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Treekitkarnmongkol W, Shah V, Kai K, Katayama H, Wong J, Ladha FA, Nguyen T, Menegaz B, Lu W, Yang F, Mino B, Tang X, Gagea M, Batra H, Raso MG, Wistuba II, Krishnamurthy S, Pinder SE, Sawyer EJ, Thompson AM, Sen S. Epigenetic activation of SOX11 is associated with recurrence and progression of ductal carcinoma in situ to invasive breast cancer. Br J Cancer 2024; 131:171-183. [PMID: 38760444 DOI: 10.1038/s41416-024-02697-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 03/26/2024] [Accepted: 04/15/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Risk of recurrence and progression of ductal carcinoma in situ (DCIS) to invasive cancer remains uncertain, emphasizing the need for developing predictive biomarkers of aggressive DCIS. METHODS Human cell lines and mouse models of disease progression were analyzed for candidate risk predictive biomarkers identified and validated in two independent DCIS cohorts. RESULTS RNA profiling of normal mammary and DCIS tissues (n = 48) revealed that elevated SOX11 expression correlates with MKI67, EZH2, and DCIS recurrence score. The 21T human cell line model of DCIS progression to invasive cancer and two mouse models developing mammary intraepithelial neoplasia confirmed the findings. AKT activation correlated with chromatin accessibility and EZH2 enrichment upregulating SOX11 expression. AKT and HER2 inhibitors decreased SOX11 expression along with diminished mammosphere formation. SOX11 was upregulated in HER2+ and basal-like subtypes (P < 0.001). Longitudinal DCIS cohort (n = 194) revealed shorter recurrence-free survival in SOX11+ than SOX11- patients (P = 0.0056 in all DCIS; P < 0.0001 in HER2+ subtype) associated with increased risk of ipsilateral breast event/IBE (HR = 1.9, 95%CI = 1.2-2.9; P = 0.003). DISCUSSION Epigenetic activation of SOX11 drives recurrence of DCIS and progression to invasive cancer, suggesting SOX11 as a predictive biomarker of IBE.
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MESH Headings
- Humans
- Female
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Breast Neoplasms/metabolism
- Animals
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Carcinoma, Intraductal, Noninfiltrating/metabolism
- SOXC Transcription Factors/genetics
- SOXC Transcription Factors/metabolism
- Mice
- Disease Progression
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/pathology
- Epigenesis, Genetic
- Cell Line, Tumor
- Neoplasm Invasiveness
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Gene Expression Regulation, Neoplastic
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- Enhancer of Zeste Homolog 2 Protein/genetics
- Enhancer of Zeste Homolog 2 Protein/metabolism
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Affiliation(s)
- Warapen Treekitkarnmongkol
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vandna Shah
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Kazuharu Kai
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hiroshi Katayama
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Justin Wong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Farah A Ladha
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tristian Nguyen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brian Menegaz
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Wei Lu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fei Yang
- Department of Anatomic Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Barbara Mino
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ximing Tang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mihai Gagea
- Department of Veterinary Medicine & Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Harsh Batra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maria Gabriela Raso
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Savitri Krishnamurthy
- Department of Anatomic Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sarah E Pinder
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Elinor J Sawyer
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London, UK
| | - Alastair M Thompson
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
| | - Subrata Sen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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2
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Psilopatis I, Schaefer JI, Arsenakis D, Bolovis D, Levidou G. SOX11 and Epithelial-Mesenchymal Transition in Metastatic Serous Ovarian Cancer. Biomedicines 2023; 11:2540. [PMID: 37760985 PMCID: PMC10526401 DOI: 10.3390/biomedicines11092540] [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: 08/09/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Ovarian cancer is the leading cause of death from gynecological malignancies, with serous carcinoma being the most common histopathologic subtype. Epithelial-mesenchymal transition (EMT) correlates with increased metastatic potential, whereas the transcription factor SRY-box transcription factor 11 (SOX11) is overexpressed in diverse malignancies. METHODS In the present study, we aimed to evaluate the potential role of the immunohistochemical expression of SOX11 in 30 serous ovarian carcinomas in association with E-cadherin and vimentin expression as well as with patients' clinicopathological data. RESULTS Most of the examined cases showed concurrent expression of E-cadherin and vimentin, whereas SOX11 was expressed in a minority of the cases (26.7%). Interestingly, the positive cases more frequently had a metastatic disease at the time of diagnosis compared with the negative cases (p = 0.09), an association, however, of marginal significance. Moreover, there was a negative correlation between E-cadherin and SOX11 expression (p = 0.0077) and a positive correlation between vimentin and SOX11 expression (p = 0.0130). CONCLUSIONS The present work, for the first time, provides preliminary evidence of a possible implication of SOX11 overexpression in the promotion of EMT in metastatic serous ovarian cancer, thereby endorsing tumor metastasis.
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Affiliation(s)
- Iason Psilopatis
- Department of Pathology, Medical School, Klinikum Nuremberg, Paracelsus University, 90419 Nuremberg, Germany
- Department of Obstetrics and Gynecology, University Erlangen, Universitaetsstrasse 21–23, 91054 Erlangen, Germany
| | - Jule Ida Schaefer
- Department of Pathology, Medical School, Klinikum Nuremberg, Paracelsus University, 90419 Nuremberg, Germany
| | - Dimitrios Arsenakis
- Department of Gynecology, Medical School, Klinikum Nuremberg, Paracelsus University, 90419 Nuremberg, Germany
| | - Dimitrios Bolovis
- Department of Gynecology, Medical School, Klinikum Nuremberg, Paracelsus University, 90419 Nuremberg, Germany
| | - Georgia Levidou
- Department of Pathology, Medical School, Klinikum Nuremberg, Paracelsus University, 90419 Nuremberg, Germany
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3
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Ouyang D, Liang Y, Li L, Ai N, Lu S, Yu M, Liu X, Xie S. Integration of multi-omics data using adaptive graph learning and attention mechanism for patient classification and biomarker identification. Comput Biol Med 2023; 164:107303. [PMID: 37586201 DOI: 10.1016/j.compbiomed.2023.107303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/08/2023] [Accepted: 07/28/2023] [Indexed: 08/18/2023]
Abstract
With the rapid development and accumulation of high-throughput sequencing technology and omics data, many studies have conducted a more comprehensive understanding of human diseases from a multi-omics perspective. Meanwhile, graph-based methods have been widely used to process multi-omics data due to its powerful expressive ability. However, most existing graph-based methods utilize fixed graphs to learn sample embedding representations, which often leads to sub-optimal results. Furthermore, treating embedding representations of different omics equally usually cannot obtain more reasonable integrated information. In addition, the complex correlation between omics is not fully taken into account. To this end, we propose an end-to-end interpretable multi-omics integration method, named MOGLAM, for disease classification prediction. Dynamic graph convolutional network with feature selection is first utilized to obtain higher quality omic-specific embedding information by adaptively learning the graph structure and discover important biomarkers. Then, multi-omics attention mechanism is applied to adaptively weight the embedding representations of different omics, thereby obtaining more reasonable integrated information. Finally, we propose omic-integrated representation learning to capture complex common and complementary information between omics while performing multi-omics integration. Experimental results on three datasets show that MOGLAM achieves superior performance than other state-of-the-art multi-omics integration methods. Moreover, MOGLAM can identify important biomarkers from different omics data types in an end-to-end manner.
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Affiliation(s)
- Dong Ouyang
- Peng Cheng Laboratory, Shenzhen, 518055, China; School of Computer Science and Engineering, Faculty of Innovation Engineering, Macau University of Science and Technology, 999078, Macao Special Administrative Region of China
| | - Yong Liang
- Peng Cheng Laboratory, Shenzhen, 518055, China.
| | - Le Li
- School of Computer Science and Engineering, Faculty of Innovation Engineering, Macau University of Science and Technology, 999078, Macao Special Administrative Region of China
| | - Ning Ai
- School of Computer Science and Engineering, Faculty of Innovation Engineering, Macau University of Science and Technology, 999078, Macao Special Administrative Region of China
| | - Shanghui Lu
- School of Computer Science and Engineering, Faculty of Innovation Engineering, Macau University of Science and Technology, 999078, Macao Special Administrative Region of China
| | - Mingkun Yu
- School of Computer Science and Engineering, Faculty of Innovation Engineering, Macau University of Science and Technology, 999078, Macao Special Administrative Region of China
| | - Xiaoying Liu
- Computer Engineering Technical College, Guangdong Polytechnic of Science and Technology, Zhuhai, 519090, China
| | - Shengli Xie
- Guangdong-HongKong-Macao Joint Laboratory for Smart Discrete Manufacturing, Guangzhou, 510000, China
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4
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Lu DY, Ellegast JM, Ross KN, Malone CF, Lin S, Mabe NW, Dharia NV, Meyer A, Conway A, Su AH, Selich-Anderson J, Taslim C, Byrum AK, Seong BKA, Adane B, Gray NS, Rivera MN, Lessnick SL, Stegmaier K. The ETS transcription factor ETV6 constrains the transcriptional activity of EWS-FLI to promote Ewing sarcoma. Nat Cell Biol 2023; 25:285-297. [PMID: 36658220 PMCID: PMC9928584 DOI: 10.1038/s41556-022-01059-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 11/24/2022] [Indexed: 01/21/2023]
Abstract
Transcription factors (TFs) are frequently mutated in cancer. Paediatric cancers exhibit few mutations genome-wide but frequently harbour sentinel mutations that affect TFs, which provides a context to precisely study the transcriptional circuits that support mutant TF-driven oncogenesis. A broadly relevant mechanism that has garnered intense focus involves the ability of mutant TFs to hijack wild-type lineage-specific TFs in self-reinforcing transcriptional circuits. However, it is not known whether this specific type of circuitry is equally crucial in all mutant TF-driven cancers. Here we describe an alternative yet central transcriptional mechanism that promotes Ewing sarcoma, wherein constraint, rather than reinforcement, of the activity of the fusion TF EWS-FLI supports cancer growth. We discover that ETV6 is a crucial TF dependency that is specific to this disease because it, counter-intuitively, represses the transcriptional output of EWS-FLI. This work discovers a previously undescribed transcriptional mechanism that promotes cancer.
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Affiliation(s)
- Diana Y Lu
- Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jana M Ellegast
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kenneth N Ross
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clare F Malone
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shan Lin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathaniel W Mabe
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashleigh Meyer
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy Conway
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Angela H Su
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Selich-Anderson
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Cenny Taslim
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Andrea K Byrum
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Bo Kyung A Seong
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Biniam Adane
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Miguel N Rivera
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Stephen L Lessnick
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- Division of Pediatric Hematology, Oncology and BMT, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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5
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Sun Q, Du J, Dong J, Pan S, Jin H, Han X, Zhang J. Systematic Investigation of the Multifaceted Role of SOX11 in Cancer. Cancers (Basel) 2022; 14:cancers14246103. [PMID: 36551589 PMCID: PMC9776339 DOI: 10.3390/cancers14246103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/23/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
SRY-box transcription factor 11 (SOX11), as a member of the SOX family, is a transcription factor involved in the regulation of specific biological processes and has recently been found to be a prognostic marker for certain cancers. However, the roles of SOX11 in cancer remain controversial. Our study aimed to explore the various aspects of SOX11 in pan-cancer. The expression of SOX11 was investigated by the Genotype Tissue-Expression (GTEX) dataset and the Cancer Genome Atlas (TCGA) database. The protein level of SOX11 in tumor tissues and tumor-adjacent tissues was verified by human pan-cancer tissue microarray. Additionally, we used TCGA pan-cancer data to analyze the correlations among SOX11 expression and survival outcomes, clinical features, stemness, microsatellite instability (MSI), tumor mutation burden (TMB), mismatch repair (MMR) related genes and the tumor immune microenvironment. Furthermore, the cBioPortal database was applied to investigate the gene alterations of SOX11. The main biological processes of SOX11 in cancers were analyzed by Gene Set Enrichment Analysis (GSEA). As a result, aberrant expression of SOX11 has been implicated in 27 kinds of cancer types. Aberrant SOX11 expression was closely associated with survival outcomes, stage, tumor recurrence, MSI, TMB and MMR-related genes. In addition, the most frequent alteration of the SOX11 genome was mutation. Our study also showed the correlations of SOX11 with the level of immune infiltration in various cancers. In summary, our findings underline the multifaceted role and prognostic value of SOX11 in pan-cancer.
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Affiliation(s)
- Qingqing Sun
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei 230001, China
- Department of Medical Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Jun Du
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Jie Dong
- Department of Medical Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Shuaikang Pan
- Department of Medical Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Hongwei Jin
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei 230001, China
| | - Xinghua Han
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei 230001, China
- Department of Medical Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Correspondence: (X.H.); (J.Z.)
| | - Jinguo Zhang
- Department of Medical Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Correspondence: (X.H.); (J.Z.)
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Proteomics-Based Identification of Dysregulated Proteins in Breast Cancer. Proteomes 2022; 10:proteomes10040035. [PMID: 36278695 PMCID: PMC9590004 DOI: 10.3390/proteomes10040035] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022] Open
Abstract
Immunohistochemistry (IHC) is still widely used as a morphology-based assay for in situ analysis of target proteins as specific tumor antigens. However, as a very heterogeneous collection of neoplastic diseases, breast cancer (BC) requires an accurate identification and characterization of larger panels of candidate biomarkers, beyond ER, PR, and HER2 proteins, for diagnosis and personalized treatment, without the limited availability of antibodies that are required to identify specific proteins. Top-down, middle-down, and bottom-up mass spectrometry (MS)-based proteomics approaches complement traditional histopathological tissue analysis to examine expression, modification, and interaction of hundreds to thousands of proteins simultaneously. In this review, we discuss the proteomics-based identification of dysregulated proteins in BC that are essential for the following issues: discovery and validation of new biomarkers by analysis of solid and liquid/non-invasive biopsies, cell lines, organoids and xenograft models; identification of panels of biomarkers for early detection and accurate discrimination between cancer, benign and normal tissues; identification of subtype-specific and stage-specific protein expression profiles in BC grading and measurement of disease progression; characterization of new subtypes of BC; characterization and quantitation of post-translational modifications (PTMs) and aberrant protein-protein interactions (PPI) involved in tumor development; characterization of the global remodeling of BC tissue homeostasis, diagnosis and prognostic information; and deciphering of molecular functions, biological processes and mechanisms through which the dysregulated proteins cause tumor initiation, invasion, and treatment resistance.
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7
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Xu J, Qin S, Yi Y, Gao H, Liu X, Ma F, Guan M. Delving into the Heterogeneity of Different Breast Cancer Subtypes and the Prognostic Models Utilizing scRNA-Seq and Bulk RNA-Seq. Int J Mol Sci 2022; 23:ijms23179936. [PMID: 36077333 PMCID: PMC9456551 DOI: 10.3390/ijms23179936] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Breast cancer (BC) is the most common malignancy in women with high heterogeneity. The heterogeneity of cancer cells from different BC subtypes has not been thoroughly characterized and there is still no valid biomarker for predicting the prognosis of BC patients in clinical practice. Methods: Cancer cells were identified by calculating single cell copy number variation using the inferCNV algorithm. SCENIC was utilized to infer gene regulatory networks. CellPhoneDB software was used to analyze the intercellular communications in different cell types. Survival analysis, univariate Cox, least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox analysis were used to construct subtype specific prognostic models. Results: Triple-negative breast cancer (TNBC) has a higher proportion of cancer cells than subtypes of HER2+ BC and luminal BC, and the specifically upregulated genes of the TNBC subtype are associated with antioxidant and chemical stress resistance. Key transcription factors (TFs) of tumor cells for three subtypes varied, and most of the TF-target genes are specifically upregulated in corresponding BC subtypes. The intercellular communications mediated by different receptor–ligand pairs lead to an inflammatory response with different degrees in the three BC subtypes. We establish a prognostic model containing 10 genes (risk genes: ATP6AP1, RNF139, BASP1, ESR1 and TSKU; protective genes: RPL31, PAK1, STARD10, TFPI2 and SIAH2) for luminal BC, seven genes (risk genes: ACTR6 and C2orf76; protective genes: DIO2, DCXR, NDUFA8, SULT1A2 and AQP3) for HER2+ BC, and seven genes (risk genes: HPGD, CDC42 and PGK1; protective genes: SMYD3, LMO4, FABP7 and PRKRA) for TNBC. Three prognostic models can distinguish high-risk patients from low-risk patients and accurately predict patient prognosis. Conclusions: Comparative analysis of the three BC subtypes based on cancer cell heterogeneity in this study will be of great clinical significance for the diagnosis, prognosis and targeted therapy for BC patients.
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Place E, Manning E, Kim DW, Kinjo A, Nakamura G, Ohyama K. SHH and Notch regulate SOX9+ progenitors to govern arcuate POMC neurogenesis. Front Neurosci 2022; 16:855288. [PMID: 36033614 PMCID: PMC9404380 DOI: 10.3389/fnins.2022.855288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 07/20/2022] [Indexed: 12/05/2022] Open
Abstract
Pro-opiomelanocortin (POMC)-expressing neurons in the hypothalamic arcuate nucleus (ARC) play key roles in feeding and energy homoeostasis, hence their development is of great research interest. As the process of neurogenesis is accompanied by changes in adhesion, polarity, and migration that resemble aspects of epithelial-to-mesenchymal transitions (EMTs), we have characterised the expression and regulation within the prospective ARC of transcription factors with context-dependent abilities to regulate aspects of EMT. Informed by pseudotime meta-analysis of recent scRNA-seq data, we use immunohistochemistry and multiplex in situ hybridisation to show that SOX2, SRY-Box transcription factor 9 (SOX9), PROX1, Islet1 (ISL1), and SOX11 are sequentially expressed over the course of POMC neurogenesis in the embryonic chick. Through pharmacological studies ex vivo, we demonstrate that while inhibiting either sonic hedgehog (SHH) or Notch signalling reduces the number of SOX9+ neural progenitor cells, these treatments lead, respectively, to lesser and greater numbers of differentiating ISL1+/POMC+ neurons. These results are consistent with a model in which SHH promotes the formation of SOX9+ progenitors, and Notch acts to limit their differentiation. Both pathways are also required to maintain normal levels of proliferation and to suppress apoptosis. Together our findings demonstrate that hypothalamic neurogenesis is accompanied by dynamic expression of transcription factors (TFs) that mediate EMTs, and that SHH and Notch signalling converge to regulate hypothalamic cellular homoeostasis.
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Affiliation(s)
- Elsie Place
- School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | - Elizabeth Manning
- School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | - Dong Won Kim
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Arisa Kinjo
- Department of Histology and Neuroanatomy, Tokyo Medical University, Tokyo, Japan
| | - Go Nakamura
- Department of Histology and Neuroanatomy, Tokyo Medical University, Tokyo, Japan
| | - Kyoji Ohyama
- Department of Histology and Neuroanatomy, Tokyo Medical University, Tokyo, Japan
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9
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Mass Spectrometry Imaging Spatial Tissue Analysis toward Personalized Medicine. LIFE (BASEL, SWITZERLAND) 2022; 12:life12071037. [PMID: 35888125 PMCID: PMC9318569 DOI: 10.3390/life12071037] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/04/2022] [Accepted: 07/10/2022] [Indexed: 12/19/2022]
Abstract
Novel profiling methodologies are redefining the diagnostic capabilities and therapeutic approaches towards more precise and personalized healthcare. Complementary information can be obtained from different omic approaches in combination with the traditional macro- and microscopic analysis of the tissue, providing a more complete assessment of the disease. Mass spectrometry imaging, as a tissue typing approach, provides information on the molecular level directly measured from the tissue. Lipids, metabolites, glycans, and proteins can be used for better understanding imbalances in the DNA to RNA to protein translation, which leads to aberrant cellular behavior. Several studies have explored the capabilities of this technology to be applied to tumor subtyping, patient prognosis, and tissue profiling for intraoperative tissue evaluation. In the future, intercenter studies may provide the needed confirmation on the reproducibility, robustness, and applicability of the developed classification models for tissue characterization to assist in disease management.
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Kurani H, Razavipour SF, Harikumar KB, Dunworth M, Ewald AJ, Nasir A, Pearson G, Van Booven D, Zhou Z, Azzam D, Wahlestedt C, Slingerland J. DOT1L Is a Novel Cancer Stem Cell Target for Triple-Negative Breast Cancer. Clin Cancer Res 2022; 28:1948-1965. [PMID: 35135840 PMCID: PMC9365344 DOI: 10.1158/1078-0432.ccr-21-1299] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 12/01/2021] [Accepted: 02/04/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE Although chemotherapies kill most cancer cells, stem cell-enriched survivors seed metastasis, particularly in triple-negative breast cancers (TNBC). TNBCs arise from and are enriched for tumor stem cells. Here, we tested if inhibition of DOT1L, an epigenetic regulator of normal tissue stem/progenitor populations, would target TNBC stem cells. EXPERIMENTAL DESIGN Effects of DOT1L inhibition by EPZ-5676 on stem cell properties were tested in three TNBC lines and four patient-derived xenograft (PDX) models and in isolated cancer stem cell (CSC)-enriched ALDH1+ and ALDH1- populations. RNA sequencing compared DOT1L regulated pathways in ALDH1+ and ALDH1- cells. To test if EPZ-5676 decreases CSC in vivo, limiting dilution assays of EPZ-5676/vehicle pretreated ALDH1+ and ALDH1- cells were performed. Tumor latency, growth, and metastasis were evaluated. Antitumor activity was also tested in TNBC PDX and PDX-derived organoids. RESULTS ALDH1+ TNBC cells exhibit higher DOT1L and H3K79me2 than ALDH1-. DOT1L maintains MYC expression and self-renewal in ALDH1+ cells. Global profiling revealed that DOT1L governs oxidative phosphorylation, cMyc targets, DNA damage response, and WNT activation in ALDH1+ but not in ALDH1- cells. EPZ-5676 reduced tumorspheres and ALDH1+ cells in vitro and decreased tumor-initiating stem cells and metastasis in xenografts generated from ALDH1+ but not ALDH1- populations in vivo. EPZ-5676 significantly reduced growth in vivo of one of two TNBC PDX tested and decreased clonogenic 3D growth of two other PDX-derived organoid cultures. CONCLUSIONS DOT1L emerges as a key CSC regulator in TNBC. Present data support further clinical investigation of DOT1L inhibitors to target stem cell-enriched TNBC.
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Affiliation(s)
- Hetakshi Kurani
- Braman Family Breast Cancer Institute at Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida.,Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida.,Breast Cancer Program, Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington, District of Columbia
| | - Seyedeh Fatemeh Razavipour
- Breast Cancer Program, Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington, District of Columbia
| | - Kuzhuvelil B. Harikumar
- Braman Family Breast Cancer Institute at Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida.,Cancer Research Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India
| | - Matthew Dunworth
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Andrew J. Ewald
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Cancer Invasion and Metastasis Program, Sidney Kimmel Comprehensive Cancer Center, and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Apsra Nasir
- Breast Cancer Program, Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington, District of Columbia
| | - Gray Pearson
- Breast Cancer Program, Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington, District of Columbia
| | - Derek Van Booven
- John P. Hussman Institute of Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Zhiqun Zhou
- Braman Family Breast Cancer Institute at Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Diana Azzam
- Department of Environmental Health Sciences, Florida International University, Miami, Florida
| | - Claes Wahlestedt
- Center for Therapeutic Innovation, Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, Florida
| | - Joyce Slingerland
- Breast Cancer Program, Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington, District of Columbia.,Corresponding Author: Joyce Slingerland, Lombardi Comprehensive Cancer Center, Georgetown University, New Research Building, Room E212, 3970 Reservoir Road NW, Washington, DC 20007. Phone: 305-898-9910; E-mail:
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11
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Spina E, Simundza J, Incassati A, Chandramouli A, Kugler MC, Lin Z, Khodadadi-Jamayran A, Watson CJ, Cowin P. Gpr125 is a unifying hallmark of multiple mammary progenitors coupled to tumor latency. Nat Commun 2022; 13:1421. [PMID: 35302059 PMCID: PMC8931046 DOI: 10.1038/s41467-022-28937-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/16/2022] [Indexed: 12/15/2022] Open
Abstract
Gpr125 is an orphan G-protein coupled receptor, with homology to cell adhesion and axonal guidance factors, that is implicated in planar polarity and control of cell movements. By lineage tracing we demonstrate that Gpr125 is a highly specific marker of bipotent mammary stem cells in the embryo and of multiple long-lived unipotent basal mammary progenitors in perinatal and postnatal glands. Nipple-proximal Gpr125+ cells express a transcriptomic profile indicative of chemo-repulsion and cell movement, whereas Gpr125+ cells concentrated at invasive ductal tips display a hybrid epithelial-mesenchymal phenotype and are equipped to bind chemokine and growth factors and secrete a promigratory matrix. Gpr125 progenitors acquire bipotency in the context of transplantation and cancer and are greatly expanded and massed at the pushing margins of short latency MMTV-Wnt1 tumors. High Gpr125 expression identifies patients with particularly poor outcome within the basal breast cancer subtype highlighting its potential utility as a factor to stratify risk. Gpr125 has emerged as a specific marker of mammary stem cells and basal progenitors. Here they show that Gpr125 cells congregate at ductal tips during morphogenesis and amass at tumor margins, and that high Gpr125 predicts early tumor onset and poor outcome in basal breast cancer.
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Affiliation(s)
- Elena Spina
- Department of Cell Biology, New York University School of Medicine, New York, USA.
| | - Julia Simundza
- Department of Cell Biology, New York University School of Medicine, New York, USA
| | - Angela Incassati
- Department of Cell Biology, New York University School of Medicine, New York, USA
| | - Anupama Chandramouli
- Department of Cell Biology, New York University School of Medicine, New York, USA.,Department of Dermatology, New York University School of Medicine, New York, USA
| | - Matthias C Kugler
- Division of Pulmonary and Critical Care Medicine, New York University School of Medicine, New York, USA
| | - Ziyan Lin
- Department of Applied Bioinformatics, New York University School of Medicine, New York, USA
| | | | | | - Pamela Cowin
- Department of Cell Biology, New York University School of Medicine, New York, USA. .,Department of Dermatology, New York University School of Medicine, New York, USA.
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12
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Dey A, Kundu M, Das S, Jena BC, Mandal M. Understanding the function and regulation of Sox2 for its therapeutic potential in breast cancer. Biochim Biophys Acta Rev Cancer 2022; 1877:188692. [PMID: 35122882 DOI: 10.1016/j.bbcan.2022.188692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/11/2022] [Accepted: 01/28/2022] [Indexed: 12/12/2022]
Abstract
Sox family of transcriptional factors play essential functions in development and are implicated in multiple clinical disorders, including cancer. Sox2 being their most prominent member and performing a critical role in reprogramming differentiated adult cells to an embryonic phenotype is frequently upregulated in multiple cancers. High Sox2 levels are detected in breast tumor tissues and correlate with a worse prognosis. In addition, Sox2 expression is connected with resistance to conventional anticancer therapy. Together, it can be said that inhibiting Sox2 expression can reduce the malignant features associated with breast cancer, including invasion, migration, proliferation, stemness, and chemoresistance. This review highlights the critical roles played by the Sox gene family members in initiating or suppressing breast tumor development, while primarily focusing on Sox2 and its role in breast tumor initiation, maintenance, and progression, elucidates the probable mechanisms that control its activity, and puts forward potential therapeutic strategies to inhibit its expression.
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Affiliation(s)
- Ankita Dey
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur (IIT Kharagpur), Kharagpur, West Bengal, India..
| | - Moumita Kundu
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur (IIT Kharagpur), Kharagpur, West Bengal, India..
| | - Subhayan Das
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur (IIT Kharagpur), Kharagpur, West Bengal, India..
| | - Bikash Chandra Jena
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur (IIT Kharagpur), Kharagpur, West Bengal, India..
| | - Mahitosh Mandal
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur (IIT Kharagpur), Kharagpur, West Bengal, India..
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13
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ATPR regulates human mantle cell lymphoma cells differentiation via SOX11/CyclinD1/Rb/E2F1. Cell Signal 2022; 93:110280. [DOI: 10.1016/j.cellsig.2022.110280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/01/2022] [Accepted: 02/04/2022] [Indexed: 11/20/2022]
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14
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Yu L, Dong Y, Xue J, Xu S, Wang G, Kuang D, Duan Y. SOX11 is a sensitive and specific marker for pulmonary high-grade neuroendocrine tumors. Diagn Pathol 2022; 17:2. [PMID: 34996493 PMCID: PMC8742448 DOI: 10.1186/s13000-021-01186-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 12/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Synaptophysin (SYN), chromogranin A (CGA), CD56 and insulinoma-associated protein 1 (INSM1) are proposed neuroendocrine (NE) markers used for diagnosis of pulmonary NE tumors. These NE markers have been identified in subsets of non-NE tumors requiring differential diagnosis, thus we sought to explore new NE markers. METHODS We evaluated the immunohistochemical expression of SOX11, a transcription factor involved in neurogenesis, in pulmonary NE tumors and large cell carcinomas (LCCs). RESULTS We found that SOX11 showed a sensitivity similar to INSM1 and CGA, and less than SYN and CD56 in small cell lung carcinomas (SCLCs) and large cell neuroendocrine carcinomas (LCNECs). While SOX11 is more specific than the other four markers for diagnosis of high-grade neuroendocrine carcinomas (HG-NECs) because 1) None of LCCs (0/63), the most challenging non-NE tumor type for differential diagnosis due to overlapped morphology with LCNECs displayed SOX11 positivity. While expression of at least one of SYN, CGA, CD56 or INSM1 was identified in approximately 60% (18/30) of LCCs. 2) SOX11 was only expressed in 1 of 37 carcinoid tumors in contrast to diffuse expression of SYN, CGA, CD56 and INSM1. In HG-NECs, we noticed that SOX11 was a good complementary marker for SCLC diagnosis as it was positive in 7 of 18 SYN-/CGA-/CD56- SCLCs and 3 of 8 SYN-/CGA-/CD56-/INSM1- SCLCs, and SOX11 positivity in 4 of 6 SYN-/CGA-/CD56- cases previously diagnosed as LCCs with NE morphology provides additional evidence of NE differentiation for reclassification into LCNECs, which was further confirmed by electromicroscopical identification of neurosecretory granules. We also found SOX11 expression cannot predict the prognosis in patients with HG-NECs. CONCLUSIONS Therefore, SOX11 is a useful complementary transcriptional NE marker for diagnosis and differential diagnosis of SCLC and LCNEC.
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Affiliation(s)
- Lu Yu
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, People's Republic of China.,Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, People's Republic of China
| | - Yuting Dong
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, People's Republic of China.,Department of Pathology, School of Basic Medical Science, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Jin Xue
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, People's Republic of China.,Department of Pathology, School of Basic Medical Science, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Sanpeng Xu
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, People's Republic of China.,Department of Pathology, School of Basic Medical Science, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Guoping Wang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, People's Republic of China.,Department of Pathology, School of Basic Medical Science, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Dong Kuang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, People's Republic of China. .,Department of Pathology, School of Basic Medical Science, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China.
| | - Yaqi Duan
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, People's Republic of China. .,Department of Pathology, School of Basic Medical Science, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China.
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15
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Tian Y, Wang L, Zhang Y, Li L, Fei Y, Zhang X, Lin G. Association between miR-212-3p and SOX11, and the effects of miR-212-3p on cell proliferation and migration in mantle cell lymphoma. Oncol Lett 2021; 22:709. [PMID: 34457064 PMCID: PMC8358606 DOI: 10.3892/ol.2021.12970] [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: 07/23/2020] [Accepted: 05/21/2021] [Indexed: 01/01/2023] Open
Abstract
To the best of our knowledge, the effect of miR-212-3p on sex-determining region Y-box 11 (SOX11) expression has not been previously investigated and how this effect affects cell proliferation and migration in lymphoma remains unclear. The present study aimed to assess the association between microRNA-212-3p (miR-212-3p) and SOX11, and the effects of miR-212-3p on cell proliferation and migration in mantle cell lymphoma. Cancer tissue and corresponding paracancerous tissue samples were collected from 65 patients with mantle cell lymphoma. The mRNA expression levels of miR-212-3p and SOX11 were analyzed using quantitative PCR, and SOX11 protein expression was determined using western blotting. Following transfection, the miR-212-3p mimic group exhibited a significantly lower SOX11 mRNA and protein expression than the miR-NC group. After 48–72 h of transfection, cell proliferation in the miR-212-3p mimic group was significantly lower than that in the miR-NC group. Furthermore, the miR-212-3p mimic group exhibited significantly lower cell invasion and significantly higher apoptosis than the miR-NC group. The current results suggested that miR-212-3p inhibited lymphoma cell proliferation and migration, and promoted their apoptosis by specifically regulating SOX11. Therefore, miR-212-3p may serve as a novel therapeutic target and marker for lymphoma.
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Affiliation(s)
- Yuyang Tian
- Department of Hematology, Hainan Cancer Hospital, Haikou, Hainan 571000, P.R. China
| | - Li Wang
- Department of Hematology, Huai'an Hospital Affiliated to Xuzhou Medical College and Huai'an Second People's Hospital, Huai'an, Jiangsu 223002, P.R. China
| | - Yanming Zhang
- Department of Hematology, Huai'an Hospital Affiliated to Xuzhou Medical College and Huai'an Second People's Hospital, Huai'an, Jiangsu 223002, P.R. China
| | - Lianqiao Li
- Department of Hematology, Hainan Cancer Hospital, Haikou, Hainan 571000, P.R. China
| | - Yingying Fei
- Department of Radiotherapy, Huai'an Hospital Affiliated to Xuzhou Medical College and Huai'an Second People's Hospital, Huai'an, Jiangsu 223002, P.R. China
| | - Xingxia Zhang
- Department of Hematology, Huai'an Hospital Affiliated to Xuzhou Medical College and Huai'an Second People's Hospital, Huai'an, Jiangsu 223002, P.R. China
| | - Guoqiang Lin
- Department of Hematology, Huai'an Hospital Affiliated to Xuzhou Medical College and Huai'an Second People's Hospital, Huai'an, Jiangsu 223002, P.R. China
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16
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Seok J, Gil M, Dayem AA, Saha SK, Cho SG. Multi-Omics Analysis of SOX4, SOX11, and SOX12 Expression and the Associated Pathways in Human Cancers. J Pers Med 2021; 11:jpm11080823. [PMID: 34442467 PMCID: PMC8400412 DOI: 10.3390/jpm11080823] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/06/2021] [Accepted: 08/20/2021] [Indexed: 01/08/2023] Open
Abstract
The Sry-related HMG BOX (SOX) gene family encodes transcription factors containing highly conserved high-mobility group domains that bind to the minor groove in DNA. Although some SOX genes are known to be associated with tumorigenesis and cancer progression, their expression and prognostic value have not been systematically studied. We performed multi-omic analysis to investigate the expression of SOX genes in human cancers. Expression and phylogenetic tree analyses of the SOX gene family revealed that the expression of three closely related SOX members, SOX4, SOX11, and SOX12, was increased in multiple cancers. Expression, mutation, and alteration of the three SOX members were evaluated using the Oncomine and cBioPortal databases, and the correlation between these genes and clinical outcomes in various cancers was examined using the Kaplan–Meier, PrognoScan, and R2 database analyses. The genes commonly correlated with the three SOX members were categorized in key pathways related to the cell cycle, mitosis, immune system, and cancer progression in liver cancer and sarcoma. Additionally, functional protein partners with three SOX proteins and their probable signaling pathways were explored using the STRING database. This study suggests the prognostic value of the expression of three SOX genes and their associated pathways in various human cancers.
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Affiliation(s)
| | | | | | | | - Ssang-Goo Cho
- Correspondence: ; Tel.: +82-2-450-4207 or +82-2-444-4207
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17
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Jatiani SS, Christie S, Leshchenko VV, Jain R, Kapoor A, Bisignano P, Lee C, Kaniskan HÜ, Edwards D, Meng F, Laganà A, Youssef Y, Wiestner A, Alinari L, Jin J, Filizola M, Aggarwal AK, Parekh S. SOX11 Inhibitors Are Cytotoxic in Mantle Cell Lymphoma. Clin Cancer Res 2021; 27:4652-4663. [PMID: 34158358 PMCID: PMC8364871 DOI: 10.1158/1078-0432.ccr-20-5039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/19/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Mantle cell lymphoma (MCL) is a fatal subtype of non-Hodgkin lymphoma. SOX11 transcription factor is overexpressed in the majority of nodal MCL. We have previously reported that B cell-specific overexpression of SOX11 promotes MCL pathogenesis via critically increasing BCR signaling in vivo. SOX11 is an attractive target for MCL therapy; however, no small-molecule inhibitor of SOX11 has been identified to date. Although transcription factors are generally considered undruggable, the ability of SOX11 to bind to the minor groove of DNA led us to hypothesize that there may exist cavities at the protein-DNA interface that are amenable to targeting by small molecules. EXPERIMENTAL DESIGN Using a combination of in silico predictions and experimental validations, we report here the discovery of three structurally related compounds (SOX11i) that bind SOX11, perturb its interaction with DNA, and effect SOX11-specific anti-MCL cytotoxicity. RESULTS We find mechanistic validation of on-target activity of these SOX11i in the inhibition of BCR signaling and the transcriptional modulation of SOX11 target genes, specifically, in SOX11-expressing MCL cells. One of the three SOX11i exhibits relatively superior in vitro activity and displays cytotoxic synergy with ibrutinib in SOX11-expressing MCL cells. Importantly, this SOX11i induces cytotoxicity specifically in SOX11-positive ibrutinib-resistant MCL patient samples and inhibits Bruton tyrosine kinase phosphorylation in a xenograft mouse model derived from one of these subjects. CONCLUSIONS Taken together, our results provide a foundation for therapeutically targeting SOX11 in MCL by a novel class of small molecules.
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Affiliation(s)
- Shashidhar S Jatiani
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Stephanie Christie
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Violetta V Leshchenko
- Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rinku Jain
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Abhijeet Kapoor
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Paola Bisignano
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Clement Lee
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - H Ümit Kaniskan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Donna Edwards
- Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Fanye Meng
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alessandro Laganà
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Youssef Youssef
- Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Adrian Wiestner
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland
| | - Lapo Alinari
- Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Jian Jin
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Aneel K Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Samir Parekh
- Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
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18
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Sun Q, Peng Y, Liu J. A reference-free approach for cell type classification with scRNA-seq. iScience 2021; 24:102855. [PMID: 34381979 PMCID: PMC8335627 DOI: 10.1016/j.isci.2021.102855] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/07/2021] [Accepted: 07/08/2021] [Indexed: 11/29/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has become a revolutionary technology to characterize cells under different biological conditions. Unlike bulk RNA-seq, gene expression from scRNA-seq is highly sparse due to limited sequencing depth per cell. This is worsened by tossing away a significant portion of reads that attribute to gene quantification. To overcome data sparsity and fully utilize original reads, we propose scSimClassify, a reference-free and alignment-free approach to classify cell types with k-mer level features. The compressed k-mer groups (CKGs), identified by the simhash method, contain k-mers with similar abundance profiles and serve as the cells’ features. Our experiments demonstrate that CKG features lend themselves to better performance than gene expression features in scRNA-seq classification accuracy in the majority of experimental cases. Because CKGs are derived from raw reads without alignment to reference genome, scSimClassify offers an effective alternative to existing methods especially when reference genome is incomplete or insufficient to represent subject genomes. Compressed k-mer groups (CKGs) are used to classify cell types without references CKGs are competitive to gene expression features for cell type classification CKGs are associated with genes sharing gene specific k-mers
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Affiliation(s)
- Qi Sun
- Department of Computer Science, University of Kentucky, Lexington, KY, 40508, USA
| | - Yifan Peng
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jinze Liu
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, USA
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19
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Wang T, Shao W, Huang Z, Tang H, Zhang J, Ding Z, Huang K. MOGONET integrates multi-omics data using graph convolutional networks allowing patient classification and biomarker identification. Nat Commun 2021; 12:3445. [PMID: 34103512 PMCID: PMC8187432 DOI: 10.1038/s41467-021-23774-w] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 05/04/2021] [Indexed: 12/18/2022] Open
Abstract
To fully utilize the advances in omics technologies and achieve a more comprehensive understanding of human diseases, novel computational methods are required for integrative analysis of multiple types of omics data. Here, we present a novel multi-omics integrative method named Multi-Omics Graph cOnvolutional NETworks (MOGONET) for biomedical classification. MOGONET jointly explores omics-specific learning and cross-omics correlation learning for effective multi-omics data classification. We demonstrate that MOGONET outperforms other state-of-the-art supervised multi-omics integrative analysis approaches from different biomedical classification applications using mRNA expression data, DNA methylation data, and microRNA expression data. Furthermore, MOGONET can identify important biomarkers from different omics data types related to the investigated biomedical problems.
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Affiliation(s)
- Tongxin Wang
- Department of Computer Science, Indiana University Bloomington, Bloomington, IN, USA
| | - Wei Shao
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Zhi Huang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, USA
| | - Haixu Tang
- Department of Computer Science, Indiana University Bloomington, Bloomington, IN, USA
| | - Jie Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Zhengming Ding
- Department of Computer Science, Tulane University, New Orleans, LA, USA.
| | - Kun Huang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA.
- Regenstrief Institute, Indianapolis, IN, USA.
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20
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Beleaua MA, Jung I, Braicu C, Milutin D, Gurzu S. SOX11, SOX10 and MITF Gene Interaction: A Possible Diagnostic Tool in Malignant Melanoma. Life (Basel) 2021; 11:life11040281. [PMID: 33801642 PMCID: PMC8065671 DOI: 10.3390/life11040281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/24/2022] Open
Abstract
Malignant melanoma (MM) is a highly heterogenic tumor whose histological diagnosis might be difficult. This study aimed to investigate the diagnostic and prognostic utility of the conventional pan-melanoma cocktail members (HMB-45, melan-A and tyrosinase), in conjunction with SOX10 and SOX11 immunohistochemical (IHC) expression. In 105 consecutive cases of MMs and 44 of naevi, the IHC examination was performed using the five-abovementioned markers, along with microphthalmia transcription factor (MITF), S100, and Ki67. Correlation with the clinicopathological factors and a long-term follow-up was also done. Survival analysis was performed with Kaplan–Meier curves and compared with TCGA public datasets. None of the 44 naevi expressed SOX11, but its positivity was seen in 52 MMs (49.52%), being directly correlated with lymphovascular invasion, the Ki67 index, and SOX10 expression. HMB-45, SOX10, and tyrosinase, but not melan-A, proved to differentiate the naevi from MMs successfully, with high specificity. Triple MITF/SOX10/SOX11 co-expression was seen in 9 out of 15 negative conventional pan-melanoma-cocktail cases. The independent prognostic value was proved for the conventional pan-melanoma cocktail (triple positivity for HMB-45, melan-A, and tyrosinase) and, independently for HMB-45 and tyrosinase, but not for melan-A, SOX10, or SOX11. As consequence, to differentiate MMs from benign naevi, melan-A should be substituted by SOX10 in the conventional cocktail. Although the conventional pan-melanoma cocktail, along with S100 can be used for the identification of melanocytic origin of tumor cells and predicting prognosis of MMs, the conventional-adapted cocktail (triple positivity for HMB-45, SOX10, and tyrosinase) has a slightly higher diagnostic specificity. SOX11 can be added to identify the aggressive MMs with risk for lymphatic dissemination and the presence of circulating tumor cells.
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Affiliation(s)
- Marius-Alexandru Beleaua
- Department of Pathology, Clinical County Emergency Hospital, Targu-Mures, Romania, 540139 Targu Mures, Romania; (M.-A.B.); (D.M.)
- Department of Pathology, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology, 38 Gheorghe Marinescu Street, 540139 Targu Mures, Romania;
| | - Ioan Jung
- Department of Pathology, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology, 38 Gheorghe Marinescu Street, 540139 Targu Mures, Romania;
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania;
- Research Center (CCAMF), George Emil Palade University of Medicine, Pharmacy, Sciences and Technology, 540139 Targu Mures, Romania
| | - Doina Milutin
- Department of Pathology, Clinical County Emergency Hospital, Targu-Mures, Romania, 540139 Targu Mures, Romania; (M.-A.B.); (D.M.)
| | - Simona Gurzu
- Department of Pathology, Clinical County Emergency Hospital, Targu-Mures, Romania, 540139 Targu Mures, Romania; (M.-A.B.); (D.M.)
- Department of Pathology, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology, 38 Gheorghe Marinescu Street, 540139 Targu Mures, Romania;
- Research Center (CCAMF), George Emil Palade University of Medicine, Pharmacy, Sciences and Technology, 540139 Targu Mures, Romania
- Correspondence: ; Tel.: +40-745-673550; Fax: +40-265-210407
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21
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Liu Y, Guo W. SOX factors as cell-state regulators in the mammary gland and breast cancer. Semin Cell Dev Biol 2021; 114:126-133. [PMID: 33583737 DOI: 10.1016/j.semcdb.2021.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 01/17/2021] [Accepted: 01/17/2021] [Indexed: 12/27/2022]
Abstract
Emerging evidence has shown that several SOX family transcription factors are key regulators of stem/progenitor cell fates in the mammary gland. These cell-fate regulators are often upregulated in breast cancer and contribute to tumor initiation and progression. They induce lineage plasticity and the epithelial-mesenchymal transition, which promotes tumor invasion, metastasis, and therapeutic resistance. SOX factors act through modulating multiple oncogenic signaling pathways in breast cancer. In addition to the cell-autonomous functions, new evidence suggests they can shape the tumor immune microenvironment. Here, we will review the molecular and functional evidence linking SOX factors with mammary gland development and discuss how these cell-fate regulators are co-opted in breast cancer.
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Affiliation(s)
- Yu Liu
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Wenjun Guo
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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22
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Sun N, Gao P, Li Y, Yan Z, Peng Z, Zhang Y, Han F, Qi X. Screening and Identification of Key Common and Specific Genes and Their Prognostic Roles in Different Molecular Subtypes of Breast Cancer. Front Mol Biosci 2021; 8:619110. [PMID: 33644115 PMCID: PMC7905399 DOI: 10.3389/fmolb.2021.619110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/08/2021] [Indexed: 01/27/2023] Open
Abstract
Breast cancer is one of the most common cancers. Although the present molecular classification improves the treatment effect and prognosis of breast cancer, the heterogeneity of the molecular subtype remains very complex, and the applicability and effectiveness of treatment methods are still limited leading to poorer patient prognosis than expected. Further identification of more refined molecular typing based on gene expression profile will yield better understanding of the heterogeneity, improving treatment effects and prolonging prognosis of patients. Here, we downloaded the mRNA expression profiles and corresponding clinical data of patients with breast cancer from public databases and performed typical molecular typing using PAM50 (Prediction Analysis of Microarray 50) method. Comparative analyses were performed to screen the common and specific differentially expressed genes (DEGs) between cancer and corresponding para-cancerous tissues in each breast cancer subtype. The GO and KEGG analyses of the DEGs were performed to enrich the common and specific functional progress and signaling pathway involved in breast cancer subtypes. A total of 38 key common and specific DEGs were identified and selected based on the validated results, GO/KEGG enrichments, and the priority of expression, including four common DEGs and 34 specific DEGs in different subtypes. The prognostic value of these key common and specific DEGs was further analyzed to obtain useful potential markers in clinic. Finally, the potential roles and the specific prognostic values of the common and specific DEGs were speculated and summarized in total breast cancer and different subtype breast cancer based on the results of these analyses. The findings of our study provide the basis of more refined molecular typing of breast cancer, potential new therapeutic targets and prognostic markers for different breast cancer subtypes
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Affiliation(s)
- Na Sun
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Pingping Gao
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Yanling Li
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Zexuan Yan
- Institute of Pathology and Southwest Cancer Center, Key Laboratory of the Ministry of Education, Southwest Hospital, Army Medical University, Chongqing, China
| | - Zaihui Peng
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Yi Zhang
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Fei Han
- Institute of Toxicology, College of Preventive Medicine, Army Medical University, Chongqing, China
| | - Xiaowei Qi
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
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23
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MiR-211 determines brain metastasis specificity through SOX11/NGN2 axis in triple-negative breast cancer. Oncogene 2021; 40:1737-1751. [PMID: 33536579 PMCID: PMC7932919 DOI: 10.1038/s41388-021-01654-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 12/11/2020] [Accepted: 01/13/2021] [Indexed: 11/08/2022]
Abstract
Brian metastasis, which is diagnosed in 30% of triple-negative breast cancer (TNBC) patients with metastasis, causes poor survival outcomes. Growing evidence has characterized miRNAs involving in breast cancer brain metastasis; however, currently, there is a lack of prognostic plasma-based indicator for brain metastasis. In this study, high level of miR-211 can act as brain metastatic prognostic marker in vivo. High miR-211 drives early and specific brain colonization through enhancing trans-blood-brain barrier (BBB) migration, BBB adherence, and stemness properties of tumor cells and causes poor survival in vivo. SOX11 and NGN2 are the downstream targets of miR-211 and negatively regulate miR-211-mediated TNBC brain metastasis in vitro and in vivo. Most importantly, high miR-211 is correlated with poor survival and brain metastasis in TNBC patients. Our findings suggest that miR-211 may be used as an indicator for TNBC brain metastasis.
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24
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Ni M, Sun W, Li Y, Ding L, Lin W, Peng H, Zheng Q, Sun J, Li J, Liu H, Yang Y, Xu L, Zhang G. Sox11 Modified Tendon-Derived Stem Cells Promote the Repair of Osteonecrosis of Femoral Head. Cell Transplant 2021; 30:9636897211053870. [PMID: 34699265 PMCID: PMC8552377 DOI: 10.1177/09636897211053870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/26/2021] [Accepted: 09/29/2021] [Indexed: 11/23/2022] Open
Abstract
Osteonecrosis of the femoral head (ONFH) is a leading cause of mobility impairment which may lead to a total hip replacement. Recent studies have found tendon derived stem cells (TDSCs) might be an ideal cell source for musculoskeletal tissue regeneration. And our previous study has shown Sox11 could promote osteogenesis of bone marrow-derived MSCs. However, the effect of TDSCs or Sox11 over-expressing TDSCs (TDSCs-Sox11) on bone regeneration in ONFH has not been investigated. In the present study, TDSCs were infected with AAV carrying Sox11 or empty vector. We showed that Sox11 could promote the proliferation and osteogenic differentiation of TDSCs, as well as angiogenesis in vitro. The western blot analysis showed that Sox11 could activate the PI3K/Akt signaling pathway to promote osteogenesis of TDSCs. Finally, using a rabbit model of hormone-induced ONFH, our result demonstrated that local administration of TDSCs or TDSCs overexpressing Sox11 could accelerate bone regeneration in necrotic femoral heads, and TDSCs overexpressing Sox11 showed better effects. TDSCs over-expressing Sox11 might be a promising cell source for stem cell therapy to promote bone regeneration, such as ONFH, fracture, bone defect, and so on.
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Affiliation(s)
- Ming Ni
- Department of Orthopedics, the First Medical Center, Chinese PLA General Hospital, Beijing, P.R. China
- Contributed equally as first authors
| | - Weiwei Sun
- Department of Anesthesiology, the First Medical Center, Chinese People’s Liberation Army (PLA) General Hospital, Beijing, P.R. China
- Contributed equally as first authors
| | - Yucong Li
- Department of Orthopedics and Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Lingli Ding
- Lingnan Medical Research Center, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weiping Lin
- Department of Orthopedics and Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Haiwen Peng
- Department of Orthopedics, the First Medical Center, Chinese PLA General Hospital, Beijing, P.R. China
| | - Qingyuan Zheng
- Department of Orthopedics, the First Medical Center, Chinese PLA General Hospital, Beijing, P.R. China
| | - Jingyang Sun
- Department of Orthopedics, the First Medical Center, Chinese PLA General Hospital, Beijing, P.R. China
| | - Juncheng Li
- Department of Orthopedics, the First Medical Center, Chinese PLA General Hospital, Beijing, P.R. China
| | - Hao Liu
- Department of Orthopedics, the First Medical Center, Chinese PLA General Hospital, Beijing, P.R. China
| | - Yi Yang
- Central Laboratory, Department of Cardiology, Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Liangliang Xu
- Lingnan Medical Research Center, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Guoqiang Zhang
- Department of Orthopedics, the First Medical Center, Chinese PLA General Hospital, Beijing, P.R. China
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25
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Xu J, Zhang J, Li L, Mao J, You T, Li Y. SOX12 expression is associated with progression and poor prognosis in human breast cancer. Am J Transl Res 2020; 12:8162-8174. [PMID: 33437389 PMCID: PMC7791485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/19/2020] [Indexed: 06/12/2023]
Abstract
The sex-determining region Y-box 12 (SOX12) is implicated in several oncogenic signaling pathways of multiple types of cancer; however, the biological effects of SOX12 on breast cancer has yet to be elucidated. Here, we assessed SOX12 expression using real-time quantitative PCR in 142 pairs of breast cancer and adjacent normal tissues (ANTs) and immunohistochemistry in 524 breast cancer and 147 ANTs. The effects of SOX12 on breast cancer progression, clinicopathological variables, and prognostic value were then investigated. SOX12 expression was markedly elevated in breast cancer tissues relative to that in ANTs at both mRNA and protein levels. Positive SOX12 expression was correlated to tumor size (P = 0.005), estrogen receptor (ER) (P = 0.018) and human epidermal growth factor receptor (HER2) (P = 0.004) status, lymph node metastasis (P < 0.001), and the tumor-node-metastasis (TNM) stage (P < 0.001). Notably, the positive rate of SOX12 expression gradually increased with breast cancer progression. Multivariate analysis indicated that SOX12 was an independent prognostic factor for overall survival (OS, P = 0.023) and distant metastasis-free survival (DMFS, P = 0.012). Subgroup analysis revealed that luminal and HER2 patients with positive SOX12 expression had a shorter OS period than those with negative SOX12 expression. Moreover, SOX12 expression was associated with a high risk of distant metastasis in invasive carcinoma with the lymph node metastasis subgroup. In summary, SOX12 correlates with progression and poor prognosis in human breast cancer, suggesting that SOX12 is a potential target for breast cancer treatment and warrants further functional research.
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Affiliation(s)
- Junming Xu
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Jinyan Zhang
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Lei Li
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Jieqi Mao
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
| | - Tiangeng You
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical UniversityShanghai, China
| | - Yang Li
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai, China
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26
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Tsang SM, Oliemuller E, Howard BA. Regulatory roles for SOX11 in development, stem cells and cancer. Semin Cancer Biol 2020; 67:3-11. [DOI: 10.1016/j.semcancer.2020.06.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 05/29/2020] [Accepted: 06/12/2020] [Indexed: 12/17/2022]
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27
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Prediction of genome-wide effects of single nucleotide variants on transcription factor binding. Sci Rep 2020; 10:17632. [PMID: 33077858 PMCID: PMC7572467 DOI: 10.1038/s41598-020-74793-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/07/2020] [Indexed: 11/26/2022] Open
Abstract
Single nucleotide variants (SNVs) located in transcriptional regulatory regions can result in gene expression changes that lead to adaptive or detrimental phenotypic outcomes. Here, we predict gain or loss of binding sites for 741 transcription factors (TFs) across the human genome. We calculated ‘gainability’ and ‘disruptability’ scores for each TF that represent the likelihood of binding sites being created or disrupted, respectively. We found that functional cis-eQTL SNVs are more likely to alter TF binding sites than rare SNVs in the human population. In addition, we show that cancer somatic mutations have different effects on TF binding sites from different TF families on a cancer-type basis. Finally, we discuss the relationship between these results and cancer mutational signatures. Altogether, we provide a blueprint to study the impact of SNVs derived from genetic variation or disease association on TF binding to gene regulatory regions.
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28
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Xiao Y, Xie Q, Qin Q, Liang Y, Lin H, Zeng D. Upregulation of SOX11 enhances tamoxifen resistance and promotes epithelial-to-mesenchymal transition via slug in MCF-7 breast cancer cells. J Cell Physiol 2020; 235:7295-7308. [PMID: 32043610 PMCID: PMC7496966 DOI: 10.1002/jcp.29629] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/30/2020] [Indexed: 02/05/2023]
Abstract
Resistance to tamoxifen remains a prominent conundrum in the therapy of hormone-sensitive breast cancer. Also, the molecular underpinnings leading to tamoxifen resistance remain unclear. In the present study, we utilized the Gene Expression Omnibus database to identify that SOX11 might exert a pivotal function in conferring tamoxifen resistance of breast cancer. SOX11 was found to be markedly upregulated at both the messenger RNA and protein levels in established MCF-7-Tam-R cells compared to the parental counterparts. Moreover, SOX11 was able to activate the transcription of slug via binding to its promoter, resulting in promoting the progress of epithelial-to-mesenchymal transition and suppressing the expression of ESR1. Downregulating SOX11 expression can restore the sensitivity to 4-hydroxytamoxifen in MCF-7-Tam-R cells. Survival analysis from large sample datasets indicated that SOX11 was closely related to poorer survival in patients with breast cancer. These findings suggest a novel feature of SOX11 in contributing to tamoxifen resistance. Hence, targeting SOX11 could be a potential therapeutic strategy to tackle tamoxifen resistance in breast cancer.
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Affiliation(s)
- Yingsheng Xiao
- Department of Thyroid SurgeryShantou Central HospitalShantouChina
| | - Qin Xie
- Department of Medical OncologyCancer Hospital of Shantou University Medical CollegeShantouChina
- Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast CancerShantouGuangdongChina
| | - Qingsong Qin
- Laboratory of Human Virology and OncologyShantou University Medical CollegeShantouChina
| | - Yuanke Liang
- Department of Thyroid and Breast SurgeryThe First Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
| | - Haoyu Lin
- Department of Thyroid and Breast SurgeryThe First Affiliated Hospital of Shantou University Medical CollegeShantouGuangdongChina
| | - De Zeng
- Department of Medical OncologyCancer Hospital of Shantou University Medical CollegeShantouChina
- Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast CancerShantouGuangdongChina
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29
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Hirokawa YS, Kanayama K, Kagaya M, Shimojo N, Uchida K, Imai H, Ishii K, Watanabe M. SOX11-induced decrease in vimentin and an increase in prostate cancer cell migration attributed to cofilin activity. Exp Mol Pathol 2020; 117:104542. [PMID: 32971115 DOI: 10.1016/j.yexmp.2020.104542] [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: 08/06/2019] [Revised: 08/13/2020] [Accepted: 09/18/2020] [Indexed: 12/23/2022]
Abstract
SOX11 is a transcription factor in the SOX family of genes that regulate multiple cellular events by influencing the expression of key genes in developmental, physiological, and tumorigenic cells. To elucidate the role of SOX11 in prostate cancer cells, PC-3 prostate cancer cells were cloned (S6 and S9 cells) to highly express SOX11. We demonstrated that both S6 and S9 lose vimentin expression, acquiring epithelial marker proteins, which indicates the Epithelial state phenotype. S6 and S9 cells have cancer-promoting characteristics that include higher migratory properties compared with control cells. The mechanisms that are responsible for the enhanced migration are cofilin activity and keratin 18 expression. TCGA (The Cancer Genome Atlas) dataset analysis revealed that metastatic prostate cancer tumors tend to have more SOX11 gene amplification compared with primary tumors. These results suggest the tumor promotive role and epithelial protein induction of SOX11 in prostate cancer cell.
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Affiliation(s)
- Yoshifumi S Hirokawa
- Department of Oncologic Pathology, Mie University Graduate School of Medicine, Tsu, Mie 514-8507, Japan.
| | - Kazuki Kanayama
- Department of Clinical Nutrition, Suzuka University of Medical Science, Suzuka, Mie 510-0293, Japan
| | - Michiko Kagaya
- Department of Oncologic Pathology, Mie University Graduate School of Medicine, Tsu, Mie 514-8507, Japan
| | - Naoshi Shimojo
- Department of Pathology and Matrix Biology, Mie University Graduate School of Medicine, Tsu, Mie 514-8507, Japan
| | - Katsunori Uchida
- Department of Oncologic Pathology, Mie University Graduate School of Medicine, Tsu, Mie 514-8507, Japan
| | - Hiroshi Imai
- Pathology Division, Mie University Hospital, Tsu, Mie 514-8507, Japan
| | - Kenichiro Ishii
- Department of Oncologic Pathology, Mie University Graduate School of Medicine, Tsu, Mie 514-8507, Japan
| | - Masatoshi Watanabe
- Department of Oncologic Pathology, Mie University Graduate School of Medicine, Tsu, Mie 514-8507, Japan
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30
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Oliemuller E, Newman R, Tsang SM, Foo S, Muirhead G, Noor F, Haider S, Aurrekoetxea-Rodríguez I, Vivanco MDM, Howard BA. SOX11 promotes epithelial/mesenchymal hybrid state and alters tropism of invasive breast cancer cells. eLife 2020; 9:58374. [PMID: 32909943 PMCID: PMC7518891 DOI: 10.7554/elife.58374] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022] Open
Abstract
SOX11 is an embryonic mammary epithelial marker that is normally silenced prior to birth. High SOX11 levels in breast tumours are significantly associated with distant metastasis and poor outcome in breast cancer patients. Here, we show that SOX11 confers distinct features to ER-negative DCIS.com breast cancer cells, leading to populations enriched with highly plastic hybrid epithelial/mesenchymal cells, which display invasive features and alterations in metastatic tropism when xenografted into mice. We found that SOX11+DCIS tumour cells metastasize to brain and bone at greater frequency and to lungs at lower frequency compared to cells with lower SOX11 levels. High levels of SOX11 leads to the expression of markers associated with mesenchymal state and embryonic cellular phenotypes. Our results suggest that SOX11 may be a potential biomarker for breast tumours with elevated risk of developing metastases and may require more aggressive therapies.
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Affiliation(s)
- Erik Oliemuller
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Richard Newman
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Siu Man Tsang
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Shane Foo
- Translational Immunotherapy Team, Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom
| | - Gareth Muirhead
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Farzana Noor
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | | | - Maria dM Vivanco
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Beatrice A Howard
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
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31
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Ma Y, Shepherd J, Zhao D, Bollu LR, Tahaney WM, Hill J, Zhang Y, Mazumdar A, Brown PH. SOX9 Is Essential for Triple-Negative Breast Cancer Cell Survival and Metastasis. Mol Cancer Res 2020; 18:1825-1838. [PMID: 32661114 DOI: 10.1158/1541-7786.mcr-19-0311] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/21/2020] [Accepted: 07/06/2020] [Indexed: 12/16/2022]
Abstract
Triple-negative breast cancer (TNBC) has the worst prognosis of all breast cancers, and lacks effective targeted treatment strategies. Previously, we identified 33 transcription factors highly expressed in TNBC. Here, we focused on six sex determining region Y-related HMG-box (SOX) transcription factors (SOX4, 6, 8, 9, 10, and 11) highly expressed in TNBCs. Our siRNA screening assay demonstrated that SOX9 knockdown suppressed TNBC cell growth and invasion in vitro. Thus, we hypothesized that SOX9 is an important regulator of breast cancer survival and metastasis, and demonstrated that knockout of SOX9 reduced breast tumor growth and lung metastasis in vivo. In addition, we found that loss of SOX9 induced profound apoptosis, with only a slight impairment of G1 to S progression within the cell cycle, and that SOX9 directly regulates genes controlling apoptosis. On the basis of published CHIP-seq data, we demonstrated that SOX9 binds to the promoter of apoptosis-regulating genes (tnfrsf1b, fadd, tnfrsf10a, tnfrsf10b, and ripk1), and represses their expression. SOX9 knockdown upregulates these genes, consistent with the induction of apoptosis. Analysis of available CHIP-seq data showed that SOX9 binds to the promoters of several epithelial-mesenchymal transition (EMT)- and metastasis-regulating genes. Using CHIP assays, we demonstrated that SOX9 directly binds the promoters of genes involved in EMT (vim, cldn1, ctnnb1, and zeb1) and that SOX9 knockdown suppresses the expression of these genes. IMPLICATIONS: Our studies identified the SOX9 protein as a "master regulator" of breast cancer cell survival and metastasis, and provide preclinical rationale to develop SOX9 inhibitors for the treatment of women with metastatic triple-negative breast cancer.
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Affiliation(s)
- Yanxia Ma
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Jonathan Shepherd
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Dekuang Zhao
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Lakshmi Reddy Bollu
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - William M Tahaney
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Houston, Texas.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Jamal Hill
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Yun Zhang
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Abhijit Mazumdar
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Powel H Brown
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Houston, Texas. .,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas.,Department of Breast Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
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Terkelsen T, Russo F, Gromov P, Haakensen VD, Brunak S, Gromova I, Krogh A, Papaleo E. Secreted breast tumor interstitial fluid microRNAs and their target genes are associated with triple-negative breast cancer, tumor grade, and immune infiltration. Breast Cancer Res 2020; 22:73. [PMID: 32605588 PMCID: PMC7329449 DOI: 10.1186/s13058-020-01295-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 05/14/2020] [Indexed: 12/21/2022] Open
Abstract
Background Studies on tumor-secreted microRNAs point to a functional role of these in cellular communication and reprogramming of the tumor microenvironment. Uptake of tumor-secreted microRNAs by neighboring cells may result in the silencing of mRNA targets and, in turn, modulation of the transcriptome. Studying miRNAs externalized from tumors could improve cancer patient diagnosis and disease monitoring and help to pinpoint which miRNA-gene interactions are central for tumor properties such as invasiveness and metastasis. Methods Using a bioinformatics approach, we analyzed the profiles of secreted tumor and normal interstitial fluid (IF) microRNAs, from women with breast cancer (BC). We carried out differential abundance analysis (DAA), to obtain miRNAs, which were enriched or depleted in IFs, from patients with different clinical traits. Subsequently, miRNA family enrichment analysis was performed to assess whether any families were over-represented in the specific sets. We identified dysregulated genes in tumor tissues from the same cohort of patients and constructed weighted gene co-expression networks, to extract sets of co-expressed genes and co-abundant miRNAs. Lastly, we integrated miRNAs and mRNAs to obtain interaction networks and supported our findings using prediction tools and cancer gene databases. Results Network analysis showed co-expressed genes and miRNA regulators, associated with tumor lymphocyte infiltration. All of the genes were involved in immune system processes, and many had previously been associated with cancer immunity. A subset of these, BTLA, CXCL13, IL7R, LAMP3, and LTB, was linked to the presence of tertiary lymphoid structures and high endothelial venules within tumors. Co-abundant tumor interstitial fluid miRNAs within this network, including miR-146a and miR-494, were annotated as negative regulators of immune-stimulatory responses. One co-expression network encompassed differences between BC subtypes. Genes differentially co-expressed between luminal B and triple-negative breast cancer (TNBC) were connected with sphingolipid metabolism and predicted to be co-regulated by miR-23a. Co-expressed genes and TIF miRNAs associated with tumor grade were BTRC, CHST1, miR-10a/b, miR-107, miR-301a, and miR-454. Conclusion Integration of IF miRNAs and mRNAs unveiled networks associated with patient clinicopathological traits, and underlined molecular mechanisms, specific to BC sub-groups. Our results highlight the benefits of an integrative approach to biomarker discovery, placing secreted miRNAs within a biological context.
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Affiliation(s)
- Thilde Terkelsen
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Francesco Russo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pavel Gromov
- Breast Cancer Biology Group, Genome Integrity Unit, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Vilde Drageset Haakensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Irina Gromova
- Breast Cancer Biology Group, Genome Integrity Unit, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Anders Krogh
- Unit of Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark. .,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Yeh CM, Lin CW, Lu HJ, Chuang CY, Chou CH, Yang SF, Chen MK. Impact of SRY-Box Transcription Factor 11 Gene Polymorphisms on Oral Cancer Risk and Clinicopathologic Characteristics. Int J Mol Sci 2020; 21:ijms21124468. [PMID: 32586027 PMCID: PMC7352504 DOI: 10.3390/ijms21124468] [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] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/22/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Oral cancer is among the most common cancers worldwide and has become a major global health problem because of its relatively high morbidity and mortality rates. The sex-determining region on the Y-chromosome-related high-mobility-group box (SOX) transcription factor 11 (SOX11) plays a key role in human development and differentiation and is frequently increased in various human cancers. However, the clinical significance of SOX11 polymorphisms in oral cancer and their association with oral cancer risk are unclear. In this study, we included 1196 patients with oral cancer and 1200 controls. Real-time polymerase chain reaction was applied to analyze three SOX11 single-nucleotide polymorphisms (rs77996007, rs66465560, and rs68114586). Our results shown that SOX11 polymorphisms carriers with betel quid chewing were found to have an 8.38- to 9.23-fold risk to have oral cancer compared to SOX11 wild-type carriers without betel quid chewing. Furthermore, oral cancer patients who carried SOX11 rs77996007 “TC + CC” variants were significantly associated with large tumor size (AOR, 1.324; 95% CI, 1.047–1.674; p = 0.019). Moreover, a database analysis using the Cancer Genome Atlas suggested that SOX11 mRNA expression was high during the tumor development process. In conclusion, our results suggest that SOX11 rs77996007 is involved in oral cancer progression and clinical characteristics.
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Affiliation(s)
- Chia-Ming Yeh
- Institute of Medicine, Chung Shan Medical University, Taichung 402, Taiwan; (C.-M.Y.); (C.-H.C.)
- Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
- Department of Otorhinolaryngology-Head and Neck Surgery, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Chiao-Wen Lin
- Institute of Oral Sciences, Chung Shan Medical University, Taichung 402, Taiwan;
- Department of Dentistry, Chung Shan Medical University Hospital, Taichung 402, Taiwan
| | - Hsueh-Ju Lu
- Division of Medical Oncology, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung 402, Taiwan;
- School of Medicine, Chung Shan Medical University, Taichung 402, Taiwan;
| | - Chun-Yi Chuang
- School of Medicine, Chung Shan Medical University, Taichung 402, Taiwan;
- Department of Otolaryngology, Chung Shan Medical University Hospital, Taichung 402, Taiwan
| | - Chia-Hsuan Chou
- Institute of Medicine, Chung Shan Medical University, Taichung 402, Taiwan; (C.-M.Y.); (C.-H.C.)
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung 402, Taiwan; (C.-M.Y.); (C.-H.C.)
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung 402, Taiwan
- Correspondence: (S.-F.Y.); (M.-K.C.)
| | - Mu-Kuan Chen
- Institute of Medicine, Chung Shan Medical University, Taichung 402, Taiwan; (C.-M.Y.); (C.-H.C.)
- Cancer Research Center, Changhua Christian Hospital, Changhua 500, Taiwan
- Department of Otorhinolaryngology-Head and Neck Surgery, Changhua Christian Hospital, Changhua 500, Taiwan
- Correspondence: (S.-F.Y.); (M.-K.C.)
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34
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Silva TC, Coetzee SG, Gull N, Yao L, Hazelett DJ, Noushmehr H, Lin DC, Berman BP. ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. Bioinformatics 2020; 35:1974-1977. [PMID: 30364927 PMCID: PMC6546131 DOI: 10.1093/bioinformatics/bty902] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/01/2018] [Accepted: 10/25/2018] [Indexed: 12/18/2022] Open
Abstract
Motivation DNA methylation has been used to identify functional changes at transcriptional enhancers and other cis-regulatory modules (CRMs) in tumors and other disease tissues. Our R/Bioconductor package ELMER (Enhancer Linking by Methylation/Expression Relationships) provides a systematic approach that reconstructs altered gene regulatory networks (GRNs) by combining enhancer methylation and gene expression data derived from the same sample set. Results We present a completely revised version 2 of ELMER that provides numerous new features including an optional web-based interface and a new Supervised Analysis mode to use pre-defined sample groupings. We show that Supervised mode significantly increases statistical power and identifies additional GRNs and associated Master Regulators, such as SOX11 and KLF5 in Basal-like breast cancer. Availability and implementation ELMER v.2 is available as an R/Bioconductor package at http://bioconductor.org/packages/ELMER/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tiago C Silva
- Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Simon G Coetzee
- Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Nicole Gull
- Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lijing Yao
- Bioinformatics Research & Early Development, Roche Sequencing Solutions, Belmont, CA, USA
| | - Dennis J Hazelett
- Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Houtan Noushmehr
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.,Department of Neurosurgery, Henry Ford Hospital, Detroit, MI, USA
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Benjamin P Berman
- Department of Biomedical Sciences, Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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35
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Exploring the role of post-translational modulators of transcription factors in triple-negative breast cancer gene expression. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
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36
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Su X, Long Q, Bo J, Shi Y, Zhao LN, Lin Y, Luo Q, Ghazanfar S, Zhang C, Liu Q, Wang L, He K, He J, Cui X, Yang JYH, Han ZG, Yang G, Sha JJ. Mutational and transcriptomic landscapes of a rare human prostate basal cell carcinoma. Prostate 2020; 80:508-517. [PMID: 32119131 DOI: 10.1002/pros.23965] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/11/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND As a rare subtype of prostate carcinoma, basal cell carcinoma (BCC) has not been studied extensively and thus lacks systematic molecular characterization. METHODS Here, we applied single-cell genomic amplification and RNA-Seq to a specimen of human prostate BCC (CK34βE12+ /P63+ /PAP- /PSA- ). The mutational landscape was obtained via whole exome sequencing of the amplification mixture of 49 single cells, and the transcriptomes of 69 single cells were also obtained. RESULTS The five putative driver genes mutated in BCC are CASC5, NUTM1, PTPRC, KMT2C, and TBX3, and the top three nucleotide substitutions are C>T, T>C, and C>A, similar to common prostate cancer. The distribution of the variant allele frequency values indicated that these single cells are from the same tumor clone. The 69 single cells were clustered into tumor, stromal, and immune cells based on their global transcriptomic profiles. The tumor cells specifically express basal cell markers like KRT5, KRT14, and KRT23 and epithelial markers EPCAM, CDH1, and CD24. The transcription factor covariance network analysis showed that the BCC tumor cells have distinct regulatory networks. By comparison with current prostate cancer datasets, we found that some of the bulk samples exhibit basal cell signatures. Interestingly, at single-cell resolution the gene expression patterns of prostate BCC tumor cells show uniqueness compared with that of common prostate cancer-derived circulating tumor cells. CONCLUSIONS This study, for the first time, discloses the comprehensive mutational and transcriptomic landscapes of prostate BCC, which lays a foundation for the understanding of its tumorigenesis mechanism and provides new insights into prostate cancers in general.
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Affiliation(s)
- Xianbin Su
- Department of Urology and Key Laboratory of Systems Biomedicine (Ministry of Education), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qi Long
- Key Laboratory for Regenerative Medicine (Ministry of Education), School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Juanjie Bo
- Department of Urology and Key Laboratory of Systems Biomedicine (Ministry of Education), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Li-Nan Zhao
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yingxin Lin
- Department of Statistics, Charles Perkins Center and School of Mathematics and Statistics, The University of Sydney, Sydney, Australia
| | - Qing Luo
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shila Ghazanfar
- Department of Statistics, Charles Perkins Center and School of Mathematics and Statistics, The University of Sydney, Sydney, Australia
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Chao Zhang
- Department of Urology, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Qiang Liu
- Department of Pathology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lan Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kunyan He
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jian He
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaofang Cui
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jean Y H Yang
- Department of Statistics, Charles Perkins Center and School of Mathematics and Statistics, The University of Sydney, Sydney, Australia
| | - Ze-Guang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guoliang Yang
- Department of Urology and Key Laboratory of Systems Biomedicine (Ministry of Education), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jian-Jun Sha
- Department of Urology and Key Laboratory of Systems Biomedicine (Ministry of Education), Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Grönroos T, Mäkinen A, Laukkanen S, Mehtonen J, Nikkilä A, Oksa L, Rounioja S, Marincevic-Zuniga Y, Nordlund J, Pohjolainen V, Paavonen T, Heinäniemi M, Lohi O. Clinicopathological features and prognostic value of SOX11 in childhood acute lymphoblastic leukemia. Sci Rep 2020; 10:2043. [PMID: 32029838 PMCID: PMC7005266 DOI: 10.1038/s41598-020-58970-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/22/2020] [Indexed: 12/11/2022] Open
Abstract
Acute lymphoblastic leukemia is marked by aberrant transcriptional features that alter cell differentiation, self-renewal, and proliferative features. We sought to identify the transcription factors exhibiting altered and subtype-specific expression patterns in B-ALL and report here that SOX11, a developmental and neuronal transcription factor, is aberrantly expressed in the ETV6-RUNX1 and TCF3-PBX1 subtypes of acute B-cell leukemias. We show that a high expression of SOX11 leads to alterations of gene expression that are typically associated with cell adhesion, migration, and differentiation. A high expression is associated with DNA hypomethylation at the SOX11 locus and a favorable outcome. The results indicate that SOX11 expression marks a group of patients with good outcomes and thereby prompts further study of its use as a biomarker.
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Affiliation(s)
- Toni Grönroos
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
| | - Artturi Mäkinen
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Saara Laukkanen
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Juha Mehtonen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Atte Nikkilä
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Laura Oksa
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Samuli Rounioja
- Fimlab Laboratories, Department of Hematology, Tampere University Hospital, Tampere, Finland
| | - Yanara Marincevic-Zuniga
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Virva Pohjolainen
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Timo Paavonen
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland.,Department of Pathology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Olli Lohi
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Department of Pediatrics, Tampere University Hospital, Tampere, Finland
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38
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Umeh-Garcia M, Simion C, Ho PY, Batra N, Berg AL, Carraway KL, Yu A, Sweeney C. A Novel Bioengineered miR-127 Prodrug Suppresses the Growth and Metastatic Potential of Triple-Negative Breast Cancer Cells. Cancer Res 2019; 80:418-429. [PMID: 31694904 DOI: 10.1158/0008-5472.can-19-0656] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 09/21/2019] [Accepted: 11/01/2019] [Indexed: 12/31/2022]
Abstract
miR-127 is downregulated in breast cancer, where it has been shown to suppress the proliferation, migration, and invasion of breast cancer cells. In triple-negative breast cancer (TNBC), miR-127 downregulation correlates with decreased disease-free and overall patient survival. Tumor suppressor miRNAs may hold therapeutic promise but progress has been limited by several factors, including the lability and high cost of miRNA mimics. Here, we take a novel approach to produce a miR-127 prodrug (miR-127PD), which we demonstrate is processed to mature, functional miR-127-3p in TNBC tumor cells. miR-127PD decreased the viability and motility of TNBC cells, sensitized TNBC cells to chemotherapy, and restricted the TNBC stem cell population. Furthermore, systemic delivery of miR-127PD suppressed tumor growth of MDA-MB-231 and MDA-MB-468 TNBC cells and spontaneous metastasis of MDA-MB-231 cells. In addition, CERK, NANOS1, FOXO6, SOX11, SOX12, FASN, and SUSD2 were identified as novel, functionally important targets of miR-127. In conclusion, our study demonstrates that miR-127 functions as a tumor and metastasis suppressor in TNBC and that delivery of miR-127 may hold promise as a novel therapy. SIGNIFICANCE: Exogenous administration of miR-127, which is functionally activated in target cells, inhibits growth and spontaneous metastasis of triple-negative breast cancer.
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Affiliation(s)
- Maxine Umeh-Garcia
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California
| | - Catalina Simion
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California
| | - Pui-Yan Ho
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California
| | - Neelu Batra
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California
| | - Anastasia L Berg
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California
| | - Kermit L Carraway
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California
| | - Aiming Yu
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California
| | - Colleen Sweeney
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, California.
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Mehta GA, Khanna P, Gatza ML. Emerging Role of SOX Proteins in Breast Cancer Development and Maintenance. J Mammary Gland Biol Neoplasia 2019; 24:213-230. [PMID: 31069617 PMCID: PMC6790170 DOI: 10.1007/s10911-019-09430-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/21/2019] [Indexed: 12/26/2022] Open
Abstract
The SOX genes encode a family of more than 20 transcription factors that are critical regulators of embryogenesis and developmental processes and, when aberrantly expressed, have been shown to contribute to tumor development and progression in both an oncogenic and tumor suppressive role. Increasing evidence demonstrates that the SOX proteins play essential roles in multiple cellular processes that mediate or contribute to oncogenic transformation and tumor progression. In the context of breast cancer, SOX proteins function both as oncogenes and tumor suppressors and have been shown to be associated with tumor stage and grade and poor prognosis. Experimental evidence demonstrates that a subset of SOX proteins regulate critical aspects of breast cancer biology including cancer stemness and multiple signaling pathways leading to altered cell proliferation, survival, and tumor development; EMT, cell migration and metastasis; as well as other tumor associated characteristics. This review will summarize the role of SOX family members as important mediators of tumorigenesis in breast cancer, with an emphasis on the triple negative or basal-like subtype of breast cancer, as well as examine the therapeutic potential of these genes and their downstream targets.
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Affiliation(s)
- Gaurav A Mehta
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, CINJ 4558, New Brunswick, NJ, 08903, USA
- Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Pooja Khanna
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, CINJ 4558, New Brunswick, NJ, 08903, USA
- Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Michael L Gatza
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, CINJ 4558, New Brunswick, NJ, 08903, USA.
- Department of Radiation Oncology, Robert Wood Johnson Medical School, New Brunswick, NJ, USA.
- Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.
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40
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Yang Z, Jiang S, Lu C, Ji T, Yang W, Li T, Lv J, Hu W, Yang Y, Jin Z. SOX11: friend or foe in tumor prevention and carcinogenesis? Ther Adv Med Oncol 2019; 11:1758835919853449. [PMID: 31210798 PMCID: PMC6547177 DOI: 10.1177/1758835919853449] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 04/26/2019] [Indexed: 12/12/2022] Open
Abstract
Sex-determining region Y-related high-mobility-group box transcription factor 11
(SOX11) is an essential member of the SOX transcription factors and has been
highlighted as an important regulator in embryogenesis. SOX11 studies have only
recently shifted focus from its role in embryogenesis and development to its
function in disease. In particular, the role of SOX11 in carcinogenesis has
become of major interest in the field. SOX11 expression is elevated in a wide
variety of tumors. In many cancers, dysfunctional expression of SOX11 has been
correlated with increased cancer cell survival, inhibited cell differentiation,
and tumor progression through the induction of metastasis and angiogenesis.
Nevertheless, in a limited number of malignancies, SOX11 has also been
identified to function as a tumor suppressor. Herein, we review the correlation
between the expression of SOX11 and tumor behaviors. We also summarize the
mechanisms underlying the regulation of SOX11 expression and activity in
pathological conditions. In particular, we focus on the pathological processes
of cancer targeted by SOX11 and discuss whether SOX11 is protective or
detrimental during tumor progression. Moreover, SOX11 is highlighted as a
clinical biomarker for the diagnosis and prognosis of various human cancer. The
information reviewed here should assist in future experimental designs and
emphasize the potential of SOX11 as a therapeutic target for cancer.
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Affiliation(s)
- Zhi Yang
- Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Shuai Jiang
- Department of Aerospace Medicine, The Fourth Military Medical University, Xi'an, China
| | - Chenxi Lu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences, Northwest University, Xi'an, China
| | - Ting Ji
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences, Northwest University, Xi'an, China
| | - Wenwen Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences, Northwest University, Xi'an, China
| | - Tian Li
- Department of Biomedical Engineering, The Fourth Military Medical University, Xi'an, China
| | - Jianjun Lv
- Department of Biomedical Engineering, The Fourth Military Medical University, Xi'an, China
| | - Wei Hu
- Department of Immunology, The Fourth Military Medical University, Xi'an, China
| | - Yang Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Faculty of Life Sciences, Northwest University, Xi'an, China
| | - Zhenxiao Jin
- Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, 127 Changle West Road, Xi'an 710032, China
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Phillips L, Gill AJ, Baxter RC. Novel Prognostic Markers in Triple-Negative Breast Cancer Discovered by MALDI-Mass Spectrometry Imaging. Front Oncol 2019; 9:379. [PMID: 31139569 PMCID: PMC6527753 DOI: 10.3389/fonc.2019.00379] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 04/23/2019] [Indexed: 11/29/2022] Open
Abstract
There are no widely-accepted prognostic markers currently available to predict outcomes in patients with triple-negative breast cancer (TNBC), and no targeted therapies with confirmed benefit. We have used MALDI mass spectrometry imaging (MSI) of tryptic peptides to compare regions of cancer and benign tissue in 10 formalin-fixed, paraffin-embedded sections of TNBC tumors. Proteins were identified by reference to a peptide library constructed by LC-MALDI-MS/MS analyses of the same tissues. The prognostic significance of proteins that distinguished between cancer and benign regions was estimated by Kaplan-Meier analysis of their gene expression from public databases. Among peptides that distinguished between cancer and benign tissue in at least 3 tissues with a ROC area under the curve >0.7, 14 represented proteins identified from the reference library, including proteins not previously associated with breast cancer. Initial network analysis using the STRING database showed no obvious functional relationships except among collagen subunits COL1A1, COL1A2, and COL63A, but manual curation, including the addition of EGFR to the analysis, revealed a unique network connecting 10 of the 14 proteins. Kaplan-Meier survival analysis to examine the relationship between tumor expression of genes encoding the 14 proteins, and recurrence-free survival (RFS) in patients with basal-like TNBC showed that, compared to low expression, high expression of nine of the genes was associated with significantly worse RFS, most with hazard ratios >2. In contrast, in estrogen receptor-positive tumors, high expression of these genes showed only low, or no, association with worse RFS. These proteins are proposed as putative markers of RFS in TNBC, and some may also be considered as possible targets for future therapies.
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Affiliation(s)
- Leo Phillips
- Hormones and Cancer Group, University of Sydney, Kolling Institute, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Anthony J Gill
- Cancer Diagnosis and Pathology Group, University of Sydney, Kolling Institute, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Robert C Baxter
- Hormones and Cancer Group, University of Sydney, Kolling Institute, Royal North Shore Hospital, St Leonards, NSW, Australia
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Shan T, Uyar DS, Wang LS, Mutch DG, Huang THM, Rader JS, Sheng X, Huang YW. SOX11 hypermethylation as a tumor biomarker in endometrial cancer. Biochimie 2019; 162:8-14. [PMID: 30935961 DOI: 10.1016/j.biochi.2019.03.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 03/27/2019] [Indexed: 01/24/2023]
Abstract
We previously reported that SOX4 is overexpressed in endometrial cancer and that it partially contributes to hypermethylation of miR-129-2 and miR-203. The current study seeks to identify methylation and expression levels of the SOX gene family in endometrial carcinomas. Methylation levels of the 16 SOX gene family members were measured by combining bisulfite restriction analysis (COBRA), MassARRAY, and pyrosequencing assays of cell lines and endometrial cancer samples. Gene expression was determined by RT-qPCR. The methylation level of the SOX11 locus was correlated with clinicopathologic factors in primary endometrial tumors and in TCGA endometrial cohort. It was also examined in DNA of serum and endometrial specimens from a longitudinal cohort of early stage endometrial cancer patients. COBRA assays indicated that hypermethylation of SOX1, SOX2, SOX11, SOX14, SOX15, SOX17, and SOX18 was present in endometrial cancer cell lines and not in the normal control. SOX11 expression was reactivated only by a DNA methylation inhibitor. Moreover, aberrant DNA methylation of SOX11 was detected in the majority of endometrioid endometrial carcinomas (n=114) and none of the 22 adjacent normal endometrial samples (P<0.0001). The methylation status of SOX11 associated significantly with microsatellite instability and MLH1 methylation in endometrial tumors (P<0.0001), and this finding was validated in TCGA endometrial cohort. Furthermore, SOX11 was not hypermethylated in serum DNA from early stage endometrial cancer patients. This study found that hypermethylation of SOX11 is common in endometrial carcinomas and strongly associates with microsatellite instability and MLH1 methylation.
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Affiliation(s)
- Tianjiao Shan
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA; Shandong Cancer Hospital Affiliated to Shandong University, Jinan, 250117, Shandong, China
| | - Denise S Uyar
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Li-Shu Wang
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - David G Mutch
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tim H-M Huang
- Department of Molecular Medicine and Cancer Therapy & Research Center, University of Texas Health Science Center, San Antonio, TX, 78229, USA
| | - Janet S Rader
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Xiugui Sheng
- Shandong Cancer Hospital Affiliated to Shandong University, Jinan, 250117, Shandong, China; National Cancer Center, National Clinical Research Center for Cancer and Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, Guangdong, 518116, China.
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
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The role of SOX family members in solid tumours and metastasis. Semin Cancer Biol 2019; 67:122-153. [PMID: 30914279 DOI: 10.1016/j.semcancer.2019.03.004] [Citation(s) in RCA: 212] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/07/2019] [Accepted: 03/21/2019] [Indexed: 02/07/2023]
Abstract
Cancer is a heavy burden for humans across the world with high morbidity and mortality. Transcription factors including sex determining region Y (SRY)-related high-mobility group (HMG) box (SOX) proteins are thought to be involved in the regulation of specific biological processes. The deregulation of gene expression programs can lead to cancer development. Here, we review the role of the SOX family in breast cancer, prostate cancer, renal cell carcinoma, thyroid cancer, brain tumours, gastrointestinal and lung tumours as well as the entailing therapeutic implications. The SOX family consists of more than 20 members that mediate DNA binding by the HMG domain and have regulatory functions in development, cell-fate decision, and differentiation. SOX2, SOX4, SOX5, SOX8, SOX9, and SOX18 are up-regulated in different cancer types and have been found to be associated with poor prognosis, while the up-regulation of SOX11 and SOX30 appears to be favourable for the outcome in other cancer types. SOX2, SOX4, SOX5 and other SOX members are involved in tumorigenesis, e.g. SOX2 is markedly up-regulated in chemotherapy resistant cells. The SoxF family (SOX7, SOX17, SOX18) plays an important role in angio- and lymphangiogenesis, with SOX18 seemingly being an attractive target for anti-angiogenic therapy and the treatment of metastatic disease in cancer. In summary, SOX transcription factors play an important role in cancer progression, including tumorigenesis, changes in the tumour microenvironment, and metastasis. Certain SOX proteins are potential molecular markers for cancer prognosis and putative potential therapeutic targets, but further investigations are required to understand their physiological functions.
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Liu Z, Zhong Y, Chen YJ, Chen H. SOX11 regulates apoptosis and cell cycle in hepatocellular carcinoma via Wnt/β-catenin signaling pathway. Biotechnol Appl Biochem 2018; 66:240-246. [PMID: 30517979 DOI: 10.1002/bab.1718] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/02/2018] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is the most common type of liver cancer with high mortality. Identifying key molecules involved in the regulation of HCC development is of great clinical significance. SOX11 is a transcription factor belonging to group C of Sry-related high mobility group box family whose abnormal expression is frequently seen in many kinds of human cancers. Here, we noted that the expression of SOX11 was decreased in human HCC tumors compared with that in matched normal tissues. Overexpression of SOX11 promoted growth inhibition and apoptosis in HCC cell line HuH-7. Mechanistically, SOX11 enhanced the expression of nemo-like kinase and the phosphorylation of TCF4, thereby blunting the activation of oncogenic Wnt/β-catenin signaling pathway in HuH-7 cells. Finally, SOX11 was also found to sensitize HuH-7 cells to chemotherapy drugs cisplatin and 5-fluorouraci. Therefore, our study identifies SOX11 as a potential tumor suppressor in HCC and may hopefully be beneficial for the clinical diagnosis or treatment of HCC.
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Affiliation(s)
- Zhi Liu
- Department of Hepatobiliary Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, People's Republic of China.,Institute of Hepatobiliary, Pancreatic and Intestinal Disease, North Sichuan Medical College, Nanchong, People's Republic of China
| | - Yang Zhong
- Department of Hepatobiliary Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, People's Republic of China.,Institute of Hepatobiliary, Pancreatic and Intestinal Disease, North Sichuan Medical College, Nanchong, People's Republic of China
| | - Yu Jian Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, People's Republic of China.,Institute of Hepatobiliary, Pancreatic and Intestinal Disease, North Sichuan Medical College, Nanchong, People's Republic of China
| | - Hui Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of North Sichuan Medical College, Nanchong, People's Republic of China.,Institute of Hepatobiliary, Pancreatic and Intestinal Disease, North Sichuan Medical College, Nanchong, People's Republic of China
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Regulation of SOX11 expression through CCND1 and STAT3 in mantle cell lymphoma. Blood 2018; 133:306-318. [PMID: 30530749 DOI: 10.1182/blood-2018-05-851667] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/30/2018] [Indexed: 12/26/2022] Open
Abstract
The neural transcription factor SOX11 is usually highly expressed in typical mantle cell lymphoma (MCL), but it is absent in the more indolent form of MCL. Despite being an important diagnostic marker for this hard-to-treat malignancy, the mechanisms of aberrant SOX11 expression are largely unknown. Herein, we describe 2 modes of SOX11 regulation by the cell-cycle regulator cyclin D1 (CCND1) and the signal transducer and activator of transcription 3 (STAT3). We found that ectopic expression of CCND1 in multiple human MCL cell lines resulted in increased SOX11 transcription, which correlated with increased acetylated histones H3K9 and H3K14 (H3K9/14Ac). Increased H3K9/14Ac and SOX11 expression was also observed after histone deacetylase 1 (HDAC1) or HDAC2 was depleted by RNA interference or inhibited by the HDAC inhibitor vorinostat. Mechanistically, we showed that CCND1 interacted with and sequestered HDAC1 and HDAC2 from the SOX11 locus, leading to SOX11 upregulation. Interestingly, our data revealed a potential inverse relationship between phosphorylated Y705 STAT3 and SOX11 expression in MCL cell lines, primary tumors, and patient-derived xenografts. Functionally, inactivation of STAT3 by inhibiting the upstream Janus kinase (JAK) 1 or JAK2 or by STAT3 knockdown was found to increase SOX11 expression, whereas interleukin-21 (IL-21)-induced STAT3 activation or overexpression of the constitutively active form of STAT3 decreased SOX11 expression. In addition, targeting SOX11 directly by RNA interference or indirectly by IL-21 treatment induced toxicity in SOX11+ MCL cells. Collectively, we demonstrate the involvement of CCND1 and STAT3 in the regulation of SOX11 expression, providing new insights and therapeutic implications in MCL.
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46
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Xu S, Dong Y, Huo Z, Yu L, Xue J, Wang G, Duan Y. SOX11: a potentially useful marker in surgical pathology: a systematic analysis of SOX11 expression in epithelial and non-epithelial tumours. Histopathology 2018; 74:391-405. [PMID: 30221780 DOI: 10.1111/his.13757] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 09/13/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Sanpeng Xu
- Institute of Pathology; Tongji Hospital; Huazhong University of Science and Technology; Wuhan China
| | - Yuting Dong
- Institute of Pathology; Tongji Hospital; Huazhong University of Science and Technology; Wuhan China
- Department of Pathology; School of Basic Medical Science; Huazhong University of Science and Technology; Wuhan China
| | - Zitian Huo
- Institute of Pathology; Tongji Hospital; Huazhong University of Science and Technology; Wuhan China
- Department of Pathology; School of Basic Medical Science; Huazhong University of Science and Technology; Wuhan China
| | - Lu Yu
- Institute of Pathology; Tongji Hospital; Huazhong University of Science and Technology; Wuhan China
- Department of Pathology; School of Basic Medical Science; Huazhong University of Science and Technology; Wuhan China
| | - Jin Xue
- Institute of Pathology; Tongji Hospital; Huazhong University of Science and Technology; Wuhan China
- Department of Pathology; School of Basic Medical Science; Huazhong University of Science and Technology; Wuhan China
| | - Guoping Wang
- Institute of Pathology; Tongji Hospital; Huazhong University of Science and Technology; Wuhan China
- Department of Pathology; School of Basic Medical Science; Huazhong University of Science and Technology; Wuhan China
| | - Yaqi Duan
- Institute of Pathology; Tongji Hospital; Huazhong University of Science and Technology; Wuhan China
- Department of Pathology; School of Basic Medical Science; Huazhong University of Science and Technology; Wuhan China
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47
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Lord M, Arvidsson G, Wasik AM, Christensson B, Wright AP, Grandien A, Sander B. Impact of Sox11 over-expression in Ba/F3 cells. Haematologica 2018; 103:e594-e597. [PMID: 29954934 DOI: 10.3324/haematol.2018.197467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Martin Lord
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital
| | - Gustav Arvidsson
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet
| | - Agata M Wasik
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital
| | - Birger Christensson
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital
| | - Anthony P Wright
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet
| | - Alf Grandien
- Department of Medicine, Center for Hematology and Regenerative Medicine (HERM), Karolinska Institutet, Stockholm, Sweden
| | - Birgitta Sander
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital
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48
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Early lineage segregation of multipotent embryonic mammary gland progenitors. Nat Cell Biol 2018; 20:666-676. [PMID: 29784918 PMCID: PMC5985933 DOI: 10.1038/s41556-018-0095-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/26/2018] [Indexed: 12/19/2022]
Abstract
The mammary gland (MG) is composed of basal cells (BCs) and luminal cells (LCs). While it is generally believed that MG arises from embryonic multipotent progenitors (EMPs), it remains unclear when lineage restriction occurs and what are the mechanisms responsible for the switch from multipotency to unipotency during MG morphogenesis. Here, we performed multicolor lineage tracing and assessed the fate of single progenitors and demonstrated the existence of a developmental switch from multipotency to unipotency during embryonic MG development. Molecular profiling and single cell RNA-seq revealed that EMPs express a unique hybrid basal and luminal signature and the factors associated with the different lineages. Sustained p63 expression in EMPs promotes unipotent BC fate and was sufficient to reprogram adult LCs into BCs by promoting an intermediate hybrid multipotent like state. Altogether, this study identifies the timing and the mechanisms mediating the early lineage segregation of multipotent progenitors during MG development.
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49
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Li M, Sun Q, Wang X. Transcriptional landscape of human cancers. Oncotarget 2018; 8:34534-34551. [PMID: 28427185 PMCID: PMC5470989 DOI: 10.18632/oncotarget.15837] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 02/08/2017] [Indexed: 12/21/2022] Open
Abstract
The homogeneity and heterogeneity in somatic mutations, copy number alterations and methylation across different cancer types have been extensively explored. However, the related exploration based on transcriptome data is lacking. In this study we explored gene expression profiles across 33 human cancer types using The Cancer Genome Atlas (TCGA) data. We identified consistently upregulated genes (such as E2F1, EZH2, FOXM1, MYBL2, PLK1, TTK, AURKA/B and BUB1) and consistently downregulated genes (such as SCARA5, MYOM1, NKAPL, PEG3, USP2, SLC5A7 and HMGCLL1) across various cancers. The dysregulation of these genes is likely to be associated with poor clinical outcomes in cancer. The dysregulated pathways commonly in cancers include cell cycle, DNA replication, repair, and recombination, Notch signaling, p53 signaling, Wnt signaling, TGFβ signaling, immune response etc. We also identified genes consistently upregulated or downregulated in highly-advanced cancers compared to lowly-advanced cancers. The highly (low) expressed genes in highly-advanced cancers are likely to have higher (lower) expression levels in cancers than in normal tissue, indicating that common gene expression perturbations drive cancer initiation and cancer progression. In addition, we identified a substantial number of genes exclusively dysregulated in a single cancer type or inconsistently dysregulated in different cancer types, demonstrating the intertumor heterogeneity. More importantly, we found a number of genes commonly dysregulated in various cancers such as PLP1, MYOM1, NKAPL and USP2 which were investigated in few cancer related studies, and thus represent our novel findings. Our study provides comprehensive portraits of transcriptional landscape of human cancers.
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Affiliation(s)
- Mengyuan Li
- School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Qingrong Sun
- School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaosheng Wang
- Department of Basic Medicine, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
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50
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Magne J, Jenvrin A, Chauchet A, Casasnovas O, Donzel A, Jego L, Aral B, Guy J, Nadal N, Vernerey D, Callier P, Garnache-Ottou F, Ferrand C. Potential added value of a RT-qPCR method of SOX 11 expression, in the context of a multidisciplinary diagnostic assessment of B cell malignancies. Exp Hematol Oncol 2018; 7:5. [PMID: 29484276 PMCID: PMC5819690 DOI: 10.1186/s40164-018-0097-6] [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: 11/14/2017] [Accepted: 02/02/2018] [Indexed: 01/24/2023] Open
Abstract
Background Expression of SRY [sex-determining region Y]-box11 (SOX11) is specific to mantle cell lymphoma (MCL) and contributes, in conjunction with immunoglobulin variable heavy chain gene mutation status, to the identification of two forms of this disease. Methods The aim of this report was firstly, to design an easy and suitable RT-qPCR method to quantify SOX11 mRNA expression in mantle cell lymphoma and other B cell malignancies with the proper reference gene; secondly, to define the best threshold of relative quantity of SOX11 mRNA in order to reach the best compromise between sensitivity and specificity. Results For best discrimination of MCL and non-MCL groups we determined an area under the curve (AUC) of 0.9750 and a threshold of 1.76 with 100% sensitivity and 88% specificity. AUC and threshold values of respectively 0.91/1.346 [87% sensitivity, 80% specificity] and 0.9525/1.7120 [100% sensitivity, 88% specificity] for GAPDH and RPLP0 respectively denote that the RPLP0 reference gene alone is sufficient for PCR housekeeping gene. Conclusion This work describes an RT-qPCR assay for SOX11 expression in order to better characterize MCL at diagnosis. Further studies on larger cohorts are needed to evaluate this molecular tool, especially for the follow-up of minimal residual disease. Electronic supplementary material The online version of this article (10.1186/s40164-018-0097-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julien Magne
- 1INSERM, UMR866, Faculté des Sciences de Santé, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Alizée Jenvrin
- INSERM, EFS BFC, UMR1098, Univ. Bourgogne Franche-Comté, Besançon, 25000 France
| | - Adrien Chauchet
- 3Department of Hematology, University Hospital of Besancon, 25000 Besançon, France
| | - Olivier Casasnovas
- 4Department of Hematology, University Hospital of Dijon, 21000 Dijon, France
| | - Anne Donzel
- 1INSERM, UMR866, Faculté des Sciences de Santé, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Laurence Jego
- 1INSERM, UMR866, Faculté des Sciences de Santé, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Bernard Aral
- 1INSERM, UMR866, Faculté des Sciences de Santé, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Julien Guy
- 1INSERM, UMR866, Faculté des Sciences de Santé, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Nathalie Nadal
- 1INSERM, UMR866, Faculté des Sciences de Santé, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Dewi Vernerey
- Univ. Bourgogne Franche-Comté, EA 3181, 25000 Besançon, France
| | - Patrick Callier
- 1INSERM, UMR866, Faculté des Sciences de Santé, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Christophe Ferrand
- INSERM, EFS BFC, UMR1098, Univ. Bourgogne Franche-Comté, Besançon, 25000 France.,Laboratoire de Thérapeutique Immuno-Moléculaire et cellulaire des cancers, INSERM UMR1098, Etablissement Français du Sang Bourgogne/Franche-Comté, 8, rue du Docteur Jean-François-Xavier Girod, 25020 Besançon, France
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