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Thiery J, Fahrner M. Integration of proteomics in the molecular tumor board. Proteomics 2024; 24:e2300002. [PMID: 38143279 DOI: 10.1002/pmic.202300002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/26/2023]
Abstract
Cancer remains one of the most complex and challenging diseases in mankind. To address the need for a personalized treatment approach for particularly complex tumor cases, molecular tumor boards (MTBs) have been initiated. MTBs are interdisciplinary teams that perform in-depth molecular diagnostics to cooperatively and interdisciplinarily advise on the best therapeutic strategy. Current molecular diagnostics are routinely performed on the transcriptomic and genomic levels, aiming to identify tumor-driving mutations. However, these approaches can only partially capture the actual phenotype and the molecular key players of tumor growth and progression. Thus, direct investigation of the expressed proteins and activated signaling pathways provide valuable complementary information on the tumor-driving molecular characteristics of the tissue. Technological advancements in mass spectrometry-based proteomics enable the robust, rapid, and sensitive detection of thousands of proteins in minimal sample amounts, paving the way for clinical proteomics and the probing of oncogenic signaling activity. Therefore, proteomics is currently being integrated into molecular diagnostics within MTBs and holds promising potential in aiding tumor classification and identifying personalized treatment strategies. This review introduces MTBs and describes current clinical proteomics, its potential in precision oncology, and highlights the benefits of multi-omic data integration.
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Affiliation(s)
- Johanna Thiery
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
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2
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Rypens C, Van Berckelaer C, Berditchevski F, van Dam P, Van Laere S. Deciphering the molecular biology of inflammatory breast cancer through molecular characterization of patient samples and preclinical models. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 384:77-112. [PMID: 38637101 DOI: 10.1016/bs.ircmb.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Inflammatory breast cancer is an aggressive subtype of breast cancer with dismal patient prognosis and a unique clinical presentation. In the past two decades, molecular profiling technologies have been used in order to gain insight into the molecular biology of IBC and to search for possible targets for treatment. Although a gene signature that accurately discriminates between IBC and nIBC patient samples and preclinical models was identified, the overall genomic and transcriptomic differences are small and ambiguous, mainly due to the limited sample sizes of the evaluated patient series and the failure to correct for confounding effects of the molecular subtypes. Nevertheless, data collected over the past 20 years by independent research groups increasingly support the existence of several IBC-specific biological characteristics. In this review, these features are classified as established, emerging and conceptual hallmarks based on the level of evidence reported in the literature. In addition, a synoptic model is proposed that integrates all hallmarks and that can explain how cancer cell intrinsic mechanisms (i.e. NF-κB activation, genomic instability, MYC-addiction, TGF-β resistance, adaptive stress response, chromatin remodeling, epithelial-to-mesenchymal transition) can contribute to the establishment of the dynamic immune microenvironment associated with IBC. It stands to reason that future research projects are needed to further refine (parts of) this model and to investigate its clinical translatability.
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Affiliation(s)
- Charlotte Rypens
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium; CellCarta N V, Wilrijk, Belgium
| | - Christophe Van Berckelaer
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium
| | - Fedor Berditchevski
- Institute of Cancer and Genomic Sciences, The University of Birmingham, Birmingham, United Kingdom
| | - Peter van Dam
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium; Multidisciplinary Oncological Centre Antwerp (MOCA), Antwerp University Hospital, Drie Eikenstraat 655, Edegem, Belgium
| | - Steven Van Laere
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, Antwerp, Belgium.
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Ortiz-Soto G, Babilonia-Díaz NS, Lacourt-Ventura MY, Rivera-Rodríguez DM, Quiñones-Rodríguez JI, Colón-Vargas M, Almodóvar-Rivera I, Ferrer-Torres LE, Suárez-Arroyo IJ, Martínez-Montemayor MM. Metadherin Regulates Inflammatory Breast Cancer Invasion and Metastasis. Int J Mol Sci 2023; 24:4694. [PMID: 36902125 PMCID: PMC10002532 DOI: 10.3390/ijms24054694] [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: 01/05/2023] [Revised: 02/25/2023] [Accepted: 02/26/2023] [Indexed: 03/05/2023] Open
Abstract
Inflammatory breast cancer (IBC) is one of the most lethal subtypes of breast cancer (BC), accounting for approximately 1-5% of all cases of BC. Challenges in IBC include accurate and early diagnosis and the development of effective targeted therapies. Our previous studies identified the overexpression of metadherin (MTDH) in the plasma membrane of IBC cells, further confirmed in patient tissues. MTDH has been found to play a role in signaling pathways related to cancer. However, its mechanism of action in the progression of IBC remains unknown. To evaluate the function of MTDH, SUM-149 and SUM-190 IBC cells were edited with CRISPR/Cas9 vectors for in vitro characterization studies and used in mouse IBC xenografts. Our results demonstrate that the absence of MTDH significantly reduces IBC cell migration, proliferation, tumor spheroid formation, and the expression of NF-κB and STAT3 signaling molecules, which are crucial oncogenic pathways in IBC. Furthermore, IBC xenografts showed significant differences in tumor growth patterns, and lung tissue revealed epithelial-like cells in 43% of wild-type (WT) compared to 29% of CRISPR xenografts. Our study emphasizes the role of MTDH as a potential therapeutic target for the progression of IBC.
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Affiliation(s)
- Gabriela Ortiz-Soto
- Department of Biochemistry, Universidad Central del Caribe-School of Medicine, Bayamón, PR 00960, USA
| | - Natalia S. Babilonia-Díaz
- Department of Biochemistry, Universidad Central del Caribe-School of Medicine, Bayamón, PR 00960, USA
| | | | | | - Jailenne I. Quiñones-Rodríguez
- Department of Clinical Anatomy, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
- Department of Anatomy and Cell Biology, School of Medicine, Universidad Central del Caribe, Bayamón, PR 00960, USA
| | - Mónica Colón-Vargas
- Department of Mathematical Sciences, University of Puerto Rico at Mayagüez, Mayagüez, PR 00681, USA
| | - Israel Almodóvar-Rivera
- Department of Mathematical Sciences, University of Puerto Rico at Mayagüez, Mayagüez, PR 00681, USA
| | - Luis E. Ferrer-Torres
- Department of Pathology and Laboratory Medicine, Hospital Interamericano de Medicina Avanzada (H.I.M.A.)—San Pablo Caguas, Caguas, PR 00725, USA
- Department of Immunopathology, Hato Rey Pathology Associates Inc. (HRPLABS), San Juan, PR 00936, USA
| | - Ivette J. Suárez-Arroyo
- Department of Biochemistry, Universidad Central del Caribe-School of Medicine, Bayamón, PR 00960, USA
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Comparative transcriptional analyses of preclinical models and patient samples reveal MYC and RELA driven expression patterns that define the molecular landscape of IBC. NPJ Breast Cancer 2022; 8:12. [PMID: 35042871 PMCID: PMC8766434 DOI: 10.1038/s41523-021-00379-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022] Open
Abstract
Inflammatory breast cancer (IBC) is an aggressive disease for which the spectrum of preclinical models was rather limited in the past. More recently, novel cell lines and xenografts have been developed. This study evaluates the transcriptome of an extended series of IBC preclinical models and performed a comparative analysis with patient samples to determine the extent to which the current models recapitulate the molecular characteristics of IBC observed clinically. We demonstrate that the IBC preclinical models are exclusively estrogen receptor (ER)-negative and of the basal-like subtype, which reflects to some extent the predominance of these subtypes in patient samples. The IBC-specific 79-signature we previously reported was retrained and discriminated between IBC and non-IBC preclinical models, but with a relatively high rate of false positive predictions. Further analyses of gene expression profiles revealed important roles for cell proliferation, MYC transcriptional activity, and TNFɑ/NFκB in the biology of IBC. Patterns of MYC expression and transcriptional activity were further explored in patient samples, which revealed interactions with ESR1 expression that are contrasting in IBC and nIBC and notable given the comparatively poor outcomes of ER+ IBC. Our analyses also suggest important roles for NMYC, MXD3, MAX, and MLX in shaping MYC signaling in IBC. Overall, we demonstrate that the IBC preclinical models can be used to unravel cancer cell intrinsic molecular features, and thus constitute valuable research tools. Nevertheless, the current lack of ER-positive IBC models remains a major hurdle, particularly since interactions with the ER pathway appear to be relevant for IBC.
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Shafei MA, Flemban A, Daly C, Kendrick P, White P, Dean S, Qualtrough D, Conway ME. Differential expression of the BCAT isoforms between breast cancer subtypes. Breast Cancer 2020; 28:592-607. [PMID: 33367952 PMCID: PMC8065012 DOI: 10.1007/s12282-020-01197-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/19/2020] [Indexed: 01/08/2023]
Abstract
Background Biological characterisation of breast cancer subtypes is essential as it informs treatment regimens especially as different subtypes have distinct locoregional patterns. This is related to metabolic phenotype, where altered cellular metabolism is a fundamental adaptation of cancer cells during rapid proliferation. In this context, the metabolism of the essential branched-chain amino acids (BCAAs), catalysed by the human branched-chain aminotransferase proteins (hBCAT), offers multiple benefits for tumour growth. Upregulation of the cytosolic isoform of hBCAT (hBCATc), regulated by c-Myc, has been demonstrated to increase cell migration, tumour aggressiveness and proliferation in gliomas, ovarian and colorectal cancer but the importance of the mitochondrial isoform, hBCATm has not been fully investigated. Methods Using immunohistochemistry, the expression profile of metabolic proteins (hBCAT, IDH) was assessed between breast cancer subtypes, HER2 + , luminal A, luminal B and TNBC. Correlations between the percentage and the intensity of protein expression/co-expression with clinical parameters, such as hormone receptor status, tumour stage, lymph-node metastasis and survival, were determined. Results We show that hBCATc expression was found to be significantly associated with the more aggressive HER2 + and luminal B subtypes, whilst hBCATm and IDH1 associated with luminal A subtype. This was concomitant with better prognosis indicating a differential metabolic reliance between these two subtypes, in which enhanced expression of IDH1 may replenish the α-ketoglutarate pool in cells with increased hBCATm expression. Conclusion The cytosolic isoform of BCAT is associated with tumours that express HER2 receptors, whereas the mitochondrial isoform is highly expressed in tumours that are ER + , indicating that the BCAT proteins are regulated through different signalling pathways, which may lead to the identification of novel targets for therapeutic applications targeting dysregulated cancer metabolism.
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Affiliation(s)
- Mai Ahmed Shafei
- Faculty of Health and Life Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK
| | - Arwa Flemban
- Faculty of Health and Life Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.,Department of Pathology, Faculty of Medicine, Umm Al-Qura University, Makkah, 24382, Saudi Arabia
| | - Carl Daly
- Faculty of Health and Life Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK
| | - Paul Kendrick
- Faculty of Health and Life Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK
| | - Paul White
- Faculty of Health and Life Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK
| | - Sarah Dean
- Faculty of Health and Life Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK
| | - David Qualtrough
- Faculty of Health and Life Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK
| | - Myra E Conway
- Faculty of Health and Life Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.
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Shou Y, Yang L, Yang Y, Zhu X, Li F, Xu J. Identification of Signatures of Prognosis Prediction for Melanoma Using a Hypoxia Score. Front Genet 2020; 11:570530. [PMID: 33133157 PMCID: PMC7550673 DOI: 10.3389/fgene.2020.570530] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/08/2020] [Indexed: 01/16/2023] Open
Abstract
Melanoma is one of the most aggressive cancers. Hypoxic microenvironment affects multiple cellular pathways and contributes to tumor progression. The purpose of the research was to investigate the association between hypoxia and melanoma, and identify the prognostic value of hypoxia-related genes. Based on the GSVA algorithm, gene expression profile collected from The Cancer Genome Atlas (TCGA) was used for calculating the hypoxia score. The Kaplan–Meier plot suggested that a high hypoxia score was correlated with the inferior survival of melanoma patients. Using differential gene expression analysis and WGCNA, a total of 337 overlapping genes associated with hypoxia were determined. Protein-protein interaction network and functional enrichment analysis were conducted, and Lasso Cox regression was performed to establish the prognostic gene signature. Lasso regression showed that seven genes displayed the best features. A novel seven-gene signature (including ABCA12, PTK6, FERMT1, GSDMC, KRT2, CSTA, and SPRR2F) was constructed for prognosis prediction. The ROC curve inferred good performance in both the TCGA cohort and validation cohorts. Therefore, our study determined the prognostic implication of the hypoxia score in melanoma and showed a novel seven-gene signature to predict prognosis, which may provide insights into the prognosis evaluation and clinical decision making.
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Affiliation(s)
- Yanhong Shou
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Lu Yang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yongsheng Yang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaohua Zhu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Feng Li
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jinhua Xu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Dermatology, Shanghai, China
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Caveolin-1 Expression in Benign and Malignant Breast Lesions and Its Correlation with Expression of Estrogen Receptor (ER), Progesterone Receptor (PR), and Human Epidermal Growth Factor Receptor 2 (HER2), Lymph Node Metastasis, Tumor Grade, and Survival of the Patients. INTERNATIONAL JOURNAL OF CANCER MANAGEMENT 2020. [DOI: 10.5812/ijcm.97468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Zhang YH, Xing YQ, Chen Z, Ma XC, Lu Q. Association between interleukin-10 genetic polymorphisms and risk of primary open angle glaucoma in a Chinese Han population: a case-control study. Int J Ophthalmol 2019; 12:1605-1611. [PMID: 31637197 DOI: 10.18240/ijo.2019.10.13] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 07/04/2019] [Indexed: 01/10/2023] Open
Abstract
AIM To investigate the association between interleukin-10 (IL-10) genetic polymorphisms and risk of POAG through a case-control study in a Han population of China. METHODS A total of 210 patients with POAG and 420 normal subjects were recruited during the period from Dec. 2013 to Dec. 2016. The IL-10 -1082A>G (rs1800870), -819T>C (rs1800871) and -592C>A (rs1800872) polymorphisms were determined using iPlex GOLD SNP genotyping analysis (the SequenomMassARRAY® System, Sequenom, San Diego, USA). The association between IL-10 -1082A>G (rs1800870), -819T>C (rs1800871), and -592C>A (rs1800872) polymorphisms and risk of POAG was assessed by singlelogistic regression analysis. RESULTS We observed that those carrying the CC genotype of rs1800871 was associated with an increased risk of POAG when compared with those harboring the TT genotype (OR=1.84, 95%CI=1.01-3.38). Those with AA genotype of rs1800872 had a 10.62 fold risk of POAG in comparison to the CC genotype (OR=10.62, 95%CI, 3.41-33.09). A completely linkage disequilibrium was found between IL-10 rs1800871-rs1800872 (D'=1.00, r 2=0.16). The A-C-A (OR=2.60, 95%CI, 1.48-4.58) and G-T-A (OR=2.34, 95%CI, 1.42-3.86) haplotypes were associated with an increased risk of POAG, while the A-T-C haplotype showed a decreased risk of POAG (OR=0.63, 95%CI, 0.49-0.81). CONCLUSION Our data suggest that IL-10 rs1800871 and rs1800872 can be predictive factors for the pathogenesis of POAG in the Chinese population.
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Affiliation(s)
- Yi-Hui Zhang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Pronvince, China.,Ophthalmology Department of Inner Mongolia People's Hospital, Hohhot 010017, Inner Mongolia Autonomous Region, China
| | - Yi-Qiao Xing
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Pronvince, China
| | - Zhen Chen
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Pronvince, China
| | - Xiao-Cheng Ma
- Ophthalmology Department of Inner Mongolia People's Hospital, Hohhot 010017, Inner Mongolia Autonomous Region, China
| | - Qiang Lu
- Ophthalmology Department of Inner Mongolia People's Hospital, Hohhot 010017, Inner Mongolia Autonomous Region, China
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Zeng B, Zhang X, Zhao J, Wei Z, Zhu H, Fu M, Zou D, Feng Y, Luo H, Lei Y. The role of DNMT1/hsa-miR-124-3p/BCAT1 pathway in regulating growth and invasion of esophageal squamous cell carcinoma. BMC Cancer 2019; 19:609. [PMID: 31226958 PMCID: PMC6588861 DOI: 10.1186/s12885-019-5815-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/10/2019] [Indexed: 01/16/2023] Open
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is the major subtype of esophageal cancer with high aggressiveness and poor prognosis. There is an urgent need for understanding the molecular mechanism underlying the development and progression of ESCC. Methods ESCC tissues and corresponding non-neoplastic tissues were collected. The expression and function of miR-124-3p and BCAT1 in two cell lines KYSE-150 and Eca109 were determined. Results We show downregulation of miR-124-3p expression in ESCC tissues, which is highly correlated with proliferation and migration of ESCC cell lines KYSE-150 and Eca109. miR-124-3p show high correlation with TNM stage and differentiation grade. Furthermore, miR-124-3p directly targets mRNA 3’UTR region of BCAT1, which results in upregulation of BCAT1 expression as observed in ESCC tissues and cell lines. Also, our data indicates that BCAT1 high expression is strongly linked to the disease-free survival, tumor size, pathologic stage, T classification and differentiation grade. On the other hand, we clarified the upstream mechanism regulating miR-124-3p expression in ESCC, which involves in the hypermethylation-silencing regulation mediated by DNA methyltransferase 1(DNMT1), which is of high expression in ESCC tissues and cell lines in the present study. In addition, DNMT1 knockdown or inhibition of DNMT1 function contributes to downregulation of miR-124-3p and BCAT1 expression. Conclusions Our study thus clarifies a new mechanism that DNMT1/miR-124/BCAT1 axis regulates the development and progression of ESCC.
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Affiliation(s)
- Bo Zeng
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xin Zhang
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jingling Zhao
- Department of Burns, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhewei Wei
- Department of Gastrointestinal Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Haoshuai Zhu
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Minyi Fu
- Surgical and anesthesia center, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dawei Zou
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanfen Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China. .,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China. .,, Guangzhou, China.
| | - Honghe Luo
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China. .,, Guangzhou, China.
| | - Yiyan Lei
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China. .,, Guangzhou, China.
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Circular RNAs in Vascular Functions and Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1087:287-297. [PMID: 30259375 DOI: 10.1007/978-981-13-1426-1_23] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Vascular disease is one of the top five causes of death and affects a variety of other diseases, such as heart, nervous system, and metabolic disorders. Vascular dysfunction is a hallmark of ischemia, cancer, and inflammatory diseases and can accelerate the progression of diseases. Circular RNAs (circRNAs) are a new type of noncoding RNAs with covalent bond ring structure, which have been reported to be abnormally expressed in many human diseases. circRNAs regulate gene expression through the sponging of microRNAs (miRNAs) and can also be used as disease biomarkers. Here we will summarize the functions of circRNAs in vascular diseases, including vascular dysfunction, atherosclerosis, diabetes mellitus-related retinal vascular dysfunction, chronic thromboembolic pulmonary hypertension, carotid atherosclerotic disease, hepatic vascular invasion in hepatocellular carcinoma, aortic aneurysm, coronary artery disease, and type 2 diabetes mellitus.
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11
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Identification of frequent somatic mutations in inflammatory breast cancer. Breast Cancer Res Treat 2017; 163:263-272. [PMID: 28243898 DOI: 10.1007/s10549-017-4165-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 02/15/2017] [Indexed: 12/12/2022]
Abstract
PURPOSE Inflammatory breast cancer is an aggressive form of breast cancer that shows distinct clinical features from non-inflammatory breast cancer. Genomic understanding of inflammatory breast cancer will shed light on biological targets for this disease. Our objective was to identify targeted hotspot mutations using multiplex genome sequencing in inflammatory breast cancer and compare the findings with those for patients with non-inflammatory breast cancer to further recognize novel targets. METHODS We studied 400 patients with metastatic breast cancer who had somatic hotspot mutation testing using a 46- or 50-gene multiplex platform from March 2012 to December 2014. Among this population, 24 patients had inflammatory breast cancer and 376 patients had non-inflammatory breast cancer. We tested a total of 26 samples from 24 patients with inflammatory breast cancer. RESULTS The average number of mutations per patient was higher in inflammatory breast cancer than in non-inflammatory breast cancer (1.23 vs. 0.65, respectively). Identified somatic mutations in inflammatory breast cancer were TP53 (n = 18, 75%), PIK3CA (n = 10, 41.7%), and ERBB2 (n = 4, 16.7%). TP53 and ERBB2 mutations were significantly more prevalent in inflammatory breast cancer than in non-inflammatory breast cancer (P < 0.01). All patients with ERBB2 mutations had hormone receptor (HR)+ primary tumors. CONCLUSIONS TP53, PIK3CA, and ERBB2 were detected as three major somatic mutations in metastatic inflammatory breast cancer patients. While the inflammatory breast cancer TP53 and PIK3CA mutations mirrored previously reported data for metastatic non-inflammatory breast cancer, this is the first report of higher frequency of ERBB2 mutation in inflammatory breast cancer, especially in the HR+ subtype. Once validated in a larger cohort of inflammatory breast cancer patients, this novel finding could lead to development of treatments for HR+ inflammatory breast cancer.
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Anwar SL, Wahyono A, Aryandono T, Haryono SJ. Caveolin-1 in Breast Cancer: Single Molecule Regulation of Multiple Key Signaling Pathways. Asian Pac J Cancer Prev 2016; 16:6803-12. [PMID: 26514450 DOI: 10.7314/apjcp.2015.16.16.6803] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Caveolin-1 is a 22-kD trans-membrane protein enriched in particular plasma membrane invaginations known as caveolae. Cav-1 expression is often dysregulated in human breast cancers, being commonly upregulated in cancer cells and downregulated in stromal cells. As an intracellular scaffolding protein, Cav-1, is involved in several vital biological regulations including endocytosis, transcytosis, vesicular transport, and signaling pathways. Several pathways are modulated by Cav-1 including estrogen receptor, EGFR, Her2/neu, TGFβ, and mTOR and represent as major drivers in mammary carcinogenesis. Expression and role of Cav-1 in breast carcinogenesis is highly variable depending on the stage of tumor development as well as context of the cell. However, recent data have shown that downregulation of Cav-1 expression in stromal breast tumors is associated with frequent relapse, resistance to therapy, and poor outcome. Modification of Cav-1 expression for translational cancer therapy is particularly challenging since numerous signaling pathways might be affected. This review focuses on present understanding of Cav-1 in breast carcinogenesis and its potential role as a new biomarker for predicting therapeutic response and prognosis as well as new target for therapeutic manipulation.
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Affiliation(s)
- Sumadi Lukman Anwar
- Department of Surgery, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia E-mail :
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Suárez-Arroyo IJ, Feliz-Mosquea YR, Pérez-Laspiur J, Arju R, Giashuddin S, Maldonado-Martínez G, Cubano LA, Schneider RJ, Martínez-Montemayor MM. The proteome signature of the inflammatory breast cancer plasma membrane identifies novel molecular markers of disease. Am J Cancer Res 2016; 6:1720-1740. [PMID: 27648361 PMCID: PMC5004075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 07/10/2016] [Indexed: 06/06/2023] Open
Abstract
Inflammatory Breast Cancer (IBC) is the most lethal form of breast cancer with a 35% 5-year survival rate. The accurate and early diagnosis of IBC and the development of targeted therapy against this deadly disease remain a great medical challenge. Plasma membrane proteins (PMPs) such as E-cadherin and EGFR, play an important role in the progression of IBC. Because the critical role of PMPs in the oncogenic processes they are the perfect candidates as molecular markers and targets for cancer therapies. In the present study, Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) followed by mass spectrometry analysis was used to compare the relative expression levels of membrane proteins (MP) between non-cancerous mammary epithelial and IBC cells, MCF-10A and SUM-149, respectively. Six of the identified PMPs were validated by immunoblotting using the membrane fractions of non-IBC and IBC cell lines, compared with MCF-10A cells. Immunohistochemical analysis using IBC, invasive ductal carcinoma or normal mammary tissue samples was carried out to complete the validation method in nine of the PMPs. We identified and quantified 278 MPs, 76% of which classified as PMPs with 1.3-fold or higher change. We identified for the first time the overexpression of the novel plasminogen receptor, PLGRKT in IBC and of the carrier protein, SCAMP3. Furthermore, we describe the positive relationship between L1CAM expression and metastasis in IBC patients and the role of SCAMP3 as a tumor-related protein. Overall, the membrane proteomic signature of IBC reflects a global change in cellular organization and suggests additional strategies for cancer progression. Together, this study provides insight into the specialized IBC plasma membrane proteome with the potential to identify a number of novel therapeutic targets for IBC.
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Affiliation(s)
| | | | | | - Rezina Arju
- New York University School of Medicine, Alexandria Center for Life SciencesNew York, NY, USA
| | - Shah Giashuddin
- Department of Pathology and Laboratory Medicine, New York Methodist HospitalNew York, NY, USA
| | | | - Luis A Cubano
- Universidad Central del Caribe-School of MedicineBayamón, PR
| | - Robert J Schneider
- New York University School of Medicine, Alexandria Center for Life SciencesNew York, NY, USA
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14
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Kingsbury JM, Sen ND, Cardenas ME. Branched-Chain Aminotransferases Control TORC1 Signaling in Saccharomyces cerevisiae. PLoS Genet 2015; 11:e1005714. [PMID: 26659116 PMCID: PMC4684349 DOI: 10.1371/journal.pgen.1005714] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/09/2015] [Indexed: 11/18/2022] Open
Abstract
The conserved target of rapamycin complex 1 (TORC1) integrates nutrient signals to orchestrate cell growth and proliferation. Leucine availability is conveyed to control TORC1 activity via the leu-tRNA synthetase/EGOC-GTPase module in yeast and mammals, but the mechanisms sensing leucine remain only partially understood. We show here that both leucine and its α-ketoacid metabolite, α-ketoisocaproate, effectively activate the yeast TORC1 kinase via both EGOC GTPase-dependent and -independent mechanisms. Leucine and α-ketoisocaproate are interconverted by ubiquitous branched-chain aminotransferases (BCAT), which in yeast are represented by the mitochondrial and cytosolic enzymes Bat1 and Bat2, respectively. BCAT yeast mutants exhibit severely compromised TORC1 activity, which is partially restored by expression of Bat1 active site mutants, implicating both catalytic and structural roles of BCATs in TORC1 control. We find that Bat1 interacts with branched-chain amino acid metabolic enzymes and, in a leucine-dependent fashion, with the tricarboxylic acid (TCA)-cycle enzyme aconitase. BCAT mutation perturbed TCA-cycle intermediate levels, consistent with a TCA-cycle block, and resulted in low ATP levels, activation of AMPK, and TORC1 inhibition. We propose the biosynthetic capacity of BCAT and its role in forming multicomplex metabolons connecting branched-chain amino acids and TCA-cycle metabolism governs TCA-cycle flux to activate TORC1 signaling. Because mammalian mitochondrial BCAT is known to form a supramolecular branched-chain α-keto acid dehydrogenase enzyme complex that links leucine metabolism to the TCA-cycle, these findings establish a precedent for understanding TORC1 signaling in mammals. In all organisms from yeasts to mammals the target of rapamycin TORC1 pathway controls growth in response to nutrients such as leucine, but the leucine sensing mechanisms are only partially characterized. We show that both leucine and its α-ketoacid metabolite, α-ketoisocaproate, are similarly capable of activating TORC1 kinase via EGOC GTPase-dependent and -independent mechanisms. Activation of TORC1 by leucine or α-ketoisocaproate is only partially mediated via EGOC-GTPase. Leucine and α-ketoisocaproate are interconverted by ubiquitous branched-chain aminotransferases (BCAT). Disruption of BCAT caused reduced TORC1 activity, which was partially restored by expression of BCAT active site mutants, arguing for both structural and catalytic roles of BCAT in TORC1 control. We find BCAT interacts with several branched-chain amino acid metabolic enzymes, and in a leucine-dependent fashion with the tricarboxylic acid (TCA)-cycle enzyme aconitase. Both aconitase mutation or TCA-cycle inhibition impaired TORC1 activity. Mutation of BCAT resulted in a TCA-cycle intermediate profile consistent with a TCA-cycle block, low ATP levels, activation of AMPK, and TORC1 inhibition. Our results suggest a model whereby BCAT coordinates leucine and TCA cycle metabolism to control TORC1 signaling. Taken together, our findings forge key insights into how the TORC1 signaling cascade senses nutrients to control cell growth.
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Affiliation(s)
- Joanne M Kingsbury
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Neelam D Sen
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Maria E Cardenas
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
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15
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Yan JF, Kim H, Jeong SK, Lee HJ, Sethi MK, Lee LY, Beavis RC, Im H, Snyder MP, Hofree M, Ideker T, Wu SL, Paik YK, Fanayan S, Hancock WS. Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues. J Proteome Res 2015; 14:4995-5006. [PMID: 26435392 DOI: 10.1021/acs.jproteome.5b00827] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
V-erb-b2 erythroblastic leukemia viral oncogene homologue 2, known as ERBB2, is an important oncogene in the development of certain cancers. It can form a heterodimer with other epidermal growth factor receptor family members and activate kinase-mediated downstream signaling pathways. ERBB2 gene is located on chromosome 17 and is amplified in a subset of cancers, such as breast, gastric, and colon cancer. Of particular interest to the Chromosome-Centric Human Proteome Project (C-HPP) initiative is the amplification mechanism that typically results in overexpression of a set of genes adjacent to ERBB2, which provides evidence of a linkage between gene location and expression. In this report we studied patient samples from ERBB2-positive together with adjacent control nontumor tissues. In addition, non-ERBB2-expressing patient samples were selected as comparison to study the effect of expression of this oncogene. We detected 196 proteins in ERBB2-positive patient tumor samples that had minimal overlap (29 proteins) with the non-ERBB2 tumor samples. Interaction and pathway analysis identified extracellular signal regulated kinase (ERK) cascade and actin polymerization and actinmyosin assembly contraction as pathways of importance in ERBB2+ and ERBB2- gastric cancer samples, respectively. The raw data files are deposited at ProteomeXchange (identifier: PXD002674) as well as GPMDB.
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Affiliation(s)
- Julia Fangfei Yan
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Hoguen Kim
- Yonsei University College of Medicine, Yonsei University , 50-1 Yonsei-Ro, Seodaemun-gu, Seoul 120-752, Korea
| | - Seul-Ki Jeong
- Yonsei Proteome Research Center, Yonsei University , 262 Seongsanno, Seodaemun-gu, Seoul 120-749, Korea
| | - Hyoung-Joo Lee
- Yonsei Proteome Research Center, Yonsei University , 262 Seongsanno, Seodaemun-gu, Seoul 120-749, Korea
| | - Manveen K Sethi
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Ling Y Lee
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Ronald C Beavis
- Department of Biochemistry and Medical Genetics, Faculty of Health Sciences, University of Manitoba , 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - Hogune Im
- Department of Genetics, Stanford University , Stanford, California 94305, United States
| | - Michael P Snyder
- Department of Genetics, Stanford University , Stanford, California 94305, United States
| | - Matan Hofree
- Department of Computer Science and Engineering, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Trey Ideker
- Program in Bioinformatics, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Shiaw-Lin Wu
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Young-Ki Paik
- Yonsei University College of Medicine, Yonsei University , 50-1 Yonsei-Ro, Seodaemun-gu, Seoul 120-752, Korea.,Yonsei Proteome Research Center, Yonsei University , 262 Seongsanno, Seodaemun-gu, Seoul 120-749, Korea
| | - Susan Fanayan
- Department of Biomedical Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - William S Hancock
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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16
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Chang IW, Wu WJ, Wang YH, Wu TF, Liang PI, He HL, Yeh BW, Li CF. BCAT1 overexpression is an indicator of poor prognosis in patients with urothelial carcinomas of the upper urinary tract and urinary bladder. Histopathology 2015; 68:520-32. [DOI: 10.1111/his.12778] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/06/2015] [Indexed: 02/06/2023]
Affiliation(s)
- I-Wei Chang
- Department of Pathology; E-DA Hospital; I-Shou University; Kaohsiung Taiwan
- School of Medicine for International Students; I-Shou University; Kaohsiung Taiwan
| | - Wen-Jen Wu
- Graduate Institute of Medicine; College of Medicine; Kaohsiung Medical University; Kaohsiung Taiwan
- Department of Urology; School of Medicine; College of Medicine; Kaohsiung Medical University; Kaohsiung Taiwan
- Department of Urology; Kaohsiung Medical University Hospital; Kaohsiung Taiwan
- Department of Urology; Kaohsiung Municipal Hsiao-Kang Hospital; Kaohsiung Taiwan
- Center for Stem Cell Research; Kaohsiung Medical University; Kaohsiung Taiwan
| | - Yu-Hui Wang
- Institute of Bioinformatics and Biosignal Transduction; National Cheng Kung University; Tainan Taiwan
| | - Ting-Feng Wu
- Department of Biotechnology; Southern Taiwan University of Science and Technology; Tainan Taiwan
| | - Peir-In Liang
- Department of Pathology; Kaohsiung Medical University Hospital; Kaohsiung Medical University; Kaohsiung Taiwan
| | - Hong-Lin He
- Department of Pathology; E-DA Hospital; I-Shou University; Kaohsiung Taiwan
| | - Bi-Wen Yeh
- Graduate Institute of Medicine; College of Medicine; Kaohsiung Medical University; Kaohsiung Taiwan
- Department of Urology; School of Medicine; College of Medicine; Kaohsiung Medical University; Kaohsiung Taiwan
- Department of Urology; Kaohsiung Medical University Hospital; Kaohsiung Taiwan
- Department of Urology; Kaohsiung Municipal Hsiao-Kang Hospital; Kaohsiung Taiwan
- Center for Stem Cell Research; Kaohsiung Medical University; Kaohsiung Taiwan
| | - Chien-Feng Li
- Department of Biotechnology; Southern Taiwan University of Science and Technology; Tainan Taiwan
- Department of Pathology; Chi-Mei Medical Center; Tainan Taiwan
- National Cancer Research Institute; National Health Research Institutes; Tainan Taiwan
- Institute of Clinical Medicine; Kaohsiung Medical University; Kaohsiung Taiwan
- Department of Internal Medicine and Cancer Center; Kaohsiung Medical University Hospital; Kaohsiung Medical University; Kaohsiung Taiwan
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17
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Abstract
Breast cancer is among the most commonly diagnosed cancer types in women worldwide and is the second leading cause of cancer-related disease in the USA. SH2 domains recruit signaling proteins to phosphotyrosine residues on aberrantly activated growth factor and cytokine receptors and contribute to cancer cell cycling, metastasis, angiogenesis and so on. Herein we review phosphopeptide mimetic and small-molecule approaches targeting the SH2 domains of Grb2, Grb7 and STAT3 that inhibit their targets and reduce proliferation in in vitro breast cancer models. Only STAT3 inhibitors have been evaluated in in vivo models and have led to tumor reduction. Taken together, these studies suggest that targeting SH2 domains is an important approach to the treatment of breast cancer.
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18
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Panwar B, Menon R, Eksi R, Omenn GS, Guan Y. MI-PVT: A Tool for Visualizing the Chromosome-Centric Human Proteome. J Proteome Res 2015. [PMID: 26204236 DOI: 10.1021/acs.jproteome.5b00525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We have developed the web-based Michigan Proteome Visualization Tool (MI-PVT) to visualize and compare protein expression and isoform-level function across human chromosomes and tissues (http://guanlab.ccmb.med.umich.edu/mipvt). As proof of principle, we have populated the tool with Human Proteome Map (HPM) data. We were able to observe many biologically interesting features. From the vantage point of our chromosome 17 team, for example, we found more than 300 proteins from chromosome 17 expressed in each of the 30 tissues and cell types studied, with the highest number of expressed proteins being 685 in testis. Comparisons of expression levels across tissues showed low numbers of proteins expressed in esophagus, but esophagus had 12 cytoskeletal proteins coded on chromosome 17 with very high expression (>1000 spectral counts). This customized MI-PVT should be helpful for biologists to browse and study specific proteins and protein data sets across tissues and chromosomes. Users can upload any data of interest in MI-PVT for visualization. Our aim is to integrate extensive mass-spectrometric proteomic data into the tool to facilitate finding chromosome-centric protein expression and correlation across tissues.
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Affiliation(s)
- Bharat Panwar
- Department of Computational Medicine and Bioinformatics, ‡Department of Internal Medicine, §Department of Human Genetics and School of Public Health, ∥Department of Electrical Engineering and Computer Science, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, ‡Department of Internal Medicine, §Department of Human Genetics and School of Public Health, ∥Department of Electrical Engineering and Computer Science, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Ridvan Eksi
- Department of Computational Medicine and Bioinformatics, ‡Department of Internal Medicine, §Department of Human Genetics and School of Public Health, ∥Department of Electrical Engineering and Computer Science, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, ‡Department of Internal Medicine, §Department of Human Genetics and School of Public Health, ∥Department of Electrical Engineering and Computer Science, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, ‡Department of Internal Medicine, §Department of Human Genetics and School of Public Health, ∥Department of Electrical Engineering and Computer Science, University of Michigan , Ann Arbor, Michigan 48109, United States
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19
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Investigation of HER2 expression in canine mammary tumors by antibody-based, transcriptomic and mass spectrometry analysis: is the dog a suitable animal model for human breast cancer? Tumour Biol 2015; 36:9083-91. [PMID: 26088453 DOI: 10.1007/s13277-015-3661-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/09/2015] [Indexed: 11/27/2022] Open
Abstract
Canine mammary tumors (CMTs) share many features with human breast cancer (HBC), specifically concerning cancer-related pathways. Although the human epidermal growth factor receptor 2 (HER2) plays a significant role as a therapeutic and prognostic biomarker in HBC, its relevance in the pathogenesis and prognosis of CMT is still controversial. The aim of this study was to investigate HER2 expression in canine mammary hyperplasic and neoplastic tissues as well as to evaluate the specificity of the most commonly used polyclonal anti HER2 antibody by multiple molecular approaches. HER2 protein and RNA expression were determined by immunohistochemistry (IHC) and by quantitative real-time (qRT) PCR. A strong cell membrane associated with non-specific cytoplasmic staining was observed in 22% of carcinomas by IHC. Adenomas and carcinomas exhibited a significantly higher HER2 mRNA expression when compared to normal mammary glands, although no significant difference between benign and malignant tumors was noticed by qRT-PCR. The IHC results suggest a lack of specificity of the FDA-approved antibody in CMT samples as further demonstrated by Western immunoblotting (WB) and reverse phase protein arrays (RPPA). Furthemore, HER2 was not detected by mass spectrometry (MS) in a protein-expressing carcinoma at the IHC investigation. This study highlights that caution needs to be used when trying to translate from human to veterinary medicine information concerning cancer-related biomarkers and pathways. Further investigations are necessary to carefully assess the diagnostic and biological role specifically exerted by HER2 in CMTs and the use of canine mammary tumors as a model of HER2 over-expressing breast cancer.
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20
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Quantitative proteomic analysis of paired colorectal cancer and non-tumorigenic tissues reveals signature proteins and perturbed pathways involved in CRC progression and metastasis. J Proteomics 2015; 126:54-67. [PMID: 26054784 DOI: 10.1016/j.jprot.2015.05.037] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 05/18/2015] [Accepted: 05/31/2015] [Indexed: 02/07/2023]
Abstract
Modern proteomics has proven instrumental in our understanding of the molecular deregulations associated with the development and progression of cancer. Herein, we profile membrane-enriched proteome of tumor and adjacent normal tissues from eight CRC patients using label-free nanoLC-MS/MS-based quantitative proteomics and advanced pathway analysis. Of the 948 identified proteins, 184 proteins were differentially expressed (P<0.05, fold change>1.5) between the tumor and non-tumor tissue (69 up-regulated and 115 down-regulated in tumor tissues). The CRC tumor and non-tumor tissues clustered tightly in separate groups using hierarchical cluster analysis of the differentially expressed proteins, indicating a strong CRC-association of this proteome subset. Specifically, cancer associated proteins such as FN1, TNC, DEFA1, ITGB2, MLEC, CDH17, EZR and pathways including actin cytoskeleton and RhoGDI signaling were deregulated. Stage-specific proteome signatures were identified including up-regulated ribosomal proteins and down-regulated annexin proteins in early stage CRC. Finally, EGFR(+) CRC tissues showed an EGFR-dependent down-regulation of cell adhesion molecules, relative to EGFR(-) tissues. Taken together, this study provides a detailed map of the altered proteome and associated protein pathways in CRC, which enhances our mechanistic understanding of CRC biology and opens avenues for a knowledge-driven search for candidate CRC protein markers.
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21
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Robichaux JP, Hallett RM, Fuseler JW, Hassell JA, Ramsdell AF. Mammary glands exhibit molecular laterality and undergo left-right asymmetric ductal epithelial growth in MMTV-cNeu mice. Oncogene 2015; 34:2003-10. [PMID: 24909172 PMCID: PMC4261057 DOI: 10.1038/onc.2014.149] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 04/01/2014] [Accepted: 04/21/2014] [Indexed: 02/07/2023]
Abstract
Significant left-right (L-R) differences in tumor incidence and disease outcome occur for cancers of paired organs, including the breasts; however, the basis for this laterality is unknown. Here, we show that despite their morphologic symmetry, left versus right mammary glands in wild-type mice have baseline differences in gene expression that are L-R independently regulated during pubertal development, including genes that regulate luminal progenitor cell renewal, luminal cell differentiation, mammary tumorigenesis, tamoxifen sensitivity and chemotherapeutic resistance. In MMTV-cNeu(Tg/Tg) mice, which model HER2/Neu-amplified breast cancer, baseline L-R differences in mammary gene expression are amplified, sustained or inverted in a gene-specific manner and the mammary ductal epithelium undergoes L-R asymmetric growth and patterning. Comparative genomic analysis of mouse L-R mammary gene expression profiles with gene expression profiles of human breast tumors revealed significant linkage between right-sided gene expression and decreased breast cancer patient survival. Collectively, these findings are the first to demonstrate that mammary glands are lateralized organs, and, moreover, that mammary glands have L-R differential susceptibility to HER2/Neu oncogene-mediated effects on ductal epithelial growth and differentiation. We propose that intrinsic molecular laterality may have a role in L-R asymmetric breast tumor incidence and, furthermore, that interplay between the L-R molecular landscape and oncogene activity may contribute to the differential disease progression and patient outcome that are associated with tumor situs.
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Affiliation(s)
- Jacqulyne P. Robichaux
- Department of Regenerative Medicine and Cell Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425
| | - Robin M. Hallett
- Department of Biochemistry and Biomedical Sciences, Centre for Functional Genomics, McMaster University, Ontario, Canada
| | - John W. Fuseler
- Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, SC 29208
| | - John A. Hassell
- Department of Biochemistry and Biomedical Sciences, Centre for Functional Genomics, McMaster University, Ontario, Canada
| | - Ann F. Ramsdell
- Department of Regenerative Medicine and Cell Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425
- Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, SC 29208
- Program In Women’s and Gender Studies, College of Arts and Sciences, University of South Carolina, Columbia, SC 29208
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22
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Identifying the impact of inflammatory breast cancer on survival: a retrospective multi-center cohort study. Arch Gynecol Obstet 2015; 292:655-64. [DOI: 10.1007/s00404-015-3691-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 03/13/2015] [Indexed: 01/08/2023]
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23
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Abstract
Lung cancer is the most frequently occurring cancer in the world and continually leads in mortality among cancers. The overall 5-year survival rate for lung cancer has risen only 4% (from 12% to 16%) over the past 4 decades, and late diagnosis is a major obstacle in improving lung cancer prognosis. Survival of patients undergoing lung resection is greater than 80%, suggesting that early detection and diagnosis of cancers before they become inoperable and lethal will greatly improve mortality. Lung cancer biomarkers can be used for screening, detection, diagnosis, prognosis, prediction, stratification, therapy response monitoring, and so on. This review focuses on noninvasive diagnostic and prognostic biomarkers. For that purpose, our discussion in this review will focus on biological fluid-based biomarkers. The body fluids include blood (serum or plasma), sputum, saliva, BAL, pleural effusion, and VOC. Since it is rich in different cellular and molecular elements and is one of the most convenient and routine clinical procedures, serum or plasma is the main source for the development and validation of many noninvasive biomarkers. In terms of molecular aspects, the most widely validated ones are proteins, some of which are used in the clinical sector, though in limited accessory purposes. We will also discuss the lung cancer (protein) biomarkers in clinical trials and currently in the validation phase with hundreds of samples. After proteins, we will discuss microRNAs, methylated DNA, and circulating tumor cells, which are being vigorously developed and validated as potential lung cancer biomarkers. The main aim of this review is to provide researchers and clinicians with an understanding of the potential noninvasive lung cancer biomarkers in biological fluids that have recently been discovered.
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24
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Guo C, Liu S, Sun MZ. The role of CT10 regulation of kinase-like in cancer. Future Oncol 2014; 10:2687-97. [DOI: 10.2217/fon.14.199] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
ABSTRACT V-crk avian sarcoma virus CT10 oncogene homolog-like (CRKL) is a member of CRK family. It acts as an adaptor protein in intracellular signal transduction. CRKL has been reported overexpressed in a variety of cancers affecting the aggressive and malignant behaviors of cancer cells. CRKL seems to show a tumor-promotion role in gastric cancer, glioblastoma multiforme, hepatocellular carcinoma, bladder cancer, lung cancer, colon cancer, ovarian cancer, leukemia, breast cancer, head and neck cancer, rhabdomyosarcoma and neuroblastoma. The association of CRKL with malignant tumors and its potential action mechanisms were summarized. CRKL has the potential to be used as a biomarker for the diagnosis, treatment and prognosis of certain tumors.
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Affiliation(s)
- Chunmei Guo
- Department of Biotechnology, Dalian Medical University, Dalian, China
| | - Shuqing Liu
- Department of Biochemistry, Dalian Medical University, Dalian, China
| | - Ming-Zhong Sun
- Department of Biotechnology, Dalian Medical University, Dalian, China
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25
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Bertucci F, Finetti P, Vermeulen P, Van Dam P, Dirix L, Birnbaum D, Viens P, Van Laere S. Genomic profiling of inflammatory breast cancer: a review. Breast 2014; 23:538-45. [PMID: 24998451 DOI: 10.1016/j.breast.2014.06.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 06/02/2014] [Accepted: 06/08/2014] [Indexed: 01/04/2023] Open
Abstract
Inflammatory breast cancer (IBC) is a rare but aggressive form of breast cancer. Despite efforts in the past decade to delineate the molecular biology of IBC by applying high-throughput molecular profiling technologies to clinical samples, IBC remains insufficiently characterized. The reasons for that include limited sizes of the study population, heterogeneity with respect to the composition of the IBC and non-IBC control groups and technological differences across studies. In 2008, the World IBC Consortium was founded to foster collaboration between research groups focusing on IBC. One of the initial projects was to redefine the molecular profile of IBC using an unprecedented number of samples and search for gene signatures associated with survival and response to neo-adjuvant chemotherapy. Here, we provide an overview of all the molecular profiling studies that have been performed on IBC clinical samples to date.
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Affiliation(s)
- François Bertucci
- Département d'Oncologie Moléculaire, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes and UMR1068 Inserm, Marseille, France; Département d'Oncologie Médicale, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes and UMR1068 Inserm, Marseille, France; Faculté de Médecine, Université de la Méditerranée, Marseille, France.
| | - Pascal Finetti
- Département d'Oncologie Moléculaire, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes and UMR1068 Inserm, Marseille, France
| | - Peter Vermeulen
- Translational Cancer Research Unit, GZA Hospitals Sint-Augustinus, Wilrijk, Belgium; Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Peter Van Dam
- Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Luc Dirix
- Translational Cancer Research Unit, GZA Hospitals Sint-Augustinus, Wilrijk, Belgium; Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Daniel Birnbaum
- Département d'Oncologie Moléculaire, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes and UMR1068 Inserm, Marseille, France
| | - Patrice Viens
- Département d'Oncologie Médicale, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes and UMR1068 Inserm, Marseille, France; Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - Steven Van Laere
- Translational Cancer Research Unit, GZA Hospitals Sint-Augustinus, Wilrijk, Belgium; Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Department of Oncology, KU Leuven, Leuven, Belgium.
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Bai Y, Hassler J, Ziyar A, Li P, Wright Z, Menon R, Omenn GS, Cavalcoli JD, Kaufman RJ, Sartor MA. Novel bioinformatics method for identification of genome-wide non-canonical spliced regions using RNA-Seq data. PLoS One 2014; 9:e100864. [PMID: 24991935 PMCID: PMC4084626 DOI: 10.1371/journal.pone.0100864] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/31/2014] [Indexed: 12/03/2022] Open
Abstract
Setting During endoplasmic reticulum (ER) stress, the endoribonuclease (RNase) Ire1α initiates removal of a 26 nt region from the mRNA encoding the transcription factor Xbp1 via an unconventional mechanism (atypically within the cytosol). This causes an open reading frame-shift that leads to altered transcriptional regulation of numerous downstream genes in response to ER stress as part of the unfolded protein response (UPR). Strikingly, other examples of targeted, unconventional splicing of short mRNA regions have yet to be reported. Objective Our goal was to develop an approach to identify non-canonical, possibly very short, splicing regions using RNA-Seq data and apply it to ER stress-induced Ire1α heterozygous and knockout mouse embryonic fibroblast (MEF) cell lines to identify additional Ire1α targets. Results We developed a bioinformatics approach called the Read-Split-Walk (RSW) pipeline, and evaluated it using two Ire1α heterozygous and two Ire1α-null samples. The 26 nt non-canonical splice site in Xbp1 was detected as the top hit by our RSW pipeline in heterozygous samples but not in the negative control Ire1α knockout samples. We compared the Xbp1 results from our approach with results using the alignment program BWA, Bowtie2, STAR, Exonerate and the Unix “grep” command. We then applied our RSW pipeline to RNA-Seq data from the SKBR3 human breast cancer cell line. RSW reported a large number of non-canonical spliced regions for 108 genes in chromosome 17, which were identified by an independent study. Conclusions We conclude that our RSW pipeline is a practical approach for identifying non-canonical splice junction sites on a genome-wide level. We demonstrate that our pipeline can detect novel splice sites in RNA-Seq data generated under similar conditions for multiple species, in our case mouse and human.
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Affiliation(s)
- Yongsheng Bai
- Department of Computational Medicine and Bioinformatics, and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Justin Hassler
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Ahdad Ziyar
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Philip Li
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Zachary Wright
- Department of Computational Medicine and Bioinformatics, and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Departments of Internal Medicine and Human Genetics, and School of Public Health, University of Michigan, United States of America
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - James D. Cavalcoli
- Department of Computational Medicine and Bioinformatics, and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Randal J. Kaufman
- Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
- * E-mail: (RJK); (MAS)
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (RJK); (MAS)
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Udensi UK, Tackett AJ, Byrum S, Avaritt NL, Sengupta D, Moreland LW, Tchounwou PB, Isokpehi RD. Proteomics-Based Identification of Differentially Abundant Proteins from Human Keratinocytes Exposed to Arsenic Trioxide. JOURNAL OF PROTEOMICS & BIOINFORMATICS 2014; 7:166-178. [PMID: 25419056 PMCID: PMC4240501 DOI: 10.4172/jpb.1000317] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Arsenic is a widely distributed environmental toxicant that can cause multi-tissue pathologies. Proteomic assays allow for the identification of biological processes modulated by arsenic in diverse tissue types. METHOD The altered abundance of proteins from HaCaT human keratinocyte cell line exposed to arsenic was quantified using a label-free LC-MS/MS mass spectrometry workflow. Selected proteomics results were validated using western blot and RT-PCR. A functional annotation analytics strategy that included visual analytical integration of heterogeneous data sets was developed to elucidate functional categories. The annotations integrated were mainly tissue localization, biological process and gene family. RESULT The abundance of 173 proteins was altered in keratinocytes exposed to arsenic; in which 96 proteins had increased abundance while 77 proteins had decreased abundance. These proteins were also classified into 69 Gene Ontology biological process terms. The increased abundance of transferrin receptor protein (TFRC) was validated and also annotated to participate in response to hypoxia. A total of 33 proteins (11 increased abundance and 22 decreased abundance) were associated with 18 metabolic process terms. The Glutamate--cysteine ligase catalytic subunit (GCLC), the only protein annotated with the term sulfur amino acid metabolism process, had increased abundance while succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial precursor (SDHB), a tumor suppressor, had decreased abundance. CONCLUSION A list of 173 differentially abundant proteins in response to arsenic trioxide was grouped using three major functional annotations covering tissue localization, biological process and protein families. A possible explanation for hyperpigmentation pathologies observed in arsenic toxicity is that arsenic exposure leads to increased iron uptake in the normally hypoxic human skin. The proteins mapped to metabolic process terms and differentially abundant are candidates for evaluating metabolic pathways perturbed by arsenicals.
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Affiliation(s)
- Udensi K Udensi
- RCMI Center for Environmental Health, College of Science, Engineering and Technology, Jackson State University, Jackson Mississippi 39217, USA
| | - Alan J Tackett
- Proteomics Facility, University of Arkansas for Medical Sciences, Department of Biochemistry and Molecular Biology, Little Rock, AR 72205, USA
| | - Stephanie Byrum
- Proteomics Facility, University of Arkansas for Medical Sciences, Department of Biochemistry and Molecular Biology, Little Rock, AR 72205, USA
| | - Nathan L Avaritt
- Proteomics Facility, University of Arkansas for Medical Sciences, Department of Biochemistry and Molecular Biology, Little Rock, AR 72205, USA
| | - Deepanwita Sengupta
- Proteomics Facility, University of Arkansas for Medical Sciences, Department of Biochemistry and Molecular Biology, Little Rock, AR 72205, USA
| | - Linley W Moreland
- Proteomics Facility, University of Arkansas for Medical Sciences, Department of Biochemistry and Molecular Biology, Little Rock, AR 72205, USA
| | - Paul B Tchounwou
- RCMI Center for Environmental Health, College of Science, Engineering and Technology, Jackson State University, Jackson Mississippi 39217, USA
| | - Raphael D Isokpehi
- RCMI Center for Environmental Health, College of Science, Engineering and Technology, Jackson State University, Jackson Mississippi 39217, USA
- Department of Biology, School of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach FL 32114, USA
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Omenn GS, Guan Y, Menon R. A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines. J Proteomics 2014; 107:103-12. [PMID: 24802673 DOI: 10.1016/j.jprot.2014.04.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/09/2014] [Accepted: 04/10/2014] [Indexed: 02/07/2023]
Abstract
Combined RNA-Seq and proteomics analyses reveal striking differential expression of splice isoforms of key proteins in important cancer pathways and networks. Even between primary tumor cell lines from histologically similar inflammatory breast cancers, we find striking differences in hormone receptor-negative cell lines that are ERBB2 (Her2/neu)-amplified versus ERBB1 (EGFR) over-expressed with low ERBB2 activity. We have related these findings to protein-protein interaction networks, signaling and metabolic pathways, and methods for predicting functional variants among multiple alternative isoforms. Understanding the upstream ligands and regulators and the downstream pathways and interaction networks for ERBB receptors is certain to be important for explanation and prediction of the variable levels of expression and therapeutic responses of ERBB+tumors in the breast and in other organ sites. Alternative splicing is a remarkable evolutionary development that increases protein diversity from multi-exonic genes without requiring expansion of the genome. It is no longer sufficient to report the up- or down-expression of genes and proteins without dissecting the complexity due to alternative splicing. This article is part of a Special Issue entitled: 20Years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini , Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.
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Affiliation(s)
- Gilbert S Omenn
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA
| | - Yuanfang Guan
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA
| | - Rajasree Menon
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA
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Paik YK, Omenn GS, Thongboonkerd V, Marko-Varga G, Hancock WS. Genome-wide proteomics, Chromosome-Centric Human Proteome Project (C-HPP), part II. J Proteome Res 2013; 13:1-4. [PMID: 24328071 DOI: 10.1021/pr4011958] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center, Departments of Integrated Omics for Biomedical Science and Biochemistry, Yonsei University , 50 Yonsei-ro, Sudaemoon-ku, Seoul 120-749, Korea
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Gbormittah FO, Haab BB, Partyka K, Garcia-Ott C, Hancapie M, Hancock WS. Characterization of glycoproteins in pancreatic cyst fluid using a high-performance multiple lectin affinity chromatography platform. J Proteome Res 2013; 13:289-99. [PMID: 24303806 DOI: 10.1021/pr400813u] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Currently, pancreatic cancer is the fourth cause of cancer death. In 2013, it is estimated that ∼38 460 people will die of pancreatic cancer. Early detection of malignant cyst (pancreatic cancer precursor) is necessary to help prevent late diagnosis of the tumor. In this study, we characterized glycoproteins and nonglycoproteins on pooled mucinous (n = 10) and nonmucinous (n = 10) pancreatic cyst fluid to identify "proteins of interest" to differentiate between mucinous cyst from nonmucinous cyst and investigate these proteins as potential biomarker targets. An automated multilectin affinity chromatography (M-LAC) platform was utilized for glycoprotein enrichment followed by nano-LC-MS/MS analysis. Spectral count quantitation allowed for the identification of proteins with significant differential levels in mucinous cysts from nonmucinous cysts of which one protein (periostin) was confirmed via immunoblotting. To exhaustively evaluate differentially expressed proteins, we used a number of proteomic tools including gene ontology classification, pathway and network analysis, Novoseek data mining, and chromosome gene mapping. Utilization of complementary proteomic tools revealed that several of the proteins such as mucin 6 (MUC6), bile salt-activated lipase (CEL), and pyruvate kinase lysozyme M1/M2 with significant differential expression have strong association with pancreatic cancer. Furthermore, chromosome gene mapping demonstrated coexpressions and colocalization of some proteins of interest including 14-3-3 protein epsilon (YWHAE), pigment epithelium derived factor (SERPINF1), and oncogene p53.
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Affiliation(s)
- Francisca Owusu Gbormittah
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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Ponomarenko E, Baranova A, Lisitsa A, Albar JP, Archakov A. The chromosome-centric human proteome project at FEBS Congress. Proteomics 2013; 14:147-52. [PMID: 24285571 DOI: 10.1002/pmic.201300373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 11/07/2013] [Accepted: 11/20/2013] [Indexed: 11/10/2022]
Abstract
In the summer of 2013, distinguished global representatives of proteome science gathered to discuss the futuristic visions of the chromosome-centric human proteome project (C-HPP) (Cochairs: Y. K. Paik, G. Omenn; hosted by A. Archakov, Institute of Biomedical Chemistry, Russia) that was broadcast to the annual Federation of European Biochemical Societies Congress (St. Petersburg, Russia, July 10-11, 2013). Technology breakthroughs presented included a new ultra-sensitive Tribrid mass-spectrometer from Thermo and SOMAmers-Slow Off-rate Modified Aptamers (SOMAlogic, USA), a new type of protein capture reagents. Professor Archakov's group introduced the "rectangle" concept of proteome size as a product of proteome width and depth. The discussion on proteome width culminated with the introduction of digital biomarkers-low-copied aberrant proteins that differ from their typical forms by PTMs, alternative splicing, or single amino acid polymorphisms. The aberrant proteoforms, a complement to whole-genome proteomic surveys, were presented as an ultimate goal for the proteomic community.
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Affiliation(s)
- Elena Ponomarenko
- Institute of Biomedical Chemistry, Moscow, Russia; RHUPO, Russian Human Proteome Organization, Moscow, Russia
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Omenn GS. Plasma proteomics, the Human Proteome Project, and cancer-associated alternative splice variant proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:866-73. [PMID: 24211518 DOI: 10.1016/j.bbapap.2013.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 10/17/2013] [Accepted: 10/31/2013] [Indexed: 12/24/2022]
Abstract
This article addresses three inter-related subjects: the development of the Human Plasma Proteome Peptide Atlas, the launch of the Human Proteome Project, and the emergence of alternative splice variant transcripts and proteins as important features of evolution and pathogenesis. The current Plasma Peptide Atlas provides evidence on which peptides have been detected for every protein confidently identified in plasma; there are links to their spectra and their estimated abundance, facilitating the planning of targeted proteomics for biomarker studies. The Human Proteome Project (HPP) combines a chromosome-centric C-HPP with a biology and disease-driven B/D-HPP, upon a foundation of mass spectrometry, antibody, and knowledgebase resource pillars. The HPP aims to identify the approximately 7000 "missing proteins" and to characterize all proteins and their many isoforms. Success will enable the larger research community to utilize newly-available peptides, spectra, informative MS transitions, and databases for targeted analyses of priority proteins for each organ and disease. Among the isoforms of proteins, splice variants have the special feature of greatly enlarging protein diversity without enlarging the genome; evidence is accumulating of striking differential expression of splice variants in cancers. In this era of RNA-sequencing and advanced mass spectrometry, it is no longer sufficient to speak simply of increased or decreased expression of genes or proteins without carefully examining the splice variants in the protein mixture produced from each multi-exon gene. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan, Ann Arbor, MI, USA; Institute for Systems Biology, Seattle, WA, USA
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Menon R, Im H, Zhang EY, Wu SL, Chen R, Snyder M, Hancock WS, Omenn GS. Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes. J Proteome Res 2013; 13:212-27. [PMID: 24111759 DOI: 10.1021/pr400773v] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This study was conducted as a part of the Chromosome-Centric Human Proteome Project (C-HPP) of the Human Proteome Organization. The United States team of C-HPP is focused on characterizing the protein-coding genes in chromosome 17. Despite its small size, chromosome 17 is rich in protein-coding genes; it contains many cancer-associated genes, including BRCA1, ERBB2, (Her2/neu), and TP53. The goal of this study was to examine the splice variants expressed in three ERBB2 expressed breast cancer cell-line models of hormone-receptor-negative breast cancers by integrating RNA-Seq and proteomic mass spectrometry data. The cell lines represent distinct phenotypic variations subtype: SKBR3 (ERBB2+ (overexpression)/ER-/PR-; adenocarcinoma), SUM190 (ERBB2+ (overexpression)/ER-/PR-; inflammatory breast cancer), and SUM149 (ERBB2 (low expression) ER-/PR-; inflammatory breast cancer). We identified more than one splice variant for 1167 genes expressed in at least one of the three cancer cell lines. We found multiple variants of genes that are in the signaling pathways downstream of ERBB2 along with variants specific to one cancer cell line compared with the other two cancer cell lines and with normal mammary cells. The overall transcript profiles based on read counts indicated more similarities between SKBR3 and SUM190. The top-ranking Gene Ontology and BioCarta pathways for the cell-line specific variants pointed to distinct key mechanisms including: amino sugar metabolism, caspase activity, and endocytosis in SKBR3; different aspects of metabolism, especially of lipids in SUM190; cell-to-cell adhesion, integrin, and ERK1/ERK2 signaling; and translational control in SUM149. The analyses indicated an enrichment in the electron transport chain processes in the ERBB2 overexpressed cell line models and an association of nucleotide binding, RNA splicing, and translation processes with the IBC models, SUM190 and SUM149. Detailed experimental studies on the distinct variants identified from each of these three breast cancer cell line models that may open opportunities for drug target discovery and help unveil their specific roles in cancer progression and metastasis.
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Affiliation(s)
- Rajasree Menon
- Department of Computational Medicine & Bioinformatics, University of Michigan , 100 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
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