1
|
Karri K, Waxman DJ. Dysregulation of murine long noncoding single-cell transcriptome in nonalcoholic steatohepatitis and liver fibrosis. RNA (NEW YORK, N.Y.) 2023; 29:977-1006. [PMID: 37015806 PMCID: PMC10275269 DOI: 10.1261/rna.079580.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
LncRNAs comprise a heterogeneous class of RNA-encoding genes typified by low expression, nuclear enrichment, high tissue-specificity, and functional diversity, but the vast majority remain uncharacterized. Here, we assembled the mouse liver noncoding transcriptome from >2000 bulk RNA-seq samples and discovered 48,261 liver-expressed lncRNAs, a majority novel. Using these lncRNAs as a single-cell transcriptomic reference set, we elucidated lncRNA dysregulation in mouse models of high fat diet-induced nonalcoholic steatohepatitis and carbon tetrachloride-induced liver fibrosis. Trajectory inference analysis revealed lncRNA zonation patterns across the liver lobule in each major liver cell population. Perturbations in lncRNA expression and zonation were common in several disease-associated liver cell types, including nonalcoholic steatohepatitis-associated macrophages, a hallmark of fatty liver disease progression, and collagen-producing myofibroblasts, a central feature of liver fibrosis. Single-cell-based gene regulatory network analysis using bigSCale2 linked individual lncRNAs to specific biological pathways, and network-essential regulatory lncRNAs with disease-associated functions were identified by their high network centrality metrics. For a subset of these lncRNAs, promoter sequences of the network-defined lncRNA target genes were significantly enriched for lncRNA triplex formation, providing independent mechanistic support for the lncRNA-target gene linkages predicted by the gene regulatory networks. These findings elucidate liver lncRNA cell-type specificities, spatial zonation patterns, associated regulatory networks, and temporal patterns of dysregulation during hepatic disease progression. A subset of the liver disease-associated regulatory lncRNAs identified have human orthologs and are promising candidates for biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Kritika Karri
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
| | - David J Waxman
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
| |
Collapse
|
2
|
Zhang Y, He L, Huang L, Yao S, Lin N, Li P, Xu H, Wu X, Xu J, Lu Y, Li Y, Zhu S. Oncogenic PAX6 elicits CDK4/6 inhibitor resistance by epigenetically inactivating the LATS2-Hippo signaling pathway. Clin Transl Med 2021; 11:e503. [PMID: 34459131 PMCID: PMC8382979 DOI: 10.1002/ctm2.503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 07/04/2021] [Accepted: 07/11/2021] [Indexed: 12/13/2022] Open
Abstract
Intrinsic resistance to CDK4/6 inhibitors hinders their clinical utility in cancer treatment. Furthermore, the predictive markers of CDK4/6 inhibitors in gastric cancer (GC) remain incompletely described. Here, we found that PAX6 expression was negatively correlated with the response to palbociclib in vitro and in vivo in GC. We observed that the PAX6 expression level was negatively correlated with the overall survival of GC patients and further showed that PAX6 can promote GC cell proliferation and the cell cycle. The cell cycle is regulated by the interaction of cyclins with their partner serine/threonine cyclin-dependent kinases (CDKs), and the G1/S-phase transition is the main target of CDK4/6 inhibitors. Therefore, we tested whether PAX6 expression was correlated with the GC response to palbociclib. We found that PAX6 hypermethylates the promoter of LATS2 and inactivates the Hippo pathway, which upregulates cyclin D1 (CCND1) expression. This results in a suppressed response to palbociclib in GC. Furthermore, we found that the induction of the Hippo signaling pathway or treatment with a DNA methylation inhibitor could overcome PAX6-induced palbociclib resistance in GC. These findings uncover a tumor promoter function of PAX6 in GC and establish overexpressed PAX6 as a mechanism of resistance to palbociclib.
Collapse
Affiliation(s)
- Yi Zhang
- Department of Gastroenterology and Hepatology, the First Affiliated HospitalSun Yat‐sen UniversityNo.58 Zhongshan 2nd RoadGuangzhou510630China
- Department of Hepatobiliary surgery, the Third Affiliated HospitalSun Yat‐sen UniversityNo.600 Tian he RoadGuangzhou510630China
- Department of Hepatic surgery, the First Affiliated HospitalSun Yat‐sen UniversityNo.58 Zhongshan 2nd RoadGuangzhou510080China
| | - Long‐Jun He
- State Key Laboratory of Oncology in South ChinaCancer CenterSun Yat‐sen UniversityNo.651 Dongfeng Road EastGuangzhou510060China
| | - Lin‐Lin Huang
- Department of Gastroenterology and Hepatology, the First Affiliated HospitalSun Yat‐sen UniversityNo.58 Zhongshan 2nd RoadGuangzhou510630China
- Department of Gastroenterology and HepatologyGuangdong Provincial People's Hospital/Guangdong Academy of Medical
SciencesNo.106 Zhongshan 2nd RoadGuangzhou510080China
| | - Sheng Yao
- Department of Gastroenterology and Hepatology, the First Affiliated HospitalSun Yat‐sen UniversityNo.58 Zhongshan 2nd RoadGuangzhou510630China
| | - Nan Lin
- Department of Hepatobiliary surgery, the Third Affiliated HospitalSun Yat‐sen UniversityNo.600 Tian he RoadGuangzhou510630China
| | - Ping Li
- Department of Gastroenterology and Hepatology, the First Affiliated HospitalSun Yat‐sen UniversityNo.58 Zhongshan 2nd RoadGuangzhou510630China
| | - Hui‐Wen Xu
- Department of Gastroenterology and Hepatology, the First Affiliated HospitalSun Yat‐sen UniversityNo.58 Zhongshan 2nd RoadGuangzhou510630China
| | - Xi‐Wen Wu
- Department of Hepatic surgery, the First Affiliated HospitalSun Yat‐sen UniversityNo.58 Zhongshan 2nd RoadGuangzhou510080China
| | - Jian‐Liang Xu
- Department of Hepatobiliary surgery, the Third Affiliated HospitalSun Yat‐sen UniversityNo.600 Tian he RoadGuangzhou510630China
| | - Yi Lu
- Department of Hepatobiliary surgery, the Third Affiliated HospitalSun Yat‐sen UniversityNo.600 Tian he RoadGuangzhou510630China
| | - Yan‐Jie Li
- Department of Hepatobiliary surgery, the Third Affiliated HospitalSun Yat‐sen UniversityNo.600 Tian he RoadGuangzhou510630China
| | - Sen‐Lin Zhu
- Department of Gastroenterology and Hepatology, the First Affiliated HospitalSun Yat‐sen UniversityNo.58 Zhongshan 2nd RoadGuangzhou510630China
| |
Collapse
|
3
|
Su PH, Huang RL, Lai HC, Chen LY, Weng YC, Wang CC, Wu CC. NKX6-1 mediates cancer stem-like properties and regulates sonic hedgehog signaling in leiomyosarcoma. J Biomed Sci 2021; 28:32. [PMID: 33906647 PMCID: PMC8077933 DOI: 10.1186/s12929-021-00726-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/09/2021] [Indexed: 01/04/2023] Open
Abstract
Background Leiomyosarcoma (LMS), the most common soft tissue sarcoma, exhibits heterogeneous and complex genetic karyotypes with severe chromosomal instability and rearrangement and poor prognosis. Methods Clinical variables associated with NKX6-1 were obtained from The Cancer Genome Atlas (TCGA). NKX6-1 mRNA expression was examined in 49 human uterine tissues. The in vitro effects of NXK6-1 in LMS cells were determined by reverse transcriptase PCR, western blotting, colony formation, spheroid formation, and cell viability assays. In vivo tumor growth was evaluated in nude mice. Results Using The Cancer Genome Atlas (TCGA) and human uterine tissue datasets, we observed that NKX6-1 expression was associated with poor prognosis and malignant potential in LMS. NKX6-1 enhanced in vitro tumor cell aggressiveness via upregulation of cell proliferation and anchorage-independent growth and promoted in vivo tumor growth. Moreover, overexpression and knockdown of NKX6-1 were associated with upregulation and downregulation, respectively, of stem cell transcription factors, including KLF8, MYC, and CD49F, and affected sphere formation, chemoresistance, NOTCH signaling and Sonic hedgehog (SHH) pathways in human sarcoma cells. Importantly, treatment with an SHH inhibitor (RU-SKI 43) but not a NOTCH inhibitor (DAPT) reduced cell survival in NKX6-1-expressing cancer cells, indicating that an SHH inhibitor could be useful in treating LMS. Finally, using the TCGA dataset, we demonstrated that LMS patients with high expression of NKX6-1 and HHAT, an SHH pathway acyltransferase, had poorer survival outcomes compared to those without. Conclusions Our findings indicate that NKX6-1 and HHAT play critical roles in the pathogenesis of LMS and could be promising diagnostic and therapeutic targets for LMS patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12929-021-00726-6.
Collapse
Affiliation(s)
- Po-Hsuan Su
- Translational Epigenetics Center, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Rui-Lan Huang
- Translational Epigenetics Center, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Hung-Cheng Lai
- Translational Epigenetics Center, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Obstetrics and Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Lin-Yu Chen
- Translational Epigenetics Center, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Yu-Chun Weng
- Translational Epigenetics Center, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Chih-Chien Wang
- Department of Orthopaedics, Tri-Service General Hospital, National Defense Medical Center, Neihu District, No. 325, Sec. 2, Chengong Road, Taipei, 11490, Taiwan
| | - Chia-Chun Wu
- Department of Orthopaedics, Tri-Service General Hospital, National Defense Medical Center, Neihu District, No. 325, Sec. 2, Chengong Road, Taipei, 11490, Taiwan.
| |
Collapse
|
4
|
Meier T, Timm M, Montani M, Wilkens L. Gene networks and transcriptional regulators associated with liver cancer development and progression. BMC Med Genomics 2021; 14:41. [PMID: 33541355 PMCID: PMC7863452 DOI: 10.1186/s12920-021-00883-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 01/24/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Treatment options for hepatocellular carcinoma (HCC) are limited, and overall survival is poor. Despite the high frequency of this malignoma, its basic disease mechanisms are poorly understood. Therefore, the aim of this study was to use different methodological approaches and combine the results to improve our knowledge on the development and progression of HCC. METHODS Twenty-three HCC samples were characterized by histological, morphometric and cytogenetic analyses, as well as comparative genomic hybridization (aCGH) and genome-wide gene expression followed by a bioinformatic search for potential transcriptional regulators and master regulatory molecules of gene networks. RESULTS Histological evaluation revealed low, intermediate and high-grade HCCs, and gene expression analysis split them into two main sets: GE1-HCC and GE2-HCC, with a low and high proliferation gene expression signature, respectively. Array-based comparative genomic hybridization demonstrated a high level of chromosomal instability, with recurrent chromosomal gains of 1q, 6p, 7q, 8q, 11q, 17q, 19p/q and 20q in both HCC groups and losses of 1p, 4q, 6q, 13q and 18q characteristic for GE2-HCC. Gene expression and bioinformatics analyses revealed that different genes and gene regulatory networks underlie the distinct biological features observed in GE1-HCC and GE2-HCC. Besides previously reported dysregulated genes, the current study identified new candidate genes with a putative role in liver cancer, e.g. C1orf35, PAFAH1B3, ZNF219 and others. CONCLUSION Analysis of our findings, in accordance with the available published data, argues in favour of the notion that the activated E2F1 signalling pathway, which can be responsible for both inappropriate cell proliferation and initial chromosomal instability, plays a pivotal role in HCC development and progression. A dedifferentiation switch that manifests in exaggerated gene expression changes might be due to turning on transcriptional co-regulators with broad impact on gene expression, e.g. POU2F1 (OCT1) and NFY, as a response to accumulating cell stress during malignant development. Our findings point towards the necessity of different approaches for the treatment of HCC forms with low and high proliferation signatures and provide new candidates for developing appropriate HCC therapies.
Collapse
Affiliation(s)
- Tatiana Meier
- Institute of Pathology, Nordstadtkrankenhaus, Hanover, Germany.
| | - Max Timm
- Institute of Pathology, Nordstadtkrankenhaus, Hanover, Germany
- Clinic for Laryngology, Rhinology and Otology, Medical School Hanover, Hanover, Germany
| | - Matteo Montani
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Ludwig Wilkens
- Institute of Pathology, Nordstadtkrankenhaus, Hanover, Germany
- Institute of Human Genetics, Medical School Hanover, Hanover, Germany
| |
Collapse
|
5
|
Chung HH, Lee CT, Hu JM, Chou YC, Lin YW, Shih YL. NKX6.1 Represses Tumorigenesis, Metastasis, and Chemoresistance in Colorectal Cancer. Int J Mol Sci 2020; 21:ijms21145106. [PMID: 32707737 PMCID: PMC7404324 DOI: 10.3390/ijms21145106] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 12/28/2022] Open
Abstract
Accumulating evidence suggests that NKX6.1 (NK homeobox 1) plays a role in various types of cancer. In our previous studies, we identified NKX6.1 hypermethylation as a promising marker and demonstrated that the NKX6.1 gene functions as a metastasis suppressor through the epigenetic regulation of the epithelial-to-mesenchymal transition (EMT) in cervical cancer. More recently, we have demonstrated that NKX6.1 methylation is related to the chemotherapy response in colorectal cancer (CRC). Nevertheless, the biological function of NKX6.1 in the tumorigenesis of CRC remains unclear. In this study, we showed that NKX6.1 suppresses tumorigenic and metastatic ability both in vitro and in vivo. NKX6.1 represses cell invasion partly through the modulation of EMT. The overexpression of NKX6.1 enhances chemosensitivity in CRC cells. To further explore how NKX6.1 exerts its tumor-suppressive function, we used RNA sequencing technology for comprehensive analysis. The results showed that differentially expressed genes (DEGs) were mainly related to cell migration, response to drug, transcription factor activity, and growth factor activity, suggesting that these DEGs are involved in the function of NKX6.1 suppressing cancer invasion and metastasis. Our results demonstrated that NKX6.1 functions as a tumor suppressor partly by repressing EMT and enhancing chemosensitivity in CRC, making it a potential therapeutic target.
Collapse
Affiliation(s)
- Hsin-Hua Chung
- Graduate Institute of Medical Sciences, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan; (H.-H.C.); (J.-M.H.); (Y.-W.L.)
| | - Chun-Te Lee
- Division of Urological Surgery, Department of Surgery, Tri-Service General Hospital Songshan Branch, No.131, Jiankang Rd., Songshan District, Taipei 10581, Taiwan;
| | - Je-Ming Hu
- Graduate Institute of Medical Sciences, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan; (H.-H.C.); (J.-M.H.); (Y.-W.L.)
- Division of Colorectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, No.325, Sec.2, Chenggong Rd., Neihu District, Taipei 11490, Taiwan
| | - Yu-Ching Chou
- School of Public Health, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan;
| | - Ya-Wen Lin
- Graduate Institute of Medical Sciences, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan; (H.-H.C.); (J.-M.H.); (Y.-W.L.)
- Department and Graduate Institute of Microbiology and Immunology, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan
- Graduate Institute of Life Sciences, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan
| | - Yu-Lueng Shih
- Graduate Institute of Medical Sciences, National Defense Medical Center, No.161, Sec.6, Minquan East Rd., Neihu District, Taipei 11490, Taiwan; (H.-H.C.); (J.-M.H.); (Y.-W.L.)
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, No. 325, Sec. 2, Chenggong Rd., Neihu District, Taipei 11490, Taiwan
- Correspondence: ; Tel./Fax: +886-2-87917654
| |
Collapse
|
6
|
Zhang Y, Wang W, Wang Y, Huang X, Zhang Z, Chen B, Xie W, Li S, Shen S, Peng B. NEK2 promotes hepatocellular carcinoma migration and invasion through modulation of the epithelial-mesenchymal transition. Oncol Rep 2018; 39:1023-1033. [PMID: 29399700 PMCID: PMC5802024 DOI: 10.3892/or.2018.6224] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/31/2017] [Indexed: 11/06/2022] Open
Abstract
Never in mitosis gene-A (NIMA)-related expressed kinase 2 (NEK2) has been recently reported to play a role in tumor progression, drug resistance and tumorigenesis. However, little is known about the effects of NEK2 in hepatocellular carcinoma (HCC) metastasis and the underlying mechanism. NEK2 expression levels were examined by immunochemistry, qRT-PCR and western blot analyses in HCC cell lines and HCC tissues. A Transwell assay was used to determine the migration and invasion capacity of NEK2-silenced or NEK2-overexpressing HCC cells. Cell proliferation was investigated by MTT [(3-(4,5)-dimethylthiazol(-z-y1)-3,5-di-phenytetrazolium bromide] assay. The expression levels of epithelial-mesenchymal transition (EMT) markers in NEK2-silenced or NEK2-overexpressing HCC cells were examined by western blot analyses and qRT-PCR. The correlations between NEK2 expression and clinicopathological characteristics were further analyzed. Gene microarray was further used to analyze the effect of NEK2 expression on downstream cell signals. Our study showed that NEK2 was overexpressed in human HCC (37.84%; 98/259). NEK2 overexpression was significantly associated with liver non-capsulation and predicted poor survival outcomes in HCC patients after hepatectomy. In addition, NEK2 significantly enhanced HCC cell invasive ability. Mechanistically, we found that the epithelial-mesenchymal transition (EMT) plays a pivotal role in the NEK2-mediated promotion of HCC cell invasion. Furthermore, we provided evidence that signaling through the Wnt, NF-κB, focal adhesion, VEGF, Hippo and p53 pathways may be downstream of NEK2. Our findings highlight the importance of NEK2 in HCC metastasis and suggest that NEK2 is a reliable prognostic marker for HCC patients after hepatectomy.
Collapse
Affiliation(s)
- Yi Zhang
- Department of Hepatic Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Wei Wang
- Department of Medical Ultrasonics, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Yifei Wang
- Department of Hepatic Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Xiaohui Huang
- Department of General Surgical Laboratory, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Zhaohui Zhang
- Department of Hepatic Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Bin Chen
- Department of Hepatic Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Wenxuan Xie
- Department of Hepatic Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Shaoqiang Li
- Department of Hepatic Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Shunli Shen
- Department of Hepatic Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Baogang Peng
- Department of Hepatic Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, P.R. China
| |
Collapse
|