1
|
Fang J, Singh S, Cheng C, Natarajan S, Sheppard H, Abu-Zaid A, Durbin AD, Lee HW, Wu Q, Steele J, Connelly JP, Jin H, Chen W, Fan Y, Pruett-Miller SM, Rehg JE, Koo SC, Santiago T, Emmons J, Cairo S, Wang R, Glazer ES, Murphy AJ, Chen T, Davidoff AM, Armengol C, Easton J, Chen X, Yang J. Genome-wide mapping of cancer dependency genes and genetic modifiers of chemotherapy in high-risk hepatoblastoma. Nat Commun 2023; 14:4003. [PMID: 37414763 PMCID: PMC10326052 DOI: 10.1038/s41467-023-39717-6] [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: 03/21/2022] [Accepted: 06/27/2023] [Indexed: 07/08/2023] Open
Abstract
A lack of relevant genetic models and cell lines hampers our understanding of hepatoblastoma pathogenesis and the development of new therapies for this neoplasm. Here, we report an improved MYC-driven hepatoblastoma-like murine model that recapitulates the pathological features of embryonal type of hepatoblastoma, with transcriptomics resembling the high-risk gene signatures of the human disease. Single-cell RNA-sequencing and spatial transcriptomics identify distinct subpopulations of hepatoblastoma cells. After deriving cell lines from the mouse model, we map cancer dependency genes using CRISPR-Cas9 screening and identify druggable targets shared with human hepatoblastoma (e.g., CDK7, CDK9, PRMT1, PRMT5). Our screen also reveals oncogenes and tumor suppressor genes in hepatoblastoma that engage multiple, druggable cancer signaling pathways. Chemotherapy is critical for human hepatoblastoma treatment. A genetic mapping of doxorubicin response by CRISPR-Cas9 screening identifies modifiers whose loss-of-function synergizes with (e.g., PRKDC) or antagonizes (e.g., apoptosis genes) the effect of chemotherapy. The combination of PRKDC inhibition and doxorubicin-based chemotherapy greatly enhances therapeutic efficacy. These studies provide a set of resources including disease models suitable for identifying and validating potential therapeutic targets in human high-risk hepatoblastoma.
Collapse
Affiliation(s)
- Jie Fang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shivendra Singh
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Changde Cheng
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sivaraman Natarajan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather Sheppard
- Comparative Pathology Core, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ahmed Abu-Zaid
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adam D Durbin
- Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ha Won Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Qiong Wu
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jacob Steele
- Center for Advanced Genome Engineering (CAGE), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jon P Connelly
- Center for Advanced Genome Engineering (CAGE), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering (CAGE), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jerold E Rehg
- Comparative Pathology Core, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Selene C Koo
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Teresa Santiago
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Joseph Emmons
- VPC Diagnostic Laboratory, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stefano Cairo
- Champions Oncology, 1330 Piccard dr, Rockville, MD, USA
| | - Ruoning Wang
- Center for Childhood Cancer and Blood Disease, Hematology/Oncology & BMT, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
| | - Evan S Glazer
- Department of Surgery, College of Medicine, The University of Tennessee Health Science Center, 910 Madison Ave., Suite 325, Memphis, TN, USA
| | - Andrew J Murphy
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Surgery, College of Medicine, The University of Tennessee Health Science Center, 910 Madison Ave., Suite 325, Memphis, TN, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Surgery, College of Medicine, The University of Tennessee Health Science Center, 910 Madison Ave., Suite 325, Memphis, TN, USA
- St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Carolina Armengol
- Childhood Liver Oncology Group, Germans Trias i Pujol Research Institute (IGTP), Translational Program in Cancer Research (CARE), Badalona, Spain
- CIBER, Hepatic and Digestive Diseases, Barcelona, Spain
- CIBERehd, Madrid, Spain
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Jun Yang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN, USA.
- St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Pathology, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN, USA.
| |
Collapse
|
2
|
Su SY, Lee WC. Age-period-cohort analysis with a constant-relative-variation constraint for an apportionment of period and cohort slopes. PLoS One 2019; 14:e0226678. [PMID: 31856261 PMCID: PMC6922428 DOI: 10.1371/journal.pone.0226678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 11/28/2019] [Indexed: 01/01/2023] Open
Abstract
Age-period-cohort analysis of incidence and/or mortality data has received much attention in the literature. To circumvent the non-identifiability problem inherent in the age-period-cohort model, additional constraints are necessary on the parameters estimates. We propose setting the constraint to reflect the different nature of the three temporal variables: age, period, and birth cohort. There are two assumptions in our method. Recognizing age effects to be deterministic (first assumption), we do not explicitly incorporate the age parameters into constraint. For the stochastic period and cohort effects, we set a constant-relative-variation constraint on their trends (second assumption). The constant-relative-variation constraint dictates that between two stochastic effects, one with a larger curvature gets a larger (absolute) slope, and one with zero curvature gets no slope. We conducted Monte-Carlo simulations to examine the statistical properties of the proposed method and analyzed the data of prostate cancer incidence for whites from 1973-2012 to illustrate the methodology. A driver for the period and/or cohort effect may be lacking in some populations. In that case, the CRV method automatically produces an unbiased age effect and no period and/or cohort effect, thereby addressing the situation properly. However, the method proposed in this paper is not a general purpose model and will produce biased results in many other real-life data scenarios. It is only useful in situations when the age effects are deterministic and dominant, and the period and cohort effects are stochastic and minor.
Collapse
Affiliation(s)
- Shih-Yung Su
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
- Innovation and Policy Center for Population Health and Sustainable Environment, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Wen-Chung Lee
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
- Innovation and Policy Center for Population Health and Sustainable Environment, College of Public Health, National Taiwan University, Taipei, Taiwan
- Taiwan Cancer Registry, Taipei, Taiwan
| |
Collapse
|
4
|
Elhassan MM, Mohamedani AA, Yousif NO, Elhaj NM, Qaddoumi I, Abuidres DO. Epidemiological review of childhood cancers in central Sudan. SOUTH AFRICAN JOURNAL OF ONCOLOGY 2018. [DOI: 10.4102/sajo.v2i0.37] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Background: Epidemiological studies of paediatric cancer incidence in Sudan are rare.Objectives: The aim of this study was to provide baseline information about the epidemiology of childhood cancers in patients treated at the National Cancer Institute (NCI) in Wad Medani, Sudan.Methods: We performed a retrospective health facility–based study of cancer incidence and patient characteristics of children who were treated at the NCI from January 1999 to December 2015. The changing patterns of cancers incidence during the study period were also recorded.Results: Of 15 387 new patients with cancer who were registered at the NCI during the study period, 1159 (7.5%) were children (younger than 15 years). The mean age of the paediatric patients was 7 years, with standard deviation of 5. Most of the patients (36%) were 10 to 15 years old, 33% were 0 to 4 years old and 31% were 5 to 10 years old. Among the study population, 60% were males and 40% were females. Approximately 76% of children lived in rural areas in Sudan. Leukaemias (29%) and lymphomas (26%) comprised 55% of all paediatric cancers. Central nervous system (CNS) tumours constituted 6% of all paediatric tumours, whereas non-CNS embryonal tumours (i.e. nephroblastoma, neuroblastoma, hepatoblastoma and retinoblastoma) accounted for 20%. The average number of cases per year increased from 42 in 1999–2005 to 75 in 2006–2010 and 106 in 2011–2015.Conclusion: The number of patients seeking treatment for childhood cancers has increased every year in central Sudan. Leukaemias and lymphomas constitute more than half of these cancers. A population-based cancer registry is needed to determine the true incidence of childhood cancers in Sudan.
Collapse
|
5
|
Bihari C, Rastogi A, Shasthry SM, Bajpai M, Bhadoria AS, Rajesh S, Mukund A, Kumar A, Sarin SK. Platelets contribute to growth and metastasis in hepatocellular carcinoma. APMIS 2016; 124:776-86. [PMID: 27457354 DOI: 10.1111/apm.12574] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 06/04/2016] [Indexed: 12/13/2022]
Abstract
To determine the association of platelets with hepatocellular carcinoma (HCC) growth and its metastasis. We examined platelets, laboratory, and radiological data of consecutive 420 HCC and 1008 cirrhosis cases. Follow-up information of platelet count in cirrhosis to HCC, pre- to post-therapy, and post-therapy to HCC outcome was analyzed. Cytokine profiling was performed in HCC and cirrhosis (n = 10 each). On the basis of imaging, HCC was divided into six subgroups. Cytosmears of HCC were assessed for platelet clustering around tumor cells. An in vitro Matrigel invasion assay was performed on human HCC cell lines using graded concentration of platelets. Baseline platelet numbers and platelet/lymphocyte ratios (PLRs) were significantly higher (p < 0.001) in HCC than cirrhosis. IL-1, IL-6, FGF, G-CSF, thrombopoietin, and VEGF were higher in HCC than cirrhosis. Platelet counts were increased after HCC conversion of cirrhosis (p < 0.001) and decreased (p < 0.001) after therapy. Platelets and PLR in recurrence cases were higher than in responders at baseline. AFP, PIVKAII, platelets, and PLR increase (p < 0.001 each) with advancement in HCC growth. Multivariate analysis showed platelets (p = 0.002), PLR (p = 0.004), and AFP (p < 0.001) associated with distant metastasis. Platelet clustering seen in 75.7% of HCC group 3, 45% in group 2, and 12.5% in group 1 cases (p < 0.001). Invaded cells in Matrigel assay positively correlated with platelet concentration. Platelets can contribute to the development, growth, invasion, and metastasis of HCC. Rising platelet count after HCC therapy is indicative of incomplete response or recurrence.
Collapse
Affiliation(s)
- Chhagan Bihari
- Department of Pathology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Archana Rastogi
- Department of Pathology, Institute of Liver and Biliary Sciences, New Delhi, India
| | | | - Meenu Bajpai
- Department of Tranfusion Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Ajeet Singh Bhadoria
- Department of Research, Institute of Liver and Biliary Sciences, New Delhi, India
| | - S Rajesh
- Department of Radiology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Amar Mukund
- Department of Radiology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Anupam Kumar
- Department of Research, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Shiv K Sarin
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
| |
Collapse
|
10
|
Shih YW, Lee YC, Wu PF, Lee YB, Chiang TA. Plumbagin inhibits invasion and migration of liver cancer HepG2 cells by decreasing productions of matrix metalloproteinase-2 and urokinase- plasminogen activator. Hepatol Res 2009; 39:998-1009. [PMID: 19624766 DOI: 10.1111/j.1872-034x.2009.00540.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
AIM To investigate the inhibitory effects of plumbagin (5-hydroxy-2 methyl-1,4-naphthoquinone) on the invasion and migration and its correlation with matrix metalloproteinase-2 (MMP-2) and urokinase-plasminogen activator (u-PA) in liver cancer HepG2 cells under non-cytotoxic concentrations. METHODS The cell viability was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The adhesion, migration and invasion were measured by cell-matrix adhesion assay and Boyden chamber assay. The MMP-2 and u-PA activities were estimated by gelatin and casein-plasminogen zymography. The mRNA and protein levels of MMP-2, u-PA, urokinase-plasminogen activator receptor (u-PAR), tissue inhibitor of metalloproteinase-2 (TIMP-2), plasminogen activator inhibitor-1 (PAI-1), nuclear factor kappa B (NF-kappaB), c-Fos and c-Jun were evaluated by semi-quantitative reverse transcription polymerase chain reaction and western blotting. Also, the binding abilities of NF-kappaB and activator protein-1 (AP-1) were analyzed by electrophoretic mobility shift assay (EMSA). RESULTS In this study, plumbagin had exhibited an inhibitory effect on the abilities of adhesion, migration and invasion. The results from zymography showed plumbagin treatment may decrease the activities of MMP-2 and u-PA. Further, the mRNA and protein levels of MMP-2, u-PA and u-PAR were significantly reduced, while TIMP-2 and PAI-1 were elevated by plumbagin treatment. Next, plumbagin significantly decreased the nuclear levels of NF-kappaB, c-Fos and c-Jun. Also, treating HepG2 cells with plumbagin leads to dose-dependent inhibition on the binding abilities of NF-kappaB and AP-1. CONCLUSION We demonstrated the inhibitory effects of plumbagin on the invasion, migration and adhesion of HepG2 cells, while plumbagin treatment may decrease the expressions of MMP-2 and u-PA and enhance the expressions of TIMP-2 and PAI-1.
Collapse
Affiliation(s)
- Yuan-Wei Shih
- Department of Biological Science and Technology, and Graduate Institute of Biomedical Science, Chung Hwa Universit of Medical Technology, Tainan, Taiwan
| | | | | | | | | |
Collapse
|