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Xu D, Zhang D, Wei W, Zhang C. UBA5 inhibition restricts lung adenocarcinoma via blocking macrophage M2 polarization and cisplatin resistance. Exp Cell Res 2024; 440:114148. [PMID: 38936760 DOI: 10.1016/j.yexcr.2024.114148] [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: 04/09/2024] [Revised: 06/22/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024]
Abstract
UBA5, a ubiquitin-like activated enzyme involved in ufmylation and sumoylation, presents a viable target for pancreatic and breast cancer treatments, yet its role in lung adenocarcinoma (LUAD) remains underexplored. This study reveals UBA5's tumor-promoting effect in LUAD, as evidenced by its upregulation in patients and positive correlation with TNM stages. Elevated UBA5 levels predict poor outcomes for these patients. Pharmacological inhibition of UBA5 using DKM 2-93 significantly curtails the growth of A549, H1299, and cisplatin-resistant A549 (A549/DDP) LUAD cells in vitro. Additionally, UBA5 knockdown via shRNA lentivirus suppresses tumor growth both in vitro and in vivo. High UBA5 expression adversely alters the tumor immune microenvironment, affecting immunostimulators, MHC molecules, chemokines, receptors, and immune cell infiltration. Notably, UBA5 expression correlates positively with M2 macrophage infiltration, the predominant immune cells in LUAD. Co-culture experiments further demonstrate that UBA5 knockdown directly inhibits M2 macrophage polarization and lactate production in LUAD. Moreover, in vivo studies show reduced M2 macrophage infiltration following UBA5 knockdown. UBA5 expression is also associated with increased tumor heterogeneity, including tumor mutational burden, microsatellite instability, neoantigen presence, and homologous recombination deficiency. Experiments indicate that UBA5 overexpression promotes cisplatin resistance in vitro, whereas UBA5 inhibition enhances cisplatin sensitivity in both in vitro and in vivo settings. Overall, these findings suggest that targeting UBA5 inhibits LUAD by impeding cancer cell proliferation, M2 macrophage polarization, and cisplatin resistance.
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Affiliation(s)
- Dacai Xu
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Zhanjiang, 524033, PR China; Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, 524033, PR China.
| | - Donghui Zhang
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Zhanjiang, 524033, PR China; Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, 524033, PR China
| | - Wenlu Wei
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Zhanjiang, 524033, PR China; Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, 524033, PR China
| | - Chong Zhang
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Zhanjiang, 524033, PR China; Zhanjiang Central Hospital, Guangdong Medical University, Zhanjiang, 524033, PR China
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2
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Siberski-Cooper CJ, Mayes MS, Gorden PJ, Kramer L, Bhatia V, Koltes JE. The genetic architecture of complete blood counts in lactating Holstein dairy cows. Front Genet 2024; 15:1360295. [PMID: 38601075 PMCID: PMC11004310 DOI: 10.3389/fgene.2024.1360295] [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: 12/22/2023] [Accepted: 03/04/2024] [Indexed: 04/12/2024] Open
Abstract
Complete blood counts (CBCs) measure the abundance of individual immune cells, red blood cells, and related measures such as platelets in circulating blood. These measures can indicate the health status of an animal; thus, baseline circulating levels in a healthy animal may be related to the productive life, resilience, and production efficiency of cattle. The objective of this study is to determine the heritability of CBC traits and identify genomic regions that are associated with CBC measurements in lactating Holstein dairy cattle. The heritability of CBCs was estimated using a Bayes C0 model. The study population consisted of 388 cows with genotypes at roughly 75,000 markers and 16 different CBC phenotypes taken at one to three time points (n = 33, 131, and 224 for 1, 2, and 3 time points, respectively). Heritabilities ranged from 0.00 ± 0.00 (red cell distribution width) to 0.68 ± 0.06 (lymphocytes). A total of 96 different 1-Mb windows were identified that explained more than 1% of the genetic variance for at least one CBC trait, with 10 windows explaining more than 1% of the genetic variance for two or more traits. Multiple genes in the identified regions have functions related to immune response, cell differentiation, anemia, and disease. Positional candidate genes include RAD52 motif-containing protein 1 (RDM1), which is correlated with the degree of immune infiltration of immune cells, and C-X-C motif chemokine ligand 12 (CXCL12), which is critically involved in neutrophil bone marrow storage and release regulation and enhances neutrophil migration. Since animal health directly impacts feed intake, understanding the genetics of CBCs may be useful in identifying more disease-resilient and feed-efficient dairy cattle. Identification of genes responsible for variation in CBCs will also help identify the variability in how dairy cattle defend against illness and injury.
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Affiliation(s)
| | - Mary S. Mayes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Patrick J. Gorden
- Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, United States
| | - Luke Kramer
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Vishesh Bhatia
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - James E. Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
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Pandey M, Shah SK, Gromiha MM. Computational approaches for identifying disease-causing mutations in proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 139:141-171. [PMID: 38448134 DOI: 10.1016/bs.apcsb.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Advancements in genome sequencing have expanded the scope of investigating mutations in proteins across different diseases. Amino acid mutations in a protein alter its structure, stability and function and some of them lead to diseases. Identification of disease-causing mutations is a challenging task and it will be helpful for designing therapeutic strategies. Hence, mutation data available in the literature have been curated and stored in several databases, which have been effectively utilized for developing computational methods to identify deleterious mutations (drivers), using sequence and structure-based properties of proteins. In this chapter, we describe the contents of specific databases that have information on disease-causing and neutral mutations followed by sequence and structure-based properties. Further, characteristic features of disease-causing mutations will be discussed along with computational methods for identifying cancer hotspot residues and disease-causing mutations in proteins.
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Affiliation(s)
- Medha Pandey
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Suraj Kumar Shah
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India; International Research Frontiers Initiative, School of Computing, Tokyo Institute of Technology, Yokohama, Japan.
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Schibler AC, Jevtic P, Pegoraro G, Levy DL, Misteli T. Identification of epigenetic modulators as determinants of nuclear size and shape. eLife 2023; 12:e80653. [PMID: 37219077 PMCID: PMC10259489 DOI: 10.7554/elife.80653] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 05/04/2023] [Indexed: 05/24/2023] Open
Abstract
The shape and size of the human cell nucleus is highly variable among cell types and tissues. Changes in nuclear morphology are associated with disease, including cancer, as well as with premature and normal aging. Despite the very fundamental nature of nuclear morphology, the cellular factors that determine nuclear shape and size are not well understood. To identify regulators of nuclear architecture in a systematic and unbiased fashion, we performed a high-throughput imaging-based siRNA screen targeting 867 nuclear proteins including chromatin-associated proteins, epigenetic regulators, and nuclear envelope components. Using multiple morphometric parameters, and eliminating cell cycle effectors, we identified a set of novel determinants of nuclear size and shape. Interestingly, most identified factors altered nuclear morphology without affecting the levels of lamin proteins, which are known prominent regulators of nuclear shape. In contrast, a major group of nuclear shape regulators were modifiers of repressive heterochromatin. Biochemical and molecular analysis uncovered a direct physical interaction of histone H3 with lamin A mediated via combinatorial histone modifications. Furthermore, disease-causing lamin A mutations that result in disruption of nuclear shape inhibited lamin A-histone H3 interactions. Oncogenic histone H3.3 mutants defective for H3K27 methylation resulted in nuclear morphology abnormalities. Altogether, our results represent a systematic exploration of cellular factors involved in determining nuclear morphology and they identify the interaction of lamin A with histone H3 as an important contributor to nuclear morphology in human cells.
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Affiliation(s)
| | - Predrag Jevtic
- Department of Molecular Biology, University of WyomingLaramieUnited States
| | - Gianluca Pegoraro
- High Throughput Imaging Facility (HiTIF), National Cancer Institute, NIHBethesdaUnited States
| | - Daniel L Levy
- Department of Molecular Biology, University of WyomingLaramieUnited States
| | - Tom Misteli
- National Cancer InstituteBethesdaUnited States
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Kong K, Hu S, Yue J, Yang Z, Jabbour SK, Deng Y, Zhao B, Li F. Integrative genomic profiling reveals characteristics of lymph node metastasis in small cell lung cancer. Transl Lung Cancer Res 2023; 12:295-311. [PMID: 36895932 PMCID: PMC9989804 DOI: 10.21037/tlcr-22-785] [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: 08/05/2022] [Accepted: 01/10/2023] [Indexed: 02/17/2023]
Abstract
Background Small cell lung cancer (SCLC) is the most aggressive lung cancer subtype, with more than 70% of patients having metastatic disease and a poor prognosis. However, no integrated multi-omics analysis has been performed to explore novel differentially expressed genes (DEGs) or significantly mutated genes (SMGs) associated with lymph node metastasis (LNM) in SCLC. Methods In this study, whole-exome sequencing (WES) and RNA-sequencing were performed on tumor specimens to investigate the association between genomic and transcriptome alterations and LNM in SCLC patients with (N+, n=15) or without (N0, n=11) LNM. Results The results of WES revealed that the most common mutations occurred in TTN (85%) and TP53 (81%). The SMGs, including ZNF521, CDH10, ZNF429, POLE, and FAM135B, were associated with LNM. Cosmic signature analysis showed that mutation signatures 2, 4, and 7 were associated with LNM. Meanwhile, DEGs, including MAGEA4, FOXI3, RXFP2, and TRHDE, were found to be associated with LNM. Furthermore, we found that the messenger RNA (mRNA) levels of RB1 (P=0.0087), AFF3 (P=0.058), TDG (P=0.05), and ANKRD28 (P=0.042) were significantly correlated with copy number variants (CNVs), and ANKRD28 expression was consistently lower in N+ tumors than in N0 tumors. Further validation in cBioPortal revealed a significant correlation between LNM and poor prognosis in SCLC (P=0.014), although there was no significant correlation between LNM and overall survival (OS) in our cohort (P=0.75). Conclusions To our knowledge, this is the first integrative genomics profiling of LNM in SCLC. Our findings are particularly important for early detection and the provision of reliable therapeutic targets.
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Affiliation(s)
- Kangle Kong
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shan Hu
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaqi Yue
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ziheng Yang
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Salma K Jabbour
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Yu Deng
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Zhao
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fan Li
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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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.
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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
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In Silico Analysis of Ion Channels and Their Correlation with Epithelial to Mesenchymal Transition in Breast Cancer. Cancers (Basel) 2022; 14:cancers14061444. [PMID: 35326596 PMCID: PMC8946083 DOI: 10.3390/cancers14061444] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Breast cancer involves changes in the healthy cells of the breast resulting in rapid and abnormal division of cells that later spread to other parts of the body through the process of metastasis, which involves epithelial mesenchymal transition (EMT). Ion channels play a significant role in the switch from epithelial to mesenchymal transition through their contributions to cellular motility, cell volume regulation and cell cycle progression. Comprehensive computational analyses were performed to understand the role of ion channels in tumor/metastatic samples of breast cancer and their correlation with EMT. Abstract Uncontrolled growth of breast cells due to altered gene expression is a key feature of breast cancer. Alterations in the expression of ion channels lead to variations in cellular activities, thus contributing to attributes of cancer hallmarks. Changes in the expression levels of ion channels were observed as a consequence of EMT. Additionally, ion channels were reported in the activation of EMT and maintenance of a mesenchymal phenotype. Here, to identify altered ion channels in breast cancer patients, differential gene expression and weighted gene co-expression network analyses were performed using transcriptomic data. Protein–protein interactions network analysis was carried out to determine the ion channels interacting with hub EMT-related genes in breast cancer. Thirty-two ion channels were found interacting with twenty-six hub EMT-related genes. The identified ion channels were further correlated with EMT scores, indicating mesenchymal phenotype. Further, the pathway map was generated to represent a snapshot of deregulated cellular processes by altered ion channels and EMT-related genes. Kaplan–Meier five-year survival analysis and Cox regressions indicated the expression of CACNA1B, ANO6, TRPV3, VDAC1 and VDAC2 to be potentially associated with poor survival. Deregulated ion channels correlate with EMT-related genes and have a crucial role in breast cancer-associated tumorigenesis. Most likely, they are potential candidates for the determination of prognosis in patients with breast cancer.
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NMU Is a Poor Prognostic Biomarker in Patients with Lung Adenocarcinoma. DISEASE MARKERS 2021; 2021:5031479. [PMID: 34336003 PMCID: PMC8292091 DOI: 10.1155/2021/5031479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/31/2021] [Accepted: 07/02/2021] [Indexed: 12/17/2022]
Abstract
Lung adenocarcinoma (LUAD) is the most prevalent histologic type of lung cancer, associated with a high incidence rate and substantial mortality rate worldwide. Accumulating evidence shows that the aberrant expression of neuromedin U (NMU) contributes to the initiation and progression of cancer. Herein, we explored whether NMU could be adopted as a new diagnostic and therapeutic marker in LUAD. The UALCAN and GEPIA web resources were employed to assess data on the NMU expression in LUAD. The STRING web resource was used to develop the PPI (protein-protein interaction) network of NMU, whereas Cytoscape was applied for module analysis. The Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of NMU and the interacting proteins were examined using the WebGestalt tool. Survival analysis was performed with the Kaplan-Meier plotter tool. Results revealed that the NMU expression in LUAD was significantly higher than in the nonmalignant tissues. Moreover, higher NMU levels were dramatically related to shorter overall survival, first progression survival, and postprogression survival. The specific gene mutations G45V, R143T, and F152L of NMU occurred in LUAD samples and were associated with a worse prognosis in patients. KEGG and western blot analyses demonstrated an association of NMU with the cell cycle and the cAMP signaling cascade. Bioinformatic analysis and the in vitro experiments implicated NMU as a promising prognostic signature and treatment target for LUAD.
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Lu J, Ding Y, Chen Y, Jiang J, Chen Y, Huang Y, Wu M, Li C, Kong M, Zhao W, Wang H, Zhang J, Li Z, Lu Y, Yu X, Jin K, Zhou D, Zhou T, Teng F, Zhang H, Zhou Z, Wang H, Teng L. Whole-exome sequencing of alpha-fetoprotein producing gastric carcinoma reveals genomic profile and therapeutic targets. Nat Commun 2021; 12:3946. [PMID: 34168152 PMCID: PMC8225795 DOI: 10.1038/s41467-021-24170-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 06/01/2021] [Indexed: 02/05/2023] Open
Abstract
Alpha-fetoprotein producing gastric carcinoma (AFPGC) is a rare and aggressive subtype of gastric cancer. However, little is known about the genomic features of this disease. We perform whole-exome sequencing analysis of AFPGC, and identify 34 significantly mutated genes. Somatic copy number alterations analysis reveals several significant focal amplifications (e.g. 19q12, 17q12) and focal deletions (e.g. 1p36.11, 9p21.3), and some of these negatively affect the patient prognosis. Comparative analyses reveal that AFPGC has distinct genomic features from gastric cancer of The Cancer Genome Atlas as well as four molecular subtypes. Several frequently altered genes with potential as therapeutic targets are identified in AFPGC. Further analysis reveals that AFPGC with amplification of CCNE1 at 19q12 and/or ERBB2 at 17q12 show poorer survival and more aggressive. Subsequently, based on our established patient-derived xenograft models for AFPGC, translational research is performed and the therapeutic value of targeting CCNE1 and ERBB2 is validated. In this work, we provide an understanding of genomic characteristics of AFPGC and propose a platform to explore and validate the genome-guided personalized treatment for this disease.
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Affiliation(s)
- Jun Lu
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yongfeng Ding
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yanyan Chen
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Junjie Jiang
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yiran Chen
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yingying Huang
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Mengjie Wu
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Chengzhi Li
- Department of Pathology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Mei Kong
- Department of Pathology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Wenyi Zhao
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences and Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Zhejiang University, Hangzhou, China
| | - Haohao Wang
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jing Zhang
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhongqi Li
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yimin Lu
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiongfei Yu
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ketao Jin
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Donghui Zhou
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Tianhua Zhou
- Institute of Gastroenterology, Cancer center, Zhejiang University, Hangzhou, China
| | - Fei Teng
- Hangzhou Oncocare Co. Ltd, Hangzhou, China
| | - Haibin Zhang
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhan Zhou
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences and Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Zhejiang University, Hangzhou, China.
| | - Haiyong Wang
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
| | - Lisong Teng
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
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Chamberlin K, Chamberlin G, Saunders K, Khagi S. Next-generation sequencing reveals novel mutations in a collision tumor of glioblastoma and meningioma. CNS Oncol 2021; 10:CNS70. [PMID: 34015961 PMCID: PMC8162195 DOI: 10.2217/cns-2020-0029] [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] [Indexed: 12/26/2022] Open
Abstract
Primary intracranial collision tumors are rare in patients without predisposing factors. We report such a case in a 42-year-old female who presented with headaches and altered mental status. Imaging revealed a single heterogeneous, rim-enhancing lesion in the left parieto-occipital periventricular region, involving the corpus callosum. Stereotactic biopsy demonstrated glioblastoma. Subsequent tumor resection showed histologic evidence of glioblastoma and meningioma. Next-generation sequencing was performed on both tumor components. The glioblastoma exhibited a CDKN2A homozygous deletion and novel missense mutations in TAF1L and CSMD3, while no definitive genetic alterations were identified in the meningioma. Next-generation sequencing may yield insight into molecular drivers of intracranial collision tumors and aid in identifying future therapeutic targets. Next-generation sequencing (NGS) reveals novel mutations in a collision tumor of GBM and meningioma. NGS has the potential to yield insight into molecular drivers of intracranial tumors and identify therapeutic targets.
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Affiliation(s)
- Kelly Chamberlin
- Department of Neurosurgery, UNC Hospitals, Chapel Hill, NC 27514, USA
| | - Gregory Chamberlin
- Department of Pathology & Laboratory Medicine, UNC Hospitals, Chapel Hill, NC 27514, USA
| | - Katherine Saunders
- Department of Pathology & Laboratory Medicine, UNC Hospitals, Chapel Hill, NC 27514, USA
| | - Simon Khagi
- Department of Neurosurgery, UNC Hospitals, Chapel Hill, NC 27514, USA.,Department of Medicine, Division of Medical Oncology, UNC Hospitals, Chapel Hill, NC 27514, USA
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Shang S, Li X, Gao Y, Guo S, Sun D, Zhou H, Sun Y, Wang P, Zhi H, Bai J, Ning S, Li X. MeImmS: Predict Clinical Benefit of Anti-PD-1/PD-L1 Treatments Based on DNA Methylation in Non-small Cell Lung Cancer. Front Genet 2021; 12:676449. [PMID: 34093667 PMCID: PMC8173132 DOI: 10.3389/fgene.2021.676449] [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: 03/05/2021] [Accepted: 04/26/2021] [Indexed: 01/13/2023] Open
Abstract
Immunotherapy has become an effective therapy for cancer treatment. However, the development of biomarkers to predict immunotherapy response still remains a challenge. We have developed the DNA Methylation Immune Score, named “MeImmS,” which can predict clinical benefits of non-small cell lung cancer (NSCLC) patients based on DNA methylation of 8 CpG sites. The 8 CpG sites regulate the expression of immune-related genes and MeImmS was related to immune-associated pathways, exhausted T cell markers and immune cells. Copy-number loss in 1p36.33 may affect the response of cancer patients to immunotherapy. In addition, SAA1, CXCL10, CCR5, CCL19, CXCL11, CXCL13, and CCL5 were found to be key immune regulatory genes in immunotherapy. Together, MeImmS discovered the heterogeneous of NSCLC patients and guided the immunotherapy of cancer patients in the future.
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Affiliation(s)
- Shipeng Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shuang Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Dailin Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hanxiao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yue Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Bai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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12
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Kazemi-Sefat GE, Keramatipour M, Talebi S, Kavousi K, Sajed R, Kazemi-Sefat NA, Mousavizadeh K. The importance of CDC27 in cancer: molecular pathology and clinical aspects. Cancer Cell Int 2021; 21:160. [PMID: 33750395 PMCID: PMC7941923 DOI: 10.1186/s12935-021-01860-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/01/2021] [Indexed: 12/17/2022] Open
Abstract
Background CDC27 is one of the core components of Anaphase Promoting complex/cyclosome. The main role of this protein is defined at cellular division to control cell cycle transitions. Here we review the molecular aspects that may affect CDC27 regulation from cell cycle and mitosis to cancer pathogenesis and prognosis. Main text It has been suggested that CDC27 may play either like a tumor suppressor gene or oncogene in different neoplasms. Divergent variations in CDC27 DNA sequence and alterations in transcription of CDC27 have been detected in different solid tumors and hematological malignancies. Elevated CDC27 expression level may increase cell proliferation, invasiveness and metastasis in some malignancies. It has been proposed that CDC27 upregulation may increase stemness in cancer stem cells. On the other hand, downregulation of CDC27 may increase the cancer cell survival, decrease radiosensitivity and increase chemoresistancy. In addition, CDC27 downregulation may stimulate efferocytosis and improve tumor microenvironment. Conclusion CDC27 dysregulation, either increased or decreased activity, may aggravate neoplasms. CDC27 may be suggested as a prognostic biomarker in different malignancies. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-01860-9.
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Affiliation(s)
- Golnaz Ensieh Kazemi-Sefat
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Shahid Hemmat Highway, P.O. Box: 14665-354, Tehran, 14496-14535, Iran
| | - Mohammad Keramatipour
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeed Talebi
- Department of Medical Genetics, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Roya Sajed
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Shahid Hemmat Highway, P.O. Box: 14665-354, Tehran, 14496-14535, Iran
| | | | - Kazem Mousavizadeh
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Shahid Hemmat Highway, P.O. Box: 14665-354, Tehran, 14496-14535, Iran. .,Cellular and Molecular Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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13
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Kim M, Na JM, Lee GW, Lee SJ, Kim JD, Yang JW. EGFR-mutated pulmonary adenocarcinoma with concurrent PIK3CA mutation, and with acquired RET fusion and EGFR T790M mutation after afatinib therapy. J Pathol Transl Med 2020; 55:79-82. [PMID: 33260286 PMCID: PMC7829570 DOI: 10.4132/jptm.2020.11.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/02/2020] [Indexed: 11/17/2022] Open
Affiliation(s)
- Minhye Kim
- Department of Pathology, Gyeonsang National University Hospital, Jinju, Korea
| | - Ji Min Na
- Department of Pathology, Gyeonsang National University Hospital, Jinju, Korea
| | - Gyeong-Won Lee
- Division of Hematology-Oncology, Department of Internal Medicine, Gyeonsang National University Hospital, Gyeongsang National University College of Medicine, Jinju, Korea
| | - Seung Jun Lee
- Division of Pulmonology and Allergy, Department of Internal Medicine, Gyeonsang National University Hospital, Gyeongsang National University College of Medicine, Jinju, Korea
| | - Jong Duk Kim
- Department of Cardiothoracic Surgery, Gyeonsang National University Hospital, Jinju, Korea
| | - Jung Wook Yang
- Department of Pathology, Gyeonsang National University Hospital, Gyeongsang National University College of Medicine, Jinju, Korea
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14
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Ahn S, Lim J, Park SY, Kim H, Kwon HJ, Han YB, Lee CT, Cho S, Chung JH. Genetic Alterations in Preinvasive Lung Synchronous Lesions. Cancer Res Treat 2020; 52:1120-1134. [PMID: 32599981 PMCID: PMC7577825 DOI: 10.4143/crt.2020.307] [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] [Received: 04/14/2020] [Accepted: 06/04/2020] [Indexed: 12/24/2022] Open
Abstract
Purpose Despite advances in treatment, lung cancer remains the leading cause of cancer mortality. This study aimed to characterise genome-wide tumorigenesis events and to understand the hypothesis of the multistep carcinogenesis of lung adenocarcinoma (LUAD). Materials and Methods We conducted multiregion whole-exome sequencing of LUAD with synchronous atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ, or minimally invasive adenocarcinoma of 19 samples from three patients to characterize genome-wide tumorigenesis events and validate the hypothesis of the multistep carcinogenesis of LUAD. We identified potential pathogenic mutations preserved in preinvasive lesions and supplemented the finding by allelic variant level from RNA sequencing. Results Overall, independent mutational profiles were observed per patient and between patients. Some shared mutations including epidermal growth factor receptor (EGFR, p.L858R) were present across synchronous lesions. Conclusion Here, we show that there are driver gene mutations in AAH, and they may exacerbate as a sequence in a histological continuum, supporting the Darwinian evolution model of cancer genome. The intertumoral and intratumoral heterogeneity of synchronous LUAD implies that multi-biomarker strategies might be necessary for appropriate treatment.
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Affiliation(s)
- Soyeon Ahn
- Division of Statistics, Medical Research Collaborating Center, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Jisun Lim
- Division of Statistics, Medical Research Collaborating Center, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Soo Young Park
- Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Hyojin Kim
- Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Hyun Jung Kwon
- Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Yeon Bi Han
- Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Choon-Taek Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Sukki Cho
- Department of Thoracic and Cardiovascular Surgery, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Jin-Haeng Chung
- Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
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15
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Aguiar TFM, Rivas MP, Costa S, Maschietto M, Rodrigues T, Sobral de Barros J, Barbosa AC, Valieris R, Fernandes GR, Bertola DR, Cypriano M, Caminada de Toledo SR, Major A, Tojal I, Apezzato MLDP, Carraro DM, Rosenberg C, Lima da Costa CM, Cunha IW, Sarabia SF, Terrada DL, Krepischi ACV. Insights Into the Somatic Mutation Burden of Hepatoblastomas From Brazilian Patients. Front Oncol 2020; 10:556. [PMID: 32432034 PMCID: PMC7214543 DOI: 10.3389/fonc.2020.00556] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/27/2020] [Indexed: 12/23/2022] Open
Abstract
Hepatoblastoma is a very rare embryonal liver cancer supposed to arise from the impairment of hepatocyte differentiation during embryogenesis. In this study, we investigated by exome sequencing the burden of somatic mutations in a cohort of 10 hepatoblastomas, including a congenital case. Our data disclosed a low mutational background and pointed out to a novel set of candidate genes for hepatoblastoma biology, which were shown to impact gene expression levels. Only three recurrently mutated genes were detected: CTNNB1 and two novel candidates, CX3CL1 and CEP164. A relevant finding was the identification of a recurrent mutation (A235G) in two hepatoblastomas at the CX3CL1 gene; evaluation of RNA and protein expression revealed upregulation of CX3CL1 in tumors. The analysis was replicated in two independents cohorts, substantiating that an activation of the CX3CL1/CX3CR1 pathway occurs in hepatoblastomas. In inflammatory regions of hepatoblastomas, CX3CL1/CX3CR1 were not detected in the infiltrated lymphocytes, in which they should be expressed in normal conditions, whereas necrotic regions exhibited negative labeling in tumor cells, but strongly positive infiltrated lymphocytes. Altogether, these data suggested that CX3CL1/CX3CR1 upregulation may be a common feature of hepatoblastomas, potentially related to chemotherapy response and progression. In addition, three mutational signatures were identified in hepatoblastomas, two of them with predominance of either the COSMIC signatures 1 and 6, found in all cancer types, or the COSMIC signature 29, mostly related to tobacco chewing habit; a third novel mutational signature presented an unspecific pattern with an increase of C>A mutations. Overall, we present here novel candidate genes for hepatoblastoma, with evidence that CX3CL1/CX3CR1 chemokine signaling pathway is likely involved with progression, besides reporting specific mutational signatures.
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Affiliation(s)
- Talita Ferreira Marques Aguiar
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil.,Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Maria Prates Rivas
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Silvia Costa
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | - Tatiane Rodrigues
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Juliana Sobral de Barros
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Anne Caroline Barbosa
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Renan Valieris
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Gustavo R Fernandes
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Debora R Bertola
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Monica Cypriano
- Adolescent and Child With Cancer Support Group (GRAACC), Department of Pediatric, Federal University of São Paulo, São Paulo, Brazil
| | - Silvia Regina Caminada de Toledo
- Adolescent and Child With Cancer Support Group (GRAACC), Department of Pediatric, Federal University of São Paulo, São Paulo, Brazil
| | - Angela Major
- Department of Pathology and Immunology, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, United States
| | - Israel Tojal
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | | | - Dirce Maria Carraro
- International Center for Research, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | - Isabela W Cunha
- Department of Pathology, Rede D'OR-São Luiz, São Paulo, Brazil.,Department of Pathology, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Stephen Frederick Sarabia
- Department of Pathology and Immunology, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, United States
| | - Dolores-López Terrada
- Department of Pathology and Immunology, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, United States.,Department of Pediatrics, Texas Children's Cancer Center, Houston, TX, United States.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, United States
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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16
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Chun YJ, Choi JW, Hong MH, Jung D, Son H, Cho EK, Min YJ, Kim SW, Park K, Lee SS, Kim S, Kim HR, Cho BC. Molecular characterization of lung adenocarcinoma from Korean patients using next generation sequencing. PLoS One 2019; 14:e0224379. [PMID: 31765373 PMCID: PMC6876835 DOI: 10.1371/journal.pone.0224379] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 10/13/2019] [Indexed: 02/07/2023] Open
Abstract
The treatment of Lung adenocarcinoma (LUAD) could benefit from the incorporation of precision medicine. This study was to identify cancer-related genetic alterations by next generation sequencing (NGS) in resected LUAD samples from Korean patients and to determine their associations with clinical features. A total of 201 tumors and their matched peripheral blood samples were analyzed using targeted sequencing via the Illumina HiSeq 2500 platform of 242 genes with a median depth of coverage greater than 500X. One hundred ninety-two tumors were amenable to data analysis. EGFR was the most frequently mutated gene, occurring in 106 (55%) patients, followed by TP53 (n = 67, 35%) and KRAS (n = 11, 6%). EGFR mutations were strongly increased in patients that were female and never-smokers. Smokers had a significantly higher tumor mutational burden (TMB) than never-smokers (average 4.84 non-synonymous mutations/megabase [mt/Mb] vs. 2.84 mt/Mb, p = 0.019). Somatic mutations of APC, CTNNB1, and AMER1 in the WNT signaling pathway were highly associated with shortened disease-free survival (DFS) compared to others (median DFS of 89 vs. 27 months, p = 0.018). Patients with low TMB, annotated as less than 2 mt/Mb, had longer DFS than those with high TMB (p = 0.041). A higher frequency of EGFR mutations and a lower of KRAS mutations were observed in Korean LUAD patients. Profiles of 242 genes mapped in this study were compared with whole exome sequencing genetic profiles generated in The Cancer Genome Atlas Lung Adenocarcinoma. NGS-based diagnostics can provide clinically relevant information such as mutations or TMB from readily available formalin-fixed paraffin-embedded tissue.
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Affiliation(s)
- You Jin Chun
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Woo Choi
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Korea
| | - Min Hee Hong
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Dongmin Jung
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Hyeonju Son
- Department of Biomedical Systems Informatics, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Kyung Cho
- Division of Hematology-Oncology, Department of Internal Medicine, Gachon Medical School, Gil Medical Center, Incheon, Korea
| | - Young Joo Min
- Division of Hematology and Oncology, Department of Internal Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, Korea
| | - Sang-We Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Keunchil Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sung Sook Lee
- Department of Hematology-Oncology, Inje University Haeundae Paik Hospital, Busan, Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Hye Ryun Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Byoung Chul Cho
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
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17
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Lusk CM, Watza D, Dyson G, Craig D, Ratliff V, Wenzlaff AS, Lonardo F, Bollig-Fischer A, Bepler G, Purrington K, Gadgeel S, Schwartz AG. Profiling the Mutational Landscape in Known Driver Genes and Novel Genes in African American Non-Small Cell Lung Cancer Patients. Clin Cancer Res 2019; 25:4300-4308. [PMID: 30979741 PMCID: PMC6635071 DOI: 10.1158/1078-0432.ccr-18-2439] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 12/07/2018] [Accepted: 04/05/2019] [Indexed: 12/26/2022]
Abstract
PURPOSE Identifying novel driver genes and mutations in African American non-small cell lung cancer (NSCLC) cases can inform targeted therapy and improve outcomes for this traditionally underrepresented population. EXPERIMENTAL DESIGN Tumor DNA, RNA, and germline DNA were collected from African American NSCLC patients who participated in research conducted at the Karmanos Cancer Institute (KCI) in Detroit, Michigan. Known mutations were ascertained through the Sequenom LungCarta panel of 214 mutations in 26 genes, RET/ROS1 fusions, amplification of FGFR1, and expression of ALK. Paired tumor and normal DNA was whole-exome sequenced for a subset of cases without known driver mutations. RESULTS Of the 193 tumors tested, 77 known driver mutations were identified in 66 patients (34.2%). Sixty-seven of the 127 patients without a known driver mutation were sequenced. In 54 of these patients, 50 nonsynonymous mutations were predicted to have damaging effects among the 26 panel genes, 47 of which are not found in The Cancer Genome Atlas NSCLC white or African American samples. Analyzing the whole-exome sequence data using MutSig2CV identified a total of 88 genes significantly mutated at FDR q < 0.1. Only 5 of these genes were previously reported as oncogenic. CONCLUSIONS These findings suggest that broader mutation profiling including both known and novel driver genes in African Americans with NSCLC will identify additional mutations that may be useful in treatment decision-making.
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Affiliation(s)
- Christine M Lusk
- Karmanos Cancer Institute, Detroit, Michigan
- Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Donovan Watza
- Karmanos Cancer Institute, Detroit, Michigan
- Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Greg Dyson
- Karmanos Cancer Institute, Detroit, Michigan
- Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Douglas Craig
- Karmanos Cancer Institute, Detroit, Michigan
- Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Valerie Ratliff
- Karmanos Cancer Institute, Detroit, Michigan
- Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Angela S Wenzlaff
- Karmanos Cancer Institute, Detroit, Michigan
- Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Fulvio Lonardo
- Karmanos Cancer Institute, Detroit, Michigan
- Department of Pathology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Aliccia Bollig-Fischer
- Karmanos Cancer Institute, Detroit, Michigan
- Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Gerold Bepler
- Karmanos Cancer Institute, Detroit, Michigan
- Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Kristen Purrington
- Karmanos Cancer Institute, Detroit, Michigan
- Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Shirish Gadgeel
- Karmanos Cancer Institute, Detroit, Michigan
- Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
- Currently at the Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Ann G Schwartz
- Karmanos Cancer Institute, Detroit, Michigan.
- Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
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18
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He ZH, Lv W, Wang LM, Wang YQ, Hu J. Identification of Genes Associated with Lung Adenocarcinoma Prognosis. Comb Chem High Throughput Screen 2019; 22:220-224. [PMID: 30947660 DOI: 10.2174/1386207322666190404152140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/14/2018] [Accepted: 12/11/2018] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Lung cancer is the most prevalent cancer in the world, and lung adenocarcinoma is the most common lung cancer subtype. Identification and determination of relevant prognostic markers are the key steps to personalized cancer management. METHODS We collected the gene expression profiles from 265 tumor tissues of stage I patients from The Cancer Genome Atlas (TCGA) databases. Using Cox regression model, we evaluated the association between gene expression and the overall survival time of patients adjusting for gender and age at initial pathologic diagnosis. RESULTS Age at initial pathologic diagnosis was identified to be associated with the survival, while gender was not. We identified that 15 genes were significantly associated with overall survival time of patients (FDR < 0.1). The 15-mRNA signature- based risk score was helpful to distinguish patients of high-risk group from patients of low-risk group. CONCLUSION Our findings reveal novel genes associated with lung adenocarcinoma survival and extend our understanding of how gene expression contributes to lung adenocarcinoma survival. These results are helpful for the prediction of the prognosis and personalized cancer management.
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Affiliation(s)
- Zhe-Hao He
- Department of Thoracic Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310000, China
| | - Wang Lv
- Department of Thoracic Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310000, China
| | - Lu-Ming Wang
- Department of Thoracic Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310000, China
| | - Yi-Qing Wang
- Department of Thoracic Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310000, China
| | - Jian Hu
- Department of Thoracic Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310000, China
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19
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Curtis NL, Bolanos-Garcia VM. The Anaphase Promoting Complex/Cyclosome (APC/C): A Versatile E3 Ubiquitin Ligase. Subcell Biochem 2019; 93:539-623. [PMID: 31939164 DOI: 10.1007/978-3-030-28151-9_18] [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] [Indexed: 03/25/2023]
Abstract
In the present chapter we discuss the essential roles of the human E3 ubiquitin ligase Anaphase Promoting Complex/Cyclosome (APC/C) in mitosis as well as the emerging evidence of important APC/C roles in cellular processes beyond cell division control such as regulation of genomic integrity and cell differentiation of the nervous system. We consider the potential incipient role of APC/C dysregulation in the pathophysiology of the neurological disorder Alzheimer's disease (AD). We also discuss how certain Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA) viruses take control of the host's cell division regulatory system through harnessing APC/C ubiquitin ligase activity and hypothesise the plausible molecular mechanisms underpinning virus manipulation of the APC/C. We also examine how defects in the function of this multisubunit protein assembly drive abnormal cell proliferation and lastly argue the potential of APC/C as a promising therapeutic target for the development of innovative therapies for the treatment of chronic malignancies such as cancer.
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Affiliation(s)
- Natalie L Curtis
- Faculty of Health and Life Sciences, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, England, UK
| | - Victor M Bolanos-Garcia
- Faculty of Health and Life Sciences, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, England, UK.
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20
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Lee H, Joung JG, Shin HT, Kim DH, Kim Y, Kim H, Kwon OJ, Shim YM, Lee HY, Lee KS, Choi YL, Park WY, Hayes DN, Um SW. Genomic alterations of ground-glass nodular lung adenocarcinoma. Sci Rep 2018; 8:7691. [PMID: 29769567 PMCID: PMC5955945 DOI: 10.1038/s41598-018-25800-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/30/2018] [Indexed: 12/20/2022] Open
Abstract
In-depth molecular pathogenesis of ground-glass nodular lung adenocarcinoma has not been well understood. The objectives of this study were to identify genomic alterations in ground-glass nodular lung adenocarcinomas and to investigate whether viral transcripts were detected in these tumors. Nine patients with pure (n = 4) and part-solid (n = 5) ground-glass nodular adenocarcinomas were included. Six were females with a median age of 58 years. We performed targeted exon sequencing and RNA sequencing. EGFR (n = 10), IDH2 (n = 2), TP53 (n = 1), PTEN (n = 1), EPHB4 (n = 1), and BRAF (n = 1) were identified as driver mutations by targeted exon sequencing. Vasculogenesis-associated genes including NOTCH4 and TGFBR3 expression were significantly downregulated in adenocarcinoma tissue versus normal tissue (adjusted P values < 0.001 for both NOTCH4 and TGFBR3). In addition, five novel fusion gene loci were identified in four lung adenocarcinomas. However, no significant virus-associated transcripts were detected in tumors. In conclusions, EGFR, IDH2, TP53, PTEN, EPHB4, and BRAF were identified as putative driver mutations of ground-glass nodular adenocarcinomas. Five novel fusion genes were also identified in four tumors. Viruses do not appear to be involved in the tumorigenesis of ground-glass nodular lung adenocarcinoma.
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Affiliation(s)
- Hyun Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Je-Gun Joung
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Hyun-Tae Shin
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Duk-Hwan Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Yujin Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Hojoong Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - O Jung Kwon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young Mog Shim
- Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ho Yun Lee
- Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyung Soo Lee
- Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoon-La Choi
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - D Neil Hayes
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sang-Won Um
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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21
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Qiu L, Tan X, Lin J, Liu RY, Chen S, Geng R, Wu J, Huang W. CDC27 Induces Metastasis and Invasion in Colorectal Cancer via the Promotion of Epithelial-To-Mesenchymal Transition. J Cancer 2017; 8:2626-2635. [PMID: 28900500 PMCID: PMC5595092 DOI: 10.7150/jca.19381] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 05/22/2017] [Indexed: 12/21/2022] Open
Abstract
Distant metastasis is the primary cause of cancer-related death among patients with colorectal cancer (CRC), and the discovery of novel therapeutic targets by further exploring the molecular mechanisms of CRC metastasis is therefore urgently needed. We previously illustrated that CDC27 overexpression promoted proliferation in CRC, but no studies have emphasized the role of CDC27 in cancer metastasis thus far. Our previous data indicated that the expression of CDC27 was significantly associated with distant metastasis in patient tissues, and therefore, in this study, we focused on the investigation of the potential mechanisms of CDC27 in CRC metastasis. The results revealed that CDC27 promoted the metastasis, invasion and sphere-formation capacity of DLD1 cells, but that the inhibition of CDC27 in HCT116 cells suppressed metastasis both in vitro and in vivo. Mechanistic analyses revealed that CDC27 promoted epithelial-to-mesenchymal transition (EMT), as demonstrated by the reduced expression of the epithelial markers ZO-1 and E-cadherin and the enhanced expression of the mesenchymal markers ZEB1 and Snail in HCT116 and DLD1 cells. Further mechanistic investigation indicated that CDC27 promoted metastasis and sphere-formation capacity in an ID1-dependent manner. In conclusion, we first demonstrated the role of CDC27 in cancer metastasis and showed that CDC27 may serve as a promising therapeutic target for CRC.
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Affiliation(s)
- Lin Qiu
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou.,Department of Hematology/Oncology, Guangzhou Women and Children's Medical center, Guangzhou Medical University, Guangzhou, Guangdong
| | - Xin Tan
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou
| | - Jiaxin Lin
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou.,Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou
| | - Ran-Yi Liu
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou
| | - Shuai Chen
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou
| | - Rong Geng
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou
| | - Jiangxue Wu
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou
| | - Wenlin Huang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou
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22
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Sundaresan V, Lin VT, Liang F, Kaye FJ, Kawabata-Iwakawa R, Shiraishi K, Kohno T, Yokota J, Zhou L. Significantly mutated genes and regulatory pathways in SCLC-a meta-analysis. Cancer Genet 2017; 216-217:20-28. [PMID: 29025592 DOI: 10.1016/j.cancergen.2017.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 05/06/2017] [Accepted: 05/31/2017] [Indexed: 02/08/2023]
Abstract
Small cell lung cancer (SCLC) accounts for approximately 15% of all lung cancers and demands effective targeted therapeutic strategies. In this meta-analysis study, we aim to identify significantly mutated genes and regulatory pathways to help us better understand the progression of SCLC and to identify potential biomarkers. Besides ranking genes based on their mutation frequencies, we sought to identify statistically significant mutations in SCLC with the MutSigCV software. Our analysis identified several genes with relatively low mutation frequency, including PTEN, as highly significant (p < 0.001), suggesting these genes may play an important role in the progression of SCLC. Our results also indicated mutations in genes involved in the axon guidance pathways likely play an important role in SCLC progression. In addition, we observed that the mutation rate was significantly higher in samples with RB1 gene mutated when compared to samples with wild type RB1, suggesting that RB1 status has significant impact on the mutation profile and disease progression in SCLC.
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Affiliation(s)
- Varsha Sundaresan
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA; UF Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Victor T Lin
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Faming Liang
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Frederic J Kaye
- UF Health Cancer Center, University of Florida, Gainesville, FL, USA; Department of Medicine, University of Florida, Gainesville, FL, USA; UF Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Reika Kawabata-Iwakawa
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Division of Translational Research, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Tokyo 104-0045, Japan
| | - Jun Yokota
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Cancer Genome Biology Group, Institute of Predictive and Personalized Medicine of Cancer, Barcelona 08916, Spain
| | - Lei Zhou
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA; UF Health Cancer Center, University of Florida, Gainesville, FL, USA; UF Genetics Institute, University of Florida, Gainesville, FL, USA.
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23
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Yi X, Tao Y, Lin X, Dai Y, Yang T, Yue X, Jiang X, Li X, Jiang DS, Andrade KC, Chang J. Histone methyltransferase Setd2 is critical for the proliferation and differentiation of myoblasts. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:697-707. [PMID: 28130125 DOI: 10.1016/j.bbamcr.2017.01.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 01/19/2017] [Accepted: 01/23/2017] [Indexed: 01/05/2023]
Abstract
Skeletal muscle cell proliferation and differentiation are tightly regulated. Epigenetic regulation is a major component of the regulatory mechanism governing these processes. Histone modification is part of the epigenetic code used for transcriptional regulation of chromatin through the establishment of an active or repressive state for genes involved in myogenesis in a temporal manner. Here, we uncovered the function of SET domain containing 2 (Setd2), an essential histone 3 lysine 36 trimethyltransferase, in regulating the proliferation and differentiation of myoblasts. Setd2 was silenced in the skeletal muscle myoblast cell line, C2C12, using the CRISPR/CAS9 system. The mutant cells exhibited defect in myotube formation. The myotube formation marker, myosin heavy chain (MHC), was downregulated earlier in Setd2 silenced cells compared to wild-type myoblasts during differentiation. The deficiency in Setd2 also resulted in repression of Myogenin (MyoG) expression, a key myogenic regulator during differentiation. In addition to the myoblast differentiation defect, decreased proliferation rate with significantly reduced levels of histone 3 phosphorylation, indicative of cell proliferation defect, were observed in the Setd2 silenced cells; suggesting an impaired proliferation phenotype. Furthermore, compromised G1/S- and G2/M-phase transition and decreased expression levels of major regulators of cell cycle G1/S checkpoints, cyclin D1, CDK4, CDK6, and cyclin E2 were detected in Setd2 silenced cells. Consistent with the cell cycle arrested phenotype, cyclin-dependent kinase inhibitor p21 was upregulated in Setd2 silenced cells. Together, this study demonstrates an essential role of Setd2 in myoblast proliferation and differentiation, and uncovers Setd2-mediated molecular mechanism through regulating MyoG and p21.
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Affiliation(s)
- Xin Yi
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China; Texas A&M University Health Science Center, Institute of Biosciences and Technology, Houston, TX 77030, USA
| | - Ye Tao
- Texas A&M University Health Science Center, Institute of Biosciences and Technology, Houston, TX 77030, USA
| | - Xi Lin
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Yuan Dai
- Texas A&M University Health Science Center, Institute of Biosciences and Technology, Houston, TX 77030, USA
| | - Tingli Yang
- Texas A&M University Health Science Center, Institute of Biosciences and Technology, Houston, TX 77030, USA
| | - Xiaojing Yue
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xuejun Jiang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Xiaoyan Li
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Ding-Sheng Jiang
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kelsey C Andrade
- Texas A&M University Health Science Center, Institute of Biosciences and Technology, Houston, TX 77030, USA
| | - Jiang Chang
- Texas A&M University Health Science Center, Institute of Biosciences and Technology, Houston, TX 77030, USA.
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24
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Chandler JD, Wongtrakool C, Banton SA, Li S, Orr ML, Barr DB, Neujahr DC, Sutliff RL, Go YM, Jones DP. Low-dose oral cadmium increases airway reactivity and lung neuronal gene expression in mice. Physiol Rep 2016; 4:e12821. [PMID: 27401458 PMCID: PMC4945833 DOI: 10.14814/phy2.12821] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/15/2016] [Indexed: 01/05/2023] Open
Abstract
Inhalation of cadmium (Cd) is associated with lung diseases, but less is known concerning pulmonary effects of Cd found in the diet. Cd has a decades-long half-life in humans and significant bioaccumulation occurs with chronic dietary intake. We exposed mice to low-dose CdCl2 (10 mg/L in drinking water) for 20 weeks, which increased lung Cd to a level similar to that of nonoccupationally exposed adult humans. Cd-treated mice had increased airway hyperresponsiveness to methacholine challenge, and gene expression array showed that Cd altered the abundance of 443 mRNA transcripts in mouse lung. In contrast to higher doses, low-dose Cd did not elicit increased metallothionein transcripts in lung. To identify pathways most affected by Cd, gene set enrichment of transcripts was analyzed. Results showed that major inducible targets of low-dose Cd were neuronal receptors represented by enriched olfactory, glutamatergic, cholinergic, and serotonergic gene sets. Olfactory receptors regulate chemosensory function and airway hypersensitivity, and these gene sets were the most enriched. Targeted metabolomics analysis showed that Cd treatment also increased metabolites in pathways of glutamatergic (glutamate), serotonergic (tryptophan), cholinergic (choline), and catecholaminergic (tyrosine) receptors in the lung tissue. Protein abundance measurements showed that the glutamate receptor GRIN2A was increased in mouse lung tissue. Together, these results show that in mice, oral low-dose Cd increased lung Cd to levels comparable to humans, increased airway hyperresponsiveness and disrupted neuronal pathways regulating bronchial tone. Therefore, dietary Cd may promote or worsen airway hyperresponsiveness in multiple lung diseases including asthma.
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Affiliation(s)
- Joshua D Chandler
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia
| | - Cherry Wongtrakool
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia Atlanta VA Medical Center, Decatur, Georgia
| | - Sophia A Banton
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia
| | - Shuzhao Li
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia
| | - Michael L Orr
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia
| | - Dana Boyd Barr
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - David C Neujahr
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia
| | - Roy L Sutliff
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia Atlanta VA Medical Center, Decatur, Georgia
| | - Young-Mi Go
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia
| | - Dean P Jones
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, Georgia
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25
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Jiang L, Huang J, Higgs BW, Hu Z, Xiao Z, Yao X, Conley S, Zhong H, Liu Z, Brohawn P, Shen D, Wu S, Ge X, Jiang Y, Zhao Y, Lou Y, Morehouse C, Zhu W, Sebastian Y, Czapiga M, Oganesyan V, Fu H, Niu Y, Zhang W, Streicher K, Tice D, Zhao H, Zhu M, Xu L, Herbst R, Su X, Gu Y, Li S, Huang L, Gu J, Han B, Jallal B, Shen H, Yao Y. Genomic Landscape Survey Identifies SRSF1 as a Key Oncodriver in Small Cell Lung Cancer. PLoS Genet 2016; 12:e1005895. [PMID: 27093186 PMCID: PMC4836692 DOI: 10.1371/journal.pgen.1005895] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/03/2016] [Indexed: 11/19/2022] Open
Abstract
Small cell lung cancer (SCLC) is an aggressive disease with poor survival. A few sequencing studies performed on limited number of samples have revealed potential disease-driving genes in SCLC, however, much still remains unknown, particularly in the Asian patient population. Here we conducted whole exome sequencing (WES) and transcriptomic sequencing of primary tumors from 99 Chinese SCLC patients. Dysregulation of tumor suppressor genes TP53 and RB1 was observed in 82% and 62% of SCLC patients, respectively, and more than half of the SCLC patients (62%) harbored TP53 and RB1 mutation and/or copy number loss. Additionally, Serine/Arginine Splicing Factor 1 (SRSF1) DNA copy number gain and mRNA over-expression was strongly associated with poor survival using both discovery and validation patient cohorts. Functional studies in vitro and in vivo demonstrate that SRSF1 is important for tumorigenicity of SCLC and may play a key role in DNA repair and chemo-sensitivity. These results strongly support SRSF1 as a prognostic biomarker in SCLC and provide a rationale for personalized therapy in SCLC. SCLC patients are initially highly chemo-sensitive with response rates of greater than 80% in both limited and extensive diseases, but suffer uniform disease recurrence or progression in a very short period of time. In the absence of well-defined genomic biomarkers and insights into the resistance mechanism, many targeted treatments have yielded negative results in the last decade Using integrated next generation sequencing (NGS) technology in combination with a high quality surgical sample set with comprehensive clinical annotation, our study not only identified novel recurrent genetic alterations in genes such as CDH10 and DNA repair pathways which may influence outcomes in SCLC patients, but also discovered the expression of SRSF1, an RNA-splicing factor which can both regulate key oncogenic and survival pathways such as BCL2, and play a critical role in patient survival.
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Affiliation(s)
- Liyan Jiang
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jiaqi Huang
- Medimmune, Gaithersburg, Maryland, United States of America
| | | | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhan Xiao
- Medimmune, Gaithersburg, Maryland, United States of America
| | - Xin Yao
- Medimmune, Gaithersburg, Maryland, United States of America
| | - Sarah Conley
- Medimmune, Gaithersburg, Maryland, United States of America
| | - Haihong Zhong
- Medimmune, Gaithersburg, Maryland, United States of America
| | - Zheng Liu
- Medimmune, Gaithersburg, Maryland, United States of America
| | - Philip Brohawn
- Medimmune, Gaithersburg, Maryland, United States of America
| | - Dong Shen
- Medimmune, Gaithersburg, Maryland, United States of America
| | - Song Wu
- Medimmune, Gaithersburg, Maryland, United States of America
| | - Xiaoxiao Ge
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Jiang
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yizhuo Zhao
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yuqing Lou
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | | | - Wei Zhu
- Medimmune, Gaithersburg, Maryland, United States of America
| | | | - Meggan Czapiga
- Medimmune, Gaithersburg, Maryland, United States of America
| | | | - Haihua Fu
- Asia & Emerging Markets iMed, AstraZeneca R&D, Shanghai, China
| | - Yanjie Niu
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Zhang
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | | | - David Tice
- Medimmune, Gaithersburg, Maryland, United States of America
| | - Heng Zhao
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Meng Zhu
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lin Xu
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ronald Herbst
- Medimmune, Gaithersburg, Maryland, United States of America
| | - Xinying Su
- Asia & Emerging Markets iMed, AstraZeneca R&D, Shanghai, China
| | - Yi Gu
- Asia & Emerging Markets iMed, AstraZeneca R&D, Shanghai, China
| | - Shyoung Li
- Beijing Genomics Institute, Shenzhen GuangDong, China
| | - Lihua Huang
- Beijing Genomics Institute, Shenzhen GuangDong, China
| | - Jianren Gu
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Baohui Han
- Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Bahija Jallal
- Medimmune, Gaithersburg, Maryland, United States of America
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, School of Public Health, Nanjing Medical University, Nanjing, China
- * E-mail: (HS); (YY)
| | - Yihong Yao
- Medimmune, Gaithersburg, Maryland, United States of America
- * E-mail: (HS); (YY)
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26
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Li C, Gao Z, Li F, Li X, Sun Y, Wang M, Li D, Wang R, Li F, Fang R, Pan Y, Luo X, He J, Zheng L, Xia J, Qiu L, He J, Ye T, Zhang R, He M, Zhu M, Hu H, Shi T, Zhou X, Sun M, Tian S, Zhou Y, Wang Q, Chen L, Yin G, Lu J, Wu R, Guo G, Li Y, Hu X, Li L, Asan A, Wang Q, Yin Y, Feng Q, Wang B, Wang H, Wang M, Yang X, Zhang X, Yang H, Jin L, Wang CY, Ji H, Chen H, Wang J, Wei Q. Whole Exome Sequencing Identifies Frequent Somatic Mutations in Cell-Cell Adhesion Genes in Chinese Patients with Lung Squamous Cell Carcinoma. Sci Rep 2015; 5:14237. [PMID: 26503331 PMCID: PMC4621504 DOI: 10.1038/srep14237] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 08/19/2015] [Indexed: 02/07/2023] Open
Abstract
Lung squamous cell carcinoma (SQCC) accounts for about 30% of all lung cancer cases. Understanding of mutational landscape for this subtype of lung cancer in Chinese patients is currently limited. We performed whole exome sequencing in samples from 100 patients with lung SQCCs to search for somatic mutations and the subsequent target capture sequencing in another 98 samples for validation. We identified 20 significantly mutated genes, including TP53, CDH10, NFE2L2 and PTEN. Pathways with frequently mutated genes included those of cell-cell adhesion/Wnt/Hippo in 76%, oxidative stress response in 21%, and phosphatidylinositol-3-OH kinase in 36% of the tested tumor samples. Mutations of Chromatin regulatory factor genes were identified at a lower frequency. In functional assays, we observed that knockdown of CDH10 promoted cell proliferation, soft-agar colony formation, cell migration and cell invasion, and overexpression of CDH10 inhibited cell proliferation. This mutational landscape of lung SQCC in Chinese patients improves our current understanding of lung carcinogenesis, early diagnosis and personalized therapy.
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Affiliation(s)
- Chenguang Li
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhibo Gao
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Fei Li
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Science, Shanghai, 200031, China
| | - Xiangchun Li
- BGI-Shenzhen, Shenzhen, 518083, China
- Department of Medicine and Therapeutics, State Key Laboratory of Digestive. Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - 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
| | - Mengyun Wang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Dan Li
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Rui Wang
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Fuming Li
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Science, Shanghai, 200031, China
| | - Rong Fang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Science, Shanghai, 200031, China
| | - Yunjian Pan
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xiaoyang Luo
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jing He
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | | | - Jufeng Xia
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Science, Shanghai, 200031, China
| | - Lixin Qiu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Jun He
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Ting Ye
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ruoxin Zhang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | | | - Meiling Zhu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Haichuan Hu
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Tingyan Shi
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Xiaoyan Zhou
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Menghong Sun
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | | | - Yong Zhou
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | | | | | - Jingya Lu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Renhua Wu
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | | | - Xueda Hu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Lin Li
- BGI-Shenzhen, Shenzhen, 518083, China
| | - A Asan
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Qin Wang
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Ye Yin
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Bin Wang
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Hang Wang
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Xiaonan Yang
- BGI-Shanghai, Eastern CHINA, BGI-Shenzhen, Shanghai, 201100, China
| | | | | | - Li Jin
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Cun-Yu Wang
- Lab of Molecular Signaling, Division of Oral Biology and Medicine, School of Dentistry and Jonsson Cancer Center, UCLA, Los Angeles, California, 90095, USA
| | - Hongbin Ji
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Science, Shanghai, 200031, 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
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 2200, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Qingyi Wei
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Duke Cancer Institute, Duke University Medical Center, and Department of Medicine, Duke University School of Medicine, Durham, North Carolina, 27710, USA
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Yoon JK, Ahn J, Kim HS, Han SM, Jang H, Lee MG, Lee JH, Bang D. microDuMIP: target-enrichment technique for microarray-based duplex molecular inversion probes. Nucleic Acids Res 2014; 43:e28. [PMID: 25414325 PMCID: PMC4357688 DOI: 10.1093/nar/gku1188] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Molecular inversion probe (MIP)-based capture is a scalable and effective target-enrichment technology that can use synthetic single-stranded oligonucleotides as probes. Unlike the straightforward use of synthetic oligonucleotides for low-throughput target capture, high-throughput MIP capture has required laborious protocols to generate thousands of single-stranded probes from DNA microarray because of multiple enzymatic steps, gel purifications and extensive PCR amplifications. Here, we developed a simple and efficient microarray-based MIP preparation protocol using only one enzyme with double-stranded probes and improved target capture yields by designing probes with overlapping targets and unique barcodes. To test our strategy, we produced 11 510 microarray-based duplex MIPs (microDuMIPs) and captured 3554 exons of 228 genes in a HapMap genomic DNA sample (NA12878). Under our protocol, capture performance and precision of calling were compatible to conventional MIP capture methods, yet overlapping targets and unique barcodes allowed us to precisely genotype with as little as 50 ng of input genomic DNA without library preparation. microDuMIP method is simpler and cheaper, allowing broader applications and accurate target sequencing with a scalable number of targets.
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Affiliation(s)
- Jung-Ki Yoon
- College of Medicine, Seoul National University, Seoul 110-799, Korea
| | - Jinwoo Ahn
- Department of Chemistry, Yonsei University, Seoul 120-752, Korea
| | - Han Sang Kim
- Department of Pharmacology, Pharmacogenomic Research Center for Membrane Transporters, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 120-752, Korea Yonsei Cancer Center, Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 120-752, Korea
| | - Soo Min Han
- Department of Pharmacology, Pharmacogenomic Research Center for Membrane Transporters, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 120-752, Korea
| | - Hoon Jang
- Department of Chemistry, Yonsei University, Seoul 120-752, Korea
| | - Min Goo Lee
- Department of Pharmacology, Pharmacogenomic Research Center for Membrane Transporters, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 120-752, Korea
| | - Ji Hyun Lee
- Department of Oral Biology, Yonsei University College of Dentistry, Seoul 120-752, Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul 120-752, Korea
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28
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Hao C, Wang L, Peng S, Cao M, Li H, Hu J, Huang X, Liu W, Zhang H, Wu S, Pataer A, Heymach JV, Eterovic AK, Zhang Q, Shaw KR, Chen K, Futreal A, Wang M, Hofstetter W, Mehran R, Rice D, Roth JA, Sepesi B, Swisher SG, Vaporciyan A, Walsh GL, Johnson FM, Fang B. Gene mutations in primary tumors and corresponding patient-derived xenografts derived from non-small cell lung cancer. Cancer Lett 2014; 357:179-185. [PMID: 25444907 DOI: 10.1016/j.canlet.2014.11.024] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 11/11/2014] [Accepted: 11/12/2014] [Indexed: 12/20/2022]
Abstract
Molecular annotated patient-derived xenograft (PDX) models are useful for the preclinical investigation of anticancer drugs and individualized anticancer therapy. We established 23 PDXs from 88 surgical specimens of lung cancer patients and determined gene mutations in these PDXs and their paired primary tumors by ultradeep exome sequencing on 202 cancer-related genes. The numbers of primary tumors with deleterious mutations in TP53, KRAS, PI3KCA, ALK, STK11, and EGFR were 43.5%, 21.7%, 17.4%, 17.4%, 13.0%, and 8.7%, respectively. Other genes with deleterious mutations in ≥3 (13.0%) primary tumors were MLL3, SETD2, ATM, ARID1A, CRIPAK, HGF, BAI3, EP300, KDR, PDGRRA and RUNX1. Of 315 mutations detected in the primary tumors, 293 (93%) were also detected in their corresponding PDXs, indicating that PDXs have the capacity to recapitulate the mutations in primary tumors. Nevertheless, a substantial number of mutations had higher allele frequencies in the PDXs than in the primary tumors, or were not detectable in the primary tumor, suggesting the possibility of tumor cell enrichment in PDXs or heterogeneity in the primary tumors. The molecularly annotated PDXs generated from this study could be useful for future translational studies.
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Affiliation(s)
- Chuncheng Hao
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Li Wang
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Shaohua Peng
- Department of Thoracic and Head/Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Mengru Cao
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Hongyu Li
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jing Hu
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Xiao Huang
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Wei Liu
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Hui Zhang
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Shuhong Wu
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Apar Pataer
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - John V Heymach
- Department of Thoracic and Head/Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; The University of Texas Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Agda Karina Eterovic
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Qingxiu Zhang
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Kenna R Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computation Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Michael Wang
- Department of Lymphoma, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Wayne Hofstetter
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Reza Mehran
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - David Rice
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jack A Roth
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Stephen G Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ara Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Garrett L Walsh
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Faye M Johnson
- Department of Thoracic and Head/Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; The University of Texas Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Bingliang Fang
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; The University of Texas Graduate School of Biomedical Sciences, Houston, Texas, USA.
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29
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An eight-miRNA signature as a potential biomarker for predicting survival in lung adenocarcinoma. J Transl Med 2014; 12:159. [PMID: 24893932 PMCID: PMC4062505 DOI: 10.1186/1479-5876-12-159] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/14/2014] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Lung adenocarcinoma is a heterogernous disease that creates challenges for classification and management. The purpose of this study is to identify specific miRNA markers closely associated with the survival of LUAD patients from a large dataset of significantly altered miRNAs, and to assess the prognostic value of this miRNA expression profile for OS in patients with LUAD. METHODS We obtained miRNA expression profiles and corresponding clinical information for 372 LUAD patients from The Cancer Genome Atlas (TCGA), and identified the most significantly altered miRNAs between tumor and normal samples. Using survival analysis and supervised principal components method, we identified an eight-miRNA signature for the prediction of overall survival (OS) of LUAD patients. The relationship between OS and the identified miRNA signature was self-validated in the TCGA cohort (randomly classified into two subgroups: n = 186 for the training set and n = 186 for the testing set). Survival receiver operating characteristic (ROC) analysis was used to assess the performance of survival prediction. The biological relevance of putative miRNA targets was also analyzed using bioinformatics. RESULTS Sixteen of the 111 most significantly altered miRNAs were associated with OS across different clinical subclasses of the TCGA-derived LUAD cohort. A linear prognostic model of eight miRNAs (miR-31, miR-196b, miR-766, miR-519a-1, miR-375, miR-187, miR-331 and miR-101-1) was constructed and weighted by the importance scores from the supervised principal component method to divide patients into high- and low-risk groups. Patients assigned to the high-risk group exhibited poor OS compared with patients in the low-risk group (hazard ratio [HR] = 1.99, P <0.001). The eight-miRNA signature is an independent prognostic marker of OS of LUAD patients and demonstrates good performance for predicting 5-year OS (Area Under the respective ROC Curves [AUC] = 0.626, P = 0.003), especially for non-smokers (AUC = 0.686, P = 0.023). CONCLUSIONS We identified an eight-miRNA signature that is prognostic of LUAD. The miRNA signature, if validated in other prospective studies, may have important implications in clinical practice, in particular identifying a subgroup of patients with LUAD who are at high risk of mortality.
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