+ TILs from predefined ROIs in QuPath. Results: The average estimated total stromal cell count per case was 520 (range: 282–816) by QuPath and 551 (range: 265–744) by pathologists. The DIA-estimated CD8+ TIL density (mean = 16.9%) was comparable to pathologists' manual estimates (mean = 15.9%). A paired t-test showed no statistically significant difference between DIA and pathologist estimates of CD8+ TIL density among both training (n = 25, P = 0.55) and test (n = 25, P = 0.34) cases. There was an almost perfect agreement between QuPath and each pathologist's estimates of CD8+ TIL density (κ = 0.85–0.86). Conclusions: These findings demonstrate the feasibility of applying a DIA workflow for estimating stromal CD8+ TIL density in NSCLC. DIA has the potential to provide an efficient and standardized approach for estimating stromal CD8+ TIL density.
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Affiliation(s)
- Iny Jhun
- Department of Pathology, Stanford Health Care, Palo Alto, CA, USA
| | - Daniel Shepherd
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Yin P Hung
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Emilio Madrigal
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Long P Le
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
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22
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Behring M, Ye Y, Elkholy A, Bajpai P, Agarwal S, Kim H, Ojesina AI, Wiener HW, Manne U, Shrestha S, Vazquez AI. Immunophenotype-associated gene signature in ductal breast tumors varies by receptor subtype, but the expression of individual signature genes remains consistent. Cancer Med 2021; 10:5712-5720. [PMID: 34189853 PMCID: PMC8366080 DOI: 10.1002/cam4.4095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/25/2021] [Accepted: 05/10/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In silico deconvolution of invasive immune cell infiltration in bulk breast tumors helps characterize immunophenotype, expands treatment options, and influences survival endpoints. In this study, we identify the differential expression (DE) of the LM22 signature to classify immune-rich and -poor breast tumors and evaluate immune infiltration by receptor subtype and lymph node metastasis. METHODS Using publicly available data, we applied the CIBERSORT algorithm to estimate immune cells infiltrating the tumor into immune-rich and immune-poor groups. We then tested the association of receptor subtype and nodal status with immune-rich/poor phenotype. We used DE to test individual signature genes and over-representation analysis for related pathways. RESULTS CCL19 and CXCL9 expression differed between rich/poor signature groups regardless of subtype. Overexpression of CHI3L2 and FES was observed in triple negative breast cancers (TNBCs) relative to other subtypes in immune-rich tumors. Non-signature genes, LYZ, C1QB, CORO1A, EVI2B, GBP1, PSMB9, and CD52 were consistently overexpressed in immune-rich tumors, and SCUBE2 and GRIA2 were associated with immune-poor tumors. Immune-rich tumors had significant upregulation of genes/pathways while none were identified in immune-poor tumors. CONCLUSIONS Overall, the proportion of immune-rich/poor tumors differed by subtype; however, a subset of 10 LM22 genes that marked immune-rich status remained the same across subtype. Non-LM22 genes differentially expressed between the phenotypes suggest that the biologic processes responsible for immune-poor phenotype are not yet well characterized.
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MESH Headings
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/genetics
- Breast Neoplasms/immunology
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/immunology
- Carcinoma, Ductal, Breast/pathology
- Datasets as Topic
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/immunology
- Humans
- Immunophenotyping
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Up-Regulation/immunology
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Affiliation(s)
- Michael Behring
- Department of EpidemiologyUniversity of Alabama at BirminghamBirminghamALUSA
- Department of Pathology and SurgeryUniversity of Alabama at BirminghamBirminghamALUSA
| | - Yuanfan Ye
- Department of EpidemiologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Amr Elkholy
- Department of Pathology and SurgeryUniversity of Alabama at BirminghamBirminghamALUSA
| | - Prachi Bajpai
- Department of Pathology and SurgeryUniversity of Alabama at BirminghamBirminghamALUSA
| | - Sumit Agarwal
- Department of Pathology and SurgeryUniversity of Alabama at BirminghamBirminghamALUSA
| | - Hyung‐Gyoon Kim
- Department of Pathology and SurgeryUniversity of Alabama at BirminghamBirminghamALUSA
| | - Akinyemi I. Ojesina
- Department of EpidemiologyUniversity of Alabama at BirminghamBirminghamALUSA
- Comprehensive Cancer CenterUniversity of Alabama at BirminghamBirminghamALUSA
| | - Howard W Wiener
- Department of EpidemiologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Upender Manne
- Department of Pathology and SurgeryUniversity of Alabama at BirminghamBirminghamALUSA
- Comprehensive Cancer CenterUniversity of Alabama at BirminghamBirminghamALUSA
| | - Sadeep Shrestha
- Department of EpidemiologyUniversity of Alabama at BirminghamBirminghamALUSA
| | - Ana I. Vazquez
- Department of Epidemiology and BiostatisticsMichigan State UniversityEast LansingMIUSA
- Institute for Quantitative Health Science & EngineeringEast LansingMIUSA
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23
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Crosstalk between Tumor-Infiltrating Immune Cells and Cancer-Associated Fibroblasts in Tumor Growth and Immunosuppression of Breast Cancer. J Immunol Res 2021; 2021:8840066. [PMID: 34337083 PMCID: PMC8294979 DOI: 10.1155/2021/8840066] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 03/04/2021] [Accepted: 06/30/2021] [Indexed: 02/08/2023] Open
Abstract
Signals from the tumor microenvironment (TME) have a profound influence on the maintenance and progression of cancers. Chronic inflammation and the infiltration of immune cells in breast cancer (BC) have been strongly associated with early carcinogenic events and a switch to a more immunosuppressive response. Cancer-associated fibroblasts (CAFs) are the most abundant stromal component and can modulate tumor progression according to their secretomes. The immune cells including tumor-infiltrating lymphocytes (TILs) (cytotoxic T cells (CTLs), regulatory T cells (Tregs), and helper T cell (Th)), monocyte-infiltrating cells (MICs), myeloid-derived suppressor cells (MDSCs), mast cells (MCs), and natural killer cells (NKs) play an important part in the immunological balance, fluctuating TME between protumoral and antitumoral responses. In this review article, we have summarized the impact of these immunological players together with CAF secreted substances in driving BC progression. We explain the crosstalk of CAFs and tumor-infiltrating immune cells suppressing antitumor response in BC, proposing these cellular entities as predictive markers of poor prognosis. CAF-tumor-infiltrating immune cell interaction is suggested as an alternative therapeutic strategy to regulate the immunosuppressive microenvironment in BC.
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24
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Wang J, Liu Y, Zhang S. Prognostic and immunological value of ATP6AP1 in breast cancer: implications for SARS-CoV-2. Aging (Albany NY) 2021; 13:16904-16921. [PMID: 34228637 PMCID: PMC8312471 DOI: 10.18632/aging.203229] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 05/11/2021] [Indexed: 12/24/2022]
Abstract
Abnormal ATPase H+ Transporting Accessory Protein 1 (ATP6AP1) expression may promote carcinogenesis. We investigated the association of ATP6AP1 with breast cancer (BC) and COVID-19. The Oncomine, Gene Expression Profiling Interactive Analysis, Human Protein Atlas and Kaplan-Meier plotter databases were used to evaluate the expression and prognostic value of ATP6AP1 in BC. ATP6AP1 was upregulated in BC tissues, and higher ATP6AP1 expression was associated with poorer outcomes. Data from the Tumor Immune Estimation Resource, Tumor-Immune System Interaction Database and Kaplan-Meier plotter indicated that ATP6AP1 expression correlated with immune infiltration, and that its prognostic effects in BC depended on tumor-infiltrating immune cell subtype levels. Multiple databases were used to evaluate the association of ATP6AP1 with clinicopathological factors, assess the mutation and methylation of ATP6AP1, and analyze gene co-expression and enrichment. The ATP6AP1 promoter was hypomethylated in BC tissues and differentially methylated between different disease stages and subtypes. Data from the Gene Expression Omnibus indicated that ATP6AP1 levels in certain cell types were reduced after SARS-CoV-2 infections. Ultimately, higher ATP6AP1 expression was associated with a poorer prognosis and with higher or lower infiltration of particular immune cells in BC. BC patients may be particularly susceptible to SARS-CoV-2 infections, which may alter their prognoses.
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Affiliation(s)
- Jintian Wang
- Department of Breast Surgery, The Fourth Hospital of Hebei Medical University, Hebei, Shijiazhuang 050011, China
| | - Yunjiang Liu
- Department of Breast Surgery, The Fourth Hospital of Hebei Medical University, Hebei, Shijiazhuang 050011, China
| | - Shuo Zhang
- Department of Breast Surgery, The Fourth Hospital of Hebei Medical University, Hebei, Shijiazhuang 050011, China
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25
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Huo Q, Li Z, Chen S, Wang J, Li J, Xie N. VWCE as a potential biomarker associated with immune infiltrates in breast cancer. Cancer Cell Int 2021; 21:272. [PMID: 34020650 PMCID: PMC8140436 DOI: 10.1186/s12935-021-01955-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 04/27/2021] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Von Willebrand Factor C and EGF Domains (VWCE) is an important gene that regulates cell adhesion, migration, and interaction. However, the correlation between VWCE expression and immune infiltrating in breast cancer remain unclear. In this study, we investigated the correlation between VWCE expression and immune infiltration levels in breast cancer. METHODS The expression of VWCE was analyzed by the tumor immune estimation resource (TIMER) and DriverDB databases. Furthermore, genes co-expressed with VWCE and gene ontology (GO) enrichment analysis were investigated by the STRING and Enrichr web servers. Also, we performed the single nucleotide variation (SNV), copy number variation (CNV), and pathway activity analysis through GSCALite. Subsequently, the relationship between VWCE expression and tumor immunity was analyzed by TIMER and TISIDB databases, and further verified the results using Quantitative Real-Time PCR (RT-PCR), Western blotting, and immunohistochemistry. RESULTS The results showed that the expression of VWCE mRNA in breast cancer tissue was significantly lower than that in normal tissues. We found that the expression level of VWCE was associated with subtypes, estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor-2 (HER2) status of breast cancer patients, but there was no significant difference in the expression of VWCE was found in age and nodal status. Further analyses indicated that VWCE was correlated with the activation or inhibition of multiple oncogenic pathways. Additionally, VWCE expression was negatively correlated with the expression of STAT1 (Th1 marker, r = - 0.12, p = 6e-05), but positively correlated with the expression of MS4A4A (r = 0.28, p = 0). These results suggested that the expression of VWCE was correlated with immune infiltration levels of Th1 and M2 macrophage in breast cancer. CONCLUSIONS In our study, VWCE expression was associated with a better prognosis and was immune infiltration in breast cancer. These findings demonstrate that VWCE is a potential prognostic biomarker and correlated with tumor immune cell infiltration, and maybe a promising therapeutic target in breast cancer.
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Affiliation(s)
- Qin Huo
- Biobank, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University , Shenzhen, 518035, China
| | - Zhenwei Li
- Biobank, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University , Shenzhen, 518035, China
| | - Siqi Chen
- Biobank, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University , Shenzhen, 518035, China
| | - Juan Wang
- Department of Clinical Medicine , University of South China , Hengyang , 421001 , China
| | - Jiaying Li
- Department of Clinical Medicine , University of South China , Hengyang , 421001 , China
| | - Ni Xie
- Biobank, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University , Shenzhen, 518035, China.
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Identification of Five Immune-Related lncRNAs Predicting Survival and Tumor Microenvironment Characteristics in Breast Cancer. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:6676692. [PMID: 33727952 PMCID: PMC7937456 DOI: 10.1155/2021/6676692] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/14/2021] [Accepted: 02/06/2021] [Indexed: 02/07/2023]
Abstract
A common cancer in females, breast cancer (BRCA) mortality has been recently reduced; however, the prognosis of BRCA patients remains poor. This study attempted to develop prognostic immune-related long noncoding RNAs (lncRNAs) for BRCA and identify the effects of these lncRNAs on the tumor microenvironment (TME). Gene expression data from The Cancer Genome Atlas (TCGA) database were collected in order to select differentially expressed lncRNAs. Immune-related lncRNAs were downloaded from the ImmLnc database, where 316 immune-related lncRNAs were identified, 12 of which were found to be significantly related to the prognosis of BRCA patients. Multivariate cox regression analysis was then applied to construct prognostic immune-related lncRNAs as the risk model, including C6orf99, LINC00987, SIAH2-AS1, LINC01010, and ELOVL2-AS1. High-risk and low-risk groups were distinguished according to the median of immune-related risk scores. Accordingly, the overall survival (OS) in the high-risk group was observed to be shorter than that in the low-risk group. qRT-PCR analysis demonstrated that lncRNA expression levels in BRCA cell lines were in basic agreement with predictions except for LINC00987. By validating numerous clinical samples, lncRNA C6orf99 was shown to be highly expressed in the advanced stage, while LINC01010 and SIAH2-AS1 decreased in the advanced T-stage and M-stage. Moreover, the expression of LINC0098 was found to be significantly decreased among the groups (>50 years old). Gene set enrichment analysis (GSEA) was applied to analyze the cancer hallmarks and immunological characteristics of the high-risk and low-risk groups. Importantly, the TIMER database demonstrated that this immune-related lncRNA risk model for breast cancer is related to the infiltration of immune cells. In conclusion, the results indicated that five immune-related lncRNAs could be used as a prognostic model and may even accelerate immunotherapy for BRCA patients.
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Meneveau MO, Sahli ZT, Lynch KT, Mauldin IS, Slingluff CL. Immunotyping and Quantification of Melanoma Tumor-Infiltrating Lymphocytes. Methods Mol Biol 2021; 2265:515-528. [PMID: 33704737 DOI: 10.1007/978-1-0716-1205-7_36] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The density of tumour-infiltrating lymphocytes (TILs) in melanoma is correlated with improved clinical prognosis; however, standardized TIL immunotyping and quantification protocols are lacking. Herein, we provide a review of the technologies being utilized for the immunotyping and quantification of melanoma TILs.
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Affiliation(s)
- Max O Meneveau
- Department of Surgery, The University of Virginia Health System, Charlottesville, VA, USA
| | - Zeyad T Sahli
- Department of Surgery, The University of Virginia Health System, Charlottesville, VA, USA
| | - Kevin T Lynch
- Department of Surgery, The University of Virginia Health System, Charlottesville, VA, USA
| | - Ileana S Mauldin
- Department of Surgery, The University of Virginia Health System, Charlottesville, VA, USA
| | - Craig L Slingluff
- Department of Surgery, The University of Virginia Health System, Charlottesville, VA, USA.
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Pei J, Li Y, Su T, Zhang Q, He X, Tao D, Wang Y, Yuan M, Li Y. Identification and Validation of an Immunological Expression-Based Prognostic Signature in Breast Cancer. Front Genet 2020; 11:912. [PMID: 33193571 PMCID: PMC7526716 DOI: 10.3389/fgene.2020.00912] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 07/22/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Emerging evidence suggests that the immune system plays a crucial role in the regulation of the response to therapy and long-term outcomes of patients with breast cancer (BRCA). In this study, we aimed to identify a significant signature based on immune-related genes to predict the prognosis of BRCA patients. Methods: The expression data were downloaded from The Cancer Genome Atlas (TCGA). The immune-related gene list, the transcription factor (TF) gene list, and the immune infiltrate scores of samples in the TCGA database were acquired from the ImmPort database, the Cistrome Cancer database, and the TIMER database, respectively. Univariate Cox regression analysis was utilized to identify prognostic immune-related differentially expressed genes (DEGs) (PIRDEGs) in BRCA. A prognostic immune signature containing 15 PIRDEGs in BRCA was established using the least absolute shrinkage and selection operator (LASSO) model with 1,000 iterations followed by a stepwise Cox proportional hazards model with a training set of 508 samples in TCGA. An independent assessment of the prognostic prediction ability of the signature was conducted using Kaplan–Meier survival analysis with a testing set of 505 samples in TCGA. Results: We identified 466 PIRDEGs and 80 TFs among the DEGs. A gene signature containing 15 PIRDEGs was constructed. Risk scores of BRCA patients were calculated using this model, which showed a high accuracy of prognosis prediction in both the training set and testing set and could be an independent prognostic factor of BRCA patients. Conclusions: Our study revealed that a PIRDEG signature could be a candidate prognostic biomarker for predicting the overall survival (OS) of patients with BRCA.
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Affiliation(s)
- Jianying Pei
- Department of Clinical Laboratory, The First Clinical Medical College of Lanzhou University, Lanzhou, China.,Institute of Clinical Medicine, Gansu Province Maternal and Child-Care Hospital, Lanzhou, China
| | - Yan Li
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Tianxiong Su
- Department of Clinical Laboratory, People's Hospital of Qingyang, Qingyang, China
| | - Qiaomei Zhang
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Xin He
- Department of Clinical Laboratory, The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Dan Tao
- Department of Clinical Laboratory, The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Yanyun Wang
- Department of Clinical Laboratory, The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Manqiu Yuan
- Department of Clinical Laboratory, The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Yanping Li
- Department of Clinical Laboratory, The First Clinical Medical College of Lanzhou University, Lanzhou, China.,Department of Clinical Laboratory, The First Hospital of Lanzhou University, Lanzhou, China
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Gao S, Chen J, Han X, Wei D, Wu Z, Gao C. LC3B in Malignant Cells Correlates With Immune Infiltrate in Hypopharyngeal Squamous Cell Carcinoma. Technol Cancer Res Treat 2020; 19:1533033820970664. [PMID: 33176581 PMCID: PMC7672751 DOI: 10.1177/1533033820970664] [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] [Indexed: 12/24/2022] Open
Abstract
The objective of this study was to investigate the between autophagy activity and local immune response in hypopharyngeal squamous cell carcinoma (HSCC). Herein, we observed the expression of autophagy marker microtubule-associated protein light chain 3B (MAP1LC3B), CD8 cytotoxic T lymphocytes (CTLs), CD39 (regulatory T cells Tregs) and CD163 (tumor-associated macrophages TAMs) in HSCC, and determined the prognostic roles of CD8+/CD39+ and CD8+/CD163+ in patients with HSCC. The expression of light chain 3B (LC3B) and CD8+/CD39+ was found to be significantly lower in HSCC tissues than in adjacent non-tumor mucosa tissue samples; LC3B expression was positively correlated with the infiltration rate of CD8+/CD39+ in HSCC. Further studies revealed that the ratio of CD8+/CD39+ immune cells was negatively correlated with tumor lymph node metastasis and TNM classification, while the ratio of CD8+/CD163+ immune cells was negatively correlated with TNM classification. Moreover, the expression of LC3B was analyzed and the patients were grouped according to their immune infiltration characteristics. The 5-year cumulative survival rates of LC3B+, CD8+/CD39+, and CD8+/CD163+ patients were significantly higher than those of other group patients. Collectively, our studies indicated that the expression of LC3B in HSCC was correlated with the infiltration ratio of immune cells, and a change in autophagy activity may affect the cellular immunity in HSCC. The ratios of tCD8+/CD39+ and tCD8+/CD163+ may serve as prognostic factors for HSCC.
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Affiliation(s)
- Sifan Gao
- Department of Otorhinolaryngology, Head and Neck Surgery, 36639The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jun Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, 36639The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xiaowen Han
- Department of Pathology, 12485Anhui Medical University, Hefei, China
| | - Dangjun Wei
- Department of Otorhinolaryngology, Head and Neck Surgery, Taihe County Hospital of Traditional Chinese Medicine, Fuyang, Anhui, China
| | - Zhengsheng Wu
- Department of Pathology, 12485Anhui Medical University, Hefei, China
| | - Chaobing Gao
- Department of Otorhinolaryngology, Head and Neck Surgery, 36639The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
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Ye Q, Han X, Wu Z. Bioinformatics analysis to screen key prognostic genes in the breast cancer tumor microenvironment. Bioengineered 2020; 11:1280-1300. [PMID: 33164640 PMCID: PMC8291857 DOI: 10.1080/21655979.2020.1840731] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Increasing evidence has shown that the tumor microenvironment (TME) plays an important role in tumor occurrence and development and can also affect patient prognosis. In this study, we screened key prognostic genes in the breast cancer (BC) TME by analyzing the immune and stromal scores of tumor samples to detect differentially expressed genes (DEGs) and also constructed a TME-related prognostic model. First, we obtained mRNA-Seq and related clinical information for patients with BC from The Cancer Genome Atlas (TCGA) and calculated the stromal and immune scores of tumor tissues using the ESTIMATE algorithm. Next, we performed functional enrichment analysis and generated protein-protein interaction networks from the DEGs that were highly related to the TME. Finally, Cox proportional hazards regression analysis was performed on BC datasets from TCGA, and analyses were conducted on infiltrating immune cells and the human protein atlas. Together, these analyses indicated that the KLRB1 and SIT1 genes could be used as independent prognostic factors for BC, while risk score, age, and clinical stage could be used as prognostic factors. In summary, we found that the prognosis of BC is closely related to immune regulation in the TME.
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Affiliation(s)
- Qian Ye
- Department of Pathology, School of Basic Medicine, Anhui Medical University , Hefei, China
| | - Xiaowen Han
- Department of Pathology, School of Basic Medicine, Anhui Medical University , Hefei, China
| | - Zhengsheng Wu
- Department of Pathology, School of Basic Medicine, Anhui Medical University , Hefei, China
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Heat Shock Protein 90 Family Isoforms as Prognostic Biomarkers and Their Correlations with Immune Infiltration in Breast Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2148253. [PMID: 33145341 PMCID: PMC7596464 DOI: 10.1155/2020/2148253] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 08/09/2020] [Accepted: 10/05/2020] [Indexed: 02/08/2023]
Abstract
Background The heat shock protein 90 (HSP90s) family is composed of molecular chaperones composed of four isoforms in humans, which has been widely reported as unregulated in various kinds of cancers. Nevertheless, the role of each HSP90s isoform in prognosis and immune infiltration in distinct subtypes of breast cancer (BRAC) remains unclear. Methods Public online databases including the Oncomine, UALCAN, Kaplan-Meier Plotter, Tumor IMmune Estimation Resource (TIMER), Gene Expression Profiling Interactive Analysis (GEPIA), GeneMANIA, and Database for Annotation, Visualization, and Integrated Discovery (DAVID) were integrated to perform bioinformatic analyses and to explore the possible associations among HSP90s gene expression, prognosis, and immune infiltration in BRAC. Results The mRNA expression of all HSP90s members was elevated in distinct clinical stages and subtypes of BRAC, compared with the normal breast tissue (P < 0.05). Overexpressed HSP90AA1 was associated with poor prognosis, particularly, both short overall survival (OS) and release-free survival (RFS) in Basal-like BRAC patients; overexpressed HSP90AB1 and HSP90B1 were both associated with poor RFS in Luminal A BRAC patients, while overexpressed TRAP1 was associated with favorable RFS in Luminal A BRAC patients. Moreover, HSP90s gene expression in BRAC showed correlations with the infiltration of CD8+ T cells, neutrophils, macrophages, and dendritic cells (DCs), as well as the activation of tumor-associated macrophages (TAMs), DCs, and CD4+ helper T (Th) cells. The underlying mechanisms of HSP90s modulating tumor-infiltrating immune cells (TIICs) might be related with their functions in antigen processing and presentation, major histocompatibility complex (MHC) binding, and assisting client proteins. Conclusion This study demonstrated that HSP90s family genes were overexpressed and might be serve as prognostic biomarkers in subtypes of BRAC. It might be a novel breakthrough point of BRAC treatment to regulate immune infiltration in BRAC microenvironment for more effective anticancer immunity through pharmacological intervention of HSP90s.
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32
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Pan X, Chen Y, Gao S. Four genes relevant to pathological grade and prognosis in ovarian cancer. Cancer Biomark 2020; 29:169-178. [PMID: 32444534 DOI: 10.3233/cbm-191162] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND: Ovarian cancer is the common tumor in female, the prognostic of which is influenced by a series of factors. In this study, 4 genes relevant to pathological grade in ovarian cancer were screened out by the construction of weighted gene co-expression network analysis. METHODS: GSE9891 with 298 ovarian cancer cases had been used to construct co-expression networks. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses was used to analyze the possible mechanism of genes involved in the malignant process of ovarian cancer. Hub genes were validated in other independent datasets, such as GSE63885, GSE26193 and GSE30161. Survival analysis based on the hub genes was performed by website of Kaplan Meier-plotter. RESULTS: The result based on weighted gene co-expression network analysis indicated that turquoise module has the highest association with pathological grade. Gene Ontology enrichment analysis revealed that the genes in turquoise module main enrichment in inflammatory response and immune response. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that the genes in turquoise module main enrichment in cytokine-cytokine receptor interaction and chemokine signaling pathway. In turquoise module, a total of 4 hub genes (MS4A4A, CD163, CPR65, MS4A6A) were identified. Then, 4 hub genes were effectively verified in the test datasets (GSE63885, GSE26193 and GSE30161) and tissue samples from Shengjing Hospital of China Medical University. Survival analysis indicated that the 4 hub genes were associated with poor progression-free survival of ovarian cancer. CONCLUSIONS: In conclusion, 4 hub genes (MS4A4A, CD163, CPR65, MS4A6A) were verified associated with pathological grade of ovarian cancer. Moreover, MS4A4A, CD163, MS4A6A may serve as a surface marker for M2 macrophages. Targeting the 4 hub genes may can improve the prognosis of ovarian cancer.
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Affiliation(s)
- Xue Pan
- Department of Gynecological Tumors, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ying Chen
- Department of Ultrasound, Jiangnan Hospital Affiliated to Zhejiang University of Traditional Chinese Medicine, Hangzhou, Zhejiang, China
| | - Song Gao
- Department of Gynecological Tumors, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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Piasecka D, Braun M, Mieszkowska M, Kowalczyk L, Kopczynski J, Kordek R, Sadej R, Romanska HM. Upregulation of HIF1-α via an NF-κB/COX2 pathway confers proliferative dominance of HER2-negative ductal carcinoma in situ cells in response to inflammatory stimuli. Neoplasia 2020; 22:576-589. [PMID: 32980776 PMCID: PMC7522292 DOI: 10.1016/j.neo.2020.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 12/31/2022] Open
Abstract
There are data to suggest that some ductal carcinoma in situ (DCIS) may evolve through an evolutionary bottleneck, where minor clones susceptible to the imposed selective pressure drive disease progression. Here, we tested the hypothesis that an impact of the inflammatory environment on DCIS evolution is HER2-dependent, conferring proliferative dominance of HER2-negative cells. In tissue samples, density of tumour-infiltrating immune cells (TIICs) was associated only with high tumour nuclear grade, but in 9% of predominantly HER2-negative cases, the presence of tumoral foci ('hot-spots') of basal-like cells with HIF1-α activity adjacent to the areas of dense stromal infiltration was noted. Results of in vitro analyses further demonstrated that IL-1β and TNF-α as well as macrophage-conditioned medium triggered phosphorylation of NF-κB and subsequent upregulation of COX2 and HIF1-α, exclusively in HER2-negative cells. Treatment with both IL-1β and TNF-α resulted in growth stimulation and inhibition of HER2-negative and HER2-positive cells, respectively. Moreover, ectopic overexpression of HIF1-α rescued HER2-positive cells from the negative effect of IL-1β and TNF-α on cell growth. Our data provide novel insight into the molecular basis of HER2-dependent proliferation of DCIS cells and indicate the NF-κB/COX2 → HIF1-α signalling axis as a dominant mechanism of DCIS evolution induced by inflammatory microenvironment. Presented findings also highlight the clinical significance of heterogeneity of DCIS tumours and suggest that HIF1-α might be considered as a predictive marker of disease progression.
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Affiliation(s)
- Dominika Piasecka
- Department of Pathology, Chair of Oncology, Medical University of Lodz, Lodz, Poland; Department of Molecular Enzymology and Oncology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Marcin Braun
- Department of Pathology, Chair of Oncology, Medical University of Lodz, Lodz, Poland
| | - Magdalena Mieszkowska
- Department of Molecular Enzymology and Oncology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Lukasz Kowalczyk
- Department of Pathology, Chair of Oncology, Medical University of Lodz, Lodz, Poland
| | - Janusz Kopczynski
- Department of Surgical Pathology, Holycross Cancer Center, Kielce, Poland
| | - Radzislaw Kordek
- Department of Pathology, Chair of Oncology, Medical University of Lodz, Lodz, Poland
| | - Rafal Sadej
- Department of Molecular Enzymology and Oncology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland.
| | - Hanna M Romanska
- Department of Pathology, Chair of Oncology, Medical University of Lodz, Lodz, Poland.
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A four-gene signature in the tumor microenvironment that significantly associates with the prognosis of patients with breast cancer. Gene 2020; 761:145049. [PMID: 32791092 DOI: 10.1016/j.gene.2020.145049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/27/2020] [Accepted: 08/07/2020] [Indexed: 12/15/2022]
Abstract
Breast cancer (BRCA) is a highly heterogeneous disease due to the complicated microenvironment in the tumor, making the treatment benefits varied. Therefore, this study aims to identify a gene signature in the tumor microenvironment (TME) associated with the prognosis of BRCA patients. We downloaded the immune, stromal, and proliferation (ISP)-associated genes from the literature on BRCA. mRNA expression and clinical information obtained from The Cancer Genome Atlas (TCGA) were performed to identify the initial biomarker. Furthermore, we validated the robustness of the gene signature in the independent validation data set GSE20685. A four-gene signature in TME, including CD74, MMP9, RPA3, and SHCBP1, was constructed to predict the overall survival of BRCA. The survival time of the high-risk group was significantly worse than that of the low-risk group. Univariate and multivariate Cox regression analysis showed that our four-gene ISP signature was an independent prognostic factor in TCGA and GSE20685 data sets. The AUC suggested that our four-gene ISP signature was comparable to TNM classification at predicting the overall survival of BRCA patients. Interestingly, BRCA patients with high-risk scores were more likely to be associated with stromal and proliferation of cancer. In contrast, those with high-risk scores were more likely to be associated with tumor immunity-related pathway. We found an innovative biomarker in TME to predict the prognosis of BRCA. This signal might reflect the imbalance of TME and provide potential biomarkers for the individualized and precise treatment of BRCA.
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Levels of different subtypes of tumour-infiltrating lymphocytes correlate with each other, with matched circulating lymphocytes, and with survival in breast cancer. Breast Cancer Res Treat 2020; 183:49-59. [PMID: 32577938 PMCID: PMC7376517 DOI: 10.1007/s10549-020-05757-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/16/2020] [Indexed: 02/08/2023]
Abstract
Purpose Breast cancer tumour-infiltrating lymphocytes associate with clinico-pathological factors, including survival, although the literature includes many conflicting findings. Our aim was to assess these associations for key lymphocyte subtypes and in different tumour compartments, to determine whether these provide differential correlations and could, therefore, explain published inconsistencies. Uniquely, we also examine whether infiltrating levels merely reflect systemic lymphocyte levels or whether local factors are predominant in recruitment. Methods Immunohistochemistry was used to detect tumour-infiltrating CD20+ (B), CD4+ (helper T), CD8+ (cytotoxic T) and FoxP3+ (regulatory T) cells in breast cancers from 62 patients, with quantification in tumour stroma, tumour cell nests, and tumour margins. Levels were analysed with respect to clinico-pathological characteristics and matched circulating levels (determined by flow-cytometry). Results CD4+ lymphocytes were the most prevalent subtype in tumour stroma and at tumour edge and CD8+ lymphocytes were most prevalent in tumour nests; FoxP3+ lymphocytes were rarest in all compartments. High grade or hormone receptor negative tumours generally had significantly increased lymphocytes, especially in tumour stroma. Only intra-tumoural levels of CD8+ lymphocytes correlated significantly with matched circulating levels (p < 0.03), suggesting that recruitment is mainly unrelated to systemic activity. High levels of stromal CD4+ and CD20+ cells associated with improved survival in hormone receptor negative cases (p < 0.04), while tumour nest CD8+ and FoxP3+ cells associated with poor survival in hormone receptor positives (p < 0.005). Conclusions Lymphocyte subtype and location define differential impacts on tumour biology, therefore, roles of tumour-infiltrating lymphocytes will only be unravelled through thorough analyses that take this into account. Electronic supplementary material The online version of this article (10.1007/s10549-020-05757-5) contains supplementary material, which is available to authorized users.
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Lv Z, Zhang P, Li D, Qin M, Nie L, Wang X, Ai L, Feng Z, Odhiambo WO, Ma Y, Ji Y. CD19-targeting fusion protein combined with PD1 antibody enhances anti-tumor immunity in mouse models. Oncoimmunology 2020; 9:1747688. [PMID: 32363119 PMCID: PMC7185221 DOI: 10.1080/2162402x.2020.1747688] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/04/2020] [Accepted: 03/17/2020] [Indexed: 12/24/2022] Open
Abstract
In our previous studies, using a B cell vaccine (scFv-Her2), the targeting of tumor-associated antigen Her2 (human epidermal growth factor receptor-2) to B cells via the anti-CD19 single chain variable fragment (scFv) was shown to augment tumor-specific immunity, which enhanced tumor control in the prophylactic and therapeutic setting. However, the fusion protein displayed limited activity against established tumors, and local relapses often occurred following scFv-Her2 treatment, indicating that scFv-Her2-induced responses are inadequate to maintain anti-tumor immunity. In this study, targeting the IV region (D4) of the extracellular region of Her2 to B cells via CD19 molecules (scFv-Her2D4) was found to enhance IFN-γ-producing-CD8+ T cell infiltration in tumor tissues and reduced the number of tumor-infiltrating myeloid-derived suppressor cells (MDSCs). However, negative co-stimulatory molecules such as programmed cell death protein-1 (PD-1), CD160, and LAG-3 on T cells and programmed death protein ligand-1 (PD-L1) on tumor cells were upregulated in the tumor microenvironment after scFv-Her2D4 treatment. Further, anti-PD1 administration enhanced the efficacy of scFv-Her2D4 and anti-tumor immunity, as evidenced by the reversal of tumor-infiltrating CD8+ T cell exhaustion and the reduction of MDSCs and Treg cells, which suppress T cells and alter the tumor immune microenvironment. Moreover, combining this with anti-PD1 antibodies promoted complete tumor rejection. Our data provide evidence of a close interaction among tumor vaccines, T cells, and the PD-L1/PD-1 axis and establish a basis for the rational design of combination therapy with immune modulators and tumor vaccine therapy.
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Affiliation(s)
- Zhuangwei Lv
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Infection and Immunity, Xi'an Jiaotong University Translational Medicine Center, Xi'an, China
| | - Ping Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Infection and Immunity, Xi'an Jiaotong University Translational Medicine Center, Xi'an, China
| | - Dandan Li
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Infection and Immunity, Xi'an Jiaotong University Translational Medicine Center, Xi'an, China
| | - Mengting Qin
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Infection and Immunity, Xi'an Jiaotong University Translational Medicine Center, Xi'an, China
| | - Longzhu Nie
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiaoqian Wang
- The Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Li Ai
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Zhaozu Feng
- School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Woodvine Otieno Odhiambo
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yunfeng Ma
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Infection and Immunity, Xi'an Jiaotong University Translational Medicine Center, Xi'an, China
| | - Yanhong Ji
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Institute of Infection and Immunity, Xi'an Jiaotong University Translational Medicine Center, Xi'an, China.,Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of China, Xi'an Jiaotong University, Xi'an, P. R. China
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Schirosi L, Saponaro C, Giotta F, Popescu O, Pastena MI, Scarpi E, Mangia A. Tumor Infiltrating Lymphocytes and NHERF1 Impact on Prognosis of Breast Cancer Patients. Transl Oncol 2019; 13:186-192. [PMID: 31865181 PMCID: PMC6931214 DOI: 10.1016/j.tranon.2019.10.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/31/2019] [Accepted: 10/31/2019] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Breast cancer (BC) is a heterogeneous disease, and patients with apparently similar clinicopathological characteristics in clinical practice show different outcome. This study evaluated in primary BCs and in the subgroup of the triple-negative breast cancers (TNBCs) the level of tumor infiltrating lymphocytes (TILs), Na+/H+ exchanger regulatory factor 1 (NHERF1) expression, and their association respect to the clinical outcome of patients. MATERIAL AND METHODS NHERF1 expression was assessed by immunohistochemistry in 338 BC samples; the analysis of TILs was examined using hematoxylin and eosin stained slides, according to International TILs Working Group 2014. RESULTS Multivariate analysis identified TILs as an independent prognostic factor for DFS in the entire cohort and in the TNBC subgroup (HR, 0.32; 95% CI, 0.12-0.87; P = 0.026; and HR, 0.22; 95% CI, 0.06-0.80; P = 0.022, respectively). Univariate and survival analysis by Kaplan-Meier method revealed that patients with cytoplasmic (c) NHERF1-/TILs+ expression had better DFS than other patients (P = 0.049), and this result was also found in the TNBC subgroup (P = 0.031). Moreover, TNBC patients with cNHERF1-/TILs- expression had a worse DFS and OS than other patients (P = 0.057 and P = 0.002, respectively). CONCLUSIONS In the complex scenario of BC and in the era of tumor immunogenicity and immunotherapy, we found an association of TIL levels and cNHERF1 expression that could be useful to identify BCs and particularly TNBC patients with different prognosis and clinical outcome.
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Affiliation(s)
- Laura Schirosi
- Pathology Department, IRCCS Istituto Tumori "Giovanni Paolo II" di Bari, 70124, Italy
| | - Concetta Saponaro
- Functional Biomorphology Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II" di Bari, 70124, Italy
| | - Francesco Giotta
- Medical Oncology Unit, IRCCS Istituto Tumori "Giovanni Paolo II" di Bari, 70124, Italy
| | - Ondina Popescu
- Pathology Department, IRCCS Istituto Tumori "Giovanni Paolo II" di Bari, 70124, Italy
| | - Maria Irene Pastena
- Pathology Department, IRCCS Istituto Tumori "Giovanni Paolo II" di Bari, 70124, Italy
| | - Emanuela Scarpi
- Unit of Biostatistics and Clinical Trials, (IRST)-IRCCS Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori, Meldola, FC 47014, Italy
| | - Anita Mangia
- Functional Biomorphology Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II" di Bari, 70124, Italy.
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Zhang C, Shen L, Qi F, Wang J, Luo J. Multi-omics analysis of tumor mutation burden combined with immune infiltrates in bladder urothelial carcinoma. J Cell Physiol 2019; 235:3849-3863. [PMID: 31596511 DOI: 10.1002/jcp.29279] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/27/2019] [Indexed: 12/24/2022]
Abstract
To explore the prognosis of tumor mutation burden (TMB) and underlying relationships with tumor-infiltrating immune cells in bladder cancer (BLCA). Transcriptome profiles and somatic mutation data from The Cancer Genome Atlas database by the GDC tool. A total of 437 samples were included, consisted of 412 BLCA patients and matched 25 normal samples. Specific mutation information was summarized and illustrated in waterfall plot. Higher TMB levels revealed improved overall survival (OS) and lower tumor recurrence. We found 68 differentially expressed genes in two TMB groups and identified eight independent hub TMB-related signature. Pathway analysis suggested that differential TMB-related signature correlated with multiple cancer-related crosstalk, including cell cycle, DNA replication, cellular senescence, and p53 signaling pathway. Besides, the tumor mutation burden related signature (TMBRS) model based on eight signature possessed well predictive value with area under curve (AUC) = 0.753, and patients with higher TMBRS scores showed worse OS outcomes (p < .001). Moreover, we exhibited the inferred immune cell fractions in box plot and differential abundance of immune cells were shown in the heatmap. The Wilcoxon rank-sum test suggested that CD8+ T cell (p = .001) and memory activated CD4+ T cell (p = .004) showed higher infiltrating levels in high-TMB group, while the density of resting mast cells showed lower infiltrating level in high-TMB group (p = .016). Finally, it is significant to note that CD8+ T cell and memory activated CD4+ T cell subsets not only revealed higher infiltrating abundance in high-TMB group but correlated with prolonged OS and lower risk of tumor recurrence, respectively.
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Affiliation(s)
- Chuanjie Zhang
- Department of Urinary Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Luping Shen
- Institute for Stem Cell and Neural Regeneration, School of Pharmacy, Nanjing Medical University, Nanjing, China
| | - Feng Qi
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - JinCheng Wang
- Department of Hepatobiliary Surgery of Drum Tower Clinical Medical College, Nanjing Medical University, Nanjing, China
| | - Jun Luo
- Department of Urology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
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