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Zhu E, Xie Q, Huang X, Zhang Z. Application of spatial omics in gastric cancer. Pathol Res Pract 2024; 262:155503. [PMID: 39128411 DOI: 10.1016/j.prp.2024.155503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 07/25/2024] [Accepted: 07/27/2024] [Indexed: 08/13/2024]
Abstract
Gastric cancer (GC), a globally prevalent and lethal malignancy, continues to be a key research focus. However, due to its considerable heterogeneity and complex pathogenesis, the treatment and diagnosis of gastric cancer still face significant challenges. With the rapid development of spatial omics technology, which provides insights into the spatial information within tumor tissues, it has emerged as a significant tool in gastric cancer research. This technology affords new insights into the pathology and molecular biology of gastric cancer for scientists. This review discusses recent advances in spatial omics technology for gastric cancer research, highlighting its applications in the tumor microenvironment (TME), tumor heterogeneity, tumor genesis and development mechanisms, and the identification of potential biomarkers and therapeutic targets. Moreover, this article highlights spatial omics' potential in precision medicine and summarizes existing challenges and future directions. It anticipates spatial omics' continuing impact on gastric cancer research, aiming to improve diagnostic and therapeutic approaches for patients. With this review, we aim to offer a comprehensive overview to scientists and clinicians in gastric cancer research, motivating further exploration and utilization of spatial omics technology. Our goal is to improve patient outcomes, including survival rates and quality of life.
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Affiliation(s)
- Erran Zhu
- Department of Clinical Medicine, Grade 20, Hengyang Medical College, University of South China, Hengyang, Hunan, 421001, China
| | - Qi Xie
- Department of Clinical Medicine, Grade 20, Hengyang Medical College, University of South China, Hengyang, Hunan, 421001, China
| | - Xinqi Huang
- Excellent Class, Clinical Medicine, Grade 20, Hengyang Medical College, University of South China, Hengyang, Hunan, 421001, China
| | - Zhiwei Zhang
- Cancer Research Institute of Hengyang Medical College, University of South China; Key Laboratory of Cancer Cellular and Molecular Pathology of Hunan; Department of Pathology, Department of Pathology of Hengyang Medical College, University of South China; The First Affiliated Hospital of University of South China, China.
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2
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Sicinska E, Kola VSR, Kerfoot JA, Taddei ML, Al-Ibraheemi A, Hsieh YH, Church AJ, Landesman-Bollag E, Landesman Y, Hemming ML. ASPSCR1::TFE3 Drives Alveolar Soft Part Sarcoma by Inducing Targetable Transcriptional Programs. Cancer Res 2024; 84:2247-2264. [PMID: 38657118 PMCID: PMC11250573 DOI: 10.1158/0008-5472.can-23-2115] [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: 07/15/2023] [Revised: 02/09/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024]
Abstract
Alveolar soft part sarcoma (ASPS) is a rare mesenchymal malignancy driven by the ASPSCR1::TFE3 fusion. A better understanding of the mechanisms by which this oncogenic transcriptional regulator drives cancer growth is needed to help identify potential therapeutic targets. In this study, we characterized the transcriptional and chromatin landscapes of ASPS tumors and preclinical models, identifying the essential role of ASPSCR1::TFE3 in tumor cell viability by regulating core transcriptional programs involved in cell proliferation, angiogenesis, and mitochondrial biology. ASPSCR1::TFE3 directly interacted with key epigenetic regulators at enhancers and promoters to support ASPS-associated transcription. Among the effector programs driven by ASPSCR1::TFE3, cell proliferation was driven by high levels of cyclin D1 expression. Disruption of cyclin D1/CDK4 signaling led to a loss of ASPS proliferative capacity, and combined inhibition of CDK4/6 and angiogenesis halted tumor growth in xenografts. These results define the ASPS oncogenic program, reveal mechanisms by which ASPSCR1::TFE3 controls tumor biology, and identify a strategy for therapeutically targeting tumor cell-intrinsic vulnerabilities. Significance: The ASPSCR1::TFE3 fusion propels the growth of alveolar soft part sarcoma by activating transcriptional programs that regulate proliferation, angiogenesis, mitochondrial biogenesis, and differentiation and can be therapeutically targeted to improve treatment.
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MESH Headings
- Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism
- Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics
- Sarcoma, Alveolar Soft Part/genetics
- Sarcoma, Alveolar Soft Part/pathology
- Sarcoma, Alveolar Soft Part/metabolism
- Humans
- Animals
- Mice
- Cell Proliferation/genetics
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Gene Expression Regulation, Neoplastic
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Cell Line, Tumor
- Xenograft Model Antitumor Assays
- Cyclin-Dependent Kinase 4/genetics
- Cyclin-Dependent Kinase 4/metabolism
- Cyclin-Dependent Kinase 4/antagonists & inhibitors
- Female
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/pathology
- Neovascularization, Pathologic/metabolism
- Intracellular Signaling Peptides and Proteins
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Affiliation(s)
- Ewa Sicinska
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Vijaya S R Kola
- Division of Hematology and Oncology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts
| | - Joseph A Kerfoot
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Madeleine L Taddei
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alyaa Al-Ibraheemi
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yi-Hsuan Hsieh
- Division of Hematology and Oncology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts
| | - Alanna J Church
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Esther Landesman-Bollag
- Department of Medicine, Section of Hematology and Oncology, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts
| | - Yosef Landesman
- Cure Alveolar Soft Part Sarcoma International, Brookline, Massachusetts
| | - Matthew L Hemming
- Division of Hematology and Oncology, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts
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3
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Gu Y, Chen G, Ning X. Homeobox Protein BarH-like 1 Promotes Gastric Cancer Progression by Activating Coiled-Coil Domain-Containing Protein 178. Dig Dis Sci 2024; 69:1182-1199. [PMID: 38358459 DOI: 10.1007/s10620-024-08312-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND Coiled-coil domain-containing protein 178 (CCDC178) has been revealed to exert metastasis-promoting properties in hepatocellular carcinoma, whereas its function in gastric cancer (GC) has not been fully understood. AIMS We evaluated its role in GC and the molecular mechanism. METHODS The differentially expressed genes in datasets related to GC metastasis were intersected with survival-related genes in GC, followed by prognostic significance prediction. Loss- and gain-of-function assays were conducted to examine the involvement of CCDC178, Homeobox protein BarH-like 1 (BARX1), and the extracellular signal-regulated kinase (ERK) pathway in GC cell malignant phenotype and the polarization of tumor-associated macrophages (TAM). The corresponding functions were verified in the in vivo animal experiment. RESULTS High CCDC178 expression predicted a poor prognosis for GC patients, and CCDC178 correlated significantly with macrophage infiltration in GC tissues. CCDC178 activated the ERK pathway in GC. Silencing of CCDC178 reduced the colony formation, migratory and invasive potential of GC cells, and the M2-like polarization of TAM, which was reversed by TBHQ (an ERK activator). BARX1 bound to the promoter region of CCDC178, thus inducing its transcriptional level. Silencing of BARX1 suppressed the M2-type polarization of TAM in vitro and in vivo, and CCDC178 mitigated the repressing role of BARX1 knockdown. CONCLUSIONS BARX1 activates the transcription of CCDC178 to induce the ERK pathway, thereby supporting macrophage recruitment and M2-like polarization in GC.
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Affiliation(s)
- Yue Gu
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang District, 150001, Harbin, Heilongjiang, People's Republic of China.
| | - Gang Chen
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang District, 150001, Harbin, Heilongjiang, People's Republic of China
| | - Xinwei Ning
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, No. 37, Yiyuan Street, Nangang District, 150001, Harbin, Heilongjiang, People's Republic of China
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4
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Zhou S, Abdihamid O, Tan F, Zhou H, Liu H, Li Z, Xiao S, Li B. KIT mutations and expression: current knowledge and new insights for overcoming IM resistance in GIST. Cell Commun Signal 2024; 22:153. [PMID: 38414063 PMCID: PMC10898159 DOI: 10.1186/s12964-023-01411-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/25/2023] [Indexed: 02/29/2024] Open
Abstract
Gastrointestinal stromal tumor (GIST) is the most common sarcoma located in gastrointestinal tract and derived from the interstitial cell of Cajal (ICC) lineage. Both ICC and GIST cells highly rely on KIT signal pathway. Clinically, about 80-90% of treatment-naive GIST patients harbor primary KIT mutations, and special KIT-targeted TKI, imatinib (IM) showing dramatic efficacy but resistance invariably occur, 90% of them was due to the second resistance mutations emerging within the KIT gene. Although there are multiple variants of KIT mutant which did not show complete uniform biologic characteristics, most of them have high KIT expression level. Notably, the high expression level of KIT gene is not correlated to its gene amplification. Recently, accumulating evidences strongly indicated that the gene coding, epigenetic regulation, and pre- or post- protein translation of KIT mutants in GIST were quite different from that of wild type (WT) KIT. In this review, we elucidate the biologic mechanism of KIT variants and update the underlying mechanism of the expression of KIT gene, which are exclusively regulated in GIST, providing a promising yet evidence-based therapeutic landscape and possible target for the conquer of IM resistance. Video Abstract.
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Affiliation(s)
- Shishan Zhou
- Division of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China, Xiangya road 87
| | - Omar Abdihamid
- Garissa Cancer Center, Garissa County Referral Hospital, Kismayu road, Garissa town, P.O BOX, 29-70100, Kenya
| | - Fengbo Tan
- Division of Surgery, Xiangya Hospital, Central South University, China, Hunan, Changsha
| | - Haiyan Zhou
- Division of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Heli Liu
- Division of Surgery, Xiangya Hospital, Central South University, China, Hunan, Changsha
| | - Zhi Li
- Center for Molecular Medicine of Xiangya Hospital, Collaborative Innovation Center for Cancer Medicine, Central South University, Changsha, Hunan, China, 410008
| | - Sheng Xiao
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, 410008, MA, USA
| | - Bin Li
- Division of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China, Xiangya road 87#.
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5
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Wang P, Yan J, Qiu H, Huang J, Yang Z, Shi Q, Yan C. A radiomics-clinical combined nomogram-based on non-enhanced CT for discriminating the risk stratification in GISTs. J Cancer Res Clin Oncol 2023; 149:12993-13003. [PMID: 37464150 DOI: 10.1007/s00432-023-05170-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/09/2023] [Indexed: 07/20/2023]
Abstract
PURPOSE To discriminate the risk stratification in gastrointestinal stromal tumors (GISTs) by preoperatively constructing a model of nonenhanced computed tomography (NECT). METHODS A total of 111 GISTs patients (77 in the training group and 34 in the validation Group) from two hospitals between 2015 and 2022 were collected retrospectively. One thousand and thirty-seven radiomics features were extracted from non-contract CT images, and the optimal radiomics signature was determined by univariate analysis and LASSO regression. The radiomics model was developed and validated from the ten optimal radiomics features by three methods. Covariates (clinical features, CT findings, and immunohistochemical characteristics) were collected to establish the clinical model, and both the radiomics features and the covariates were used to build the combined model. The effectiveness of the three models was evaluated by the Delong test. RESULTS The experimental results showed that the clinical models (75.3%, 70.6%), the radiomics models (79.2%, 79.4%) and the combined models (81.8%, 82.4%) all had high accuracy in predicting the pathological risk of GIST in both training and validation groups. The AUC values of the combined models were significantly higher in both the training groups (0.921 vs 0.822, p= 0.032) and the validation groups (0.913 vs 0.792, p= 0.019) than that of the clinical models. According to the calibration curve, the combined model nomogram is clinically useful. CONCLUSIONS The clinical-radiomics combined model and based on NECT performed well in discriminating the risk stratification in GISTs. As a quantitative technique, radiomics is capable of predicting the malignant potential and guiding treatment preoperatively.
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Affiliation(s)
- Peizhe Wang
- Department of Medical Imaging, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, Shandong, China
| | - Jingrui Yan
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Hui Qiu
- Department of Medical Imaging, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, Shandong, China
| | - Jingying Huang
- Department of Medical Imaging, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Zhe Yang
- Department of Medical Imaging, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, Shandong, China
| | - Qiang Shi
- Department of Medical Imaging, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, Shandong, China
| | - Chengxin Yan
- Department of Medical Imaging, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, Shandong, China.
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6
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Durand M, Brehaut V, Clement G, Kelemen Z, Macé J, Feil R, Duville G, Launay-Avon A, Roux CPL, Lunn JE, Roudier F, Krapp A. The Arabidopsis transcription factor NLP2 regulates early nitrate responses and integrates nitrate assimilation with energy and carbon skeleton supply. THE PLANT CELL 2023; 35:1429-1454. [PMID: 36752317 PMCID: PMC10118280 DOI: 10.1093/plcell/koad025] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Nitrate signaling improves plant growth under limited nitrate availability and, hence, optimal resource use for crop production. Whereas several transcriptional regulators of nitrate signaling have been identified, including the Arabidopsis thaliana transcription factor NIN-LIKE PROTEIN7 (NLP7), additional regulators are expected to fine-tune this pivotal physiological response. Here, we characterized Arabidopsis NLP2 as a top-tier transcriptional regulator of the early nitrate response gene regulatory network. NLP2 interacts with NLP7 in vivo and shares key molecular features such as nitrate-dependent nuclear localization, DNA-binding motif, and some target genes with NLP7. Genetic, genomic, and metabolic approaches revealed a specific role for NLP2 in the nitrate-dependent regulation of carbon and energy-related processes that likely influence plant growth under distinct nitrogen environments. Our findings highlight the complementarity and specificity of NLP2 and NLP7 in orchestrating a multitiered nitrate regulatory network that links nitrate assimilation with carbon and energy metabolism for efficient nitrogen use and biomass production.
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Affiliation(s)
- Mickaël Durand
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
- UMR CNRS 7267, EBI Ecologie et Biologie des Interactions, Université de Poitiers, Poitiers, France
| | - Virginie Brehaut
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
| | - Gilles Clement
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
| | - Zsolt Kelemen
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
| | - Julien Macé
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm D-14476, Germany
| | - Garry Duville
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
| | - Alexandra Launay-Avon
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette 91190, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette 91190, France
| | - Christine Paysant-Le Roux
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette 91190, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette 91190, France
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm D-14476, Germany
| | - François Roudier
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France
| | - Anne Krapp
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles 78000, France
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Yue L, Sun Y, Wang X, Hu W. Advances of endoscopic and surgical management in gastrointestinal stromal tumors. Front Surg 2023; 10:1092997. [PMID: 37123546 PMCID: PMC10130460 DOI: 10.3389/fsurg.2023.1092997] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
As one of the most common mesenchymal malignancies in the digestive system, gastrointestinal stromal tumors (GISTs) occur throughout the alimentary tract with diversified oncological characteristics. With the advent of the tyrosine kinase inhibitor era, the treatment regimens of patients with GISTs have been revolutionized and GISTs have become the paradigm of multidisciplinary therapy. However, surgery resection remains recognized as the potentially curative management for the radical resection and provided with favorable oncological outcomes. The existing available surgery algorithms in clinical practice primarily incorporate open procedure, and endoscopic and laparoscopic surgery together with combined operation techniques. The performance of various surgery methods often refers to the consideration of risk evaluation of recurrence and metastases; the degree of disease progression; size, location, and growth pattern of tumor; general conditions of selected patients; and indications and safety profile of various techniques. In the present review, we summarize the fundamental principle of surgery of GISTs based on risk assessment as well as tumor size, location, and degree of progress with an emphasis on the indications, strengths, and limitations of current surgery techniques.
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Affiliation(s)
- Lei Yue
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Medical School, Zhejiang University, Hangzhou, China
| | - Yingchao Sun
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Medical School, Zhejiang University, Hangzhou, China
| | - Xinjie Wang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Medical School, Zhejiang University, Hangzhou, China
| | - Weiling Hu
- Department of Gastroenterology, Sir Run Run Shaw Hospital, Medical School, Zhejiang University, Hangzhou, China
- Institute of Gastroenterology, Zhejiang University (IGZJU), Hangzhou, China
- Zhejiang University Cancer Center, Hangzhou, China
- Correspondence: Weiling Hu
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Andrzejewska M, Czarny J, Derwich K. Latest Advances in the Management of Pediatric Gastrointestinal Stromal Tumors. Cancers (Basel) 2022; 14:4989. [PMID: 36291774 PMCID: PMC9599787 DOI: 10.3390/cancers14204989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/28/2022] [Accepted: 10/10/2022] [Indexed: 11/21/2022] Open
Abstract
Gastrointestinal stromal tumor is the most common mesenchymal neoplasm of the gastrointestinal tract, usually found in elderly adults. It is infrequent among pediatric patients and usually differs biologically from adult-type diseases presenting mutations of KIT and PDGFR genes. In this population, more frequent is the wild-type GIST possessing SDH, TRK, RAS, NF1 mutations, among others. Both tumor types require individualized treatment with kinase inhibitors that are still being tested in the pediatric population due to the different neoplasm biology. We review the latest updates to the management of pediatric gastrointestinal tumors with a particular focus on the advances in molecular biology of the disease that enables the definition of possible resistance. Emerging treatment with kinase inhibitors that could serve as targeted therapy is discussed, especially with multikinase inhibitors of higher generation, the effectiveness of which has already been confirmed in the adult population.
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Affiliation(s)
- Marta Andrzejewska
- Faculty of Medicine, Poznan University of Medical Sciences, 61-701 Poznan, Poland or
| | - Jakub Czarny
- Faculty of Medicine, Poznan University of Medical Sciences, 61-701 Poznan, Poland or
| | - Katarzyna Derwich
- Department of Pediatric Oncology, Hematology and Transplantology, Institute of Pediatrics, Poznan University of Medical Sciences, 60-355 Poznan, Poland
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9
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Sun J, Zhang Q, Sun X, Xue A, Gao X, Shen K. THZ1 targeting CDK7 suppresses c-KIT transcriptional activity in gastrointestinal stromal tumours. Cell Commun Signal 2022; 20:138. [PMID: 36076237 PMCID: PMC9454178 DOI: 10.1186/s12964-022-00928-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/05/2022] [Indexed: 11/19/2022] Open
Abstract
Background Gastrointestinal stromal tumours (GISTs) are the most common mesenchymal tumours of the gastrointestinal tract and are characterized by activating mutations of c-KIT or PDGFRa receptor tyrosine kinases (RTKs). Despite the clinical success of tyrosine kinase inhibitors (TKIs), more than half of GIST patients develop resistance due to a second mutation. Cyclin-dependent kinase 7 (CDK7) is the catalytic subunit of CDK-activating kinase (CAK), and it plays an important role in the regulation of cell cycle transitions and gene transcription. THZ1, a CDK7 inhibitor, exhibits a dose-dependent inhibitory effect in various cancers. Methods Data from the public GEO database and tissue microarray were used to analyse the gene expression levels of CDKs in GISTs. The impact of CDK7 knockdown and the CDK7 inhibitor THZ1 on GIST progression was investigated in vitro using CCK-8, colony formation, and flow cytometry assays and in vivo using a xenograft mouse model. RNA sequencing was performed to investigate the mechanism of GIST cell viability impairment mediated by THZ1 treatment. Results Our study demonstrated that CDK7 is relatively overexpressed in high-risk GISTs and predicts a poor outcome. A low concentration of THZ1 exhibited a pronounced antineoplastic effect in GIST cells in vivo and in vitro. Moreover, THZ1 exerted synergistic anticancer effects with imatinib. THZ1 treatment resulted in transcriptional modulation by inhibiting the phosphorylation of Ser2, Ser5, and Ser7 within RNA polymerase II (RNAPII). c-KIT, an oncogene driver of GIST, was transcriptionally repressed by THZ1 treatment or CDK7 knockdown. Transcriptome sequencing analysis showed that OSR1 acts as a downstream target of CDK7 and regulates c-KIT expression. Taken together, our results highlight elevated CDK7 expression as a predictor of poor outcome in GIST and present the combination of CDK7 and RTK inhibitors as a potent therapeutic strategy to improve the efficacy of GIST treatment. Video abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-022-00928-x.
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Affiliation(s)
- Jianyi Sun
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China
| | - Qiang Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China
| | - Xiangfei Sun
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China
| | - Anwei Xue
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China
| | - Xiaodong Gao
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China.
| | - Kuntang Shen
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China.
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10
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Hemming ML, Benson MR, Loycano MA, Anderson JA, Andersen JL, Taddei ML, Krivtsov AV, Aubrey BJ, Cutler JA, Hatton C, Sicinska E, Armstrong SA. MOZ and Menin-MLL Complexes Are Complementary Regulators of Chromatin Association and Transcriptional Output in Gastrointestinal Stromal Tumor. Cancer Discov 2022; 12:1804-1823. [PMID: 35499757 PMCID: PMC9453853 DOI: 10.1158/2159-8290.cd-21-0646] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 03/23/2022] [Accepted: 04/27/2022] [Indexed: 01/09/2023]
Abstract
Gastrointestinal stromal tumor (GIST) is commonly characterized by activating mutations in the receptor tyrosine kinase KIT. Tyrosine kinase inhibitors are the only approved therapy for GIST, and complementary treatment strategies are urgently needed. As GIST lacks oncogene amplification and relies upon an established network of transcription factors, we hypothesized that unique chromatin-modifying enzymes are essential in orchestrating the GIST epigenome. We identified through genome-scale CRISPR screening that MOZ and Menin-MLL chromatin regulatory complexes are cooperative and unique dependencies in GIST. These complexes were enriched at GIST-relevant genes and regulated their transcription. Inhibition of MOZ and Menin-MLL complexes decreased GIST cell proliferation by disrupting interactions with transcriptional/chromatin regulators, such as DOT1L. MOZ and Menin inhibition caused significant reductions in tumor burden in vivo, with superior effects observed with combined Menin and KIT inhibition. These results define unique chromatin regulatory dependencies in GIST and identify potential therapeutic strategies for clinical application. SIGNIFICANCE Although many malignancies rely on oncogene amplification, GIST instead depends upon epigenetic regulation of KIT and other essential genes. Utilizing genome-scale CRISPR dependency screens, we identified complementary chromatin-modifying complexes essential to GIST and characterize the consequences of their disruption, elucidating a novel therapeutic approach to this disease. This article is highlighted in the In This Issue feature, p. 1599.
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Affiliation(s)
- Matthew L. Hemming
- Department of Medical Oncology, Sarcoma Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Morgan R. Benson
- Department of Pediatric Oncology and Division of Hematology/Oncology, Dana-Farber Cancer Institute, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Michael A. Loycano
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Justin A. Anderson
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Jessica L. Andersen
- Department of Medical Oncology, Sarcoma Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Madeleine L. Taddei
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrei V. Krivtsov
- Department of Pediatric Oncology and Division of Hematology/Oncology, Dana-Farber Cancer Institute, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Brandon J. Aubrey
- Department of Pediatric Oncology and Division of Hematology/Oncology, Dana-Farber Cancer Institute, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jevon A. Cutler
- Department of Pediatric Oncology and Division of Hematology/Oncology, Dana-Farber Cancer Institute, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Charlie Hatton
- Department of Pediatric Oncology and Division of Hematology/Oncology, Dana-Farber Cancer Institute, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ewa Sicinska
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Scott A. Armstrong
- Department of Pediatric Oncology and Division of Hematology/Oncology, Dana-Farber Cancer Institute, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
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11
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Zhong ME, Huang ZP, Wang X, Cai D, Li CH, Gao F, Wu XJ, Wang W. A Transcription Factor Signature Can Identify the CMS4 Subtype and Stratify the Prognostic Risk of Colorectal Cancer. Front Oncol 2022; 12:902974. [PMID: 35847938 PMCID: PMC9280271 DOI: 10.3389/fonc.2022.902974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/26/2022] [Indexed: 12/24/2022] Open
Abstract
BackgroundColorectal cancer (CRC) is a heterogeneous disease, and current classification systems are insufficient for stratifying patients with different risks. This study aims to develop a generalized, individualized prognostic consensus molecular subtype (CMS)-transcription factors (TFs)-based signature that can predict the prognosis of CRC.MethodsWe obtained differentially expressed TF signature and target genes between the CMS4 and other CMS subtypes of CRC from The Cancer Genome Atlas (TCGA) database. A multi-dimensional network inference integrative analysis was conducted to identify the master genes and establish a CMS4-TFs-based signature. For validation, an in-house clinical cohort (n = 351) and another independent public CRC cohort (n = 565) were applied. Gene set enrichment analysis (GSEA) and prediction of immune cell infiltration were performed to interpret the biological significance of the model.ResultsA CMS4-TFs-based signature termed TF-9 that includes nine TF master genes was developed. Patients in the TF-9 high-risk group have significantly worse survival, regardless of clinical characteristics. The TF-9 achieved the highest mean C-index (0.65) compared to all other signatures reported (0.51 to 0.57). Immune infiltration revealed that the microenvironment in the high-risk group was highly immune suppressed, as evidenced by the overexpression of TIM3, CD39, and CD40, suggesting that high-risk patients may not directly benefit from the immune checkpoint inhibitors.ConclusionsThe TF-9 signature allows a more precise categorization of patients with relevant clinical and biological implications, which may be a valuable tool for improving the tailoring of therapeutic interventions in CRC patients.
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Affiliation(s)
- Min-Er Zhong
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ze-Ping Huang
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xun Wang
- Department of Biomedical Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Du Cai
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Cheng-Hang Li
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Feng Gao
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Wei Wang, ; Xiao-Jian Wu, ; Feng Gao,
| | - Xiao-Jian Wu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Wei Wang, ; Xiao-Jian Wu, ; Feng Gao,
| | - Wei Wang
- Biomedical Big Data Centre, Department of Gynaecology, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
- *Correspondence: Wei Wang, ; Xiao-Jian Wu, ; Feng Gao,
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12
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MiRNA-196-5p Promotes Proliferation and Migration in Cholangiocarcinoma via HAND1/Wnt/β-Catenin Signaling Pathway. JOURNAL OF ONCOLOGY 2022; 2022:4599676. [PMID: 35466323 PMCID: PMC9019430 DOI: 10.1155/2022/4599676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 02/09/2022] [Accepted: 03/14/2022] [Indexed: 11/17/2022]
Abstract
Accumulating evidence has indicated the crucial role of microRNA-196 in mediating tumor progression, while its significance in cholangiocarcinoma (CCA) remains unclear. In this study, we provided the first evidence that the expression level of miR-196-5p is elevated in both CCA cell lines and clinic specimen. MiR-196-5p inhibition notably suppressed cell proliferation as well as metastasis in CCA cell line HuCCT1. Furthermore, the interaction between miR-196-5p and its downstream molecule HAND1 was verified. Moreover, a series of rescue assay verified that both HAND1 and β-catenin silencing could reverse the abnormal elevated cell proliferation and migration brought by miR-196-5p elevation, indicating that HAND1/Wnt/β-catenin signaling pathway activation is essential for miR-196-5p to exert its roles. In summary, we successfully depict the oncogenic role of miR-196-5p in promoting cell proliferation and migration in CCA via HAND1/Wnt/β-catenin axis.
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13
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Gu L, Jiang C, Xu C, Liu Y, Zhou H. Based on Molecular Subtypes, Immune Characteristics and Genomic Variation to Constructing and Verifying Multi-Gene Prognostic Characteristics of Colorectal Cancer. Front Cell Dev Biol 2022; 10:828415. [PMID: 35281077 PMCID: PMC8905350 DOI: 10.3389/fcell.2022.828415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/31/2022] [Indexed: 11/25/2022] Open
Abstract
Background: Colon cancer (COAD) has been identified as being among the most prevalent tumors globally and ranked the third major contributor to cancer-related mortality. COAD is a molecularly heterogeneous disease. There are great differences in clinical manifestations and prognosis among different molecular subtypes. Methods:379 TCGA-COAD samples were divided into four subtypes: primary proliferative, with collective, crypt-like, and EMT invasion. The differences among the four subtypes were analyzed from the multidimensional perspectives of immunity, genomic variation, and prognosis. The limma package was utilized to identify differentially expressed genes (DEGs) amongst different molecular subtypes. Phenotype-related coexpressed gene modules were identified using WGCNA. The polygenic prognosis model was created utilizing the lasso Cox analysis and verified by time-dependent subject operating characteristics (ROC). Results: There are some differences in prognosis, TMB and common gene variation, immune score, and immunotherapy/chemotherapy between proliferative and three invasive molecular subtypes. 846 differential genes (DEGs) were obtained by limma packet analysis. Differential gene analysis was utilized to screen the DEGs among distinct subtypes, which were significantly enriched in the pathways related to tumorigenesis and development. Co-expression network analysis found 46 co-expressed genes correlated with proliferative and three invasive phenotypes. Based on differentially co-expressed genes, we developed a prognostic risk model of 8-genes signature, which exhibited strong stability regardless of external and internal validation. RT-PCR experiments proved the expression of eight genes in tumor and normal samples. Conclusion: We have developed an eight-gene signature prognostic stratification system. Furthermore, we proposed that this classifier can serve as a molecular diagnostic tool to assess the prognosis of colon cancer patients.
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Affiliation(s)
- Lei Gu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chunhui Jiang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chunjie Xu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ye Liu
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hong Zhou
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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14
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Li Z, Zou W, Sun J, Zhou S, Zhou Y, Cai X, Zhang J. A comprehensive gene expression profile of allergic rhinitis-derived nasal fibroblasts and the potential mechanism for its phenotype. Hum Exp Toxicol 2022; 41:9603271211069038. [PMID: 35133179 DOI: 10.1177/09603271211069038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND Allergic rhinitis (AR) is a common immunoglobulin E-mediated immune response involved various cell types, while the role of nasal fibroblasts (NFs) in the pathogenesis of AR is less understood. PURPOSE The study aimed to uncover the gene expression profile of AR-derived NFs and the potential mechanism for the changed phenotype of AR-NFs. RESEARCH DESIGN The primary NFs were isolated from 3 AR patients (AR-NFs) and 3 controls (Ctrl-NFs), and the proliferation, migration and interleukins production abilities of NFs were detected respectively. RNA-sequence was used to identify differentially expressed genes (DEGs) in AR-NFs. Transcription factor (TF) regulatory network and bioinformatic analyses were both conducted to clarify the biological roles of DEGs including the TFs. The DEG with the highest validated |fold change (FC)| value, detected by qPCR, was selected for further confirmation. RESULTS AR-NFs showed a higher proliferation and migration abilities as well as released higher levels of IL-33 and IL-6, compared to Ctrl-NFs. A total of 729 DEGs were screened out in AR-NFs. TF regulatory network indicated that BARX homeobox 1 (BARX1) and forkhead box L1 were the major node TFs. Bioinformatic analyses showed that a large number of DEGs including several target genes of BARX1 were both enriched cytokine-related GO terms, and immune- or inflammation-related pathways. BARX1 had the highest |FC| value, and silencing BARX1 in AR-NFs resulted in the significant downregulation of proliferation and migration abilities, and the production of interleukins. CONCLUSIONS Our study for the first time provided the gene expression profile of AR-derived NFs, and BARX1 could be developed as a potent target to alleviate the pathogenesis of AR.
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Affiliation(s)
- Zhengwen Li
- Department of Otorhinolaryngology, 278245Shanghai Tenth Peoples' Hospital, Tongji University, Shanghai, China
| | - Wentao Zou
- Department of Otorhinolaryngology, 278245Shanghai Tenth Peoples' Hospital, Tongji University, Shanghai, China
| | - Jingwen Sun
- Department of Otorhinolaryngology, 278245Shanghai Tenth Peoples' Hospital, Tongji University, Shanghai, China
| | - Shuang Zhou
- Department of Otorhinolaryngology, 278245Shanghai Tenth Peoples' Hospital, Tongji University, Shanghai, China
| | - Yue Zhou
- Department of Otorhinolaryngology, 278245Shanghai Tenth Peoples' Hospital, Tongji University, Shanghai, China
| | - Xiaojing Cai
- Department of Otorhinolaryngology, 278245Shanghai Tenth Peoples' Hospital, Tongji University, Shanghai, China
| | - Jiaxiong Zhang
- Department of Otorhinolaryngology, 278245Shanghai Tenth Peoples' Hospital, Tongji University, Shanghai, China
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15
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Chen Y, Tang L, Huang W, Zhang Y, Abisola FH, Li L. Identification and validation of a novel cuproptosis-related signature as a prognostic model for lung adenocarcinoma. Front Endocrinol (Lausanne) 2022; 13:963220. [PMID: 36353226 PMCID: PMC9637654 DOI: 10.3389/fendo.2022.963220] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/10/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Cuproptosis is a novel form of copper-induced cell death that targets lipoylated tricarboxylic acid (TCA) cycle proteins. However, its prognostic role in lung adenocarcinoma (LUAD) remains unclear. This study aimed to establish a cuproptosis-related prognostic signature for patients with LUAD. METHODS Transcriptome data of LUAD samples were extracted from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The prognostic value of cuproptosis-related genes (CRGs) was investigated using Cox regression analysis to develop a cuproptosis-related prognostic model. Kyoto Encyclopedia of Genes and Genomes (KEGG), gene ontology (GO) and gene set variation analysis (GSVA) were conducted to characterize different biological activities or pathways between high- or low-CRG groups. The expression pattern and prognostic values of CRGs were validated in 37 paired tumor-normal samples using quantitative PCR. Furthermore, in vitro experiments were performed to investigate the relationship between cuproptosis and CRG expression and to explore the function of target genes in cuproptosis. RESULTS Among the 36 CRGs, 17 genes were upregulated, and 3 genes were downregulated in LUAD. A total of 385 CRGs were identified using Pearson correlation analysis. A cuproptosis-related signature was constructed using least absolute shrinkage and selection operator (LASSO) analysis. The prognostic value of the cuproptosis-related signature was validated in six external validation cohorts and in LUAD specimens from our facility. Patients in the high-risk group based on the CRG signature score had shorter overall survival than those in the low-risk group in both the datasets and clinical specimens. In vitro experiments revealed that the expression of BARX1, GFRA3, and KHDRBS2 was upregulated after cuproptosis was induced by elesclomol-CuCL2, whereas the upregulation was suppressed on pretreatment with tetrathiomolybdate (TTM), a chelator of copper. Further, the cell proliferation assay revealed that the BARX1 and GFRA3 deficiency facilities the cuproptosis induced by elesclomol-CuCL2. CONCLUSION This study established a new CRG signature that can be used to predict the OS of LUAD patients. Moreover, the knockdown of BARX1 and GFRA3 could increase the sensitivity of LUAD cells to the cuproptosis.
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Affiliation(s)
- Yuqiao Chen
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lu Tang
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wentao Huang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Youyu Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fakolade Hannah Abisola
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Linfeng Li
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China
- Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
- *Correspondence: Linfeng Li,
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