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Ayyappan V, Jenkinson NM, Tressler CM, Tan Z, Cheng M, Shen XE, Guerrero A, Sonkar K, Cai R, Adelaja O, Roy S, Meeker A, Argani P, Glunde K. Context-dependent roles for ubiquitous mitochondrial creatine kinase CKMT1 in breast cancer progression. Cell Rep 2024; 43:114121. [PMID: 38615320 PMCID: PMC11100297 DOI: 10.1016/j.celrep.2024.114121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/14/2024] [Accepted: 03/31/2024] [Indexed: 04/16/2024] Open
Abstract
Metabolic reprogramming is a hallmark of cancer, enabling cancer cells to rapidly proliferate, invade, and metastasize. We show that creatine levels in metastatic breast cancer cell lines and secondary metastatic tumors are driven by the ubiquitous mitochondrial creatine kinase (CKMT1). We discover that, while CKMT1 is highly expressed in primary tumors and promotes cell viability, it is downregulated in metastasis. We further show that CKMT1 downregulation, as seen in breast cancer metastasis, drives up mitochondrial reactive oxygen species (ROS) levels. CKMT1 downregulation contributes to the migratory and invasive potential of cells by ROS-induced upregulation of adhesion and degradative factors, which can be reversed by antioxidant treatment. Our study thus reconciles conflicting evidence about the roles of metabolites in the creatine metabolic pathway in breast cancer progression and reveals that tight, context-dependent regulation of CKMT1 expression facilitates cell viability, cell migration, and cell invasion, which are hallmarks of metastatic spread.
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Affiliation(s)
- Vinay Ayyappan
- Johns Hopkins University In Vivo Cellular and Molecular Imaging Center, Division of Cancer Imaging Research, Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicole M Jenkinson
- Johns Hopkins University In Vivo Cellular and Molecular Imaging Center, Division of Cancer Imaging Research, Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Caitlin M Tressler
- Johns Hopkins University In Vivo Cellular and Molecular Imaging Center, Division of Cancer Imaging Research, Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zheqiong Tan
- Johns Hopkins University In Vivo Cellular and Molecular Imaging Center, Division of Cancer Imaging Research, Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Medical Laboratory, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Menglin Cheng
- Johns Hopkins University In Vivo Cellular and Molecular Imaging Center, Division of Cancer Imaging Research, Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xinyi Elaine Shen
- Johns Hopkins University In Vivo Cellular and Molecular Imaging Center, Division of Cancer Imaging Research, Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alejandro Guerrero
- Johns Hopkins University In Vivo Cellular and Molecular Imaging Center, Division of Cancer Imaging Research, Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kanchan Sonkar
- Johns Hopkins University In Vivo Cellular and Molecular Imaging Center, Division of Cancer Imaging Research, Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ruoqing Cai
- Johns Hopkins University In Vivo Cellular and Molecular Imaging Center, Division of Cancer Imaging Research, Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Oluwatobi Adelaja
- Johns Hopkins University In Vivo Cellular and Molecular Imaging Center, Division of Cancer Imaging Research, Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sujayita Roy
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alan Meeker
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pedram Argani
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kristine Glunde
- Johns Hopkins University In Vivo Cellular and Molecular Imaging Center, Division of Cancer Imaging Research, Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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2
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Romero-Arias JR, González-Castro CA, Ramírez-Santiago G. A multiscale model of the role of microenvironmental factors in cell segregation and heterogeneity in breast cancer development. PLoS Comput Biol 2023; 19:e1011673. [PMID: 37992135 DOI: 10.1371/journal.pcbi.1011673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 12/06/2023] [Accepted: 11/08/2023] [Indexed: 11/24/2023] Open
Abstract
We analyzed a quantitative multiscale model that describes the epigenetic dynamics during the growth and evolution of an avascular tumor. A gene regulatory network (GRN) formed by a set of ten genes that are believed to play an important role in breast cancer development was kinetically coupled to the microenvironmental agents: glucose, estrogens, and oxygen. The dynamics of spontaneous mutations was described by a Yule-Furry master equation whose solution represents the probability that a given cell in the tissue undergoes a certain number of mutations at a given time. We assumed that the mutation rate is modified by a spatial gradient of nutrients. The tumor mass was simulated by means of cellular automata supplemented with a set of reaction diffusion equations that described the transport of microenvironmental agents. By analyzing the epigenetic state space described by the GRN dynamics, we found three attractors that were identified with cellular epigenetic states: normal, precancer and cancer. For two-dimensional (2D) and three-dimensional (3D) tumors we calculated the spatial distribution of the following quantities: (i) number of mutations, (ii) mutation of each gene and, (iii) phenotypes. Using estrogen as the principal microenvironmental agent that regulates cell proliferation process, we obtained tumor shapes for different values of estrogen consumption and supply rates. It was found that he majority of mutations occurred in cells that were located close to the 2D tumor perimeter or close to the 3D tumor surface. Also, it was found that the occurrence of different phenotypes in the tumor are controlled by estrogen concentration levels since they can change the individual cell threshold and gene expression levels. All results were consistently observed for 2D and 3D tumors.
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Affiliation(s)
- J Roberto Romero-Arias
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Ottaiano A, Ianniello M, Santorsola M, Ruggiero R, Sirica R, Sabbatino F, Perri F, Cascella M, Di Marzo M, Berretta M, Caraglia M, Nasti G, Savarese G. From Chaos to Opportunity: Decoding Cancer Heterogeneity for Enhanced Treatment Strategies. BIOLOGY 2023; 12:1183. [PMID: 37759584 PMCID: PMC10525472 DOI: 10.3390/biology12091183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
Cancer manifests as a multifaceted disease, characterized by aberrant cellular proliferation, survival, migration, and invasion. Tumors exhibit variances across diverse dimensions, encompassing genetic, epigenetic, and transcriptional realms. This heterogeneity poses significant challenges in prognosis and treatment, affording tumors advantages through an increased propensity to accumulate mutations linked to immune system evasion and drug resistance. In this review, we offer insights into tumor heterogeneity as a crucial characteristic of cancer, exploring the difficulties associated with measuring and quantifying such heterogeneity from clinical and biological perspectives. By emphasizing the critical nature of understanding tumor heterogeneity, this work contributes to raising awareness about the importance of developing effective cancer therapies that target this distinct and elusive trait of cancer.
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Affiliation(s)
- Alessandro Ottaiano
- Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (M.S.); (F.P.); (M.C.); (M.D.M.); (G.N.)
| | - Monica Ianniello
- AMES, Centro Polidiagnostico Strumentale srl, Via Padre Carmine Fico 24, 80013 Casalnuovo Di Napoli, Italy; (M.I.); (R.R.); (R.S.); (G.S.)
| | - Mariachiara Santorsola
- Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (M.S.); (F.P.); (M.C.); (M.D.M.); (G.N.)
| | - Raffaella Ruggiero
- AMES, Centro Polidiagnostico Strumentale srl, Via Padre Carmine Fico 24, 80013 Casalnuovo Di Napoli, Italy; (M.I.); (R.R.); (R.S.); (G.S.)
| | - Roberto Sirica
- AMES, Centro Polidiagnostico Strumentale srl, Via Padre Carmine Fico 24, 80013 Casalnuovo Di Napoli, Italy; (M.I.); (R.R.); (R.S.); (G.S.)
| | - Francesco Sabbatino
- Oncology Unit, Department of Medicine, Surgery and Dentistry, University of Salerno, 84081 Baronissi, Italy;
| | - Francesco Perri
- Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (M.S.); (F.P.); (M.C.); (M.D.M.); (G.N.)
| | - Marco Cascella
- Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (M.S.); (F.P.); (M.C.); (M.D.M.); (G.N.)
| | - Massimiliano Di Marzo
- Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (M.S.); (F.P.); (M.C.); (M.D.M.); (G.N.)
| | - Massimiliano Berretta
- Department of Clinical and Experimental Medicine, University of Messina, 98122 Messina, Italy;
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania “L. Vanvitelli”, Via Luigi De Crecchio 7, 80138 Naples, Italy;
| | - Guglielmo Nasti
- Istituto Nazionale Tumori di Napoli, IRCCS “G. Pascale”, Via M. Semmola, 80131 Naples, Italy; (M.S.); (F.P.); (M.C.); (M.D.M.); (G.N.)
| | - Giovanni Savarese
- AMES, Centro Polidiagnostico Strumentale srl, Via Padre Carmine Fico 24, 80013 Casalnuovo Di Napoli, Italy; (M.I.); (R.R.); (R.S.); (G.S.)
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4
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Stevens LE, Peluffo G, Qiu X, Temko D, Fassl A, Li Z, Trinh A, Seehawer M, Jovanović B, Alečković M, Wilde CM, Geck RC, Shu S, Kingston NL, Harper NW, Almendro V, Pyke AL, Egri SB, Papanastasiou M, Clement K, Zhou N, Walker S, Salas J, Park SY, Frank DA, Meissner A, Jaffe JD, Sicinski P, Toker A, Michor F, Long HW, Overmoyer BA, Polyak K. JAK-STAT Signaling in Inflammatory Breast Cancer Enables Chemotherapy-Resistant Cell States. Cancer Res 2023; 83:264-284. [PMID: 36409824 PMCID: PMC9845989 DOI: 10.1158/0008-5472.can-22-0423] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 09/23/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022]
Abstract
Inflammatory breast cancer (IBC) is a difficult-to-treat disease with poor clinical outcomes due to high risk of metastasis and resistance to treatment. In breast cancer, CD44+CD24- cells possess stem cell-like features and contribute to disease progression, and we previously described a CD44+CD24-pSTAT3+ breast cancer cell subpopulation that is dependent on JAK2/STAT3 signaling. Here we report that CD44+CD24- cells are the most frequent cell type in IBC and are commonly pSTAT3+. Combination of JAK2/STAT3 inhibition with paclitaxel decreased IBC xenograft growth more than either agent alone. IBC cell lines resistant to paclitaxel and doxorubicin were developed and characterized to mimic therapeutic resistance in patients. Multi-omic profiling of parental and resistant cells revealed enrichment of genes associated with lineage identity and inflammation in chemotherapy-resistant derivatives. Integrated pSTAT3 chromatin immunoprecipitation sequencing and RNA sequencing (RNA-seq) analyses showed pSTAT3 regulates genes related to inflammation and epithelial-to-mesenchymal transition (EMT) in resistant cells, as well as PDE4A, a cAMP-specific phosphodiesterase. Metabolomic characterization identified elevated cAMP signaling and CREB as a candidate therapeutic target in IBC. Investigation of cellular dynamics and heterogeneity at the single cell level during chemotherapy and acquired resistance by CyTOF and single cell RNA-seq identified mechanisms of resistance including a shift from luminal to basal/mesenchymal cell states through selection for rare preexisting subpopulations or an acquired change. Finally, combination treatment with paclitaxel and JAK2/STAT3 inhibition prevented the emergence of the mesenchymal chemo-resistant subpopulation. These results provide mechanistic rational for combination of chemotherapy with inhibition of JAK2/STAT3 signaling as a more effective therapeutic strategy in IBC. SIGNIFICANCE Chemotherapy resistance in inflammatory breast cancer is driven by the JAK2/STAT3 pathway, in part via cAMP/PKA signaling and a cell state switch, which can be overcome using paclitaxel combined with JAK2 inhibitors.
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Affiliation(s)
- Laura E Stevens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Guillermo Peluffo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Daniel Temko
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
| | - Zheqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Anne Trinh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Marco Seehawer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Bojana Jovanović
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Maša Alečković
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Callahan M Wilde
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Renee C Geck
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Shaokun Shu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Natalie L Kingston
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nicholas W Harper
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Vanessa Almendro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Alanna L Pyke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shawn B Egri
- The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | | | - Kendell Clement
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts.,The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Ningxuan Zhou
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sarah Walker
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jacqueline Salas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - So Yeon Park
- Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - David A Frank
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts.,The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Jacob D Jaffe
- The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
| | - Alex Toker
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts.,The Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts.,The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts.,The Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts.,Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Beth A Overmoyer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts.,The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts.,The Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts.,Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, Massachusetts
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Sun R, He J, Xiang Q, Feng Y, Gong Y, Ning Y, Deng C, Sun K, Zhang M, Cheng Z, Le X, Xiong Q, Dai F, Wu Y, Xiang T. NTF4 plays a dual role in breast cancer in mammary tumorigenesis and metastatic progression. Int J Biol Sci 2023; 19:641-657. [PMID: 36632451 PMCID: PMC9830504 DOI: 10.7150/ijbs.79435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/15/2022] [Indexed: 01/04/2023] Open
Abstract
Breast cancer metastasis can happen even when the primary tumor is relatively small. But the mechanism for such early metastasis is poorly understood. Herein, we report that neurotrophin 4 (NTF4) plays a dual role in breast cancer proliferation and metastasis. Clinical data showed high levels of NTF4, especially in the early stage, to be associated with poor clinical outcomes, supporting the notion that metastasis, rather than primary cancer, was the major determinant of breast cancer mortality for patients. NTF4 promoted epithelial-mesenchymal transition (EMT), cell motility, and invasiveness of breast cancer cells in vitro and in vivo. Interestingly, NTF4 inhibited cell proliferation while promoting cellular apoptosis in vitro and inhibited xenograft tumorigenicity in vivo. Mechanistically, NTF4 elicited its pro-metastatic effects by activating PRKDC/AKT and ANXA1/NF-κB pathways to stabilize SNAIL protein, therefore decreasing the level of E-cadherin. Conversely, NTF4 increased ANXA1 phosphorylation and sumoylation and the interaction with importin β, leading to nuclear import and retention of ANXA1, which in turn activates the caspase-3 apoptosis cascade. Our findings identified an unexpected dual role for NTF4 in breast cancer which contributes to early metastasis of the disease. Therefore, NTF4 may serve as a prognostic marker and a potential therapeutic target for breast cancer.
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Affiliation(s)
- Ran Sun
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.,Department of Oncology, Jiulongpo People's Hospital, Chongqing 400050, China
| | - Jin He
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Qin Xiang
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yixiao Feng
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yijia Gong
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yijiao Ning
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Chaoqun Deng
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Kexin Sun
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Mingjun Zhang
- Department of Laboratory Medicine, Jiulongpo People's Hospital, Chongqing 400050, China
| | - Zhaobo Cheng
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Xin Le
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Qi Xiong
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Fengsheng Dai
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yongzhong Wu
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China.,✉ Corresponding authors: Tingxiu Xiang. Tel: (023) 65079282. E-mail: and Yongzhong Wu. E-mail:
| | - Tingxiu Xiang
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.,Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China.,✉ Corresponding authors: Tingxiu Xiang. Tel: (023) 65079282. E-mail: and Yongzhong Wu. E-mail:
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Li Y, Jiang X, Zhong M, Yu B, Yuan H. Whole Genome Sequencing of Single-Circulating Tumor Cell Ameliorates Unraveling Breast Cancer Heterogeneity. BREAST CANCER (DOVE MEDICAL PRESS) 2022; 14:505-513. [PMID: 36597488 PMCID: PMC9805725 DOI: 10.2147/bctt.s388653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 12/07/2022] [Indexed: 12/29/2022]
Abstract
Objective Because tumor tissues are most frequently heterogeneous and hard to characterize, the resulting therapeutic strategy could be misled. The most active and invasive tumor cells are circulating tumor cells (CTCs). In this study, we investigated the feasibility of individualized treatment of breast cancer patients based on whole genome sequencing (WGS) of single cell CTC. Methods Twenty-four CTCs were identified in three breast cancer patients. For each patient, one polyploid CTC was captured, and on which the WGS was performed. WGS was considered due to its sequencing robustness compared to conventional sequencing approaches. Based on the histopathological Her-2 status in tumor tissue and the HER2 gene status in WGS results of CTC, we adjusted treatment strategies and monitored disease progression. Results Patients ID1 and ID2 are found to be Her-2 positive in primary tumors and HER2 gene amplification in the DNA of CTCs. In-patient ID3, histopathological examination of the primary tumor and liver metastases revealed Her-2 negative, but the WGS analysis of CTC showed HER2 gene amplification. After adjusting treatment by adding Her-2 inhibitors according to the results of CTC sequencing, liver metastases and pleural effusion were significantly reduced two months later, CTC number and ctDNA burden were decreased, and 18-months progression-free survival (PFS) was recorded. In addition, some potential therapeutic targets and mutations in drug-resistant genes were detected. Conclusion The results of CTC sequencing effectively guided the treatment of a patient with HER2 gene amplification in CTC but with Her-2 negative on tumor tissue. Therefore, CTC sequencing could help resolve the heterogeneity of tumors and provide precision medicine for patients.
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Affiliation(s)
- Yongping Li
- Department of Breast Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, People’s Republic of China
| | - Xiaofei Jiang
- Department of Breast Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, People’s Republic of China
| | - Ming Zhong
- Department of Breast Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, People’s Republic of China
| | - Bo Yu
- Department of Vascular Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, People’s Republic of China,Bo Yu, Department of Vascular Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong New Area, Shanghai, 201399, People’s Republic of China, Tel +86 18918922698, Email
| | - Hao Yuan
- Department of Breast Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, People’s Republic of China,Correspondence: Hao Yuan, Department of Breast Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 2800 Gongwei Road, Pudong New Area, Shanghai, 201399, People’s Republic of China, Tel +86 18918790382, Email
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7
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Wang R, Wang X, Yin L, Yin L, Chu GCY, Hu P, Ou Y, Zhang Y, Lewis MS, Pandol SJ. Breast Cancer MCF-7 Cells Acquire Heterogeneity during Successive Co-Culture with Hematopoietic and Bone Marrow-Derived Mesenchymal Stem/Stromal Cells. Cells 2022; 11:3553. [PMID: 36428982 PMCID: PMC9688235 DOI: 10.3390/cells11223553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
During disease progression and bone metastasis, breast tumor cells interact with various types of bystander cells residing in the tumor microenvironment. Such interactions prompt tumor cell heterogeneity. We used successive co-culture as an experimental model to examine cancer-bystander cell interaction. RMCF7-2, a clone of the human breast cancer MCF-7 cells tagged with a red fluorescent protein, was tracked for morphologic, behavioral, and gene expression changes. Co-cultured with various types of hematopoietic cells, RMCF7-2 adopted stable changes to a rounded shape in suspension growth of red fluorescent cells, from which derivative clones displayed marked expressional changes of marker proteins, including reduced E-cadherin and estrogen receptor α, and loss of progesterone receptor. In a successive co-culture with bone marrow-derived mesenchymal stem/stromal cells, the red fluorescent clones in suspension growth changed once more, adopting an attachment growth, but in diversified shapes. Red fluorescent clones recovered from the second-round co-culture were heterogeneous in morphology, but retained the altered marker protein expression while displaying increased proliferation, migration, and xenograft tumor formation. Interaction with bystander cells caused permanent morphologic, growth behavioral, and gene expressional changes under successive co-culture, which is a powerful model for studying cancer cell heterogeneity during breast cancer progression and metastasis.
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Affiliation(s)
- Ruoxiang Wang
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Xudong Wang
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Liyuan Yin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Lijuan Yin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Gina Chia-Yi Chu
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Peizhen Hu
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yan Ou
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yi Zhang
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Michael S. Lewis
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Pathology, VA Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
| | - Stephen J. Pandol
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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8
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Khatib SA, Ma L, Dang H, Forgues M, Chung JY, Ylaya K, Hewitt SM, Chaisaingmongkol J, Rucchirawat M, Wang XW. Single-cell biology uncovers apoptotic cell death and its spatial organization as a potential modifier of tumor diversity in HCC. Hepatology 2022; 76:599-611. [PMID: 35034369 DOI: 10.1002/hep.32345] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS HCC is a highly aggressive and heterogeneous cancer type with limited treatment options. Identifying drivers of tumor heterogeneity may lead to better therapeutic options and favorable patient outcomes. We investigated whether apoptotic cell death and its spatial architecture is linked to tumor molecular heterogeneity using single-cell in situ hybridization analysis. APPROACH AND RESULTS We analyzed 254 tumor samples from two HCC cohorts using tissue microarrays. We developed a mathematical model to quantify cellular diversity among HCC samples using two tumor markers, cyclin-dependent kinase inhibitor 3 and protein regulator of cytokinesis 1 as surrogates for heterogeneity and caspase 3 (CASP3) as an apoptotic cell death marker. We further explored the impact of potential dying-cell hubs on tumor cell diversity and patient outcome by density contour mapping and spatial proximity analysis. We also developed a selectively controlled in vitro model of cell death using CRISPR/CRISPR-associated 9 to determine therapy response and growth under hypoxic conditions. We found that increasing levels of CASP3+ tumor cells are associated with higher tumor diversity. Interestingly, we discovered regions of densely populated CASP3+ , which we refer to as CASP3+ cell islands, in which the nearby cellular heterogeneity was found to be the greatest compared to cells farther away from these islands and that this phenomenon was associated with survival. Additionally, cell culture experiments revealed that higher levels of cell death, accompanied by increased CASP3 expression, led to greater therapy resistance and growth under hypoxia. CONCLUSIONS These results are consistent with the hypothesis that increased apoptotic cell death may lead to greater tumor heterogeneity and thus worse patient outcomes.
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Affiliation(s)
- Subreen A Khatib
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.,Department of Tumor Biology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Lichun Ma
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Hien Dang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.,Division of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Joon-Yong Chung
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Kris Ylaya
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Jittporn Chaisaingmongkol
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, Thailand.,Center of Excellence on Environmental Health and Toxicology, Office of the Higher Education Commission, Ministry of Education, Bangkok, Thailand
| | - Mathuros Rucchirawat
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, Thailand.,Center of Excellence on Environmental Health and Toxicology, Office of the Higher Education Commission, Ministry of Education, Bangkok, Thailand
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.,Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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9
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Wolf Y, Samuels Y. Intratumor Heterogeneity and Antitumor Immunity Shape One Another Bidirectionally. Clin Cancer Res 2022; 28:2994-3001. [PMID: 35380639 PMCID: PMC9306293 DOI: 10.1158/1078-0432.ccr-21-1355] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/10/2022] [Accepted: 03/28/2022] [Indexed: 01/07/2023]
Abstract
Over the last decade, it has become clear that the genomic landscapes of tumors profoundly impact their immunogenicity and how tumor cells interact with immune cells. Whereas past discoveries mainly focused on the interplay between tumor immunogenicity and tumor mutational burden (TMB), under the assumption that a higher mutation load would give rise to a better patient response to immune checkpoint blockade therapies, we and others have underlined intratumor heterogeneity (ITH) as an important determinant of the magnitude of the antitumor response and the nature of the tumor microenvironment. In this review, we define TMB versus ITH and how the two factors are being inferred from data, examine key findings in the cancer immunogenomics literature deciphering the complex cross-talk between TMB, ITH, and antitumor immunity in human cancers and in vivo models, and discuss the mutual influence of ITH and immunity-how the antitumor response can give rise to tumors with higher ITH, and how higher ITH can put shackles on the antitumor response.
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Affiliation(s)
- Yochai Wolf
- Ella Lemelbaum Institute for Immuno-Oncology and Skin Cancer, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Corresponding Authors: Yochai Wolf, Ella Lemelbaum Institute for Immuno-Oncology and Skin Cancer, Sheba Medical Center, Tel Hashomer, Ramat Gan 5265601, Israel. E-mail: ; and Yardena Samuels, Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 761000, Israel. E-mail:
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Corresponding Authors: Yochai Wolf, Ella Lemelbaum Institute for Immuno-Oncology and Skin Cancer, Sheba Medical Center, Tel Hashomer, Ramat Gan 5265601, Israel. E-mail: ; and Yardena Samuels, Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 761000, Israel. E-mail:
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10
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Pohl L, Friedhoff J, Jurcic C, Teroerde M, Schindler I, Strepi K, Schneider F, Kaczorowski A, Hohenfellner M, Duensing A, Duensing S. Kidney Cancer Models for Pre-Clinical Drug Discovery: Challenges and Opportunities. Front Oncol 2022; 12:889686. [PMID: 35619925 PMCID: PMC9128013 DOI: 10.3389/fonc.2022.889686] [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: 03/04/2022] [Accepted: 04/13/2022] [Indexed: 11/25/2022] Open
Abstract
Renal cell carcinoma (RCC) is among the most lethal urological malignancies once metastatic. The introduction of immune checkpoint inhibitors has revolutionized the therapeutic landscape of metastatic RCC, nevertheless, a significant proportion of patients will experience disease progression. Novel treatment options are therefore still needed and in vitro and in vivo model systems are crucial to ultimately improve disease control. At the same time, RCC is characterized by a number of molecular and functional peculiarities that have the potential to limit the utility of pre-clinical model systems. This includes not only the well-known genomic intratumoral heterogeneity (ITH) of RCC but also a remarkable functional ITH that can be shaped by influences of the tumor microenvironment. Importantly, RCC is among the tumor entities, in which a high number of intratumoral cytotoxic T cells is associated with a poor prognosis. In fact, many of these T cells are exhausted, which represents a major challenge for modeling tumor-immune cell interactions. Lastly, pre-clinical drug development commonly relies on using phenotypic screening of 2D or 3D RCC cell culture models, however, the problem of “reverse engineering” can prevent the identification of the precise mode of action of drug candidates thus impeding their translation to the clinic. In conclusion, a holistic approach to model the complex “ecosystem RCC” will likely require not only a combination of model systems but also an integration of concepts and methods using artificial intelligence to further improve pre-clinical drug discovery.
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Affiliation(s)
- Laura Pohl
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, Heidelberg, Germany
| | - Jana Friedhoff
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christina Jurcic
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, Heidelberg, Germany
| | - Miriam Teroerde
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, Heidelberg, Germany
| | - Isabella Schindler
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, Heidelberg, Germany
| | - Konstantina Strepi
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Schneider
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, Heidelberg, Germany
| | - Adam Kaczorowski
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, Heidelberg, Germany
| | - Markus Hohenfellner
- Department of Urology, University Hospital Heidelberg and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Anette Duensing
- Department of Urology, University Hospital Heidelberg and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany.,Precision Oncology of Urological Malignancies, Department of Urology University Hospital Heidelberg, Heidelberg, Germany.,Cancer Therapeutics Program, UPMC Hillman Cancer Center, Pittsburgh, PA, United States.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Stefan Duensing
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, Heidelberg, Germany.,Department of Urology, University Hospital Heidelberg and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
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11
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Evans JA, Carlotti E, Lin ML, Hackett RJ, Haughey MJ, Passman AM, Dunn L, Elia G, Porter RJ, McLean MH, Hughes F, ChinAleong J, Woodland P, Preston SL, Griffin SM, Lovat L, Rodriguez-Justo M, Huang W, Wright NA, Jansen M, McDonald SAC. Clonal Transitions and Phenotypic Evolution in Barrett's Esophagus. Gastroenterology 2022; 162:1197-1209.e13. [PMID: 34973296 PMCID: PMC8972067 DOI: 10.1053/j.gastro.2021.12.271] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 01/10/2023]
Abstract
BACKGROUND & AIMS Barrett's esophagus (BE) is a risk factor for esophageal adenocarcinoma but our understanding of how it evolves is poorly understood. We investigated BE gland phenotype distribution, the clonal nature of phenotypic change, and how phenotypic diversity plays a role in progression. METHODS Using immunohistochemistry and histology, we analyzed the distribution and the diversity of gland phenotype between and within biopsy specimens from patients with nondysplastic BE and those who had progressed to dysplasia or had developed postesophagectomy BE. Clonal relationships were determined by the presence of shared mutations between distinct gland types using laser capture microdissection sequencing of the mitochondrial genome. RESULTS We identified 5 different gland phenotypes in a cohort of 51 nondysplastic patients where biopsy specimens were taken at the same anatomic site (1.0-2.0 cm superior to the gastroesophageal junction. Here, we observed the same number of glands with 1 and 2 phenotypes, but 3 phenotypes were rare. We showed a common ancestor between parietal cell-containing, mature gastric (oxyntocardiac) and goblet cell-containing, intestinal (specialized) gland phenotypes. Similarly, we have shown a clonal relationship between cardiac-type glands and specialized and mature intestinal glands. Using the Shannon diversity index as a marker of gland diversity, we observed significantly increased phenotypic diversity in patients with BE adjacent to dysplasia and predysplasia compared to nondysplastic BE and postesophagectomy BE, suggesting that diversity develops over time. CONCLUSIONS We showed that the range of BE phenotypes represents an evolutionary process and that changes in gland diversity may play a role in progression. Furthermore, we showed a common ancestry between gastric and intestinal-type glands in BE.
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Affiliation(s)
- James A Evans
- Clonal Dynamics in Epithelia Laboratory, Queen Mary University of London, London, United Kingdom
| | - Emanuela Carlotti
- Clonal Dynamics in Epithelia Laboratory, Queen Mary University of London, London, United Kingdom
| | - Meng-Lay Lin
- Clonal Dynamics in Epithelia Laboratory, Queen Mary University of London, London, United Kingdom
| | - Richard J Hackett
- Clonal Dynamics in Epithelia Laboratory, Queen Mary University of London, London, United Kingdom
| | - Magnus J Haughey
- School of Mathematical Sciences, Queen Mary University of London, London, United Kingdom
| | - Adam M Passman
- Clonal Dynamics in Epithelia Laboratory, Queen Mary University of London, London, United Kingdom
| | - Lorna Dunn
- Northern Institute for Cancer Research, Newcastle University, Newcastle, United Kingdom
| | - George Elia
- Clonal Dynamics in Epithelia Laboratory, Queen Mary University of London, London, United Kingdom
| | - Ross J Porter
- Department of Gastroenterology, University of Aberdeen, Aberdeen, United Kingdom
| | - Mairi H McLean
- Department of Gastroenterology, University of Aberdeen, Aberdeen, United Kingdom
| | - Frances Hughes
- Department of Surgery, Barts Health NHS Trust, Royal London Hospital, London, United Kingdom
| | - Joanne ChinAleong
- Department of Histopathology, Barts Health NHS Trust, Royal London Hospital, London, United Kingdom
| | - Philip Woodland
- Endoscopy Unit, Barts Health NHS Trust, Royal London Hospital, London, United Kingdom
| | - Sean L Preston
- Endoscopy Unit, Barts Health NHS Trust, Royal London Hospital, London, United Kingdom
| | - S Michael Griffin
- School of Mathematical Sciences, Queen Mary University of London, London, United Kingdom; Royal College of Surgeons of Edinburgh, Edinburgh, United Kingdom
| | - Laurence Lovat
- Oeosophagogastric Disorders Centre, Department of Gastroenterology, University College London Hospitals, London, United Kingdom; Research Department of Tissue and Energy, University College London Division of Surgical and Interventional Science, University College London, London, United Kingdom
| | - Manuel Rodriguez-Justo
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | - Weini Huang
- School of Mathematical Sciences, Queen Mary University of London, London, United Kingdom
| | - Nicholas A Wright
- Epithelial Stem Cell Laboratory, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Marnix Jansen
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom; UCL Cancer Institute, University College London, London, United Kingdom
| | - Stuart A C McDonald
- Clonal Dynamics in Epithelia Laboratory, Queen Mary University of London, London, United Kingdom.
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12
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Foo MA, You M, Chan SL, Sethi G, Bonney GK, Yong WP, Chow EKH, Fong ELS, Wang L, Goh BC. Clinical translation of patient-derived tumour organoids- bottlenecks and strategies. Biomark Res 2022; 10:10. [PMID: 35272694 PMCID: PMC8908618 DOI: 10.1186/s40364-022-00356-6] [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: 12/19/2021] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
Multiple three-dimensional (3D) tumour organoid models assisted by multi-omics and Artificial Intelligence (AI) have contributed greatly to preclinical drug development and precision medicine. The intrinsic ability to maintain genetic and phenotypic heterogeneity of tumours allows for the reconciliation of shortcomings in traditional cancer models. While their utility in preclinical studies have been well established, little progress has been made in translational research and clinical trials. In this review, we identify the major bottlenecks preventing patient-derived tumour organoids (PDTOs) from being used in clinical setting. Unsuitable methods of tissue acquisition, disparities in establishment rates and a lengthy timeline are the limiting factors for use of PDTOs in clinical application. Potential strategies to overcome this include liquid biopsies via circulating tumour cells (CTCs), an automated organoid platform and optical metabolic imaging (OMI). These proposed solutions accelerate and optimize the workflow of a clinical organoid drug screening. As such, PDTOs have the potential for potential applications in clinical oncology to improve patient outcomes. If remarkable progress is made, cancer patients can finally benefit from this revolutionary technology.
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Affiliation(s)
- Malia Alexandra Foo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Mingliang You
- Hangzhou Cancer Institute, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Hangzhou, 31002, China.,Affiliated Hangzhou Cancer Hospital, Zhejiang University School of Medicine, Hangzhou, 31002, China
| | - Shing Leng Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Surgery, National University Hospital, Singapore, Singapore
| | - Gautam Sethi
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Glenn K Bonney
- Department of Surgery, National University Hospital, Singapore, Singapore.,NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wei-Peng Yong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Haematology-Oncology, National University Hospital, National University Health System, Singapore, Singapore
| | - Edward Kai-Hua Chow
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Eliza Li Shan Fong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Lingzhi Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore. .,NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Boon-Cher Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore. .,NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Department of Haematology-Oncology, National University Hospital, National University Health System, Singapore, Singapore.
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13
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Mehraj U, Mushtaq U, Mir MA, Saleem A, Macha MA, Lone MN, Hamid A, Zargar MA, Ahmad SM, Wani NA. Chemokines in Triple-Negative Breast Cancer Heterogeneity: New Challenges for Clinical Implications. Semin Cancer Biol 2022; 86:769-783. [PMID: 35278636 DOI: 10.1016/j.semcancer.2022.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/01/2022] [Accepted: 03/07/2022] [Indexed: 12/12/2022]
Abstract
Tumor heterogeneity is a hallmark of cancer and one of the primary causes of resistance to therapies. Triple-negative breast cancer (TNBC), which accounts for 15% to 20% of all breast cancers and is the most aggressive subtype, is very diverse, connected to metastatic potential and response to therapy. It is a very diverse disease at the molecular, pathologic, and clinical levels. TNBC is substantially more likely to recur and has a worse overall survival rate following diagnosis than other breast cancer subtypes. Chemokines, low molecular weight proteins that stimulate chemotaxis, have been shown to control the cues responsible for TNBC heterogeneity. In this review, we have focused on tumor heterogeneity and the role of chemokines in modulating tumor heterogeneity, since this is the most critical issue in treating TNBC. Additionally, we examined numerous cues mediated by chemokine networks that contribute to the heterogeneity of TNBC. Recent developments in our knowledge of the chemokine networks that regulate TNBC heterogeneity may pave the door for developing difficult-to-treat TNBC treatment options.
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Affiliation(s)
- Umar Mehraj
- Department of Bioresources, School of Life Sciences, University of Kashmir, Srinagar, Jammu & Kashmir India
| | - Umer Mushtaq
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Ganderbal, J&K, India
| | - Manzoor A Mir
- Department of Bioresources, School of Life Sciences, University of Kashmir, Srinagar, Jammu & Kashmir India
| | - Afnan Saleem
- Division of Animal Biotechnology Faculty of Veterinary Sciences and Animal Husbandry, Shuhama Sher-e- Kashmir University of Agricultural Sciences and Technology-Kashmir, India
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science & Technology Awantipora, Jammu & Kashmir, India
| | - Mohammad Nadeem Lone
- Department of Chemistry, School of Physical & Chemical Sciences, Central University of Kashmir, Ganderbal J & K, India
| | - Abid Hamid
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Ganderbal, J&K, India
| | - Mohammed A Zargar
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Ganderbal, J&K, India
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology Faculty of Veterinary Sciences and Animal Husbandry, Shuhama Sher-e- Kashmir University of Agricultural Sciences and Technology-Kashmir, India
| | - Nissar Ahmad Wani
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Ganderbal, J&K, India.
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14
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Kusi M, Zand M, Lin LL, Chen M, Lopez A, Lin CL, Wang CM, Lucio ND, Kirma NB, Ruan J, Huang THM, Mitsuya K. 2-Hydroxyglutarate destabilizes chromatin regulatory landscape and lineage fidelity to promote cellular heterogeneity. Cell Rep 2022; 38:110220. [PMID: 35021081 PMCID: PMC8811753 DOI: 10.1016/j.celrep.2021.110220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/23/2021] [Accepted: 12/15/2021] [Indexed: 02/07/2023] Open
Abstract
The epigenome delineates lineage-specific transcriptional programs and restricts cell plasticity to prevent non-physiological cell fate transitions. Although cell diversification fosters tumor evolution and therapy resistance, upstream mechanisms that regulate the stability and plasticity of the cancer epigenome remain elusive. Here we show that 2-hydroxyglutarate (2HG) not only suppresses DNA repair but also mediates the high-plasticity chromatin landscape. A combination of single-cell epigenomics and multi-omics approaches demonstrates that 2HG disarranges otherwise well-preserved stable nucleosome positioning and promotes cell-to-cell variability. 2HG induces loss of motif accessibility to the luminal-defining transcriptional factors FOXA1, FOXP1, and GATA3 and a shift from luminal to basal-like gene expression. Breast tumors with high 2HG exhibit enhanced heterogeneity with undifferentiated epigenomic signatures linked to adverse prognosis. Further, ascorbate-2-phosphate (A2P) eradicates heterogeneity and impairs growth of high 2HG-producing breast cancer cells. These findings suggest 2HG as a key determinant of cancer plasticity and provide a rational strategy to counteract tumor cell evolution. Kusi et al. show that the oncometabolite 2-hydroxyglutarate (2HG) initiates cell-level epigenome fluctuations in the chromatin regulatory landscape, accompanied by loss of lineage fidelity. Breast tumors with high 2HG accumulation exhibit enhanced cellular heterogeneity with undifferentiated stem-like epigenomic signatures. The findings suggest metabolic derangement as a molecular origin of breast cancer heterogeneity.
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Affiliation(s)
- Meena Kusi
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Maryam Zand
- Department of Computer Science, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Li-Ling Lin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Meizhen Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Anthony Lopez
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Chun-Lin Lin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Chiou-Miin Wang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Nicholas D Lucio
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Nameer B Kirma
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Jianhua Ruan
- Department of Computer Science, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Tim H-M Huang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
| | - Kohzoh Mitsuya
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
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15
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Kashyap A, Rapsomaniki MA, Barros V, Fomitcheva-Khartchenko A, Martinelli AL, Rodriguez AF, Gabrani M, Rosen-Zvi M, Kaigala G. Quantification of tumor heterogeneity: from data acquisition to metric generation. Trends Biotechnol 2021; 40:647-676. [PMID: 34972597 DOI: 10.1016/j.tibtech.2021.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 01/18/2023]
Abstract
Tumors are unique and complex ecosystems, in which heterogeneous cell subpopulations with variable molecular profiles, aggressiveness, and proliferation potential coexist and interact. Understanding how heterogeneity influences tumor progression has important clinical implications for improving diagnosis, prognosis, and treatment response prediction. Several recent innovations in data acquisition methods and computational metrics have enabled the quantification of spatiotemporal heterogeneity across different scales of tumor organization. Here, we summarize the most promising efforts from a common experimental and computational perspective, discussing their advantages, shortcomings, and challenges. With personalized medicine entering a new era of unprecedented opportunities, our vision is that of future workflows integrating across modalities, scales, and dimensions to capture intricate aspects of the tumor ecosystem and to open new avenues for improved patient care.
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Affiliation(s)
- Aditya Kashyap
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland
| | | | - Vesna Barros
- Department of Healthcare Informatics, IBM Research, IBM R&D Labs, University of Haifa Campus, Mount Carmel, Haifa, 3498825, Israel; The Hebrew University, The Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Anna Fomitcheva-Khartchenko
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland; Eidgenössische Technische Hochschule (ETH-Zurich), Vladimir-Prelog-Weg 1-5/10, 8099 Zurich, Switzerland
| | | | | | - Maria Gabrani
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland
| | - Michal Rosen-Zvi
- Department of Healthcare Informatics, IBM Research, IBM R&D Labs, University of Haifa Campus, Mount Carmel, Haifa, 3498825, Israel; The Hebrew University, The Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Govind Kaigala
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland.
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16
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Lacaze JL, Aziza R, Chira C, De Maio E, Izar F, Jouve E, Massabeau C, Pradines A, Selmes G, Ung M, Zerdoud S, Dalenc F. Diagnosis, biology and epidemiology of oligometastatic breast cancer. Breast 2021; 59:144-156. [PMID: 34252822 PMCID: PMC8441842 DOI: 10.1016/j.breast.2021.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 05/31/2021] [Accepted: 06/23/2021] [Indexed: 11/01/2022] Open
Abstract
Does oligometastatic breast cancer (OMBC) deserve a dedicated treatment? Although some authors recommend multidisciplinary management of OMBC with a curative intent, there is no evidence proving this strategy beneficial in the absence of a randomized trial. The existing literature sheds little light on OMBC. Incidence is unknown; data available are either obsolete or biased; there is no consensus on the definition of OMBC and metastatic sites, nor on necessary imaging techniques. However, certain proposals merit consideration. Knowledge of eventual specific OMBC biological characteristics is limited to circulating tumor cell (CTC) counts. Given the data available for other cancers, studies on microRNAs (miRNAs), circulating tumor DNA (ctDNA) and genomic alterations should be developed Finally, safe and effective therapies do exist, but results of randomized trials will not be available for many years. Prospective observational cohort studies need to be implemented.
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Affiliation(s)
- Jean-Louis Lacaze
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département d'Oncologie Médicale, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France.
| | - Richard Aziza
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département d'Imagerie Médicale, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Ciprian Chira
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département de Radiothérapie, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Eleonora De Maio
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département d'Oncologie Médicale, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Françoise Izar
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département de Radiothérapie, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Eva Jouve
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département de Chirurgie, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Carole Massabeau
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département de Radiothérapie, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Anne Pradines
- Institut Claudius Regaud (ICR), Département Biologie Médicale Oncologique, Centre de Recherche en Cancérologie de Toulouse, (CRCT), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), INSERM UMR-1037, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Gabrielle Selmes
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département de Chirurgie, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Mony Ung
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département d'Oncologie Médicale, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Slimane Zerdoud
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département de Médecine Nucléaire, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
| | - Florence Dalenc
- Institut Claudius Regaud (ICR), Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Département d'Oncologie Médicale, Université de Toulouse, UPS, 1 av. Irène Joliot Curie, 31059, Toulouse Cedex 9, France
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17
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Penzhorn IH, Schubert PT. Metastatic olfactory neuroblastoma: A small round blue cell puzzle on fine-needle aspiration cytology. Diagn Cytopathol 2021; 50:E13-E17. [PMID: 34491630 DOI: 10.1002/dc.24868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 11/09/2022]
Abstract
Small round blue cell tumors (SRBCTs) are a heterogeneous group of malignant neoplasms that can be challenging to distinguish on fine-needle aspiration (FNA) cytology. Ancillary tests as well as clinico-radiological correlation are often required to make an accurate diagnosis. FNA is a low-cost, low-infrastructure test, making it a coveted diagnostic tool, especially in low-resource settings. Olfactory neuroblastoma (ONB) is a rare SRBCT encountered in both pediatric and adult patients. Awareness of the cytomorphologic and immunocytochemical features of ONB is important in the workup of a SRBCT. This case report describes the primary diagnosis of metastatic ONB on FNA cytology.
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Affiliation(s)
- Ingrid H Penzhorn
- Division of Anatomical Pathology, Tygerberg Hospital, National Health Laboratory Service, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Pawel T Schubert
- Division of Anatomical Pathology, Tygerberg Hospital, National Health Laboratory Service, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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18
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Hamdi Y, Boujemaa M, Mighri N, Mejri N, Jaidane O, Ben Nasr S, Bouaziz H, Hassouna JB, Zribi A, Berrazaga Y, Rachdi H, Daoud N, El Benna H, Labidi S, Haddaoui A, Rahal K, Benna F, Boussen H, Abdelhak S, Boubaker S. Identification of BRCA2 Cis Double Heterozygous Breast Cancer Cases Using Whole Exome Sequencing: Phenotypic Expression and Impact on Personalized Oncology. Front Genet 2021; 12:674990. [PMID: 34456966 PMCID: PMC8397457 DOI: 10.3389/fgene.2021.674990] [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: 04/17/2021] [Accepted: 07/08/2021] [Indexed: 12/24/2022] Open
Abstract
BRCA1 and BRCA2 are the most commonly mutated breast cancer susceptibility genes that convey a high risk of breast and ovarian cancer. Most BRCA1 or BRCA2 mutation carriers have inherited a single heterozygous mutation. In recent years, very rare cases with biallelic or trans double heterozygous mutations on BRCA1 and or BRCA2 have been identified and seem to be associated with distinctive phenotypes. Given that this genotype-phenotype correlation in cancer predisposing hereditary conditions is of relevance for oncological prevention and genetic testing, it is important to investigate these rare BRCA genotypes for better clinical management of BRCA mutation carriers. Here we present the first report on Cis double heterozygosity (Cis DH) on BRCA2 gene identified using Whole exome sequencing (WES) in a Tunisian family with two BRCA2 mutations namely: c.632-1G>A and c.1310_1313DelAAGA that are both reported as pathogenic in ClinVar database. Subsequent analysis in 300 high-risk Tunisian breast cancer families detected this Cis double heterozygous genotype in 8 additional individuals belonging to 5 families from the same geographic origin suggesting a founder effect. Moreover, the observed Cis DH seems to be associated with an early age of onset (mean age = 35.33 years) and severe phenotype of the disease with high breast cancer grade and multiple cancer cases in the family. The identification of unusual BRCA genotypes in this Tunisian cohort highlights the importance of performing genetic studies in under-investigated populations. This will also potentially help avoiding erroneous classifications of genetic variants in African population and therefore avoiding clinical misdiagnosis of BRCA related cancers. Our findings will also have an impact on the genetic testing and the clinical management of North African breast cancer patients as well as patients from different other ethnic groups in regard to several emerging target therapies such as PARP inhibitors.
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Affiliation(s)
- Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Najah Mighri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nesrine Mejri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Olfa Jaidane
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Sonia Ben Nasr
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Department of Medical Oncology, Military Hospital, Tunis, Tunisia
| | - Hanen Bouaziz
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Jamel Ben Hassouna
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Aref Zribi
- Department of Medical Oncology, Military Hospital, Tunis, Tunisia
| | - Yossra Berrazaga
- Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Haifa Rachdi
- Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Nouha Daoud
- Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Houda El Benna
- Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Soumaya Labidi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | | | - Khaled Rahal
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Farouk Benna
- Department of Radiation Oncology, University of Tunis, Tunis, Tunisia
| | - Hamouda Boussen
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia.,Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
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19
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Rakha E, Toss M, Quinn C. Specific cell differentiation in breast cancer: a basis for histological classification. J Clin Pathol 2021; 75:76-84. [PMID: 34321225 DOI: 10.1136/jclinpath-2021-207487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 02/20/2021] [Indexed: 11/03/2022]
Abstract
Breast parenchyma progenitor cells show a high degree of phenotypic plasticity reflected in the wide range of morphology observed in benign and malignant breast tumours. Although there is evidence suggesting that all breast cancer (BC) arises from a common epithelial progenitor or stem cell located at the terminal duct lobular units (TDLUs), BC shows a broad spectrum of morphology with extensive variation in histological type and grade. This is related to the complexity of BC carcinogenesis including initial genetic changes in the cell of origin, subsequent genetic and epigenetic alterations and reprogramming that occur at various stages of BC development and the interplay with the surrounding microenvironment, factors which influence the process of differentiation. Differentiation in BC determines the morphology, which can be measured using histological grade and tumour type. Histological grade, which measures the similarity to the TDLUs, reflects the degree of differentiation whereas tumour type reflects the type of differentiation. Understanding BC phenotypic differentiation facilitates the accurate diagnosis and histological classification of BC with corresponding clinical implications in terms of disease behaviour, prognosis and management plans. In this review, we highlight the potential pathways that BC stem cells follow resulting in the development of different histological types of BC and how knowledge of these pathways impacts our ability to classify BC in diagnostic practice. We also discuss the role of cellular differentiation in producing metaplastic and neuroendocrine carcinomas of the breast and how the latter differ from their counterparts in other organs, with emphasis on clinical relevance.
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Affiliation(s)
- Emad Rakha
- School of Medicine, The University of Nottingham, Nottingham, UK
| | - Michael Toss
- School of Medicine, The University of Nottingham, Nottingham, UK
| | - Cecily Quinn
- Histopathology, St. Vincent's Hospital, Dublin, Ireland.,Belfield, University College Dublin - National University of Ireland, Dublin, Ireland
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20
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Evolutionary Trajectories and Genomic Divergence in Localized Breast Cancers after Ipsilateral Breast Tumor Recurrence. Cancers (Basel) 2021; 13:cancers13081821. [PMID: 33920370 PMCID: PMC8069481 DOI: 10.3390/cancers13081821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/30/2022] Open
Abstract
Simple Summary Ipsilateral breast tumor relapse (IBTR) occurs in 5–10% of localized breast cancers (BCs) within 10 years of incidence, despite proper treatment of the primary lesion. However, the clinical consequences of evolutionary trajectories of BC cells and their impact on IBTR remain poorly understood. Here, we conducted a longitudinal genomic analysis of 10 matched localized BC patients with IBTR. Overall, we identified the differences in homologous recombination deficiency, chromosomal instability, and somatic mutation drivers between primary and relapsed lesions. Our analyses highlighted three clonal architectures that shape by distinct mutagenic processes and subclonal diversification during relapse progression. Finally, this study provided a framework, which integrated actionable biomarkers with clonal architectures, towards improvement of future treatment decisions. Abstract The evolutionary trajectories that drive clinical and therapeutic consequences in localized breast cancers (BCs) with ipsilateral breast tumor relapse (IBTR) remain largely unknown. Analyses of longitudinal paired whole-exome sequencing data from 10 localized BC patients with IBTR reveal that, compared to primary breast tumors, homologous recombination (HR) deficiency, inactivation of the HR pathway, chromosomal instability, and somatic driver mutations are more frequent. Furthermore, three major models of evolution in IBTR are summarized, through which relative contributions of mutational signatures shift, and the subclonal diversity expansions are shown. Optimal treatment regimens are suggested by the clinically relevant molecular features, such as HR deficiency (20%) or specific alterations (30%) with sensitivity to available FDA-approved drugs. Finally, a rationale for the development of the therapeutic management framework is provided. This study sheds light on the complicated evolution patterns in IBTR and has significant clinical implications for future improvement of treatment decisions.
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21
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Abstract
Tumor heterogeneity can arise from a variety of extrinsic and intrinsic sources and drives unfavorable outcomes. With recent technological advances, single-cell RNA sequencing has become a way for researchers to easily assay tumor heterogeneity at the transcriptomic level with high resolution. However, ongoing research focuses on different ways to analyze this big data and how to compare across multiple different samples. In this chapter, we provide a practical guide to calculate inter- and intrasample diversity metrics from single-cell RNA sequencing datasets. These measures of diversity are adapted from commonly used metrics in statistics and ecology to quantify and compare sample heterogeneity at single-cell resolution.
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22
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Tarabichi M, Salcedo A, Deshwar AG, Ni Leathlobhair M, Wintersinger J, Wedge DC, Van Loo P, Morris QD, Boutros PC. A practical guide to cancer subclonal reconstruction from DNA sequencing. Nat Methods 2021; 18:144-155. [PMID: 33398189 PMCID: PMC7867630 DOI: 10.1038/s41592-020-01013-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 11/09/2020] [Indexed: 01/28/2023]
Abstract
Subclonal reconstruction from bulk tumor DNA sequencing has become a pillar of cancer evolution studies, providing insight into the clonality and relative ordering of mutations and mutational processes. We provide an outline of the complex computational approaches used for subclonal reconstruction from single and multiple tumor samples. We identify the underlying assumptions and uncertainties in each step and suggest best practices for analysis and quality assessment. This guide provides a pragmatic resource for the growing user community of subclonal reconstruction methods.
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Affiliation(s)
- Maxime Tarabichi
- The Francis Crick Institute, London, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Adriana Salcedo
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Amit G Deshwar
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Máire Ni Leathlobhair
- Big Data Institute, University of Oxford, Oxford, UK
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Jeff Wintersinger
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - David C Wedge
- Big Data Institute, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford, UK
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK
| | | | - Quaid D Morris
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
- Vector Institute, Toronto, Ontario, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.
- Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
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23
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Robb TJ, Tse R, Blenkiron C. Reviving the Autopsy for Modern Cancer Evolution Research. Cancers (Basel) 2021; 13:409. [PMID: 33499137 PMCID: PMC7866143 DOI: 10.3390/cancers13030409] [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: 11/25/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 12/14/2022] Open
Abstract
Outstanding questions plaguing oncologists, centred around tumour evolution and heterogeneity, include the development of treatment resistance, immune evasion, and optimal drug targeting strategies. Such questions are difficult to study in limited cancer tissues collected during a patient's routine clinical care, and may be better investigated in the breadth of cancer tissues that may be permissible to collect during autopsies. We are starting to better understand key tumour evolution challenges based on advances facilitated by autopsy studies completed to date. This review article explores the great progress in understanding that cancer tissues collected at autopsy have already enabled, including the shared origin of metastatic cells, the importance of early whole-genome doubling events for amplifying genes needed for tumour survival, and the creation of a wealth of tissue resources powered to answer future questions, including patient-derived xenografts, cell lines, and a wide range of banked tissues. We also highlight the future role of these programmes in advancing our understanding of cancer evolution. The research autopsy provides a special opportunity for cancer patients to give the ultimate gift-to selflessly donate their tissues towards better cancer care.
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Affiliation(s)
- Tamsin Joy Robb
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1051, New Zealand;
| | - Rexson Tse
- Department of Forensic Pathology, LabPLUS, Auckland City Hospital, Auckland 1051, New Zealand;
| | - Cherie Blenkiron
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1051, New Zealand;
- Auckland Cancer Society Research Centre, University of Auckland, Auckland 1051, New Zealand
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24
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Delaney LM, Farias N, Ghassemi Rad J, Fernando W, Annan H, Hoskin DW. The Natural Alkaloid Piperlongumine Inhibits Metastatic Activity and Epithelial-to-Mesenchymal Transition of Triple-Negative Mammary Carcinoma Cells. Nutr Cancer 2020; 73:2397-2410. [PMID: 33019824 DOI: 10.1080/01635581.2020.1825755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/11/2020] [Indexed: 01/06/2023]
Abstract
In this study, we determined the effect of low dose piperlongumine on the motility/invasive capacity and epithelial-to-mesenchymal transition (EMT) of MDA-MB-231 triple-negative breast cancer (TNBC) cells and the metastasis of 4T1 mouse mammary carcinoma cells. MTT assays measured the effect of piperlongumine on TNBC cell growth. Motility/invasiveness were determined by gap closure/transwell assays. Western blotting assessed ZEB1, Slug, and matrix metalloproteinase (MMP) 9 expression. Interleukin (IL) 6 was detected by ELISA. MMP2, E-cadherin, and miR-200c expression was determined by real-time quantitative polymerase chain reaction. Reactive oxygen species (ROS) were measured by flow cytometry. The orthotopic 4T1 mouse model of breast cancer was used to examine metastasis. Piperlongumine-treated MDA-MB-231 cells showed reduced motility/invasiveness, decreased MMP2 and MMP9 expression, increased miR-200c expression, reduced IL-6 synthesis, decreased expression of ZEB1 and Slug, increased E-cadherin expression, and epithelial-like morphology. Piperlongumine also inhibited transforming growth factor β-induced ZEB1 and Slug expression. ROS accumulated in piperlongumine-treated cells, while changes in metastasis-associated gene expression were ablated by exogenous glutathione. Metastasis of 4T1 cells to the lungs of BALB/c mice was dramatically reduced in piperlongumine-treated animals. These findings reveal a previously unknown capacity of low dose piperlongumine to interfere with TNBC metastasis via an oxidative stress-dependent mechanism.
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Affiliation(s)
- Leanne M Delaney
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Nathan Farias
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Javad Ghassemi Rad
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Wasundara Fernando
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Henry Annan
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David W Hoskin
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Surgery, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
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25
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Shah OS, Soran A, Sahin M, Knapick BA, Ugras S, Celik E, Lucas PC, Lee AV. Identifying Genomic Alterations in Patients With Stage IV Breast Cancer Using MammaSeq: An International Collaborative Study. Clin Breast Cancer 2020; 21:210-217. [PMID: 33191115 DOI: 10.1016/j.clbc.2020.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/01/2020] [Accepted: 08/13/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Identification of genomic alterations present in cancer patients may aid in cancer diagnosis, prognosis and therapeutic target discovery. In this study, we aimed to identify clinically actionable variants present in stage IV breast cancer (BC) samples. MATERIALS AND METHODS DNA was extracted from formalin-fixed paraffin-embedded samples of BC (n = 41). DNA was sequenced using MammaSeq, a BC-specific next-generation sequencing panel targeting 79 genes and 1369 mutations. Ion Torrent Suite 4.0 was used to make variant calls on the raw data, and the resulting single nucleotide variants were annotated using the CRAVAT toolkit. Single nucleotide variations (SNVs) were filtered to remove common polymorphisms and germline variants. CNVkit was employed to identify copy number variations (CNVs). The Precision Medicine Knowledgebase (PMKB) and OncoKB Precision Oncology Database were used to associate clinical significance with the identified variants. RESULTS A total of 41 samples from Turkish patients with BC were sequenced (read depth of 94-13,340; median of 1529). These patients were diagnosed with various BC subtypes including invasive ductal carcinoma, invasive lobular carcinoma, apocrine BC, and micropapillary BC. In total, 59 different alterations (49 SNVs and 10 CNVs) were identified. From these, 8 alterations (3 CNVs - ERBB2, FGFR1, and AR copy number gains and 5 SNVs - IDH1.R132H, TP53.E204∗, PI3KCA.E545K, PI3KCA.H1047R, and PI3KCA.R88Q) were identified to have some clinical significance by PMKB and OncoKB. Moreover, the top 5 genes with the most SNVs included PIK3CA, TP53, MAP3K1, ATM, and NCOR1. Additionally, copy number gains and losses were found in ERBB2, GRB7, IGFR1, AR, FGFR1, MYC, and IKBKB, and BRCA2, RUNX1, and RB1, respectively. CONCLUSION We identified 59 unique alterations in 38 genes in 41 stage IV BC tissue samples using MammaSeqTM. Eight of these alterations were found to have some clinical significance by OncoKB and PKMB. This study highlights the potential use of cancer specific next-generation sequencing panels in clinic to get better insight into the patient-specific genomic alterations.
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Affiliation(s)
- Osama Shiraz Shah
- Magee-Womens Research Institute, Pittsburgh, PA; Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA
| | | | - Mustafa Sahin
- Department of General Surgery, Selçuk University, Konya, Turkey
| | | | - Serdar Ugras
- Department of Pathology, Selçuk University, Konya, Turkey
| | - Esin Celik
- Department of Pathology, Selçuk University, Konya, Turkey
| | - Peter C Lucas
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA; UPMC Hillman Cancer Center, Pittsburgh, PA
| | - Adrian V Lee
- Magee-Womens Research Institute, Pittsburgh, PA; Women's Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh, PA; UPMC Hillman Cancer Center, Pittsburgh, PA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA; Institute for Precision Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, PA.
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26
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Chen N, Feng Q, Deng J, Xiong Y, Deng YJ, Wang MM, Zhou L, Yu QW, Hu JP, Deng H. Hdc-expressing myeloid-derived suppressor cells promote basal-like transition and metastasis of breast cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2020; 13:1431-1443. [PMID: 32661481 PMCID: PMC7344006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
Metastases are the greatest contributors to death from breast cancer. Here, we identified a distinct subpopulation of luminal breast cancer characterized by cytokeratin 14 (CK14) expression in secondary colonies rather than primary tumors. This entity possessed a poorer prognosis compared to their CK14- counterparts. Immunohistochemical analysis showed that myeloid-derived suppressor cells (MDSCs) were recruited into the tumor microenvironment and exhibited a close spatial relationship with CK14+ cancer cells. We demonstrated that histidine decarboxylase (Hdc) is capable of labeling myeloid-biased hematopoietic stem cell/progenitor cell (HSC/HSPC) and immature myeloid cells infiltrating in tumor tissues. FACS data obtained from Hdc-CreERT2; eGFP; MMTV-PyVT female mice revealed an increased percentage of Hdc+ PMN-MDSCs in metastatic masses. Hdc+ PMN-MDSCs expressed high levels of canonical Wnts, including Wnt2, Wnt4, Wnt5a, and Wnt7b, to aberrantly activate Wnt/β-catenin signaling in CK14+ malignant cells. β-catenin translocated from the membrane into the cytoplasm and nucleus. Targeted ablation of Hdc+ PMN-MDSCs-derived Wnts through porcupineflox/flox and iDTR transgenic models hampered the metastatic cascade, making Hdc+ immature myeloid cells an attractive candidate for tailed immunotherapies.
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Affiliation(s)
- Na Chen
- Department of Breast Surgery, The Fourth Affiliated Hospital of Nanchang UniversityNanchang, China
| | - Qiong Feng
- Department of Pathology, The Second Affiliated Hospital of Nanchang UniversityNanchang, China
| | - Jun Deng
- Department of Emergency, The First Affiliated Hospital of Nanchang UniversityNanchang, China
| | - Yin Xiong
- Department of General Medicine, The Second Affiliated Hospital of Nanchang UniversityNanchang, China
| | - Yan-Juan Deng
- Department of Pathology, The Fourth Affiliated Hospital of Nanchang UniversityNanchang, China
- Tumor Immunology Institute, Nanchang UniversityNanchang, China
| | - Meng-Meng Wang
- Department of Pathology, The Fourth Affiliated Hospital of Nanchang UniversityNanchang, China
- Tumor Immunology Institute, Nanchang UniversityNanchang, China
| | - Lv Zhou
- Department of Pathology, The Fourth Affiliated Hospital of Nanchang UniversityNanchang, China
- Tumor Immunology Institute, Nanchang UniversityNanchang, China
| | - Qi-Wen Yu
- Department of Pathology, The Fourth Affiliated Hospital of Nanchang UniversityNanchang, China
- Tumor Immunology Institute, Nanchang UniversityNanchang, China
| | - Jin-Ping Hu
- Department of Pathology, The Fourth Affiliated Hospital of Nanchang UniversityNanchang, China
- Tumor Immunology Institute, Nanchang UniversityNanchang, China
| | - Huan Deng
- Department of Pathology, The Fourth Affiliated Hospital of Nanchang UniversityNanchang, China
- Tumor Immunology Institute, Nanchang UniversityNanchang, China
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Sharick JT, Walsh CM, Sprackling CM, Pasch CA, Pham DL, Esbona K, Choudhary A, Garcia-Valera R, Burkard ME, McGregor SM, Matkowskyj KA, Parikh AA, Meszoely IM, Kelley MC, Tsai S, Deming DA, Skala MC. Metabolic Heterogeneity in Patient Tumor-Derived Organoids by Primary Site and Drug Treatment. Front Oncol 2020; 10:553. [PMID: 32500020 PMCID: PMC7242740 DOI: 10.3389/fonc.2020.00553] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/27/2020] [Indexed: 12/16/2022] Open
Abstract
New tools are needed to match cancer patients with effective treatments. Patient-derived organoids offer a high-throughput platform to personalize treatments and discover novel therapies. Currently, methods to evaluate drug response in organoids are limited because they overlook cellular heterogeneity. In this study, non-invasive optical metabolic imaging (OMI) of cellular heterogeneity was characterized in breast cancer (BC) and pancreatic cancer (PC) patient-derived organoids. Baseline heterogeneity was analyzed for each patient, demonstrating that single-cell techniques, such as OMI, are required to capture the complete picture of heterogeneity present in a sample. Treatment-induced changes in heterogeneity were also analyzed, further demonstrating that these measurements greatly complement current techniques that only gauge average cellular response. Finally, OMI of cellular heterogeneity in organoids was evaluated as a predictor of clinical treatment response for the first time. Organoids were treated with the same drugs as the patient's prescribed regimen, and OMI measurements of heterogeneity were compared to patient outcome. OMI distinguished subpopulations of cells with divergent and dynamic responses to treatment in living organoids without the use of labels or dyes. OMI of organoids agreed with long-term therapeutic response in patients. With these capabilities, OMI could serve as a sensitive high-throughput tool to identify optimal therapies for individual patients, and to develop new effective therapies that address cellular heterogeneity in cancer.
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Affiliation(s)
- Joe T Sharick
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, United States.,Morgridge Institute for Research, Madison, WI, United States
| | | | | | - Cheri A Pasch
- University of Wisconsin Carbone Cancer Center, Madison, WI, United States
| | - Dan L Pham
- Morgridge Institute for Research, Madison, WI, United States.,Department of Biomedical Engineering, University of Wisconsin, Madison, WI, United States
| | - Karla Esbona
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, United States
| | - Alka Choudhary
- University of Wisconsin Carbone Cancer Center, Madison, WI, United States.,Department of Medicine, University of Wisconsin, Madison, WI, United States
| | - Rebeca Garcia-Valera
- University of Wisconsin Carbone Cancer Center, Madison, WI, United States.,Department of Medicine, University of Wisconsin, Madison, WI, United States.,Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, Zapopan, Mexico
| | - Mark E Burkard
- University of Wisconsin Carbone Cancer Center, Madison, WI, United States.,Department of Medicine, University of Wisconsin, Madison, WI, United States
| | - Stephanie M McGregor
- University of Wisconsin Carbone Cancer Center, Madison, WI, United States.,Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, United States
| | - Kristina A Matkowskyj
- University of Wisconsin Carbone Cancer Center, Madison, WI, United States.,Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, United States.,William S. Middleton Memorial Veterans Hospital, Madison, WI, United States
| | - Alexander A Parikh
- Division of Surgical Oncology, East Carolina University Brody School of Medicine, Greenville, NC, United States
| | - Ingrid M Meszoely
- Department of Surgery, Vanderbilt University, Nashville, TN, United States
| | - Mark C Kelley
- Department of Surgery, Vanderbilt University, Nashville, TN, United States
| | - Susan Tsai
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Dustin A Deming
- University of Wisconsin Carbone Cancer Center, Madison, WI, United States.,Division of Hematology and Oncology, Department of Medicine, University of Wisconsin, Madison, WI, United States.,McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin, Madison, WI, United States
| | - Melissa C Skala
- Morgridge Institute for Research, Madison, WI, United States.,University of Wisconsin Carbone Cancer Center, Madison, WI, United States.,Department of Biomedical Engineering, University of Wisconsin, Madison, WI, United States
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28
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Assessing Cell Activities rather than Identities to Interpret Intra-Tumor Phenotypic Diversity and Its Dynamics. iScience 2020; 23:101061. [PMID: 32361272 PMCID: PMC7195534 DOI: 10.1016/j.isci.2020.101061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/02/2020] [Accepted: 04/09/2020] [Indexed: 12/26/2022] Open
Abstract
Despite advances in single-cell and molecular techniques, it is still unclear how to best quantify phenotypic heterogeneity in cancer cells that evolved beyond normal, known classifications. We present an approach to phenotypically characterize cells based on their activities rather than static classifications. We validated the detectability of specific activities (epithelial-mesenchymal transition, glycolysis) in single cells, using targeted RT-qPCR analyses and in vitro inductions. We analyzed 50 established activity signatures as a basis for phenotypic description in public data and computed cell-cell distances in 28,513 cells from 85 patients and 8 public datasets. Despite not relying on any classification, our measure correlated with standard diversity indices in populations of known structure. We identified bottlenecks as phenotypic diversity reduced upon colorectal cancer initiation. This suggests that focusing on what cancer cells do rather than what they are can quantify phenotypic diversity in universal fashion, to better understand and predict intra-tumor heterogeneity dynamics. Cells categorized as having the same identity can perform different activities Single-cell expression data can be used to infer the activities cells take part in Activity profiles provide a basis to measure phenotypic cell-cell divergence Cell activity can quantify intra-tumor heterogeneity more fully than identity
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29
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Wang X, He X, Guo H, Tong Y. Variants in the 8q24 region associated with risk of breast cancer: Systematic research synopsis and meta-analysis. Medicine (Baltimore) 2020; 99:e19217. [PMID: 32080114 PMCID: PMC7034712 DOI: 10.1097/md.0000000000019217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Breast cancer is a molecularly heterogeneous disorder associated with high lethal malignant tumors among women worldwide. Genetic factors play an important role in breast cancer development. Several single nucleotide polymorphisms in the 8q24 region associated with risk of breast cancer have been identified. Fifteen studies including 32,955 cases and 43,716 controls were collected to conduct a meta-analysis to evaluate the associations between variants in 8q24 region and risk of breast cancer. Our study showed that only rs13281615 is associated with breast cancer risk in this large-scale research synopsis and meta-analysis. Further studies are needed to explore the role of the 8q24 variants in the development of breast cancer.
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Affiliation(s)
- Xuedong Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
| | - Xian He
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
| | - Hui Guo
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yu Tong
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan Province, China
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30
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Hutchinson KE, Yost SE, Chang CW, Johnson RM, Carr AR, McAdam PR, Halligan DL, Chang CC, Schmolze D, Liang J, Yuan Y. Comprehensive Profiling of Poor-Risk Paired Primary and Recurrent Triple-Negative Breast Cancers Reveals Immune Phenotype Shifts. Clin Cancer Res 2020; 26:657-668. [PMID: 31611282 PMCID: PMC8568263 DOI: 10.1158/1078-0432.ccr-19-1773] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/07/2019] [Accepted: 10/09/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Emerging data suggest immune checkpoint inhibitors have reduced efficacy in heavily pretreated triple-negative breast cancers (TNBC), but underlying mechanisms are poorly understood. To better understand the phenotypic evolution of TNBCs, we studied the genomic and transcriptomic profiles of paired tumors from patients with TNBC. EXPERIMENTAL DESIGN We collected paired primary and metastatic TNBC specimens from 43 patients and performed targeted exome sequencing and whole-transcriptome sequencing. From these efforts, we ascertained somatic mutation profiles, tumor mutational burden (TMB), TNBC molecular subtypes, and immune-related gene expression patterns. Stromal tumor-infiltrating lymphocytes (stromal TIL), recurrence-free survival, and overall survival were also analyzed. RESULTS We observed a typical TNBC mutational landscape with minimal shifts in copy number or TMB over time. However, there were notable TNBC molecular subtype shifts, including increases in the Lehmann/Pietenpol-defined basal-like 1 (BL1, 11.4%-22.6%) and mesenchymal (M, 11.4%-22.6%) phenotypes, and a decrease in the immunomodulatory phenotype (IM, 31.4%-3.2%). The Burstein-defined basal-like immune-activated phenotype was also decreased (BLIA, 42.2%-17.2%). Among downregulated genes from metastases, we saw enrichment of immune-related Kyoto Encyclopedia of Genes and Genomes pathways and gene ontology (GO) terms, and decreased expression of immunomodulatory gene signatures (P < 0.03) and percent stromal TILs (P = 0.03). There was no clear association between stromal TILs and survival. CONCLUSIONS We observed few mutational shifts, but largely consistent transcriptomic shifts in longitudinally paired TNBCs. Transcriptomic and IHC analyses revealed significantly reduced immune-activating gene expression signatures and TILs in recurrent TNBCs. These data may explain the observed lack of efficacy of immunotherapeutic agents in heavily pretreated TNBCs. Further studies are ongoing to better understand these initial observations.See related commentary by Savas and Loi, p. 526.
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Affiliation(s)
| | - Susan E Yost
- Department of Medical Oncology and Therapeutic Research, City of Hope National Medical Center, Duarte, California
| | - Ching-Wei Chang
- Oncology Biostatistics, Genentech, Inc., South San Francisco, California
| | | | | | | | | | - Chun-Chieh Chang
- Oncology Biostatistics, Genentech, Inc., South San Francisco, California
| | - Daniel Schmolze
- Department of Pathology, City of Hope National Medical Center, Duarte, California
| | - Jackson Liang
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, California
| | - Yuan Yuan
- Department of Medical Oncology and Therapeutic Research, City of Hope National Medical Center, Duarte, California.
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31
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Cheng J, Wang R, Zhong G, Chen X, Cheng Y, Li W, Yang Y. ST6GAL2 Downregulation Inhibits Cell Adhesion and Invasion and is Associated with Improved Patient Survival in Breast Cancer. Onco Targets Ther 2020; 13:903-914. [PMID: 32099394 PMCID: PMC6996233 DOI: 10.2147/ott.s230847] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 12/30/2019] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE Breast cancer is one of the most common and serious types of cancer, with a particularly unfavorable prognosis. Although dysregulation of β-galactoside α 2,6-sialyltransferase 2 (ST6GAL2) has been observed in multiple cancers, the mechanism involved remains to be clarified. In this study, we focused on the potential function of ST6GAL2 in the regulation of breast cancer. METHODS Flow cytometry and CCK-8 were used to measure markers of the cell cycle proliferation, adhesion, and invasion. Real-time PCR and immunohistochemistry analysis were used to detect the expression levels of ST6GAL2 in breast cancer tissues. Western blot was used to analyze the expression level of genes correlated with focal adhesion and metastasis pathways in breast cancer cells. RESULTS ST6GAL2 expression levels were higher in breast cancer tissues as compared to healthy tissues. ST6GAL2 expression was associated with tumor stage, survival time, and estrogen receptor (ER)/progesterone receptor (PR)/human epidermal growth factor receptor 2 (HER2) status of breast cancer patients. Silence of ST6GAL2 inhibited cancer progression by arresting cell cycle progression at G0/G1 phase and inhibiting cell adhesion and invasion. ST6GAL2 was positively correlated with focal adhesion and metastasis pathways, and its downregulation inhibited the expression of ICAM-1, VCAM-1, CD24, MMP2, MMP9, and CXCR4. CONCLUSION These findings indicated that ST6GAL2 might serve as a useful potential target for treatment of breast cancer.
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Affiliation(s)
- Junchi Cheng
- Department of Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou310000, People’s Republic of China
| | - Rong Wang
- Department of Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou310000, People’s Republic of China
| | - Guansheng Zhong
- Department of Breast Surgery, The First Affiliated Hospital, Zhejiang University, Hangzhou310003, People’s Republic of China
| | - Xi Chen
- Department of Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou310000, People’s Republic of China
| | - Yun Cheng
- Department of Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou310000, People’s Republic of China
| | - Wei Li
- Department of Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou310000, People’s Republic of China
| | - Yunshan Yang
- Department of Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou310000, People’s Republic of China
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32
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Li J, Ge Y, Huang JX, Strømgaard K, Zhang X, Xiong XF. Heterotrimeric G Proteins as Therapeutic Targets in Drug Discovery. J Med Chem 2019; 63:5013-5030. [PMID: 31841625 DOI: 10.1021/acs.jmedchem.9b01452] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Heterotrimeric G proteins are molecular switches in GPCR signaling pathways and regulate a plethora of physiological and pathological processes. GPCRs are efficient drug targets, and more than 30% of the drugs in use target them. However, selectively targeting an individual GPCR may be undesirable in various multifactorial diseases in which multiple receptors are involved. In addition, abnormal activation or expression of G proteins is frequently associated with diseases. Furthermore, G proteins harboring mutations often result in malignant diseases. Thus, targeting G proteins instead of GPCRs might provide alternative approaches for combating these diseases. In this review, we discuss the biochemistry of heterotrimeric G proteins, describe the G protein-associated diseases, and summarize the currently known modulators that can regulate the activities of G proteins. The outlook for targeting G proteins to treat diverse diseases is also included in this manuscript.
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Affiliation(s)
- Jian Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Yang Ge
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Jun-Xiang Huang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Xiaolei Zhang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Xiao-Feng Xiong
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
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33
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Barrow-McGee R, Procter J, Owen J, Woodman N, Lombardelli C, Kothari A, Kovacs T, Douek M, George S, Barry PA, Ramsey K, Gibson A, Buus R, Holgersen E, Natrajan R, Haider S, Shattock MJ, Gillett C, Tutt AN, Pinder SE, Naidoo K. Real-time ex vivo perfusion of human lymph nodes invaded by cancer (REPLICANT): a feasibility study. J Pathol 2019; 250:262-274. [PMID: 31755096 PMCID: PMC7065097 DOI: 10.1002/path.5367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/06/2019] [Accepted: 11/18/2019] [Indexed: 01/18/2023]
Abstract
Understanding how breast cancer (BC) grows in axillary lymph nodes (ALNs), and refining how therapies might halt that process, is clinically important. However, modelling the complex ALN microenvironment is difficult, and no human models exist at present. We harvested ALNs from ten BC patients, and perfused them at 37 °C ex vivo for up to 24 h. Controlled autologous testing showed that ALNs remain viable after 24 h of ex vivo perfusion: haematoxylin and eosin-stained histological appearance and proliferation (by Ki67 immunohistochemistry) did not change significantly over time for any perfused ALN compared with a control from time-point zero. Furthermore, targeted gene expression analysis (NanoString PanCancer IO360 panel) showed that only 21/750 genes were differentially expressed between control and perfused ALNs (|log2 FC| > 1 and q < 0.1): none were involved in apoptosis and metabolism, but rather all 21 genes were involved in immune function and angiogenesis. During perfusion, tissue acid-base balance remained stable. Interestingly, the flow rate increased (p < 0.001) in cancer-replaced (i.e. metastasis occupied more than 90% of the surface area on multiple levels) compared to cancer-free nodes (i.e. nodes with no metastasis on multiple sections). CXCL11 transcripts were significantly more abundant in cancer-replaced nodes, while CXCL12 transcripts were significantly more abundant in cancer-free nodes. These cytokines were also detected in the circulating perfusate. Monoclonal antibodies (nivolumab and trastuzumab) were administered into a further three ALNs to confirm perfusion efficacy. These drugs saturated the nodes; nivolumab even induced cancer cell death. Normothermic ALN perfusion is not only feasible but sustains the tumour microenvironment ex vivo for scientific investigation. This model could facilitate the identification of actionable immuno-oncology targets. © 2019 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Rachel Barrow-McGee
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK
| | - Julia Procter
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK
| | - Julie Owen
- King's Health Partners Cancer Biobank, Guy's Comprehensive Cancer Centre, London, UK
| | - Natalie Woodman
- King's Health Partners Cancer Biobank, Guy's Comprehensive Cancer Centre, London, UK
| | - Cristina Lombardelli
- King's Health Partners Cancer Biobank, Guy's Comprehensive Cancer Centre, London, UK
| | | | - Tibor Kovacs
- Guy's and St. Thomas' Hospital NHS Foundation Trust, London, UK
| | - Michael Douek
- School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Comprehensive Cancer Centre, London, UK
| | - Simi George
- Department of Cellular Pathology, Guy's and St. Thomas' Hospital NHS Foundation Trust, London, UK
| | | | | | - Amy Gibson
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK
| | - Richard Buus
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK.,Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | - Erle Holgersen
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK
| | - Syed Haider
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK
| | - Michael J Shattock
- British Heart Foundation Centre of Research Excellence, King's College London, St Thomas' Hospital, London, UK
| | - Cheryl Gillett
- King's Health Partners Cancer Biobank, Guy's Comprehensive Cancer Centre, London, UK
| | - Andrew Nj Tutt
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK
| | - Sarah E Pinder
- School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Comprehensive Cancer Centre, London, UK
| | - Kalnisha Naidoo
- Toby Robins Breast Cancer Now Research Centre, Breast Cancer Research Division, The Institute of Cancer Research, London, UK.,Department of Cellular Pathology, Guy's and St. Thomas' Hospital NHS Foundation Trust, London, UK
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34
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Waninger JJ, Green MD, Cheze Le Rest C, Rosen B, El Naqa I. Integrating radiomics into clinical trial design. THE QUARTERLY JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING : OFFICIAL PUBLICATION OF THE ITALIAN ASSOCIATION OF NUCLEAR MEDICINE (AIMN) [AND] THE INTERNATIONAL ASSOCIATION OF RADIOPHARMACOLOGY (IAR), [AND] SECTION OF THE SOCIETY OF RADIOPHARMACEUTICAL CHEMISTRY AND BIOLOGY 2019; 63:339-346. [PMID: 31527581 DOI: 10.23736/s1824-4785.19.03217-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In radiomics, quantitative features that describe phenotypic tumor characteristics are derived from radiographic images. Because radiomics generates information from routine medical images, it is a powerful way to non-invasively examine the spatial and temporal heterogeneity of disease, and thus has potential to significantly impact clinical trial design, execution, and ultimately patient care. The aim of this review article is to discuss how radiomics may address some of the current challenges in clinical randomized control trials, and the difficulties of integrating robust and repeatable radiomics analysis into trial design. Each step of the radiomics process, including image acquisition and reconstruction, image segmentation, feature extraction, and computational analysis, requires extensive standardization in order to be successfully incorporated into clinical trials and inform clinical decision making. By addressing these challenges, the potential of radiomics may be realized.
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Affiliation(s)
- Jessica J Waninger
- Department of Medical Education, University of Michigan School of Medicine, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Michael D Green
- Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, MI, USA.,University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | | | - Benjamin Rosen
- Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Issam El Naqa
- Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, MI, USA -
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35
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Martín-Pardillos A, Valls Chiva Á, Bande Vargas G, Hurtado Blanco P, Piñeiro Cid R, Guijarro PJ, Hümmer S, Bejar Serrano E, Rodriguez-Casanova A, Diaz-Lagares Á, Castellvi J, Miravet-Verde S, Serrano L, Lluch-Senar M, Sebastian V, Bribian A, López-Mascaraque L, López-López R, Ramón Y Cajal S. The role of clonal communication and heterogeneity in breast cancer. BMC Cancer 2019; 19:666. [PMID: 31277602 PMCID: PMC6612119 DOI: 10.1186/s12885-019-5883-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 06/26/2019] [Indexed: 12/13/2022] Open
Abstract
Background Cancer is a rapidly evolving, multifactorial disease that accumulates numerous genetic and epigenetic alterations. This results in molecular and phenotypic heterogeneity within the tumor, the complexity of which is further amplified through specific interactions between cancer cells. We aimed to dissect the molecular mechanisms underlying the cooperation between different clones. Methods We produced clonal cell lines derived from the MDA-MB-231 breast cancer cell line, using the UbC-StarTrack system, which allowed tracking of multiple clones by color: GFP C3, mKO E10 and Sapphire D7. Characterization of these clones was performed by growth rate, cell metabolic activity, wound healing, invasion assays and genetic and epigenetic arrays. Tumorigenicity was tested by orthotopic and intravenous injections. Clonal cooperation was evaluated by medium complementation, co-culture and co-injection assays. Results Characterization of these clones in vitro revealed clear genetic and epigenetic differences that affected growth rate, cell metabolic activity, morphology and cytokine expression among cell lines. In vivo, all clonal cell lines were able to form tumors; however, injection of an equal mix of the different clones led to tumors with very few mKO E10 cells. Additionally, the mKO E10 clonal cell line showed a significant inability to form lung metastases. These results confirm that even in stable cell lines heterogeneity is present. In vitro, the complementation of growth medium with medium or exosomes from parental or clonal cell lines increased the growth rate of the other clones. Complementation assays, co-growth and co-injection of mKO E10 and GFP C3 clonal cell lines increased the efficiency of invasion and migration. Conclusions These findings support a model where interplay between clones confers aggressiveness, and which may allow identification of the factors involved in cellular communication that could play a role in clonal cooperation and thus represent new targets for preventing tumor progression. Electronic supplementary material The online version of this article (10.1186/s12885-019-5883-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana Martín-Pardillos
- Translational Molecular Pathology Group, Vall d'Hebron Research Institute, Barcelona, Spain. .,CIBERONC (Centro de Investigación Biomédica en Red de Cáncer), Madrid, Spain.
| | - Ángeles Valls Chiva
- Translational Molecular Pathology Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Gemma Bande Vargas
- Translational Molecular Pathology Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | | | - Roberto Piñeiro Cid
- CIBERONC (Centro de Investigación Biomédica en Red de Cáncer), Madrid, Spain.,Cancer Modelling Lab, Roche-CHUS Joint Unit, Santiago de Compostela, Spain
| | - Pedro J Guijarro
- Translational Molecular Pathology Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Stefan Hümmer
- Translational Molecular Pathology Group, Vall d'Hebron Research Institute, Barcelona, Spain.,CIBERONC (Centro de Investigación Biomédica en Red de Cáncer), Madrid, Spain
| | - Eva Bejar Serrano
- Translational Molecular Pathology Group, Vall d'Hebron Research Institute, Barcelona, Spain.,CIBERONC (Centro de Investigación Biomédica en Red de Cáncer), Madrid, Spain
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain
| | - Ángel Diaz-Lagares
- CIBERONC (Centro de Investigación Biomédica en Red de Cáncer), Madrid, Spain.,Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain
| | - Josep Castellvi
- Hospital Vall d'Hebron, Anatomía Patológica, Barcelona, Spain
| | - Samuel Miravet-Verde
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Institute of Science and Technology, Barcelona, Spain
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - María Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Institute of Science and Technology, Barcelona, Spain
| | - Víctor Sebastian
- Department of Chemical Engineering, Aragon Institute of Nanoscience (INA), University of Zaragoza, Zaragoza, Spain.,Networking Research Centre on Bioengineering, Biomaterials and Nanomedicine, CIBER-BBN, Madrid, Spain
| | - Ana Bribian
- Department of Molecular, Cellular and Developmental Neurobiology, Instituto Cajal-CSIC, Madrid, Spain
| | - Laura López-Mascaraque
- Department of Molecular, Cellular and Developmental Neurobiology, Instituto Cajal-CSIC, Madrid, Spain
| | - Rafael López-López
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain.,Roche-CHUS Joint Unit, University Clinical Hospital of Santiago (CHUS), Santiago de Compostela, Spain
| | - Santiago Ramón Y Cajal
- Translational Molecular Pathology Group, Vall d'Hebron Research Institute, Barcelona, Spain. .,CIBERONC (Centro de Investigación Biomédica en Red de Cáncer), Madrid, Spain. .,Hospital Vall d'Hebron, Anatomía Patológica, Barcelona, Spain.
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36
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Metastasis as a systemic disease: molecular insights and clinical implications. Biochim Biophys Acta Rev Cancer 2019; 1872:89-102. [PMID: 31202687 DOI: 10.1016/j.bbcan.2019.06.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/06/2019] [Accepted: 06/09/2019] [Indexed: 12/18/2022]
Abstract
Metastasis is a complex systemic disease that develops as a result of interactions between tumor cells and their local and distant microenvironments. Local and systemic immune-related changes play especially critical roles in limiting or enabling the development of metastatic disease. Although anti-tumor immune responses likely eliminate most early primary and metastatic lesions, factors secreted by cancer or stromal cells in the primary tumor can mobilize and activate cells in distant organs in a way that promotes the outgrowth of disseminated cancer cells into macrometastatic lesions. Therefore, the prevention, detection, and effective treatment of metastatic disease require a deeper understanding of the systemic effects of primary tumors as well as predisposing hereditary and acquired host factors including chronic inflammatory conditions. The success of immunotherapy in a subset of cancer patients is an example of how modulating the microenvironment and tumor-immune cell interactions can be exploited for the effective eradiation of even advanced-stage tumors. Here, we highlight emerging insights and clinical implications of cancer as a systemic disease.
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37
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Ramón Y Cajal S, Hümmer S, Peg V, Guiu XM, De Torres I, Castellvi J, Martinez-Saez E, Hernandez-Losa J. Integrating clinical, molecular, proteomic and histopathological data within the tissue context: tissunomics. Histopathology 2019; 75:4-19. [PMID: 30667539 PMCID: PMC6851567 DOI: 10.1111/his.13828] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/19/2019] [Indexed: 12/14/2022]
Abstract
Malignant tumours show a marked degree of morphological, molecular and proteomic heterogeneity. This variability is closely related to microenvironmental factors and the location of the tumour. The activation of genetic alterations is very tissue‐dependent and only few tumours have distinct genetic alterations. Importantly, the activation state of proteins and signaling factors is heterogeneous in the primary tumour and in metastases and recurrences. The molecular diagnosis based only on genetic alterations can lead to treatments with unpredictable responses, depending on the tumour location, such as the tumour response in melanomas versus colon carcinomas with BRAF mutations. Therefore, we understand that the correct evaluation of tumours requires a system that integrates both morphological, molecular and protein information in a clinical and pathological context, where intratumoral heterogeneity can be assessed. Thus, we propose the term ‘tissunomics’, where the diagnosis will be contextualised in each tumour based on the complementation of the pathological, molecular, protein expression, environmental cells and clinical data.
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Affiliation(s)
- Santiago Ramón Y Cajal
- Translational Molecular Pathology, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
| | - Stefan Hümmer
- Translational Molecular Pathology, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
| | - Vicente Peg
- Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
| | - Xavier M Guiu
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain.,Department of Pathology, Bellvitge University Hospital, Barcelona, Spain
| | - Inés De Torres
- Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Josep Castellvi
- Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
| | - Elena Martinez-Saez
- Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Javier Hernandez-Losa
- Translational Molecular Pathology, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
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38
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Sharick JT, Jeffery JJ, Karim MR, Walsh CM, Esbona K, Cook RS, Skala MC. Cellular Metabolic Heterogeneity In Vivo Is Recapitulated in Tumor Organoids. Neoplasia 2019; 21:615-626. [PMID: 31078067 PMCID: PMC6514366 DOI: 10.1016/j.neo.2019.04.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 12/14/2022] Open
Abstract
Heterogeneous populations within a tumor have varying metabolic profiles, which can muddle the interpretation of bulk tumor imaging studies of treatment response. Although methods to study tumor metabolism at the cellular level are emerging, these methods provide a single time point “snapshot” of tumor metabolism and require a significant time and animal burden while failing to capture the longitudinal metabolic response of a single tumor to treatment. Here, we investigated a novel method for longitudinal, single-cell tracking of metabolism across heterogeneous tumor cell populations using optical metabolic imaging (OMI), which measures autofluorescence of metabolic coenzymes as a report of metabolic activity. We also investigated whether in vivo cellular metabolic heterogeneity can be accurately captured using tumor-derived three-dimensional organoids in a genetically engineered mouse model of breast cancer. OMI measurements of response to paclitaxel and the phosphatidylinositol-3-kinase inhibitor XL147 in tumors and organoids taken at single cell resolution revealed parallel shifts in metaboltruic heterogeneity. Interestingly, these previously unappreciated heterogeneous metabolic responses in tumors and organoids could not be attributed to tumor cell fate or varying leukocyte content within the microenvironment, suggesting that heightened metabolic heterogeneity upon treatment is largely due to heterogeneous metabolic shifts within tumor cells. Together, these studies show that OMI revealed remarkable heterogeneity in response to treatment, which could provide a novel approach to predict the presence of potentially unresponsive tumor cell subpopulations lurking within a largely responsive bulk tumor population, which might otherwise be overlooked by traditional measurements.
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Affiliation(s)
- Joe T Sharick
- Department of Biomedical Engineering, Vanderbilt University, PMB 351631, 2301 Vanderbilt Place, Nashville, TN, 37235, USA; Morgridge Institute for Research, 330 N. Orchard Street, Madison, WI, 53715, USA
| | - Justin J Jeffery
- University of Wisconsin Carbone Cancer Center, 600 Highland Avenue, Madison, WI, 53792, USA
| | - Mohammad R Karim
- Morgridge Institute for Research, 330 N. Orchard Street, Madison, WI, 53715, USA
| | - Christine M Walsh
- Morgridge Institute for Research, 330 N. Orchard Street, Madison, WI, 53715, USA
| | - Karla Esbona
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, 3170 UW Medical Foundation Centennial Building, 1685 Highland Avenue, Madison, WI, 53705, USA
| | - Rebecca S Cook
- Department of Biomedical Engineering, Vanderbilt University, PMB 351631, 2301 Vanderbilt Place, Nashville, TN, 37235, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, PMB 407935 U-3218, Medical Research Building III, Nashville, TN, 37240, USA;; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN; Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Melissa C Skala
- Morgridge Institute for Research, 330 N. Orchard Street, Madison, WI, 53715, USA; Department of Biomedical Engineering, University of Wisconsin-Madison, Engineering Centers Building, 1550 Engineering Drive Room #2130, Madison, WI, 53706.
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39
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Molecular Heterogeneity of Renal Cell Carcinoma. Urol Oncol 2019. [DOI: 10.1007/978-3-319-42623-5_59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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40
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Kalinowski L, Saunus JM, McCart Reed AE, Lakhani SR. Breast Cancer Heterogeneity in Primary and Metastatic Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1152:75-104. [DOI: 10.1007/978-3-030-20301-6_6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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41
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Vitamin D-induced vitamin D receptor expression induces tamoxifen sensitivity in MCF-7 stem cells via suppression of Wnt/β-catenin signaling. Biosci Rep 2018; 38:BSR20180595. [PMID: 30314996 PMCID: PMC6435469 DOI: 10.1042/bsr20180595] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 09/17/2018] [Accepted: 10/05/2018] [Indexed: 12/18/2022] Open
Abstract
Objective: Cancer stem cells (CSCs) are responsible for the drug resistance of breast cancers. Vitamin D deficiency promotes tumor resistance. The present study examined the effect of vitamin D and vitamin D receptor (VDR) expression on the tamoxifen resistance of CSCs. Methods: MCF-7 cells were treated with 1,25(OH)2D3 and their levels of VDR expression, viability, and apoptosis were detected. CD133+ MCF-7 stem cells were identified and transfected with a VDR-overexpression plasmid. The tamoxifen concentration that reduced MCF-7 cell viability by 50% (IC50) was determined. The activation of Wnt/β-catenin signaling was also investigated. Results: Vitamin D reduced the viability of MCF-7 cells and promoted their apoptosis. Vitamin D enhanced VDR expression and induced DNA damage. When CD133+ stem cells were separated from MCF-7 cells, the IC50 of tamoxifen for stem cells was significantly higher than that of parental MCF-7 cells, suggesting a higher tamoxifen resistance in MCF-7 stem cells. Levels of VDR expression and Wnt/β-catenin signaling in CD133+ cells were markedly lower and higher than those in CD133− cells, respectively. Stem cells transfected with VDR overexpression plasmids showed decreased tamoxifen IC50 values, viability, spheroid formation, and expression of Wnt and β-catenin proteins when compared with control cells. Cell apoptosis was increased by transfection with a VDR overexpression plasmid. Finally, the inhibitory effects induced by VDR overexpression could be reversed by the VDR inhibitor, calcifediol. Conclusion: Stem cells contributed to the tamoxifen resistance of MCF-7 cells. Vitamin D-induced VDR expression increased the sensitivity of MCF-7 stem cells to tamoxifen by inhibiting Wnt/β-catenin signaling.
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42
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High-resolution clonal mapping of multi-organ metastasis in triple negative breast cancer. Nat Commun 2018; 9:5079. [PMID: 30498242 PMCID: PMC6265294 DOI: 10.1038/s41467-018-07406-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/30/2018] [Indexed: 12/31/2022] Open
Abstract
Most triple negative breast cancers (TNBCs) are aggressively metastatic with a high degree of intra-tumoral heterogeneity (ITH), but how ITH contributes to metastasis is unclear. Here, clonal dynamics during metastasis were studied in vivo using two patient-derived xenograft (PDX) models established from the treatment-naive primary breast tumors of TNBC patients diagnosed with synchronous metastasis. Genomic sequencing and high-complexity barcode-mediated clonal tracking reveal robust alterations in clonal architecture between primary tumors and corresponding metastases. Polyclonal seeding and maintenance of heterogeneous populations of low-abundance subclones is observed in each metastasis. However, lung, liver, and brain metastases are enriched for an identical population of high-abundance subclones, demonstrating that primary tumor clones harbor properties enabling them to seed and thrive in multiple organ sites. Further, clones that dominate multi-organ metastases share a genomic lineage. Thus, intrinsic properties of rare primary tumor subclones enable the seeding and colonization of metastases in secondary organs in these models. It is unclear how intra-tumoral heterogeneity contributes to metastasis. Here the authors study the clonal dynamics of triple negative breast cancer metastasis using patient derived xenografts and demonstrate that primary tumor clones harbor properties that support seeding and colonization of multiple organs.
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43
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Stoppacciaro A, Di Vito S, Filetici P. Epigenetic Factors and Mitochondrial Biology in Yeast: A New Paradigm for the Study of Cancer Metabolism? Front Pharmacol 2018; 9:1349. [PMID: 30524288 PMCID: PMC6258771 DOI: 10.3389/fphar.2018.01349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/02/2018] [Indexed: 12/14/2022] Open
Abstract
Bidirectional cross-talk between nuclear and mitochondrial DNA is fundamental for cell homeostasis. Epigenetic mechanisms regulate the inter-organelle communication between nucleus and mitochondria. Recent research highlights not only the retrograde activation of nuclear gene transcription in case of mitochondria dysfunction, but also the role of post-translational modifications of mitochondrial proteins in respiratory metabolism. Here we discuss some aspects and novel findings in Saccharomyces cerevisiae. In yeast, KAT-Gcn5 and DUB-Ubp8 have a role in respiration and are localized, as single proteins, into mitochondria. These findings, beside the canonical and widely known nuclear activity of SAGA complex in chromatin regulation, provide novel clues on promising aspects linking evolutionary conserved epigenetic factors to the re-programmed metabolism of cancer cells.
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Affiliation(s)
- Antonella Stoppacciaro
- Surgical Pathology Units, Department of Clinical and Molecular Medicine, Ospedale Sant'Andrea, Sapienza University of Rome, Rome, Italy
| | - Serena Di Vito
- Institute of Molecular Biology and Pathology, CNR, Sapienza University of Rome, Rome, Italy
| | - Patrizia Filetici
- Institute of Molecular Biology and Pathology, CNR, Sapienza University of Rome, Rome, Italy
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44
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Klaassen R, Larue RTHM, Mearadji B, van der Woude SO, Stoker J, Lambin P, van Laarhoven HWM. Feasibility of CT radiomics to predict treatment response of individual liver metastases in esophagogastric cancer patients. PLoS One 2018; 13:e0207362. [PMID: 30440002 PMCID: PMC6237370 DOI: 10.1371/journal.pone.0207362] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 10/30/2018] [Indexed: 02/06/2023] Open
Abstract
In this study we investigate a CT radiomics approach to predict response to chemotherapy of individual liver metastases in patients with esophagogastric cancer (EGC). In eighteen patients with metastatic EGC treated with chemotherapy, all liver metastases were manually delineated in 3D on the pre-treatment and evaluation CT. From the pre-treatment CT scans 370 radiomics features were extracted per lesion. Random forest (RF) models were generated to discriminate partial responding (PR, >65% volume decrease, including 100% volume decrease), and complete remission (CR, only 100% volume decrease) lesions from other lesions. RF-models were build using a leave one out strategy where all lesions of a single patient were removed from the dataset and used as validation set for a model trained on the lesions of the remaining patients. This process was repeated for all patients, resulting in 18 trained models and one validation set for both the PR and CR datasets. Model performance was evaluated by receiver operating characteristics with corresponding area under the curve (AUC). In total 196 liver metastases were delineated on the pre-treatment CT, of which 99 (51%) lesions showed a decrease in size of more than 65% (PR). From the PR set a total of 47 (47% of RL, 24% of initial) lesions were no longer detected in CT scan 2 (CR). The RF-model for PR lesions showed an average training AUC of 0.79 (range: 0.74-0.83) and 0.65 (95% ci: 0.57-0.73) for the combined validation set. The RF-model for CR lesions had an average training AUC of 0.87 (range: 0.83-0.90) and 0.79 (95% ci 0.72-0.87) for the validation set. Our findings show that individual response of liver metastases varies greatly within and between patients. A CT radiomics approach shows potential in discriminating responding from non-responding liver metastases based on the pre-treatment CT scan, although further validation in an independent patient cohort is needed to validate these findings.
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Affiliation(s)
- Remy Klaassen
- Amsterdam UMC, University of Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
- Amsterdam UMC, University of Amsterdam, LEXOR, Laboratory for Experimental Oncology and Radiobiology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Ruben T. H. M. Larue
- The D-Lab: Decision Support for Precision Medicine, GROW-School for Oncology and Developmental Biology, Maastricht Comprehensive Cancer Centre, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Banafsche Mearadji
- Amsterdam UMC, University of Amsterdam, Department of Radiology and Nuclear Medicine, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Stephanie O. van der Woude
- Amsterdam UMC, University of Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Jaap Stoker
- Amsterdam UMC, University of Amsterdam, Department of Radiology and Nuclear Medicine, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Philippe Lambin
- The D-Lab: Decision Support for Precision Medicine, GROW-School for Oncology and Developmental Biology, Maastricht Comprehensive Cancer Centre, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Hanneke W. M. van Laarhoven
- Amsterdam UMC, University of Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, Netherlands
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45
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Chung YR, Kim HJ, Kim M, Ahn S, Park SY. Clinical implications of changes in the diversity of c-MYC copy number variation after neoadjuvant chemotherapy in breast cancer. Sci Rep 2018; 8:16668. [PMID: 30420657 PMCID: PMC6232091 DOI: 10.1038/s41598-018-35072-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 10/30/2018] [Indexed: 12/25/2022] Open
Abstract
Chemotherapy can alter the makeup of a tumor cell population by exerting selection pressure. We examined the change in Shannon index, a mathematical diversity measure used in ecology, for c-MYC copy number variation (CNV) after neoadjuvant chemotherapy and evaluated its clinical significance in breast cancer. Associations between Shannon indices for c-MYC CNV in pre- and post-neoadjuvant chemotherapy breast cancer samples and clinicopathologic features of tumors as well as patient survival were analyzed in 144 patients. A change in c-MYC amplification and copy number gain status was found in 14.3% and 33.6% with most cases showing positive to negative conversion. The chemo-sensitive group showed a significant decrease in Shannon index after neoadjuvant chemotherapy. However, there was no difference in diversity indices between pre- and post-neoadjuvant chemotherapy specimens in the chemo-resistant group. In survival analyses, high Shannon indices for c-MYC CNV in post-neoadjuvant chemotherapy samples as well as those in pre-neoadjuvant chemotherapy samples were revealed as independent prognostic factors for poor disease-free survival not only in the whole group but also in the chemo-resistant subgroup. These findings suggest that a change in Shannon index for c-MYC CNV after neoadjuvant chemotherapy reflects chemo-responsiveness and that Shannon indices after neoadjuvant chemotherapy have a prognostic value in breast cancer patients who receive neoadjuvant chemotherapy.
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Affiliation(s)
- Yul Ri Chung
- Department of pathology, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Republic of Korea.,Department of pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyun Jeong Kim
- Department of pathology, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Republic of Korea
| | - Milim Kim
- Department of pathology, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Republic of Korea.,Department of pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Soomin Ahn
- Department of pathology, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Republic of Korea
| | - So Yeon Park
- Department of pathology, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Republic of Korea. .,Department of pathology, Seoul National University College of Medicine, Seoul, Republic of Korea.
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46
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Stereotactic radiotherapy in metastatic breast cancer. Breast 2018; 41:57-66. [DOI: 10.1016/j.breast.2018.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/09/2018] [Accepted: 06/21/2018] [Indexed: 12/19/2022] Open
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47
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Lee JY, Schizas M, Geyer FC, Selenica P, Piscuoglio S, Sakr RA, Ng CKY, Carniello JVS, Towers R, Giri DD, de Andrade VP, Papanastasiou AD, Viale A, Harris RS, Solit DB, Weigelt B, Reis-Filho JS, King TA. Lobular Carcinomas In Situ Display Intralesion Genetic Heterogeneity and Clonal Evolution in the Progression to Invasive Lobular Carcinoma. Clin Cancer Res 2018; 25:674-686. [PMID: 30185420 DOI: 10.1158/1078-0432.ccr-18-1103] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/26/2018] [Accepted: 08/31/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE Lobular carcinoma in situ (LCIS) is a preinvasive lesion of the breast. We sought to define its genomic landscape, whether intralesion genetic heterogeneity is present in LCIS, and the clonal relatedness between LCIS and invasive breast cancers.Experimental Design: We reanalyzed whole-exome sequencing (WES) data and performed a targeted amplicon sequencing validation of mutations identified in 43 LCIS and 27 synchronous more clinically advanced lesions from 24 patients [9 ductal carcinomas in situ (DCIS), 13 invasive lobular carcinomas (ILC), and 5 invasive ductal carcinomas (IDC)]. Somatic genetic alterations, mutational signatures, clonal composition, and phylogenetic trees were defined using validated computational methods. RESULTS WES of 43 LCIS lesions revealed a genomic profile similar to that previously reported for ILCs, with CDH1 mutations present in 81% of the lesions. Forty-two percent (18/43) of LCIS were found to be clonally related to synchronous DCIS and/or ILCs, with clonal evolutionary patterns indicative of clonal selection and/or parallel/branched progression. Intralesion genetic heterogeneity was higher among LCIS clonally related to DCIS/ILC than in those nonclonally related to DCIS/ILC. A shift from aging to APOBEC-related mutational processes was observed in the progression from LCIS to DCIS and/or ILC in a subset of cases. CONCLUSIONS Our findings support the contention that LCIS has a repertoire of somatic genetic alterations similar to that of ILCs, and likely constitutes a nonobligate precursor of breast cancer. Intralesion genetic heterogeneity is observed in LCIS and should be considered in studies aiming to develop biomarkers of progression from LCIS to more advanced lesions.
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Affiliation(s)
- Ju Youn Lee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michail Schizas
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Institute of Pathology and Medical Genetics, University Hospital Basel, Basel, Switzerland
| | - Rita A Sakr
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Institute of Pathology and Medical Genetics, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Russell Towers
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dilip D Giri
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Victor P de Andrade
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Agnes Viale
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Reuben S Harris
- Howard Hughes Medical Institute, Masonic Cancer Center, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - David B Solit
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tari A King
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
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48
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Joseph C, Papadaki A, Althobiti M, Alsaleem M, Aleskandarany MA, Rakha EA. Breast cancer intratumour heterogeneity: current status and clinical implications. Histopathology 2018; 73:717-731. [PMID: 29722058 DOI: 10.1111/his.13642] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Breast cancer (BC) is a heterogeneous disease that varies in presentation, morphological features, behaviour, and response to therapy. High-throughput molecular profiling studies have revolutionised our understanding of BC heterogeneity, and have demonstrated that molecular profiles of tumours are variable not only between tumours, but also within individual tumours. Current evidence indicates that spatial and temporal intratumour heterogeneity of BC exists at levels beyond what are commonly expected. Intratumour heterogeneity poses critical challenges in the diagnosis, prediction of behaviour and management of BC. For instance, heterogeneous expression of oestrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 can be seen not only in primary tumours between different regions, but also between primary tumours and their corresponding metastatic/recurrent lesions. The demonstration of molecularly distinct subclones within individual tumours may explain, at least in part, the mechanisms controlling the variable behaviour of BC, and may change our approach to BC sampling and treatment. In this review, BC intratumour heterogeneity is highlighted, with a special emphasis on the current knowledge pertaining to the relationship between intratumour heterogeneity and BC pathogenesis, evolution, and progression, with consideration of its impact on disease diagnosis, management, and the emergence of novel therapeutic targets. The key role of high-throughput molecular and imaging techniques is also addressed.
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Affiliation(s)
- Chitra Joseph
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, UK
| | - Athanasia Papadaki
- Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Maryam Althobiti
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, UK
| | - Mansour Alsaleem
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, UK
| | - Mohammed A Aleskandarany
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, UK
| | - Emad A Rakha
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, UK.,Cellular Pathology, Nottingham University Hospitals NHS Trust, Nottingham, UK
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49
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Sun R, Xie HY, Qian JX, Huang YN, Yang F, Zhang FL, Shao ZM, Li DQ. FBXO22 Possesses Both Protumorigenic and Antimetastatic Roles in Breast Cancer Progression. Cancer Res 2018; 78:5274-5286. [PMID: 29945959 DOI: 10.1158/0008-5472.can-17-3647] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 06/04/2018] [Accepted: 06/22/2018] [Indexed: 11/16/2022]
Abstract
The molecular underpinnings behind malignant progression of breast cancer from a localized lesion to an invasive and ultimately metastatic disease are incompletely understood. Here, we report that F-box only protein 22 (FBXO22) plays a dual role in mammary tumorigenesis and metastasis. FBXO22 was upregulated in primary breast tumors and promoted cell proliferation and colony formation in vitro and xenograft tumorigenicity in vivo Surprisingly, FBXO22 suppressed epithelial-mesenchymal transition (EMT), cell motility, and invasiveness in vitro and metastatic lung colonization in vivo Clinical data showed that expression levels of FBXO22 were associated with favorable clinical outcomes, supporting the notion that metastasis, rather than primary cancer, is the major determinant of the mortality of patients with breast cancer. Mechanistic investigations further revealed that FBXO22 elicits its antimetastatic effects by targeting SNAIL, a master regulator of EMT and breast cancer metastasis, for ubiquitin-mediated proteasomal degradation in a glycogen synthase kinase 3β phosphorylation-dependent manner. Importantly, expression of SNAIL rescued FBXO22-mediated suppression of EMT, cell migration, and invasion. A patient-derived tryptophan-to-arginine mutation at residue 52 (W52R) within the F-box domain impaired FBXO22 binding to the SKP1-Cullin1 complex and blocked FBXO22-mediated SNAIL degradation, thus abrogating the ability of FBXO22 to suppress cell migration, invasion, and metastasis. Collectively, these findings uncover an unexpected dual role for FBXO22 in mammary tumorigenesis and metastatic progression and delineate the mechanism of an oncogenic mutation of FBXO22 in breast cancer progression.Significance: These findings highlight the paradoxical roles of FBXO22 in breast cancer, as it promotes breast tumor cell proliferation but prevents EMT and metastasis. Cancer Res; 78(18); 5274-86. ©2018 AACR.
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Affiliation(s)
- Rui Sun
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hong-Yan Xie
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Cancer Institute, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jin-Xian Qian
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yan-Ni Huang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai, China.,Key Laboratory of Breast Cancer in Shanghai, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fan Yang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai, China.,Key Laboratory of Breast Cancer in Shanghai, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fang-Lin Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China. .,Cancer Institute, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhi-Min Shao
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China. .,Cancer Institute, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai, China.,Key Laboratory of Breast Cancer in Shanghai, Shanghai Medical College, Fudan University, Shanghai, China.,Key Laboratory of Medical Epigenetics and Metabolism, Shanghai Medical College, Fudan University, Shanghai, China
| | - Da-Qiang Li
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China. .,Cancer Institute, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai, China.,Key Laboratory of Breast Cancer in Shanghai, Shanghai Medical College, Fudan University, Shanghai, China.,Key Laboratory of Medical Epigenetics and Metabolism, Shanghai Medical College, Fudan University, Shanghai, China
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50
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Kurland BF, Oesterreich S. Heterogeneity in Metastatic Breast Cancer 18F-Fluoroestradiol Uptake: Clinically Actionable, Biologically Illuminating? J Nucl Med 2018; 59:1210-1211. [PMID: 29903931 DOI: 10.2967/jnumed.118.214304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 06/13/2018] [Indexed: 11/16/2022] Open
Affiliation(s)
- Brenda F Kurland
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania .,UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania; and
| | - Steffi Oesterreich
- UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania; and.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
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