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Tong Z, Yan C, Dong YA, Yao M, Zhang H, Liu L, Zheng Y, Zhao P, Wang Y, Fang W, Zhang F, Jiang W. Whole-exome sequencing reveals potential mechanisms of drug resistance to FGFR3-TACC3 targeted therapy and subsequent drug selection: towards a personalized medicine. BMC Med Genomics 2020; 13:138. [PMID: 32957974 PMCID: PMC7507681 DOI: 10.1186/s12920-020-00794-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 09/08/2020] [Indexed: 12/31/2022] Open
Abstract
Background Drug resistance is a major obstacle to effective cancer therapy. In order to detect the change in tumor genomic states under drug selection pressure, we use next-generation sequencing technology to investigate the underlying potential mechanisms of drug resistance. Methods In our study, we presented a bladder cancer patient who had been a bona fide responder to first-line gemcitabine plus cisplatin regimen and second-line pazopanib (tyrosine kinase inhibitor (TKI) for FGFR3-TACC3 fusion) but finally had disease progression as an ideal case for showing genomic alteration during drug resistance. We applied whole-exome sequencing and ultra-deep target sequencing to the patient pre- and post- pazopanib resistance. Protein-protein interaction (PPI) network and Gene Ontology (GO) analyses were used to analysis protein interactions and genomic alterations. Patient-derived xenograft (PDX) model was built to test drug sensitivity. Results Twelve mutations scattered in 12 genes were identified by WES pre- pazopanib resistance, while 63 mutations in 50 genes arose post- pazopanib resistance. PPI network showed proteins from multiple epigenetic regulator families were involved post- pazopanib resistance, including subunits of chromatin remodeler SWI/SNF complex ARID1A/1B and SMARCA4, histone acetylation writers CREBBP, histone methylation writer NSD1 and erasers KDM6A/5A. GO enrichment analysis showed pazopanib resistance genes were prominently tagged for chromatin modification, transcription, as well as gland development, leaving genes with the best adaptive FGFR TKI-coping mechanisms. In addition, significantly elevated tumor mutational burden suggested possible utility of immunotherapy. Intriguingly, PDX model suggested that, sensitivity to original chemotherapy regimen (cisplatin) was restored in patient tumor post-pazopanib. Conclusions Epigenetic regulation may play a role in acquired TKI resistance. Our study traced the complete tumor genomic variation course from chemo-resistant but TKI-sensitive to TKI-resistant but chemo-(re) sensitive, revealing the potential complex dynamic drug-driven mechanisms of resistance.
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Affiliation(s)
- Zhou Tong
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Cong Yan
- Department of Medical Oncology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China
| | - Yu-An Dong
- OrigiMed, Building 3, 115 Xinjun Huan Rd. Minghang, Shanghai, 201114, China
| | - Ming Yao
- OrigiMed, Building 3, 115 Xinjun Huan Rd. Minghang, Shanghai, 201114, China
| | - Hangyu Zhang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Lulu Liu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yi Zheng
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Peng Zhao
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yimin Wang
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Weijia Fang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.,Provincial Key Laboratory of Pancreatic Disease, Hangzhou, 310003, China
| | - Feifei Zhang
- Shanghai LIDE Biotech Co.LTD, Shanghai, 201203, China
| | - Weiqin Jiang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
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Wen S, Dai L, Wang L, Wang W, Wu D, Wang K, He Z, Wang A, Chen H, Zhang P, Dong X, Dong YA, Wang K, Yao M, Wang M. Genomic Signature of Driver Genes Identified by Target Next-Generation Sequencing in Chinese Non-Small Cell Lung Cancer. Oncologist 2019; 24:e1070-e1081. [PMID: 30902917 DOI: 10.1634/theoncologist.2018-0572] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/25/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) is one of the most common human malignancies and the leading cause of cancer-related death. Over the past few decades, genomic alterations of cancer driver genes have been identified in NSCLC, and molecular testing and targeted therapies have become standard care for lung cancer patients. Here we studied the unique genomic profile of driver genes in Chinese patients with NSCLC by next-generation sequencing (NGS) assay. MATERIALS AND METHODS A total of 1,200 Chinese patients with NSCLC were enrolled in this study. The median age was 60 years (range: 26-89), and 83% cases were adenocarcinoma. NGS-based genomic profiling of major lung cancer-related genes was performed on formalin-fixed paraffin-embedded tumor samples and matched blood. RESULTS Approximately 73.9% of patients with NSCLC harbored at least one actionable alteration recommended by the National Comprehensive Cancer Network guideline, including epidermal growth factor receptor (EGFR), ALK, ERBB2, MET, BRAF, RET, and ROS1. Twenty-seven patients (2.2%) harbored inherited germline mutations of cancer susceptibility genes. The frequencies of EGFR genomic alterations (both mutations and amplification) and ALK rearrangement were identified as 50.1% and 7.8% in Chinese NSCLC populations, respectively, and significantly higher than the Western population. Fifty-six distinct uncommon EGFR mutations other than L858R, exon19del, exon20ins, or T790M were identified in 18.9% of patients with EGFR-mutant NSCLC. About 7.4% of patients harbored both sensitizing and uncommon mutations, and 11.6% of patients harbored only uncommon EGFR mutations. The uncommon EGFR mutations more frequently combined with the genomic alterations of ALK, CDKN2A, NTRK3, TSC2, and KRAS. In patients <40 years of age, the ALK-positive percentage was up to 28.2%. Moreover, 3.2% of ALK-positive patients harbored multi ALK rearrangements, and seven new partner genes were identified. CONCLUSION More unique features of cancer driver genes in Chinese NSCLC were identified by next-generation sequencing. These findings highlighted that NGS technology is more feasible and necessary than other molecular testing methods, and suggested that the special strategies are needed for drug development and targeted therapy for Chinese patients with NSCLC. IMPLICATIONS FOR PRACTICE Molecular targeted therapy is now the standard first-line treatment for patients with advanced non-small cell lung cancer (NSCLC). Samples of 1,200 Chinese patients with NSCLC were analyzed through next-generation sequencing to characterize the unique feature of uncommon EGFR mutations and ALK fusion. The results showed that 7.4% of EGFR-mutant patients harbored both sensitizing and uncommon mutations and 11.6% harbored only uncommon mutations. Uncommon EGFR mutations more frequently combined with the genomic alterations of ALK, CDKN2A, NTRK3, TSC2, and KRAS. ALK fusion was more common in younger patients, and the frequency decreased monotonically with age. 3.2% of ALK-positive patients harbored multi ALK rearrangement, and seven new partner genes were identified.
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Affiliation(s)
- Shiwang Wen
- Department of Thoracic Surgery, Fourth Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Lei Dai
- Department of Thoracic Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Lei Wang
- Department of Thoracic Surgery, Fourth Hospital of Hebei Medical University, Shijiazhuang, People's Republic of China
| | - Wenjian Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Duoguang Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Kefeng Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Zhanghai He
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Aodi Wang
- OrigiMed, Shanghai, People's Republic of China
| | - Hui Chen
- OrigiMed, Shanghai, People's Republic of China
| | - Peng Zhang
- OrigiMed, Shanghai, People's Republic of China
| | | | - Yu-An Dong
- OrigiMed, Shanghai, People's Republic of China
| | - Kai Wang
- OrigiMed, Shanghai, People's Republic of China
- Zhejiang University International Hospital, Hangzhou, People's Republic of China
| | - Ming Yao
- OrigiMed, Shanghai, People's Republic of China
| | - Minghui Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
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Hu J, Guo Y, Lin J, Liu X, Guo H, Ma R, Zhang Y, Dong YA, Shi W, Yao M. Genomic feature differences in APC-mutant and wild-type colorectal cancer patients. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.e15609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Jing Hu
- First People's Hospital of Yunnan Province, Kunming, China
| | - Yun Guo
- First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jie Lin
- The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiaojian Liu
- First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Jia J, Zhang P, Liu W, Mu S, Chirn GW, Wang W, Wang K, Dong YA. Correlation of tumor mutational burden and predicted functional impact of mutations across cancer types. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.e24296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Jun Jia
- Dongguan people's Hospital, Dongguan, China
| | | | | | | | | | | | - Kai Wang
- OrigiMed & Zhejiang University International Hospital, China, China
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Abstract
Recent experiments established that a culture of
Saccharomyces cerevisiae (baker’s yeast) survives sudden high temperatures by specifically duplicating the entire chromosome III and two chromosomal fragments (from IV and XII). Heat shock proteins (HSPs) are not significantly over-abundant in the duplication. In contrast, we suggest a simple algorithm to “
postdict” the experimental results: Find a small enough chromosome with minimal protein disorder and duplicate this region. This algorithm largely explains all observed duplications. In particular, all regions duplicated in the experiment reduced the overall content of protein disorder. The differential analysis of the functional makeup of the duplication remained inconclusive. Gene Ontology (GO) enrichment suggested over-representation in processes related to reproduction and nutrient uptake. Analyzing the protein-protein interaction network (PPI) revealed that few network-central proteins were duplicated. The predictive hypothesis hinges upon the concept of reducing proteins with long regions of disorder in order to become less sensitive to heat shock attack.
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Affiliation(s)
- Esmeralda Vicedo
- Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany ; Institute of Experimental Physics, Division of Biophysics, University of Warsaw, Warsaw, Poland
| | - Zofia Gasik
- Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany ; Graduate School of Information Science in Health, TUM, Munich, Germany
| | - Yu-An Dong
- Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany ; Institute of Systems Biology, Shanghai University, Shanghai, China
| | - Tatyana Goldberg
- Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany
| | - Burkhard Rost
- Department of Informatics, Bioinformatics & Computational Biology, TUM, Munich, Germany ; Institute of Advanced Study, TUM, Munich, Germany ; Institute for Food and Plant Sciences WZW, TUM, Freising, Germany
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Fossum E, Friedel CC, Rajagopala SV, Titz B, Baiker A, Schmidt T, Kraus T, Stellberger T, Rutenberg C, Suthram S, Bandyopadhyay S, Rose D, von Brunn A, Uhlmann M, Zeretzke C, Dong YA, Boulet H, Koegl M, Bailer SM, Koszinowski U, Ideker T, Uetz P, Zimmer R, Haas J. Evolutionarily conserved herpesviral protein interaction networks. PLoS Pathog 2009; 5:e1000570. [PMID: 19730696 PMCID: PMC2731838 DOI: 10.1371/journal.ppat.1000570] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 08/10/2009] [Indexed: 01/21/2023] Open
Abstract
Herpesviruses constitute a family of large DNA viruses widely spread in vertebrates and causing a variety of different diseases. They possess dsDNA genomes ranging from 120 to 240 kbp encoding between 70 to 170 open reading frames. We previously reported the protein interaction networks of two herpesviruses, varicella-zoster virus (VZV) and Kaposi's sarcoma-associated herpesvirus (KSHV). In this study, we systematically tested three additional herpesvirus species, herpes simplex virus 1 (HSV-1), murine cytomegalovirus and Epstein-Barr virus, for protein interactions in order to be able to perform a comparative analysis of all three herpesvirus subfamilies. We identified 735 interactions by genome-wide yeast-two-hybrid screens (Y2H), and, together with the interactomes of VZV and KSHV, included a total of 1,007 intraviral protein interactions in the analysis. Whereas a large number of interactions have not been reported previously, we were able to identify a core set of highly conserved protein interactions, like the interaction between HSV-1 UL33 with the nuclear egress proteins UL31/UL34. Interactions were conserved between orthologous proteins despite generally low sequence similarity, suggesting that function may be more conserved than sequence. By combining interactomes of different species we were able to systematically address the low coverage of the Y2H system and to extract biologically relevant interactions which were not evident from single species. Herpesvirus proteins interact with each other in a complex manner throughout the infectious cycle. This is probably best exemplified in the process where a large number of viral proteins come together to form new viral particles which are subsequently released from the infected cell. A more detailed understanding of how viral proteins interact with each other might assist the development of drugs which may inhibit these interactions and consequently block viral replication. Here we present three genome-wide studies of protein-protein interactions in the herpesviruses herpes simplex virus I, murine cytomegalovirus and Epstein-Barr virus. Altogether we identified 735 interactions in the three viruses, most of which have not previously been reported. By combining these studies with our previously published studies for Kaposi's sarcoma-associated herpesvirus and varicella-zoster virus we were able to perform a comparative analysis of interactions in five related viral species. We observed that a high proportion of interactions were conserved between the different species, despite a low degree of sequence conservation. This implies that by comparing interaction data, we were able to increase the coverage of our viral networks and thus obtain a better and more complete picture of interactions between herpesviral proteins.
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Affiliation(s)
- Even Fossum
- Max-von-Pettenkofer Institut, Ludwig-Maximilians-Universität, München, Germany
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Uetz P, Dong YA, Zeretzke C, Atzler C, Baiker A, Berger B, Rajagopala SV, Roupelieva M, Rose D, Fossum E, Haas J. Herpesviral protein networks and their interaction with the human proteome. Science 2005; 311:239-42. [PMID: 16339411 DOI: 10.1126/science.1116804] [Citation(s) in RCA: 330] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The comprehensive yeast two-hybrid analysis of intraviral protein interactions in two members of the herpesvirus family, Kaposi sarcoma-associated herpesvirus (KSHV) and varicella-zoster virus (VZV), revealed 123 and 173 interactions, respectively. Viral protein interaction networks resemble single, highly coupled modules, whereas cellular networks are organized in separate functional submodules. Predicted and experimentally verified interactions between KSHV and human proteins were used to connect the viral interactome into a prototypical human interactome and to simulate infection. The analysis of the combined system showed that the viral network adopts cellular network features and that protein networks of herpesviruses and possibly other intracellular pathogens have distinguishing topologies.
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Affiliation(s)
- Peter Uetz
- Institut für Genetik, Forschungszentrum Karlsruhe, Postfach 3640, Karlsruhe, D-76021 Germany
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Abstract
Although cloned viral ORFeomes are particularly well suited for genome-wide interaction mapping due to the limited size of viral genomes, only a few such studies have been published. Here, we summarize virus interaction mapping projects involving vaccinia virus, hepatitis C virus (HCV), potato virus A (PVA), pea seed-borne mosaic virus (PSbMV), and bacteriophage T7, as well as some projects in progress. The studies reported suggest that virus-specific coding and replication strategies must be taken into account to yield accurate numbers of protein interactions. In particular, the number of false negatives can be significant for RNA viruses expressing precursor polyproteins (because interactions between full-length mature proteins are often not detected due to incorrect processing) and for viruses replicating in the cytoplasm whose transcripts have not been selected for splicing signals. In conclusion, the studies on viral protein interaction maps suggest that cloned pathogen ORFeomes will contribute to a holistic picture of the pathogenesis of infectious diseases and are ideal starting points for new approaches in systems biology. Both viral ORFeome and interaction mapping projects are being documented on our Web site (http://itgmv1.fzk.de/www/itg/uetz/virus/).
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Affiliation(s)
- Peter Uetz
- Institut für Genetik, Forschungszentrum Karlsruhe, D-76021 Karlsruhe, Germany.
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