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Ren X, Zhang Q, Guo W, Wang L, Wu T, Zhang W, Liu M, Kong D. Cell-cycle and apoptosis related and proteomics-based signaling pathways of human hepatoma Huh-7 cells treated by three currently used multi-RTK inhibitors. Front Pharmacol 2022; 13:944893. [PMID: 36071844 PMCID: PMC9444053 DOI: 10.3389/fphar.2022.944893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/29/2022] [Indexed: 11/18/2022] Open
Abstract
Sorafenib, lenvatinib and regorafenib, the multi-RTK inhibitors with potent anti-angiogenesis effects, are currently therapeutic drugs generally recommended for the patients with advanced hepatocellular carcinoma (HCC). To date, however, there have been no published studies on the mechanism underling differential effects of the three drugs on HCC cell proliferation, and the proteomic analysis in HCC cell lines treated by regorafenib or lenvatinib. The present study for the first time performed a direct comparison of the cell cycle arrest and apoptosis induction in the Huh-7 cells caused by sorafenib, regorafenib and lenvatinib at respective IC50 using flow cytometry technique, as well as their pharmacological interventions for influencing whole cell proteomics using tandem mass tag-based peptide-labeling coupled with the nLC-HRMS technique. Sorafenib, regorafenib and lenvatinib at respective IC50 drove the remaining surviving Huh-7 cells into a G0/G1 arrest, but lenvatinib and regorafenib were much more effective than sorafenib. Lenvatinib produced a much stronger induction of Huh-7 cells into early apoptosis than sorafenib and regorafenib, while necrotic cell proportion induced by regorafenib was 2.4 times as large as that by lenvatinib. The proteomic study revealed 419 proteins downregulated commonly by the three drugs at respective IC50. KEGG pathway analysis of the downregulated proteins indicated the ranking of top six signaling pathways including the spliceosome, DNA replication, cell cycle, mRNA surveillance, P53 and nucleotide excision repair involved in 33 proteins, all of which were directly related to their pharmacological effects on cell cycle and cell apoptosis. Notably, lenvatinib and regorafenib downregulated the proteins of PCNA, Cyclin B1, BCL-xL, TSP1, BUD31, SF3A1 and Mad2 much more strongly than sorafenib. Moreover, most of the proteins in the P53 signaling pathway were downregulated with lenvatinib and regorafenib by more than 36% at least. In conclusion, lenvatinib and regorafenib have much stronger potency against Huh-7 cell proliferation than sorafenib because of their more potent effects on cell cycle arrest and apoptosis induction. The underling mechanism may be at least due to the 33 downregulated proteins centralizing the signal pathways of cell cycle, p53 and DNA synthesis based on the present proteomics study.
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Affiliation(s)
- Xuejiao Ren
- Department of Radiotherapy, Third Hospital of Hebei Medical University, Shijiazhuang, China
- Department of Radiotherapy, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Qingning Zhang
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
| | - Wenyan Guo
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
| | - Lan Wang
- Department of Radiotherapy, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Tao Wu
- Department of Radiotherapy, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Wei Zhang
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
| | - Ming Liu
- Department of Radiotherapy, Third Hospital of Hebei Medical University, Shijiazhuang, China
- *Correspondence: Ming Liu, ; Dezhi Kong,
| | - Dezhi Kong
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
- *Correspondence: Ming Liu, ; Dezhi Kong,
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Hull R, Mbele M, Makhafola T, Hicks C, Wang SM, Reis RM, Mehrotra R, Mkhize-Kwitshana Z, Kibiki G, Bates DO, Dlamini Z. Cervical cancer in low and middle-income countries. Oncol Lett 2020; 20:2058-2074. [PMID: 32782524 PMCID: PMC7400218 DOI: 10.3892/ol.2020.11754] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/16/2019] [Indexed: 12/11/2022] Open
Abstract
Cervical cancer is a malignant tumour that occurs in the cervix and is classified into two histological types, adenocarcinoma and squamous cell carcinoma (SCC); SCC is more common and accounts for 70% of all cases. In 2018 there were ~569,000 new cases of cervical cancer diagnosed worldwide and ~311,000 deaths were attributed to cervical cancer. Of these, between 84 and 90% occurred in low- and middle-income countries (LMICs) such as South Africa, India, China and Brazil. The most common cause of cervical cancer is persistent infection caused by the sexually transmitted human papilloma virus. Other factors that contribute to the incidence of cervical cancer include geography, traditional practices and beliefs, the screening levels, socioeconomic status, healthcare access, public awareness, use of oral contraceptives, smoking and co-infection with HIV. An estimated 11 million women from LMICs will be diagnosed with cervical cancer in the next 10-20 years. The aim of this review was to explore various types of genetic and epigenetic factors that influence the development, progression or suppression of cervical cancer.
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Affiliation(s)
- Rodney Hull
- SA-MRC/UP Precision Prevention and Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, Faculty of Health Sciences, University of Pretoria, Hatfield 0028, South Africa
| | - Mzwandile Mbele
- SA-MRC/UP Precision Prevention and Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, Faculty of Health Sciences, University of Pretoria, Hatfield 0028, South Africa
| | - Tshepiso Makhafola
- SA-MRC/UP Precision Prevention and Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, Faculty of Health Sciences, University of Pretoria, Hatfield 0028, South Africa
| | - Chindo Hicks
- Bioinformatics and Genomics Centre, School of Medicine, Department of Genetics, Louisiana State University, New Orleans, LA 70112, USA
| | - Shao-Ming Wang
- National Cancer Centre, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, P.R. China
| | - Rui Manuel Reis
- Molecular Oncology Research Centre, Barretos Cancer Hospital, Sao Paulo 14784-400, Brazil
| | - Ravi Mehrotra
- Indian Council of Medical Research, New Delhi, Delhi 110029, India
| | | | - Gibson Kibiki
- East African Health Research Commission, East African Community, Bujumbura, Bujumbura Mairie 350, Burundi
| | - David O Bates
- Queen's Medical Centre, University of Nottingham, Nottingham, Nottinghamshire NG7 2UH, UK
| | - Zodwa Dlamini
- SA-MRC/UP Precision Prevention and Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, Faculty of Health Sciences, University of Pretoria, Hatfield 0028, South Africa
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Yang L, He Y, Zhang Z, Wang W. Systematic analysis and prediction model construction of alternative splicing events in hepatocellular carcinoma: a study on the basis of large-scale spliceseq data from The Cancer Genome Atlas. PeerJ 2019; 7:e8245. [PMID: 31844595 PMCID: PMC6907093 DOI: 10.7717/peerj.8245] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/19/2019] [Indexed: 02/05/2023] Open
Abstract
Growing evidence showed that alternative splicing (AS) event is significantly related to tumor occurrence and progress. This study was performed to make a systematic analysis of AS events and constructed a robust prediction model of hepatocellular carcinoma (HCC). The clinical information and the genes expression profile data of 335 HCC patients were collected from The Cancer Genome Atlas (TCGA). Information of seven types AS events were collected from the TCGA SpliceSeq database. Overall survival (OS) related AS events and splicing factors (SFs) were identified using univariate Cox regression analysis. The corresponding genes of OS-related AS events were sent for gene network analysis and functional enrichment analysis. Optimal OS-related AS events were selected by LASSO regression to construct prediction model using multivariate Cox regression analysis. Prognostic value of the prediction models were assessed by receiver operating characteristic (ROC) curve and KaplanMeir survival analysis. The relationship between the Percent Spliced In (PSI) value of OS-related AS events and SFs expression were analyzed using Spearman correlation analysis. And the regulation network was generated by Cytoscape. A total of 34,163 AS events were identified, which consist of 3,482 OS-related AS events. UBB, UBE2D3, SF3A1 were the hub genes in the gene network of the top 800 OS-related AS events. The area under the curve (AUC) of the final prediction model based on seven types OS-related AS events was 0.878, 0.843, 0.821 in 1, 3, 5 years, respectively. Upon multivariate analysis, risk score (All) served as the risk factor to independently predict OS for HCC patients. SFs HNRNPH3 and HNRNPL were overexpressed in tumor samples and were signifcantly associated with the OS of HCC patients. The regulation network showed prominent correlation between the expression of SFs and OS-related AS events in HCC patients. The final prediction model performs well in predicting the prognosis of HCC patients. And the findings in this study improve our understanding of the association between AS events and HCC.
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Affiliation(s)
- Lingpeng Yang
- Department of Liver Surgery & Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Yang He
- Department of Liver Surgery & Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Zifei Zhang
- Department of Liver Surgery & Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Wentao Wang
- Department of Liver Surgery & Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
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Idris M, Harmston N, Petretto E, Madan B, Virshup DM. Broad regulation of gene isoform expression by Wnt signaling in cancer. RNA (NEW YORK, N.Y.) 2019; 25:1696-1713. [PMID: 31506381 PMCID: PMC6859862 DOI: 10.1261/rna.071506.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/06/2019] [Indexed: 05/08/2023]
Abstract
Differential gene isoform expression is a ubiquitous mechanism to enhance proteome diversity and maintain cell homeostasis. Mechanisms such as splicing that drive gene isoform variability are highly dynamic and responsive to changes in cell signaling pathways. Wnt/β-catenin signaling has profound effects on cell activity and cell fate and is known to modify several splicing events by altering the expression of individual splicing factors. However, a global assessment of how extensively Wnt signaling regulates splicing and other mechanisms that determine mRNA isoform composition in cancer is lacking. We used deep time-resolved RNA-seq in two independent in vivo Wnt-addicted tumor models during treatment with the potent Wnt inhibitor ETC-159 and examined Wnt regulated splicing events and splicing regulators. We found 1025 genes that underwent Wnt regulated variable exon usage leading to isoform expression changes. This was accompanied by extensive Wnt regulated changes in the expression of splicing regulators. Many of these Wnt regulated events were conserved in multiple human cancers, and many were linked to previously defined cancer-associated splicing quantitative trait loci. This suggests that the Wnt regulated splicing events are components of fundamental oncogenic processes. These findings demonstrate the wide-ranging effects of Wnt signaling on the isoform composition of the cell and provides an extensive resource of expression changes of splicing regulators and gene isoforms regulated by Wnt signaling.
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Affiliation(s)
- Muhammad Idris
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
| | - Nathan Harmston
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
- Centre for Computational Biology and Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857
- Science Division, Yale-NUS College, Singapore, 138527
| | - Enrico Petretto
- Centre for Computational Biology and Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857
| | - Babita Madan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
| | - David M Virshup
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina 27705, USA
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Lee G, Bang L, Kim SY, Kim D, Sohn KA. Identifying subtype-specific associations between gene expression and DNA methylation profiles in breast cancer. BMC Med Genomics 2017; 10:28. [PMID: 28589855 PMCID: PMC5461552 DOI: 10.1186/s12920-017-0268-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Breast cancer is a complex disease in which different genomic patterns exists depending on different subtypes. Recent researches present that multiple subtypes of breast cancer occur at different rates, and play a crucial role in planning treatment. To better understand underlying biological mechanisms on breast cancer subtypes, investigating the specific gene regulatory system via different subtypes is desirable. METHODS Gene expression, as an intermediate phenotype, is estimated based on methylation profiles to identify the impact of epigenomic features on transcriptomic changes in breast cancer. We propose a kernel weighted l1-regularized regression model to incorporate tumor subtype information and further reveal gene regulations affected by different breast cancer subtypes. For the proper control of subtype-specific estimation, samples from different breast cancer subtype are learned at different rate based on target estimates. Kolmogorov Smirnov test is conducted to determine learning rate of each sample from different subtype. RESULTS It is observed that genes that might be sensitive to breast cancer subtype show prediction improvement when estimated using our proposed method. Comparing to a standard method, overall performance is also enhanced by incorporating tumor subtypes. In addition, we identified subtype-specific network structures based on the associations between gene expression and DNA methylation. CONCLUSIONS In this study, kernel weighted lasso model is proposed for identifying subtype-specific associations between gene expressions and DNA methylation profiles. Identification of subtype-specific gene expression associated with epigenomic changes might be helpful for better planning treatment and developing new therapies.
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Affiliation(s)
- Garam Lee
- Department of Software and Computer Engineering, Ajou University, Suwon, 16499, South Korea
| | - Lisa Bang
- Biomedical & Translational Informatics Institute, Geisinger Health System, Danville, PA, USA
| | - So Yeon Kim
- Department of Software and Computer Engineering, Ajou University, Suwon, 16499, South Korea
| | - Dokyoon Kim
- Biomedical & Translational Informatics Institute, Geisinger Health System, Danville, PA, USA. .,The Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
| | - Kyung-Ah Sohn
- Department of Software and Computer Engineering, Ajou University, Suwon, 16499, South Korea.
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Thutkawkorapin J, Picelli S, Kontham V, Liu T, Nilsson D, Lindblom A. Exome sequencing in one family with gastric- and rectal cancer. BMC Genet 2016; 17:41. [PMID: 26872740 PMCID: PMC4752738 DOI: 10.1186/s12863-016-0351-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/08/2016] [Indexed: 12/18/2022] Open
Abstract
Background Heritable factors are well known to increase the risk of cancer in families. Known susceptibility genes account for a small proportion of all colorectal cancer cases. The aim of this study was to identify the genetic background in a family suggested to segregate a dominant cancer syndrome with a high risk of rectal- and gastric cancer. We performed whole exome sequencing in three family members, 2 with rectal cancer and 1 with gastric cancer and followed it up in additional family members, other patients and controls. Results We identified 12 novel non-synonymous single nucleotide variants, which were shared among 5 affected members of this family. The mutations were found in 12 different genes; DZIP1L, PCOLCE2, IGSF10, SUCNR1, OR13C8, EPB41L4B, SEC16A, NOTCH1, TAS2R7, SF3A1, GAL3ST1, and TRIOBP. None of the mutations was suggested as a high penetrant mutation. It was not possible to completely rule out any of the mutations as contributing to disease, although seven were more unlikely than the others. Neither did we rule out the effect of all thousands of intronic, intergenic and synonymous variants shared between the three persons used for exome sequencing. Conclusions We propose this family, suggested to segregate dominant disease, could be an example of complex inheritance.
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Affiliation(s)
| | - Simone Picelli
- Karolinska Institutet, Department of Molecular Medicine and Surgery, Stockholm, Sweden. .,Eukaryotic Single Cell Genomics facility, Science for Life Laboratory, Stockholm, Sweden.
| | - Vinaykumar Kontham
- Karolinska Institutet, Department of Molecular Medicine and Surgery, Stockholm, Sweden.
| | - Tao Liu
- Karolinska Institutet, Department of Molecular Medicine and Surgery, Stockholm, Sweden.
| | - Daniel Nilsson
- Karolinska Institutet, Department of Molecular Medicine and Surgery, Stockholm, Sweden.
| | - Annika Lindblom
- Karolinska Institutet, Department of Molecular Medicine and Surgery, Stockholm, Sweden.
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