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Fleischer T, Haugen MH, Ankill J, Silwal-Pandit L, Børresen-Dale AL, Hedenfalk I, Hatschek T, Tost J, Engebraaten O, Kristensen VN. An integrated omics approach highlights how epigenetic events can explain and predict response to neoadjuvant chemotherapy and bevacizumab in breast cancer. Mol Oncol 2024. [PMID: 38671580 DOI: 10.1002/1878-0261.13656] [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: 07/11/2023] [Revised: 02/09/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Treatment with the anti-angiogenic drug bevacizumab in addition to chemotherapy has shown efficacy for breast cancer in some clinical trials, but better biomarkers are needed to optimally select patients for treatment. Here, we present an omics approach where DNA methylation profiles are integrated with gene expression and results from proteomic data in breast cancer patients to predict response to therapy and pinpoint response-related epigenetic events. Fresh-frozen tumor biopsies taken before, during, and after treatment from human epidermal growth factor receptor 2 negative non-metastatic patients receiving neoadjuvant chemotherapy with or without bevacizumab were subjected to molecular profiling. Here, we report that DNA methylation at enhancer CpGs related to cell cycle regulation can predict response to chemotherapy and bevacizumab for the estrogen receptor positive subset of patients (AUC = 0.874), and we validated this observation in an independent patient cohort with a similar treatment regimen (AUC = 0.762). Combining the DNA methylation scores with the scores from a previously published protein signature resulted in a slight increase in the prediction performance (AUC = 0.784). We also show that tumors receiving the combination treatment underwent more extensive epigenetic alterations. Finally, we performed an integrative expression-methylation quantitative trait loci analysis on alterations in DNA methylation and gene expression levels, showing that the epigenetic alterations that occur during treatment are different between responders and non-responders and that these differences may be explained by the proliferation-epithelial-to-mesenchymal transition axis through the activity of grainyhead like transcription factor 2. Using tumor purity computed from copy number data, we developed a method for estimating cancer cell-specific methylation to confirm that the association to response reflects DNA methylation in cancer cells. Taken together, these results support the potential for clinical benefit of the addition of bevacizumab to chemotherapy when administered to the correct patients.
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Affiliation(s)
- Thomas Fleischer
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Mads Haugland Haugen
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Jørgen Ankill
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Laxmi Silwal-Pandit
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ingrid Hedenfalk
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Thomas Hatschek
- Breast Cancer Center, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, Université Paris Saclay, Evry, France
| | - Olav Engebraaten
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Division of Cancer Medicine, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Vessela N Kristensen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
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2
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Wild SA, Cannell IG, Nicholls A, Kania K, Bressan D, Hannon GJ, Sawicka K. Clonal transcriptomics identifies mechanisms of chemoresistance and empowers rational design of combination therapies. eLife 2022; 11:e80981. [PMID: 36525288 PMCID: PMC9757829 DOI: 10.7554/elife.80981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/10/2022] [Indexed: 12/23/2022] Open
Abstract
Tumour heterogeneity is thought to be a major barrier to successful cancer treatment due to the presence of drug resistant clonal lineages. However, identifying the characteristics of such lineages that underpin resistance to therapy has remained challenging. Here, we utilise clonal transcriptomics with WILD-seq; Wholistic Interrogation of Lineage Dynamics by sequencing, in mouse models of triple-negative breast cancer (TNBC) to understand response and resistance to therapy, including BET bromodomain inhibition and taxane-based chemotherapy. These analyses revealed oxidative stress protection by NRF2 as a major mechanism of taxane resistance and led to the discovery that our tumour models are collaterally sensitive to asparagine deprivation therapy using the clinical stage drug L-asparaginase after frontline treatment with docetaxel. In summary, clonal transcriptomics with WILD-seq identifies mechanisms of resistance to chemotherapy that are also operative in patients and pin points asparagine bioavailability as a druggable vulnerability of taxane-resistant lineages.
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Affiliation(s)
- Sophia A Wild
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson WayCambridgeUnited Kingdom
| | - Ian G Cannell
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson WayCambridgeUnited Kingdom
| | - Ashley Nicholls
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson WayCambridgeUnited Kingdom
| | - Katarzyna Kania
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson WayCambridgeUnited Kingdom
| | - Dario Bressan
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson WayCambridgeUnited Kingdom
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson WayCambridgeUnited Kingdom
| | - Kirsty Sawicka
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson WayCambridgeUnited Kingdom
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3
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Gong Q, Guo Z, Sun W, Du X, Jiang Y, Liu F. CX3CL1 promotes cell sensitivity to ferroptosis and is associated with the tumor microenvironment in clear cell renal cell carcinoma. BMC Cancer 2022; 22:1184. [PMCID: PMC9670481 DOI: 10.1186/s12885-022-10302-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
Abstract
Background
An increasing number of studies have demonstrated that CX3CL1 is involved in the development of tumors and may thus be considered a new potential therapeutic target for them. However, the function of CX3CL1 in clear cell renal cell carcinoma (ccRCC) remains poorly defined.
Methods
The pan-cancer expression pattern and prognostic value of CX3CL1 were evaluated in this study. Moreover, the relationship of CX3CL1 expression with the tumor microenvironment, especially the tumor immune microenvironment, was analyzed. Our analyses employed public repository data. Additionally, we generated stable CX3CL1-overexpressing 786-O cells to determine the role of CX3CL1 in vitro via cell viability and transwell assays. A xenograft tumor model was used to determine the role of CX3CL1 in vivo. The association between CX3CL1 and ferroptosis sensitivity of tumor cells was assessed using Ferrostatin-1.
Results
Our findings indicated the involvement of CX3CL1 in the occurrence and development of ccRCC by acting as a tumor suppressor. We also found that ccRCC patients with high CX3CL1 expression showed better clinical outcomes than those with low CX3CL1 expression. The findings of our epigenetic study suggested that the expression of CX3CL1 in ccRCC is correlated with its DNA methylation level. Furthermore, the CX3CL1 expression level was closely related to the infiltration level of CD8+ T cells into the tumor microenvironment (TME). CX3CL1 showed different predictive values in different immunotherapy cohorts. Finally, CX3CL1 overexpression inhibited tumor cell proliferation and metastasis and promoted tumor ferroptosis sensitivity in ccRCC.
Conclusions
This study revealed the role of CX3CL1 as a tumor suppressor in ccRCC. Our findings indicated that CX3CL1 plays a crucial role in regulating the ccRCC TME and is a potential predictor of immunotherapy outcomes in ccRCC. We also found that CX3CL1 can promote ferroptosis sensitivity in ccRCC cells.
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4
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Shen R, Liu D, Wang X, Guo Z, Sun H, Song Y, Wang D. DNA Damage and Activation of cGAS/STING Pathway Induce Tumor Microenvironment Remodeling. Front Cell Dev Biol 2022; 9:828657. [PMID: 35265630 PMCID: PMC8900217 DOI: 10.3389/fcell.2021.828657] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/27/2021] [Indexed: 12/11/2022] Open
Abstract
DNA damage occurs throughout tumorigenesis and development. The immunogenicity of DNA makes it an immune stimulatory molecule that initiates strong inflammatory responses. The cGAS/STING pathway has been investigated as a critical receptor in both exogenous and endogenous DNA sensing to activate the innate immune response. Growing lines of evidence have indicated that activation of the cGAS/STING pathway is critical in antitumor immunity. Recent studies have demonstrated the outstanding advancement of this pathway in tumor-combined immunotherapy; accordingly, increased studies focus on exploration of STING pathway agonists and analogues. However, current studies propose the potential use of the cGAS/STING pathway in tumor initiation and metastasis. Here, we review the molecular mechanisms and activation of the cGAS/STING pathway, and the relationship between DNA damage and this pathway, particularly highlighting the remodeling of immune contexture in tumor environment (TME) triggered by cascade inflammatory signals. A detailed understanding of TME reprogramming initiated by this pathway may pave the way for the development of new therapeutic strategies and rational clinical application.
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Affiliation(s)
- Rong Shen
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Disheng Liu
- The First Hospital of Lanzhou University, Lanzhou, China
| | - Xiaoning Wang
- School of Medicine, Shandong University, Jinan, China
| | - Zhao Guo
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Haonan Sun
- The First Hospital of Lanzhou University, Lanzhou, China
| | - Yanfeng Song
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Degui Wang
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
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5
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Liu X, Qiu R, Xu M, Meng M, Zhao S, Ji J, Yang Y. KMT2C is a potential biomarker of prognosis and chemotherapy sensitivity in breast cancer. Breast Cancer Res Treat 2021; 189:347-361. [PMID: 34240274 DOI: 10.1007/s10549-021-06325-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 07/05/2021] [Indexed: 12/27/2022]
Abstract
PURPOSE Epigenetic regulation plays critical roles in cancer progression, and high-frequency mutations or expression variations in epigenetic regulators have been frequently observed in tumorigenesis, serving as biomarkers and targets for cancer therapy. Here, we aimed to explore the function of epigenetic regulators in breast cancer. METHODS The mutational landscape of epigenetic regulators in breast cancer samples was investigated based on datasets from the Cancer Genome Atlas. The Kaplan-Meier method was used for survival analysis. RNA sequencing (RNA-seq) in MCF-7 cells transfected with control siRNA or KMT2C siRNA was performed. Quantitative reverse transcription-PCR and chromatin immunoprecipitation were used to validate the RNA-seq results. RESULTS Among the 450 epigenetic regulators, KMT2C was frequently mutated in breast cancer samples. The tumor mutational burden (TMB) was elevated in breast cancer samples with KMT2C mutations or low KMT2C mRNA levels compared to their counterparts with wild-type KMT2C or high KMT2C mRNA levels. Somatic mutation and low expression of KMT2C were independently correlated with the poor overall survival (OS) and disease-free survival (DFS) of the breast cancer samples, respectively. RNA-seq analysis combined with chromatin immunoprecipitation and qRT-PCR assays revealed that the depletion of KMT2C remarkably affected the expression of DNA damage repair-related genes. More importantly, the low expression of KMT2C was related to breast cancer cell sensitivity to chemotherapy and longer OS of breast cancer patients who underwent chemotherapy. CONCLUSION We conclude that KMT2C could serve as a potential biomarker of prognosis and chemotherapy sensitivity by affecting the DNA damage repair-related genes of breast cancer.
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Affiliation(s)
- Xinhua Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Rongfang Qiu
- Zhejiang Provincial Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, School of Medicine, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China.,Department of Radiology, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Min Xu
- Zhejiang Provincial Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, School of Medicine, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China.,Department of Radiology, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China
| | - Miaomiao Meng
- Zhejiang Provincial Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, School of Medicine, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China.,Department of Radiology, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China
| | - Siyu Zhao
- Zhejiang Provincial Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, School of Medicine, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China.,Department of Radiology, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China
| | - Jiansong Ji
- Zhejiang Provincial Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, School of Medicine, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China. .,Department of Radiology, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China.
| | - Yang Yang
- Zhejiang Provincial Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, School of Medicine, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China. .,Department of Radiology, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China. .,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
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6
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Izadi F, Sharpe BP, Breininger SP, Secrier M, Gibson J, Walker RC, Rahman S, Devonshire G, Lloyd MA, Walters ZS, Fitzgerald RC, Rose-Zerilli MJJ, Underwood TJ. Genomic Analysis of Response to Neoadjuvant Chemotherapy in Esophageal Adenocarcinoma. Cancers (Basel) 2021; 13:3394. [PMID: 34298611 PMCID: PMC8308111 DOI: 10.3390/cancers13143394] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 01/04/2023] Open
Abstract
Neoadjuvant therapy followed by surgery is the standard of care for locally advanced esophageal adenocarcinoma (EAC). Unfortunately, response to neoadjuvant chemotherapy (NAC) is poor (20-37%), as is the overall survival benefit at five years (9%). The EAC genome is complex and heterogeneous between patients, and it is not yet understood whether specific mutational patterns may result in chemotherapy sensitivity or resistance. To identify associations between genomic events and response to NAC in EAC, a comparative genomic analysis was performed in 65 patients with extensive clinical and pathological annotation using whole-genome sequencing (WGS). We defined response using Mandard Tumor Regression Grade (TRG), with responders classified as TRG1-2 (n = 27) and non-responders classified as TRG4-5 (n =38). We report a higher non-synonymous mutation burden in responders (median 2.08/Mb vs. 1.70/Mb, p = 0.036) and elevated copy number variation in non-responders (282 vs. 136/patient, p < 0.001). We identified copy number variants unique to each group in our cohort, with cell cycle (CDKN2A, CCND1), c-Myc (MYC), RTK/PIK3 (KRAS, EGFR) and gastrointestinal differentiation (GATA6) pathway genes being specifically altered in non-responders. Of note, NAV3 mutations were exclusively present in the non-responder group with a frequency of 22%. Thus, lower mutation burden, higher chromosomal instability and specific copy number alterations are associated with resistance to NAC.
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Affiliation(s)
- Fereshteh Izadi
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
- Centre for NanoHealth, Swansea University Medical School, Singleton Campus, Swansea SA2 8PP, UK
| | - Benjamin P. Sharpe
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Stella P. Breininger
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
| | - Maria Secrier
- UCL Genetics Institute, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK;
| | - Jane Gibson
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Robert C. Walker
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
| | - Saqib Rahman
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
| | - Ginny Devonshire
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK;
| | - Megan A. Lloyd
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
| | - Zoë S. Walters
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Rebecca C. Fitzgerald
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 OXZ, UK;
| | - Matthew J. J. Rose-Zerilli
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Tim J. Underwood
- School of Cancer Sciences, Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK; (F.I.); (B.P.S.); (S.P.B.); (J.G.); (R.C.W.); (S.R.); (M.A.L.); (Z.S.W.); (M.J.J.R.-Z.)
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
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7
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De Mattos-Arruda L, Cortes J, Blanco-Heredia J, Tiezzi DG, Villacampa G, Gonçalves-Ribeiro S, Paré L, Souza CA, Ortega V, Sammut SJ, Cusco P, Fasani R, Chin SF, Perez-Garcia J, Dienstmann R, Nuciforo P, Villagrasa P, Rubio IT, Prat A, Caldas C. The temporal mutational and immune tumour microenvironment remodelling of HER2-negative primary breast cancers. NPJ Breast Cancer 2021; 7:73. [PMID: 34099718 PMCID: PMC8185105 DOI: 10.1038/s41523-021-00282-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 05/03/2021] [Indexed: 12/30/2022] Open
Abstract
The biology of breast cancer response to neoadjuvant therapy is underrepresented in the literature and provides a window-of-opportunity to explore the genomic and microenvironment modulation of tumours exposed to therapy. Here, we characterised the mutational, gene expression, pathway enrichment and tumour-infiltrating lymphocytes (TILs) dynamics across different timepoints of 35 HER2-negative primary breast cancer patients receiving neoadjuvant eribulin therapy (SOLTI-1007 NEOERIBULIN-NCT01669252). Whole-exome data (N = 88 samples) generated mutational profiles and candidate neoantigens and were analysed along with RNA-Nanostring 545-gene expression (N = 96 samples) and stromal TILs (N = 105 samples). Tumour mutation burden varied across patients at baseline but not across the sampling timepoints for each patient. Mutational signatures were not always conserved across tumours. There was a trend towards higher odds of response and less hazard to relapse when the percentage of subclonal mutations was low, suggesting that more homogenous tumours might have better responses to neoadjuvant therapy. Few driver mutations (5.1%) generated putative neoantigens. Mutation and neoantigen load were positively correlated (R2 = 0.94, p = <0.001); neoantigen load was weakly correlated with stromal TILs (R2 = 0.16, p = 0.02). An enrichment in pathways linked to immune infiltration and reduced programmed cell death expression were seen after 12 weeks of eribulin in good responders. VEGF was downregulated over time in the good responder group and FABP5, an inductor of epithelial mesenchymal transition (EMT), was upregulated in cases that recurred (p < 0.05). Mutational heterogeneity, subclonal architecture and the improvement of immune microenvironment along with remodelling of hypoxia and EMT may influence the response to neoadjuvant treatment.
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Affiliation(s)
- Leticia De Mattos-Arruda
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain.
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK.
| | - Javier Cortes
- Oncology Department International Breast Cancer Center (IBCC), Quiron Group, Barcelona, Spain
- Medica Scientia Innovation Research (MedSIR), Barcelona, Spain
- Medica Scientia Innovation Research (MedSIR), Ridgewood, NJ, USA
- Breast Cancer Research program, Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Universidad Europea de Madrid, Faculty of Biomedical and Health Sciences, Department of Medicine, Madrid, Spain
| | - Juan Blanco-Heredia
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Daniel G Tiezzi
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
- Breast Disease Division, Ribeirão Preto School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Guillermo Villacampa
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | | | - Laia Paré
- Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain
- SOLTI Breast Cancer Research Group, Barcelona, Spain
- Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute, Barcelona, Spain
| | - Carla Anjos Souza
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Vanesa Ortega
- Breast Cancer Research program, Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Stephen-John Sammut
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Pol Cusco
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - Roberta Fasani
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - Suet-Feung Chin
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Jose Perez-Garcia
- Oncology Department International Breast Cancer Center (IBCC), Quiron Group, Barcelona, Spain
- Medica Scientia Innovation Research (MedSIR), Barcelona, Spain
- Medica Scientia Innovation Research (MedSIR), Ridgewood, NJ, USA
| | - Rodrigo Dienstmann
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | | | - Isabel T Rubio
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - Aleix Prat
- Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain
- SOLTI Breast Cancer Research Group, Barcelona, Spain
- Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute, Barcelona, Spain
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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8
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Chen X, Gao Y, Zhang G, Li B, Ma T, Ma Y, Wang X. Bevacizumab Plays a double-edged role in Neoadjuvant Therapy for Non-metastatic Breast Cancer: A Systemic Review and Meta-Analysis. J Cancer 2021; 12:2643-2653. [PMID: 33854624 PMCID: PMC8040714 DOI: 10.7150/jca.53303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/04/2021] [Indexed: 12/04/2022] Open
Abstract
The anti-angiogenic drug Bevacizumab (Bev) is engaged in neoadjuvant therapy for non-metastatic breast cancer (NMBC). However, whether neoadjuvant Bev providing a greater benefit to patients is debatable. Our study aimed to review Bev's role in Neoadjuvant therapy (NAT) in NMBC and identify predictive markers associated with its efficacy by systemic review and meta-analysis. Eligible trials were retrieved from the Pubmed, Embase, and Cochrane Library, and random or fixed effects models were applied to synthesize data. Power of pCR to predict DFS or OS was evaluated by nonlinear mixed effect model. In NMBC, Bev significantly improved the rate of patients achieving pCR, but this benefit discontinued in DFS or OS. Biomarkers such as PAM50 intrinsic subtype, VEGF overexpression, regulation of VEGF signaling pathway, hypoxia-related genes, BRCA1/2 mutation, P53 mutation and immune phenotype can be used to predict Bev-inducing pCR and/or DFS/OS. Unfortunately, although patients with pCR survived longer than those without pCR when ignoring the use of Bev, but patients achieving pCR with Bev might survive shorter than those achieving pCR without Bev. Subgroup analyses found Bev prolonged patients' OS when given pre- and post-surgery. Lastly, adding Bev increased adverse effects. Overall, Bev offered limited effect for patients with NMBC in an unscreened population. However, in biomarkers - identified subgroup, Bev could be promising to ameliorate the prognosis of specific patients with NMBC.
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Affiliation(s)
- XinJie Chen
- Beijing University of Chinese Medicine, No. 11, Bei San Huan Dong Lu, Chaoyang District, Beijing, 100029, China.,Oncology Department, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, No.23 Back Road of Art Gallery, Dongcheng District, Beijing, 100010, China
| | - Yu Gao
- Beijing University of Chinese Medicine, No. 11, Bei San Huan Dong Lu, Chaoyang District, Beijing, 100029, China.,Oncology Department, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, No.23 Back Road of Art Gallery, Dongcheng District, Beijing, 100010, China
| | - GanLin Zhang
- Oncology Department, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, No.23 Back Road of Art Gallery, Dongcheng District, Beijing, 100010, China
| | - BingXue Li
- Beijing University of Chinese Medicine, No. 11, Bei San Huan Dong Lu, Chaoyang District, Beijing, 100029, China.,Oncology Department, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, No.23 Back Road of Art Gallery, Dongcheng District, Beijing, 100010, China
| | - TingTing Ma
- Oncology Department, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, No.23 Back Road of Art Gallery, Dongcheng District, Beijing, 100010, China
| | - YunFei Ma
- Oncology Department, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, No.23 Back Road of Art Gallery, Dongcheng District, Beijing, 100010, China
| | - XiaoMin Wang
- Oncology Department, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, No.23 Back Road of Art Gallery, Dongcheng District, Beijing, 100010, China
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9
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Haugen MH, Lingjærde OC, Hedenfalk I, Garred Ø, Borgen E, Loman N, Hatschek T, Børresen-Dale AL, Naume B, Mills GB, Mælandsmo GM, Engebraaten O. Protein Signature Predicts Response to Neoadjuvant Treatment With Chemotherapy and Bevacizumab in HER2-Negative Breast Cancers. JCO Precis Oncol 2021; 5:PO.20.00086. [PMID: 34036235 PMCID: PMC8140811 DOI: 10.1200/po.20.00086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 10/21/2020] [Accepted: 12/07/2020] [Indexed: 12/17/2022] Open
Abstract
PURPOSE Antiangiogenic therapy using bevacizumab has proven effective for a number of cancers; however, in breast cancer (BC), there is an unmet need to identify patients who benefit from such treatment. PATIENTS AND METHODS In the NeoAva phase II clinical trial, patients (N = 132) with large (≥ 25 mm) human epidermal growth factor receptor 2 (HER2)-negative primary tumors were randomly assigned 1:1 to treatment with neoadjuvant chemotherapy (CTx) alone or in combination with bevacizumab (Bev plus CTx). The ratio of the tumor size after relative to before treatment was calculated into a continuous response scale. Tumor biopsies taken prior to neoadjuvant treatment were analyzed by reverse-phase protein arrays (RPPA) for expression levels of 210 BC-relevant (phospho-) proteins. Lasso regression was used to derive a predictor of tumor shrinkage from the expression of selected proteins prior to treatment. RESULTS We identified a nine-protein signature score named vascular endothelial growth factor inhibition response predictor (ViRP) for use in the Bev plus CTx treatment arm able to predict with accuracy pathologic complete response (pCR) (area under the curve [AUC] = 0.85; 95% CI, 0.74 to 0.97) and low residual cancer burden (RCB 0/I) (AUC = 0.80; 95% CI, 0.68 to 0.93). The ViRP score was significantly lower in patients with pCR (P < .001) and in patients with low RCB (P < .001). The ViRP score was internally validated on mRNA data and the resultant surrogate mRNA ViRP score significantly separated the pCR patients (P = .016). Similarly, the mRNA ViRP score was validated (P < .001) in an independent phase II clinical trial (PROMIX). CONCLUSION Our ViRP score, integrating the expression of nine proteins and validated on mRNA data both internally and in an independent clinical trial, may be used to increase the likelihood of benefit from treatment with bevacizumab combined with chemotherapy in patients with HER2-negative BC.
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Affiliation(s)
- Mads H Haugen
- Department of Tumor Biology, Institute for Cancer Research, Division of Cancer Medicine, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Ole Christian Lingjærde
- Department of Genetics, Institute for Cancer Research, Division of Cancer Medicine, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway.,Department of Informatics-Biomedical Informatics, University of Oslo, Oslo, Norway.,K.G. Jebsen-Centre for B Cell Malignancies, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ingrid Hedenfalk
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Øystein Garred
- Division of Laboratory Medicine-Pathology, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Elin Borgen
- Division of Laboratory Medicine-Pathology, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Niklas Loman
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden.,Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Skåne, Sweden
| | - Thomas Hatschek
- Department of Oncology-Pathology, Karolinska University Hospital, Stockholm, Sweden
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Division of Cancer Medicine, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Bjørn Naume
- Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Oncology, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Gordon B Mills
- Department of Cell, Developmental and Cancer Biology, School of Medicine, Oregon Health Science University, Portland, OR
| | - Gunhild M Mælandsmo
- Department of Tumor Biology, Institute for Cancer Research, Division of Cancer Medicine, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway.,Institute for Medical Biology, Faculty of Health Sciences, University of Tromsø, The Arctic University of Norway, Tromsø, Norway
| | - Olav Engebraaten
- Department of Tumor Biology, Institute for Cancer Research, Division of Cancer Medicine, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway.,Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Oncology, Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway
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10
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Tan S, Zang G, Wang Y, Sun Z, Li Y, Lu C, Wang Z. Differences of Angiogenesis Factors in Tumor and Diabetes Mellitus. Diabetes Metab Syndr Obes 2021; 14:3375-3388. [PMID: 34335038 PMCID: PMC8318726 DOI: 10.2147/dmso.s315362] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/04/2021] [Indexed: 12/11/2022] Open
Abstract
Angiogenesis, as a process occurring under the regulation of a variety of factors, is one of the important ways of vascular development. It coexists in a variety of pathological and physiological processes. Now a large number of studies have proved that tumor growth, metastasis, and various vascular complications of diabetes are closely related to angiogenesis, and an increasing number of studies have shown that there are many common factors between the two. But angiogenesis is the opposite of the two: it is enhanced in tumors and suppressed in diabetes. Therefore, this review discusses the causes of the phenomenon from the expression of various factors affecting angiogenesis in these two diseases and their effects on angiogenesis in the relevant microenvironment, as well as the application status of these factors or cells as therapeutic targets in the treatment of these two diseases.
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Affiliation(s)
- Shidong Tan
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, People’s Republic of China
| | - Guangyao Zang
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, People’s Republic of China
| | - Ying Wang
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, People’s Republic of China
| | - Zhen Sun
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, People’s Republic of China
| | - Yalan Li
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, People’s Republic of China
| | - Cheng Lu
- General Office, Affiliated Hospital of Jiangsu University, Zhenjiang, People’s Republic of China
- Correspondence: Cheng Lu General Office, Affiliated Hospital of Jiangsu University, 438 Jiefang Road, Zhenjiang, 212001, People's Republic of China, +86 511 88986902 Email
| | - Zhongqun Wang
- Department of Cardiology, Affiliated Hospital of Jiangsu University, Zhenjiang, People’s Republic of China
- Zhongqun Wang Department of Cardiology, Affiliated Hospital of Jiangsu University, 438 Jiefang Road, Zhenjiang, 212001, People’s Republic of ChinaTel +86 511 85030586 Email
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11
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Feng H, Liu K, Shen X, Liang J, Wang C, Qiu W, Cheng X, Zhao R. Targeting tumor cell-derived CCL2 as a strategy to overcome Bevacizumab resistance in ETV5 + colorectal cancer. Cell Death Dis 2020; 11:916. [PMID: 33099574 PMCID: PMC7585575 DOI: 10.1038/s41419-020-03111-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 02/06/2023]
Abstract
In our previous study, ETV5 mediated-angiogenesis was demonstrated to be dependent upon the PDGF-BB/PDGFR-β/Src/STAT3/VEGFA pathway in colorectal cancer (CRC). However, the ability of ETV5 to affect the efficacy of anti-angiogenic therapy in CRC requires further investigation. Gene set enrichment analysis (GSEA) and a series of experiments were performed to identify the critical candidate gene involved in Bevacizumab resistance. Furthermore, the ability of treatment targeting the candidate gene to enhance Bevacizumab sensitivity in vitro and in vivo was investigated. Our results revealed that ETV5 directly bound to the VEGFA promoter to promote translation of VEGFA. However, according to in vitro and in vivo experiments, ETV5 unexpectedly accelerated antiVEGF therapy (Bevacizumab) resistance. GSEA and additional assays confirmed that ETV5 could promote angiogenesis by inducing the secretion of another tumor angiogenesis factor (CCL2) in CRC cells to facilitate Bevacizumab resistance. Mechanistically, ETV5 upregulated CCL2 by activating STAT3 to facilitate binding with the CCL2 promoter. ETV5 induced-VEGFA translation and CCL2 secretion were mutually independent mechanisms, that induced angiogenesis by activating the PI3K/AKT and p38/MAPK signaling pathways in human umbilical vein endothelial cells (HUVECs). In CRC tissues, ETV5 protein levels were positively associated with CD31, CCL2, and VEGFA protein expression. CRC patients possessing high expression of ETV5/VEGFA or ETV5/CCL2 exhibited a poorer prognosis compared to that of other patients. Combined antiCCL2 and antiVEGFA (Bevacizumab) treatment could inhibit tumor angiogenesis and growth more effectively than single treatments in CRCs with high expression of ETV5 (ETV5+ CRCs). In conclusion, our results not only revealed ETV5 as a novel biomarker for anti-angiogenic therapy, but also indicated a potential combined therapy strategy that involved in targeting of both CCL2 and VEGFA in ETV5+ CRC.
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Affiliation(s)
- Haoran Feng
- Department of General Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, 200025, Shanghai, China.,Shanghai Institute of Digestive Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, 200025, Shanghai, China
| | - Kun Liu
- Department of General Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, 200025, Shanghai, China.,Department of General Surgery, Ruijin Hospital North, School of Medicine, Shanghai Jiao Tong University, 201800, Shanghai, China
| | - Xiaonan Shen
- Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, 200001, Shanghai, China
| | - Juyong Liang
- Department of General Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, 200025, Shanghai, China.,Shanghai Institute of Digestive Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, 200025, Shanghai, China
| | - Changgang Wang
- Department of General Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, 200025, Shanghai, China.,Department of General Surgery, Ruijin Hospital North, School of Medicine, Shanghai Jiao Tong University, 201800, Shanghai, China
| | - Weihua Qiu
- Department of General Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, 200025, Shanghai, China. .,Shanghai Institute of Digestive Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, 200025, Shanghai, China. .,Department of General Surgery, Ruijin Hospital North, School of Medicine, Shanghai Jiao Tong University, 201800, Shanghai, China.
| | - Xi Cheng
- Department of General Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, 200025, Shanghai, China. .,Shanghai Institute of Digestive Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, 200025, Shanghai, China. .,Department of General Surgery, Ruijin Hospital North, School of Medicine, Shanghai Jiao Tong University, 201800, Shanghai, China.
| | - Ren Zhao
- Department of General Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, 200025, Shanghai, China. .,Shanghai Institute of Digestive Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, 200025, Shanghai, China. .,Department of General Surgery, Ruijin Hospital North, School of Medicine, Shanghai Jiao Tong University, 201800, Shanghai, China.
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12
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Karn T, Meissner T, Weber KE, Solbach C, Denkert C, Engels K, Fasching PA, Sinn BV, Schrader I, Budczies J, Marmé F, Müller V, Holtrich U, Gerber B, Schem C, Young BM, Hanusch C, Stickeler E, Huober J, van Mackelenbergh M, Leyland-Jones B, Fehm T, Nekljudova V, Untch M, Loibl S. A Small Hypoxia Signature Predicted pCR Response to Bevacizumab in the Neoadjuvant GeparQuinto Breast Cancer Trial. Clin Cancer Res 2020; 26:1896-1904. [PMID: 31932495 DOI: 10.1158/1078-0432.ccr-19-1954] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 11/19/2019] [Accepted: 01/08/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE In breast cancer, bevacizumab increased pCR rate but not long-term survival and no predictive markers are available to identify patients with long-term benefit from the drug. EXPERIMENTAL DESIGN We profiled 289 pretherapeutic formalin-fixed, paraffin-embedded (FFPE) biopsies of HER2-negative patients from the GeparQuinto trial of neoadjuvant chemotherapy ± bevacizumab by exome-capture RNA-sequencing (RNA-seq). In a prospectively planned study, we tested molecular signatures for response prediction. IHC validation was performed using tissue microarrays. RESULTS We found strong agreement of molecular and pathologic parameters as hormone receptors, grading, and lymphocyte infiltration in 221 high-quality samples. Response rates (49.3% pCR overall) were higher in basal-like (68.9%) and HER2-enriched (45.5%) than in luminal B (35.7%), luminal A (17.9%), and normal-like (20.0%) subtypes. T-cell (OR = 1.60; 95% confidence interval, 1.21-2.12; P = 0.001), proliferation (OR = 2.88; 95% CI, 2.00-4.15; P < 0.001), and hypoxia signatures (OR = 1.92; 95% CI, 1.41-2.60; P < 0.001) significantly predicted pCR in univariate analysis. In a prespecified multivariate logistic regression, a small hypoxia signature predicted pCR (OR = 2.40; 95% CI, 1.28-4.51; P = 0.006) with a significant interaction with bevacizumab treatment (P = 0.020). IHC validation using NDRG1 as marker revealed highly heterogenous expression within tissue leading to profound loss of sensitivity in TMA analysis, still a significant predictive value for pCR was detected (P = 0.025). CONCLUSIONS Exome-capture RNA-seq characterizes small FFPE core biopsies by reliably detecting factors as for example ER status, grade, and tumor-infiltrating lymphocytes levels. Beside molecular subtypes and immune signatures, a small hypoxia signature predicted pCR to bevacizumab, which could be validated by IHC. The signature can have important applications for bevacizumab treatment in different cancer types and might also have a role for novel combination therapies of bevacizumab with immune checkpoint inhibition.
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Affiliation(s)
- Thomas Karn
- Goethe University Hospital Frankfurt, Frankfurt, Germany.
| | | | | | | | | | - Knut Engels
- Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Germany
| | | | - Iris Schrader
- Gynäkologisch-Onkologische Praxis Hannover, Hannover, Germany
| | | | | | - Volkmar Müller
- University Hospital Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Uwe Holtrich
- Goethe University Hospital Frankfurt, Frankfurt, Germany
| | | | | | | | | | | | | | | | | | - Tanja Fehm
- University Hospital Tübingen, Tübingen, Germany
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13
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Lindholm EM, Ragle Aure M, Haugen MH, Kleivi Sahlberg K, Kristensen VN, Nebdal D, Børresen‐Dale A, Lingjærde OC, Engebraaten O. miRNA expression changes during the course of neoadjuvant bevacizumab and chemotherapy treatment in breast cancer. Mol Oncol 2019; 13:2278-2296. [PMID: 31402562 PMCID: PMC6763780 DOI: 10.1002/1878-0261.12561] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/26/2019] [Accepted: 08/09/2019] [Indexed: 12/24/2022] Open
Abstract
One of the hallmarks of cancer is sustained angiogenesis. Favorable results have been reported in some breast cancer (BC) patients receiving antiangiogenic therapy with bevacizumab (Bev) in combination with chemotherapy, and further knowledge on how Bev can be optimally combined with conventional treatment to increase efficacy is strongly needed. In this randomized, neoadjuvant phase II clinical trial, 132 patients with HER2-negative, nonmetastatic BC were treated with Bev in combination with sequential chemotherapy. Biopsies were sampled before treatment, after 12 weeks with anthracycline and after taxane therapy at week 25. MicroRNA (miRNA) expression profiling was performed on biopsies from each time point. Altogether, 241 biopsies were analyzed with the aim of identifying miRNA-based biomarkers of response to therapy. Results from the miRNA analyses were reported for the ER-positive cohort, which were previously demonstrated to benefit from antiangiogenic therapy in this study. For both treatment arms of this cohort, significantly different expression was observed for 217 miRNAs between objective responding and nonresponding patients before treatment initiation. These miRNAs have been linked to regulation of epithelial-mesenchymal transition, metastasis, and tumor growth, among other processes. Bev in combination with chemotherapy resulted in similar miRNA changes to chemotherapy alone. However, the deregulation of miRNA expression occurred earlier in the Bev arm. In both arms, tumor suppressor miRNAs were found upregulated after treatment, while oncogenic miRNAs were downregulated in the Bev arm. Patients responding to Bev showed a strong correlation between deregulated miRNAs and decreased proliferation score during the course of treatment, with downregulation of miR-4465 as the strongest indicator of reduced proliferation. Integrative analyses at miRNA-, gene-, and protein expression further indicated a longitudinal decrease in proliferation. Altogether, the results indicate that proliferation might represent a predictive factor for increased Bev sensitivity, which may aid in the identification of patients who could potentially benefit from Bev.
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Affiliation(s)
- Evita Maria Lindholm
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium HospitalOslo University HospitalNorway
| | - Miriam Ragle Aure
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium HospitalOslo University HospitalNorway
| | - Mads Haugland Haugen
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium HospitalOslo University HospitalNorway
- Department of Tumor biology, Institute for Cancer Research, The Norwegian Radium HospitalOslo University HospitalNorway
| | - Kristine Kleivi Sahlberg
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium HospitalOslo University HospitalNorway
- Department of Research and InnovationVestre Viken Hospital TrustDrammenNorway
| | - Vessela N. Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium HospitalOslo University HospitalNorway
- Department of Clinical Molecular Biology (EpiGen), Division of MedicineAkershus University HospitalLørenskogNorway
| | - Daniel Nebdal
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium HospitalOslo University HospitalNorway
| | - Anne‐Lise Børresen‐Dale
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium HospitalOslo University HospitalNorway
- Insitute for Clinical MedicineUniversity of OsloNorway
| | - Ole Christian Lingjærde
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium HospitalOslo University HospitalNorway
- Department of Computer Science, Faculty of Mathematics and Natural SciencesUniversity of OsloNorway
| | - Olav Engebraaten
- Department of Tumor biology, Institute for Cancer Research, The Norwegian Radium HospitalOslo University HospitalNorway
- Insitute for Clinical MedicineUniversity of OsloNorway
- Department of OncologyOslo University HospitalNorway
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14
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Hovhannisyan G, Harutyunyan T, Aroutiounian R, Liehr T. DNA Copy Number Variations as Markers of Mutagenic Impact. Int J Mol Sci 2019; 20:ijms20194723. [PMID: 31554154 PMCID: PMC6801639 DOI: 10.3390/ijms20194723] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 12/26/2022] Open
Abstract
DNA copy number variation (CNV) occurs due to deletion or duplication of DNA segments resulting in a different number of copies of a specific DNA-stretch on homologous chromosomes. Implications of CNVs in evolution and development of different diseases have been demonstrated although contribution of environmental factors, such as mutagens, in the origin of CNVs, is poorly understood. In this review, we summarize current knowledge about mutagen-induced CNVs in human, animal and plant cells. Differences in CNV frequencies induced by radiation and chemical mutagens, distribution of CNVs in the genome, as well as adaptive effects in plants, are discussed. Currently available information concerning impact of mutagens in induction of CNVs in germ cells is presented. Moreover, the potential of CNVs as a new endpoint in mutagenicity test-systems is discussed.
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Affiliation(s)
- Galina Hovhannisyan
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, 0025 Yerevan, Armenia.
| | - Tigran Harutyunyan
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, 0025 Yerevan, Armenia.
| | - Rouben Aroutiounian
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, 0025 Yerevan, Armenia.
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany.
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15
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Debik J, Euceda LR, Lundgren S, Gythfeldt HVDL, Garred Ø, Borgen E, Engebraaten O, Bathen TF, Giskeødegård GF. Assessing Treatment Response and Prognosis by Serum and Tissue Metabolomics in Breast Cancer Patients. J Proteome Res 2019; 18:3649-3660. [DOI: 10.1021/acs.jproteome.9b00316] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | | | - Steinar Lundgren
- Department of Oncology, St. Olav’s University Hospital, 7006 Trondheim, Norway
| | | | - Øystein Garred
- Department of Tumor Biology, Oslo University Hospital, 0424 Oslo, Norway
| | - Elin Borgen
- Department of Tumor Biology, Oslo University Hospital, 0424 Oslo, Norway
| | - Olav Engebraaten
- Department of Oncology, Oslo University Hospital, 0424 Oslo, Norway
- Department of Tumor Biology, Oslo University Hospital, 0424 Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0318 Oslo, Norway
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