1
|
Portolés I, Ribera J, Fernandez-Galán E, Lecue E, Casals G, Melgar-Lesmes P, Fernández-Varo G, Boix L, Sanduzzi M, Aishwarya V, Reig M, Jiménez W, Morales-Ruiz M. Identification of Dhx15 as a Major Regulator of Liver Development, Regeneration, and Tumor Growth in Zebrafish and Mice. Int J Mol Sci 2024; 25:3716. [PMID: 38612527 PMCID: PMC11011938 DOI: 10.3390/ijms25073716] [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: 02/26/2024] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
RNA helicase DHX15 plays a significant role in vasculature development and lung metastasis in vertebrates. In addition, several studies have demonstrated the overexpression of DHX15 in the context of hepatocellular carcinoma. Therefore, we hypothesized that this helicase may play a significant role in liver regeneration, physiology, and pathology. Dhx15 gene deficiency was generated by CRISPR/Cas9 in zebrafish and by TALEN-RNA in mice. AUM Antisense-Oligonucleotides were used to silence Dhx15 in wild-type mice. The hepatocellular carcinoma tumor induction model was generated by subcutaneous injection of Hepa 1-6 cells. Homozygous Dhx15 gene deficiency was lethal in zebrafish and mouse embryos. Dhx15 gene deficiency impaired liver organogenesis in zebrafish embryos and liver regeneration after partial hepatectomy in mice. Also, heterozygous mice presented decreased number and size of liver metastasis after Hepa 1-6 cells injection compared to wild-type mice. Dhx15 gene silencing with AUM Antisense-Oligonucleotides in wild-type mice resulted in 80% reduced expression in the liver and a significant reduction in other major organs. In addition, Dhx15 gene silencing significantly hindered primary tumor growth in the hepatocellular carcinoma experimental model. Regarding the potential use of DHX15 as a diagnostic marker for liver disease, patients with hepatocellular carcinoma showed increased levels of DHX15 in blood samples compared with subjects without hepatic affectation. In conclusion, Dhx15 is a key regulator of liver physiology and organogenesis, is increased in the blood of cirrhotic and hepatocellular carcinoma patients, and plays a key role in controlling hepatocellular carcinoma tumor growth and expansion in experimental models.
Collapse
Affiliation(s)
- Irene Portolés
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
| | - Jordi Ribera
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
| | - Esther Fernandez-Galán
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
| | - Elena Lecue
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
| | - Gregori Casals
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
- Commission for the Biochemical Evaluation of the Hepatic Disease-SEQCML, 08036 Barcelona, Spain
| | - Pedro Melgar-Lesmes
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
- Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Guillermo Fernández-Varo
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
| | - Loreto Boix
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
- Barcelona Clinic Liver Cancer Group, Liver Unit, Hospital Clinic, University of Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Marco Sanduzzi
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
- Barcelona Clinic Liver Cancer Group, Liver Unit, Hospital Clinic, University of Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Veenu Aishwarya
- AUM LifeTech, Inc., 3675 Market Street, Suite 200, Philadelphia, PA 19104, USA;
| | - Maria Reig
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
- Barcelona Clinic Liver Cancer Group, Liver Unit, Hospital Clinic, University of Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Wladimiro Jiménez
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
- Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Manuel Morales-Ruiz
- Biochemistry and Molecular Genetics Department-CDB, Hospital Clínic of Barcelona, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 170 Villarroel St. Barcelona, 08036 Barcelona, Spain; (I.P.); (J.R.); (E.F.-G.); (E.L.); (G.C.); (P.M.-L.); (G.F.-V.); (W.J.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28222 Madrid, Spain; (L.B.); (M.S.); (M.R.)
- Commission for the Biochemical Evaluation of the Hepatic Disease-SEQCML, 08036 Barcelona, Spain
- Biomedicine Department, Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| |
Collapse
|
2
|
Fan L, Guo X, Zhang J, Wang Y, Wang J, Li Y. Relationship between DHX15 expression and survival in colorectal cancer. REVISTA ESPANOLA DE ENFERMEDADES DIGESTIVAS 2023; 115:234-240. [PMID: 36177832 DOI: 10.17235/reed.2022.8838/2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
OBJECTIVE to explore the relationship between the expression of DEAH-box RNA helicase 15 (DHX15) in colorectal cancer (CRC), its clinical pathological features and survival. METHOD DHX15 expression data with clinical pathological features from the Cancer Gene Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) were statistically analyzed for the association between DHX15 expression and overall survival in CRC. The expression of DHX15 was performed by immunohistochemical staining (IHC) using tumor and the adjacent normal tissue, mounted in tissue microarrays. The significance of DHX15 expression to predict survival and prognosis of CRC were analyzed using the Kaplan-Meier method, univariate and multivariate Cox regression analysis. RESULTS low expression of DHX15 mRNA and DHX15 protein in CRC were both negative factors for survival. Overall survival of patients with low-expression of DHX15 was significantly lower (χ2 = 8.452, p = 0.004) by Kaplan-Meier evaluation. Low expression of DHX15 in CRC tissues correlated with distal lymph node metastasis (χ² = 7.120, p = 0.008), TNM stage (χ² = 3.935, p = 0.047) and disease recurrence (χ² = 9.524, p = 0.002) in CRC. Low expression of DHX15 (HR = 4.012, 95 % CI: 1.462-11.013, p = 0.007), late TNM stage (HR = 0.067, 95 % CI: 0.029-0.156, p < 0.001) and recurrence (HR = 0.008, 95 % CI: 0.002-0.034, p < 0.001) were risk factors related to the prognosis of CRC patients by univariate Cox regression analysis. CONCLUSION our findings reveal a key role for DHX15 in the progress of CRC metastasis and recurrence. DHX15 may be a potential biomarker for CRC targeted therapy.
Collapse
Affiliation(s)
- Leqi Fan
- Pharmacology, Capital Medical University
| | | | - Jiyi Zhang
- Medical Chemistry, Capital Medical University
| | - Yuji Wang
- Medical Chemistry, Capital Medical University
| | - Jinhui Wang
- Pharmaceutical Science, Harbin Medical University
| | - Ye Li
- Pharmacology, Capital Medical University, China
| |
Collapse
|
3
|
Miao Y, Yuan Q, Wang C, Feng X, Ren J, Wang C. Comprehensive Characterization of RNA-Binding Proteins in Colon Adenocarcinoma Identifies a Novel Prognostic Signature for Predicting Clinical Outcomes and Immunotherapy Responses Based on Machine Learning. Comb Chem High Throughput Screen 2023; 26:163-182. [PMID: 35379120 DOI: 10.2174/1386207325666220404125228] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND RNA-binding proteins (RBPs) are crucial factors that function in the posttranscriptional modification process and are significant in cancer. OBJECTIVE This research aimed for a multigene signature to predict the prognosis and immunotherapy response of patients with colon adenocarcinoma (COAD) based on the expression profile of RNA-binding proteins (RBPs). METHODS COAD samples retrieved from the TCGA and GEO datasets were utilized for a training dataset and a validation dataset. Totally, 14 shared RBP genes with prognostic significance were identified. Non-negative matrix factorization clusters defined by these RBPs could stratify COAD patients into two molecular subtypes. Cox regression analysis and identification of 8-gene signature categorized COAD patients into high- and low-risk populations with significantly different prognosis and immunotherapy responses. RESULTS Our prediction signature was superior to another five well-established prediction models. A nomogram was generated to quantificationally predict the overall survival (OS) rate, validated by calibration curves. Our findings also indicated that high-risk populations possessed an enhanced immune evasion capacity and low-risk populations might benefit immunotherapy, especially for the joint combination of PD-1 and CTLA4 immunosuppressants. DHX15 and LARS2 were detected with significantly different expressions in both datasets, which were further confirmed by qRTPCR and immunohistochemical staining. CONCLUSION Our observations supported an eight-RBP-related signature that could be applied for survival prediction and immunotherapy response of patients with COAD.
Collapse
Affiliation(s)
- Ye Miao
- Department of Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Department of Neurosurgery, First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Qihang Yuan
- Department of Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Chao Wang
- Department of Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Xiaoshi Feng
- Department of Endocrinology, First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Jie Ren
- Department of Oncology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Changmiao Wang
- Department of Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| |
Collapse
|
4
|
Sers C, Schäfer R. Silencing effects of mutant RAS signalling on transcriptomes. Adv Biol Regul 2023; 87:100936. [PMID: 36513579 DOI: 10.1016/j.jbior.2022.100936] [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: 11/19/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Mutated genes of the RAS family encoding small GTP-binding proteins drive numerous cancers, including pancreatic, colon and lung tumors. Besides the numerous effects of mutant RAS gene expression on aberrant proliferation, transformed phenotypes, metabolism, and therapy resistance, the most striking consequences of chronic RAS activation are changes of the genetic program. By performing systematic gene expression studies in cellular models that allow comparisons of pre-neoplastic with RAS-transformed cells, we and others have estimated that 7 percent or more of all transcripts are altered in conjunction with the expression of the oncogene. In this context, the number of up-regulated transcripts approximates that of down-regulated transcripts. While up-regulated transcription factors such as MYC, FOSL1, and HMGA2 have been identified and characterized as RAS-responsive drivers of the altered transcriptome, the suppressed factors have been less well studied as potential regulators of the genetic program and transformed phenotype in the breadth of their occurrence. We therefore have collected information on downregulated RAS-responsive factors and discuss their potential role as tumor suppressors that are likely to antagonize active cancer drivers. To better understand the active mechanisms that entail anti-RAS function and those that lead to loss of tumor suppressor activity, we focus on the tumor suppressor HREV107 (alias PLAAT3 [Phospholipase A and acyltransferase 3], PLA2G16 [Phospholipase A2, group XVI] and HRASLS3 [HRAS-like suppressor 3]). Inactivating HREV107 mutations in tumors are extremely rare, hence epigenetic causes modulated by the RAS pathway are likely to lead to down-regulation and loss of function.
Collapse
Affiliation(s)
- Christine Sers
- Laboratory of Molecular Tumor Pathology and systems Biology, Institute of Pathology, Charité Universitätstmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany; German Cancer Consortium, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany
| | - Reinhold Schäfer
- Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; German Cancer Consortium, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
| |
Collapse
|
5
|
The RNA helicase DHX15 is a critical regulator of natural killer-cell homeostasis and functions. Cell Mol Immunol 2022; 19:687-701. [PMID: 35322175 DOI: 10.1038/s41423-022-00852-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/28/2022] [Indexed: 11/08/2022] Open
Abstract
The RNA helicase DHX15 is widely expressed in immune cells and traditionally thought to be an RNA splicing factor or a viral RNA sensor. However, the role of DHX15 in NK-cell activities has not been studied thus far. Here, we generated Dhx15-floxed mice and found that conditional deletion of Dhx15 in NK cells (Ncr1CreDhx15fl/fl mice) resulted in a marked reduction in NK cells in the periphery and that the remaining Dhx15-deleted NK cells failed to acquire a mature phenotype. As a result, Dhx15-deleted NK cells exhibited profound defects in their cytolytic functions. We also found that deletion of Dhx15 in NK cells abrogated their responsiveness to IL-15, which was associated with inhibition of IL-2/IL-15Rβ (CD122) expression and IL-15R signaling. The defects in Dhx15-deleted NK cells were rescued by ectopic expression of a constitutively active form of STAT5. Mechanistically, DHX15 did not affect CD122 mRNA splicing and stability in NK cells but instead facilitated the surface expression of CD122, likely through interaction with its 3'UTR, which was dependent on the ATPase domain of DHX15 rather than its splicing domain. Collectively, our data identify a key role for DHX15 in regulating NK-cell activities and provide novel mechanistic insights into how DHX15 regulates the IL-15 signaling pathway in NK cells.
Collapse
|
6
|
Xing J, Zhou X, Fang M, Zhang E, Minze LJ, Zhang Z. DHX15 is required to control RNA virus-induced intestinal inflammation. Cell Rep 2021; 35:109205. [PMID: 34161762 PMCID: PMC8276442 DOI: 10.1016/j.celrep.2021.109205] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/10/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023] Open
Abstract
RNA helicases play critical roles in various biological processes, including serving as viral RNA sensors in innate immunity. Here, we find that RNA helicase DEAH-box helicase 15 (DHX15) is essential for type I interferon (IFN-I, IFN-β), type III IFN (IFN-λ3), and inflammasome-derived cytokine IL-18 production by intestinal epithelial cells (IECs) in response to poly I:C and RNA viruses with preference of enteric RNA viruses, but not DNA virus. Importantly, we generate IEC-specific Dhx15-knockout mice and demonstrate that DHX15 is required for controlling intestinal inflammation induced by enteric RNA virus rotavirus in suckling mice and reovirus in adult mice in vivo, which owes to impaired IFN-β, IFN-λ3, and IL-18 production in IECs from Dhx15-deficient mice. Mechanistically, DHX15 interacts with NLRP6 to trigger NLRP6 inflammasome assembly and activation for inducing IL-18 secretion in IECs. Collectively, our report reveals critical roles for DHX15 in sensing enteric RNA viruses in IECs and controlling intestinal inflammation.
Collapse
Affiliation(s)
- Junji Xing
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Xiaojing Zhou
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Biochemistry, Clinical Medical College, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Mingli Fang
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Evan Zhang
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Laurie J Minze
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Zhiqiang Zhang
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Surgery, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA.
| |
Collapse
|
7
|
Zhao M, Ying L, Wang R, Yao J, Zhu L, Zheng M, Chen Z, Yang Z. DHX15 Inhibits Autophagy and the Proliferation of Hepatoma Cells. Front Med (Lausanne) 2021; 7:591736. [PMID: 33644083 PMCID: PMC7904900 DOI: 10.3389/fmed.2020.591736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 12/10/2020] [Indexed: 12/14/2022] Open
Abstract
Autophagy is a highly conserved process by which superfluous or harmful components in eukaryotic cells are degraded by autophagosomes. This cytoprotective mechanism is strongly related to various human diseases, such as cancer, autoimmune diseases, and diabetes. DEAH-box helicase 15 (DHX15), a member of the DEAH box family, is mainly involved in RNA splicing and ribosome maturation. Recently, DHX15 was identified as a tumor-related factor. Although both autophagy and DHX15 are involved in cellular metabolism and cancer progression, their exact relationship and mechanism remain elusive. In this study, we discovered a non-classic function of DHX15 and identified DHX15 as a suppressive protein in autophagy for the first time. We further found that mTORC1 is involved in DHX15-mediated regulation of autophagy and that DHX15 inhibits proliferation of hepatocellular carcinoma (HCC) cells by suppressing autophagy. In conclusion, our study demonstrates a non-classical function of DHX15 as a negative regulator of autophagy related to the mTORC1 pathway and reveals that DHX15-related autophagy dysfunction promotes HCC cell proliferation, indicating that DHX15 may be a target for liver cancer treatment.
Collapse
Affiliation(s)
- Miaomiao Zhao
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Lixiong Ying
- Pathology Department, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Rusha Wang
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Jiping Yao
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Liming Zhu
- Department of Chemotherapy, Zhejiang Cancer Hospital, Hangzhou, China
| | - Min Zheng
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Zhi Chen
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Zhenggang Yang
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| |
Collapse
|
8
|
The RNA helicase Dhx15 mediates Wnt-induced antimicrobial protein expression in Paneth cells. Proc Natl Acad Sci U S A 2021; 118:2017432118. [PMID: 33483420 PMCID: PMC7848544 DOI: 10.1073/pnas.2017432118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RNA helicases play roles in various essential biological processes such as RNA splicing and editing. Recent in vitro studies show that RNA helicases are involved in immune responses toward viruses, serving as viral RNA sensors or immune signaling adaptors. However, there is still a lack of in vivo data to support the tissue- or cell-specific function of RNA helicases owing to the lethality of mice with complete knockout of RNA helicases; further, there is a lack of evidence about the antibacterial role of helicases. Here, we investigated the in vivo role of Dhx15 in intestinal antibacterial responses by generating mice that were intestinal epithelial cell (IEC)-specific deficient for Dhx15 (Dhx15 f/f Villin1-cre, Dhx15ΔIEC). These mice are susceptible to infection with enteric bacteria Citrobacter rodentium (C. rod), owing to impaired α-defensin production by Paneth cells. Moreover, mice with Paneth cell-specific depletion of Dhx15 (Dhx15 f/f Defensinα6-cre, Dhx15ΔPaneth) are more susceptible to DSS (dextran sodium sulfate)-induced colitis, which phenocopy Dhx15ΔIEC mice, due to the dysbiosis of the intestinal microbiota. In humans, reduced protein levels of Dhx15 are found in ulcerative colitis (UC) patients. Taken together, our findings identify a key regulator of Wnt-induced α-defensins in Paneth cells and offer insights into its role in the antimicrobial response as well as intestinal inflammation.
Collapse
|
9
|
Zhao MM, Wang RS, Zhou YL, Yang ZG. Emerging relationship between RNA helicases and autophagy. J Zhejiang Univ Sci B 2020; 21:767-778. [PMID: 33043643 PMCID: PMC7606199 DOI: 10.1631/jzus.b2000245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 08/10/2020] [Indexed: 01/15/2023]
Abstract
RNA helicases, the largest family of proteins that participate in RNA metabolism, stabilize the intracellular environment through various processes, such as translation and pre-RNA splicing. These proteins are also involved in some diseases, such as cancers and viral diseases. Autophagy, a self-digestive and cytoprotective trafficking process in which superfluous organelles and cellular garbage are degraded to stabilize the internal environment or maintain basic cellular survival, is associated with human diseases. Interestingly, similar to autophagy, RNA helicases play important roles in maintaining cellular homeostasis and are related to many types of diseases. According to recent studies, RNA helicases are closely related to autophagy, participate in regulating autophagy, or serve as a bridge between autophagy and other cellular activities that widely regulate some pathophysiological processes or the development and progression of diseases. Here, we summarize the most recent studies to understand how RNA helicases function as regulatory proteins and determine their association with autophagy in various diseases.
Collapse
Affiliation(s)
- Miao-miao Zhao
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Ru-sha Wang
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Yan-lin Zhou
- Department of Gastroenterology, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310006, China
| | - Zheng-gang Yang
- The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| |
Collapse
|
10
|
McElderry J, Carrington B, Bishop K, Kim E, Pei W, Chen Z, Ramanagoudr-Bhojappa R, Prakash A, Burgess SM, Liu PP, Sood R. Splicing factor DHX15 affects tp53 and mdm2 expression via alternate splicing and promoter usage. Hum Mol Genet 2020; 28:4173-4185. [PMID: 31691804 DOI: 10.1093/hmg/ddz261] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/18/2019] [Accepted: 10/24/2019] [Indexed: 12/21/2022] Open
Abstract
DHX15, a DEAH box containing RNA helicase, is a splicing factor required for the last step of splicing. Recent studies identified a recurrent mutational hotspot, R222G, in DHX15 in ∼ 6% of acute myeloid leukemia (AML) patients that carry the fusion protein RUNX1-RUNX1T1 produced by t (8;21) (q22;q22). Studies using yeast mutants showed that substitution of G for the residue equivalent to R222 leads to loss of its helicase function, suggesting that it is a loss-of-function mutation. To elucidate the role of DHX15 during development, we established the first vertebrate knockout model with CRISPR/Cas9 in zebrafish. Our data showed that dhx15 expression is enriched in the brain, eyes, pectoral fin primordia, liver and intestinal bulb during embryonic development. Dhx15 deficiency leads to pleiotropic morphological phenotypes in homozygous mutant embryos starting at 3 days post fertilization (dpf) that result in lethality by 7 dpf, revealing an essential role during embryonic development. RNA-seq analysis suggested important roles of Dhx15 in chromatin and nucleosome assembly and regulation of the Mdm2-p53 pathway. Interestingly, exons corresponding to the alternate transcriptional start sites for tp53 and mdm2 were preferentially expressed in the mutant embryos, leading to significant upregulation of their alternate isoforms, Δ113p53 (orthologous to Δ133p53 isoform in human) and mdm2-P2 (isoform using distal promoter P2), respectively. We speculate that these alterations in the Mdm2-p53 pathway contribute to the development of AML in patients with t(8;21) and somatically mutated DHX15.
Collapse
Affiliation(s)
- John McElderry
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Blake Carrington
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Bishop
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erika Kim
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wuhong Pei
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zelin Chen
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ramanagouda Ramanagoudr-Bhojappa
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anupam Prakash
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shawn M Burgess
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - P Paul Liu
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raman Sood
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
11
|
Yao G, Chen K, Qin Y, Niu Y, Zhang X, Xu S, Zhang C, Feng M, Wang K. Long Non-coding RNA JHDM1D-AS1 Interacts with DHX15 Protein to Enhance Non-Small-Cell Lung Cancer Growth and Metastasis. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 18:831-840. [PMID: 31739208 PMCID: PMC6861564 DOI: 10.1016/j.omtn.2019.09.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 09/04/2019] [Accepted: 09/21/2019] [Indexed: 01/16/2023]
Abstract
JHDM1D antisense 1 (JHDM1D-AS1), a long non-coding RNA (lncRNA), has been shown to promote pancreatic cancer growth by inducing an angiogenic response. However, its biological and clinical significance in non-small-cell lung cancer (NSCLC) is still unclear. In this study, we examined the expression and prognostic significance of JHDM1D-AS1 in NSCLC. The effects of JHDM1D-AS1 knockdown or overexpression on NSCLC growth and metastasis were investigated. We show that JHDM1D-AS1 is upregulated in NSCLC relative to adjacent normal lung tissues. High JHDM1D-AS1 expression is significantly correlated with advanced tumor, node, and metastasis (TNM) stage and lymph node metastasis. JHDM1D-AS1 expression serves as an independent prognostic factor for overall survival of patients with NSCLC. Functionally, JHDM1D-AS1 knockdown inhibits NSCLC cell aggressiveness both in vitro and in vivo, which is rescued by ectopic expression of JHDM1D-AS1. JHDM1D-AS1 binding stabilizes DHX15 protein in NSCLC cells. DHX15 overexpression enhances NSCLC cell proliferation and invasion, whereas knockdown of DHX15 exerts opposite effects. JHDM1D-AS1-mediated aggressive phenotype is impaired when DHX15 is silenced. Ectopic expression of DHX15 restores the defects in proliferation and invasion of JHDM1D-AS1-depleted NSCLC cells. Collectively, the interaction between JHDM1D-AS1 and DHX15 accounts for NSCLC growth and metastasis. This work provides potential additional therapeutic targets for treatment of NSCLC.
Collapse
Affiliation(s)
- Guodong Yao
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Kexin Chen
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yu Qin
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yangyang Niu
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xuefang Zhang
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shidong Xu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Chi Zhang
- Brandeis University, Waltham, MA, USA
| | - Meiyan Feng
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China.
| | - Kuan Wang
- Department of Gastrointestinal Surgery, Harbin Medical University Cancer Hospital, Harbin, China.
| |
Collapse
|
12
|
Xu Y, Song Q, Pascal LE, Zhong M, Zhou Y, Zhou J, Deng F, Huang J, Wang Z. DHX15 is up-regulated in castration-resistant prostate cancer and required for androgen receptor sensitivity to low DHT concentrations. Prostate 2019; 79:657-666. [PMID: 30714180 PMCID: PMC6823643 DOI: 10.1002/pros.23773] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/11/2019] [Indexed: 01/04/2023]
Abstract
BACKGROUND DHX15 is a member of the DEAH-box (DHX) RNA helicase family. Our previous study identified it as an AR coactivator which contributes to prostate cancer progression. METHODS We investigated DHX15 expression in castration resistant prostate cancer specimens and the influence of DHX15 on the responsiveness of prostate cancer cells to DHT stimulation. We also explored the role DHX15 played in enzalutamide resistance and the interacting domain in DHX15 with AR. DHX15 expression level in human CRPC specimens and prostate cancer specimens was detected by tissue microarray (TMA) immunostaining analysis. Colony formation assay was performed to determine the proliferation of cells treated with enzalutamide or DHT. siRNAs were used to knockdown DHX15. The interactions between DHX15 and AR were detected using co-immunoprecipitation assay. RESULTS The expression level of DHX15 was upregulated in human CRPC specimens compared with hormone naïve prostate cancer specimens. DHX15 knockdown reduced AR sensitivity to low DHT concentrations in C4-2 cells. Inactivation of DHX15 sensitizes the enzalutamide treatment in C4-2 cells. Deletion mutagenesis indicated that DHX1 5 interacts with AR through its N terminal domain. CONCLUSIONS These findings suggest that DHX15 contributes to prostate cancer progression. DHX15 is required for androgen receptor sensitivity to low DHT concentrations and contributes to enzalutamide resistance in C4-2 cells. Targeting DHX15 may improve the ADT treatment.
Collapse
Affiliation(s)
- Yadong Xu
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, China
- The Third Xiangya Hospital of Central South University, Changsha, China
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Qiong Song
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Center for Translational Medicine, Guangxi Medical University, Nanning, China
| | - Laura E. Pascal
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Mingming Zhong
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yibin Zhou
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jianhua Zhou
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Fang‐Ming Deng
- Department of Pathology, NYU School of Medicine, New York, New York
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina
| | - Zhou Wang
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| |
Collapse
|
13
|
Xie C, Liao H, Zhang C, Zhang S. Overexpression and clinical relevance of the RNA helicase DHX15 in hepatocellular carcinoma. Hum Pathol 2018; 84:213-220. [PMID: 30339968 DOI: 10.1016/j.humpath.2018.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/29/2018] [Accepted: 10/04/2018] [Indexed: 01/06/2023]
Abstract
DHX15 is an outstanding member of the DEAH-box RNA helicase family. A few studies suggest that DHX15 contributes to carcinogenesis in several tumor cell lines. However, whether DHX15 acts as an oncogene or tumor suppressor and its association with hepatocellular carcinoma (HCC) prognosis are still poorly understood. To address this question, we used immunohistochemistry to evaluate DHX15 expression patterns and their association with clinicopathological factors and the prognosis of patients with HCC. Our results showed that DHX15 expression was significantly higher in cancerous tissues than that in nontumor tissues (P < .0001). DHX15 expression in HCC patients was associated with differentiation status (P = .018), tumor number (P = .048), intrahepatic or extrahepatic metastasis (P = .001), serum α-fetoprotein (P = .006), hepatitis B virus level (P = .018), and recurrence (P < .001). In addition, the survival analysis revealed that the DHX15-high group had significantly decreased overall survival time (P = .004) and lower 1-year survival rates (P = .002) compared with the DHX15-low group. Furthermore, multivariate analysis identified DHX15 expression as an independent factor associated with poor prognosis in HCC (P = .036). In summary, these findings demonstrate, for the first time, that DHX15 is significantly upregulated in HCC and its high expression was correlated with poor prognosis, suggesting its pivotal role in the progression of HCC. The present results suggest that DHX15 may serve as a potential prognostic biomarker for HCC patients.
Collapse
Affiliation(s)
- Chengrong Xie
- Fujian Provincial Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma (Xiamen University Affiliated Zhongshan Hospital), Fujian, China
| | - Hongfeng Liao
- Department of Pathology, Xiamen University Affiliated Zhongshan Hospital, Fujian, China
| | - Changmao Zhang
- School of Clinical Medicine, Fujian Medical University, Fujian, China
| | - Sheng Zhang
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| |
Collapse
|
14
|
Zhang Y, Fang L, Zang Y, Xu Z. Identification of Core Genes and Key Pathways via Integrated Analysis of Gene Expression and DNA Methylation Profiles in Bladder Cancer. Med Sci Monit 2018; 24:3024-3033. [PMID: 29739919 PMCID: PMC5968840 DOI: 10.12659/msm.909514] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Background Bladder cancer (BC) is the most common urological malignant tumor. In BC, aberrant DNA methylation is believed to be associated with carcinogenesis. Therefore, the identification of key genes and pathways could help determine the potential molecular mechanisms of BC development. Material/Methods Microarray data on gene expression and gene methylation were downloaded from the Gene Expression Omnibus (GEO) database. Abnormal methylated/expressed genes were analyzed by GEO2R and statistical software R. Gene Ontology term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed using the DAVID database and KOBAS 3.0. STRING and Cytoscape software were used to construct protein–protein interaction (PPI) networks and analyze modules of the PPI network. Results A total of 71 hypomethylated/upregulated genes were significantly enriched in cell–cell adhesion and blood vessel development. KEGG pathway analysis highlighted p53 signaling and metabolic pathways. Five core genes in the PPI network were determined: CDH1, DDOST, CASP8, DHX15, and PTPRF. Additionally, 89 hypermethylated/downregulated genes were found. These genes were enriched mostly in cell adhesion and signal transduction. KEGG pathway analysis revealed enrichment in focal adhesion. The top 5 core genes in the PPI network were GNG4, ADCY9, NPY, ADRA2B, and PENK. We found most of the core genes were also significantly altered in the Cancer Genome Atlas database. Conclusions Abnormal methylated/expressed genes and key signaling pathways involved in BC were identified through integrated bioinformatics analysis. In the future, these genes may serve as biomarkers for diagnosis and therapeutic targets in BC.
Collapse
Affiliation(s)
- Yongzhen Zhang
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
| | - Liang Fang
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
| | - Yuanwei Zang
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
| | - Zhonghua Xu
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
| |
Collapse
|