1
|
Lee YF, Phua CZJ, Yuan J, Zhang B, Lee MY, Kannan S, Chiu YHJ, Koh CWQ, Yap CK, Lim EKH, Chen J, Lim Y, Lee JJH, Skanderup AJ, Wang Z, Zhai W, Tan NS, Verma CS, Tay Y, Tan DSW, Tam WL. PARP4 interacts with hnRNPM to regulate splicing during lung cancer progression. Genome Med 2024; 16:91. [PMID: 39034402 PMCID: PMC11265163 DOI: 10.1186/s13073-024-01328-1] [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: 02/17/2023] [Accepted: 04/02/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND The identification of cancer driver genes from sequencing data has been crucial in deepening our understanding of tumor biology and expanding targeted therapy options. However, apart from the most commonly altered genes, the mechanisms underlying the contribution of other mutations to cancer acquisition remain understudied. Leveraging on our whole-exome sequencing of the largest Asian lung adenocarcinoma (LUAD) cohort (n = 302), we now functionally assess the mechanistic role of a novel driver, PARP4. METHODS In vitro and in vivo tumorigenicity assays were used to study the functional effects of PARP4 loss and mutation in multiple lung cancer cell lines. Interactomics analysis by quantitative mass spectrometry was conducted to identify PARP4's interaction partners. Transcriptomic data from cell lines and patient tumors were used to investigate splicing alterations. RESULTS PARP4 depletion or mutation (I1039T) promotes the tumorigenicity of KRAS- or EGFR-driven lung cancer cells. Disruption of the vault complex, with which PARP4 is commonly associated, did not alter tumorigenicity, indicating that PARP4's tumor suppressive activity is mediated independently. The splicing regulator hnRNPM is a potentially novel PARP4 interaction partner, the loss of which likewise promotes tumor formation. hnRNPM loss results in splicing perturbations, with a propensity for dysregulated intronic splicing that was similarly observed in PARP4 knockdown cells and in LUAD cohort patients with PARP4 copy number loss. CONCLUSIONS PARP4 is a novel modulator of lung adenocarcinoma, where its tumor suppressive activity is mediated not through the vault complex-unlike conventionally thought, but in association with its novel interaction partner hnRNPM, thus suggesting a role for splicing dysregulation in LUAD tumorigenesis.
Collapse
Affiliation(s)
- Yi Fei Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Cheryl Zi Jin Phua
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Ju Yuan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Bin Zhang
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - May Yin Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix, Singapore, 138671, Singapore
| | - Yui Hei Jasper Chiu
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Casslynn Wei Qian Koh
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Choon Kong Yap
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Edwin Kok Hao Lim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Jianbin Chen
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Yuhua Lim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Jane Jia Hui Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Anders Jacobsen Skanderup
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
| | - Zhenxun Wang
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
- Centre for Vision Research, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Weiwei Zhai
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Nguan Soon Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Chandra S Verma
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix, Singapore, 138671, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore
| | - Daniel Shao Weng Tan
- Division of Medical Oncology, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Singapore.
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.
| |
Collapse
|
2
|
Zolotarenko A, Bruskin S. IQGAP3 Is an Important Mediator of Skin Inflammatory Diseases. Int J Mol Sci 2024; 25:4545. [PMID: 38674130 PMCID: PMC11050236 DOI: 10.3390/ijms25084545] [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: 02/14/2024] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
IQGAP3 (IQ Motif Containing GTPase Activating Protein 3) is member of the IQGAP family of scaffold proteins, which are essential for assembling multiprotein complexes that coordinate various intracellular signaling pathways. Previous research has shown that IQGAP3 is overexpressed in psoriatic skin lesions. Given its involvement in processes like cell proliferation and chemokine signaling, we sought to explore its molecular role in driving the psoriatic phenotype of keratinocytes. By conducting transcriptome profiling of HaCaT keratinocytes, we identified numerous psoriasis-associated pathways that were affected when IQGAP3 was knocked down. These included alterations in NFkB signaling, EGFR signaling, activation of p38/MAPK and ERK1/ERK2, lipid metabolism, cytokine production, and the response to inflammatory cytokine stimulation. Real-time analysis further revealed changes in cell growth dynamics, including proliferation and wound healing. The balance between cell proliferation and apoptosis was altered, as were skin barrier functions and the production of IL-6 and IFNγ. Despite these significant findings, the diversity of the alterations observed in the knockdown cells led us to conclude that IQGAP3 may not be the best target for the therapeutic inhibition to normalize the phenotype of keratinocytes in psoriasis.
Collapse
Affiliation(s)
- Alena Zolotarenko
- Laboratory of Functional genomics, Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sergey Bruskin
- Laboratory of Functional genomics, Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia
| |
Collapse
|
3
|
He G, Wang X, Li B, Wang L, Zhang J, Shi Y, Zhu W, Shi M. Genetic Analysis of a Mosaic Fra(16)(q22)/Del(16)(q22) Karyotype in a Primary Infertile Woman. Int J Womens Health 2024; 16:637-644. [PMID: 38645979 PMCID: PMC11032136 DOI: 10.2147/ijwh.s450272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/29/2024] [Indexed: 04/23/2024] Open
Abstract
Purpose Fragile sites are specific chromosomal regions showing gaps, poor staining, contractions, or even breaks in the chromosomes. These spontaneous and heritable fragile sites are prone to structural variations which can lead to adverse reproductive outcomes. This paper aims to present a specific case study of a female patient, with a mosaic karyotype involving chromosome 16q22 fragile site which is very rare in clinic and her experience of infertility. Case Presentation A 37-year-old woman is diagnosed with ten-year primary infertility. She worked in a factory, and she was occasionally exposed to paint. She underwent two cycles of follicular monitoring with intrauterine insemination (IUI) using her husband's sperm six years ago but failed. Most of her prepregnancy tests were normal, except a not smooth right fallopian tube. Her G-band karyotype of peripheral blood lymphocytes was mos 46, XX, del(16)(q22)[40]/46, XX, fra(16)(q22)[29]/46, XX, fra(16)tr(16)(q22)[3]/46, XX[28] which inherited from her mother. The SCE assay detected a significantly higher frequency of SCEs in the 16q region of the patient's chromosomes compared to her mother and a healthy control. However, the average SCEs per chromosome were quite close. Moreover, copy number variation (CNV) sequencing showed no deletion nor duplication at 16q22. Conclusion Infertility cannot be completely attributed to the fragile site on chromosome 16q22. Assisted reproductive technology combined with preimplantation genetic testing may help in achieving a healthy live birth.
Collapse
Affiliation(s)
- Guiyuan He
- Centre for Reproductive and Genetic Medicine, Dalian Women and Children’s Medical Group, Dalian, People’s Republic of China
| | - Xi Wang
- Centre for Reproductive and Genetic Medicine, Dalian Women and Children’s Medical Group, Dalian, People’s Republic of China
| | - Beiqing Li
- Centre for Reproductive and Genetic Medicine, Dalian Women and Children’s Medical Group, Dalian, People’s Republic of China
| | - Lei Wang
- Centre for Reproductive and Genetic Medicine, Dalian Women and Children’s Medical Group, Dalian, People’s Republic of China
| | - Jing Zhang
- Department of Clinical Laboratory, Central Hospital of Dalian University of Technology, Dalian Municipal Central Hospital, Dalian, People’s Republic of China
| | - Yang Shi
- Centre for Reproductive and Genetic Medicine, Dalian Women and Children’s Medical Group, Dalian, People’s Republic of China
| | - Wenxiu Zhu
- Centre for Reproductive and Genetic Medicine, Dalian Women and Children’s Medical Group, Dalian, People’s Republic of China
| | - Ming Shi
- Centre for Reproductive and Genetic Medicine, Dalian Women and Children’s Medical Group, Dalian, People’s Republic of China
- Department of Clinical Laboratory, Dalian Women and Children’s Medical Group, Dalian, People’s Republic of China
| |
Collapse
|
4
|
Mei W, Dong Y, Gu Y, Kapoor A, Lin X, Su Y, Vega Neira S, Tang D. IQGAP3 is relevant to prostate cancer: A detailed presentation of potential pathomechanisms. J Adv Res 2023; 54:195-210. [PMID: 36681115 DOI: 10.1016/j.jare.2023.01.015] [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: 10/30/2022] [Revised: 12/12/2022] [Accepted: 01/15/2023] [Indexed: 01/20/2023] Open
Abstract
INTRODUCTION IQGAP3 possesses oncogenic actions; its impact on prostate cancer (PC) remains unclear. OBJECTIVE We will investigate IQGAP3's association with PC progression, key mechanisms, prognosis, and immune evasion. METHODS IQGAP3 expression in PC was examined by immunohistochemistry and using multiple datasets. IQGAP3 network was analyzed for pathway alterations and used to construct a multigene signature (SigIQGAP3NW). SigIQGAP3NW was characterized using LNCaP cell-derived castration-resistant PCs (CRPCs), analyzed for prognostic value in 26 human cancer types, and studied for association with immune evasion. RESULTS Increases in IQGAP3 expression associated with PC tumorigenesis, tumor grade, metastasis, and p53 mutation. IQGAP3 correlative genes were dominantly involved in mitosis. IQGAP3 correlated with PLK1 and TOP2A expression at Spearman correlation/R = 0.89 (p ≤ 3.069e-169). Both correlations were enriched in advanced PCs and Taxane-treated CRPCs and occurred at high levels (R > 0.8) in multiple cancer types. SigIQGAP3NW effectively predicted cancer recurrence and poor prognosis in independent PC cohorts and across 26 cancer types. SigIQGAP3NW stratified PC recurrence after adjustment for age at diagnosis, grade, stage, and surgical margin. SigIQGAP3NW component genes were upregulated in PC, metastasis, LNCaP cell-produced CRPC, and showed an association with p53 mutation. SigIQGAP3NW correlated with immune cell infiltration, including Treg in PC and other cancers. RELT, a SigIQGAP3NW component gene, was associated with elevations of multiple immune checkpoints and the infiltration of Treg and myeloid-derived suppressor cells in PC and across cancer types. RELT and SigIQGAP3NW predict response to immune checkpoint blockade (ICB) therapy. CONCLUSIONS In multiple cancers, IQGAP3 robustly correlates with PLK1 and TOP2A expression, and SigIQGAP3NW and/or RELT effectively predict mortality risk and/or resistance to ICB therapy. PLK1 and TOP2A inhibitors should be investigated for treating cancers with elevated IQGAP3 expression. SigIQGAP3NW and/or RELT can be developed for clinical applications in risk stratification and management of ICB therapy.
Collapse
Affiliation(s)
- Wenjuan Mei
- Department of Nephrology, The First Affiliated Hospital of Nanchang University, Jiangxi, China; Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada; Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada; The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada.
| | - Ying Dong
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada; Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada; The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Yan Gu
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada; Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada; The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Anil Kapoor
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada; Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada; The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Xiaozeng Lin
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada; Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada; The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Yingying Su
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada; Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada; The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Sandra Vega Neira
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada; Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada; The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada
| | - Damu Tang
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada; Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada; The Research Institute of St Joe's Hamilton, St Joseph's Hospital, Hamilton, ON L8N 4A6, Canada.
| |
Collapse
|
5
|
Fei T, Zhou EC, Wang XJ. FOXD2 regulations IQGAP3 mediated Ca 2+ signaling pathway to facilitate gastric adenocarcinoma cell promotion. Kaohsiung J Med Sci 2023; 39:1087-1095. [PMID: 37724892 DOI: 10.1002/kjm2.12756] [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: 02/21/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 09/21/2023] Open
Abstract
As a transcriptional factor, the Forkhead box (FOX) gene family is closely connected with apoptosis, proliferation, and other cellular processes. FOXD2, as one descendant of the FOX gene family, has been mentioned in many articles to show a high expression in several cancers. However, whether FOXD2 has a connection with gastric adenocarcinoma remains an unanswered question. Expression of FOXD2 and IQGAP3 in gastric adenocarcinoma was evaluated by bioinformatics analysis, which was further detected by real-time quantitative PCR (qRT-PCR) and western blot. The downstream target genes of FOXD2 were also mined by bioinformatics analysis. Pathway enrichment analysis was then performed on the target genes. Chromatin immunoprecipitation assay (ChIP) and dual-luciferase reporter assay were conducted to validate the regulatory relationship between FOXD2 and its downstream target gene IQGAP3. Methyl thiazolyl tetrazolium assay (MTT), combined with cell colony formation assay, was employed to assess the effect of FOXD2 and IQGAP3 on the proliferation of gastric adenocarcinoma cells. Intracytoplasmic Ca2+ concentration was measured by Fluo-3 fluorescence staining. FOXD2 showed a high expression in gastric adenocarcinoma tissues and cells, and FOXD2 silencing considerably attenuated gastric adenocarcinoma cell proliferation. IQGAP3, a downstream target gene of FOXD2, had a positive connection with the expression of FOXD2. The binding relationship between FOXD2 and the promoter region of IQGAP3 was further verified by ChIP and dual-luciferase reporter assays. The results of cell function experiments indicated that FOXD2 could promote gastric adenocarcinoma cell proliferation by transcriptionally activating IQGAP3 to induce an increase in intracellular Ca2+ level. This study confirmed that FOXD2 increased intracellular Ca2+ level through transcriptional activation of IQGAP3, which in turn propelled the proliferation of gastric adenocarcinoma cells, revealing the considerable significance of FOXD2 in the development of gastric adenocarcinoma.
Collapse
Affiliation(s)
- Ting Fei
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - En-Cheng Zhou
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Xiao-Jun Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| |
Collapse
|
6
|
Huang J, Zhao G, Peng Q, Yi X, Ji L, Li J, Li P, Guan Y, Ge J, Chen L, Chen R, Hu X, Lee W, Reuben A, Futreal PA, Xia X, Ma J, Zhang J, Chen Z. Analysis of genomic and immune intratumor heterogeneity in linitis plastica via multiregional exome and T-cell receptor sequencing. Mol Oncol 2023; 17:1531-1544. [PMID: 36703611 PMCID: PMC10399711 DOI: 10.1002/1878-0261.13381] [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: 06/09/2022] [Revised: 11/25/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
The molecular landscape and the intratumor heterogeneity (ITH) architecture of gastric linitis plastica (LP) are poorly understood. We performed whole-exome sequencing (WES) and T-cell receptor (TCR) sequencing on 40 tumor regions from four LP patients. The landscape and ITH at the genomic and immunological levels in LP tumors were compared with multiple cancers that have previously been reported. The lymphocyte infiltration was further assessed by immunohistochemistry (IHC) in LP tumors. In total, we identified 6339 non-silent mutations from multi-samples, with a median tumor mutation burden (TMB) of 3.30 mutations per Mb, comparable to gastric adenocarcinoma from the Cancer Genome Atlas (TCGA) cohort (P = 0.53). An extremely high level of genomic ITH was observed, with only 12.42%, 5.37%, 5.35%, and 30.67% of mutations detectable across 10 regions within the same tumors of each patient, respectively. TCR sequencing revealed that TCR clonality was substantially lower in LP than in multi-cancers. IHC using antibodies against CD4, CD8, and PD-L1 demonstrated scant T-cell infiltration in the four LP tumors. Furthermore, profound TCR ITH was observed in all LP tumors, with no T-cell clones shared across tumor regions in any of the patients, while over 94% of T-cell clones were restricted to individual tumor regions. The Morisita overlap index (MOI) ranged from 0.21 to 0.66 among multi-regions within the same tumors, significantly lower than that of lung cancer (P = 0.002). Our results show that LP harbored extremely high genomic and TCR ITH and suppressed T-cell infiltration, suggesting a potential contribution to the frequent recurrence and poor therapeutic response of this adenocarcinoma.
Collapse
Affiliation(s)
- Jin Huang
- The Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal TumorXiangya Hospital, Central South UniversityChangshaHunanChina
- Department of Oncology, Xiangya HospitalXiangya HospitalCentral South UniversityChangshaChina
- Department of General Surgery, Xiangya HospitalCentral South UniversityChangshaChina
- International Joint Research Center of Minimally Invasive Endoscopic Technology Equipment & StandardizationChangshaChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalChangshaChina
| | - Guofeng Zhao
- Geneplus‐Beijing InstituteBeijingChina
- Geneplus‐BeijingBeijingChina
| | - Qiu Peng
- Cancer Research Institute, School of Basic Medical ScienceCentral South UniversityChangshaChina
| | - Xin Yi
- Geneplus‐Beijing InstituteBeijingChina
- Geneplus‐BeijingBeijingChina
| | - Liyan Ji
- Geneplus‐Beijing InstituteBeijingChina
- Geneplus‐BeijingBeijingChina
| | - Jing Li
- Geneplus‐Beijing InstituteBeijingChina
- Geneplus‐BeijingBeijingChina
| | - Pansong Li
- Geneplus‐Beijing InstituteBeijingChina
- Geneplus‐BeijingBeijingChina
| | - Yanfang Guan
- Geneplus‐Beijing InstituteBeijingChina
- Geneplus‐BeijingBeijingChina
| | - Jie Ge
- Department of General Surgery, Xiangya HospitalCentral South UniversityChangshaChina
| | - Ling Chen
- Department of General Surgery, Xiangya HospitalCentral South UniversityChangshaChina
| | - Runzhe Chen
- Department of Thoracic and Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
- Department of Genomic MedicineThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Xin Hu
- Department of Thoracic and Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
- Department of Genomic MedicineThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Won‐Chul Lee
- Department of Thoracic and Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Alexandre Reuben
- Department of Thoracic and Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - P. Andrew Futreal
- Department of Genomic MedicineThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | | | - Jian Ma
- The Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal TumorXiangya Hospital, Central South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalChangshaChina
- Cancer Research Institute, School of Basic Medical ScienceCentral South UniversityChangshaChina
| | - Jianjun Zhang
- Department of Thoracic and Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
- Department of Genomic MedicineThe University of Texas MD Anderson Cancer CenterHoustonTXUSA
| | - Zihua Chen
- The Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal TumorXiangya Hospital, Central South UniversityChangshaHunanChina
- Department of General Surgery, Xiangya HospitalCentral South UniversityChangshaChina
- International Joint Research Center of Minimally Invasive Endoscopic Technology Equipment & StandardizationChangshaChina
- National Clinical Research Center for Geriatric DisordersXiangya HospitalChangshaChina
| |
Collapse
|
7
|
Zhang J, Jiang R, Hong X, Wu H, Han X, Wu W. Metastatic insulinoma: exploration from clinicopathological signatures and genetic characteristics. Front Oncol 2023; 13:1109330. [PMID: 37251916 PMCID: PMC10213277 DOI: 10.3389/fonc.2023.1109330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 04/27/2023] [Indexed: 05/31/2023] Open
Abstract
Background Insulinoma is a rare type of pancreatic neuroendocrine tumor with low incidence and low-malignant features. While very few insulinomas present with malignant behaviours, such as lymph node and liver metastasis, only a few studies have focused on this field owing to the limitation of samples. Existing evidence suggests that metastatic insulinoma largely derive from non-functional pancreatic neuroendocrine tumor. However, we found a portion of metastatic insulinomas may derive from non-metastatic insulinomas and explored their clinicopathological signatures and genetic characteristics. Methods Four metastatic insulinoma patients with synchronous liver metastasis or lymph node metastasis at the Peking Union Medical College Hospital between October 2016 and December 2018 were enrolled, and whole exon and genome sequencing were performed on fresh frozen tissues and peripheral blood samples. Clinicopathological information and genomic sequencing results were collected and matched to explore the characteristics of the metastatic insulinomas. Results These four metastatic insulinoma patients underwent surgery or interventional therapy, and their blood glucose levels immediately increased and maintained within standard range after treatment. For these four patients, the proinsulin/insulin molar ratio <1 and primary tumors were all present as PDX1+, ARX-, and insulin+, which were similar to non-metastatic insulinomas. However, the liver metastasis showed PDX1+ and ARX+, insulin+. Meanwhile, genomic sequencing data showed no recurrently mutations and typical CNV patterns. However, one patient harboured the YY1 T372R mutation, a recurrently mutated gene in non-metastatic insulinomas. Conclusions A portion of metastatic insulinomas were largely derived from non-metastatic insulinomas in hormone secretion and ARX/PDX1 expression patterns. Meanwhile, the accumulation of ARX expression may be involved in the progression of metastatic insulinomas.
Collapse
Affiliation(s)
- Jingcheng Zhang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Rui Jiang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xiafei Hong
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xianlin Han
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Wenming Wu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| |
Collapse
|
8
|
Fan R, Xu L, Cui B, Li D, Sun X, Qi Y, Rao J, Wang K, Wang C, Zhao K, Zhao Y, Dai J, Chen W, Shen H, Liu Y, Yu D. Genomic Characterization Revealed PM 2.5-Associated Mutational Signatures in Lung Cancer Including Activation of APOBEC3B. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:6854-6864. [PMID: 37071573 DOI: 10.1021/acs.est.2c08092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Fine particulate matter (PM2.5) exposure causes DNA mutations and abnormal gene expression leading to lung cancer, but the detailed mechanisms remain unknown. Here, analysis of genomic and transcriptomic changes upon a PM2.5 exposure-induced human bronchial epithelial cell-based malignant transformed cell model in vitro showed that PM2.5 exposure led to APOBEC mutational signatures and transcriptional activation of APOBEC3B along with other potential oncogenes. Moreover, by analyzing mutational profiles of 1117 non-small cell lung cancers (NSCLCs) from patients across four different geographic regions, we observed a significantly higher prevalence of APOBEC mutational signatures in non-smoking NSCLCs than smoking in the Chinese cohorts, but this difference was not observed in TCGA or Singapore cohorts. We further validated this association by showing that the PM2.5 exposure-induced transcriptional pattern was significantly enriched in Chinese NSCLC patients compared with other geographic regions. Finally, our results showed that PM2.5 exposure activated the DNA damage repair pathway. Overall, here we report a previously uncharacterized association between PM2.5 and APOBEC activation, revealing a potential molecular mechanism of PM2.5 exposure and lung cancer.
Collapse
Affiliation(s)
- Rongrong Fan
- School of Public Health, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Lin Xu
- School of Public Health, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Bowen Cui
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Daochuan Li
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Xueying Sun
- School of Public Health, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Yuan Qi
- School of Public Health, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Jianan Rao
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Kai Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Cheng Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Kunming Zhao
- School of Public Health, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Yanjie Zhao
- School of Public Health, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Wen Chen
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Hongbing Shen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine and China International Cooperation Center for Environment and Human Health, Genomic Science and Precision Medicine Institute, Gusu School, Nanjing Medical University, Nanjing 211166, China
| | - Yu Liu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Fujian Children's Hospital, Fujian Branch of Shanghai Children's Medical Center Affiliated to Shanghai Jiao Tong University School of Medicine, Fuzhou 350000, China
| | - Dianke Yu
- School of Public Health, Qingdao University, 308 Ningxia Road, Qingdao 266071, China
| |
Collapse
|
9
|
Zhang J, Li J, Xiong Y, Li R. Circ_0000284 upregulates RHPN2 to facilitate pancreatic cancer proliferation, metastasis, and angiogenesis through sponging miR-1179. J Biochem Mol Toxicol 2023; 37:e23274. [PMID: 36536496 DOI: 10.1002/jbt.23274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 08/15/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Circular RNA (circRNA) has been confirmed to be a key regulator for pancreatic cancer (PC) progression, but the role of circ_0000284 in PC development remains unclear. METHODS Quantitative real-time PCR was used to measure the expression of circ_0000284, microRNA (miR)-1179, and rhophilin 2 (RHPN2). PC cell proliferation, metastasis, angiogenesis, and apoptosis were assessed by EdU assay, transwell assay, tube formation assay, and flow cytometry. Relative protein expression was determined by western blot analysis. The interaction between miR-1179 and circ_0000284 or RHPN2 was confirmed by dual-luciferase reporter assay and RNA pull-down assay. RESULTS Circ_0000284 was significantly upregulated in PC tissues and cells, and its knockdown inhibited PC cell proliferation, migration, invasion, and angiogenesis while promoting apoptosis. MiR-1179 was downregulated in PC tissues and cells, and it could be sponged by circ_0000284. Moreover, the miR-1179 inhibitor reversed the regulation of circ_0000284 knockdown on PC cell progression. The highly expressed RHPN2 was found in PC tissues and cells, and it could be targeted by miR-1179. Also, circ_0000284 sponged miR-1179 to regulate RHPN2 expression. Overexpressed RHPN2 could reverse the regulation of circ_0000284 knockdown on PC cell progression. In addition, interference of circ_0000284 was discovered to repress PC tumor growth by regulating miR-1179/RHPN2.RHPN2. CONCLUSION To sum up, our data confirmed that circ_0000284 facilitated PC malignant progression depending on the regulation of miR-1179/RHPN2 axis, suggesting that circ_0000284 might be a potential target for PC treatment.
Collapse
Affiliation(s)
- Jian Zhang
- Department of Geratic Gastroenterological Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jiangwei Li
- Department of Geratic Gastroenterological Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yongqiang Xiong
- Department of Geratic Gastroenterological Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ren Li
- Department of Geratic Gastroenterological Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
10
|
Alvarez-Cubero MJ, Arance E, de Santiago E, Sanchez P, Sepúlveda MR, Marrero R, Lorente JA, Gonzalez-Cabezuelo JM, Cuenca-Lopez S, Cozar JM, Vazquez-Alonso F, Martinez-Gonzalez LJ. Follow-Up Biomarkers in the Evolution of Prostate Cancer, Levels of S100A4 as a Detector in Plasma. Int J Mol Sci 2022; 24:ijms24010547. [PMID: 36613987 PMCID: PMC9820153 DOI: 10.3390/ijms24010547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/30/2022] Open
Abstract
The management and screening of prostate cancer (PC) is still the main problem in clinical practice. In this study, we investigated the role of aggressiveness genetic markers for PC stratification. We analyzed 201 plasma samples from PC patients and controls by digital PCR. For selection and validation, 26 formalin-fixed paraffin-embedded tissues, 12 fresh tissues, and 24 plasma samples were characterized by RNA-Seq, immunochemistry, immunofluorescence, Western blot, and extracellular-vesicles analyses. We identified three novel non-invasive biomarkers; all with an increased expression pattern in patients (PCA3: p = 0.002, S100A4: p ≤ 0.0001 and MRC2: p = 0.005). S100A4 presents the most informative AUC (area under the curve) (0.735). Combination of S100A4, MRC2, and PCA3 increases the discriminatory power between patients and controls and between different more and less aggressive stages (AUC = 0.761, p ≤ 0.0001). However, although a sensitivity of 97.47% in PCA3 and a specificity of 90.32% in S100A4 was reached, the detection signal level could be variable in some analyses owing to tumor heterogeneity. This is the first time that the role of S100A4 and MRC2 has been described in PC aggressiveness. Moreover, the combination of S100A4, MRC2, and PCA3 has never been described as a non-invasive biomarker for PC screening and aggressiveness.
Collapse
Affiliation(s)
- Maria Jesus Alvarez-Cubero
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Genomics Unit, PTS Granada, Avenida de la Ilustración 114, 18016 Granada, Spain
- Nutrition, Diet and Risk Assessment Group, Bio-Health Research Institute (Instituto de Investigación Biosanitaria ibs.GRANADA), Avenida de las Fuerzas Armadas 2, 18014 Granada, Spain
- Department of Biochemistry and Molecular Biology III, Faculty of Medicine, University of Granada, PTS Granada, 18016 Granada, Spain
| | - Elena Arance
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Genomics Unit, PTS Granada, Avenida de la Ilustración 114, 18016 Granada, Spain
| | - Esperanza de Santiago
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Genomics Unit, PTS Granada, Avenida de la Ilustración 114, 18016 Granada, Spain
| | - Pilar Sanchez
- Department of Biochemistry and Molecular Biology III, Faculty of Medicine, University of Granada, PTS Granada, 18016 Granada, Spain
| | - Maria Rosario Sepúlveda
- Department of Cell Biology, Faculty of Sciences, University of Granada, Avenida de la Fuente Nueva S/N CP, 18071 Granada, Spain
| | - Raquel Marrero
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Genomics Unit, PTS Granada, Avenida de la Ilustración 114, 18016 Granada, Spain
| | - Jose Antonio Lorente
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Genomics Unit, PTS Granada, Avenida de la Ilustración 114, 18016 Granada, Spain
- Department of Legal Medicine and Toxicology, Faculty of Medicine, University of Granada, PTS Granada, 18016 Granada, Spain
| | | | - Sergio Cuenca-Lopez
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Genomics Unit, PTS Granada, Avenida de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology III, Faculty of Medicine, University of Granada, PTS Granada, 18016 Granada, Spain
| | - Jose Manuel Cozar
- Urology Department, Virgen de las Nieves Hospital, 18014 Granada, Spain
| | | | - Luis Javier Martinez-Gonzalez
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Genomics Unit, PTS Granada, Avenida de la Ilustración 114, 18016 Granada, Spain
- Correspondence: ; Tel.: +34-958-715-500 (ext. 108); Fax: +34-958-637-071
| |
Collapse
|
11
|
Zhang C, Wang K, Liu W, Lin J, Li Z, Wang H, Zhao C, Chen Y, Wu S, Yang A, Wu J, Wang H. Whole exome sequencing in Chinese mucinous pulmonary adenocarcinoma uncovers specific genetic variations different from lung adenocarcinoma. Front Oncol 2022; 12:1054845. [PMID: 36591517 PMCID: PMC9798319 DOI: 10.3389/fonc.2022.1054845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/30/2022] [Indexed: 12/16/2022] Open
Abstract
Background As a rare subtype of primary lung adenocarcinoma (LUAD), mucinous pulmonary adenocarcinoma (MPA) was considered a distinctive entity with unfavorable outcomes. Therefore, there is a great need for a better understanding of the genomic and immunological landscape of this rare tumor type, which would inform improved therapeutic strategies. Methods A total of 96 patients histologically confirmed with MPA were recruited from Shandong Cancer Hospital and Institute (SCH). Single nucleotide variation (SNV), copy number variation (CNV), genomic instability, and immunological landscape insights into 96 MPA patients were identified using WES. Results We demonstrated that MPAs had marked different genomic alterations and were more complex in genomic profiles than LUADs. Mutations in Tumor Protein 53 (TP53) and CYP7A Promoter-Binding Factor (CPF) pathways significantly shortened survival whereas mutations in Notch and Wnt pathways significantly prolonged survival in MPA. Besides, we demonstrated that mutations in immune-related genes influenced outcomes, with mutations in TP53, Ataxia Telangiectasia Mutated (ATM), Polymerase (DNA) Delta 1 (POLD1), and Epidermal Growth Factor Receptor (EGFR) correlated with worsened survival. Conclusions We not only depicted the genetic and immunologic landscape of Chinese MPA but also reveal its distinction from LUAD in genomic and immune context. Our findings may provide opportunities for therapeutic susceptibility among Chinese MPA patients.
Collapse
Affiliation(s)
- Chenyue Zhang
- Department of Integrated Therapy, Fudan University Shanghai Cancer Center, Shanghai Medical College, Shanghai, China
| | - Kai Wang
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China
| | - Wenjie Liu
- Research Institute, Berry Oncology Corporation, Beijing, China
| | - Jiamao Lin
- Department of Traditional Chinese medicine, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Zhenxiang Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Hui Wang
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Chenglong Zhao
- Department of Pathology, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Yanhua Chen
- Department of Biological Information, Berry Oncology Corporation, Beijing, China
| | - Shuangxiu Wu
- Research Institute, Berry Oncology Corporation, Beijing, China
| | - Airong Yang
- Department of Biological Information, Berry Oncology Corporation, Beijing, China
| | - Jiayan Wu
- Research Institute, Berry Oncology Corporation, Beijing, China
| | - Haiyong Wang
- Department of Internal Medicine-Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China,*Correspondence: Haiyong Wang,
| |
Collapse
|
12
|
CXCL9 influences the tumor immune microenvironment by stimulating JAK/STAT pathway in triple-negative breast cancer. Cancer Immunol Immunother 2022; 72:1479-1492. [DOI: 10.1007/s00262-022-03343-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/26/2022] [Indexed: 12/13/2022]
|
13
|
Banaganapalli B, Mallah B, Alghamdi KS, Albaqami WF, Alshaer DS, Alrayes N, Elango R, Shaik NA. Integrative weighted molecular network construction from transcriptomics and genome wide association data to identify shared genetic biomarkers for COPD and lung cancer. PLoS One 2022; 17:e0274629. [PMID: 36194576 PMCID: PMC9531836 DOI: 10.1371/journal.pone.0274629] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 09/01/2022] [Indexed: 11/05/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a multifactorial progressive airflow obstruction in the lungs, accounting for high morbidity and mortality across the world. This study aims to identify potential COPD blood-based biomarkers by analyzing the dysregulated gene expression patterns in blood and lung tissues with the help of robust computational approaches. The microarray gene expression datasets from blood (136 COPD and 6 controls) and lung tissues (16 COPD and 19 controls) were analyzed to detect shared differentially expressed genes (DEGs). Then these DEGs were used to construct COPD protein network-clusters and functionally enrich them against gene ontology annotation terms. The hub genes in the COPD network clusters were then queried in GWAS catalog and in several cancer expression databases to explore their pathogenic roles in lung cancers. The comparison of blood and lung tissue datasets revealed 63 shared DEGs. Of these DEGs, 12 COPD hub gene-network clusters (SREK1, TMEM67, IRAK2, MECOM, ASB4, C1QTNF2, CDC42BPA, DPF3, DET1, CCDC74B, KHK, and DDX3Y) connected to dysregulations of protein degradation, inflammatory cytokine production, airway remodeling, and immune cell activity were prioritized with the help of protein interactome and functional enrichment analysis. Interestingly, IRAK2 and MECOM hub genes from these COPD network clusters are known for their involvement in different pulmonary diseases. Additional COPD hub genes like SREK1, TMEM67, CDC42BPA, DPF3, and ASB4 were identified as prognostic markers in lung cancer, which is reported in 1% of COPD patients. This study identified 12 gene network- clusters as potential blood based genetic biomarkers for COPD diagnosis and prognosis.
Collapse
Affiliation(s)
- Babajan Banaganapalli
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (BB); (NAS)
| | - Bayan Mallah
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kawthar Saad Alghamdi
- Department of Biology, Faculty of Science, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| | - Walaa F. Albaqami
- Department of Science, Prince Sultan Military College of Health Sciences, Dhahran, Saudi Arabia
| | - Dalal Sameer Alshaer
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nuha Alrayes
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ramu Elango
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noor A. Shaik
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (BB); (NAS)
| |
Collapse
|
14
|
Tan AC, Saw SP, Chen J, Lai GG, Oo HN, Takano A, Lau DP, Yeong JP, Tan GS, Lim KH, Skanderup AJ, Chan JW, Teh YL, Rajasekaran T, Jain A, Tan WL, Ng QS, Kanesvaran R, Lim WT, Ang MK, Tan DS. Clinical and Genomic Features of HER2 Exon 20 Insertion Mutations and Characterization of HER2 Expression by Immunohistochemistry in East Asian Non–Small-Cell Lung Cancer. JCO Precis Oncol 2022; 6:e2200278. [DOI: 10.1200/po.22.00278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PURPOSE HER2-altered non–small-cell lung cancer (NSCLC) represents a diverse subgroup, including mutations, amplifications, and overexpression. However, HER2 exon 20 insertion mutations are emerging as a distinct molecular subtype with expanding therapeutic options. We describe the molecular epidemiology and genomic features of HER2-altered NSCLC in an Asian tertiary cancer center. METHODS We identified patients with HER2-mutated NSCLC in our institutional database, collating clinicopathological features and treatment outcomes. The genomic landscape of human epidermal growth factor receptor 2 ( HER2)–mutated NSCLC was further evaluated using whole-exome sequencing (WES) data from combined local and publicly available data sets. HER2 amplification and overexpression as selection biomarkers in NSCLC were further interrogated using HER2 immunohistochemistry and correlations with WES and RNA sequencing data. RESULTS Among 1,252 patients with consecutive lung adenocarcinoma undergoing routine next-generation sequencing, the prevalence of HER2 mutations was 3.1%—exon 20 insertion mutations comprised 2.7%. We examined the clinicopathological features in 55 patients with HER2-mutated NSCLC comprising 40 exon 20 insertion and 15 nonexon 20 insertion mutations. The most common exon 20 insertion mutation was HER2Y772_A775dup in 30 (75%), followed by HER2G776delinsVC in five patients (13%). There were limited responses to HER2-directed therapies apart from trastuzumab-deruxtecan, and no responses were seen with immunotherapy monotherapy. Evaluating the genomics features of HER2 exon 20 insertion mutations using WES data revealed low tumor mutational burden (TMB), low incidence of cancer driver comutations, and a predominance of aging mutational signature—similar to EGFR-mutated tumors. In contrast, uncommon (or nonexon 20 insertion) HER2-mutated tumors resembled EGFR wild-type tumors with higher TMB, higher frequency of cancer driver comutations, and greater presence of smoking and APOBEC mutational signature. Finally, in evaluating HER2 immunohistochemistry in all lung adenocarcinoma, there was significant discordance comparing different scoring systems and poor correlation with HER2 RNA expression and HER2 amplification. CONCLUSION The incidence of HER2 mutations is 3.1% in East Asian nonsquamous NSCLC. HER2 exon 20 insertion–mutated tumors appear genomically distinct from uncommon (nonexon 20 insertion) HER2 mutations, the latter demonstrating higher TMB, co-occurring drivers, and predominant nonaging mutational signature. The therapeutic implications of the genomic and clinical features of HER2-mutated NSCLC warrant further investigation.
Collapse
Affiliation(s)
- Aaron C. Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Stephanie P.L. Saw
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Jianbin Chen
- Genome Institute of Singapore, Singapore, Singapore
| | - Gillianne G.Y. Lai
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Hlaing Nwe Oo
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Angela Takano
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Dawn P.X. Lau
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Joe P.S. Yeong
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Gek San Tan
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Kiat Hon Lim
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | | | - Johan W.K. Chan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Yi Lin Teh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Tanujaa Rajasekaran
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Amit Jain
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Wan Ling Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Quan Sing Ng
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Ravindran Kanesvaran
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Wan-Teck Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Mei-Kim Ang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Daniel S.W. Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| |
Collapse
|
15
|
Comprehensive Multiomics Analysis Identified IQGAP3 as a Potential Prognostic Marker in Pan-Cancer. DISEASE MARKERS 2022; 2022:4822964. [PMID: 36164370 PMCID: PMC9508463 DOI: 10.1155/2022/4822964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/01/2022] [Indexed: 12/24/2022]
Abstract
Background IQGAP3 has important function in cancer progression and has become a potential therapeutic target as a transmembrane protein. But its role in tumor immunity and pan-cancer was not systematically investigated. This study evaluated the potential role of IQGAP3 and clinical significance in pan-cancer through combined multiomics analysis. Methods From Genotype Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) databases, transcriptomic datasets were first obtained, and from Gene Expression Omnibus (GEO), expression profiling microarray data were acquired and integrated to systematically assess the expression differences and prognostic relevance of IQGAP3 in pancreatic cancer. Immunohistochemical data were obtained from Human Protein Atlas (HPA) to assess IQGAP3 protein expression differences, and exome data from TCGA were used to analyze IQGAP3 expression in relation to tumor mutational burden (TMB), microsatellite instability (MSI), and mutation. Additionally, we also analyzed the relationship between IQGAP3 expression and immune checkpoints, mismatch repair (MMR), and IQGAP3 relationship with methylation and copy number variation based on expression profiles. Results Microsatellite instability (MSI), immune checkpoints, mismatch repair (MMR), and tumor mutational burden (TMB) all closely interacted with IQGAP3 mRNA. In addition, detailed relationships between the immune microenvironment and IQGAP3 mRNA as well as immune cell CD4+ Th2 and myeloid-derived suppressor cells (MDSCs) were determined. Mechanistically, IQGAP3 was involved in cytoskeleton formation, T cell receptor signaling pathways, DNA damage, cell cycle, P53 pathway, Fc gamma R-mediated phagocytosis, and apoptosis. Conclusion IQGAP3 could serve as an effective prognostic biomarker for pan-cancer immune-related therapy.
Collapse
|
16
|
Can EGFR be a therapeutic target in breast cancer? Biochim Biophys Acta Rev Cancer 2022; 1877:188789. [PMID: 36064121 DOI: 10.1016/j.bbcan.2022.188789] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/20/2022]
Abstract
Epidermal growth factor receptor (EGFR) is highly expressed in certain cancer types and is involved in regulating the biological characteristics of cancer progression, including proliferation, metastasis, and drug resistance. Various medicines targeting EGFR have been developed and approved for several cancer types, such as lung and colon cancer. To date, however, EGFR inhibitors have not achieved satisfactory clinical results in breast cancer, which continues to be the most serious malignant tumor type in females. Therefore, clarifying the underlying mechanisms related to the ineffectiveness of EGFR inhibitors in breast cancer and developing new EGFR-targeted strategies (e.g., combination therapy) remain critical challenges. Various studies have demonstrated aberrant expression and maintenance of EGFR levels in breast cancer. In this review, we summarize the regulatory mechanisms underlying EGFR protein expression in breast cancer cells, including EGFR mutations, amplification, endocytic dysfunction, recycling acceleration, and degradation disorders. We also discuss potential therapeutic strategies that act directly or indirectly on EGFR, including reducing EGFR protein expression, treating the target protein to mediate precise clearance, and inhibiting non-EGFR signaling pathways. This review should provide new therapeutic perspectives for breast cancer patients with high EGFR expression.
Collapse
|
17
|
Bae K, Kim JH, Lee JY, Kong SY, Kim YH, Kim S, Yoon KA. Oncogenic fusion of BCAR4 activates EGFR signaling and is sensitive to dual inhibition of EGFR/HER2. Front Mol Biosci 2022; 9:952651. [PMID: 36081848 PMCID: PMC9445485 DOI: 10.3389/fmolb.2022.952651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/19/2022] [Indexed: 11/05/2022] Open
Abstract
We previously reported CD63-BCAR4 fusion as a novel oncogene that significantly enhanced cell migration and metastasis in lung cancer. To identify effective inhibitors of metastatic activity induced by BCAR4 fusion, we screened a drug library of 381 FDA-approved compounds. The effect of drugs on cell migration was evaluated by monitoring wound healing. Drugs that decreased the cellular mobility of fusion-overexpressing cells compared with that of control cells were selected as candidates. Library screening revealed that erlotinib, canertinib, and lapatinib demonstrated inhibitory effects on cell migration. Activation of the EGFR signaling pathway was detected after ectopic expression of CD63-BCAR4 in normal bronchial epithelial cells, as observed by the increased phosphorylation of tyrosine residues in the EGFR protein. We also confirmed increased levels of the phosphorylated EGFR protein in resected tumors from mice injected with CD63-BCAR4 overexpressing cells. Tyrosine kinase inhibitors (TKIs) of the EGFR family significantly inhibit the migration of BCAR4 fusion-overexpressing cells and induce apoptosis at high concentrations. Among the EGFR family TKIs, canertinib, a dual EGFR/HER2 inhibitor, showed the best inhibitory effect on the migration and viability of BCAR4 fusion-overexpressing cells. We examined the effect of canertinib in vivo using a mouse xenograft model. Oral administration of canertinib to xenografted mice reduced tumor growth induced by the CD63-BCAR4 fusion gene. In addition, canertinib treatment restored E-cadherin expression and reduced the expression of epithelial-mesenchymal transition regulatory factors such as Slug and Snail. Taken together, these results suggest that EGFR/HER2 inhibitors are potential therapeutic options for BCAR4 fusion-harboring lung cancer patients, even in the absence of EGFR mutations.
Collapse
Affiliation(s)
- Kieun Bae
- College of Veterinary Medicine, Konkuk University, Seoul, South Korea
| | - Jin Hee Kim
- College of Health Science, Cheongju University, Cheongju, South Korea
| | - Ja Young Lee
- College of Veterinary Medicine, Konkuk University, Seoul, South Korea
| | - Sun-Young Kong
- Research Institute, National Cancer Center, Goyang, South Korea,National Cancer Center Graduate School of Cancer Science and Policy, Goyang, South Korea
| | - Yun-Hee Kim
- Research Institute, National Cancer Center, Goyang, South Korea,National Cancer Center Graduate School of Cancer Science and Policy, Goyang, South Korea
| | - Sunshin Kim
- Research Institute, National Cancer Center, Goyang, South Korea
| | - Kyong-Ah Yoon
- College of Veterinary Medicine, Konkuk University, Seoul, South Korea,*Correspondence: Kyong-Ah Yoon,
| |
Collapse
|
18
|
Chen K, Yang A, Carbone DP, Kanu N, Liu K, Wang R, Nie Y, Shen H, Bai J, Wu L, Li H, Shi Y, Mok T, Yu J, Yang F, Wu S, Jamal-Hanjani M, Wang J. Spatiotemporal genomic analysis reveals distinct molecular features in recurrent stage I non-small cell lung cancers. Cell Rep 2022; 40:111047. [PMID: 35830809 DOI: 10.1016/j.celrep.2022.111047] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 04/26/2022] [Accepted: 06/13/2022] [Indexed: 11/21/2022] Open
Abstract
Stage I non-small cell lung cancer (NSCLC) presents diverse outcomes. To identify molecular features leading to tumor recurrence in early-stage NSCLC, we perform multiregional whole-exome sequencing (WES), RNA sequencing, and plasma-targeted circulating tumor DNA (ctDNA) detection analysis between recurrent and recurrent-free stage I NSCLC patients (CHN-P cohort) who had undergone R0 resection with a median 5-year follow-up time. Integrated analysis indicates that the multidimensional clinical and genomic model can stratify the prognosis of stage I NSCLC in both CHN-P and EUR-T cohorts and correlates with positive pre-surgical deep next generation sequencing (NGS) ctDNA detection. Increased genomic instability related to DNA interstrand crosslinks and double-strand break repair processes is significantly associated with early tumor relapse. This study reveals important molecular insights into stage I NSCLC and may inform clinical postoperative treatment and follow-up strategies.
Collapse
Affiliation(s)
- Kezhong Chen
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Airong Yang
- Berry Oncology Corporation, Beijing 100102, China
| | | | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Ke Liu
- Berry Oncology Corporation, Beijing 100102, China
| | - Ruiru Wang
- Berry Oncology Corporation, Beijing 100102, China
| | - Yuntao Nie
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China
| | - Haifeng Shen
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China
| | - Jian Bai
- Berry Oncology Corporation, Beijing 100102, China
| | - Lin Wu
- Berry Oncology Corporation, Beijing 100102, China
| | - Hui Li
- Berry Oncology Corporation, Beijing 100102, China
| | - Yanbin Shi
- Berry Oncology Corporation, Beijing 100102, China
| | - Tony Mok
- Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jun Yu
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Fan Yang
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China.
| | - Shuangxiu Wu
- Berry Oncology Corporation, Beijing 100102, China.
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK; Department of Medical Oncology, University College London Hospitals, London, UK.
| | - Jun Wang
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China.
| |
Collapse
|
19
|
Xiang Y, Luettich K, Martin F, Battey JND, Trivedi K, Neau L, Wong ET, Guedj E, Dulize R, Peric D, Bornand D, Ouadi S, Sierro N, Büttner A, Ivanov NV, Vanscheeuwijck P, Hoeng J, Peitsch MC. Discriminating Spontaneous From Cigarette Smoke and THS 2.2 Aerosol Exposure-Related Proliferative Lung Lesions in A/J Mice by Using Gene Expression and Mutation Spectrum Data. FRONTIERS IN TOXICOLOGY 2022; 3:634035. [PMID: 35295134 PMCID: PMC8915865 DOI: 10.3389/ftox.2021.634035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/19/2021] [Indexed: 11/25/2022] Open
Abstract
Mice, especially A/J mice, have been widely employed to elucidate the underlying mechanisms of lung tumor formation and progression and to derive human-relevant modes of action. Cigarette smoke (CS) exposure induces tumors in the lungs; but, non-exposed A/J mice will also develop lung tumors spontaneously with age, which raises the question of discriminating CS-related lung tumors from spontaneous ones. However, the challenge is that spontaneous tumors are histologically indistinguishable from the tumors occurring in CS-exposed mice. We conducted an 18-month inhalation study in A/J mice to assess the impact of lifetime exposure to Tobacco Heating System (THS) 2.2 aerosol relative to exposure to 3R4F cigarette smoke (CS) on toxicity and carcinogenicity endpoints. To tackle the above challenge, a 13-gene gene signature was developed based on an independent A/J mouse CS exposure study, following by a one-class classifier development based on the current study. Identifying gene signature in one data set and building classifier in another data set addresses the feature/gene selection bias which is a well-known problem in literature. Applied to data from this study, this gene signature classifier distinguished tumors in CS-exposed animals from spontaneous tumors. Lung tumors from THS 2.2 aerosol-exposed mice were significantly different from those of CS-exposed mice but not from spontaneous tumors. The signature was also applied to human lung adenocarcinoma gene expression data (from The Cancer Genome Atlas) and discriminated cancers in never-smokers from those in ever-smokers, suggesting translatability of our signature genes from mice to humans. A possible application of this gene signature is to discriminate lung cancer patients who may benefit from specific treatments (i.e., EGFR tyrosine kinase inhibitors). Mutational spectra from a subset of samples were also utilized for tumor classification, yielding similar results. “Landscaping” the molecular features of A/J mouse lung tumors highlighted, for the first time, a number of events that are also known to play a role in human lung tumorigenesis, such as Lrp1b mutation and Ros1 overexpression. This study shows that omics and computational tools provide useful means of tumor classification where histopathological evaluation alone may be unsatisfactory to distinguish between age- and exposure-related lung tumors.
Collapse
Affiliation(s)
- Yang Xiang
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Karsta Luettich
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Florian Martin
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - James N D Battey
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Keyur Trivedi
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Laurent Neau
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Ee Tsin Wong
- Philip Morris International R&D, Philip Morris International Research Laboratories Pte. Ltd., Singapore, Singapore
| | - Emmanuel Guedj
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Remi Dulize
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Dariusz Peric
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - David Bornand
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Sonia Ouadi
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Nicolas Sierro
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | | | - Nikolai V Ivanov
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | | | - Julia Hoeng
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Manuel C Peitsch
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| |
Collapse
|
20
|
Chen Y, He Q, Ma H, Zhang L, Liu F, Han Y. Relationship of PI3K-Akt/mTOR/AMPK signaling pathway genetic mutation with efficacy and prognosis in nasopharyngeal carcinoma. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2022; 47:165-173. [PMID: 35545406 PMCID: PMC10930525 DOI: 10.11817/j.issn.1672-7347.2022.200821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Indexed: 11/03/2022]
Abstract
OBJECTIVES Genetic mutation is one of the important causes for tumor genesis and development, but genetic mutation in nasopharyngeal carcinoma (NPC) has rarely been reported. This study explored the role of phosphatidylinositol 3 kinase-protein kinase B (PI3K-Akt), mammalian target of rapamycin (mTOR), and adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK) signaling pathway in the efficacy and prognosis in patients with NPC. METHODS A total of 31 patients with advanced NPC, who came from the Affiliated Cancer Hospital of Xiangya School of Medicine of Central South University/Hunan Provincial Cancer Hospital, were enrolled. All of the exons of 288 genes, introns of 38 genes and promoters or fusion breakpoint regions from the nasopharyngeal biopsy tissues before treatment were detected by the gene sequencing platform Illumina NextSeq CN500. The coding regions of 728 genes were carried out a high-depth sequencing of target region capture, and the 4 variant types of tumor genes (including point mutations, insertion deletions of small fragments, copy number variations, and currently known fusion genes) were detected. All of 31 patients received platinum-based induction chemotherapy combined with concurrent chemoradiotherapy and were followed up for a long time. RESULTS The 3-year regional failure-free survival (RFFS) and disease-free survival (DFS) in patients with PI3K-Akt pathway mutation were significantly lower than those in unmutated patients (χ2=6.647, P<0.05). The 3-year RFFS and DFS in patients with mTOR pathway mutations were significantly lower than those in unmutated patients, and there was significant difference (χ2=5.570, P<0.05). The rate of complete response (CR) in patients with unmutated AMPK pathway was significantly higher than that in patients with mutation at 3 months after treatment (P<0.05), and the 3-year RFFS and DFS in patients with AMPK pathway mutation were significantly lower than those in unmutated patients (χ2=4.553, P<0.05). PI3K-Akt/mTOR/AMPK signaling pathway mutations and pre-treatment EB virus DNA copy numbers were independent prognostic factors for 3-year RFFS and DFS in patients with NPC (both P<0.05). CONCLUSIONS The NPC patients with PI3K-Akt/mTOR/AMPK signaling pathway mutation have poor prognosis, and the detection of PI3K-Akt, mTOR, AMPK driver genes and signaling pathways by next-generation sequencing is expected to provide new idea for basic research and targeted therapy of NPC.
Collapse
Affiliation(s)
- Yanzhu Chen
- Second Department of Head and Neck Radiotherapy, Hunan Cancer Hospital; Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China.
| | - Qian He
- Second Department of Head and Neck Radiotherapy, Hunan Cancer Hospital; Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Hongzhi Ma
- Second Department of Head and Neck Radiotherapy, Hunan Cancer Hospital; Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Lin Zhang
- Second Department of Head and Neck Radiotherapy, Hunan Cancer Hospital; Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Feng Liu
- Second Department of Head and Neck Radiotherapy, Hunan Cancer Hospital; Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China.
| | - Yaqian Han
- Second Department of Head and Neck Radiotherapy, Hunan Cancer Hospital; Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China.
| |
Collapse
|
21
|
Li Y, Li X, Chen H, Sun K, Li H, Zhou Y, Wang J, Bai F, Yang F. Single-cell RNA sequencing reveals the multi-cellular ecosystem in different radiological components of pulmonary part-solid nodules. Clin Transl Med 2022; 12:e723. [PMID: 35184398 PMCID: PMC8858630 DOI: 10.1002/ctm2.723] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Early-stage lung adenocarcinoma that radiologically manifests as part-solid nodules, consisting of both ground-glass and solid components, has distinctive growth patterns and prognosis. The characteristics of the tumour microenvironment and transcriptional features of the malignant cells of different radiological phenotypes remain poorly understood. METHODS Twelve treatment-naive patients with radiological part-solid nodules were enrolled. After frozen pathology was confirmed as lung adenocarcinoma, two regions (ground-glass and solid) from each of the 12 part-solid nodules and 5 normal lung tissues from 5 of the12 patients were subjected to single-cell sequencing by 10x Genomics. We used Seurat v3.1.5 for data integration and analysis. RESULTS We comprehensively dissected the multicellular ecosystem of the ground-glass and solid components of part-solid nodules at the single-cell resolution. In tumours, these components had comparable proportions of malignant cells. However, the angiogenesis, epithelial-to-mesenchymal transition, KRAS, p53, and cell-cycle signalling pathways were significantly up-regulated in malignant cells within solid components compared to those within ground-glass components. For the tumour microenvironment, the relative abundance of myeloid and NK cells tended to be higher in solid components than in ground-glass components. Slight subtype composition differences existed between the ground-glass and solid components. The T/NK cell subsets' cytotoxic function and the macrophages' pro-inflammation function were suppressed in solid components. Moreover, pericytes in solid components had a stronger communication related to angiogenesis promotion with endothelial cells and tumour cells. CONCLUSION The cellular landscape of ground-glass components is significantly different from that of normal tissue and similar to that of solid components. However, transcriptional differences exist in the vital signalling pathways of malignant and immune cells within these components.
Collapse
Affiliation(s)
- Yanmeng Li
- Biomedical Pioneering Innovation Center (BIOPIC)School of Life Sciences & Department of Thoracic SurgeryPeople's Hospital, Peking UniversityBeijingChina
| | - Xiao Li
- Biomedical Pioneering Innovation Center (BIOPIC)School of Life Sciences & Department of Thoracic SurgeryPeople's Hospital, Peking UniversityBeijingChina
| | - Haiming Chen
- Biomedical Pioneering Innovation Center (BIOPIC)School of Life Sciences & Department of Thoracic SurgeryPeople's Hospital, Peking UniversityBeijingChina
| | - Kunkun Sun
- Department of PathologyPeking University People's HospitalBeijingChina
| | - Hao Li
- Biomedical Pioneering Innovation Center (BIOPIC)School of Life Sciences & Department of Thoracic SurgeryPeople's Hospital, Peking UniversityBeijingChina
| | - Ying Zhou
- Department of PathologyPeking University People's HospitalBeijingChina
| | - Jun Wang
- Biomedical Pioneering Innovation Center (BIOPIC)School of Life Sciences & Department of Thoracic SurgeryPeople's Hospital, Peking UniversityBeijingChina
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC)School of Life Sciences & Department of Thoracic SurgeryPeople's Hospital, Peking UniversityBeijingChina
- Beijing Advanced Innovation Center for Genomics (ICG)Peking UniversityBeijingChina
| | - Fan Yang
- Biomedical Pioneering Innovation Center (BIOPIC)School of Life Sciences & Department of Thoracic SurgeryPeople's Hospital, Peking UniversityBeijingChina
| |
Collapse
|
22
|
Mirzaei G, Petreaca RC. Distribution of copy number variations and rearrangement endpoints in human cancers with a review of literature. Mutat Res 2022; 824:111773. [PMID: 35091282 PMCID: PMC11301607 DOI: 10.1016/j.mrfmmm.2021.111773] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022]
Abstract
Copy number variations (CNVs) which include deletions, duplications, inversions, translocations, and other forms of chromosomal re-arrangements are common to human cancers. In this report we investigated the pattern of these variations with the goal of understanding whether there exist specific cancer signatures. We used re-arrangement endpoint data deposited on the Catalogue of Somatic Mutations in Cancers (COSMIC) for our analysis. Indeed, we find that human cancers are characterized by specific patterns of chromosome rearrangements endpoints which in turn result in cancer specific CNVs. A review of the literature reveals tissue specific mutations which either drive these CNVs or appear as a consequence of CNVs because they confer an advantage to the cancer cell. We also identify several rearrangement endpoints hotspots that were not previously reported. Our analysis suggests that in addition to local chromosomal architecture, CNVs are driven by the internal cellular or nuclear physiology of each cancer tissue.
Collapse
Affiliation(s)
- Golrokh Mirzaei
- Department of Computer Science and Engineering, The Ohio State University at Marion, Marion, OH, 43302, USA
| | - Ruben C Petreaca
- Department of Molecular Genetics, The Ohio State University at Marion, Marion, OH, 43302, USA; Cancer Biology Program, The Ohio State University James Comprehensive Cancer Center, Columbus, OH, 43210, USA.
| |
Collapse
|
23
|
Gene Expression Profiles of Multiple Synchronous Lesions in Lung Adenocarcinoma. Cells 2021; 10:cells10123484. [PMID: 34943992 PMCID: PMC8700398 DOI: 10.3390/cells10123484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 11/24/2022] Open
Abstract
Many studies support a stepwise continuum of morphologic changes between atypical adenomatous hyperplasia (AAH) and lung adenocarcinoma (ADC). Here we characterized gene expression patterns and the association of differentially expressed genes and immune tumor microenvironment behaviors in AAH to ADC during ADC development. Tumor tissues from nine patients with ADC and synchronous multiple ground glass nodules/lesions (GGN/Ls) were analyzed using RNA sequencing. Using clustering, we identified genes differentially and sequentially expressed in AAH and ADC compared to normal tissues. Functional enrichment analysis using gene ontology terms was performed, and the fraction of immune cell types was estimated. We identified up-regulated genes (ACSL5 and SERINC2) with a stepwise change of expression from AAH to ADC and validated those expressions by quantitative PCR and immunohistochemistry. The immune cell profiles revealed increased B cell activities and decreased natural killer cell activities in AAH and ADC. A stepwise change of differential expression during ADC development revealed potential effects on immune function in synchronous precursors and in tumor lesions in patients with lung cancer.
Collapse
|
24
|
Angiulli F, Colombo T, Fassetti F, Furfaro A, Paci P. Mining sponge phenomena in RNA expression data. J Bioinform Comput Biol 2021; 20:2150022. [PMID: 34794369 DOI: 10.1142/s0219720021500220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In the last few years, the interactions among competing endogenous RNAs (ceRNAs) have been recognized as a key post-transcriptional regulatory mechanism in cell differentiation, tissue development, and disease. Notably, such sponge phenomena substracting active microRNAs from their silencing targets have been recognized as having a potential oncosuppressive, or oncogenic, role in several cancer types. Hence, the ability to predict sponges from the analysis of large expression data sets (e.g. from international cancer projects) has become an important data mining task in bioinformatics. We present a technique designed to mine sponge phenomena whose presence or absence may discriminate between healthy and unhealthy populations of samples in tumoral or normal expression data sets, thus providing lists of candidates potentially relevant in the pathology. With this aim, we search for pairs of elements acting as ceRNA for a given miRNA, namely, we aim at discovering miRNA-RNA pairs involved in phenomena which are clearly present in one population and almost absent in the other one. The results on tumoral expression data, concerning five different cancer types, confirmed the effectiveness of the approach in mining interesting knowledge. Indeed, 32 out of 33 miRNAs and 22 out of 25 protein-coding genes identified as top scoring in our analysis are corroborated by having been similarly associated with cancer processes in independent studies. In fact, the subset of miRNAs selected by the sponge analysis results in a significant enrichment of annotation for the KEGG32 pathway "microRNAs in cancer" when tested with the commonly used bioinformatic resource DAVID. Moreover, often the cancer datasets where our sponge analysis identified a miRNA as top scoring match the one reported already in the pertaining literature.
Collapse
|
25
|
Wang H, Wang X, Xu L, Cao H, Zhang J. Nonnegative matrix factorization-based bioinformatics analysis reveals that TPX2 and SELENBP1 are two predictors of the inner sub-consensuses of lung adenocarcinoma. Cancer Med 2021; 10:9058-9077. [PMID: 34734491 PMCID: PMC8683537 DOI: 10.1002/cam4.4386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 09/21/2021] [Accepted: 10/14/2021] [Indexed: 12/24/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is a heterogeneous disease. However the inner sub‐groups of LUAD have not been fully studied. Markers predicted the sub‐groups and prognosis of LUAD are badly needed. Aims To identify biomarkers associated with the sub‐groups and prognosis of LUAD. Materials and Methods Using nonnegative matrix factorization (NMF) clustering, LUAD patients from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) datasets and LUAD cell lines from Genomics of Drug Sensitivity in Cancer (GDSC) dataset were divided into different sub‐consensuses based on the gene expression profiling. The overall survival of LUAD patients in each sub‐consensus was determined by Kaplan‐Meier survival analysis. The common genes which were differentially expressed in each sub‐consensus of LUAD patients and LUAD cell lines were identified using TBtools. The predictive accuracy of TPX2 and SELENBP1 for theinner sub‐consensuses of LUAD was determined by Receiver operator characteristic (ROC) analysis. The Kaplan‐Meier survival analysis was also used to test the prognostic significance of TPX2 and SELENBP1 in LUAD patients. Results Using nonnegative matrix factorization clustering, LUAD patients in The Cancer Genome Atlas (TCGA), GSE30219, GSE42127, GSE50081, GSE68465, and GSE72094 datasets were divided into three sub‐consensuses. Sub‐consensus3 LUAD patients were with low overall survival and were with high TP53 mutations. Similarly, LUAD cell lines were also divided into three sub‐consensuses by NMF method, and sub‐consensus2 cell lines were resistant to EGFR inhibitors. Identification of the common genes which were differentially expressed in different sub‐consensuses of LUAD patients and LUAD cell lines revealed that TPX2 was highly expressed in sub‐consensus3 LUAD patients and sub‐consensus2 LUAD cell lines. On the contrary, SELENBP1 was highly expressed in sub‐consensus1 LUAD patients and sub‐consensus1 LUAD cell lines. The expression levels of TPX2 and SELENBP1 could distinguish sub‐consensus3 LUAD patients or sub‐consensus2 LUAD cell lines from other sub‐consensuses of LUAD patients or cell lines. Moreover, compared with normal lung tissues, TPX2 was highly expressed, while, SELENBP1 was lowly expressed in LUAD tissues. Furthermore, the higher expression levels of TPX2 were associated with the lower relapse‐free survival and the lower overall survival of LUAD patients. While, the higher expression levels of SELENBP1 were associated with the higher relapse‐free survival and higher overall survival. At last, we showed that TP53 mutant LUAD patients were with higher TPX2 and lower SELENBP1 expressions. Discussion Both iCluster and NMF method are proved to be robust LUAD classification systems. However, the LUAD patients in different iclusters had no significant clinical overall survival, while, sub‐consensus3 LUAD patients from NMF classification were with lower overall survival than other sub‐consensuses. Conclusions By integrated analysis of 1765 LUAD patients and 64 LUAD cell lines, we showed that NMF was a robust inner sub‐consensuses classification method of LUAD. TPX2 and SELENBP1 were differentially expressed in different LUAD sub‐ consensuses, and predicted the inner sub‐consensuses of LUAD with high accuracy. TPX2 was an unfavorable prognostic biomarker of LUAD which was up‐regulated in LUAD tissues and associated with the low overall survival of LUAD. SELENBP1 was a favorable prognostic biomarker of LUAD which was down‐regulated in LUAD tissues and associated with the prolonged overall survival of LUAD.
Collapse
Affiliation(s)
- Haiwei Wang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.,Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, National Health and Family Planning Commission, Fuzhou, Fujian, China
| | - Xinrui Wang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.,Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, National Health and Family Planning Commission, Fuzhou, Fujian, China
| | - Liangpu Xu
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.,Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, National Health and Family Planning Commission, Fuzhou, Fujian, China
| | - Hua Cao
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.,Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate, National Health and Family Planning Commission, Fuzhou, Fujian, China
| | - Ji Zhang
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
26
|
Chen CC, Hsu CC, Chen SL, Lin PH, Chen JP, Pan YR, Huang CE, Chen YJ, Chen YY, Wu YY, Yang MH. RAS Mediates BET Inhibitor-Endued Repression of Lymphoma Migration and Prognosticates a Novel Proteomics-Based Subgroup of DLBCL through Its Negative Regulator IQGAP3. Cancers (Basel) 2021; 13:cancers13195024. [PMID: 34638508 PMCID: PMC8508075 DOI: 10.3390/cancers13195024] [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: 09/04/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary The inhibitors of BET proteins represent a promising class of therapeutic agents that target the oncogenic activity of MYC and repress DLBCL cell migration, but the mechanism of such repression remains elusive. Herein, we found that BET inhibitor JQ1 abrogated the amoeboid movement of DLBCL cells through a small GTPase-driven mechanism, including both restrained RAS signaling and MYC-mediated suppression of GTP-RhoA activity. BET inhibition drastically increased the expression of a GTPase regulatory protein, the IQ motif containing GTPase activating protein 3 (IQGAP3), in DLBCL. Proteomics-based re-stratification identified a specific subgroup of DLBCL patients whose tumors harbored an enhanced PI3K activity and had an inferior survival, whereas a lower IQGAP3 expression level further portended a very dismal outcome for those patients. The inhibitors of both BET and RAS (through attenuated PI3K signaling) activities effectively ameliorated the outspread of in vivo DLBCL tumors, indicating the potential of their synergism in the treatment of specific DLBCL subtypes. Abstract Phenotypic heterogeneity and molecular diversity make diffuse large B-cell lymphoma (DLBCL) a challenging disease. We recently illustrated that amoeboid movement plays an indispensable role in DLBCL dissemination and inadvertently identified that the inhibitor of bromodomain and extra-terminal (BET) proteins JQ1 could repress DLBCL migration. To explore further, we dissected the impacts of BET inhibition in DLBCL. We found that JQ1 abrogated amoeboid movement of DLBCL cells through both restraining RAS signaling and suppressing MYC-mediated RhoA activity. We also demonstrated that BET inhibition resulted in the upregulation of a GTPase regulatory protein, the IQ motif containing GTPase activating protein 3 (IQGAP3). IQGAP3 similarly exhibited an inhibitory effect on RAS activity in DLBCL cells. Through barcoded mRNA/protein profiling in clinical samples, we identified a specific subgroup of DLBCL tumors with enhanced phosphatidylinositol-3-kinase (PI3K) activity, which led to an inferior survival in these patients. Strikingly, a lower IQGAP3 expression level further portended those with PI3K-activated DLBCL a very dismal outcome. The inhibition of BET and PI3K signaling activity led to effective suppression of DLBCL dissemination in vivo. Our study provides an important insight into the ongoing efforts of targeting BET proteins as a therapeutic approach for DLBCL.
Collapse
Affiliation(s)
- Chih-Cheng Chen
- Division of Hematology and Oncology, Department of Medicine, Chang Gung Memorial Hospital, Chiayi 61363, Taiwan; (C.-C.C.); (C.-C.H.); (C.-E.H.); (Y.-J.C.); (Y.-Y.C.); (Y.-Y.W.)
- School of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Chia-Chen Hsu
- Division of Hematology and Oncology, Department of Medicine, Chang Gung Memorial Hospital, Chiayi 61363, Taiwan; (C.-C.C.); (C.-C.H.); (C.-E.H.); (Y.-J.C.); (Y.-Y.C.); (Y.-Y.W.)
| | - Sung-Lin Chen
- Institute of Biotechnology in Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
| | - Po-Han Lin
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
| | - Ju-Pei Chen
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
| | - Yi-Ru Pan
- Division of General Surgery, Department of Surgery, Chang Gung Memorial Hospital, Taoyuan 33302, Taiwan;
| | - Cih-En Huang
- Division of Hematology and Oncology, Department of Medicine, Chang Gung Memorial Hospital, Chiayi 61363, Taiwan; (C.-C.C.); (C.-C.H.); (C.-E.H.); (Y.-J.C.); (Y.-Y.C.); (Y.-Y.W.)
- School of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Ying-Ju Chen
- Division of Hematology and Oncology, Department of Medicine, Chang Gung Memorial Hospital, Chiayi 61363, Taiwan; (C.-C.C.); (C.-C.H.); (C.-E.H.); (Y.-J.C.); (Y.-Y.C.); (Y.-Y.W.)
| | - Yi-Yang Chen
- Division of Hematology and Oncology, Department of Medicine, Chang Gung Memorial Hospital, Chiayi 61363, Taiwan; (C.-C.C.); (C.-C.H.); (C.-E.H.); (Y.-J.C.); (Y.-Y.C.); (Y.-Y.W.)
| | - Yu-Ying Wu
- Division of Hematology and Oncology, Department of Medicine, Chang Gung Memorial Hospital, Chiayi 61363, Taiwan; (C.-C.C.); (C.-C.H.); (C.-E.H.); (Y.-J.C.); (Y.-Y.C.); (Y.-Y.W.)
| | - Muh-Hwa Yang
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Correspondence:
| |
Collapse
|
27
|
Ye X, Ren W, Liu D, Li X, Li W, Wang X, Meng FL, Yeap LS, Hou Y, Zhu S, Casellas R, Zhang H, Wu K, Pan-Hammarström Q. Genome-wide mutational signatures revealed distinct developmental paths for human B cell lymphomas. J Exp Med 2021; 218:211517. [PMID: 33136155 PMCID: PMC7608067 DOI: 10.1084/jem.20200573] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/31/2020] [Accepted: 09/18/2020] [Indexed: 12/11/2022] Open
Abstract
Both somatic hypermutation (SHM) and class switch recombination (CSR) are initiated by activation-induced cytidine deaminase (AID). Dysregulation of these processes has been linked to B cell lymphomagenesis. Here we performed an in-depth analysis of diffuse large B cell lymphoma (DLBCL) and follicular lymphoma (FL) genomes. We characterized seven genomic mutational signatures, including two B cell tumor-specific signatures, one of which is novel and associated with aberrant SHM. We further identified two major mutational signatures (K1 and K2) of clustered mutations (kataegis) resulting from the activities of AID or error-prone DNA polymerase η, respectively. K1 was associated with the immunoglobulin (Ig) switch region mutations/translocations and the ABC subtype of DLBCL, whereas K2 was related to the Ig variable region mutations and the GCB subtype of DLBCL and FL. Similar patterns were also observed in chronic lymphocytic leukemia subtypes. Thus, alterations associated with aberrant CSR and SHM activities can be linked to distinct developmental paths for different subtypes of B cell lymphomas.
Collapse
Affiliation(s)
- Xiaofei Ye
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,BGI-Shenzhen, Shenzhen, China.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Weicheng Ren
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Dongbing Liu
- BGI-Shenzhen, Shenzhen, China.,Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, China
| | - Xiaobo Li
- BGI-Shenzhen, Shenzhen, China.,Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, China
| | - Wei Li
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Xianhuo Wang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Leng-Siew Yeap
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | | | - Rafael Casellas
- Genomics and Immunity, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD.,Center of Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Huilai Zhang
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Kui Wu
- BGI-Shenzhen, Shenzhen, China.,Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Shenzhen, China
| | - Qiang Pan-Hammarström
- Department of Lymphoma, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| |
Collapse
|
28
|
Zhang T, Joubert P, Ansari-Pour N, Zhao W, Hoang PH, Lokanga R, Moye AL, Rosenbaum J, Gonzalez-Perez A, Martínez-Jiménez F, Castro A, Muscarella LA, Hofman P, Consonni D, Pesatori AC, Kebede M, Li M, Gould Rothberg BE, Peneva I, Schabath MB, Poeta ML, Costantini M, Hirsch D, Heselmeyer-Haddad K, Hutchinson A, Olanich M, Lawrence SM, Lenz P, Duggan M, Bhawsar PMS, Sang J, Kim J, Mendoza L, Saini N, Klimczak LJ, Islam SMA, Otlu B, Khandekar A, Cole N, Stewart DR, Choi J, Brown KM, Caporaso NE, Wilson SH, Pommier Y, Lan Q, Rothman N, Almeida JS, Carter H, Ried T, Kim CF, Lopez-Bigas N, Garcia-Closas M, Shi J, Bossé Y, Zhu B, Gordenin DA, Alexandrov LB, Chanock SJ, Wedge DC, Landi MT. Genomic and evolutionary classification of lung cancer in never smokers. Nat Genet 2021; 53:1348-1359. [PMID: 34493867 PMCID: PMC8432745 DOI: 10.1038/s41588-021-00920-0] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 07/15/2021] [Indexed: 12/26/2022]
Abstract
Lung cancer in never smokers (LCINS) is a common cause of cancer mortality but its genomic landscape is poorly characterized. Here high-coverage whole-genome sequencing of 232 LCINS showed 3 subtypes defined by copy number aberrations. The dominant subtype (piano), which is rare in lung cancer in smokers, features somatic UBA1 mutations, germline AR variants and stem cell-like properties, including low mutational burden, high intratumor heterogeneity, long telomeres, frequent KRAS mutations and slow growth, as suggested by the occurrence of cancer drivers' progenitor cells many years before tumor diagnosis. The other subtypes are characterized by specific amplifications and EGFR mutations (mezzo-forte) and whole-genome doubling (forte). No strong tobacco smoking signatures were detected, even in cases with exposure to secondhand tobacco smoke. Genes within the receptor tyrosine kinase-Ras pathway had distinct impacts on survival; five genomic alterations independently doubled mortality. These findings create avenues for personalized treatment in LCINS.
Collapse
Affiliation(s)
- Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Quebec City, Quebec, Canada
| | - Naser Ansari-Pour
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Phuc H Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Rachel Lokanga
- Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Aaron L Moye
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
| | | | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francisco Martínez-Jiménez
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andrea Castro
- Department of Medicine, Division of Medical Genetics, University of California San Diego, San Diego, CA, USA
| | - Lucia Anna Muscarella
- Laboratory of Oncology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, University Hospital Federation OncoAge, Nice Hospital, University Côte d'Azur, Nice, France
| | - Dario Consonni
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela C Pesatori
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Michael Kebede
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Mengying Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Bonnie E Gould Rothberg
- Smilow Cancer Hospital, Yale-New Haven Health, New Haven, CT, USA
- Yale Comprehensive Cancer Center, New Haven, CT, USA
| | - Iliana Peneva
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Maria Luana Poeta
- Department of Bioscience, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy
| | - Manuela Costantini
- Department of Urology, Istituto di Ricovero e Cura a Carattere Scientifico Regina Elena National Cancer Institute, Rome, Italy
| | - Daniela Hirsch
- Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mary Olanich
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Scott M Lawrence
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Petra Lenz
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Maire Duggan
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Praphulla M S Bhawsar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Laura Mendoza
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, NC, USA
| | - Leszek J Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle, NC, USA
| | - S M Ashiqul Islam
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Burcak Otlu
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Nathan Cole
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Douglas R Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, NC, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jonas S Almeida
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California San Diego, San Diego, CA, USA
| | - Thomas Ried
- Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Carla F Kim
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | | | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, NC, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - David C Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
| |
Collapse
|
29
|
Li L, Shao M, He X, Ren S, Tian T. Risk of lung cancer due to external environmental factor and epidemiological data analysis. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:6079-6094. [PMID: 34517524 DOI: 10.3934/mbe.2021304] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Lung cancer is a cancer with the fastest growth in the incidence and mortality all over the world, which is an extremely serious threat to human's life and health. Evidences reveal that external environmental factors are the key drivers of lung cancer, such as smoking, radiation exposure and so on. Therefore, it is urgent to explain the mechanism of lung cancer risk due to external environmental factors experimentally and theoretically. However, it is still an open issue regarding how external environment factors affect lung cancer risk. In this paper, we summarize the main mathematical models involved the gene mutations for cancers, and review the application of the models to analyze the mechanism of lung cancer and the risk of lung cancer due to external environmental exposure. In addition, we apply the model described and the epidemiological data to analyze the influence of external environmental factors on lung cancer risk. The result indicates that radiation can cause significantly an increase in the mutation rate of cells, in particular the mutation in stability gene that leads to genomic instability. These studies not only can offer insights into the relationship between external environmental factors and human lung cancer risk, but also can provide theoretical guidance for the prevention and control of lung cancer.
Collapse
Affiliation(s)
- Lingling Li
- School of Science, Xi'an Polytechnic University, Xi'an 710048, China
| | - Mengyao Shao
- School of Science, Xi'an Polytechnic University, Xi'an 710048, China
| | - Xingshi He
- School of Science, Xi'an Polytechnic University, Xi'an 710048, China
| | - Shanjing Ren
- School of Mathematics and Big Data, GuiZhou Education University, Guiyang 550018, China
| | - Tianhai Tian
- School of Mathematical Science, Monash University, Melbourne Vic 3800, Australia
| |
Collapse
|
30
|
Zhu J, Lu Q, Li B, Li H, Wu C, Li C, Jin H. Potential of the cell-free blood-based biomarker uroplakin 2 RNA to detect recurrence after surgical resection of lung adenocarcinoma. Oncol Lett 2021; 22:520. [PMID: 34025787 PMCID: PMC8130048 DOI: 10.3892/ol.2021.12781] [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: 09/04/2019] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer, and ~30% of patients with LUAD develop cancer recurrence after surgery. The present study aimed to identify and validate biomarkers that may be used to monitor recurrence following LUAD surgery. Data from patients with LUAD were downloaded from The Cancer Genome Atlas database and postoperative recurrence samples were selected. Subsequently, weighted gene co-expression network analysis (WGCNA) was subsequently performed to identify key co-expression gene modules. Additionally, enrichment analysis of the key gene modules was performed using the Database for Annotation, Visualization and Integrated Discovery. Furthermore, survival analysis was performed on the most notable biomarker, uroplakin 2 (UPK2), which was downloaded from the Oncomine database, and its effect on prognosis was assessed. WGCNA identified 39 gene modules, of which one was most associated with recurrence. Among them, UPK2, kelch domain containing 3, galanin receptor 2 and tyrosinase-related protein 1 served a central role in the co-expression network and were significantly associated with the survival of patients. A total of 132 blood samples were collected from patients with LUAD with free UPK2 in the plasma. The expression levels of UPK2 relative to GADPH were 0.1623 and 0.2763 in non-relapsed and relapsed patients, respectively. Receiver operating characteristic curve analysis was used to detect free UPK2 mRNA in the blood in order to monitor postoperative recurrence, resulting in an area under the curve of 0.767 and a 95% CI of 0.675-0.858. Patients with high free UPK2 mRNA expression had unfavorable survival outcomes compared with those with low UPK2 expression. Therefore, free UPK2 mRNA expression in the plasma may have the potential to act as an indicator of postoperative recurrence in patients with early stage LUAD.
Collapse
Affiliation(s)
- Ji Zhu
- Department of Thoracic Surgery, First Affiliated Hospital of The Second Military Medical University, Shanghai 200433, P.R. China
| | - Qijue Lu
- Department of Thoracic Surgery, First Affiliated Hospital of The Second Military Medical University, Shanghai 200433, P.R. China
| | - Bin Li
- Department of Thoracic Surgery, Section of Esophageal Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, P.R. China
| | - Huafei Li
- School of Life Sciences, Shanghai University, Shanghai 200444, P.R. China
| | - Cong Wu
- Department of Laboratory Diagnosis, First Affiliated Hospital of The Second Military Medical University, Shanghai 200433, P.R. China
| | - Chunguang Li
- Department of Thoracic Surgery, First Affiliated Hospital of The Second Military Medical University, Shanghai 200433, P.R. China
| | - Hai Jin
- Department of Thoracic Surgery, First Affiliated Hospital of The Second Military Medical University, Shanghai 200433, P.R. China
| |
Collapse
|
31
|
Martínez-Fernández P, Pose P, Dolz-Gaitón R, García A, Trigo-Sánchez I, Rodríguez-Zarco E, Garcia-Ruiz MJ, Barba I, Izquierdo-García M, Valero-Garcia J, Ruiz C, Lázaro M, Carbonell P, Gargallo P, Méndez C, Ríos-Martín JJ, Palmeiro-Uriach A, Camarasa-Lillo N, Forteza-Vila J, Calabria I. Comprehensive NGS Panel Validation for the Identification of Actionable Alterations in Adult Solid Tumors. J Pers Med 2021; 11:jpm11050360. [PMID: 33947144 PMCID: PMC8145002 DOI: 10.3390/jpm11050360] [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: 03/24/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 01/08/2023] Open
Abstract
The increasing identification of driver oncogenic alterations and progress of targeted therapies addresses the need of comprehensive alternatives to standard molecular methods. The translation into clinical practice of next-generation sequencing (NGS) panels is actually challenged by the compliance of high quality standards for clinical accreditation. Herein, we present the analytical and clinical feasibility study of a hybridization capture-based NGS panel (Action OncoKitDx) for the analysis of somatic mutations, copy number variants (CNVs), fusions, pharmacogenetic SNPs and Microsatellite Instability (MSI) determination in formalin-fixed paraffin-embedded (FFPE) tumor samples. A total of 64 samples were submitted to extensive analytical validation for the identification of previously known variants. An additional set of 166 tumor and patient-matched normal samples were sequenced to assess the clinical utility of the assay across different tumor types. The panel demonstrated good specificity, sensitivity, reproducibility, and repeatability for the identification of all biomarkers analyzed and the 5% limit of detection set was validated. Among the clinical cohorts, the assay revealed pathogenic genomic alterations in 97% of patient cases, and in 82.7%, at least one clinically relevant variant was detected. The validation of accuracy and robustness of this assay supports the Action OncoKitDx's utility in adult solid tumors.
Collapse
Affiliation(s)
- Paula Martínez-Fernández
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Patricia Pose
- Servicio de Anatomía Patológica, Hospital Universitario de la Ribera, 46600 Alcira, Spain; (P.P.); (R.D.-G.)
| | - Raquel Dolz-Gaitón
- Servicio de Anatomía Patológica, Hospital Universitario de la Ribera, 46600 Alcira, Spain; (P.P.); (R.D.-G.)
| | - Arantxa García
- Servicio de Genética Molecular y Radiobiología, Centro Oncológico de Galicia, 15009 A Coruña, Spain;
| | - Inmaculada Trigo-Sánchez
- Servicio de Anatomía Patológica, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain; (I.T.-S.); (E.R.-Z.); (J.J.R.-M.)
| | - Enrique Rodríguez-Zarco
- Servicio de Anatomía Patológica, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain; (I.T.-S.); (E.R.-Z.); (J.J.R.-M.)
| | - MJose Garcia-Ruiz
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Ibon Barba
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Marta Izquierdo-García
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Jennifer Valero-Garcia
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Carlos Ruiz
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Marián Lázaro
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Paula Carbonell
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Pablo Gargallo
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Carlos Méndez
- Servicio de Oncología Médica, Centro Oncológico de Galicia, 15009 A Coruña, Spain;
| | - Juan José Ríos-Martín
- Servicio de Anatomía Patológica, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain; (I.T.-S.); (E.R.-Z.); (J.J.R.-M.)
| | - Alberto Palmeiro-Uriach
- Laboratorio de Anatomía Patológica, Hospital General Universitario de Castellón, 12004 Castellón, Spain;
| | | | - Jerónimo Forteza-Vila
- Anatomía Patológica, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain;
| | - Inés Calabria
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
- Correspondence:
| |
Collapse
|
32
|
Liu C, Zheng S, Wang S, Wang X, Feng X, Sun N, He J. Development and external validation of a composite immune-clinical prognostic model associated with EGFR mutation in East-Asian patients with lung adenocarcinoma. Ther Adv Med Oncol 2021; 13:17588359211006949. [PMID: 33889215 PMCID: PMC8040386 DOI: 10.1177/17588359211006949] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 03/11/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND EGFR mutation is a common oncogene driver in East Asians with lung adenocarcinoma (LUAD), conferring a favorable prognosis with effective targeted therapy. However, the EGFR mutation is a weak predictor of long-term survival. Therefore, a powerful predictive tool is urgently needed to estimate disease prognosis and patient survival for East-Asian patients with LUAD. METHODS In this first systematic analysis of the relationships among EGFR mutation, immunophenotype, and prognosis in LUAD samples from East-Asian patients, we constructed a prognostic signature consisting of EGFR-associated immune-related gene pairs (EIGPs). The predictive performance for overall survival (OS) and the clinical significance of this signature were then comprehensively investigated. RESULTS Based on transcriptome data analysis of a training set, we proposed the EIGP index (EIGPI), represented by five EIGPs, which was significantly associated with the OS of East-Asian patients with LUAD. It was also well validated in a test set. Furthermore, the prognostic performance of the EIGPI was further verified using protein levels in an additional independent set. Stratification analysis and multivariate Cox regression analysis revealed that the EIGPI was an independent prognostic factor. When combined with stage, the composite immune-clinical prognostic model index (ICPMI) showed improved prognostic accuracy in all datasets. CONCLUSION This study was the first to systematically investigate the relationships among EGFR mutation, immunophenotype, and prognosis in East Asians with LUAD and develop a composite clinical and immune model associated with EGFR mutation. This model may be a reliable and promising prognostic tool and help further personalize patient management.
Collapse
Affiliation(s)
- Chengming Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Sufei Zheng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Sihui Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinfeng Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoli Feng
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Sun
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| |
Collapse
|
33
|
Cao P, Hu S, Kong K, Han P, Yue J, Deng Y, Zhao B, Li F. Genomic landscape of ground glass opacities (GGOs) in East Asians. J Thorac Dis 2021; 13:2393-2403. [PMID: 34012587 PMCID: PMC8107556 DOI: 10.21037/jtd-21-82] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background Understanding the genomic landscape of early-stage lung adenocarcinoma (LUAD) may provide new insights into the molecular evolution in the early stages of LUAD. Methods Through sequencing of 79 spatially distinct regions from 37 patients with ground glass opacities (GGOs), we provided a comprehensive mutational landscape of GGOs, highlighting the importance of ancestry differences. Results Our study had several interesting features. First, epidermal growth factor receptor (EGFR), BRAF (v-RAF murine sarcoma viral oncogene homologue B1), and ERBB2 (Erb-B2 Receptor Tyrosine Kinase 2, also known as HER2) were more frequently mutated in our study, which supports the notion that EGFR is considered to be a major driver and tends to drive the occurrence of LUAD. Second, Signature 1, Signature 3, and Signature 6 were identified in patients with GGOs. Our results further suggested that Signature 1 was more prominent among early mutations. Third, compared with LUADs, GGOs exhibited significantly lower levers of arm-level copy number variation (CNV)—which alter the diploid status of DNA, and lower focal CNVs. Conclusions In our study, 79 samples of patients were included to analyze the GGO gene profile, revealing the genetic heterogeneity of GGO in East Asian population, and providing guidance for prognosis analysis of GGO patients by comparison with LUAD. Our study revealed that GGOs had fewer genomic alterations and simpler genomic profiles than LUADs. The most commonly altered processes were related to the receptor tyrosine kinase (RTK)/Ras/phosphatidylinositol-3-kinase (PI3K) signaling pathways in GGOs, and EGFR alterations were the dominant genetic changes across all targetable somatic changes.
Collapse
Affiliation(s)
- Peng Cao
- Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shan Hu
- Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kangle Kong
- Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Han
- Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaqi Yue
- Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Deng
- Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Zhao
- Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fan Li
- Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
34
|
Xiao D, He J, Guo Z, He H, Yang S, Huang L, Pan H, He J. Rhophilin-2 Upregulates Glutamine Synthetase by Stabilizing c-Myc Protein and Confers Resistance to Glutamine Deprivation in Lung Cancer. Front Oncol 2021; 10:571384. [PMID: 33552953 PMCID: PMC7855701 DOI: 10.3389/fonc.2020.571384] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/24/2020] [Indexed: 01/06/2023] Open
Abstract
Introduction RHPN2, a member of rhophilin family of rho-binding proteins, regulates actin cytoskeleton and vesicular trafficking, and promotes mesenchymal transformation in cancer. We have found that RHPN2 was significantly mutated in lung adenocarcinoma (LUAD). However, the role of RHPN2 in lung cancer is not fully understood. Methods In the present study, we investigated the expression of RHPN2 in 125 patients with LUAD by qRT-PCR and correlated its expression with clinical characteristics. The effects of RHPN2 on the proliferation and invasion of lung cancer cells were determined by CCK-8 and in vitro transwell assays, clonogenic assay, and xenograft mouse model. The RhoA pull down assay and Western blotting were performed to elucidate the mechanism of RNPN2 in tumorigenesis of lung cancer. Results RHPN2 was overexpressed in tumors from LUAD, and high levels of RHPN2 were associated with poor prognosis of LUAD patients. RHPN2 was required for proliferation and invasion of lung cancer cells. Intriguingly, overexpression of RHPN2 conferred the resistance to glutamine depletion in lung cancer cells. Mechanistic studies revealed that ectopic overexpression of RHPN2 promoted the stability of c-Myc protein via phosphorylation at Ser62 and increased c-Myc target glutamine synthetase (GS). Analysis of GS expression in clinical sample showed that the expression of GS was elevated in tumor cells. Kaplan-Meier analysis revealed that high levels of GS were significantly associated with worse overall survival time of the patients with LUAD. Conclusions Taken together, this study suggested that RHPN2 was involved in tumorigenesis of lung cancer via modulating c-Myc stability and the expression of its target GS in lung adenocarcinoma, which links RHPN2 and glutamine metabolism.
Collapse
Affiliation(s)
- Dakai Xiao
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Guangzhou Institute of Respiratory Disease & State Key Laboratory for Respiratory Disease, Guangzhou, China.,Research Center for Translational Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiaxi He
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Guangzhou Institute of Respiratory Disease & State Key Laboratory for Respiratory Disease, Guangzhou, China
| | - Zhihua Guo
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Guangzhou Institute of Respiratory Disease & State Key Laboratory for Respiratory Disease, Guangzhou, China.,Research Center for Translational Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huiming He
- Research Center for Translational Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shengli Yang
- Department of Thoracic Surgery, The First Hospital of Foshan City, Foshan, China
| | - Liyan Huang
- Research Center for Translational Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hui Pan
- Research Center for Translational Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jianxing He
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Guangzhou Institute of Respiratory Disease & State Key Laboratory for Respiratory Disease, Guangzhou, China
| |
Collapse
|
35
|
Wang J, Xie X, Shi J, He W, Chen Q, Chen L, Gu W, Zhou T. Denoising Autoencoder, A Deep Learning Algorithm, Aids the Identification of A Novel Molecular Signature of Lung Adenocarcinoma. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:468-480. [PMID: 33346087 PMCID: PMC8242334 DOI: 10.1016/j.gpb.2019.02.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 01/11/2019] [Accepted: 03/01/2019] [Indexed: 02/06/2023]
Abstract
Precise biomarker development is a key step in disease management. However, most of the published biomarkers were derived from a relatively small number of samples with supervised approaches. Recent advances in unsupervised machine learning promise to leverage very large datasets for making better predictions of disease biomarkers. Denoising autoencoder (DA) is one of the unsupervised deep learning algorithms, which is a stochastic version of autoencoder techniques. The principle of DA is to force the hidden layer of autoencoder to capture more robust features by reconstructing a clean input from a corrupted one. Here, a DA model was applied to analyze integrated transcriptomic data from 13 published lung cancer studies, which consisted of 1916 human lung tissue samples. Using DA, we discovered a molecular signature composed of multiple genes for lung adenocarcinoma (ADC). In independent validation cohorts, the proposed molecular signature is proved to be an effective classifier for lung cancer histological subtypes. Also, this signature successfully predicts clinical outcome in lung ADC, which is independent of traditional prognostic factors. More importantly, this signature exhibits a superior prognostic power compared with the other published prognostic genes. Our study suggests that unsupervised learning is helpful for biomarker development in the era of precision medicine.
Collapse
Affiliation(s)
- Jun Wang
- Department of Thoracic Surgery, Jiangsu Province People's Hospital and the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Xueying Xie
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Junchao Shi
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Wenjun He
- State Key Lab of Respiratory Disease, Guangzhou Medical University, Guangzhou 510000, China
| | - Qi Chen
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Liang Chen
- Department of Thoracic Surgery, Jiangsu Province People's Hospital and the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.
| | - Wanjun Gu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA.
| |
Collapse
|
36
|
Zeng Y, Jie X, Wu B, Wu G, Liu L, Xu S. IQGAP3 interacts with Rad17 to recruit the Mre11-Rad50-Nbs1 complex and contributes to radioresistance in lung cancer. Cancer Lett 2020; 493:254-265. [PMID: 32896617 DOI: 10.1016/j.canlet.2020.08.042] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/11/2020] [Accepted: 08/29/2020] [Indexed: 12/25/2022]
Abstract
IQ motif containing GTPase-activating protein 3 (IQGAP3) has been implicated in diverse cellular processes, including neuronal morphogenesis, cell proliferation and motility, and epithelial-mesenchymal transition. However, its role in cancer radioresistance is completely unknown. Here, we report that IQGAP3 is overproduced in lung cancer patients and correlates with poor clinical outcomes. Functionally, we demonstrate that depletion of IQGAP3 impairs oncogenesis and overcomes radioresistance in lung cancer in vitro and in vivo. Mechanistically, we uncover that IQGAP3 interacts with Rad17 and controls its expression to activate the ATM/Chk2 and ATR/Chk1 signaling pathways by recruiting the Mre11-Rad50-Nbs1 (MRN) complex in response to DNA damage. Moreover, Rad17 is identified as the major downstream effector that mediates the functions of IQGAP3 in lung cancer. Clinically, IQGAP3 overexpression positively correlates with Rad17 upregulation in human lung cancer tissues. Collectively, these data support key role for IQGAP3 in promoting lung cancer radioresistance by interacting with Rad17 and suggest that targeting IQGAP3 may be an attractive strategy for lung cancer radiotherapy.
Collapse
Affiliation(s)
- Yulan Zeng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xiaohua Jie
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Bian Wu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Gang Wu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Li Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Shuangbing Xu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| |
Collapse
|
37
|
A fusion of CD63-BCAR4 identified in lung adenocarcinoma promotes tumorigenicity and metastasis. Br J Cancer 2020; 124:290-298. [PMID: 33204025 PMCID: PMC7782829 DOI: 10.1038/s41416-020-01146-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 09/29/2020] [Accepted: 10/16/2020] [Indexed: 12/25/2022] Open
Abstract
Background Recently, fusion variants of the breast cancer anti-oestrogen-resistance 4 (BCAR4) gene were recurrently discovered in lung adenocarcinoma from the genome-wide studies. However, the functional characterisation of BCAR4 fusion has not been investigated. Methods Based on the analysis of RNA-sequencing data, we identified a fusion transcript of CD63–BCAR4 in a Korean patient with lung adenocarcinoma who did not harbour any known activating mutations in EGFR and KRAS genes. To investigate the oncogenic effect of CD63–BCAR4, in vitro and in vivo animal experiments were performed. Results In vitro experiments showed strongly enhanced cell migration and proliferation by the exogenous expression of CD63–BCAR4 protein in bronchial epithelial cells. Cell migration was notably reduced after knockdown of BCAR4 fusion by small-interfering RNA. The tumorigenic and metastatic capability of the CD63–BCAR4 fusion was confirmed by using the mouse xenograft model. Fusion-overexpressed cells result in metastasis to the liver and lung as well as the primary tumours after subcutaneous injection into mice. Cyclin D1, MMP1, Slug and mesenchymal markers were significantly increased after CD63–BCAR4 overexpression in the in vitro and in vivo experiments. Conclusions Taken together, our results suggest a newly identified fusion gene, CD63–BCAR4 as a potential novel oncogene in lung adenocarcinoma.
Collapse
|
38
|
Enhancement of Migration and Invasion of Gastric Cancer Cells by IQGAP3. Biomolecules 2020; 10:biom10081194. [PMID: 32824461 PMCID: PMC7465220 DOI: 10.3390/biom10081194] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/20/2020] [Accepted: 07/29/2020] [Indexed: 12/23/2022] Open
Abstract
Although gastric cancer is one of the most common causes of cancer death in the world, mechanisms underlying this type of tumor have not been fully understood. In this study, we found that IQGAP3, a member of the IQGAP gene family, was significantly up-regulated in human gastric cancer starting from the early stages of tumor progression. Overexpression of IQGAP3 in 293T and NIH3T3 cells, which have no endogenous IQGAP3 expression, resulted in morphological change with multiple dendritic-like protrusions and enhanced migration. Overexpression of IQGAP3 also led to reduced cell–cell adhesion in 293T cells, likely as a result of its interactions with e-cadherin or β-catenin proteins. Additionally, IQGAP3 accumulated along the leading edge of migrating cells and at the cleavage furrow of dividing cells. In contrast, suppression of IQGAP3 by short-interfering RNA (siRNA) markedly reduced invasion and anchorage-independent growth of MKN1 and TMK-1 gastric cancer cells. We further confirmed that IQGAP3 interacted with Rho family GTPases, and had an important role in cytokinesis. Taken together, we demonstrated that IQGAP3 plays critical roles in migration and invasion of human gastric cancer cells, and regulates cytoskeletal remodeling, cell migration and adhesion. These findings may open a new avenue for the diagnosis and treatment of gastric cancer.
Collapse
|
39
|
Wang H, Wang X, Xu L, Zhang J, Cao H. High expression levels of pyrimidine metabolic rate-limiting enzymes are adverse prognostic factors in lung adenocarcinoma: a study based on The Cancer Genome Atlas and Gene Expression Omnibus datasets. Purinergic Signal 2020; 16:347-366. [PMID: 32638267 PMCID: PMC7524999 DOI: 10.1007/s11302-020-09711-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/25/2020] [Indexed: 12/14/2022] Open
Abstract
Reprogramming of metabolism is described in many types of cancer and is associated with the clinical outcomes. However, the prognostic significance of pyrimidine metabolism signaling pathway in lung adenocarcinoma (LUAD) is unclear. Using the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets, we found that the pyrimidine metabolism signaling pathway was significantly enriched in LUAD. Compared with normal lung tissues, the pyrimidine metabolic rate–limiting enzymes were highly expressed in lung tumor tissues. The high expression levels of pyrimidine metabolic–rate limiting enzymes were associated with unfavorable prognosis. However, purinergic receptors P2RX1, P2RX7, P2RY12, P2RY13, and P2RY14 were relatively downregulated in lung cancer tissues and were associated with favorable prognosis. Moreover, we found that hypo-DNA methylation, DNA amplification, and TP53 mutation were contributing to the high expression levels of pyrimidine metabolic rate–limiting enzymes in lung cancer cells. Furthermore, combined pyrimidine metabolic rate–limiting enzymes had significant prognostic effects in LUAD. Comprehensively, the pyrimidine metabolic rate–limiting enzymes were highly expressed in bladder cancer, breast cancer, colon cancer, liver cancer, and stomach cancer. And the high expression levels of pyrimidine metabolic rate–limiting enzymes were associated with unfavorable prognosis in liver cancer. Overall, our results suggested the mRNA levels of pyrimidine metabolic rate–limiting enzymes CAD, DTYMK, RRM1, RRM2, TK1, TYMS, UCK2, NR5C2, and TK2 were predictive of lung cancer as well as other cancers.
Collapse
Affiliation(s)
- Haiwei Wang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital,, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
- Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate,, National Health and Family Planning Commission, Fuzhou, Fujian, China.
| | - Xinrui Wang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital,, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate,, National Health and Family Planning Commission, Fuzhou, Fujian, China
| | - Liangpu Xu
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital,, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate,, National Health and Family Planning Commission, Fuzhou, Fujian, China
| | - Ji Zhang
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Hua Cao
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital,, Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
- Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate,, National Health and Family Planning Commission, Fuzhou, Fujian, China.
| |
Collapse
|
40
|
Peng Y, Yuan C, Tao X, Zhao Y, Yao X, Zhuge L, Huang J, Zheng Q, Zhang Y, Hong H, Chen H, Sun Y. Integrated analysis of optical mapping and whole-genome sequencing reveals intratumoral genetic heterogeneity in metastatic lung squamous cell carcinoma. Transl Lung Cancer Res 2020; 9:670-681. [PMID: 32676329 PMCID: PMC7354123 DOI: 10.21037/tlcr-19-401] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background Intratumoral heterogeneity is a crucial factor to the outcome of patients and resistance to therapies, in which structural variants play an indispensable but undiscovered role. Methods We performed an integrated analysis of optical mapping and whole-genome sequencing on a primary tumor (PT) and matched metastases including lymph node metastasis (LNM) and tumor thrombus in the pulmonary vein (TPV). Single nucleotide variants, indels and structural variants were analyzed to reveal intratumoral genetic heterogeneity among tumor cells in different sites. Results Our results demonstrated there were less nonsynonymous somatic variants shared with PT in LNM than in TPV, while there were more structural variants shared with PT in LNM than in TPV. More private variants and its affected genes associated with tumorigenesis and progression were identified in TPV than in LNM. It should be noticed that optical mapping detected an average of 77.1% (74.5-78.5%) large structural variants (>5,000 bp) not detected by whole-genome sequencing and identified several structural variants private to metastases. Conclusions Our study does demonstrate structural variants, especially large structural variants play a crucial role in intratumoral genetic heterogeneity and optical mapping could make up for the deficiency of whole-genome sequencing to identify structural variants.
Collapse
Affiliation(s)
- Yizhou Peng
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Chongze Yuan
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xiaoting Tao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yue Zhao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xingxin Yao
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lingdun Zhuge
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | | | - Qiang Zheng
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Yue Zhang
- Berry Genomics Corporation, Beijing 100015, China
| | - Hui Hong
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Haiquan Chen
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yihua Sun
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| |
Collapse
|
41
|
Castelletti N, Kaiser JC, Simonetto C, Furukawa K, Küchenhoff H, Stathopoulos GT. Risk of lung adenocarcinoma from smoking and radiation arises in distinct molecular pathways. Carcinogenesis 2020; 40:1240-1250. [PMID: 30915466 DOI: 10.1093/carcin/bgz036] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/30/2019] [Accepted: 02/18/2019] [Indexed: 01/04/2023] Open
Abstract
KRAS mutations of lung adenocarcinoma (LADC) are associated with smoking but little is known on other exposure-oncogene associations. Hypothesizing that different inciting agents may cause different driver mutations, we aimed to identify distinct molecular pathways to LADC, applying two entirely different approaches. First, we examined clinicopathologic features and genomic signatures of environmental exposures in the large LADC Campbell data set. Second, we designed a molecular mechanistic risk model of LADC (M3LADC) that links environmental exposure to incidence risk by mathematically emulating the disease process. This model was applied to incidence data of Japanese atom-bomb survivors which contains information on radiation and smoking exposure. Grouping the clinical data by driver mutations revealed two main distinct molecular pathways to LADC: one unique to transmembrane receptor-mutant patients that displayed robust signatures of radiation exposure and one shared between submembrane transducer-mutant patients and patients with no evident driver mutation that carried the signature of smoking. Consistently, best fit of the incidence data was achieved with a M3LADC with two pathways: in one LADC risk increased with radiation exposure and in the other with cigarette consumption. We conclude there are two main molecular pathways to LADC associated with different environmental exposures. Future molecular measurements in lung cancer tissue of atom-bomb survivors may allow to further test quantitatively the M3LADC-predicted link of radiation to transmembrane receptor mutations. Moreover, the developed molecular mechanistic model showed that for low doses, as relevant e.g. for medical imaging, smokers have the same radiation risk compared with never smokers.
Collapse
Affiliation(s)
- Noemi Castelletti
- Institute of Radiation Medicine (IRM), Helmholtz Zentrum München, Neuherberg, Bavaria, Germany
| | - Jan Christian Kaiser
- Institute of Radiation Medicine (IRM), Helmholtz Zentrum München, Neuherberg, Bavaria, Germany
| | - Cristoforo Simonetto
- Institute of Radiation Medicine (IRM), Helmholtz Zentrum München, Neuherberg, Bavaria, Germany
| | - Kyoji Furukawa
- Biostatistics Center, Kurume University, Asahi-machi, Kurume, Japan
| | - Helmut Küchenhoff
- Department of Statistics, Ludwig-Maximilian University (LMU) Munich, Munich, Bavaria, Germany
| | - Georgios T Stathopoulos
- Laboratory for Molecular Respiratory Carcinogenesis, Department of Physiology, Faculty of Medicine; University of Patras; Rio, Achaia, Greece.,Comprehensive Pneumology Center (CPC) and Institute for Lung Biology and Disease (iLBD), University Hospital, Ludwig-Maximilian University (LMU) and Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Bavaria, Germany
| |
Collapse
|
42
|
Dongol S, Zhang Q, Qiu C, Sun C, Zhang Z, Wu H, Kong B. IQGAP3 promotes cancer proliferation and metastasis in high-grade serous ovarian cancer. Oncol Lett 2020; 20:1179-1192. [PMID: 32724358 PMCID: PMC7377165 DOI: 10.3892/ol.2020.11664] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/22/2020] [Indexed: 12/14/2022] Open
Abstract
Ovarian cancer is a type of gynecological cancer with the highest mortality rate worldwide. Due to a lack of effective screening methods, most cases are diagnosed at later stages where the survival rates are poor. Thus, it is termed a ‘silent killer’ and is the most lethal of all the malignancies in women. IQ motif containing GTPase Activating Protein 3 (IQGAP3) is a member of the Rho family of GTPases, and plays a crucial role in the development and progression of several types of cancer. The aim of the present study was to investigate the oncogenic functions and mechanisms of IQGAP3 on the proliferation and metastasis of high-grade serous ovarian cancer (HGSOC). Therefore, the expression levels of IQGAP3 in HGSOC and normal tissue samples were compared, and IQGAP3 knockdown was performed to examine its functional role using various in vitro and in vivo experiments. It was demonstrated that the expression of IQGAP3 was upregulated in HGSOC tissues compared with the healthy tissues; this differential expression was also observed in the ovarian cancer cell lines. Functional experimental results suggested that IQGAP3 silencing significantly reduced proliferation, migration and invasion in ovarian cancer cell lines. Moreover, in vivo experimental findings validated the in vitro results, where the tumorigenic and metastatic capacities of IQGAP3-silenced cells were significantly lower in the nude mice compared with the mice implanted with the control cells. Furthermore, knockdown of IQGAP3 resulted in increased apoptosis, and the effects of IQGAP3 expression on various epithelial-mesenchymal transition markers were identified, suggesting a possible mechanism associated with the role of IQGAP3 in metastasis. The effect of IQGAP3 silencing on chemosensitivity towards olaparib was also assessed. Collectively, the present results indicated that IQGAP3 is a potential diagnostic and prognostic marker, and a putative therapeutic target of HGSOC.
Collapse
Affiliation(s)
- Samina Dongol
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China.,Key Laboratory of Gynecologic Oncology of Shandong, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Qing Zhang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China.,Key Laboratory of Gynecologic Oncology of Shandong, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Chunping Qiu
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China.,Key Laboratory of Gynecologic Oncology of Shandong, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Chenggong Sun
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China.,Key Laboratory of Gynecologic Oncology of Shandong, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Zhiwei Zhang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China.,Key Laboratory of Gynecologic Oncology of Shandong, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Huan Wu
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China.,Key Laboratory of Gynecologic Oncology of Shandong, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Beihua Kong
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China.,Key Laboratory of Gynecologic Oncology of Shandong, Qilu Hospital of Shandong University, Ji'nan, Shandong 250012, P.R. China
| |
Collapse
|
43
|
Whole genome sequencing of colorectal neuroendocrine tumors and in-depth mutational analyses. Med Oncol 2020; 37:56. [PMID: 32424617 DOI: 10.1007/s12032-020-01356-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/28/2020] [Indexed: 02/03/2023]
Abstract
Colorectal neuroendocrine tumors (NETs) are rare neoplasms and studies on colorectal NETs are relatively few compared to other tumors. To better understand the pathogenesis of this tumor, we performed whole-genome sequencing and follow-up verification using Sanger sequencing of the colorectal NETs and paired para-tumor tissue. We analyzed the features of the gene mutation spectrum and mutation signature patterns, and analyzed the four pathways that were altered by gene mutation in pancreatic neuroendocrine tumors, including DNA damage and repair, chromatin remodeling, telomere maintenance and mTOR signaling activation. We found that PARP4 which is related to the DNA damage and repair pathway; TSC2, which is related to the mTOR signaling activation pathway; and SLX1A, which is related to telomere maintenance, were mutated in colorectal NETs. Our data analyzed characteristics of gene mutation in colorectal NETs at the whole-genome level, and may help to better understand the pathogenesis of colorectal NETs and may be helpful for potential tumor therapy in the future.
Collapse
|
44
|
EGFR-mutant lung adenocarcinoma harboring co-mutational tumor suppressor genes predicts poor prognosis. J Cancer Res Clin Oncol 2020; 146:1781-1789. [PMID: 32361787 DOI: 10.1007/s00432-020-03237-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/24/2020] [Indexed: 12/30/2022]
Abstract
INTRODUCTION EGFR mutations occur most frequently in patients with lung adenocarcinoma in East Asia. However, the prognostic and therapeutic impact of co-mutational status of EGFR and tumor suppressor genes is not fully understood. This study aims to provide a deeper understanding of lung adenocarcinoma patients with co-mutation of EGFR and tumor suppressor genes. METHODS From November 2009 to May 2016, 675 patients with lung adenocarcinoma who underwent complete surgery were included in this study. Samples were collected and pathologically examined. Whole-exome sequencing was performed on 197 samples, while direct sequencing of major driver genes, including EGFR, KRAS, ERBB2 and BRAF and Ion-torrent targeted sequencing of tumor suppressor genes, including TP53, KEAP1, MGA, NF1, RB1, SMARCA4 and STK11, were performed on 478 samples. Tumor mutational burden was calculated and survival analyses were performed. RESULTS The frequency of EGFR and TP53 mutation was 409 (60.6%) and 215 (31.9%), respectively. Co-mutation of EGFR and TP53 occured in 151 patients (22.4%), while co-mutation of EGFR and at least one tumor suppressor gene occured in 184 patients (27.3%). Compared with patients with only EGFR mutations, patients with co-mutations of EGFR and TP53 had a higher tumor mutational burden (p = 0.007) and worse recurrence-free survival (p = 0.010), while patients with co-mutations of EGFR and at least one tumor suppressor gene had a higher tumor mutational burden (p = 0.007), worse recurrence-free survival (p = 0.016) and worse overall survival (p = 0.018). CONCLUSIONS Lung adenocarcinoma patients harboring EGFR and co-mutational tumor suppressor genes should be regarded as a unique subgroup.
Collapse
|
45
|
Hong X, Qiao S, Li F, Wang W, Jiang R, Wu H, Chen H, Liu L, Peng J, Wang J, Jia C, Liang X, Dai H, Jiang J, Zhang T, Liao Q, Dai M, Cong L, Han X, Guo D, Liang Z, Li D, Zheng Z, Ye C, Li S, Zhao Y, Wu K, Wu W. Whole-genome sequencing reveals distinct genetic bases for insulinomas and non-functional pancreatic neuroendocrine tumours: leading to a new classification system. Gut 2020; 69:877-887. [PMID: 31462556 PMCID: PMC7229893 DOI: 10.1136/gutjnl-2018-317233] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 07/26/2019] [Accepted: 08/13/2019] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Insulinomas and non-functional pancreatic neuroendocrine tumours (NF-PanNETs) have distinctive clinical presentations but share similar pathological features. Their genetic bases have not been comprehensively compared. Herein, we used whole-genome/whole-exome sequencing (WGS/WES) to identify genetic differences between insulinomas and NF-PanNETs. DESIGN The mutational profiles and copy-number variation (CNV) patterns of 211 PanNETs, including 84 insulinomas and 127 NF-PanNETs, were obtained from WGS/WES data provided by Peking Union Medical College Hospital and the International Cancer Genome Consortium. Insulinoma RNA sequencing and immunohistochemistry data were assayed. RESULTS PanNETs were categorised based on CNV patterns: amplification, copy neutral and deletion. Insulinomas had CNV amplifications and copy neutral and lacked CNV deletions. CNV-neutral insulinomas exhibited an elevated rate of YY1 mutations. In contrast, NF-PanNETs had all three CNV patterns, and NF-PanNETs with CNV deletions had a high rate of loss-of-function mutations of tumour suppressor genes. NF-PanNETs with CNV alterations (amplification and deletion) had an elevated risk of relapse, and additional DAXX/ATRX mutations could predict an increased relapse risk in the first 2-year period. CONCLUSION These WGS/WES data allowed a comprehensive assessment of genetic differences between insulinomas and NF-PanNETs, reclassifying these tumours into novel molecular subtypes. We also proposed a novel relapse risk stratification system using CNV patterns and DAXX/ATRX mutations.
Collapse
Affiliation(s)
- Xiafei Hong
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Sitan Qiao
- BGI-Shenzhen, Shenzhen, China,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Fuqiang Li
- BGI-Shenzhen, Shenzhen, China,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Wenze Wang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Rui Jiang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Hao Chen
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Lulu Liu
- Department of Center Lab, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Junya Peng
- Department of Center Lab, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Jing Wang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Congwei Jia
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xiaolong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Hongmei Dai
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Jialin Jiang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Taiping Zhang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Quan Liao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Menghua Dai
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Lin Cong
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xianlin Han
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Dan Guo
- Department of Center Lab, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China,Clinical Bio-bank, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Dongjing Li
- Department of Health Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Zetian Zheng
- BGI-Shenzhen, Shenzhen, China,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Chen Ye
- BGI-Shenzhen, Shenzhen, China,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Siliang Li
- BGI-Shenzhen, Shenzhen, China,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yupei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China .,Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Kui Wu
- BGI-Shenzhen, Shenzhen, China .,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Wenming Wu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| |
Collapse
|
46
|
Chang CC, Chao KC, Huang CJ, Hung CS, Wang YC. Association between aberrant dynein cytoplasmic 1 light intermediate chain 1 expression levels, mucins and chemosensitivity in colorectal cancer. Mol Med Rep 2020; 22:185-192. [PMID: 32319648 PMCID: PMC7248515 DOI: 10.3892/mmr.2020.11086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/19/2020] [Indexed: 01/25/2023] Open
Abstract
Dynein transport along the cytoskeletal microtubules towards the minus end is essential for cell division, cell migration and other basic cellular functions. Dynein cytoplasmic 1 light intermediate chain 1 (DYNC1LI1) has been previously associated with pancreatic ductal adenocarcinoma, hepatocellular carcinoma and prostate cancer. Cytoskeletal structures are involved in the regulation of the mucosal barrier integrity. Thus, improving our understanding of the molecular mechanisms that regulate the mucosal barrier is critical for cancer management and treatment. The present study aimed to investigate DYNC1LI1 expression in colorectal cancer (CRC) tissues. The American Joint Committee on Cancer Stage II CRC cell line LS 174T was used to determine the association between the cellular expression levels of DYNC1LI1 and different types of mucin (MUC) by reverse transcription-quantitative PCR. The role of DYNC1LI1 in cell chemosensitivity and proliferation was also evaluated in the presence of the DNA analog 5-fluorouracil (5-FU) or the platinum-based drug, oxaliplatin by the MTT assay. LS 174T cells with decreased expression levels of DYNC1LI1 were discovered to be more sensitive to 5-FU compared with LS 174T cells with endogenous DYNC1LI1 expression levels. Moreover, LS 174T cells transfected with short hairpin RNA targeting DYNC1LI1 were associated with low MUC1 and high MUC2, MUC4 and MUC5AC expression levels. Notably, the CRC cells with low MUC1 expression levels and high expression levels of the other MUCs (MUC2, MU4 and MUC5AC) were shown to benefit from 5-FU treatment. In conclusion, the findings of the present study have suggested that DYNC1LI1 expression may be significantly associated with MUC expression levels and may be used to predict the chemotherapeutic efficiency. However, additional functional studies and clinical reports are required for an improved understanding of the significance of these molecular interactions in tumorigenesis.
Collapse
Affiliation(s)
- Chun-Chao Chang
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan, R.O.C
| | - Kuo-Ching Chao
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan, R.O.C
| | - Chi-Jung Huang
- Department of Medical Research, Cathay General Hospital, Taipei 10630, Taiwan, R.O.C
| | - Chih-Sheng Hung
- Division of Gastroenterology, Department of Internal Medicine, Cathay General Hospital, Taipei 10630, Taiwan, R.O.C
| | - Yen-Chieh Wang
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 24205, Taiwan, R.O.C
| |
Collapse
|
47
|
Are Synapse-Like Structures a Possible Way for Crosstalk of Cancer with Its Microenvironment? Cancers (Basel) 2020; 12:cancers12040806. [PMID: 32230806 PMCID: PMC7226151 DOI: 10.3390/cancers12040806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 01/03/2023] Open
Abstract
The failure of therapies directed at targets within cancer cells highlight the necessity for a paradigm change in cancer therapy. The attention of researchers has shifted towards the disruption of cancer cell interactions with the tumor microenvironment. A typical example of such a disruption is the immune checkpoint cancer therapy that disrupts interactions between the immune and the cancer cells. The interaction of cancer antigens with T cells occurs in the immunological synapses. This is characterized by several special features, i.e., the proximity of the immune cells and their target cells, strong intercellular adhesion, and secretion of signaling cytokines into the intercellular cleft. Earlier, we hypothesized that the cancer-associated fibroblasts interacting with cancer cells through a synapse-like adhesion might play an important role in cancer tumors. Studies of the interactions between cancer cells and cancer-associated fibroblasts showed that their clusterization on the membrane surface determined their strength and specificity. The hundreds of interacting pairs are involved in the binding that may indicate the formation of synapse-like structures. These interactions may be responsible for successful metastasis of cancer cells, and their identification and disruption may open new therapeutic possibilities.
Collapse
|
48
|
Zhou B, Xiong J. [Research Progress in Consistency of Driver Gene Status between Primary and Corresponding Metastatic Lesions in Non-small Cell Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2020; 23:196-203. [PMID: 32102137 PMCID: PMC7118335 DOI: 10.3779/j.issn.1009-3419.2020.03.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
非小细胞肺癌(non-small cell lung cancer, NSCLC)作为肺癌最常见的病理类型,具有恶性程度高和侵袭性强的特点,晚期极易发生淋巴结和不同脏器转移。近年来,随着精准医学应用的深入,不断出现NSCLC转移部位的耐药和治疗失效为分子靶向治疗带来困扰,研究证实这些可能与肿瘤转移后发生的分子学改变有关。本文旨在阐述NSCLC原发灶与转移部位驱动基因状态,系统性综述两者间驱动基因状态一致性的研究进展,为探讨转移性NSCLC的分子靶向治疗提供新的思路。
Collapse
Affiliation(s)
- Bing Zhou
- Department of Pathology, The Affiliated Jiujiang Hospital of Nanchang University, Jiujiang 332000, China
| | - Jianping Xiong
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| |
Collapse
|
49
|
Novelli G, Biancolella M, Latini A, Spallone A, Borgiani P, Papaluca M. Precision Medicine in Non-Communicable Diseases. High Throughput 2020; 9:ht9010003. [PMID: 32046063 PMCID: PMC7151056 DOI: 10.3390/ht9010003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/31/2019] [Accepted: 02/04/2020] [Indexed: 12/18/2022] Open
Abstract
The increase in life expectancy during the 20th century ranks as one of society's greatest achievements, with massive growth in the numbers and proportion of the elderly, virtually occurring in every country of the world. The burden of chronic diseases is one of the main consequences of this phenomenon, severely hampering the quality of life of elderly people and challenging the efficiency and sustainability of healthcare systems. Non-communicable diseases (NCDs) are considered a global emergency responsible for over 70% of deaths worldwide. NCDs are also the basis for complex and multifactorial diseases such as hypertension, diabetes, and obesity. The epidemics of NCDs are a consequence of a complex interaction between health, economic growth, and development. This interaction includes the individual genome, the microbiome, the metabolome, the immune status, and environmental factors such as nutritional and chemical exposure. To counteract NCDs, it is therefore essential to develop an innovative, personalized, preventative, early care model through the integration of different molecular profiles of individuals to identify both the critical biomarkers of NCD susceptibility and to discover novel therapeutic targets.
Collapse
Affiliation(s)
- Giuseppe Novelli
- Department of Biomedicine & Prevention, Genetics Unit, University of Rome “Tor Vergata”, 00133 Rome, Italy; (A.L.); (P.B.)
- IRCCS Neuromed, 86077 Pozzilli (IS), Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV 89557, USA
- Correspondence: ; Tel.: +39-0620-900-668
| | | | - Andrea Latini
- Department of Biomedicine & Prevention, Genetics Unit, University of Rome “Tor Vergata”, 00133 Rome, Italy; (A.L.); (P.B.)
| | - Aldo Spallone
- Department of Neurology and Neurosurgery, Peoples’ Friendship University of Russia (RUDN University), Moscow 117198, Russia;
| | - Paola Borgiani
- Department of Biomedicine & Prevention, Genetics Unit, University of Rome “Tor Vergata”, 00133 Rome, Italy; (A.L.); (P.B.)
| | - Marisa Papaluca
- Imperial College, Faculty of Medicine, School of Public Health, SW7 2AZ London, UK;
| |
Collapse
|
50
|
Li Y, Li X, Li H, Zhao Y, Liu Z, Sun K, Zhu X, Qi Q, An B, Shen D, Li R, Liu T, Mi J, Wang L, Yang F, Bai F, Wang J. Genomic characterisation of pulmonary subsolid nodules: mutational landscape and radiological features. Eur Respir J 2020; 55:13993003.01409-2019. [PMID: 31699841 DOI: 10.1183/13993003.01409-2019] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/23/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Lung adenocarcinomas (LUADs) that display radiologically as subsolid nodules (SSNs) exhibit more indolent biological behaviour than solid LUADs. SSNs, commonly encompassing pre-invasive and invasive yet early-stage adenocarcinomas, can be categorised as pure ground-glass nodules and part-solid nodules. The genomic characteristics of SSNs remain poorly understood. METHODS We subjected 154 SSN samples from 120 treatment-naïve Chinese patients to whole-exome sequencing. Clinical parameters and radiological features of these SSNs were collected. The genomic landscape of SSNs and differences from that of advanced-stage LUADs were defined. In addition, we investigated the intratumour heterogeneity and clonal relationship of multifocal SSNs and conducted radiogenomic analysis to link imaging and molecular characteristics of SSNs. Fisher's exact and Wilcoxon rank sum tests were used in the statistical analysis. RESULTS The median somatic mutation rate across the SSN cohort was 1.12 mutations per Mb. Mutations in EGFR were the most prominent and significant variation, followed by those in RBM10, TP53, STK11 and KRAS. The differences between SSNs and advanced-stage LUADs at a genomic level were unravelled. Branched evolution and remarkable genomic heterogeneity were demonstrated in SSNs. Although multicentric origin was predominant, we also detected early metastatic events among multifocal SSNs. Using radiogenomic analysis, we found that higher ratios of solid components in SSNs were accompanied by significantly higher mutation frequencies in EGFR, TP53, RBM10 and ARID1B, suggesting that these genes play roles in the progression of LUADs. CONCLUSIONS Our study provides the first comprehensive description of the mutational landscape and radiogenomic mapping of SSNs.
Collapse
Affiliation(s)
- Yanmeng Li
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences and Dept of Thoracic Surgery, People's Hospital, Peking University, Beijing, China.,These authors contributed equally to the study
| | - Xiao Li
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences and Dept of Thoracic Surgery, People's Hospital, Peking University, Beijing, China.,These authors contributed equally to the study
| | - Hao Li
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences and Dept of Thoracic Surgery, People's Hospital, Peking University, Beijing, China.,These authors contributed equally to the study
| | - Yifan Zhao
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences and Dept of Thoracic Surgery, People's Hospital, Peking University, Beijing, China.,These authors contributed equally to the study
| | - Ziyang Liu
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences and Dept of Thoracic Surgery, People's Hospital, Peking University, Beijing, China.,These authors contributed equally to the study
| | - Kunkun Sun
- Dept of Pathology, Peking University People's Hospital, Beijing, China
| | - Xiang Zhu
- Dept of Pathology, Peking University Third Hospital, Beijing, China
| | - Qingyi Qi
- Dept of Radiology, Peking University People's Hospital, Beijing, China
| | - Bei An
- Dept of Radiology, Peking University People's Hospital, Beijing, China
| | - Danhua Shen
- Dept of Pathology, Peking University People's Hospital, Beijing, China
| | - Ruoyan Li
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences and Dept of Thoracic Surgery, People's Hospital, Peking University, Beijing, China
| | - Taorui Liu
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences and Dept of Thoracic Surgery, People's Hospital, Peking University, Beijing, China
| | - Jiahui Mi
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences and Dept of Thoracic Surgery, People's Hospital, Peking University, Beijing, China
| | | | - Fan Yang
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences and Dept of Thoracic Surgery, People's Hospital, Peking University, Beijing, China.,These authors contributed equally to the study
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences and Dept of Thoracic Surgery, People's Hospital, Peking University, Beijing, China.,These authors contributed equally to the study
| | - Jun Wang
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences and Dept of Thoracic Surgery, People's Hospital, Peking University, Beijing, China .,These authors contributed equally to the study
| |
Collapse
|