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Kobayashi H, Imanaka S, Yoshimoto C, Matsubara S, Shigetomi H. Rethinking the pathogenesis of endometriosis: Complex interactions of genomic, epigenetic, and environmental factors. J Obstet Gynaecol Res 2024. [PMID: 39293995 DOI: 10.1111/jog.16089] [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: 06/18/2024] [Accepted: 09/01/2024] [Indexed: 09/20/2024]
Abstract
AIM Endometriosis is a complex, multifactorial disease. Recent advances in molecular biology underscore that somatic mutations within the epithelial component of the normal endometrium, alongside aberrant epigenetic alterations within endometrial stromal cells, may serve as stimulators for the proliferation of endometriotic tissue within the peritoneal cavity. Nevertheless, pivotal inquiries persist: the deterministic factors driving endometriosis development in certain women while sparing others, notwithstanding comparable experiences of retrograde menstruation. Within this review, we endeavor to synopsize the current understanding of diverse pathophysiologic mechanisms underlying the initiation and progression of endometriosis and delineate avenues for future research. METHODS A literature search without time restriction was conducted utilizing PubMed and Google Scholar. RESULTS Given that aberrant clonal expansion stemming from cancer-associated mutations is common in normal endometrial tissue, only endometrial cells harboring mutations imparting proliferative advantages may be selected for survival outside the uterus. Endometriotic cells capable of engendering metabolic plasticity and modulating mitochondrial dynamics, thereby orchestrating responses to hypoxia, oxidative stress, inflammation, hormonal stimuli, and immune surveillance, and adeptly acclimating to their harsh surroundings, stand a chance at viability. CONCLUSION The genesis of endometriosis appears to reflect the evolutionary principles of mutation, selection, clonal expansion, and adaptation to the environment.
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Affiliation(s)
- Hiroshi Kobayashi
- Department of Gynecology and Reproductive Medicine, Ms.Clinic MayOne, Kashihara, Japan
- Department of Obstetrics and Gynecology, Nara Medical University, Kashihara, Japan
| | - Shogo Imanaka
- Department of Gynecology and Reproductive Medicine, Ms.Clinic MayOne, Kashihara, Japan
- Department of Obstetrics and Gynecology, Nara Medical University, Kashihara, Japan
| | - Chiharu Yoshimoto
- Department of Obstetrics and Gynecology, Nara Medical University, Kashihara, Japan
- Department of Obstetrics and Gynecology, Nara Prefecture General Medical Center, Nara, Japan
| | - Sho Matsubara
- Department of Obstetrics and Gynecology, Nara Medical University, Kashihara, Japan
- Department of Medicine, Kei Oushin Clinic, Nishinomiya, Japan
| | - Hiroshi Shigetomi
- Department of Obstetrics and Gynecology, Nara Medical University, Kashihara, Japan
- Department of Gynecology and Reproductive Medicine, Aska Ladies Clinic, Nara, Japan
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He H, Bell SM, Davis AK, Zhao S, Sridharan A, Na CL, Guo M, Xu Y, Snowball J, Swarr DT, Zacharias WJ, Whitsett JA. PRDM3/16 regulate chromatin accessibility required for NKX2-1 mediated alveolar epithelial differentiation and function. Nat Commun 2024; 15:8112. [PMID: 39284798 PMCID: PMC11405758 DOI: 10.1038/s41467-024-52154-3] [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: 01/08/2024] [Accepted: 08/27/2024] [Indexed: 09/20/2024] Open
Abstract
While the critical role of NKX2-1 and its transcriptional targets in lung morphogenesis and pulmonary epithelial cell differentiation is increasingly known, mechanisms by which chromatin accessibility alters the epigenetic landscape and how NKX2-1 interacts with other co-activators required for alveolar epithelial cell differentiation and function are not well understood. Combined deletion of the histone methyl transferases Prdm3 and Prdm16 in early lung endoderm causes perinatal lethality due to respiratory failure from loss of AT2 cells and the accumulation of partially differentiated AT1 cells. Combination of single-cell RNA-seq, bulk ATAC-seq, and CUT&RUN data demonstrate that PRDM3 and PRDM16 regulate chromatin accessibility at NKX2-1 transcriptional targets critical for perinatal AT2 cell differentiation and surfactant homeostasis. Lineage specific deletion of PRDM3/16 in AT2 cells leads to lineage infidelity, with PRDM3/16 null cells acquiring partial AT1 fate. Together, these data demonstrate that NKX2-1-dependent regulation of alveolar epithelial cell differentiation is mediated by epigenomic modulation via PRDM3/16.
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Affiliation(s)
- Hua He
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.
- NHC Key Laboratory of Chronobiology, Sichuan University, Chengdu, Sichuan, China.
| | - Sheila M Bell
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ashley Kuenzi Davis
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Shuyang Zhao
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anusha Sridharan
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Cheng-Lun Na
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Minzhe Guo
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yan Xu
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - John Snowball
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Daniel T Swarr
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - William J Zacharias
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jeffrey A Whitsett
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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Daugan C, Boidot R, Ghiringhelli F, Borg C, Vienot A. Targeting mTOR signaling for the treatment of intrahepatic cholangiocarcinoma with TSC1/ARID1A mutations: a case report with an unexpected response. Ther Adv Med Oncol 2024; 16:17588359241271793. [PMID: 39281970 PMCID: PMC11401142 DOI: 10.1177/17588359241271793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/26/2024] [Indexed: 09/18/2024] Open
Abstract
Biliary tract cancer incidence is increasing and the prognostic remains dismal. The development of personalized medicine is a pivotal issue in proposing therapeutic options for biliary tract cancer patients. Whole exome sequencing identifies approximately 15% of IDH1 mutations and 15% of FGFR2 fusions in intrahepatic cholangiocarcinoma. Other patients are not currently eligible for targeted therapy. Here, we present a patient treated for a metastatic cholangiocarcinoma with an unexpected response to a mammalian target of rapamycin (mTOR) targeting agent. Whole exome sequencing enabled the identification of TSC1 and ARID1A mutations. Reintroduction of mTOR inhibitors with similar results sustains the main role of these targeted agents in the control of the disease. These results suggest the existence of an mTOR oncogenic addiction in biliary tract cancer. Our results support the interest in performing exome sequencing in liver cancers and the potential to identify actionable mutations with important therapeutic issues.
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Affiliation(s)
- Clémentine Daugan
- Department of Medical Oncology, University Hospital of Besançon, Besancon, France
| | - Romain Boidot
- Molecular Biology Unit, Department of Biology and Pathology of Tumors, Georges-François Leclerc Cancer Center, Dijon, France
| | - François Ghiringhelli
- Department of Medical Oncology, Georges-François Leclerc Cancer Center, Dijon, France
| | - Christophe Borg
- Department of Medical Oncology, University Hospital of Besançon, Besancon, France
- INSERM, EFS BFC, UMR1098, RIGHT, University of Bourgogne Franche-Comté, Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
- Clinical Investigational Center, CIC-1431, Besançon, France
| | - Angélique Vienot
- Department of Medical Oncology, University Hospital of Besançon, 3 Boulevard Alexandre Fleming, Besancon F-25000, France
- INSERM, EFS BFC, UMR1098, RIGHT, University of Bourgogne Franche-Comté, Interactions Greffon-Hôte-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
- Clinical Investigational Center, CIC-1431, Besançon, France
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Chen Z, Gao J, Li Z, Ma D, Wang Y, Cheng Q, Zhu J, Li Z. Integrative analysis reveals different feature of intrahepatic cholangiocarcinoma subtypes. Liver Int 2024; 44:2477-2493. [PMID: 38924592 DOI: 10.1111/liv.16015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND & AIMS Intrahepatic cholangiocarcinoma (iCCA) has two main histological subtypes: large and small duct-type iCCA, which are characterized by different clinicopathological features. This study was conducted with the purpose of expanding our understanding of their differences in molecular features and immune microenvironment. METHODS We selected 132 patients who underwent radical surgery at our department between 2015 and 2021 for clinical and survival analyses. Whole-exome sequencing was performed to analyse mutational landscapes. Bulk RNA sequencing and single-cell RNA sequencing data were used for pathway enrichment and immune infiltration analyses based on differentially expressed genes. The function of PPP1R1B was analysed both in vitro and in vivo and the gene mechanism was further investigated. RESULTS We found that large duct-type iCCA had worse overall survival and recurrence-free survival rates than small duct-type iCCA. Mutations in ARID1A, DOT1L and ELF3 usually occur in large duct-type iCCA, whereas mutations in IDH1 and BAP1 occur in small duct-type iCCA. Among the differentially expressed genes, we found that PPP1R1B was highly expressed in large duct-type iCCA tumour tissues. Expression of PPP1R1B promoted cell proliferation, migration and invasion and indicated a worse prognosis. A combination of USF2 with the promoter of PPP1R1B can enhance gene expression in iCCA, which may further affect the expression of genes such as AHNAK, C4BPA and activating the PI3K/AKT pathway. CONCLUSIONS Our findings extend our understanding of large and small duct-type iCCA. In addition, PPP1R1B may serve as a potential marker and therapeutic target for large duct-type iCCA.
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Affiliation(s)
- Zhuomiaoyu Chen
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of HCC and Liver Cirrhosis, Peking University People's Hospital, Beijing, China
| | - Jie Gao
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of HCC and Liver Cirrhosis, Peking University People's Hospital, Beijing, China
- Peking University Center of Liver Cancer Diagnosis and Treatment, Peking University People's Hospital, Beijing, China
- Peking University Institute of Organ Transplantation, Peking University People's Hospital, Beijing, China
| | - Zuyin Li
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of HCC and Liver Cirrhosis, Peking University People's Hospital, Beijing, China
| | - Delin Ma
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of HCC and Liver Cirrhosis, Peking University People's Hospital, Beijing, China
| | - Yang Wang
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of HCC and Liver Cirrhosis, Peking University People's Hospital, Beijing, China
| | - Qian Cheng
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of HCC and Liver Cirrhosis, Peking University People's Hospital, Beijing, China
| | - Jiye Zhu
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of HCC and Liver Cirrhosis, Peking University People's Hospital, Beijing, China
- Peking University Center of Liver Cancer Diagnosis and Treatment, Peking University People's Hospital, Beijing, China
- Peking University Institute of Organ Transplantation, Peking University People's Hospital, Beijing, China
| | - Zhao Li
- Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of HCC and Liver Cirrhosis, Peking University People's Hospital, Beijing, China
- Peking University Center of Liver Cancer Diagnosis and Treatment, Peking University People's Hospital, Beijing, China
- Peking University Institute of Organ Transplantation, Peking University People's Hospital, Beijing, China
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Ma Z, Sun J, Li Z, Huang S, Li B. AMDHD1 acts as a tumor suppressor and contributes to activation of TGF-β signaling pathway in cholangiocarcinoma. Cell Death Differ 2024:10.1038/s41418-024-01361-y. [PMID: 39143229 DOI: 10.1038/s41418-024-01361-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 08/16/2024] Open
Abstract
Cholangiocarcinoma (CCA) is a malignant tumor of the digestive system, characterized by its aggressive behavior and the absence of effective therapeutic biomarkers. Although recent studies have implicated AMDHD1 in tumor formation, its role in CCA development has been insufficiently explored. We utilized multiple bioinformatic datasets alongside 108 clinical samples to examine AMDHD1 expression in CCA. Then, in vitro and in vivo experiments were conducted to assess its impact on tumor growth and metastasis. Furthermore, proteomic analysis and immunoprecipitation mass spectrometry were employed to identify the downstream effectors of AMDHD1. We discovered that AMDHD1 was down-regulated in CCA and this down-regulation was associated with adverse clinicopathological features and prognosis. We also demonstrated that overexpression of AMDHD1 hindered G1/S progression in the cell cycle and promoted apoptosis, thereby inhibiting tumor growth and metastasis. Mechanistically, we found that AMDHD1 operated in a TGF-β-dependent manner and the inhibition of TGF-β signaling abrogated the effect of AMDHD1 overexpression on CCA cells. Specifically, AMDHD1 inhibited the ubiquitination and degradation of the SMAD4 protein through binding to the MH2 domain and synergistically enhanced SMAD2/3 phosphorylation, which activated of TGF-β signaling pathway and resulted in the suppression of CCA cell proliferation and migration. Our study identifies AMDHD1 as a significant prognostic biomarker and a tumor suppressor in CCA. It underscores the pivotal role of the AMDHD1/TGF-β signaling pathway in the development and progression of CCA.
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Affiliation(s)
- Zuyi Ma
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Jia Sun
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Zhenchong Li
- Junior Clinical Cooperation Unit Translational Gastrointestinal Oncology and Preclinical Models, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Shanzhou Huang
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
- Southern Medical University, Guangzhou, China.
| | - Binglu Li
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
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Liang H, Zheng X, Zhang X, Zhang Y, Zheng J. The role of SWI/SNF complexes in digestive system neoplasms. Med Oncol 2024; 41:119. [PMID: 38630164 DOI: 10.1007/s12032-024-02343-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/22/2024] [Indexed: 04/19/2024]
Abstract
Chromatin remodeling is a critical step in the DNA damage response, and the ATP-dependent chromatin remodelers are a group of epigenetic regulators that alter nucleosome assembly and regulate transcription factor accessibility to DNA, preventing genomic instability and tumorigenesis caused by DNA damage. The SWI/SNF chromatin remodeling complex is one of them, and mutations in the gene encoding the SWI/SNF subunit are frequently found in digestive tumors. We review the most recent literature on the role of SWI/SNF complexes in digestive tumorigenesis, with different SWI/SNF subunits playing different roles. They regulate the biological behavior of tumor cells, participate in multiple signaling pathways, interact with multiple genes, and have some correlation with the prognosis of patients. Their carcinogenic properties may help discover new therapeutic targets. Understanding the mutations and defects of SWI/SNF complexes, as well as the underlying functional mechanisms, may lead to new strategies for treating the digestive system by targeting relevant genes or modulating the tumor microenvironment.
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Affiliation(s)
- Hanyun Liang
- Department of Diagnostic Pathology, Shandong Second Medical University, Weifang, 261053, China
| | - Xin Zheng
- Department of Diagnostic Pathology, Shandong Second Medical University, Weifang, 261053, China
| | - Xiao Zhang
- Department of Ultrasound, Weifang People's Hospital, Weifang, 261041, China
| | - Yan Zhang
- Department of Pathology, Affiliated Hospital of Shandong Second Medical University, Weifang, 261053, China.
| | - Jie Zheng
- Department of Diagnostic Pathology, Shandong Second Medical University, Weifang, 261053, China.
- Neurologic Disorders and Regenerative Repair Lab of Shandong Higher Education, Shandong Second Medical University, Weifang, 261053, China.
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7
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Ren H, Liu C, Zhang C, Wu H, Zhang J, Wang Z, Chen L, Wang H, Shao C, Zhou L. A cuproptosis-related gene expression signature predicting clinical prognosis and immune responses in intrahepatic cholangiocarcinoma detected by single-cell RNA sequence analysis. Cancer Cell Int 2024; 24:92. [PMID: 38431620 PMCID: PMC10908169 DOI: 10.1186/s12935-024-03251-2] [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: 10/08/2023] [Accepted: 01/31/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND Cholangiocarcinoma represents a malignant neoplasm originating from the hepatobiliary tree, with a subset of tumors developing inside the liver. Intrahepatic cholangiocarcinomas (ICC) commonly exhibit an asymptomatic presentation, rendering both diagnosis and treatment challenging. Cuproptosis, an emerging regulated cell death pathway induced by copper ions, has garnered attention recently. As cancer cells show altered copper metabolism and comparatively higher copper needs, cuproptosis may play a role in the development of ICC. However, studies investigating this possibility are currently lacking. METHODS Single-cell and bulk RNA sequence data were analyzed, and correlations were established between the expression of cuproptosis-related molecules and ICC patient survival. Genes with predicting survival were used to create a CUPT score using Cox and LASSO regression and tumor mutation burden (TMB) analysis. The CIBERSORT software was employed to characterize immune cell infiltration within the tumors. Furthermore, immune infiltration prediction, biological function enrichment, and drug sensitivity analyses were conducted to explore the potential implications of the cuproptosis-related signature. The effects of silencing solute carrier family 39 member 4 gene (SLC39A4) expression using siRNA were investigated using assays measuring cell proliferation, colony formation, and cell migration. Key genes of cuproptosis were detected by western blotting. RESULTS The developed CUPT score divided patients into high and low CUPT score groups. Those with a low score had significantly better prognosis and longer survival. In contrast, high CUPT scores were associated with worse clinical outcomes and significantly higher TMB. Comparisons of the two groups also indicated differences in the immune infiltrate present in the tumors. Finally, we were able to identify 95 drugs potentially affecting the cuproptosis pathway. Some of these might be effective in the treatment of ICC. The in vitro experiments revealed that suppressing the expression of SLC39A4 in ICC cell lines resulted in reduced cell proliferation, colony formation, and cell migration. It also led to an increase in cell death and the upregulation of key genes associated with cuproptosis, namely ferredoxin 1 (FDX1) and dihydrolipoyl transacetylase (DLAT). These findings strongly suggest that this cuproptosis-associated molecule may play a pivotal role in the development and metastasis of ICC. CONCLUSIONS Changes in the expression of a cuproptosis-related gene signature can predict the clinical prognosis of ICC with considerable accuracy. This supports the notion that cuproptosis influences the diversity and complexity of the immune microenvironment, mutational landscape, and biological behavior of ICC. Understanding this pathway better may hold promise for the development of innovative strategies in the management of this disease.
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Affiliation(s)
- Hefei Ren
- Department of Laboratory Medicine, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Chang Liu
- Department of Laboratory Medicine, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Cheng Zhang
- Institute of Aging & Tissue Regeneration, State Key Laboratory of Systems Medicine for Cancer and Stress and Cancer Research Unit of Chinese Academy of Medical Sciences (No. 2019RU043), Ren-Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200127, China
| | - Hongkun Wu
- Department of Laboratory Medicine, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Jiafeng Zhang
- Department of Laboratory Medicine, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Zhenhua Wang
- Department of Laboratory Medicine, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Lei Chen
- Department of Laboratory Medicine, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Huiquan Wang
- Department of Laboratory Medicine, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Chenghao Shao
- Department of Pancreatic-Biliary Surgery, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China.
| | - Lin Zhou
- Department of Laboratory Medicine, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, China.
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Rypens C, Van Berckelaer C, Berditchevski F, van Dam P, Van Laere S. Deciphering the molecular biology of inflammatory breast cancer through molecular characterization of patient samples and preclinical models. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 384:77-112. [PMID: 38637101 DOI: 10.1016/bs.ircmb.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Inflammatory breast cancer is an aggressive subtype of breast cancer with dismal patient prognosis and a unique clinical presentation. In the past two decades, molecular profiling technologies have been used in order to gain insight into the molecular biology of IBC and to search for possible targets for treatment. Although a gene signature that accurately discriminates between IBC and nIBC patient samples and preclinical models was identified, the overall genomic and transcriptomic differences are small and ambiguous, mainly due to the limited sample sizes of the evaluated patient series and the failure to correct for confounding effects of the molecular subtypes. Nevertheless, data collected over the past 20 years by independent research groups increasingly support the existence of several IBC-specific biological characteristics. In this review, these features are classified as established, emerging and conceptual hallmarks based on the level of evidence reported in the literature. In addition, a synoptic model is proposed that integrates all hallmarks and that can explain how cancer cell intrinsic mechanisms (i.e. NF-κB activation, genomic instability, MYC-addiction, TGF-β resistance, adaptive stress response, chromatin remodeling, epithelial-to-mesenchymal transition) can contribute to the establishment of the dynamic immune microenvironment associated with IBC. It stands to reason that future research projects are needed to further refine (parts of) this model and to investigate its clinical translatability.
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Affiliation(s)
- Charlotte Rypens
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium; CellCarta N V, Wilrijk, Belgium
| | - Christophe Van Berckelaer
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium
| | - Fedor Berditchevski
- Institute of Cancer and Genomic Sciences, The University of Birmingham, Birmingham, United Kingdom
| | - Peter van Dam
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium; Multidisciplinary Oncological Centre Antwerp (MOCA), Antwerp University Hospital, Drie Eikenstraat 655, Edegem, Belgium
| | - Steven Van Laere
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium.
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9
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Huang R, Wu D, Zhang K, Hu G, Liu Y, Jiang Y, Wang C, Zheng Y. ARID1A loss induces P4HB to activate fibroblasts to support lung cancer cell growth, invasion, and chemoresistance. Cancer Sci 2024; 115:439-451. [PMID: 38100120 PMCID: PMC10859615 DOI: 10.1111/cas.16052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/27/2023] [Accepted: 12/08/2023] [Indexed: 02/13/2024] Open
Abstract
Loss of AT-interacting domain-rich protein 1A (ARID1A) frequently occurs in human malignancies including lung cancer. The biological consequence of ARID1A mutation in lung cancer is not fully understood. This study was designed to determine the effect of ARID1A-depleted lung cancer cells on fibroblast activation. Conditioned media was collected from ARID1A-depleted lung cancer cells and employed to treat lung fibroblasts. The proliferation and migration of lung fibroblasts were investigated. The secretory genes were profiled in lung cancer cells upon ARID1A knockdown. Antibody-based neutralization was utilized to confirm their role in mediating the cross-talk between lung cancer cells and fibroblasts. NOD-SCID-IL2RgammaC-null (NSG) mice received tumor tissues from patients with ARID1A-mutated lung cancer to establish patient-derived xenograft (PDX) models. Notably, ARID1A-depleted lung cancer cells promoted the proliferation and migration of lung fibroblasts. Mechanistically, ARID1A depletion augmented the expression and secretion of prolyl 4-hydroxylase beta (P4HB) in lung cancer cells, which induced the activation of lung fibroblasts through the β-catenin signaling pathway. P4HB-activated lung fibroblasts promoted the proliferation, invasion, and chemoresistance in lung cancer cells. Neutralizing P4HB hampered the tumor growth and increased cisplatin cytotoxic efficacy in two PDX models. Serum P4HB levels were higher in ARID1A-mutated lung cancer patients than in healthy controls. Moreover, increased serum levels of P4HB were significantly associated with lung cancer metastasis. Together, our work indicates a pivotal role for P4HB in orchestrating the cross-talk between ARID1A-mutated cancer cells and cancer-associated fibroblasts during lung cancer progression. P4HB may represent a promising target for improving lung cancer treatment.
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Affiliation(s)
- Risheng Huang
- Department of Thoracic SurgeryThe Dingli Clinical College of Wenzhou Medical University, Wenzhou Central HospitalWenzhouChina
| | - Danni Wu
- Department of Thoracic SurgeryThe Dingli Clinical College of Wenzhou Medical University, Wenzhou Central HospitalWenzhouChina
| | - Kangliang Zhang
- Department of Central LabThe Dingli Clinical College of Wenzhou Medical University, Wenzhou Central HospitalWenzhouChina
| | - Guanqiong Hu
- Department of NursingThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Yu Liu
- Department of Thoracic SurgeryThe First Affiliated Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Yi Jiang
- Department of PathologyThe Dingli Clinical College of Wenzhou Medical University, Wenzhou Central HospitalWenzhouChina
| | - Chichao Wang
- Department of Thoracic SurgeryThe Dingli Clinical College of Wenzhou Medical University, Wenzhou Central HospitalWenzhouChina
| | - Yuanliang Zheng
- Department of Thoracic SurgeryThe Dingli Clinical College of Wenzhou Medical University, Wenzhou Central HospitalWenzhouChina
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Li Q, Huang D, Liao W, Su X, Li J, Zhang J, Fang M, Liu Y. Tanshinone IIA regulates CCl 4 induced liver fibrosis in C57BL/6J mice via the PI3K/Akt and Nrf2/HO-1 signaling pathways. J Biochem Mol Toxicol 2024; 38:e23648. [PMID: 38348705 DOI: 10.1002/jbt.23648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 08/31/2023] [Accepted: 01/10/2024] [Indexed: 02/15/2024]
Abstract
Chronic liver diseases caused by various factors may develop into liver fibrosis (LF). Early stage of LF could be reversible. Tanshinone IIA (Tan IIA), an extract from Salvia miltiorrhiza, has been reported to be hepatoprotective. However, the potential targets and mechanism of Tan IIA in the treatment of LF are still unclear. Our study aims at the anti-LF mechanism of Tan IIA through network pharmacological analysis combined with LF-related experiments. Serum biochemical indicators and histopathological examination showed that Tan IIA could ameliorate the process of LF in the CCl4 -induced mouse model. Western blot and immunohistochemical assays showed that Tan IIA decreased the expression of Kirsten rat sarcoma viral oncogene homolog (KRAS), phosphatidylinositide 3-kinases/protein kinase B (PI3K/Akt), and nuclear factor erythroid 2-related factor/heme oxygenase-1 (Nrf2/HO-1). Compared with the model group, the Tan IIA groups increased the decreased superoxide dismutase activity and glutathione content, while decreasing the increased malondialdehyde content. These results indicate that Tan IIA may play an antioxidant role by inhibiting the expression of KRAS, PI3K/Akt, and Nrf2/HO-1 to ameliorate the progression of LF, which to some extent explains the pharmacological mechanism of Tan IIA in LF. In conclusion, our study demonstrates that Tan IIA could regulate LF via PI3K/Akt and Nrf2/HO-1 signaling pathways. It may be an effective therapeutic compound for the treatment of LF.
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Affiliation(s)
- Qingqing Li
- School of Medicine, Jianghan University, Wuhan, China
| | - Dongrui Huang
- School of Medicine, Jianghan University, Wuhan, China
| | - Wenjing Liao
- School of Medicine, Jianghan University, Wuhan, China
| | - Xinyue Su
- School of Medicine, Jianghan University, Wuhan, China
| | - Jin Li
- School of Medicine, Jianghan University, Wuhan, China
| | - Jinwei Zhang
- School of Medicine, Jianghan University, Wuhan, China
| | - Meng Fang
- School of Medicine, Jianghan University, Wuhan, China
| | - Yuwei Liu
- School of Medicine, Jianghan University, Wuhan, China
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11
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Liu W, Wang H, Zhao Q, Tao C, Qu W, Hou Y, Huang R, Sun Z, Zhu G, Jiang X, Fang Y, Gao J, Wu X, Yang Z, Ping R, Chen J, Yang R, Chu T, Zhou J, Fan J, Tang Z, Yang D, Shi Y. Multiomics analysis reveals metabolic subtypes and identifies diacylglycerol kinase α (DGKA) as a potential therapeutic target for intrahepatic cholangiocarcinoma. Cancer Commun (Lond) 2024; 44:226-250. [PMID: 38143235 PMCID: PMC10876206 DOI: 10.1002/cac2.12513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/23/2023] [Accepted: 12/14/2023] [Indexed: 12/26/2023] Open
Abstract
BACKGROUND Intrahepatic cholangiocarcinoma (iCCA) is a highly heterogeneous and lethal hepatobiliary tumor with few therapeutic strategies. The metabolic reprogramming of tumor cells plays an essential role in the development of tumors, while the metabolic molecular classification of iCCA is largely unknown. Here, we performed an integrated multiomics analysis and metabolic classification to depict differences in metabolic characteristics of iCCA patients, hoping to provide a novel perspective to understand and treat iCCA. METHODS We performed integrated multiomics analysis in 116 iCCA samples, including whole-exome sequencing, bulk RNA-sequencing and proteome analysis. Based on the non-negative matrix factorization method and the protein abundance of metabolic genes in human genome-scale metabolic models, the metabolic subtype of iCCA was determined. Survival and prognostic gene analyses were used to compare overall survival (OS) differences between metabolic subtypes. Cell proliferation analysis, 5-ethynyl-2'-deoxyuridine (EdU) assay, colony formation assay, RNA-sequencing and Western blotting were performed to investigate the molecular mechanisms of diacylglycerol kinase α (DGKA) in iCCA cells. RESULTS Three metabolic subtypes (S1-S3) with subtype-specific biomarkers of iCCA were identified. These metabolic subtypes presented with distinct prognoses, metabolic features, immune microenvironments, and genetic alterations. The S2 subtype with the worst survival showed the activation of some special metabolic processes, immune-suppressed microenvironment and Kirsten rat sarcoma viral oncogene homolog (KRAS)/AT-rich interactive domain 1A (ARID1A) mutations. Among the S2 subtype-specific upregulated proteins, DGKA was further identified as a potential drug target for iCCA, which promoted cell proliferation by enhancing phosphatidic acid (PA) metabolism and activating mitogen-activated protein kinase (MAPK) signaling. CONCLUSION Via multiomics analyses, we identified three metabolic subtypes of iCCA, revealing that the S2 subtype exhibited the poorest survival outcomes. We further identified DGKA as a potential target for the S2 subtype.
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Affiliation(s)
- Weiren Liu
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Huqiang Wang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Qianfu Zhao
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Chenyang Tao
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Weifeng Qu
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Yushan Hou
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Run Huang
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Zimei Sun
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Guiqi Zhu
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Xifei Jiang
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Yuan Fang
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Jun Gao
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Xiaoling Wu
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Zhixiang Yang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Rongyu Ping
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Jiafeng Chen
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Rui Yang
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Tianhao Chu
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Jian Zhou
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Jia Fan
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Zheng Tang
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
| | - Dong Yang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsBeijingP. R. China
| | - Yinghong Shi
- Department of Liver Surgery and TransplantationLiver Cancer Institute, Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer Invasion of Ministry of EducationShanghaiP. R. China
- Research Unit of Liver cancer Recurrence and Metastasis, Chinese Academy of Medical SciencesBeijingP. R. China
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12
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Liu L, Lu L, Qiu M, Han N, Dai S, Shi S, He S, Zhang J, Yan Q, Chen S. Comprehensive modular analyses of scar subtypes illuminate underlying molecular mechanisms and potential therapeutic targets. Int Wound J 2024; 21:e14384. [PMID: 37697692 PMCID: PMC10784627 DOI: 10.1111/iwj.14384] [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: 08/02/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 09/13/2023] Open
Abstract
Pathological scarring resulting from traumas and wounds, such as hypertrophic scars and keloids, pose significant aesthetic, functional and psychological challenges. This study provides a comprehensive transcriptomic analysis of these conditions, aiming to illuminate underlying molecular mechanisms and potential therapeutic targets. We employed a co-expression and module analysis tool to identify significant gene clusters associated with distinct pathophysiological processes and mechanisms, notably lipid metabolism, sebum production, cellular energy metabolism and skin barrier function. This examination yielded critical insights into several skin conditions including folliculitis, skin fibrosis, fibrosarcoma and congenital ichthyosis. Particular attention was paid to Module Cluster (MCluster) 3, encompassing genes like BLK, TRPV1 and GABRD, all displaying high expression and potential implications in immune modulation. Preliminary immunohistochemistry validation supported these findings, showing elevated expression of these genes in non-fibrotic samples rich in immune activity. The complex interplay of different cell types in scar formation, such as fibroblasts, myofibroblasts, keratinocytes and mast cells, was also explored, revealing promising therapeutic strategies. This study underscores the promise of targeted gene therapy for pathological scars, paving the way for more personalised therapeutic approaches. The results necessitate further research to fully ascertain the roles of these identified genes and pathways in skin disease pathogenesis and potential therapeutics. Nonetheless, our work forms a strong foundation for a new era of personalised medicine for patients suffering from pathological scarring.
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Affiliation(s)
- Liang Liu
- College of Life SciencesZhejiang UniversityHangzhouChina
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
| | - Lantian Lu
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaAustralia
| | - Min Qiu
- Hangzhou Neoantigen Therapeutics Co., LtdHangzhouChina
| | - Ning Han
- Hangzhou AI‐Nano Therapeutics Co., Ltd.HangzhouChina
| | - Shijie Dai
- School of Life SciencesZhejiang Chinese Medical UniversityHangzhouChina
| | - Shuiping Shi
- Hangzhou Neoantigen Therapeutics Co., LtdHangzhouChina
| | - Shanshan He
- College of Life SciencesZhejiang UniversityHangzhouChina
| | - Jing Zhang
- College of Life SciencesZhejiang UniversityHangzhouChina
| | - Qingfeng Yan
- College of Life SciencesZhejiang UniversityHangzhouChina
| | - Shuqing Chen
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
- College of Pharmaceutical SciencesZhejiang UniversityHangzhouChina
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13
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He H, Bell SM, Davis AK, Zhao S, Sridharan A, Na CL, Guo M, Xu Y, Snowball J, Swarr DT, Zacharias WJ, Whitsett JA. PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiation and Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.570481. [PMID: 38187557 PMCID: PMC10769259 DOI: 10.1101/2023.12.20.570481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Differential chromatin accessibility accompanies and mediates transcriptional control of diverse cell fates and their differentiation during embryogenesis. While the critical role of NKX2-1 and its transcriptional targets in lung morphogenesis and pulmonary epithelial cell differentiation is increasingly known, mechanisms by which chromatin accessibility alters the epigenetic landscape and how NKX2-1 interacts with other co-activators required for alveolar epithelial cell differentiation and function are not well understood. Here, we demonstrate that the paired domain zinc finger transcriptional regulators PRDM3 and PRDM16 regulate chromatin accessibility to mediate cell differentiation decisions during lung morphogenesis. Combined deletion of Prdm3 and Prdm16 in early lung endoderm caused perinatal lethality due to respiratory failure from loss of AT2 cell function. Prdm3/16 deletion led to the accumulation of partially differentiated AT1 cells and loss of AT2 cells. Combination of single cell RNA-seq, bulk ATAC-seq, and CUT&RUN demonstrated that PRDM3 and PRDM16 enhanced chromatin accessibility at NKX2-1 transcriptional targets in peripheral epithelial cells, all three factors binding together at a multitude of cell-type specific cis-active DNA elements. Network analysis demonstrated that PRDM3/16 regulated genes critical for perinatal AT2 cell differentiation, surfactant homeostasis, and innate host defense. Lineage specific deletion of PRDM3/16 in AT2 cells led to lineage infidelity, with PRDM3/16 null cells acquiring partial AT1 fate. Together, these data demonstrate that NKX2-1-dependent regulation of alveolar epithelial cell differentiation is mediated by epigenomic modulation via PRDM3/16.
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Affiliation(s)
- Hua He
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, West China Second University Hospital Sichuan University, Chengdu, Sichuan, 610041, China
- NHC Key Laboratory of Chronobiology, Sichuan University, Sichuan 610041, China
| | - Sheila M. Bell
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
| | - Ashley Kuenzi Davis
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
| | - Shuyang Zhao
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
| | - Anusha Sridharan
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
| | - Cheng-Lun Na
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
| | - Minzhe Guo
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
| | - Yan Xu
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
| | - John Snowball
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
| | - Daniel T. Swarr
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
| | - William J. Zacharias
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
| | - Jeffrey A. Whitsett
- Perinatal Institute, Division of Neonatology and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine
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14
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Li JJ, Lee CS. The Role of the AT-Rich Interaction Domain 1A Gene ( ARID1A) in Human Carcinogenesis. Genes (Basel) 2023; 15:5. [PMID: 38275587 PMCID: PMC10815128 DOI: 10.3390/genes15010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
The switch/sucrose non-fermentable (SWI/SNF) (SWI/SNF) complex uses energy from ATP hydrolysis to mobilise nucleosomes on chromatin. Components of SWI/SNF are mutated in 20% of all human cancers, of which mutations in AT-rich binding domain protein 1A (ARID1A) are the most common. ARID1A is mutated in nearly half of ovarian clear cell carcinoma and around one-third of endometrial and ovarian carcinomas of the endometrioid type. This review will examine in detail the molecular functions of ARID1A, including its role in cell cycle control, enhancer regulation, and the prevention of telomerase activity. ARID1A has key roles in the maintenance of genomic integrity, including DNA double-stranded break repair, DNA decatenation, integrity of the cohesin complex, and reduction in replication stress, and is also involved in mismatch repair. The role of ARID1A loss in the pathogenesis of some of the most common human cancers is discussed, with a particular emphasis on gynaecological cancers. Finally, several promising synthetic lethal strategies, which exploit the specific vulnerabilities of ARID1A-deficient cancer cells, are briefly mentioned.
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Affiliation(s)
- Jing Jing Li
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW 2170, Australia;
- Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
| | - Cheok Soon Lee
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, NSW 2170, Australia;
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, NSW 2560, Australia
- South Western Sydney Clinical School, University of New South Wales, Liverpool, NSW 2170, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW 2010, Australia
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15
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Gonzalez-Salinas F, Herrera-Gamboa J, Rojo R, Trevino V. Heterozygous Knockout of ARID4B Using CRISPR/Cas9 Attenuates Some Aggressive Phenotypes in a Breast Cancer Cell Line. Genes (Basel) 2023; 14:2184. [PMID: 38137006 PMCID: PMC10743217 DOI: 10.3390/genes14122184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Breast cancer is one of the leading causes of death in women around the world. Over time, many genes and mutations that are associated with the development of this disease have been identified. However, the specific role of many genes has not yet been fully elucidated. Higher ARID4B expression has been identified as a risk factor for diverse cancer types. Silencing experiments also showed that ARID4B is associated with developing cancer-associated characteristics. However, no transcriptomic studies have shown the overall cellular effect of loss of function in breast cancer in humans. This study addresses the impact of loss-of-function mutations in breast cancer MCF-7 cells. Using the CRISPR/Cas9 system, we generated mutations that caused heterozygous truncated proteins, isolating three monoclonal lines carrying insertions and deletions in ARID4B. We observed reduced proliferation and migration in in vitro experiments. In addition, from RNA-seq assays, a differential expression analysis shows known and novel deregulated cancer-associate pathways in mutated cells supporting the impact of ARID4B. For example, we found the AKT-PI3K pathway to be altered at the transcript level but through different genes than those reported for ARID4B. Our transcriptomic results also suggest new insights into the role of ARID4B in aggressiveness by the epithelial-to-mesenchymal transition and TGF-β pathways and in metabolism through cholesterol and mevalonate pathways. We also performed exome sequencing to show that no off-target effects were apparent. In conclusion, the ARID4B gene is associated with some aggressive phenotypes in breast cancer cells.
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Affiliation(s)
- Fernando Gonzalez-Salinas
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Ave. Morones Prieto 3000, Monterrey 64710, Nuevo Leon, Mexico; (F.G.-S.); (J.H.-G.); (R.R.)
| | - Jessica Herrera-Gamboa
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Ave. Morones Prieto 3000, Monterrey 64710, Nuevo Leon, Mexico; (F.G.-S.); (J.H.-G.); (R.R.)
- Instituto de Biotecnología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo Leon, San Nicolas de los Garza 66455, Nuevo Leon, Mexico
| | - Rocio Rojo
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Ave. Morones Prieto 3000, Monterrey 64710, Nuevo Leon, Mexico; (F.G.-S.); (J.H.-G.); (R.R.)
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City 14380, Mexico
| | - Victor Trevino
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Ave. Morones Prieto 3000, Monterrey 64710, Nuevo Leon, Mexico; (F.G.-S.); (J.H.-G.); (R.R.)
- Tecnologico de Monterrey, The Institute for Obesity Research, Eugenio Garza Sada Avenue 2501, Monterrey 64849, Nuevo Leon, Mexico
- Tecnologico de Monterrey, oriGen Project, Eugenio Garza Sada Avenue 2501, Monterrey 64849, Nuevo Leon, Mexico
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16
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Zhong B, Liao Q, Wang X, Wang X, Zhang J. The roles of epigenetic regulation in cholangiocarcinogenesis. Biomed Pharmacother 2023; 166:115290. [PMID: 37557012 DOI: 10.1016/j.biopha.2023.115290] [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: 06/22/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/11/2023] Open
Abstract
Cholangiocarcinoma (CCA), a heterogeneous malignancy of bile duct epithelial cells, is characterized by aggressiveness, difficult diagnosis, and poor prognosis due to limited understanding and lack of effective therapeutic strategies. Genetic and epigenetic alterations accumulated in CCA cells can cause the aberrant regulation of oncogenes and tumor suppressors. Epigenetic alterations with histone modification, DNA methylation, and noncoding RNA modulation are associated with the carcinogenesis of CCA. Mutation or silencing of genes by various mechanisms can be a frequent event during CCA development. Alterations in histone acetylation/deacetylation at the posttranslational level, DNA methylation at promoters, and noncoding RNA regulation contribute to the heterogeneity of CCA and drive tumor development. In this review article, we mainly focus on the roles of epigenetic regulation in cholangiocarcinogenesis. Alterations in epigenetic modification can be potential targets for the therapeutic management of CCA, and epigenetic targets may become diagnostic biomarkers of CCA.
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Affiliation(s)
- Baiyin Zhong
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Qicheng Liao
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Xin Wang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Xiaonong Wang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Jianhong Zhang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China; Ganzhou Key Laboratory of Hepatocellular Carcinoma, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China.
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17
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Yang S, Hu H, Kung H, Zou R, Dai Y, Hu Y, Wang T, Lv T, Yu J, Li F. Organoids: The current status and biomedical applications. MedComm (Beijing) 2023; 4:e274. [PMID: 37215622 PMCID: PMC10192887 DOI: 10.1002/mco2.274] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/22/2023] [Accepted: 04/27/2023] [Indexed: 05/24/2023] Open
Abstract
Organoids are three-dimensional (3D) miniaturized versions of organs or tissues that are derived from cells with stem potential and can self-organize and differentiate into 3D cell masses, recapitulating the morphology and functions of their in vivo counterparts. Organoid culture is an emerging 3D culture technology, and organoids derived from various organs and tissues, such as the brain, lung, heart, liver, and kidney, have been generated. Compared with traditional bidimensional culture, organoid culture systems have the unique advantage of conserving parental gene expression and mutation characteristics, as well as long-term maintenance of the function and biological characteristics of the parental cells in vitro. All these features of organoids open up new opportunities for drug discovery, large-scale drug screening, and precision medicine. Another major application of organoids is disease modeling, and especially various hereditary diseases that are difficult to model in vitro have been modeled with organoids by combining genome editing technologies. Herein, we introduce the development and current advances in the organoid technology field. We focus on the applications of organoids in basic biology and clinical research, and also highlight their limitations and future perspectives. We hope that this review can provide a valuable reference for the developments and applications of organoids.
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Affiliation(s)
- Siqi Yang
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Haijie Hu
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Hengchung Kung
- Krieger School of Arts and SciencesJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Ruiqi Zou
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Yushi Dai
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Yafei Hu
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Tiantian Wang
- Key Laboratory of Rehabilitation Medicine in Sichuan ProvinceWest China HospitalSichuan UniversityChengduSichuanChina
| | - Tianrun Lv
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
| | - Jun Yu
- Departments of MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Departments of OncologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Fuyu Li
- Division of Biliary Tract SurgeryDepartment of General SurgeryWest China HospitalSichuan UniversityChengduSichuan ProvinceChina
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Czegle I, Huang C, Soria PG, Purkiss DW, Shields A, Wappler-Guzzetta EA. The Role of Genetic Mutations in Mitochondrial-Driven Cancer Growth in Selected Tumors: Breast and Gynecological Malignancies. Life (Basel) 2023; 13:996. [PMID: 37109525 PMCID: PMC10145875 DOI: 10.3390/life13040996] [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: 12/28/2022] [Revised: 03/15/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
There is an increasing understanding of the molecular and cytogenetic background of various tumors that helps us better conceptualize the pathogenesis of specific diseases. Additionally, in many cases, these molecular and cytogenetic alterations have diagnostic, prognostic, and/or therapeutic applications that are heavily used in clinical practice. Given that there is always room for improvement in cancer treatments and in cancer patient management, it is important to discover new therapeutic targets for affected individuals. In this review, we discuss mitochondrial changes in breast and gynecological (endometrial and ovarian) cancers. In addition, we review how the frequently altered genes in these diseases (BRCA1/2, HER2, PTEN, PIK3CA, CTNNB1, RAS, CTNNB1, FGFR, TP53, ARID1A, and TERT) affect the mitochondria, highlighting the possible associated individual therapeutic targets. With this approach, drugs targeting mitochondrial glucose or fatty acid metabolism, reactive oxygen species production, mitochondrial biogenesis, mtDNA transcription, mitophagy, or cell death pathways could provide further tailored treatment.
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Affiliation(s)
- Ibolya Czegle
- Department of Internal Medicine and Haematology, Semmelweis University, H-1085 Budapest, Hungary
| | - Chelsea Huang
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
| | - Priscilla Geraldine Soria
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
| | - Dylan Wesley Purkiss
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
| | - Andrea Shields
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA
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