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Tapia-Valladares C, Valenzuela G, González E, Maureira I, Toro J, Freire M, Sepúlveda-Hermosilla G, Ampuero D, Blanco A, Gallegos I, Morales F, Erices JI, Barajas O, Ahumada M, Contreras HR, González J, Armisén R, Marcelain K. Distinct Driver Pathway Enrichments and a High Prevalence of TSC2 Mutations in Right Colon Cancer in Chile: A Preliminary Comparative Analysis. Int J Mol Sci 2024; 25:4695. [PMID: 38731914 PMCID: PMC11083322 DOI: 10.3390/ijms25094695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 05/13/2024] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer deaths globally. While ethnic differences in driver gene mutations have been documented, the South American population remains understudied at the genomic level, despite facing a rising burden of CRC. We analyzed tumors of 40 Chilean CRC patients (Chp) using next-generation sequencing and compared them to data from mainly Caucasian cohorts (TCGA and MSK-IMPACT). We identified 388 mutations in 96 out of 135 genes, with TP53 (45%), KRAS (30%), PIK3CA (22.5%), ATM (20%), and POLE (20%) being the most frequently mutated. TSC2 mutations were associated with right colon cancer (44.44% in RCRC vs. 6.45% in LCRC, p-value = 0.016), and overall frequency was higher compared to TCGA (p-value = 1.847 × 10-5) and MSK-IMPACT cohorts (p-value = 3.062 × 10-2). Limited sample size restricts definitive conclusions, but our data suggest potential differences in driver mutations for Chilean patients, being that the RTK-RAS oncogenic pathway is less affected and the PI3K pathway is more altered in Chp compared to TCGA (45% vs. 25.56%, respectively). The prevalence of actionable pathways and driver mutations can guide therapeutic choices, but can also impact treatment effectiveness. Thus, these findings warrant further investigation in larger Chilean cohorts to confirm these initial observations. Understanding population-specific driver mutations can guide the development of precision medicine programs for CRC patients.
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Affiliation(s)
- Camilo Tapia-Valladares
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
| | - Guillermo Valenzuela
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
| | - Evelin González
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610507, Chile
| | - Ignacio Maureira
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
- Departamento de Tecnología Médica, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
| | - Jessica Toro
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
- Centro para la Prevención y Control del Cáncer, CECAN, Universidad de Chile, Santiago 8380000, Chile
| | - Matías Freire
- CORFO Center of Excellence in Precision Medicine, Pfizer Chile, Santiago 8380000, Chile
| | | | - Diego Ampuero
- CORFO Center of Excellence in Precision Medicine, Pfizer Chile, Santiago 8380000, Chile
| | - Alejandro Blanco
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610507, Chile
| | - Iván Gallegos
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
- Centro para la Prevención y Control del Cáncer, CECAN, Universidad de Chile, Santiago 8380000, Chile
- Departamento de Patología, Hospital Clínico de la Universidad de Chile, Santiago 8380453, Chile
| | - Fernanda Morales
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
| | - José I. Erices
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
| | - Olga Barajas
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
- Centro para la Prevención y Control del Cáncer, CECAN, Universidad de Chile, Santiago 8380000, Chile
- Departamento de Medicina Interna, Hospital Clínico de la Universidad de Chile, Santiago 8380453, Chile
| | - Mónica Ahumada
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
- Centro para la Prevención y Control del Cáncer, CECAN, Universidad de Chile, Santiago 8380000, Chile
- Departamento de Medicina Interna, Hospital Clínico de la Universidad de Chile, Santiago 8380453, Chile
| | - Héctor R. Contreras
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
- Centro para la Prevención y Control del Cáncer, CECAN, Universidad de Chile, Santiago 8380000, Chile
| | - Jaime González
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
| | - Ricardo Armisén
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610507, Chile
| | - Katherine Marcelain
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
- Centro para la Prevención y Control del Cáncer, CECAN, Universidad de Chile, Santiago 8380000, Chile
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Wang R, Zhang G, Zhu X, Xu Y, Cao N, Li Z, Han C, Qin M, Shen Y, Dong J, Ma F, Zhao A. Prognostic Implications of LRP1B and Its Relationship with the Tumor-Infiltrating Immune Cells in Gastric Cancer. Cancers (Basel) 2023; 15:5759. [PMID: 38136305 PMCID: PMC10741692 DOI: 10.3390/cancers15245759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Recent studies have shown that low-density lipoprotein receptor-related protein 1b (LRP1B), as a potential tumor suppressor, is implicated in the response to immunotherapy. The frequency of LRP1B mutation gene is high in many cancers, but its role in gastric cancer (GC) has not been determined. METHODS The prognostic value of LRP1B mutation in a cohort containing 100 patients having received radical gastrectomy for stage II-III GC was explored. By analyzing the data of LRP1B mRNA, the risk score of differentially expressed genes (DEGs) between LRP1B mutation-type and wild-type was constructed based on the TCGA-STAD cohort. The infiltration of tumor immune cells was evaluated by the CYBERSORT algorithm and verified by immunohistochemistry. RESULTS LRP1B gene mutation was an independent risk factor for disease-free survival (DFS) in GC patients (HR = 2.57, 95% CI: 1.28-5.14, p = 0.008). The Kaplan-Meier curve demonstrated a shorter survival time in high-risk patients stratified according to risk score (p < 0.0001). CYBERSORT analysis showed that the DEGs were mainly concentrated in CD4+ T cells and macrophages. TIMER analysis suggested that LRP1B expression was associated with the infiltration of CD4+ T cells and macrophages. Immunohistochemistry demonstrated that LRP1B was expressed in the tumor cells (TCs) and immune cells in 16/89 and 26/89 of the cohort, respectively. LRP1B-positive TCs were associated with higher levels of CD4+ T cells, CD8+ T cells, and CD86/CD163 (p < 0.05). Multivariate analysis showed that LRP1B-positive TCs represented an independent protective factor of DFS in GC patients (HR = 0.43, 95% CI: 0.10-0.93, p = 0.042). CONCLUSIONS LRP1B has a high prognostic value in GC. LRP1B may stimulate tumor immune cell infiltration to provide GC patients with survival benefits.
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Affiliation(s)
- Rui Wang
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China; (R.W.); (G.Z.); (X.Z.); (Y.X.); (N.C.)
- Department of Gastroenterology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, China
| | - Guangtao Zhang
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China; (R.W.); (G.Z.); (X.Z.); (Y.X.); (N.C.)
| | - Xiaohong Zhu
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China; (R.W.); (G.Z.); (X.Z.); (Y.X.); (N.C.)
| | - Yan Xu
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China; (R.W.); (G.Z.); (X.Z.); (Y.X.); (N.C.)
| | - Nida Cao
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China; (R.W.); (G.Z.); (X.Z.); (Y.X.); (N.C.)
| | - Zhaoyan Li
- Department of Traditional Chinese Medicine, School of Medicine Affiliated Ruijin Hospital, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Chen Han
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China; (R.W.); (G.Z.); (X.Z.); (Y.X.); (N.C.)
| | - Mengmeng Qin
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China; (R.W.); (G.Z.); (X.Z.); (Y.X.); (N.C.)
| | - Yumiao Shen
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China; (R.W.); (G.Z.); (X.Z.); (Y.X.); (N.C.)
| | - Jiahuan Dong
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China; (R.W.); (G.Z.); (X.Z.); (Y.X.); (N.C.)
| | - Fangqi Ma
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China; (R.W.); (G.Z.); (X.Z.); (Y.X.); (N.C.)
| | - Aiguang Zhao
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China; (R.W.); (G.Z.); (X.Z.); (Y.X.); (N.C.)
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Peixoto J, Príncipe C, Pestana A, Osório H, Pinto MT, Prazeres H, Soares P, Lima RT. Using a Dual CRISPR/Cas9 Approach to Gain Insight into the Role of LRP1B in Glioblastoma. Int J Mol Sci 2023; 24:11285. [PMID: 37511044 PMCID: PMC10379115 DOI: 10.3390/ijms241411285] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
LRP1B remains one of the most altered genes in cancer, although its relevance in cancer biology is still unclear. Recent advances in gene editing techniques, particularly CRISPR/Cas9 systems, offer new opportunities to evaluate the function of large genes, such as LRP1B. Using a dual sgRNA CRISPR/Cas9 gene editing approach, this study aimed to assess the impact of disrupting LRP1B in glioblastoma cell biology. Four sgRNAs were designed for the dual targeting of two LRP1B exons (1 and 85). The U87 glioblastoma (GB) cell line was transfected with CRISPR/Cas9 PX459 vectors. To assess LRP1B-gene-induced alterations and expression, PCR, Sanger DNA sequencing, and qRT-PCR were carried out. Three clones (clones B9, E6, and H7) were further evaluated. All clones presented altered cellular morphology, increased cellular and nuclear size, and changes in ploidy. Two clones (E6 and H7) showed a significant decrease in cell growth, both in vitro and in the in vivo CAM assay. Proteomic analysis of the clones' secretome identified differentially expressed proteins that had not been previously associated with LRP1B alterations. This study demonstrates that the dual sgRNA CRISPR/Cas9 strategy can effectively edit LRP1B in GB cells, providing new insights into the impact of LRP1B deletions in GBM biology.
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Grants
- PTDC/MEC-ONC/31520/2017 FEEI, FEDER through COMPETE 2020 -POCI, Portugal 2020, and by Portuguese funds through FCT/Ministério da Ciência, Tecnologia e Ensino Superior
- POCI-01-0145-FEDER-028779 (PTDC/BIA-MIC/28779/2017) FEEI, FEDER through COMPETE 2020 -POCI, Portugal 2020, and by Portuguese funds through FCT/Ministério da Ciência, Tecnologia e Ensino Superior
- project "Institute for Research and Innovation in Health Sciences" (UID/BIM/04293/2019) FEEI, FEDER through COMPETE 2020 -POCI, Portugal 2020, and by Portuguese funds through FCT/Ministério da Ciência, Tecnologia e Ensino Superior
- "Cancer Research on Therapy Resistance: From Basic Mechanisms to Novel Targets"-NORTE-01-0145-FEDER-000051 Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF
- The Porto Comprehensive Cancer Center" with the reference NORTE-01-0145-FEDER-072678 - Consórcio PORTO.CCC - Porto.Comprehensive Cancer Center Raquel Seruca European Regional Development Fund
- ROTEIRO/0028/2013; LISBOA-01-0145-FEDER-022125 Portuguese Mass Spectrometry Network, integrated in the National Roadmap of Research Infra-structures of Strategic Relevance
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Affiliation(s)
- Joana Peixoto
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Cancer Signaling and Metabolism Group, IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4169-007 Porto, Portugal
| | - Catarina Príncipe
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Cancer Signaling and Metabolism Group, IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4169-007 Porto, Portugal
- Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Ana Pestana
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Cancer Signaling and Metabolism Group, IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4169-007 Porto, Portugal
| | - Hugo Osório
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- FMUP-Department of Pathology, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Marta Teixeira Pinto
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
| | - Hugo Prazeres
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
| | - Paula Soares
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Cancer Signaling and Metabolism Group, IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4169-007 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- FMUP-Department of Pathology, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Raquel T Lima
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Cancer Signaling and Metabolism Group, IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Rua Alfredo Allen 208, 4169-007 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- FMUP-Department of Pathology, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
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Li SS, Zhai XH, Liu HL, Liu TZ, Cao TY, Chen DM, Xiao LX, Gan XQ, Cheng K, Hong WJ, Huang Y, Lian YF, Xiao J. Whole-exome sequencing analysis identifies distinct mutational profile and novel prognostic biomarkers in primary gastrointestinal diffuse large B-cell lymphoma. Exp Hematol Oncol 2022; 11:71. [PMID: 36243813 PMCID: PMC9569083 DOI: 10.1186/s40164-022-00325-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
Background Diffuse large B-cell lymphoma (DLBCL) is the most common aggressive non-Hodgkin lymphoma, and about 10% of DLBCL cases primarily occur in the gastrointestinal tract. Previous reports have revealed that primary gastrointestinal-DLBCL (pGI-DLBCL) harbors different genetic mutations from other nodal or extranodal DLBCL. However, the exonic mutation profile of pGI-DLBCL has not been fully addressed. Methods We performed whole-exome sequencing of matched tumor tissues and blood samples from 53 pGI-DLBCL patients. The exonic mutation profiles were screened, and the correlations between genetic mutations and clinicopathological characteristics were analyzed. Results A total of 6,588 protein-altering events were found and the five most frequent mutated genes in our pGI-DLBCL cohort were IGLL5 (47%), TP53 (42%), BTG2 (28%), P2RY8 (26%) and PCLO (23%). Compared to the common DLBCL, significantly less or absence of MYD88 (0%), EZH2 (0%), BCL2 (2%) or CD79B (8%) mutations were identified in pGI-DLBCL. The recurrent potential driver genes were mainly enriched in pathways related to signal transduction, infectious disease and immune regulation. In addition, HBV infection had an impact on the mutational signature in pGI-DLBCL, as positive HBsAg was significantly associated with the TP53 and LRP1B mutations, two established tumor suppressor genes in many human cancers. Moreover, IGLL5 and LRP1B mutations were significantly correlated with patient overall survival and could serve as two novel prognostic biomarkers in pGI-DLBCL. Conclusions Our study provides a comprehensive view of the exonic mutation profile of the largest pGI-DLBCL cohort to date. The results could facilitate the clinical development of novel therapeutic and prognostic biomarkers for pGI-DLBCL. Supplementary Information The online version contains supplementary material available at 10.1186/s40164-022-00325-7.
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Affiliation(s)
- Shan-Shan Li
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Xiao-Hui Zhai
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Hai-Ling Liu
- Department of Pathology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Ting-Zhi Liu
- Department of Hematology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Tai-Yuan Cao
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Dong-Mei Chen
- Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Le-Xin Xiao
- Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Xiao-Qin Gan
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Ke Cheng
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Wan-Jia Hong
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Yan Huang
- Department of Pathology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China. .,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
| | - Yi-Fan Lian
- Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
| | - Jian Xiao
- Department of Medical Oncology, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China. .,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
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Passarella D, Ciampi S, Di Liberto V, Zuccarini M, Ronci M, Medoro A, Foderà E, Frinchi M, Mignogna D, Russo C, Porcile C. Low-Density Lipoprotein Receptor-Related Protein 8 at the Crossroad between Cancer and Neurodegeneration. Int J Mol Sci 2022; 23:ijms23168921. [PMID: 36012187 PMCID: PMC9408729 DOI: 10.3390/ijms23168921] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
The low-density-lipoprotein receptors represent a family of pleiotropic cell surface receptors involved in lipid homeostasis, cell migration, proliferation and differentiation. The family shares common structural features but also has significant differences mainly due to tissue-specific interactors and to peculiar proteolytic processing. Among the receptors in the family, recent studies place low-density lipoprotein receptor-related protein 8 (LRP8) at the center of both neurodegenerative and cancer-related pathways. From one side, its overexpression has been highlighted in many types of cancer including breast, gastric, prostate, lung and melanoma; from the other side, LRP8 has a potential role in neurodegeneration as apolipoprotein E (ApoE) and reelin receptor, which are, respectively, the major risk factor for developing Alzheimer’s disease (AD) and the main driver of neuronal migration, and as a γ-secretase substrate, the main enzyme responsible for amyloid formation in AD. The present review analyzes the contributions of LDL receptors, specifically of LRP8, in both cancer and neurodegeneration, pointing out that depending on various interactions and peculiar processing, the receptor can contribute to both proliferative and neurodegenerative processes.
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Affiliation(s)
- Daniela Passarella
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy
| | - Silvia Ciampi
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy
| | - Valentina Di Liberto
- Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, 90133 Palermo, Italy
| | - Mariachiara Zuccarini
- Department of Medical Oral and Biotechnological Sciences, University of Chieti-Pescara, 66100 Chieti, Italy
| | - Maurizio Ronci
- Department of Pharmacy, University of Chieti-Pescara, 66100 Chieti, Italy
| | - Alessandro Medoro
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy
| | - Emanuele Foderà
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy
| | - Monica Frinchi
- Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, 90133 Palermo, Italy
| | - Donatella Mignogna
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy
| | - Claudio Russo
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy
- Correspondence: ; Tel.: +39-0874404897
| | - Carola Porcile
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy
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Miao Z, Haider MS, Nazar M, Mansoor MK, Zhang H, Tang Z, Li Y. Potential molecular mechanism of ascites syndrome in broilers. WORLD POULTRY SCI J 2022. [DOI: 10.1080/00439339.2022.2075299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Zhenyan Miao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, GD, China
| | | | - Mudassar Nazar
- Veterinary Sciences, University of Agriculture Faisalabad, Sub-Campus Burewala, Burewala, Pakistan
| | - Muhammad Khalid Mansoor
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Hui Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, GD, China
| | - Zhaoxin Tang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, GD, China
| | - Ying Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, GD, China
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Shi L, Cao J, Lei X, Shi Y, Wu L. Multi-omics data identified TP53 and LRP1B as key regulatory gene related to immune phenotypes via EPCAM in HCC. Cancer Med 2022; 11:2145-2158. [PMID: 35150083 PMCID: PMC9119357 DOI: 10.1002/cam4.4594] [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: 03/19/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 12/16/2022] Open
Abstract
Background Many studies showed that the prognosis of hepatocellular carcinoma (HCC) was significantly associated with the expressions of TP53 and LRP1B. However, the potential influence of the two genes on the malignant progression of HCC is still to be expounded. Methods According to the correlation analysis between immune cells and expression levels of TP53 and LRP1B, we filtered the immune cells to perform unsupervised clustering analysis. Integration of multi‐omic data analysis identified genetic alteration and epigenetic alteration. In addition, pathway analysis was used to explore the potential function of the differentially expressed mRNAs. According to the differentially expressed genes, we established an interaction network to seek the hub gene. Least absolute shrinkage and selection operator (LASSO) regression analysis was used to build a prognosis model. Results The unsupervised clustering analysis showed that the cluster A1 showed the highest immune cell levels and the cluster B2 showed the lowest immune cell levels. Multi‐omics data analysis identified that somatic mutations, copy number variations, and DNA methylation levels had significant differences between cluster A1 and cluster B2. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that the upregulated mRNAs in the cluster A1 were mainly concentrated in T cell activation, external side of plasma membrane, receptor ligand activity, and cytokine−cytokine receptor interaction. Importantly, the EPCAM was identified as a critical node in the lncRNAs–miRNAs–mRNAs regulatory network correlated with the immune phenotypes. In addition, based on differentially expressed genes between cluster A1 and cluster B2, the prognostic model established by LASSO could predict the overall survival (OS) of HCC accurately. Conclusions The results indicated that the TP53 and LRP1B acted as the key genes in regulating the immune phenotypes of HCC via EPCAM.
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Affiliation(s)
- Liang Shi
- Department of Clinical Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.,Translational Medicine Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jie Cao
- Translational Medicine Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xin Lei
- Translational Medicine Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yifen Shi
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lili Wu
- Department of Clinical Blood Transfusion, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.,Department of Clinical Laboratory, The Central Hospital of Wenzhou, Wenzhou, China
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8
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LRP1B Expression Is Correlated With Age and Perineural Invasion in Metastatic Cutaneous Squamous Cell Carcinoma: A Pilot Study. Am J Dermatopathol 2022; 44:49-53. [PMID: 34889813 DOI: 10.1097/dad.0000000000002065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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9
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Dionísio de Sousa IJ, Cunha AI, Saraiva IA, Portugal RV, Gimba ERP, Guimarães M, Prazeres H, Lopes JM, Soares P, Lima RT. LRP1B Expression as a Putative Predictor of Response to Pegylated Liposomal Doxorubicin Treatment in Ovarian Cancer. Pathobiology 2021; 88:400-411. [PMID: 34689147 DOI: 10.1159/000517372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/11/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Pegylated liposomal doxorubicin (PLD) is among the most active therapies for recurrent/progressive ovarian cancer (OC). Low-density lipoprotein receptor-related protein 1B (LRP1B) is one of the 10 most significantly deleted genes in human cancers. It mediates endocytosis of several factors from the cellular environment including liposomes. Although the LRP1B role in cancer has not been fully disclosed, its contribution to resistance to liposomal therapies has been hypothesized. This study aimed to evaluate the impact of LRP1B protein as a possible marker of response to PLD in patients with OC. METHODS LRP1B expression and response to PLD were analyzed in OC cell lines by qRT-PCR and PrestoBlue viability assay, respectively. LRP1B protein expression was evaluated for the first time, in tumor samples from PLD-treated patients and controls (other chemotherapies) by immunohistochemistry. Association of LRP1B staining score (determined based on intensity and percentage of positively stained cells) with clinicopathological features, response to therapy and survival outcomes was evaluated. RESULTS OC cells with increased expression of LRP1B were more sensitive to PLD. LRP1B staining score was associated with clinicopathological features, response to therapy, and survival outcomes. Higher LRP1B levels were associated with prolonged progression-free survival. This association was more evident in patients treated with PLD and in responders to PLD. CONCLUSION Our results support a possible role of LRP1B as a predictor of response to PLD in patients with OC.
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Affiliation(s)
- Isabel J Dionísio de Sousa
- Department of Oncology, Centro Hospitalar Universitário de São João, Porto, Portugal.,Faculty of Medicine, University of Porto, Porto, Portugal
| | - Ana Isabel Cunha
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Cancer Signaling and Metabolism Group, IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Inês A Saraiva
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Cancer Signaling and Metabolism Group, IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,Nova University of Lisbon, Lisboa, Portugal
| | - Raquel V Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal.,Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Etel R P Gimba
- Natural Science Department, Health and Humanities Institute, Fluminense Federal University, Rio das Ostras, Brazil.,Cellular and Molecular Oncobiology Program, Research Coordination, National Institute of Cancer, Rio de Janeiro, Brazil
| | - Marcos Guimarães
- IPO-Coimbra, Portuguese Oncology Institute of Coimbra, Coimbra, Portugal
| | - Hugo Prazeres
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Cancer Signaling and Metabolism Group, IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,IPO-Coimbra, Portuguese Oncology Institute of Coimbra, Coimbra, Portugal
| | - José M Lopes
- Faculty of Medicine, University of Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Cancer Signaling and Metabolism Group, IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Paula Soares
- Faculty of Medicine, University of Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Cancer Signaling and Metabolism Group, IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Raquel T Lima
- Faculty of Medicine, University of Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Cancer Signaling and Metabolism Group, IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
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10
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Bim LV, Carneiro TNR, Buzatto VC, Colozza-Gama GA, Koyama FC, Thomaz DMD, de Jesus Paniza AC, Lee EA, Galante PAF, Cerutti JM. Molecular Signature Expands the Landscape of Driver Negative Thyroid Cancers. Cancers (Basel) 2021; 13:5184. [PMID: 34680332 PMCID: PMC8534197 DOI: 10.3390/cancers13205184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/12/2021] [Indexed: 12/04/2022] Open
Abstract
Thyroid cancer is the most common endocrine malignancy. However, the cytological diagnosis of follicular thyroid carcinoma (FTC), Hürthle cell carcinoma (HCC), and follicular variant of papillary thyroid carcinoma (FVPTC) and their benign counterparts is a challenge for preoperative diagnosis. Nearly 20-30% of biopsied thyroid nodules are classified as having indeterminate risk of malignancy and incur costs to the health care system. Based on that, 120 patients were screened for the main driver mutations previously described in thyroid cancer. Subsequently, 14 mutation-negative cases that are the main source of diagnostic errors (FTC, HCC, or FVPTC) underwent RNA-Sequencing analysis. Somatic variants in candidate driver genes (ECD, NUP98,LRP1B, NCOR1, ATM, SOS1, and SPOP) and fusions were described. NCOR1 and SPOP variants underwent validation. Moreover, expression profiling of driver-negative samples was compared to 16 BRAF V600E, RAS, or PAX8-PPARg positive samples. Negative samples were separated in two clusters, following the expression pattern of the RAS/PAX8-PPARg or BRAF V600E positive samples. Both negative groups showed distinct BRS, ERK, and TDS scores, tumor mutation burden, signaling pathways and immune cell profile. Altogether, here we report novel gene variants and describe cancer-related pathways that might impact preoperative diagnosis and provide insights into thyroid tumor biology.
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Affiliation(s)
- Larissa Valdemarin Bim
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 Andar, São Paulo 04039-032, SP, Brazil; (L.V.B.); (T.N.R.C.); (G.A.C.-G.); (D.M.D.T.); (A.C.d.J.P.)
| | - Thaise Nayane Ribeiro Carneiro
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 Andar, São Paulo 04039-032, SP, Brazil; (L.V.B.); (T.N.R.C.); (G.A.C.-G.); (D.M.D.T.); (A.C.d.J.P.)
| | - Vanessa Candiotti Buzatto
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, Rua Professor Daher Cutait 69, Bela Vista, São Paulo 01308-060, SP, Brazil; (V.C.B.); (F.C.K.); (P.A.F.G.)
| | - Gabriel Avelar Colozza-Gama
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 Andar, São Paulo 04039-032, SP, Brazil; (L.V.B.); (T.N.R.C.); (G.A.C.-G.); (D.M.D.T.); (A.C.d.J.P.)
| | - Fernanda C. Koyama
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, Rua Professor Daher Cutait 69, Bela Vista, São Paulo 01308-060, SP, Brazil; (V.C.B.); (F.C.K.); (P.A.F.G.)
| | - Debora Mota Dias Thomaz
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 Andar, São Paulo 04039-032, SP, Brazil; (L.V.B.); (T.N.R.C.); (G.A.C.-G.); (D.M.D.T.); (A.C.d.J.P.)
| | - Ana Carolina de Jesus Paniza
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 Andar, São Paulo 04039-032, SP, Brazil; (L.V.B.); (T.N.R.C.); (G.A.C.-G.); (D.M.D.T.); (A.C.d.J.P.)
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children’s Hospital and Harvard Medical School, 3 Blackfan Circle, Boston, MA 02115, USA;
| | - Pedro Alexandre Favoretto Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, Rua Professor Daher Cutait 69, Bela Vista, São Paulo 01308-060, SP, Brazil; (V.C.B.); (F.C.K.); (P.A.F.G.)
| | - Janete Maria Cerutti
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Pedro de Toledo 669, 11 Andar, São Paulo 04039-032, SP, Brazil; (L.V.B.); (T.N.R.C.); (G.A.C.-G.); (D.M.D.T.); (A.C.d.J.P.)
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11
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Han R, Chen G, Li M, Peng ZM, Xu L. Screening and clinical significance of lymph node metastasis-related genes within esophagogastric junction adenocarcinoma. Cancer Med 2021; 10:5088-5100. [PMID: 34152098 PMCID: PMC8335809 DOI: 10.1002/cam4.4065] [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: 03/01/2021] [Revised: 05/22/2021] [Accepted: 05/29/2021] [Indexed: 01/11/2023] Open
Abstract
Background Despite recent improvements in treatment technologies, such as surgical resection and chemoradiotherapy, the prognosis of patients with esophagogastric junction adenocarcinoma (EJA) remains poor due to early lymph node metastasis. Since few studies have investigated genes associated with lymph node metastasis in EJA, we aimed to screen lymph node metastasis‐associated genes and clarify their expression status and prognostic significance in EJA. Methods The differential frequency of mutations between carcinoma and para‐carcinoma tissues from 199 cases with EJA was detected using targeted next‐generation sequencing (tNGS). Following a stratified analysis to determine that gender has no effect on the frequency of gene mutations, lymph node metastasis‐related genes, including CDK6, MET, NOTCH1, and LRP1B, were screened, and CDK6 and LRP1B were selected for further study as they displayed significant differences in mutation rates. Differences in their expression status were verified using immunohistochemical (IHC) staining in 18 CDK6‐ and 17 LRP1B‐mutated samples and a randomly matched control group. Results tNGS revealed that CDK6 and LRP1B mutation frequencies were significantly different between EJA cases with (N ≥ 1) or without (N = 0) lymph node metastasis. In particular, CDK6 mutation frequency was expected less, whereas that of LRP1B was remarkably higher in cases with stage N0 than in those with stage N ≥ 1. IHC staining confirmed significant differences in CDK6 and LRP1B expression status between the study and control cohorts. Chi‐square tests revealed that a high CDK6 expression status correlated significantly with smoking history (p = 0.044), T stage (p = 0.035), N stage (p = 0.000), and advanced TNM stage (p = 0.001) in EJA, whereas a high LRP1B expression status only correlated with BMI (p = 0.013) and N stage (p = 0.000). Furthermore, as confirmed by survival status investigation, a high LRP1B expression status predicted good prognosis, and a high CDK6 expression status was an independent predictor of poor prognosis in patients with EJA. Conclusions Taken together, the findings of this study demonstrate that a high CDK6 and LRP1B expression status promotes and inhibits lymph node metastasis in patients with EJA, respectively, suggesting that both CDK6 and LRP1B are significantly potential predictors of lymph node metastasis and prognosis in EJA.
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Affiliation(s)
- Rui Han
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Shandong Province, P. R. China
| | - Gang Chen
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Shandong Province, P. R. China
| | - Meng Li
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Shandong Province, P. R. China
| | - Zhong-Min Peng
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Shandong Province, P. R. China
| | - Lin Xu
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Shandong Province, P. R. China
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12
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Inhibition of CXCR2 plays a pivotal role in re-sensitizing ovarian cancer to cisplatin treatment. Aging (Albany NY) 2021; 13:13405-13420. [PMID: 34038868 PMCID: PMC8202899 DOI: 10.18632/aging.203074] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/21/2021] [Indexed: 12/12/2022]
Abstract
cDNA microarray data conducted by our group revealed overexpression of CXCL2 and CXCL8 in ovarian cancer (OC) microenvironment. Herein, we have proven that the chemokine receptor, CXCR2, is a pivotal molecule in re-sensitizing OC to cisplatin, and its inhibition decreases cell proliferation, viability, tumor size in cisplatin-resistant cells, as well as reversed the overexpression of mesenchymal epithelium transition markers. Altogether, our study indicates a central effect of CXCR2 in preventing tumor progression, due to acquisition of cisplatin chemoresistant phenotype by tumor cells, and patients' high lethality rate. We found that the overexpression of CXCR2 by OC cells is persistent and anomalously confined to the cellular nuclei, thus pointing to an urge in developing highly lipophilic molecules that promptly permeate cells, bind to and inhibit nuclear CXCR2 to fight OC, instead of relying on the high-cost genetic engineered cells.
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13
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Giroux Leprieur E, Hélias-Rodzewicz Z, Takam Kamga P, Costantini A, Julie C, Corjon A, Dumenil C, Dumoulin J, Giraud V, Labrune S, Garinet S, Chinet T, Emile JF. Sequential ctDNA whole-exome sequencing in advanced lung adenocarcinoma with initial durable tumor response on immune checkpoint inhibitor and late progression. J Immunother Cancer 2021; 8:jitc-2020-000527. [PMID: 32581058 PMCID: PMC7319709 DOI: 10.1136/jitc-2020-000527] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Despite prolonged tumor response to immune checkpoint inhibitors (ICIs) for a subset of patients with advanced non-small cell lung cancer (NSCLC), a secondary resistance will occur for a majority of these patients. The understanding of late progression mechanisms with ICIs is important to improve future treatment strategies. METHODS We performed whole-exome sequencing (WES) on circulating tumor DNA and compared molecular profiles between the beginning of ICI treatment and tumor progression in patients with advanced NSCLC treated with ICIs and who had initial and prolonged tumor response with secondary progression, after at least 6 months of treatment. RESULTS We identified eight patients who experienced initial and durable tumor response, and secondary tumor progression after 6 months of treatment, with available paired blood samples (diagnosis and progression). All had lung adenocarcinoma, three had programmed-death ligand-1 expression ≥50% in immunohistochemistry and all presented low blood tumor mutational burden (bTMB). Seven patients received nivolumab in second-line or more, and one received pembrolizumab as first-line treatment. WES at progression showed clonal selection with molecular alterations of Wnt pathway-related genes, increase of copy number aberrations in cancer-related genes and loss of tumor-suppressor genes (such as PTEN) or of genes associated with immune response (such as B2M). No difference in term of bTMB was observed at progression. CONCLUSIONS This is the first study describing putative molecular mechanisms associated with late progression under ICI in lung cancer. Studies on treatment strategies adapted to these mechanisms are needed.
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Affiliation(s)
- Etienne Giroux Leprieur
- Université Paris-Saclay, UVSQ, EA 4340 BECCOH, Boulogne-Billancourt, France .,Department of Respiratory DIseases and Thoracic Oncology, APHP - Hopital Ambroise Pare, Boulogne-Billancourt, France
| | - Zofia Hélias-Rodzewicz
- Université Paris-Saclay, UVSQ, EA 4340 BECCOH, Boulogne-Billancourt, France.,Department of Pathology, APHP - Hopital Ambroise Pare, Boulogne-Billancourt, France
| | - Paul Takam Kamga
- Université Paris-Saclay, UVSQ, EA 4340 BECCOH, Boulogne-Billancourt, France
| | - Adrien Costantini
- Université Paris-Saclay, UVSQ, EA 4340 BECCOH, Boulogne-Billancourt, France.,Department of Respiratory DIseases and Thoracic Oncology, APHP - Hopital Ambroise Pare, Boulogne-Billancourt, France
| | - Catherine Julie
- Université Paris-Saclay, UVSQ, EA 4340 BECCOH, Boulogne-Billancourt, France.,Department of Pathology, APHP - Hopital Ambroise Pare, Boulogne-Billancourt, France
| | - Alexandre Corjon
- Université Paris-Saclay, UVSQ, EA 4340 BECCOH, Boulogne-Billancourt, France.,Department of Pathology, APHP - Hopital Ambroise Pare, Boulogne-Billancourt, France
| | - Coraline Dumenil
- Department of Respiratory DIseases and Thoracic Oncology, APHP - Hopital Ambroise Pare, Boulogne-Billancourt, France
| | - Jennifer Dumoulin
- Department of Respiratory DIseases and Thoracic Oncology, APHP - Hopital Ambroise Pare, Boulogne-Billancourt, France
| | - Violaine Giraud
- Department of Respiratory DIseases and Thoracic Oncology, APHP - Hopital Ambroise Pare, Boulogne-Billancourt, France
| | - Sylvie Labrune
- Department of Respiratory DIseases and Thoracic Oncology, APHP - Hopital Ambroise Pare, Boulogne-Billancourt, France
| | - Simon Garinet
- Department of Molecular Biology, APHP - Hopital Europeen Georges Pompidou, Paris, France
| | - Thierry Chinet
- Université Paris-Saclay, UVSQ, EA 4340 BECCOH, Boulogne-Billancourt, France.,Department of Respiratory DIseases and Thoracic Oncology, APHP - Hopital Ambroise Pare, Boulogne-Billancourt, France
| | - Jean-François Emile
- Université Paris-Saclay, UVSQ, EA 4340 BECCOH, Boulogne-Billancourt, France.,Department of Pathology, APHP - Hopital Ambroise Pare, Boulogne-Billancourt, France
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14
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Brown LC, Tucker MD, Sedhom R, Schwartz EB, Zhu J, Kao C, Labriola MK, Gupta RT, Marin D, Wu Y, Gupta S, Zhang T, Harrison MR, George DJ, Alva A, Antonarakis ES, Armstrong AJ. LRP1B mutations are associated with favorable outcomes to immune checkpoint inhibitors across multiple cancer types. J Immunother Cancer 2021; 9:e001792. [PMID: 33653800 PMCID: PMC7929846 DOI: 10.1136/jitc-2020-001792] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Low-density lipoprotein receptor-related protein 1b (encoded by LRP1B) is a putative tumor suppressor, and preliminary evidence suggests LRP1B-mutated cancers may have improved outcomes with immune checkpoint inhibitors (ICI). METHODS We conducted a multicenter, retrospective pan-cancer analysis of patients with LRP1B alterations treated with ICI at Duke University, Johns Hopkins University (JHU) and University of Michigan (UM). The primary objective was to assess the association between overall response rate (ORR) to ICI and pathogenic or likely pathogenic (P/LP) LRP1B alterations compared with LRP1B variants of unknown significance (VUS). Secondary outcomes were the associations with progression-free survival (PFS) and overall survival (OS) by LRP1B status. RESULTS We identified 101 patients (44 Duke, 35 JHU, 22 UM) with LRP1B alterations who were treated with ICI. The most common tumor types by alteration (P/LP vs VUS%) were lung (36% vs 49%), prostate (9% vs 7%), sarcoma (5% vs 7%), melanoma (9% vs 0%) and breast cancer (3% vs 7%). The ORR for patients with LRP1B P/LP versus VUS alterations was 54% and 13%, respectively (OR 7.5, 95% CI 2.9 to 22.3, p=0.0009). P/LP LRP1B alterations were associated with longer PFS (HR 0.42, 95% CI 0.26 to 0.68, p=0.0003) and OS (HR 0.62, 95% CI 0.39 to 1.01, p=0.053). These results remained consistent when excluding patients harboring microsatellite instability (MSI) and controlling for tumor mutational burden (TMB). CONCLUSIONS This multicenter study shows significantly better outcomes with ICI therapy in patients harboring P/LP versus VUS LRP1B alterations, independently of TMB/MSI status. Further mechanistic and prospective validation studies are warranted.
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Affiliation(s)
- Landon C Brown
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Matthew D Tucker
- Internal Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ramy Sedhom
- Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Eric B Schwartz
- Division of Hematology Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason Zhu
- Levine Cancer Institute, Charlotte, North Carolina, USA
| | - Chester Kao
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Matthew K Labriola
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Rajan T Gupta
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Daniele Marin
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Yuan Wu
- Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, USA
| | - Santosh Gupta
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Tian Zhang
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Michael R Harrison
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Daniel J George
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
| | - Ajjai Alva
- Division of Hematology Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Emmanuel S Antonarakis
- Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Andrew J Armstrong
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, North Carolina, USA
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15
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The Chick Chorioallantoic Membrane Model: A New In Vivo Tool to Evaluate Breast Cancer Stem Cell Activity. Int J Mol Sci 2020; 22:ijms22010334. [PMID: 33396951 PMCID: PMC7795925 DOI: 10.3390/ijms22010334] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/23/2020] [Accepted: 12/25/2020] [Indexed: 12/20/2022] Open
Abstract
The high plasticity of cancer stem-like cells (CSCs) allows them to differentiate and proliferate, specifically when xenotransplanted subcutaneously into immunocompromised mice. CSCs are highly tumorigenic, even when inoculated in small numbers. Thus, in vivo limiting dilution assays (LDA) in mice are the current gold standard method to evaluate CSC enrichment and activity. The chick embryo chorioallantoic membrane (CAM) is a low cost, naturally immune-incompetent and reproducible model widely used to evaluate the spontaneous growth of human tumor cells. Here, we established a CAM-LDA assay able to rapidly reproduce tumor specificities—in particular, the ability of the small population of CSCs to form tumors. We used a panel of organotropic metastatic breast cancer cells, which show an enrichment in a stem cell gene signature, enhanced CD44+/CD24−/low cell surface expression and increased mammosphere-forming efficiency (MFE). The size of CAM-xenografted tumors correlate with the number of inoculated cancer cells, following mice xenograft growth pattern. CAM and mice tumors are histologically comparable, displaying both breast CSC markers CD44 and CD49f. Therefore, we propose a new tool for studying CSC prevalence and function—the chick CAM-LDA—a model with easy handling, accessibility, rapid growth and the absence of ethical and regulatory constraints.
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16
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Li M, Hu J, Jin R, Cheng H, Chen H, Li L, Guo K. Effects of LRP1B Regulated by HSF1 on Lipid Metabolism in Hepatocellular Carcinoma. J Hepatocell Carcinoma 2020; 7:361-376. [PMID: 33324588 PMCID: PMC7733418 DOI: 10.2147/jhc.s279123] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/18/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND To date, aberrated lipid metabolism has been recognized as an important feature of hepatocellular carcinoma (HCC); however, it remains poorly defined. As a large member of the low-density lipoprotein receptor family, LRP1B plays a pivotal role in maintaining lipid homeostasis. Here we investigated the expression feature of LRP1B in HCC and elucidated its effects on lipid metabolism of HCC cells. MATERIALS AND METHODS LRP1B expression in HCC cells and tumor tissues was respectively examined by quantitative PCR, Western blotting and immunohistochemistry. Crispr-cas9 RNA inference and CRISPRa transcription activation system were used to downregulate and upregulate LRP1B expression, respectively. Oil red O staining, DiD staining combined with flow cytometry and transmission electron microscopy were used to evaluate the lipid content in HCC cells. Overall survival (OS) and time to recurrence (TTR) were calculated; meanwhile, Kaplan-Meier and the Cox proportional hazards model were used to assess the prognosis of HCC patients. RESULTS In contrast to inactivation expression in a majority of cancers, LRP1B showed predominantly strong expression in HCC. LRP1B knockdown induced the decrease of intracellular lipid content, downregulated expressions of lipid synthesis-related enzymes and upregulated expressions of β-oxidation-related enzymes as well as activated the AMPK signaling. Moreover, HSF1 directly regulated the transcription of LRP1B and was involved in LRP1B-mediated lipid metabolism in HCC; meanwhile, the combination of LRP1B knockdown and HSF1 inhibition suppressed synergistically the proliferation of HCC cells. In addition, simultaneous expression of HSF1 and LRP1B was an independent prognostic factor for HCC patients. CONCLUSION Altogether, the study reveals a novel unique role of LRP1B in HCC by serving as a mediator in lipid metabolism, which provides an insight for making explorable therapeutic strategies for HCC.
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Affiliation(s)
- Miaomiao Li
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, People’s Republic of China
| | - Juntao Hu
- Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, People’s Republic of China
| | - Riming Jin
- Department of First Surgery, the Third Affiliated Hospital, NAVY Medical University, Shanghai, People’s Republic of China
| | - Hongxia Cheng
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, People’s Republic of China
| | - Huaping Chen
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Limin Li
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Kun Guo
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, People’s Republic of China
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17
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Revilla G, Cedó L, Tondo M, Moral A, Pérez JI, Corcoy R, Lerma E, Fuste V, Reddy ST, Blanco-Vaca F, Mato E, Escolà-Gil JC. LDL, HDL and endocrine-related cancer: From pathogenic mechanisms to therapies. Semin Cancer Biol 2020; 73:134-157. [PMID: 33249202 DOI: 10.1016/j.semcancer.2020.11.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/19/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023]
Abstract
Cholesterol is essential for a variety of functions in endocrine-related cells, including hormone and steroid production. We have reviewed the progress to date in research on the role of the main cholesterol-containing lipoproteins; low-density lipoprotein (LDL) and high-density lipoprotein (HDL), and their impact on intracellular cholesterol homeostasis and carcinogenic pathways in endocrine-related cancers. Neither LDL-cholesterol (LDL-C) nor HDL-cholesterol (HDL-C) was consistently associated with endocrine-related cancer risk. However, preclinical studies showed that LDL receptor plays a critical role in endocrine-related tumor cells, mainly by enhancing circulating LDL-C uptake and modulating tumorigenic signaling pathways. Although scavenger receptor type BI-mediated uptake of HDL could enhance cell proliferation in breast, prostate, and ovarian cancer, these effects may be counteracted by the antioxidant and anti-inflammatory properties of HDL. Moreover, 27-hydroxycholesterol a metabolite of cholesterol promotes tumorigenic processes in breast and epithelial thyroid cancer. Furthermore, statins have been reported to reduce the incidence of breast, prostate, pancreatic, and ovarian cancer in large clinical trials, in part because of their ability to lower cholesterol synthesis. Overall, cholesterol homeostasis deregulation in endocrine-related cancers offers new therapeutic opportunities, but more mechanistic studies are needed to translate the preclinical findings into clinical therapies.
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Affiliation(s)
- Giovanna Revilla
- Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, Institut d'Investigacions Biomèdiques (IIB) Sant Pau, C/ Sant Quintí 77, 08041 Barcelona Spain; Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, C/ Antoni M. Claret 167, 08025 Barcelona, Spain
| | - Lídia Cedó
- Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, Institut d'Investigacions Biomèdiques (IIB) Sant Pau, C/ Sant Quintí 77, 08041 Barcelona Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), C/ Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Mireia Tondo
- Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, Institut d'Investigacions Biomèdiques (IIB) Sant Pau, C/ Sant Quintí 77, 08041 Barcelona Spain; Servei de Bioquímica, Hospital de la Santa Creu i Sant Pau, C/ Sant Quintí 89, 08041 Barcelona, Spain
| | - Antonio Moral
- Department of General Surgery, Hospital de la Santa Creu i Sant Pau, C/ Sant Quintí 89, 08041 Barcelona, Spain; Departament de Medicina, Universitat Autònoma de Barcelona, C/ Antoni M. Claret 167, 08025 Barcelona, Spain
| | - José Ignacio Pérez
- Department of General Surgery, Hospital de la Santa Creu i Sant Pau, C/ Sant Quintí 89, 08041 Barcelona, Spain
| | - Rosa Corcoy
- Departament de Medicina, Universitat Autònoma de Barcelona, C/ Antoni M. Claret 167, 08025 Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/ Monforte de Lemos 3-5, 28029 Madrid, Spain; Department of Endocrinology and Nutrition, Hospital de la Santa Creu i Sant Pau, C/ Sant Quintí 89, 08041 Barcelona, Spain
| | - Enrique Lerma
- Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, Institut d'Investigacions Biomèdiques (IIB) Sant Pau, C/ Sant Quintí 77, 08041 Barcelona Spain; Department of Anatomic Pathology, Hospital de la Santa Creu i Sant Pau, C/ Sant Quintí 89, 08041 Barcelona, Spain
| | - Victoria Fuste
- Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, Institut d'Investigacions Biomèdiques (IIB) Sant Pau, C/ Sant Quintí 77, 08041 Barcelona Spain; Department of Anatomic Pathology, Hospital de la Santa Creu i Sant Pau, C/ Sant Quintí 89, 08041 Barcelona, Spain
| | - Srivinasa T Reddy
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095-1736, USA
| | - Francisco Blanco-Vaca
- Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, Institut d'Investigacions Biomèdiques (IIB) Sant Pau, C/ Sant Quintí 77, 08041 Barcelona Spain; Servei de Bioquímica, Hospital de la Santa Creu i Sant Pau, C/ Sant Quintí 89, 08041 Barcelona, Spain.
| | - Eugènia Mato
- Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, Institut d'Investigacions Biomèdiques (IIB) Sant Pau, C/ Sant Quintí 77, 08041 Barcelona Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/ Monforte de Lemos 3-5, 28029 Madrid, Spain.
| | - Joan Carles Escolà-Gil
- Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau, Institut d'Investigacions Biomèdiques (IIB) Sant Pau, C/ Sant Quintí 77, 08041 Barcelona Spain.
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18
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Teng H, Wei W, Li Q, Xue M, Shi X, Li X, Mao F, Sun Z. Prevalence and architecture of posttranscriptionally impaired synonymous mutations in 8,320 genomes across 22 cancer types. Nucleic Acids Res 2020; 48:1192-1205. [PMID: 31950163 PMCID: PMC7026592 DOI: 10.1093/nar/gkaa019] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023] Open
Abstract
Somatic synonymous mutations are one of the most frequent genetic variants occurring in the coding region of cancer genomes, while their contributions to cancer development remain largely unknown. To assess whether synonymous mutations involved in post-transcriptional regulation contribute to the genetic etiology of cancers, we collected whole exome data from 8,320 patients across 22 cancer types. By employing our developed algorithm, PIVar, we identified a total of 22,948 posttranscriptionally impaired synonymous SNVs (pisSNVs) spanning 2,042 genes. In addition, 35 RNA binding proteins impacted by these identified pisSNVs were significantly enriched. Remarkably, we discovered markedly elevated ratio of somatic pisSNVs across all 22 cancer types, and a high pisSNV ratio was associated with worse patient survival in five cancer types. Intriguing, several well-established cancer genes, including PTEN, RB1 and PIK3CA, appeared to contribute to tumorigenesis at both protein function and posttranscriptional regulation levels, whereas some pisSNV-hosted genes, including UBR4, EP400 and INTS1, exerted their function during carcinogenesis mainly via posttranscriptional mechanisms. Moreover, we predicted three drugs associated with two pisSNVs, and numerous compounds associated with expression signature of pisSNV-hosted genes. Our study reveals the prevalence and clinical relevance of pisSNVs in cancers, and emphasizes the importance of considering posttranscriptional impaired synonymous mutations in cancer biology.
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Affiliation(s)
- Huajing Teng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Wenqing Wei
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinglan Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meiying Xue
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohui Shi
- Sino-Danish college, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianfeng Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Fengbiao Mao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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19
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Zheng H, Bai L. Hypoxia induced microRNA-301b-3p overexpression promotes proliferation, migration and invasion of prostate cancer cells by targeting LRP1B. Exp Mol Pathol 2019; 111:104301. [PMID: 31442444 DOI: 10.1016/j.yexmp.2019.104301] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/19/2019] [Accepted: 08/20/2019] [Indexed: 01/21/2023]
Abstract
Prostate cancer is a high burden on society worldwide due to its high morbidity and mortality. Growing evidence has implicated microRNAs (miRNAs or miRs) in the occurrence and progression of prostate cancer. The present study was conducted with main emphasis put on the possible effect of hypoxia-induced miR-301b-3p on prostate cancer by targeting low-density lipoprotein receptor-related protein 1B (LRP1B). Firstly, the differentially expressed genes were identified by conducting microarray-based gene expression profiling of prostate cancer. Next, the expression of miR-301b-3p in prostate cancer cells was examined in cells treated with 1% oxygen or dimethyloxalylglycine (DMOG), and the cell line with the highest miR-301b-3p expression was selected for subsequent experiments. Subsequently, the target relationship between miR-301b-3p and LRP1B was identified. The effect of miR-301b-3p and LRP1B on cell proliferation, migration and invasion as well as tumorigenicity of transfected cells was examined using the gain- and loss-of-function approaches. Hypoxia induced miR-301b-3p was highly expressed while LRP1B was poorly expressed in prostate cancer. Moreover, miR-301b-3p could down-regulate LRP1B by interacting with LRP1B, which acted to promote the proliferation, migration and invasion abilities of prostate cancer cells in addition to tumor growth in vivo. In addition, up-regulation of LRP1B can reverse the promoting effect of miR-301b-3p on the aforementioned factors. Collectively, up-regulation of miR-301b-3p induced by hypoxia could potentially accelerate proliferation, migration and invasion of prostate cancer cells via the inhibitory effect on LRP1B expression, highlighting that miR-301b-3p may be instrumental for the therapeutic targeting of prostate cancer.
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Affiliation(s)
- Haiying Zheng
- Department of Cardiovascular Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Huhhot 010050, PR China
| | - Ligang Bai
- Department of Urology Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Huhhot 010050, PR China.
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20
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Henriet P, Emonard H. Matrix metalloproteinase-2: Not (just) a "hero" of the past. Biochimie 2019; 166:223-232. [PMID: 31362036 DOI: 10.1016/j.biochi.2019.07.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 07/22/2019] [Indexed: 01/13/2023]
Abstract
The 72-kDa type IV collagenase or gelatinase A is the second member of the matrix metalloproteinase family, MMP-2. Since the discovery of its first two substrates within components of the extracellular matrix, denatured interstitial type I collagen and native type IV collagen, the roles and various levels of regulation of MMP-2 have been intensively studied, mainly in vitro. Its (over)expression in most if not all tumors was considered a hallmark of cancer aggressiveness and boosted investigations aiming at its inhibition. Unfortunately, the enthusiasm subsided like a soufflé after clinical trial failures, mostly because of insufficient knowledge of in vivo MMP-2 activities and detrimental side effects of broad-spectrum MMP inhibition. Nowadays, MMP-2 remains a major topic of interest in research, the second in the MMP family after MMP-9. This review presents a broad overview of the major features of this protease. This knowledge is crucial to identify diagnostic or therapeutic strategies focusing on MMP-2. In this sense, recent publications and clinical trials underline the potential value of measuring circulating or tissular MMP-2 levels as diagnostic or prognostic tools, or as a useful secondary outcome for therapies against other primary targets. Direct MMP-2 inhibition has benefited from substantial progress in the design of more specific inhibitors but their in vivo application remains challenging but certainly worth the efforts it receives.
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Affiliation(s)
- Patrick Henriet
- de Duve Institute, Université Catholique de Louvain, 1200, Brussels, Belgium
| | - Hervé Emonard
- CNRS and Université de Reims Champagne-Ardenne, UMR 7369, 51100, Reims, France.
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21
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Chen H, Chong W, Wu Q, Yao Y, Mao M, Wang X. Association of LRP1B Mutation With Tumor Mutation Burden and Outcomes in Melanoma and Non-small Cell Lung Cancer Patients Treated With Immune Check-Point Blockades. Front Immunol 2019; 10:1113. [PMID: 31164891 PMCID: PMC6536574 DOI: 10.3389/fimmu.2019.01113] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/01/2019] [Indexed: 01/04/2023] Open
Abstract
Background: Tumor mutation burden (TMB) have been served as the most prevalent biomarkers to predict immunotherapy response. LRP1B (low-density lipoprotein receptor-related protein 1B) is frequently mutated in melanoma, non-small cell lung cancer (NSCLC) and other tumors; however, its association with TMB and survival in patients with immunotherapy remains unknown. Methods: We curated somatic mutation data and clinicopathologic information from 332 melanoma immunotherapy samples for discovery and 113 NSCLC samples for further corroboration. Bayesian variants non-negative matrix factorization was used to extract tumor mutational signatures. Multivariate Cox and logistic regression models were applied to adjust confounding factors. The CIBERSORT and GSEA algorithm were separately used to infer leukocyte relative abundance and significantly enriched pathways. Results: Patients with LRP1B mutation were identified to be associated with prolonged survival in both immunotherapy cohort. Higher tumor mutation burden was found in LRP1B mutated patients, and the association remained significant after controlling for age, gender, stage, mutations in TP53 and ATR, and mutational signatures. Immune response and cell cycle regulation circuits were among the top enriched pathways in samples with LRP1B mutations. Conclusion: Our studies suggested sequencing even a single, frequently mutated gene may provide insight into genome-wide mutational burden, and may serve as a biomarker to predict immune response.
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Affiliation(s)
- Hao Chen
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China.,Key Laboratory of Cancer Prevention and Therapy of Tianjin, Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Wei Chong
- Key Laboratory of Cancer Prevention and Therapy, Department of Breast Cancer Pathology and Research Laboratory, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Qian Wu
- Department of Respiratory Medicine, Central Hospital of Zibo, Zibo, China
| | - Yueliang Yao
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Min Mao
- Key Laboratory of Tumor Immunopathology, Ministry of Education of China, Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xin Wang
- Department of Epidemiology and Biostatistics, First Affiliated Hospital, Army Medical University, Chongqing, China
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22
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miR-500 promotes cell proliferation by directly targetting LRP1B in prostate cancer. Biosci Rep 2019; 39:BSR20181854. [PMID: 30877185 PMCID: PMC6449515 DOI: 10.1042/bsr20181854] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/10/2019] [Accepted: 02/27/2019] [Indexed: 12/14/2022] Open
Abstract
Accumulating evidence suggests that miRNAs play a crucial role in the development of prostate cancer (PC); however, the role of miR-500 in PC remains poorly understood. The data presented here reveal abnormal increases in miR-500 expression in PC tissues and cell lines. Suppression of miR-500 expression significantly inhibited the proliferation of PC-3 and LnCap cells and was negatively regulative with low-density lipoprotein receptor-related protein 1B (LRP1B). Increased cell cycle arrest at the G1 stage and decreased protein expression of cyclinD1 and CDK2 was observed in response to miR-500 knockdown in PC-3 and LnCap cells, in combination with LRP1B overexpression. LRP1B was identified as a target of miR-500 and was significantly decreased in PC tissues. Taken together, these findings demonstrate that miR-500 plays an important role in the proliferation of PC cells via the inhibition of LRP1B expression.
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23
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The genetic and epigenetic association of LDL Receptor Related Protein 1B (LRP1B) gene with childhood obesity. Sci Rep 2019; 9:1815. [PMID: 30755693 PMCID: PMC6372679 DOI: 10.1038/s41598-019-38538-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 12/31/2018] [Indexed: 11/18/2022] Open
Abstract
Low-density lipoprotein Receptor Related Protein 1B (LRP1B) is homologous to the gigantic lipoprotein receptor-related protein 1 that belongs to the family of Low-density lipoprotein receptors. Previous genetic association studies of the LRP1B gene have shown its genetic association with obesity. Through exome sequencing of the LRP1B gene from a childhood severe obesity cohort (n = 692), we found novel single nucleotide polymorphism (rs431809) in intron 4, which has been significantly correlated with both body mass index (BMI) and waist-hip-ratio (WHR). Three methylations of CpG sites (cg141441481, cg01852095 and cg141441470) in the same intron were also significantly correlated with BMI and WHR. All CpG methylations had bimodal patterns, and were dependent on rs431809 genotypes. The genetic influences of obesity on the LRP1B gene may be linked to the interplay of CpG methylations in the same intron. Heritability of SNP interacts with epigenetic crosstalk in LRP1B. Genetic and epigenetic crosstalk of LRP1B gene may be implicated in the prevention and therapeutic approach to childhood obesity.
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24
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Vikova V, Jourdan M, Robert N, Requirand G, Boireau S, Bruyer A, Vincent L, Cartron G, Klein B, Elemento O, Kassambara A, Moreaux J. Comprehensive characterization of the mutational landscape in multiple myeloma cell lines reveals potential drivers and pathways associated with tumor progression and drug resistance. Theranostics 2019; 9:540-553. [PMID: 30809292 PMCID: PMC6376179 DOI: 10.7150/thno.28374] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 12/12/2018] [Indexed: 12/30/2022] Open
Abstract
Human multiple myeloma tumor cell lines (HMCLs) have been a cornerstone of research in multiple myeloma (MM) and have helped to shape our understanding of molecular processes that drive tumor progression. A comprehensive characterization of genomic mutations in HMCLs will provide a basis for choosing relevant cell line models to study a particular aspect of myeloma biology, or to screen for an antagonist of certain cancer pathways. Methods: We performed whole exome sequencing on a large cohort of 30 HMCLs, representative of a large molecular heterogeneity of MM, and 8 control samples (epstein-barr virus (EBV)-immortalized B-cells obtained from 8 different patients). We evaluated the sensitivity of HMCLs to ten drugs. Results: We identified a high confidence list of 236 protein-coding genes with mutations affecting the structure of the encoded protein. Among the most frequently mutated genes, there were known MM drivers, such as TP53, KRAS, NRAS, ATM and FAM46C, as well as novel mutated genes, including CNOT3, KMT2D, MSH3 and PMS1. We next generated a comprehensive map of altered key pathways in HMCLs. These include cell growth pathways (MAPK, JAK-STAT, PI(3)K-AKT and TP53 / cell cycle pathway), DNA repair pathway and chromatin modifiers. Importantly, our analysis highlighted a significant association between the mutation of several genes and the response to conventional drugs used in MM as well as targeted inhibitors. Conclusion: Taken together, this first comprehensive exome-wide analysis of the mutational landscape in HMCLs provides unique resources for further studies and identifies novel genes potentially associated with MM pathophysiology, some of which may be targets for future therapeutic intervention.
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Affiliation(s)
| | | | - Nicolas Robert
- CHU Montpellier, Department of Biological Hematology, Montpellier, France
| | - Guilhem Requirand
- CHU Montpellier, Department of Biological Hematology, Montpellier, France
| | - Stéphanie Boireau
- CHU Montpellier, Department of Biological Hematology, Montpellier, France
| | | | - Laure Vincent
- CHU Montpellier, Department of Clinical Hematology, Montpellier, France
| | - Guillaume Cartron
- Univ Montpellier, UFR de Médecine, Montpellier, France
- CHU Montpellier, Department of Clinical Hematology, Montpellier, France
- Univ Montpellier, UMR CNRS 5235, Montpellier, France
| | - Bernard Klein
- IGH, CNRS, Univ Montpellier, France
- CHU Montpellier, Department of Biological Hematology, Montpellier, France
- Univ Montpellier, UFR de Médecine, Montpellier, France
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY 10021, USA
| | - Alboukadel Kassambara
- IGH, CNRS, Univ Montpellier, France
- CHU Montpellier, Department of Biological Hematology, Montpellier, France
| | - Jérôme Moreaux
- IGH, CNRS, Univ Montpellier, France
- CHU Montpellier, Department of Biological Hematology, Montpellier, France
- Univ Montpellier, UFR de Médecine, Montpellier, France
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25
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Li B, Liu C, Cheng G, Peng M, Qin X, Liu Y, Li Y, Qin D. LRP1B Polymorphisms Are Associated with Multiple Myeloma Risk in a Chinese Han Population. J Cancer 2019; 10:577-582. [PMID: 30719154 PMCID: PMC6360415 DOI: 10.7150/jca.28905] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 12/08/2018] [Indexed: 12/25/2022] Open
Abstract
Multiple myeloma (MM) is an extremely complex plasma cell malignancy that is genetically heterogeneous. A recent Genome-wide association study (GWAS) indicated that variation at 2q22 (rs61070260) influences MM risk. This association has not been validated to date in a Chinese Han population. In this study, we evaluated the association between rs61070260 in LRP1B and MM risk in a Chinese Han population involving 739 MM patients and 592 healthy controls. Our results indicated that rs61070260 in LRP1B was significantly associated with MM susceptibility (P=3.937×10-37). Furthermore, the linkage disequilibrium (LD) analysis of rs61070260 revealed an LD block encompassing exons 26, 27 and 28 of the LRP1B gene, and a subsequent sequencing analysis identified three SNPs (rs762074421, rs756168629, rs113600691) in exons 26 and 28 of LRP1B. For the SNP rs756168629 in exon 26, a missense mutation which results in a transition from arginine to histidine at position 1661 of the LRP1B protein, has not been found in Chinese populations according to the Chinese Millionome Database and Genome Aggregation Database (EAS), and this mutation was predicted to be deleterious or damaging by SIFT and PolyPhen. These findings firmly establish the role of LRP1B in contributing to MM susceptibility. In addition, the identification of a rare coding mutation (p.R1661H) in LRP1B detected in MM individuals was suggested to be harmful to the encoded protein, which was characterized as a candidate tumour suppressor; thus, LRP1B is likely to be a disease-associated gene that is implicated in the development and progression of MM.
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Affiliation(s)
- Bingjie Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou 450052, Henan , P.R. China
| | - Chenxi Liu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R.China
| | - Guixue Cheng
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, P.R.China
| | - Mengle Peng
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou 450052, Henan , P.R. China
| | - Xiaosong Qin
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, P.R.China
| | - Yong Liu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning, P.R.China
| | - Yongzhe Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, P.R.China
| | - Dongchun Qin
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou 450052, Henan , P.R. China
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Leung EY, Askarian-Amiri ME, Singleton DC, Ferraro-Peyret C, Joseph WR, Finlay GJ, Broom RJ, Kakadia PM, Bohlander SK, Marshall E, Baguley BC. Derivation of Breast Cancer Cell Lines Under Physiological (5%) Oxygen Concentrations. Front Oncol 2018; 8:425. [PMID: 30370249 PMCID: PMC6194255 DOI: 10.3389/fonc.2018.00425] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 09/11/2018] [Indexed: 11/13/2022] Open
Abstract
Background: Most human breast cancer cell lines currently in use were developed and are cultured under ambient (21%) oxygen conditions. While this is convenient in practical terms, higher ambient oxygen could increase oxygen radical production, potentially modulating signaling pathways. We have derived and grown a series of four human breast cancer cell lines under 5% oxygen, and have compared their properties to those of established breast cancer lines growing under ambient oxygen. Methods: Cell lines were characterized in terms of appearance, cellular DNA content, mutation spectrum, hormone receptor status, pathway utilization and drug sensitivity. Results: Three of the four lines (NZBR1, NZBR2, and NZBR4) were triple negative (ER-, PR-, HER2-), with NZBR1 also over-expressing EGFR. NZBR3 was HER2+ and ER+ and also over-expressed EGFR. Cell lines grown in 5% oxygen showed increased expression of the hypoxia-inducible factor 1 (HIF-1) target gene carbonic anhydrase 9 (CA9) and decreased levels of ROS. As determined by protein phosphorylation, NZBR1 showed low AKT pathway utilization while NZBR2 and NZBR4 showed low p70S6K and rpS6 pathway utilization. The lines were characterized for sensitivity to 7-hydroxytamoxifen, doxorubicin, paclitaxel, the PI3K inhibitor BEZ235 and the HER inhibitors lapatinib, afatinib, dacomitinib, and ARRY-380. In some cases they were compared to established breast cancer lines. Of particular note was the high sensitivity of NZBR3 to HER inhibitors. The spectrum of mutations in the NZBR lines was generally similar to that found in commonly used breast cancer cell lines but TP53 mutations were absent and mutations in EVI2B, LRP1B, and PMS2, which have not been reported in other breast cancer lines, were detected. The results suggest that the properties of cell lines developed under low oxygen conditions (5% O2) are similar to those of commonly used breast cancer cell lines. Although reduced ROS production and increased HIF-1 activity under 5% oxygen can potentially influence experimental outcomes, no difference in sensitivity to estrogen or doxorubicin was observed between cell lines cultured in 5 vs. 21% oxygen.
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Affiliation(s)
- Euphemia Y Leung
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Marjan E Askarian-Amiri
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Dean C Singleton
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Carole Ferraro-Peyret
- Univ Lyon, Claude Bernard University, Cancer Research Center of Lyon, INSERM 1052, CNRS5286, Faculty of Pharmacy, Lyon, France.,Hospices Civils de Lyon, Molecular Biology of Tumors, GHE Hospital, Bron, France
| | - Wayne R Joseph
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Graeme J Finlay
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Reuben J Broom
- Auckland City Hospital-Oncology, Grafton, Auckland, New Zealand
| | - Purvi M Kakadia
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Stefan K Bohlander
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Elaine Marshall
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Bruce C Baguley
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
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GABPA inhibits invasion/metastasis in papillary thyroid carcinoma by regulating DICER1 expression. Oncogene 2018; 38:965-979. [PMID: 30181547 DOI: 10.1038/s41388-018-0483-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 12/13/2022]
Abstract
The ETS family transcription factor GABPA is suggested as an oncogenic element, which is further supported by the recent reporting of it as the sole ETS member to activate the mutant TERT promoter in thyroid carcinomas (TC). However, it remains unclear how GABPA contributes to TC pathogenesis. The present study is designed to address this issue. TERT expression was significantly diminished in TERT promoter-mutated TC cells upon GABPA inhibition. Surprisingly, GABPA depletion led to robustly increased cellular invasion independently of TERT promoter mutations and TERT expression. DICER1, a component of the microRNA machinery, was identified as a downstream effector of GABPA. GABPA facilitated Dicer1 transcription while its depletion reduced Dicer1 expression. The mutation of the GABPA binding site in the DICER1 promoter led to diminished basal levels of DICER1 promoter activity and abolishment of GABPA-stimulated promoter activity as well. The forced DICER1 expression abrogated the invasiveness of GABPA-depleted TC cells. Consistently, the analyses of 93 patients with papillary thyroid carcinoma (PTC) revealed a positive correlation between GABPA and DICER1 expression. GABPA expression was negatively associated with TERT expression and promoter mutations, in contrast to published observations in cancer cell lines. Lower GABPA expression was associated with distant metastasis and shorter overall/disease-free survival in PTC patients. Similar results were obtained for PTC cases in the TCGA dataset. In addition, a positive correlation between GABPA and DICER1 expression was seen in multiple types of malignancies. Taken together, despite its stimulatory effect on the mutant TERT promoter and telomerase activation, GABPA may itself act as a tumor suppressor rather than an oncogenic factor to inhibit invasion/metastasis in TCs and be a useful predictor for patient outcomes.
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28
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Liposomal therapies in oncology: does one size fit all? Cancer Chemother Pharmacol 2018; 82:741-755. [DOI: 10.1007/s00280-018-3668-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/09/2018] [Indexed: 12/23/2022]
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Rhee JK, Kim TM. Population-based statistical inference for temporal sequence of somatic mutations in cancer genomes. BMC Med Genomics 2018; 11:29. [PMID: 29697365 PMCID: PMC5918460 DOI: 10.1186/s12920-018-0352-z] [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] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It is well recognized that accumulation of somatic mutations in cancer genomes plays a role in carcinogenesis; however, the temporal sequence and evolutionary relationship of somatic mutations remain largely unknown. METHODS In this study, we built a population-based statistical framework to infer the temporal sequence of acquisition of somatic mutations. Using the model, we analyzed the mutation profiles of 1954 tumor specimens across eight tumor types. RESULTS As a result, we identified tumor type-specific directed networks composed of 2-15 cancer-related genes (nodes) and their mutational orders (edges). The most common ancestors identified in pairwise comparison of somatic mutations were TP53 mutations in breast, head/neck, and lung cancers. The known relationship of KRAS to TP53 mutations in colorectal cancers was identified, as well as potential ancestors of TP53 mutation such as NOTCH1, EGFR, and PTEN mutations in head/neck, lung and endometrial cancers, respectively. We also identified apoptosis-related genes enriched with ancestor mutations in lung cancers and a relationship between APC hotspot mutations and TP53 mutations in colorectal cancers. CONCLUSION While evolutionary analysis of cancers has focused on clonal versus subclonal mutations identified in individual genomes, our analysis aims to further discriminate ancestor versus descendant mutations in population-scale mutation profiles that may help select cancer drivers with clinical relevance.
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Affiliation(s)
- Je-Keun Rhee
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea
| | - Tae-Min Kim
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea. .,Department of Medical Informatics, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea.
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Abstract
Despite availability of sequence site-specific information resulting from years of sequencing and sequence feature curation, there have been few efforts to integrate and annotate this information. In this study, we update the number of human N-linked glycosylation sequons (NLGs), and we investigate cancer-relatedness of glycosylation-impacting somatic nonsynonymous single-nucleotide variation (nsSNV) by mapping human NLGs to cancer variation data and reporting the expected loss or gain of glycosylation sequon. We find 75.8% of all human proteins have at least one NLG for a total of 59,341 unique NLGs (includes predicted and experimentally validated). Only 27.4% of all NLGs are experimentally validated sites on 4,412 glycoproteins. With respect to cancer, 8,895 somatic-only nsSNVs abolish NLGs in 5,204 proteins and 12,939 somatic-only nsSNVs create NLGs in 7,356 proteins in cancer samples. nsSNVs causing loss of 24 NLGs on 23 glycoproteins and nsSNVs creating 41 NLGs on 40 glycoproteins are identified in three or more cancers. Of all identified cancer somatic variants causing potential loss or gain of glycosylation, only 36 have previously known disease associations. Although this work is computational, it builds on existing genomics and glycobiology research to promote identification and rank potential cancer nsSNV biomarkers for experimental validation.
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31
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Identification of a gene expression signature associated with the metastasis suppressor function of NME1: prognostic value in human melanoma. J Transl Med 2018; 98:327-338. [PMID: 29058705 PMCID: PMC5839922 DOI: 10.1038/labinvest.2017.108] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 07/19/2017] [Accepted: 07/25/2017] [Indexed: 12/18/2022] Open
Abstract
Although NME1 is well known for its ability to suppress metastasis of melanoma, the molecular mechanisms underlying this activity are not completely understood. Herein, we utilized a bioinformatics approach to systematically identify genes whose expression is correlated with the metastasis suppressor function of NME1. This was accomplished through a search for genes that were regulated by NME1, but not by NME1 variants lacking metastasis suppressor activity. This approach identified a number of novel genes, such as ALDOC, CXCL11, LRP1b, and XAGE1 as well as known targets such as NETO2, which were collectively designated as an NME1-Regulated Metastasis Suppressor Signature (MSS). The MSS was associated with prolonged overall survival in a large cohort of melanoma patients in The Cancer Genome Atlas (TCGA). The median overall survival of melanoma patients with elevated expression of the MSS genes was >5.6 years longer compared with that of patients with lower expression of the MSS genes. These data demonstrate that NMEl represents a powerful tool for identifying genes whose expression is associated with metastasis and survival of melanoma patients, suggesting their potential applications as prognostic markers and therapeutic targets in advanced forms of this lethal cancer.
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32
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Dysregulated expression of microRNAs and mRNAs in pulmonary artery remodeling in ascites syndrome in broiler chickens. Oncotarget 2018; 8:1993-2007. [PMID: 27791988 PMCID: PMC5356772 DOI: 10.18632/oncotarget.12888] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 10/19/2016] [Indexed: 12/31/2022] Open
Abstract
Ascites syndrome (AS), also known as pulmonary artery hypertension, remains a challenging disease that severely affects both humans and broiler chickens. Pulmonary artery remodeling presents a key step in the development of AS. In this study, we obtained pulmonary artery tissues from broilers with and without AS to perform miRNA sequencing analysis, miRNA-mRNA association analysis and pathological examinations. 29 significantly differentially expressed miRNAs were found both in known and novel miRNAs with 18 up-regulated and 11 down-regulated miRNAs. Their predicted potential targets were involved in a wide range of functional clusters as indicated via GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses. The upregulation of miR-155, miR-23b-3p, miR-146b-5p and miR-146b-3p were found closely associated with the pathogenesis of pulmonary artery remodeling in AS progression. The association analysis for the miRNAs-mRNAs showed that these 29 significantly differentially expressed miRNAs regulate 162 differentially expressed target genes. Among them, 20 miRNAs correlated with 18 predicted target genes that appear to be involved in pulmonary artery remodeling, mainly in three broad physiological processes: the hypoxia sensing response (HIF1α, NHE1, STAT5 and STAT3), endothelial permeability dysfunction (CD44, TRAF2, CDK2AP1, LZTFL1, JAZF1, PEBP1, LRP1B, RPS14 and THBS2) and inflammation (MEOX2, STAT5, STAT3, IRF8, MAP3K8, IL-1BETA and TNFRSF1B). Pathological pulmonary artery remodeling in the AS broilers was consistently observed in the present study. Taken together, the current analysis further illuminates the molecular mechanism of pulmonary artery remodeling underlying AS progression.
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33
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Expression of a recombinant full-length LRP1B receptor in human non-small cell lung cancer cells confirms the postulated growth-suppressing function of this large LDL receptor family member. Oncotarget 2018; 7:68721-68733. [PMID: 27626682 PMCID: PMC5356585 DOI: 10.18632/oncotarget.11897] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 08/13/2016] [Indexed: 12/26/2022] Open
Abstract
Low-density lipoprotein (LDL) receptor-related protein 1B (LRP1B), a member of the LDL receptor family, is frequently inactivated in multiple malignancies including lung cancer. LRP1B is therefore considered as a putative tumor suppressor. Due to its large size (4599 amino acids), until now only minireceptors or receptor fragments have been successfully cloned. To assess the effect of LRP1B on the proliferation of non-small cell lung cancer cells, we constructed and expressed a transfection vector containing the 13.800 bp full-length murine Lrp1b cDNA using a PCR-based cloning strategy. Expression of LRP1B was analyzed by quantitative RT-PCR (qRT-PCR) using primers specific for human LRP1B or mouse Lrp1b. Effective expression of the full length receptor was demonstrated by the appearance of a single 600 kDa band on Western Blots of HEK 293 cells. Overexpression of Lrp1b in non-small cell lung cancer cells with low or absent endogenous LRP1B expression significantly reduced cellular proliferation compared to empty vector-transfected control cells. Conversely, in Calu-1 cells, which express higher endogenous levels of the receptor, siRNA-mediated LRP1B knockdown significantly enhanced cellular proliferation. Taken together, these findings demonstrate that, consistent with the postulated tumor suppressor function, overexpression of full-length Lrp1b leads to impaired cellular proliferation, while LRP1B knockdown has the opposite effect. The recombinant Lrp1b construct represents a valuable tool to unravel the largely unknown physiological role of LRP1B and its potential functions in cancer pathogenesis.
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34
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Gu JL, Chukhman M, Lu Y, Liu C, Liu SY, Lu H. RNA-seq Based Transcription Characterization of Fusion Breakpoints as a Potential Estimator for Its Oncogenic Potential. BIOMED RESEARCH INTERNATIONAL 2017; 2017:9829175. [PMID: 29181411 PMCID: PMC5664375 DOI: 10.1155/2017/9829175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 08/23/2017] [Indexed: 12/20/2022]
Abstract
Based on high-throughput sequencing technology, the detection of gene fusions is no longer a big challenge but estimating the oncogenic potential of fusion genes remains challenging. Recent studies successfully applied machine learning methods and gene structural and functional features of fusion mutation to predict their oncogenic potentials. However, the transcription characterizations features of fusion genes have not yet been studied. In this study, based on the clonal evolution theory, we hypothesized that a fusion gene is more likely to be an oncogenic genomic alteration, if the neoplastic cells harboring this fusion mutation have larger clonal size than other neoplastic cells in a tumor. We proposed a novel method, called iFCR (internal Fusion Clone Ratio), given an estimation of oncogenic potential for fusion mutations. We have evaluated the iFCR method in three public cancer transcriptome sequencing datasets; the results demonstrated that the fusion mutations occurring in tumor samples have higher internal fusion clone ratio than normal samples. And the most frequent prostate cancer fusion mutation, TMPRSS2-ERG, appears to have a remarkably higher iFCR value in all three independent patients. The preliminary results suggest that the internal fusion clone ratio might potentially advantage current fusion mutation oncogenic potential prediction methods.
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Affiliation(s)
- Jian-lei Gu
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China
- Department of Bioinformatics, SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai 200240, China
- Key Laboratory of Molecular Embryology, Ministry of Health and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China
| | - Morris Chukhman
- Department of Bioengineering, Bioinformatics Program, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Yao Lu
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China
- Department of Bioinformatics, SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cong Liu
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China
- Department of Bioinformatics, SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Bioengineering, Bioinformatics Program, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Shi-yi Liu
- Department of Bioinformatics, SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hui Lu
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200040, China
- Department of Bioinformatics, SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai 200240, China
- Key Laboratory of Molecular Embryology, Ministry of Health and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China
- Department of Bioengineering, Bioinformatics Program, University of Illinois at Chicago, Chicago, IL 60607, USA
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35
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Zamò A, Pischimarov J, Schlesner M, Rosenstiel P, Bomben R, Horn H, Grieb T, Nedeva T, López C, Haake A, Richter J, Trümper L, Lawerenz C, Klapper W, Möller P, Hummel M, Lenze D, Szczepanowski M, Flossbach L, Schreder M, Gattei V, Ott G, Siebert R, Rosenwald A, Leich E. Differences between BCL2-break positive and negative follicular lymphoma unraveled by whole-exome sequencing. Leukemia 2017; 32:685-693. [PMID: 28824170 DOI: 10.1038/leu.2017.270] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 08/08/2017] [Indexed: 12/25/2022]
Abstract
Depending on disease stage follicular lymphoma (FL) lack the t(14;18) in ~15-~50% of cases. Nevertheless, most of these cases express BCL2. To elucidate mechanisms triggering BCL2 expression and promoting pathogenesis in t(14;18)-negative FL, exonic single-nucleotide variant (SNV) profiles of 28 t(14;18)-positive and 13 t(14;18)-negative FL were analyzed, followed by the integration of copy-number changes, copy-neutral LOH and published gene-expression data as well as the assessment of immunoglobulin N-glycosylation sites. Typical FL mutations also affected t(14;18)-negative FL. Curated gene set/pathway annotation of genes mutated in either t(14;18)-positive or t(14;18)-negative FL revealed a strong enrichment of same or similar gene sets but also a more prominent or exclusive enrichment of immune response and N-glycosylation signatures in t(14;18)-negative FL. Mutated genes showed high BCL2 association in both subgroups. Among the genes mutated in t(14;18)-negative FL 555 were affected by copy-number alterations and/or copy-neutral LOH and 96 were differently expressed between t(14;18)-positive and t(14;18)-negative FL (P<0.01). N-glycosylation sites were detected considerably less frequently in t(14;18)-negative FL. These results suggest a diverse portfolio of genetic alterations that may induce or regulate BCL2 expression or promote pathogenesis of t(14;18)-negative FL as well as a less specific but increased crosstalk with the microenvironment that may compensate for the lack of N-glycosylation.
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Affiliation(s)
- A Zamò
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Department of Diagnostic and Public Health, University of Verona, Verona, Italy.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - J Pischimarov
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - M Schlesner
- Theoretical Bioinformatics (B080), Computational Oncology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - P Rosenstiel
- Institute for Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - R Bomben
- Department of Translational Research, CRO, Aviano, Italy
| | - H Horn
- Dr Margarete Fischer-Bosch-Institute for Clinical Pharmacology, Stuttgart, Germany
| | - T Grieb
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - T Nedeva
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - C López
- Institute for Human Genetics, University Hospital Ulm, Ulm, Germany.,Institute for Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - A Haake
- Institute for Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - J Richter
- Institute for Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany.,Institute of Pathology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - L Trümper
- Department of Hematology and Medical Oncology, University Hospital, Göttingen, Germany
| | - C Lawerenz
- Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - W Klapper
- Institute of Pathology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - P Möller
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - M Hummel
- Institute of Pathology, Charité-University Hospital Berlin, Germany
| | - D Lenze
- Institute of Pathology, Charité-University Hospital Berlin, Germany
| | - M Szczepanowski
- Institute of Pathology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - L Flossbach
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - M Schreder
- Medizinische Klinik und Poliklinik II, University Hospital Würzburg, Würzburg, Germany
| | - V Gattei
- Department of Translational Research, CRO, Aviano, Italy
| | - G Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
| | - R Siebert
- Institute for Human Genetics, University Hospital Ulm, Ulm, Germany.,Institute for Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - A Rosenwald
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - E Leich
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
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Mortezaei Z, Lanjanian H, Masoudi-Nejad A. Candidate novel long noncoding RNAs, MicroRNAs and putative drugs for Parkinson's disease using a robust and efficient genome-wide association study. Genomics 2017; 109:158-164. [DOI: 10.1016/j.ygeno.2017.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 02/02/2017] [Accepted: 02/15/2017] [Indexed: 12/30/2022]
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37
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Genomic analysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations. Nat Commun 2017; 8:15290. [PMID: 28548104 PMCID: PMC5477513 DOI: 10.1038/ncomms15290] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/16/2017] [Indexed: 12/21/2022] Open
Abstract
Approximately half of the world's 500,000 new oesophageal squamous-cell carcinoma (ESCC) cases each year occur in China. Here, we show whole-genome sequencing of DNA and RNA in 94 Chinese individuals with ESCC. We identify six mutational signatures (E1-E6), and Signature E4 is unique in ESCC linked to alcohol intake and genetic variants in alcohol-metabolizing enzymes. We discover significantly recurrent mutations in 20 protein-coding genes, 4 long non-coding RNAs and 10 untranslational regions. Functional analyses show six genes that have recurrent copy-number variants in three squamous-cell carcinomas (oesophageal, head and neck and lung) significantly promote cancer cell proliferation, migration and invasion. The most frequently affected genes by structural variation are LRP1B and TTC28. The aberrant cell cycle and PI3K-AKT pathways seem critical in ESCC. These results establish a comprehensive genomic landscape of ESCC and provide potential targets for precision treatment and prevention of the cancer.
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38
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Shi E, Chmielecki J, Tang CM, Wang K, Heinrich MC, Kang G, Corless CL, Hong D, Fero KE, Murphy JD, Fanta PT, Ali SM, De Siena M, Burgoyne AM, Movva S, Madlensky L, Heestand GM, Trent JC, Kurzrock R, Morosini D, Ross JS, Harismendy O, Sicklick JK. FGFR1 and NTRK3 actionable alterations in "Wild-Type" gastrointestinal stromal tumors. J Transl Med 2016; 14:339. [PMID: 27974047 PMCID: PMC5157084 DOI: 10.1186/s12967-016-1075-6] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 11/08/2016] [Indexed: 12/22/2022] Open
Abstract
Background About 10–15% of adult, and most pediatric, gastrointestinal stromal tumors (GIST) lack mutations in KIT, PDGFRA, SDHx, or RAS pathway components (KRAS, BRAF, NF1). The identification of additional mutated genes in this rare subset of tumors can have important clinical benefit to identify altered biological pathways and select targeted therapies. Methods We performed comprehensive genomic profiling (CGP) for coding regions in more than 300 cancer-related genes of 186 GISTs to assess for their somatic alterations. Results We identified 24 GIST lacking alterations in the canonical KIT/PDGFRA/RAS pathways, including 12 without SDHx alterations. These 24 patients were mostly adults (96%). The tumors had a 46% rate of nodal metastases. These 24 GIST were more commonly mutated at 7 genes: ARID1B, ATR, FGFR1, LTK, SUFU, PARK2 and ZNF217. Two tumors harbored FGFR1 gene fusions (FGFR1–HOOK3, FGFR1–TACC1) and one harbored an ETV6–NTRK3 fusion that responded to TRK inhibition. In an independent sample set, we identified 5 GIST cases lacking alterations in the KIT/PDGFRA/SDHx/RAS pathways, including two additional cases with FGFR1–TACC1 and ETV6–NTRK3 fusions. Conclusions Using patient demographics, tumor characteristics, and CGP, we show that GIST lacking alterations in canonical genes occur in younger patients, frequently metastasize to lymph nodes, and most contain deleterious genomic alterations, including gene fusions involving FGFR1 and NTRK3. If confirmed in larger series, routine testing for these translocations may be indicated for this subset of GIST. Moreover, these findings can be used to guide personalized treatments for patients with GIST. Trial registration NCT 02576431. Registered October 12, 2015 Electronic supplementary material The online version of this article (doi:10.1186/s12967-016-1075-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eileen Shi
- School of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Chih-Min Tang
- Division of Surgical Oncology, Department of Surgery, Moores UCSD Cancer Center, UC San Diego Health Sciences, University of California San Diego, 3855 Health Sciences Drive, Room 2313, Mail Code 0987, La Jolla, CA, 92093-0987, USA
| | - Kai Wang
- Foundation Medicine, Inc., Cambridge, MA, USA
| | - Michael C Heinrich
- Portland VA Health Care System, Portland, OR, USA.,Knight Cancer Institute, Oregon Health Sciences University, Portland, OR, USA
| | - Guhyun Kang
- Knight Cancer Institute, Oregon Health Sciences University, Portland, OR, USA.,Department of Pathology, Sanggye Paik Hospital, Inje University, Seoul, Korea
| | | | - David Hong
- Division of Cancer Medicine, Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Katherine E Fero
- School of Medicine, University of California San Diego, La Jolla, CA, USA.,UCSD Department of Radiation Medicine and Applied Sciences, Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - James D Murphy
- School of Medicine, University of California San Diego, La Jolla, CA, USA.,UCSD Department of Radiation Medicine and Applied Sciences, Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Paul T Fanta
- School of Medicine, University of California San Diego, La Jolla, CA, USA.,Division of Medical Oncology, Department of Medicine, Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Siraj M Ali
- Foundation Medicine, Inc., Cambridge, MA, USA
| | - Martina De Siena
- Division of Surgical Oncology, Department of Surgery, Moores UCSD Cancer Center, UC San Diego Health Sciences, University of California San Diego, 3855 Health Sciences Drive, Room 2313, Mail Code 0987, La Jolla, CA, 92093-0987, USA
| | - Adam M Burgoyne
- School of Medicine, University of California San Diego, La Jolla, CA, USA.,Division of Medical Oncology, Department of Medicine, Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Sujana Movva
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Lisa Madlensky
- School of Medicine, University of California San Diego, La Jolla, CA, USA.,UCSD Department of Family and Preventive Medicine, Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Gregory M Heestand
- School of Medicine, University of California San Diego, La Jolla, CA, USA.,Division of Medical Oncology, Department of Medicine, Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Jonathan C Trent
- Sarcoma Medical Oncology Program, University of Miami Sylvester Cancer Center, Miami, FL, USA
| | - Razelle Kurzrock
- School of Medicine, University of California San Diego, La Jolla, CA, USA.,Division of Medical Oncology, Department of Medicine, Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA, USA
| | | | | | - Olivier Harismendy
- School of Medicine, University of California San Diego, La Jolla, CA, USA. .,Oncogenomics Laboratory, Division of Biomedical Informatics, Moores UCSD Cancer Center, UC San Diego Health Sciences, University of California San Diego, 3855 Health Sciences Drive, Room 4335, Mail Code 0820, La Jolla, CA, 92093-0820, USA.
| | - Jason K Sicklick
- School of Medicine, University of California San Diego, La Jolla, CA, USA. .,Division of Surgical Oncology, Department of Surgery, Moores UCSD Cancer Center, UC San Diego Health Sciences, University of California San Diego, 3855 Health Sciences Drive, Room 2313, Mail Code 0987, La Jolla, CA, 92093-0987, USA.
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Fridley BL, Ghosh TM, Wang A, Raghavan R, Dai J, Goode EL, Lamba JK. Genome-Wide Study of Response to Platinum, Taxane, and Combination Therapy in Ovarian Cancer: In vitro Phenotypes, Inherited Variation, and Disease Recurrence. Front Genet 2016; 7:37. [PMID: 27047539 PMCID: PMC4801852 DOI: 10.3389/fgene.2016.00037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/04/2016] [Indexed: 11/13/2022] Open
Abstract
Background: The standard treatment for epithelial ovarian cancer (EOC) patients with advanced disease is carboplatin-paclitaxel combination therapy following initial debulking surgery, yet there is wide inter-patient variation in clinical response. We sought to identify pharmacogenomic markers related to carboplatin-paclitaxel therapy. Methods: The lymphoblastoid cell lines, derived from 74 invasive EOC patients seen at the Mayo Clinic, were treated with increasing concentrations of carboplatin and/or paclitaxel and assessed for in vitro drug response using MTT viability and caspase3/7 apoptosis assays. Drug response phenotypes IC50 (effective dose at which 50% of cells are viable) and EC50 (dose resulting in 50% induction of caspase 3/7 activity) were estimated for each patient to paclitaxel and carboplatin (alone and in combination). For each of the six drug response phenotypes, a genome-wide association study was conducted. Results: Statistical analysis found paclitaxel in vitro drug response phenotypes to be moderately associated with time to EOC recurrence (p = 0.008 IC50; p = 0.058 EC50). Although no pharmacogenomic associations were significant at p < 5 × 10−8, seven genomic loci were associated with drug response at p < 10−6, including at 4q21.21 for carboplatin, 4p16.1 and 5q23.2 for paclitaxel, and 3q24, 10q, 1q44, and 13q21 for combination therapy. Nearby genes of interest include FRAS1, MGC32805, SNCAIP, SLC9A9, TIAL1, ZNF731P, and PCDH20. Conclusions: These results suggest the existence of genetic loci associated with response to platinum-taxane therapies. Further research is needed to understand the mechanism by which these loci may impact EOC clinical response to this commonly used regimen.
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Affiliation(s)
- Brooke L Fridley
- Department of Biostatistics, University of Kansas Medical Center Kansas City, KS, USA
| | - Taraswi M Ghosh
- Department of Experimental and Clinical Pharmacology, University of Minnesota Minneapolis, MN, USA
| | - Alice Wang
- Department of Biostatistics, University of Kansas Medical Center Kansas City, KS, USA
| | - Rama Raghavan
- Department of Biostatistics, University of Kansas Medical Center Kansas City, KS, USA
| | - Junqiang Dai
- Department of Biostatistics, University of Kansas Medical Center Kansas City, KS, USA
| | - Ellen L Goode
- Department of Health Sciences Research, Mayo Clinic Rochester, MN, USA
| | - Jatinder K Lamba
- Department of Pharmacotherapy and Translational Research, University of Florida Gainesville, FL, USA
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Sleeping Beauty transposon mutagenesis identifies genes that cooperate with mutant Smad4 in gastric cancer development. Proc Natl Acad Sci U S A 2016; 113:E2057-65. [PMID: 27006499 DOI: 10.1073/pnas.1603223113] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mutations in SMAD4 predispose to the development of gastrointestinal cancer, which is the third leading cause of cancer-related deaths. To identify genes driving gastric cancer (GC) development, we performed a Sleeping Beauty (SB) transposon mutagenesis screen in the stomach of Smad4(+/-) mutant mice. This screen identified 59 candidate GC trunk drivers and a much larger number of candidate GC progression genes. Strikingly, 22 SB-identified trunk drivers are known or candidate cancer genes, whereas four SB-identified trunk drivers, including PTEN, SMAD4, RNF43, and NF1, are known human GC trunk drivers. Similar to human GC, pathway analyses identified WNT, TGF-β, and PI3K-PTEN signaling, ubiquitin-mediated proteolysis, adherens junctions, and RNA degradation in addition to genes involved in chromatin modification and organization as highly deregulated pathways in GC. Comparative oncogenomic filtering of the complete list of SB-identified genes showed that they are highly enriched for genes mutated in human GC and identified many candidate human GC genes. Finally, by comparing our complete list of SB-identified genes against the list of mutated genes identified in five large-scale human GC sequencing studies, we identified LDL receptor-related protein 1B (LRP1B) as a previously unidentified human candidate GC tumor suppressor gene. In LRP1B, 129 mutations were found in 462 human GC samples sequenced, and LRP1B is one of the top 10 most deleted genes identified in a panel of 3,312 human cancers. SB mutagenesis has, thus, helped to catalog the cooperative molecular mechanisms driving SMAD4-induced GC growth and discover genes with potential clinical importance in human GC.
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Gomez-Rueda H, Palacios-Corona R, Gutiérrez-Hermosillo H, Trevino V. A robust biomarker of differential correlations improves the diagnosis of cytologically indeterminate thyroid cancers. Int J Mol Med 2016; 37:1355-62. [PMID: 27035928 DOI: 10.3892/ijmm.2016.2534] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 02/23/2016] [Indexed: 11/05/2022] Open
Abstract
The fine-needle aspiration of thyroid nodules and subsequent cytological analysis is unable to determine the diagnosis in 15 to 30% of thyroid cancer cases; patients with indeterminate cytological results undergo diagnostic surgery which is potentially unnecessary. Current gene expression biomarkers based on well-determined cytology are complex and their accuracy is inconsistent across public datasets. In the present study, we identified a robust biomarker using the differences in gene expression values specifically from cytologically indeterminate thyroid tumors and a powerful multivariate search tool coupled with a nearest centroid classifier. The biomarker is based on differences in the expression of the following genes: CCND1, CLDN16, CPE, LRP1B, MAGI3, MAPK6, MATN2, MPPED2, PFKFB2, PTPRE, PYGL, SEMA3D, SERGEF, SLC4A4 and TIMP1. This 15-gene biomarker exhibited superior accuracy independently of the cytology in six datasets, including The Cancer Genome Atlas (TCGA) thyroid dataset. In addition, this biomarker exhibited differences in the correlation coefficients between benign and malignant samples that indicate its discriminatory power, and these 15 genes have been previously related to cancer in the literature. Thus, this 15-gene biomarker provides advantages in clinical practice for the effective diagnosis of thyroid cancer.
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Affiliation(s)
- Hugo Gomez-Rueda
- Bioinformatics Research Group, Department of Research and Innovation, Medical School, Tecnológico de Monterrey, Colonia Los Doctores, 64710 Monterrey, Nuevo León, Mexico
| | - Rebeca Palacios-Corona
- Northeastern Biomedical Research Center, Instituto Mexicano del Seguro Social, Colonia Independencia, 64720 Monterrey, Nuevo León, Mexico
| | - Hugo Gutiérrez-Hermosillo
- Department of Geriatrics, UMAE 1 CMN del Bajío, Instituto Mexicano del Seguro Social, Hospital Aranda de la Parra, Colonia Centro, 37000 León, Guanajuato, Mexico
| | - Victor Trevino
- Bioinformatics Research Group, Department of Research and Innovation, Medical School, Tecnológico de Monterrey, Colonia Los Doctores, 64710 Monterrey, Nuevo León, Mexico
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Li X, Cai H, Zheng W, Tong M, Li H, Ao L, Li J, Hong G, Li M, Guan Q, Yang S, Yang D, Lin X, Guo Z. An individualized prognostic signature for gastric cancer patients treated with 5-Fluorouracil-based chemotherapy and distinct multi-omics characteristics of prognostic groups. Oncotarget 2016; 7:8743-55. [PMID: 26840027 PMCID: PMC4891001 DOI: 10.18632/oncotarget.7087] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 01/14/2016] [Indexed: 12/21/2022] Open
Abstract
5-Fluorouracil (5-FU)-based chemotherapy is currently the first-line treatment for gastric cancer. In this study, using gene expression profiles for a panel of cell lines with drug sensitivity data and two cohorts of patients, we extracted a signature consisting of two gene pairs (KCNE2 and API5, KCNE2 and PRPF3) whose within-sample relative expression orderings (REOs) could robustly predict prognoses of gastric cancer patients treated with 5-FU-based chemotherapy. This REOs-based signature was insensitive to experimental batch effects and could be directly applied to samples measured by different laboratories. Taking this unique advantage of the REOs-based signature, we classified gastric cancer samples of The Cancer Genome Atlas (TCGA) into two prognostic groups with distinct transcriptional characteristics, circumventing the usage of confounded TCGA survival data. We further showed that the two prognostic groups displayed distinct copy number, gene mutation and DNA methylation landscapes using the TCGA multi-omics data. The results provided hints for understanding molecular mechanisms determining prognoses of gastric cancer patients treated with 5-FU-based chemotherapy.
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Affiliation(s)
- Xiangyu Li
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Hao Cai
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Weicheng Zheng
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Mengsha Tong
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Hongdong Li
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Lu Ao
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Jing Li
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Guini Hong
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Mengyao Li
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Qingzhou Guan
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Sheng Yang
- Department of Medical Oncology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Da Yang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, USA
| | - Xu Lin
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Zheng Guo
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
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Tabouret E, Labussière M, Alentorn A, Schmitt Y, Marie Y, Sanson M. LRP1B deletion is associated with poor outcome for glioblastoma patients. J Neurol Sci 2015; 358:440-3. [PMID: 26428308 DOI: 10.1016/j.jns.2015.09.345] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 08/14/2015] [Accepted: 09/10/2015] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Deletion of the tumor suppressor gene LRP1B has been reported in glioblastoma, the most aggressive primary brain tumor in adults. Our objective was to analyze frequency and prognostic impact of LRP1B deletion and expression levels. METHODS We retrospectively included all the primary IDH1/2 wild-type GBM patients with available clinical follow-up, DNA and RNA from our database. Deletions were analyzed by SNP-array. LRP1B mRNA expression was analyzed by reverse transcription quantitative polymerase chain reaction. RESULTS 178 patients were included with a median age of 62.36 years. LRP1B deletions were observed for 10.1% of patients (complete: 2.8%, partial: 7.3%). LRP1B deletions were associated with poor progression-free survival (PFS) (p=0.004) and overall survival (OS) (p=0.001). By multivariate analysis, LRP1B deletions remained significant for both PFS (p=0.003, hazard ratio (HR): 2.261) and OS (p=0.001, HR: 2.609). LRP1B was down expressed with a mean relative expression of 46% comparatively to normal tissue. No association between LRP1B mRNA and patient outcome was observed. No correlation was found between the deletions and the mRNA down-expression. These results were validated using GBM TCGA data. CONCLUSION LRP1B presents with frequent molecular alterations which impact patient outcome, highlighting the potential interest of this gene for glioblastoma patients.
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Affiliation(s)
- E Tabouret
- Sorbonne Universités, Centre de Recherche de l'Institut du Cerveau et de la Moelle épinière, INSERM U1127, CNRS UMR 7225, UPMC Paris 06, Paris 75013, France; AP-HP, Service de Neurologie 2, Groupe Hospitalier Pitié-Salpêtrière, Paris 75013, France
| | - M Labussière
- Sorbonne Universités, Centre de Recherche de l'Institut du Cerveau et de la Moelle épinière, INSERM U1127, CNRS UMR 7225, UPMC Paris 06, Paris 75013, France
| | - A Alentorn
- Sorbonne Universités, Centre de Recherche de l'Institut du Cerveau et de la Moelle épinière, INSERM U1127, CNRS UMR 7225, UPMC Paris 06, Paris 75013, France; AP-HP, Service de Neurologie 2, Groupe Hospitalier Pitié-Salpêtrière, Paris 75013, France
| | - Y Schmitt
- Sorbonne Universités, Centre de Recherche de l'Institut du Cerveau et de la Moelle épinière, INSERM U1127, CNRS UMR 7225, UPMC Paris 06, Paris 75013, France
| | - Y Marie
- Institut du Cerveau et de la Moelle épinière (ICM), Plateforme de Génotypage Séquençage, Paris 75013, France; OncoNeuroTek, Paris 75013, France
| | - M Sanson
- Sorbonne Universités, Centre de Recherche de l'Institut du Cerveau et de la Moelle épinière, INSERM U1127, CNRS UMR 7225, UPMC Paris 06, Paris 75013, France; AP-HP, Service de Neurologie 2, Groupe Hospitalier Pitié-Salpêtrière, Paris 75013, France; OncoNeuroTek, Paris 75013, France.
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Cotterchio M, Lowcock E, Bider-Canfield Z, Lemire M, Greenwood C, Gallinger S, Hudson T. Association between Variants in Atopy-Related Immunologic Candidate Genes and Pancreatic Cancer Risk. PLoS One 2015; 10:e0125273. [PMID: 25945796 PMCID: PMC4422524 DOI: 10.1371/journal.pone.0125273] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/22/2015] [Indexed: 02/06/2023] Open
Abstract
Background Many epidemiology studies report that atopic conditions such as allergies are associated with reduced pancreas cancer risk. The reason for this relationship is not yet understood. This is the first study to comprehensively evaluate the association between variants in atopy-related candidate genes and pancreatic cancer risk. Methods A population-based case-control study of pancreas cancer cases diagnosed during 2011-2012 (via Ontario Cancer Registry), and controls recruited using random digit dialing utilized DNA from 179 cases and 566 controls. Following an exhaustive literature review, SNPs in 180 candidate genes were pre-screened using dbGaP pancreas cancer GWAS data; 147 SNPs in 56 allergy-related immunologic genes were retained and genotyped. Logistic regression was used to estimate age-adjusted odd ratio (AOR) for each variant and false discovery rate was used to adjust Wald p-values for multiple testing. Subsequently, a risk allele score was derived based on statistically significant variants. Results 18 SNPs in 14 candidate genes (CSF2, DENND1B, DPP10, FLG, IL13, IL13RA2, LRP1B, NOD1, NPSR1, ORMDL3, RORA, STAT4, TLR6, TRA) were significantly associated with pancreas cancer risk. After adjustment for multiple comparisons, two LRP1B SNPs remained statistically significant; for example, LRP1B rs1449477 (AA vs. CC: AOR=0.37, 95% CI: 0.22-0.62; p (adjusted)=0.04). Furthermore, the risk allele score was associated with a significant reduction in pancreas cancer risk (p=0.0007). Conclusions Preliminary findings suggest certain atopy-related variants may be associated with pancreas cancer risk. Further studies are needed to replicate this, and to elucidate the biology behind the growing body of epidemiologic evidence suggesting allergies may reduce pancreatic cancer risk.
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Affiliation(s)
- Michelle Cotterchio
- Prevention and Cancer Control, Cancer Care Ontario, Toronto, ON M5G 2L7, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
- * E-mail:
| | - Elizabeth Lowcock
- Prevention and Cancer Control, Cancer Care Ontario, Toronto, ON M5G 2L7, Canada
| | - Zoe Bider-Canfield
- Prevention and Cancer Control, Cancer Care Ontario, Toronto, ON M5G 2L7, Canada
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Celia Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Division of General Surgery, Toronto General Hospital, Toronto, ON M5G 2C4, Canada
| | - Thomas Hudson
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada
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Shapiro SG, Raghunath S, Williams C, Motsinger-Reif AA, Cullen JM, Liu T, Albertson D, Ruvolo M, Bergstrom Lucas A, Jin J, Knapp DW, Schiffman JD, Breen M. Canine urothelial carcinoma: genomically aberrant and comparatively relevant. Chromosome Res 2015; 23:311-31. [PMID: 25783786 DOI: 10.1007/s10577-015-9471-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 02/07/2015] [Accepted: 02/10/2015] [Indexed: 01/13/2023]
Abstract
Urothelial carcinoma (UC), also referred to as transitional cell carcinoma (TCC), is the most common bladder malignancy in both human and canine populations. In human UC, numerous studies have demonstrated the prevalence of chromosomal imbalances. Although the histopathology of the disease is similar in both species, studies evaluating the genomic profile of canine UC are lacking, limiting the discovery of key comparative molecular markers associated with driving UC pathogenesis. In the present study, we evaluated 31 primary canine UC biopsies by oligonucleotide array comparative genomic hybridization (oaCGH). Results highlighted the presence of three highly recurrent numerical aberrations: gain of dog chromosome (CFA) 13 and 36 and loss of CFA 19. Regional gains of CFA 13 and 36 were present in 97 % and 84 % of cases, respectively, and losses on CFA 19 were present in 77 % of cases. Fluorescence in situ hybridization (FISH), using targeted bacterial artificial chromosome (BAC) clones and custom Agilent SureFISH probes, was performed to detect and quantify these regions in paraffin-embedded biopsy sections and urine-derived urothelial cells. The data indicate that these three aberrations are potentially diagnostic of UC. Comparison of our canine oaCGH data with that of 285 human cases identified a series of shared copy number aberrations. Using an informatics approach to interrogate the frequency of copy number aberrations across both species, we identified those that had the highest joint probability of association with UC. The most significant joint region contained the gene PABPC1, which should be considered further for its role in UC progression. In addition, cross-species filtering of genome-wide copy number data highlighted several genes as high-profile candidates for further analysis, including CDKN2A, S100A8/9, and LRP1B. We propose that these common aberrations are indicative of an evolutionarily conserved mechanism of pathogenesis and harbor genes key to urothelial neoplasia, warranting investigation for diagnostic, prognostic, and therapeutic applications.
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Affiliation(s)
- S G Shapiro
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
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VanderWeele DJ, Brown CD, Taxy JB, Gillard M, Hatcher DM, Tom WR, Stadler WM, White KP. Low-grade prostate cancer diverges early from high grade and metastatic disease. Cancer Sci 2014; 105:1079-85. [PMID: 24890684 PMCID: PMC4317857 DOI: 10.1111/cas.12460] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 05/16/2014] [Accepted: 05/23/2014] [Indexed: 12/22/2022] Open
Abstract
Understanding the developmental relationship between indolent and aggressive tumors is central to understanding disease progression and making treatment decisions. For example, most men diagnosed with prostate cancer have clinically indolent disease and die from other causes. Overtreatment of prostate cancer remains a concern. Here we use laser microdissection followed by exome sequencing of low- and high-grade prostate cancer foci from four subjects, and metastatic disease from two of those subjects, to evaluate the molecular relationship of coincident cancer foci. Seventy of 79 (87%) high-confidence somatic mutations in low-grade disease were private to low-grade foci. In contrast, high-grade foci and metastases harbored many of the same mutations. In cases in which there was a metastatic focus, 15 of 80 (19%) high-confidence somatic mutations in high-grade foci were private. Seven of the 80 (9%) were shared with low-grade foci and 65 (82%) were shared with metastatic foci. Notably, mutations in cancer-associated genes and the p53 signaling pathway were found exclusively in high-grade foci and metastases. The pattern of mutations is consistent with early divergence between low- and high-grade foci and late divergence between high-grade foci and metastases. These data provide insights into the development of high-grade and metastatic prostate cancer.
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Affiliation(s)
- David J VanderWeele
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA; Department of Medicine, University of Chicago, Chicago, Illinois, USA
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Rostas JW, Pruitt HC, Metge BJ, Mitra A, Bailey SK, Bae S, Singh KP, Devine DJ, Dyess DL, Richards WO, Tucker JA, Shevde LA, Samant RS. microRNA-29 negatively regulates EMT regulator N-myc interactor in breast cancer. Mol Cancer 2014; 13:200. [PMID: 25174825 PMCID: PMC4169820 DOI: 10.1186/1476-4598-13-200] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/21/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND N-Myc Interactor is an inducible protein whose expression is compromised in advanced stage breast cancer. Downregulation of NMI, a gatekeeper of epithelial phenotype, in breast tumors promotes mesenchymal, invasive and metastatic phenotype of the cancer cells. Thus the mechanisms that regulate expression of NMI are of potential interest for understanding the etiology of breast tumor progression and metastasis. METHOD Web based prediction algorithms were used to identify miRNAs that potentially target the NMI transcript. Luciferase reporter assays and western blot analysis were used to confirm the ability of miR-29 to target NMI. Quantitive-RT-PCRs were used to examine levels of miR29 and NMI from cell line and patient specimen derived RNA. The functional impact of miR-29 on EMT phenotype was evaluated using transwell migration as well as monitoring 3D matrigel growth morphology. Anti-miRs were used to examine effects of reducing miR-29 levels from cells. Western blots were used to examine changes in GSK3β phosphorylation status. The impact on molecular attributes of EMT was evaluated using immunocytochemistry, qRT-PCRs as well as Western blot analyses. RESULTS Invasive, mesenchymal-like breast cancer cell lines showed increased levels of miR-29. Introduction of miR-29 into breast cancer cells (with robust level of NMI) resulted in decreased NMI expression and increased invasion, whereas treatment of cells with high miR-29 and low NMI levels with miR-29 antagonists increased NMI expression and decreased invasion. Assessment of 2D and 3D growth morphologies revealed an EMT promoting effect of miR-29. Analysis of mRNA of NMI and miR-29 from patient derived breast cancer tumors showed a strong, inverse relationship between the expression of NMI and the miR-29. Our studies also revealed that in the absence of NMI, miR-29 expression is upregulated due to unrestricted Wnt/β-catenin signaling resulting from inactivation of GSK3β. CONCLUSION Aberrant miR-29 expression may account for reduced NMI expression in breast tumors and mesenchymal phenotype of cancer cells that promotes invasive growth. Reduction in NMI levels has a feed-forward impact on miR-29 levels.
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Affiliation(s)
- Jack W Rostas
- />Department of Surgery, University of South Alabama, Mobile, AL USA
| | - Hawley C Pruitt
- />Department of Pathology, University of Alabama at Birmingham, WTI-320E, 1824 6th avenue South, Birmingham, AL 35294 USA
| | - Brandon J Metge
- />Department of Pathology, University of Alabama at Birmingham, WTI-320E, 1824 6th avenue South, Birmingham, AL 35294 USA
| | - Aparna Mitra
- />Mitchell Cancer Institute, University of South Alabama, Mobile, AL USA
| | - Sarah K Bailey
- />Department of Pathology, University of Alabama at Birmingham, WTI-320E, 1824 6th avenue South, Birmingham, AL 35294 USA
| | - Sejong Bae
- />BBSF-Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL USA
- />Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL USA
| | - Karan P Singh
- />BBSF-Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL USA
- />Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL USA
| | - Daniel J Devine
- />Mitchell Cancer Institute, University of South Alabama, Mobile, AL USA
| | - Donna L Dyess
- />Department of Surgery, University of South Alabama, Mobile, AL USA
| | | | - J Allan Tucker
- />Department of Pathology, University of South Alabama, Mobile, AL USA
| | - Lalita A Shevde
- />Department of Pathology, University of Alabama at Birmingham, WTI-320E, 1824 6th avenue South, Birmingham, AL 35294 USA
- />Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL USA
| | - Rajeev S Samant
- />Department of Pathology, University of Alabama at Birmingham, WTI-320E, 1824 6th avenue South, Birmingham, AL 35294 USA
- />Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL USA
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Oncogenes associated with drug resistance in ovarian cancer. J Cancer Res Clin Oncol 2014; 141:381-95. [DOI: 10.1007/s00432-014-1765-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/26/2014] [Indexed: 12/20/2022]
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Interplay among epigenetic alterations and crosstalk between genetic and epigenetic alterations in esophageal squamous cell carcinoma. Esophagus 2014. [DOI: 10.1007/s10388-014-0431-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Wang H, Ji B, Ren H, Meng C. The relationship between lysine 4 on histone H3 methylation levels of alcohol tolerance genes and changes of ethanol tolerance in Saccharomyces cerevisiae. Microb Biotechnol 2014; 7:307-14. [PMID: 24779776 PMCID: PMC4241724 DOI: 10.1111/1751-7915.12121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/31/2013] [Accepted: 01/22/2013] [Indexed: 01/09/2023] Open
Abstract
We evaluated whether epigenetic changes contributed to improve ethanol tolerance in mutant
populations of Saccharomyces cerevisiae (S. cerevisiae). Two
ethanol-tolerant variants of S. cerevisiae were used to evaluate the genetic
stability in the process of stress-free passage cultures. We found that acquired ethanol tolerance
was lost and transcription level of some genes (HSP104, PRO1,
TPS1, and SOD1) closely related to ethanol tolerance decreased
significantly after the 10th passage in ethanol-free medium. Tri-methylation of lysine 4 on histone
H3 (H3K4) enhanced at the promoter of HSP104, PRO1,
TPS1 and SOD1 in ethanol-tolerant variants of S.
cerevisiae was also diminished after tenth passage in stress-free cultures. The ethanol
tolerance was reacquired when exogenous SOD1 transferred in some tolerance-lost
strains. This showed that H3K4 methylation is involved in phenotypic variation with regard to
ethanol tolerance with respect to classic breeding methods used in yeast.
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Affiliation(s)
- Hang Wang
- Department of Bioengineering, College of Biological Science and Biotechnology, Fuzhou University, Fuzhou, Fujian, China
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