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Wang R, Lv C, Li D, Song Y, Yan Z. EEF1D stabilized by SRSF9 promotes colorectal cancer via enhancing the proliferation and metastasis. Int J Cancer 2024; 155:1487-1499. [PMID: 38771720 DOI: 10.1002/ijc.35039] [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: 11/28/2023] [Revised: 03/21/2024] [Accepted: 04/16/2024] [Indexed: 05/23/2024]
Abstract
Colorectal cancer (CRC) is the third most common cancer and causes high mortality worldwide. Although CRC has been studied widely, the molecular mechanism is not completely known. Eukaryotic translation elongation factor 1 delta (EEF1D) participates in the progression of various tumors, however, the effect of EEF1D on CRC remains unclear. Here, we aimed to identify the potential mechanism of EEF1D in CRC. The expression levels of EEF1D were assessed in CRC samples. Functional analysis of EEF1D in CRC was detected in vitro and in vivo. The regulatory mechanism of EEF1D was identified with RNA immunoprecipitation, RNA pull-down assay, and proteomics analysis. Our findings confirmed that EEF1D was upregulated in human CRC tissues. Functionally, EEF1D overexpression accelerated cell proliferation and metastasis, whereas EEF1D knockdown inhibited cell proliferation and metastasis both in vitro and in vivo CRC models. Furthermore, we showed that EEF1D was upregulated by SRSF9 via binding to 3'UTR of EEF1D mRNA. EEF1D knockdown reversed the malignant phenotype induced by SRSF9 overexpression. These findings demonstrated that EEF1D promotes CRC progression, and EEF1D may be a molecular target against CRC.
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Affiliation(s)
- Rui Wang
- Department of Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Chi Lv
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Donghao Li
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yutong Song
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhaopeng Yan
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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2
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Wang Z, Wang W, Luo Q, Song G. Plectin: Dual Participation in Tumor Progression. Biomolecules 2024; 14:1050. [PMID: 39334817 PMCID: PMC11430127 DOI: 10.3390/biom14091050] [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: 07/27/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 09/30/2024] Open
Abstract
The plectin gene can encode a cytoskeletal linking protein, plectin, known for its interaction with three critical components of the cellular cytoskeleton: intermediate filaments, microtubules, and actin filaments. In recent years, more and more studies have reported that plectin is closely related to tumorigenesis and development, exhibiting both tumor-suppressive and tumor-promoting functions. Here, we first introduce the molecular structure and function of plectin, and then we summarize the current understanding of the crucial role of plectin in cancer progression. Finally, we also discuss the possible reasons for the different roles of plectin expression in various types of cancer and highlight the double-edged sword role of plectin in tumor progression. The review aims to deepen the comprehensive understanding of plectin's role in cancer and further help to develop novel therapeutic strategies and drug targets.
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Affiliation(s)
- Zhihui Wang
- College of Bioengineering, Chongqing University, Chongqing 400030, China
- Key Laboratory of Biorheological Science & Technology, Ministry of Education, Chongqing University, Chongqing 400030, China
| | - Wenbin Wang
- College of Bioengineering, Chongqing University, Chongqing 400030, China
- Key Laboratory of Biorheological Science & Technology, Ministry of Education, Chongqing University, Chongqing 400030, China
| | - Qing Luo
- College of Bioengineering, Chongqing University, Chongqing 400030, China
- Key Laboratory of Biorheological Science & Technology, Ministry of Education, Chongqing University, Chongqing 400030, China
| | - Guanbin Song
- College of Bioengineering, Chongqing University, Chongqing 400030, China
- Key Laboratory of Biorheological Science & Technology, Ministry of Education, Chongqing University, Chongqing 400030, China
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3
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da Costa BC, Dourado MR, de Moraes EF, Panini LM, Elseragy A, Téo FH, Guimarães GN, Machado RA, Risteli M, Gurgel Rocha CA, Paranaíba LMR, González-Arriagada WA, da Silva SD, Rangel ALCA, Marques MR, Salo T, Coletta RD. Overexpression of heat-shock protein 47 impacts survival of patients with oral squamous cell carcinoma. J Oral Pathol Med 2023. [PMID: 37247331 DOI: 10.1111/jop.13455] [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: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/31/2023]
Abstract
BACKGROUND The expression of heat-shock protein 47 (HSP47) has been linked to collagen synthesis control and implicated in fibrotic disorders, but more recent studies have demonstrated its role in solid tumors. In this study, we explored the prognostic impact of HSP47 in oral squamous cell carcinomas (OSCC) and determined the in vitro effects of its loss-of-function on viability, proliferation, migration, invasion, and resistance to cisplatin of OSCC cells. METHODS The HSP47 expression in tumor samples was assessed by immunohistochemistry in two independent cohorts totaling 339 patients with OSCC, and protein levels were associated with clinicopathological features and survival outcomes. The OSCC cell lines HSC3 and SCC9 were transduced with lentivirus expressing short hairpin RNA to stably silence HSP47 and used in assays to measure cellular viability, proliferation, migration, and invasion. RESULTS HSP47 was overexpressed in OSCC samples, and its overexpression was significantly and independently associated with poor disease-specific survival and shortened disease-free survival in both OSCC cohorts. The knockdown of HSP47 showed no effects on cell viability or cisplatin sensitivity, but impaired significantly proliferation, migration, and invasion of OSCC cells, with stronger effects on SCC9 cells. CONCLUSION Our results show a significant prognostic impact of HSP47 overexpression in OSCC and reveal that HSP47 inhibition impairs the proliferation, migration, and invasion of OSCC cells. HSP47 may represent a potential therapeutic target for OSCC.
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Affiliation(s)
- Bruno Cesar da Costa
- Department of Oral Diagnosis and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Mauricio Rocha Dourado
- Department of Oral Diagnosis and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Everton Freitas de Moraes
- Department of Oral Diagnosis and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Luana Marí Panini
- Department of Oral Diagnosis and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Amr Elseragy
- Research Unit of Population Health, University of Oulu, Medical Research Centre and Oulu University Hospital, Oulu, Finland
| | - Fábio Haach Téo
- Department of Oral Diagnosis and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Gustavo Narvaes Guimarães
- Department of Biosciences and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Renato Assis Machado
- Department of Oral Diagnosis and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Maija Risteli
- Research Unit of Population Health, University of Oulu, Medical Research Centre and Oulu University Hospital, Oulu, Finland
| | - Clarissa Araujo Gurgel Rocha
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Federal University of Bahia and Dor Institute, Salvador, Bahia, Brazil
| | - Lívia Máris Ribeiro Paranaíba
- Department of Pathology and Parasitology, Institute of Biomedical Sciences, Federal University of Alfenas, Alfenas, Minas Gerais, Brazil
| | | | - Sabrina Daniela da Silva
- Lady Davis Institute for Medical Research and Segal Cancer Center, Jewish General Hospital, and Department of Otolaryngology-Head and Neck Surgery, McGill University, Montreal, Quebec, Canada
| | | | - Marcelo Rocha Marques
- Department of Biosciences and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Tuula Salo
- Research Unit of Population Health, University of Oulu, Medical Research Centre and Oulu University Hospital, Oulu, Finland
- Department of Oral and Maxillofacial Diseases and Department of Pathology, Helsinki University Central Hospital, and Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Ricardo D Coletta
- Department of Oral Diagnosis and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
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Dourado MR, Elseragy A, da Costa BC, Téo FH, Guimarães GN, Machado RA, Risteli M, Wahbi W, Gurgel Rocha CA, Paranaíba LMR, González-Arriagada WA, da Silva SD, Rangel ALCA, Marques MR, Rossa Junior C, Salo T, Coletta RD. Stress induced phosphoprotein 1 overexpression controls proliferation, migration and invasion and is associated with poor survival in oral squamous cell carcinoma. Front Oncol 2023; 12:1085917. [PMID: 36713524 PMCID: PMC9874128 DOI: 10.3389/fonc.2022.1085917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/22/2022] [Indexed: 01/12/2023] Open
Abstract
Objective Although there have been remarkable achievements in the molecular landscape of oral squamous cell carcinoma (OSCC) in recent years, bringing advances in the understanding of its pathogenesis, development and progression, little has been applied in the prognosis and choosing the optimal treatment. In this study, we explored the influence of the stress induced phosphoprotein 1 (STIP1), which is frequently reported to be highly expressed in many cancers, in OSCCs. Methods STIP1 expression was assessed in the TCGA database and in two independent cohorts by immunohistochemistry. Knockdown strategy was applied in OSCC cell lines to determine the impact of STIP1 on viability, proliferation, migration and invasion. The zebrafish model was applied for studying tumor formation and metastasis in vivo. The association of STIP1 and miR-218-5p was explored by bioinformatics and mimics transfection. Results STIP1 was highly expressed in OSCCs and significantly associated with shortened survival and higher risk of recurrence. STIP1 down-regulation decreased proliferation, migration and invasion of tumor cells, and reduced the number of metastases in the Zebrafish model. STIP1 and miR-218-5p were inversely expressed, and the transfection of miR-218-5p mimics into OSCC cells decreased STIP1 levels as well as proliferation, migration and invasion. Conclusion Our findings show that STIP1 overexpression, which is inversely associated with miR-218-5p levels, contributes to OSCC aggressiveness by controlling proliferation, migration and invasion and is a determinant of poor prognosis.
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Affiliation(s)
- Mauricio Rocha Dourado
- Department of Oral Diagnosis, and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Amr Elseragy
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, and Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Bruno Cesar da Costa
- Department of Oral Diagnosis, and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Fábio Haach Téo
- Department of Oral Diagnosis, and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Gustavo Narvaes Guimarães
- Department of Biosciences and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Renato Assis Machado
- Department of Oral Diagnosis, and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil,Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo (HRAC/USP), Bauru, São Paulo, Brazil
| | - Maija Risteli
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, and Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Wafa Wahbi
- Department of Oral and Maxillofacial Diseases, Helsinki University Central Hospital, and Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki, Finland
| | - Clarissa Araujo Gurgel Rocha
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Bahia, Brazil,Federal University of Bahia, Salvador, Bahia, Brazil,Center for Biotechnology and Cell Therapy, D’Or Institute for Research and Education (IDOR), Salvador, Brazil
| | - Lívia Máris Ribeiro Paranaíba
- Department of Pathology and Parasitology, Institute of Biomedical Sciences, Federal University of Alfenas, Alfenas, Minas Gerais, Brazil
| | | | - Sabrina Daniela da Silva
- Lady Davis Institute for Medical Research and Segal Cancer Center, Jewish General Hospital, and Department of Otolaryngology-Head and Neck Surgery, McGill University, Montreal, QC, Canada
| | | | - Marcelo Rocha Marques
- Department of Biosciences and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Carlos Rossa Junior
- Department of Diagnosis and Surgery, School of Dentistry at Araraquara, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Tuula Salo
- Cancer and Translational Medicine Research Unit, Faculty of Medicine, and Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland,Department of Oral and Maxillofacial Diseases, Helsinki University Central Hospital, and Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki, Finland,HUSLAB, Department of Pathology, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Ricardo D. Coletta
- Department of Oral Diagnosis, and Graduate Program in Oral Biology, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil,*Correspondence: Ricardo D. Coletta,
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Rezaei M, Shams Z, Rasouli BS, Amirfard KD, Sadrabadi MS, Gheysarzadeh A, Haghani K, Bakhtiyari S. New Association Between Diabetes Mellitus and Pancreatic Cancer. Curr Diabetes Rev 2023; 19:e180122200320. [PMID: 35040413 DOI: 10.2174/1573399818666220118095952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/11/2021] [Accepted: 11/24/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Diabetes mellitus is a global issue that has affected the lives of many people all over the world. This disorder, which is also called the mother of all diseases, possesses high pathogenicity and results in the emergence of many disorders. One of the known correlated diseases is pancreatic cancer which can be accompanied by diabetes mellitus. Therefore, finding the association between these diseases and common genes is urgent. OBJECTIVE In this study, in order to survey the relationship between diabetes mellitus and pancreatic cancer, the common genes of these disorders were analyzed by bioinformatics tools. METHODS For this purpose, we screened 17 shared genes from microarray data downloaded from the Gene Expression Omnibus (GEO) database. In addition, the relationship between identified genes was constructed by STRING and DAVID tools. RESULTS In total, 112 genes were identified to be differentially expressed. Among these, 17 genes were found to be common, including two genes that were down-regulated and others that were upregulated. Other analyses showed that most of the genes were enriched in Vibrio cholera infection and the mTOR signaling pathway. The biological processes of such genes included oxygen and gas transport, phagosome acidification, and GTPase activity. CONCLUSION In this study, 17 common genes that had not previously been considered in diabetes and pancreatic cancer were screened, which can be further considered for clinical approaches and in vitro studies.
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Affiliation(s)
- Monireh Rezaei
- Department of Medical Genetics, Faculty of Medical Science, Tarbiat Modares University, Tehran, Iran
| | - Zinat Shams
- Department of Biological Science, Kharazmi University, Tehran, Iran
| | - Bahareh Sadat Rasouli
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Science, Tehran, Iran
| | | | | | - Ali Gheysarzadeh
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
- Department of Clinical Biochemistry, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Karimeh Haghani
- Department of Clinical Biochemistry, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Salar Bakhtiyari
- Department of Clinical Biochemistry, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
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Negrutskii B, Shalak V, Novosylna O, Porubleva L, Lozhko D, El'skaya A. The eEF1 family of mammalian translation elongation factors. BBA ADVANCES 2022; 3:100067. [PMID: 37082266 PMCID: PMC10074971 DOI: 10.1016/j.bbadva.2022.100067] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
The eEF1 family of mammalian translation elongation factors is comprised of the two variants of eEF1A (eEF1A1 and eEF1A2), and the eEF1B complex. The latter consists of eEF1Bα, eEF1Bβ, and eEF1Bγ subunits. The two eEF1A variants have similar translation activity but may differ with respect to their secondary, "moonlighting" functions. This variability is underlined by the difference in the spatial organization of eEF1A1 and eEF1A2, and also possibly by the differences in their post-translational modifications. Here, we review the data on the spatial organization and post-translation modifications of eEF1A1 and eEF1A2, and provide examples of their involvement in various processes in addition to translation. We also describe the structural models of eEF1B subunits, their organization in the subcomplexes, and the trimeric model of the entire eEF1B complex. We discuss the functional consequences of such an assembly into a complex as well as the involvement of individual subunits in non-translational processes.
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Affiliation(s)
- B.S. Negrutskii
- Institute of Molecular Biology and Genetics, Acad. Zabolotnogo Str. 150, 03143 Kyiv, Ukraine
- Aarhus Institute of Advanced Sciences, Høegh-Guldbergs Gade 6B, DK–8000 Aarhus C, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
| | - V.F. Shalak
- Institute of Molecular Biology and Genetics, Acad. Zabolotnogo Str. 150, 03143 Kyiv, Ukraine
| | - O.V. Novosylna
- Institute of Molecular Biology and Genetics, Acad. Zabolotnogo Str. 150, 03143 Kyiv, Ukraine
| | - L.V. Porubleva
- Institute of Molecular Biology and Genetics, Acad. Zabolotnogo Str. 150, 03143 Kyiv, Ukraine
| | - D.M. Lozhko
- Institute of Molecular Biology and Genetics, Acad. Zabolotnogo Str. 150, 03143 Kyiv, Ukraine
| | - A.V. El'skaya
- Institute of Molecular Biology and Genetics, Acad. Zabolotnogo Str. 150, 03143 Kyiv, Ukraine
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Cell landscape of larval and adult Xenopus laevis at single-cell resolution. Nat Commun 2022; 13:4306. [PMID: 35879314 PMCID: PMC9314398 DOI: 10.1038/s41467-022-31949-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 07/12/2022] [Indexed: 11/09/2022] Open
Abstract
The rapid development of high-throughput single-cell RNA sequencing technology offers a good opportunity to dissect cell heterogeneity of animals. A large number of organism-wide single-cell atlases have been constructed for vertebrates such as Homo sapiens, Macaca fascicularis, Mus musculus and Danio rerio. However, an intermediate taxon that links mammals to vertebrates of more ancient origin is still lacking. Here, we construct the first Xenopus cell landscape to date, including larval and adult organs. Common cell lineage-specific transcription factors have been identified in vertebrates, including fish, amphibians and mammals. The comparison of larval and adult erythrocytes identifies stage-specific hemoglobin subtypes, as well as a common type of cluster containing both larval and adult hemoglobin, mainly at NF59. In addition, cell lineages originating from all three layers exhibits both antigen processing and presentation during metamorphosis, indicating a common regulatory mechanism during metamorphosis. Overall, our study provides a large-scale resource for research on Xenopus metamorphosis and adult organs.
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Xu Q, Liu Y, Wang S, Wang J, Liu L, Xu Y, Qin Y. Interfering with the expression of EEF1D gene enhances the sensitivity of ovarian cancer cells to cisplatin. BMC Cancer 2022; 22:628. [PMID: 35672728 PMCID: PMC9175347 DOI: 10.1186/s12885-022-09699-7] [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: 10/06/2021] [Accepted: 05/25/2022] [Indexed: 11/10/2022] Open
Abstract
Background Eukaryotic translation elongation factors 1 δ (EEF1D), has garnered much attention with regards to their role in the drug resistance of cancers. In this paper, we investigated the effects and mechanisms of increasing the sensitivity of ovarian cancer cells to cisplatin or cis-dichlorodiammine platinum (DDP) by knockdown and knockout of EEF1D gene in cellular and animal models. Methods The EEF1D gene was knocked-down or -out by siRNA or CRISPR/Cas9 respectively in human ovarian cancer cell SKOV3, DDP-resistant subline SKOV3/DDP, and EEF1D gene in human primary ovarian cancer cell from 5 ovarian cancer patients with progressive disease/stable disease (PD/SD) was transiently knocked down by siRNA interference. The mice model bearing xenografted tumor was established with subcutaneous inoculation of SKOV3/DDP. Results The results show that reducing or removing EEF1D gene expression significantly increased the sensitivity of human ovarian cancer cells to DDP in inhibiting viability and inducing apoptosis in vitro and in vivo, and also boosted DDP to inhibit xenografted tumor growth. Interfering with EEF1D gene expression in mice xenografted tumor significantly affected the levels of OPTN, p-Akt, Bcl-2, Bax, cleaved caspase-3 and ERCC1 compared to DDP treated mice alone, and had less effect on PI3K, Akt and caspase-3. Conclusions The knocking down or out EEF1D gene expression could enhance the sensitivity of ovarian cancer cells to DDP partially, which may be achieved via inactivating the PI3K/AKT signaling pathway, thus inducing cell apoptosis and decreasing repairment of DNA damage. Our study provides a novel therapeutic strategy for the treatment of ovarian cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09699-7.
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Affiliation(s)
- Qia Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Anhui Medical University, 81 Meishan Street, Hefei, Anhui, 230032, People's Republic of China
| | - Yun Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Anhui Medical University, 81 Meishan Street, Hefei, Anhui, 230032, People's Republic of China
| | - Shenyi Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Anhui Medical University, 81 Meishan Street, Hefei, Anhui, 230032, People's Republic of China
| | - Jing Wang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China
| | - Liwei Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Anhui Medical University, 81 Meishan Street, Hefei, Anhui, 230032, People's Republic of China
| | - Yin Xu
- Department of Neuropsychology, the Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, China. .,Laboratory of Molecular Neuropsychology, School of Mental Health and Psychological Sciences, Anhui Medical University, Hefei, 230032, Anhui, China.
| | - Yide Qin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Anhui Medical University, 81 Meishan Street, Hefei, Anhui, 230032, People's Republic of China.
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9
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Altered protein profile of plasma extracellular vesicles in oral squamous cell carcinoma development. J Proteomics 2022; 251:104422. [PMID: 34775099 DOI: 10.1016/j.jprot.2021.104422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/16/2021] [Accepted: 11/01/2021] [Indexed: 11/20/2022]
Abstract
Extracellular vesicles (EVs) are involved in a wide range of pathological processes and recognized as potential and novel biomarkers for oral squamous cell carcinoma (OSCC). Here, we describe the plasma EV proteome of rats with 4-nitroquinoline-1-oxide (4NQO)-induced OSCC or moderate dysplasia (MD), which can progress to OSCC, by tandem mass tag (TMT)-labeled mass spectrometry. The proteomic profiles suggest the differential expression of various proteins in MD and OSCC, some well-recognized pathological changes (e.g., translation, ATP metabolism, and mesenchymal transition), and some novel pathological changes (e.g., podosome, focal adhesion, and S100 binding). We re-examined the presence of traditional exosomal markers and the reported novel pan-EV markers. In summary, these results suggest potential EV biomarkers and underlying pathological changes in early OSCC as well as the presence of oral-derived EVs in plasma and the need for pan-EV markers. SIGNIFICANCE: This research suggests potential EV biomarkers and underlying pathological changes in early OSCC as well as the presence of oral-derived EVs in plasma and the need for pan-EV markers.
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10
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Downregulation of Methionine Cycle Genes MAT1A and GNMT Enriches Protein-Associated Translation Process and Worsens Hepatocellular Carcinoma Prognosis. Int J Mol Sci 2022; 23:ijms23010481. [PMID: 35008908 PMCID: PMC8745498 DOI: 10.3390/ijms23010481] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 01/27/2023] Open
Abstract
The major biological methyl donor, S-adenosylmethionine (adoMet) synthesis occurs mainly in the liver. Methionine adenosyltransferase 1A (MAT1A) and glycine N-methyltransferase (GNMT) are two key enzymes involved in the functional implications of that variation. We collected 42 RNA-seq data from paired hepatocellular carcinoma (HCC) and its adjacent normal liver tissue from the Cancer Genome Atlas (TCGA). There was no mutation found in MAT1A or GNMT RNA in the 42 HCC patients. The 11,799 genes were annotated in the RNA-Seq data, and their expression levels were used to investigate the phenotypes of low MAT1A and low GNMT by Gene Set Enrichment Analysis (GSEA). The REACTOME_TRANSLATION gene set was enriched and visualized in a heatmap along with corresponding differences in gene expression between low MAT1A versus high MAT1A and low GNMT versus high GNMT. We identified 43 genes of the REACTOME_TRANSLATION gene set that are powerful prognosis factors in HCC. The significantly predicted genes were referred into eukaryotic translation initiation (EIF3B, EIF3K), eukaryotic translation elongation (EEF1D), and ribosomal proteins (RPs). Cell models expressing various MAT1A and GNMT proved that simultaneous restoring the expression of MAT1A and GNMT decreased cell proliferation, invasion, as well as the REACTOME_TRANSLATION gene EEF1D, consistent with a better prognosis in human HCC. We demonstrated new findings that downregulation or defect in MAT1A and GNMT genes can enrich the protein-associated translation process that may account for poor HCC prognosis. This is the first study demonstrated that MAT1A and GNMT, the 2 key enzymes involved in methionine cycle, could attenuate the function of ribosome translation. We propose a potential novel mechanism by which the diminished GNMT and MAT1A expression may confer poor prognosis for HCC.
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11
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Xu H, Yu S, Peng K, Gao L, Chen S, Shen Z, Han Z, Chen M, Lin J, Chen S, Kang M. The role of EEF1D in disease pathogenesis: a narrative review. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1600. [PMID: 34790806 PMCID: PMC8576685 DOI: 10.21037/atm-21-5025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/16/2021] [Indexed: 11/17/2022]
Abstract
Objective The purpose of this paper was to investigate the role and mechanism of EEF1D in various diseases, especially in tumorigenesis and development, and explore the possibility of EEF1D as a biological target. Background EEF1D is a part of the EEF1 protein complex, which can produce four protein isoforms, of which three short isoforms are used as translation elongation factors. The three short isoforms play a role in anti-aging, regulating the cell cycle, and promoting the occurrence and development of malignant tumors, and the only long-form isoform plays a role in the development of the nervous system. Methods We searched the PubMed and Web of Science databases for literature up to January 2021 using relevant keywords, including “EEF1D”, “eukaryotic translation elongation factor 1 delta”, “translation elongation factor”, “translation elongation factor and cancer”, and “translation elongation factor and nervous system disease”. We then created an overview of the literature and summarized the results of the paper. Conclusions Through the review of relevant articles, we found that EEF1D is obviously overexpressed in a variety of tumors, and can regulate the proliferation of tumor cells and tumor growth, as well as play a role in tumor invasion. EEF1D is likely to become a new biological target for tumor therapy and diagnosis.
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Affiliation(s)
- Hui Xu
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shaobin Yu
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Kaiming Peng
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Lei Gao
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Sui Chen
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Zhimin Shen
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Ziyang Han
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Mingduan Chen
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Jihong Lin
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shuchen Chen
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Mingqiang Kang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China.,Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Science, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Cardio-Thoracic Surgery, Fujian Medical University, Fuzhou, China
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12
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Perez SM, Brinton LT, Kelly KA. Plectin in Cancer: From Biomarker to Therapeutic Target. Cells 2021; 10:2246. [PMID: 34571895 PMCID: PMC8469460 DOI: 10.3390/cells10092246] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/17/2022] Open
Abstract
The cytolinker and scaffolding protein, plectin, has emerged as a potent driver of malignant hallmarks in many human cancers due to its involvement in various cellular activities contributing to tumorigenesis, including cancer cell proliferation, adhesion, migration, invasion, and signal transduction. Evidence shows that beyond plectin's diverse protein interactome, its cancer-specific mislocalization to the cell surface enables its function as a potent oncoprotein. As such, therapeutic targeting of plectin, its protein interactors, and, in particular, cancer-specific plectin (CSP) presents an attractive opportunity to impede carcinogenesis directly. Here, we report on plectin's differential gene and protein expression in cancer, explore its mutational profile, and discuss the current understanding of plectin's and CSP's biological function in cancer. Moreover, we review the landscape of plectin as a prognostic marker, diagnostic biomarker, and target for imaging and therapeutic modalities. We highlight how, beyond their respective biological importance, plectin's common overexpression in cancer and CSP's cancer-specific bioavailability underscore their potential as high-value druggable targets. We discuss how recent evidence of the potent anti-cancer effects of CSP therapeutic targeting opens the door for cell-surface mislocalized proteins as novel therapeutic targets.
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Affiliation(s)
- Samantha M. Perez
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA;
| | | | - Kimberly A. Kelly
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA;
- ZielBio, Inc., Charlottesville, VA 22903, USA
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13
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Sá JDO, Trino LD, Oliveira AK, Lopes AFB, Granato DC, Normando AGC, Santos ES, Neves LX, Carnielli CM, Paes Leme AF. Proteomic approaches to assist in diagnosis and prognosis of oral cancer. Expert Rev Proteomics 2021; 18:261-284. [PMID: 33945368 DOI: 10.1080/14789450.2021.1924685] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Oral squamous cell carcinoma (OSCC) ranks among the top 10 leading causes of cancer worldwide, with 5-year survival rate of about 50%, high lymph node metastasis, and relapse rates. The OSCC diagnosis, prognosis, and treatment are mostly based on the clinical TNM classification. There is an urgent need for the discovery of biomarkers and therapeutic targets to assist in the clinical decision-making process.Areas covered: We summarize proteomic studies of the OSCC tumor, immune microenvironment, potential liquid biopsy sites, and post-translational modifications trying to retrieve information in the discovery and verification or (pre)validation phases. The search strategy was based on the combination of MeSH terms and expert refinement.Expert opinion: Untargeted combined with targeted proteomics are strategies that provide reliable and reproducible quantitation of proteins and are the methods of choice of many groups worldwide. Undoubtedly, proteomics has been contributing to the understanding of OSCC progression and uncovers potential candidates as biomarker or therapeutic targets. Nevertheless, none of these targets are available in the clinical practice yet. The scientific community needs to overcome the limitations by investing in robust experimental designs to strengthen the value of the findings, leveraging the translation of knowledge, and further supporting clinical decisions.
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Affiliation(s)
- Jamile De Oliveira Sá
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil.,Departamento De Diagnóstico Oral, Faculdade De Odontologia De Piracicaba, Universidade Estadual De Campinas (UNICAMP), Piracicaba, Brazil
| | - Luciana Daniele Trino
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Ana Karina Oliveira
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Ariane Fidelis Busso Lopes
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Daniela Campos Granato
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Ana Gabriela Costa Normando
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil.,Departamento De Diagnóstico Oral, Faculdade De Odontologia De Piracicaba, Universidade Estadual De Campinas (UNICAMP), Piracicaba, Brazil
| | - Erison Santana Santos
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil.,Departamento De Diagnóstico Oral, Faculdade De Odontologia De Piracicaba, Universidade Estadual De Campinas (UNICAMP), Piracicaba, Brazil
| | - Leandro Xavier Neves
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Carolina Moretto Carnielli
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
| | - Adriana Franco Paes Leme
- Laboratório Nacional De Biociências (Lnbio), Centro Nacional De Pesquisa Em Energia E Materiais (CNPEM), Campinas, Brazil
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14
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Joshi H, Vastrad B, Joshi N, Vastrad C, Tengli A, Kotturshetti I. Identification of Key Pathways and Genes in Obesity Using Bioinformatics Analysis and Molecular Docking Studies. Front Endocrinol (Lausanne) 2021; 12:628907. [PMID: 34248836 PMCID: PMC8264660 DOI: 10.3389/fendo.2021.628907] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 05/19/2021] [Indexed: 01/01/2023] Open
Abstract
Obesity is an excess accumulation of body fat. Its progression rate has remained high in recent years. Therefore, the aim of this study was to diagnose important differentially expressed genes (DEGs) associated in its development, which may be used as novel biomarkers or potential therapeutic targets for obesity. The gene expression profile of E-MTAB-6728 was downloaded from the database. After screening DEGs in each ArrayExpress dataset, we further used the robust rank aggregation method to diagnose 876 significant DEGs including 438 up regulated and 438 down regulated genes. Functional enrichment analysis was performed. These DEGs were shown to be significantly enriched in different obesity related pathways and GO functions. Then protein-protein interaction network, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. The module analysis was performed based on the whole PPI network. We finally filtered out STAT3, CORO1C, SERPINH1, MVP, ITGB5, PCM1, SIRT1, EEF1G, PTEN and RPS2 hub genes. Hub genes were validated by ICH analysis, receiver operating curve (ROC) analysis and RT-PCR. Finally a molecular docking study was performed to find small drug molecules. The robust DEGs linked with the development of obesity were screened through the expression profile, and integrated bioinformatics analysis was conducted. Our study provides reliable molecular biomarkers for screening and diagnosis, prognosis as well as novel therapeutic targets for obesity.
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Affiliation(s)
- Harish Joshi
- Department of Endocrinology, Endocrine and Diabetes Care Center, Hubbali, India
| | - Basavaraj Vastrad
- Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, India
| | - Nidhi Joshi
- Department of Medicine, Dr. D. Y. Patil Medical College, Kolhapur, India
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad, India
- *Correspondence: Chanabasayya Vastrad,
| | - Anandkumar Tengli
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Mysuru and JSS Academy of Higher Education & Research, Mysuru, India
| | - Iranna Kotturshetti
- Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, India
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15
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EEF1D Promotes Glioma Proliferation, Migration, and Invasion through EMT and PI3K/Akt Pathway. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7804706. [PMID: 33029523 PMCID: PMC7533006 DOI: 10.1155/2020/7804706] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/12/2020] [Accepted: 08/21/2020] [Indexed: 12/24/2022]
Abstract
Eukaryotic translation elongation factor 1δ (EEF1D), a subunit of the elongation factor 1 complex of proteins, mediates the elongation process of protein synthesis. Besides this canonical role, EEF1D was found overexpressed in many tumors, like hepatocarcinomas and medulloblastomas. In the present study, we demonstrated for the first time that EEF1D may interact with other putative proteins to regulate cell proliferation, migration, and invasion through PI3K/Akt and EMT pathways in glioma. Furthermore, knockdown of EEF1D could reduce cell proliferation and impaired epithelial-mesenchymal transition (EMT) phenotypes, including cell invasion. Taken together, these results indicate that EEF1D and its partner proteins might play a critical role in glioma and serve as a potential therapeutic target of glioma.
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16
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Domingueti CB, Castilho DAQ, de Oliveira CE, Janini JBM, González-Arriagada WA, Salo T, Coletta RD, Paranaíba LMR. Eukaryotic translation elongation factor 1δ, N-terminal propeptide of type I collagen and cancer-associated fibroblasts are prognostic markers of oral squamous cell carcinoma patients. Oral Surg Oral Med Oral Pathol Oral Radiol 2020; 130:700-707.e2. [PMID: 33132084 DOI: 10.1016/j.oooo.2020.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 08/06/2020] [Accepted: 09/07/2020] [Indexed: 12/28/2022]
Abstract
OBJECTIVE Identifying markers that influence oral squamous cell carcinoma (OSCC) prognosis is a fundamental strategy to improve the overall survival of patients. Markers such as eukaryotic translation elongation factor 1δ (EEF1D), fascin, N-terminal propeptide of type I collagen (PINP), and cancer-associated fibroblasts (CAFs) have been noticed in OSCCs and their levels are closely related to the prognosis of tumors. Our aim was to confirm the role of those markers in OSCC prognosis. STUDY DESIGN Immunohistochemistry was performed in 90 OSCC specimens. The associations between clinicopathologic features and expression of markers were assessed by χ2 test. Kaplan-Meier curves and univariate and multivariate Cox regression models were used for survival analysis. Markers were analyzed individually and in combination. RESULTS High expression of EEF1D (P = .017) and PINP (P = .02) and abundant density of CAFs in tumor stroma (P = .005) predicted significantly poor survival in OSCC patients. Multivariate analysis revealed that all 3 parameters are individually independent prognostic factors of OSCC patients, and their combination improved the discrimination of patients at high risk for poor survival. CONCLUSIONS Our results suggested that the expression of EEF1D and PINP and the density of CAFs might influence the survival of patients with OSCC.
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Affiliation(s)
- Catherine Bueno Domingueti
- Department of Pathology and Parasitology, Institute of Biomedical Sciences, Federal University of Alfenas, Alfenas, Minas Gerais, Brazil
| | - Dayana Aparecida Queiroz Castilho
- Department of Pathology and Parasitology, Institute of Biomedical Sciences, Federal University of Alfenas, Alfenas, Minas Gerais, Brazil
| | - Carine Ervolino de Oliveira
- Department of Pathology and Parasitology, Institute of Biomedical Sciences, Federal University of Alfenas, Alfenas, Minas Gerais, Brazil
| | | | | | - Tuula Salo
- Cancer and Translational Medicine Research Unit, Faculty of Medicine and Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland; Institute of Oral and Maxillofacial Disease, University of Helsinki, and HUSLAB, Department of Pathology, Helsinki University Hospital, Helsinki, Finland
| | - Ricardo D Coletta
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Lívia Máris Ribeiro Paranaíba
- Department of Pathology and Parasitology, Institute of Biomedical Sciences, Federal University of Alfenas, Alfenas, Minas Gerais, Brazil.
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17
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Negrutskii B. Non-translational Connections of eEF1B in the Cytoplasm and Nucleus of Cancer Cells. Front Mol Biosci 2020; 7:56. [PMID: 32328499 PMCID: PMC7160314 DOI: 10.3389/fmolb.2020.00056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 03/20/2020] [Indexed: 12/28/2022] Open
Abstract
The human translation machinery includes three types of supramolecular complexes involved in elongation of the polypeptide chain: the ribosome, complex of elongation factors eEF1B and multienzyme aminoacyl-tRNA synthetase complex. Of the above, eEF1B is the least investigated assembly. Recently, a number of studies provided some insights into the structure of different eEF1B subunits and changes in their expression in cancer and other diseases. There is increasing agreement that possible disease-related functions of eEF1B are not necessarily related to its role in translation. This mini-review focuses on structural and functional features of the eEF1B complex while paying special attention to possible non-canonical functions of its subunits in cancer cells.
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Affiliation(s)
- Boris Negrutskii
- Department of Structural and Functional Proteomics, Institute of Molecular Biology and Genetics, National Academy of Sciences, Kyiv, Ukraine
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18
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Biterge-Sut B. Alterations in Eukaryotic Elongation Factor complex proteins (EEF1s) in cancer and their implications in epigenetic regulation. Life Sci 2019; 238:116977. [PMID: 31639400 DOI: 10.1016/j.lfs.2019.116977] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/05/2019] [Accepted: 10/15/2019] [Indexed: 11/16/2022]
Abstract
AIMS In the cell, both transcriptional and translational processes are tightly regulated. Cancer is a multifactorial disease characterized by aberrant protein expression. Since epigenetic control mechanisms are also frequently disrupted during carcinogenesis, they have been the center of attention in cancer research within the past decades. EEF1 complex members, which are required for the elongation process in eukaryotes, have recently been implicated in carcinogenesis. This study aims to investigate genetic alterations within EEF1A1, EEF1A2, EEF1B2, EEF1D, EEF1E1 and EEF1G genes and their potential effects on epigenetic regulation mechanisms. MATERIALS AND METHODS In this study, we analyzed DNA sequencing and mRNA expression data available on The Cancer Genome Atlas (TCGA) across different cancer types to detect genetic alterations in EEF1 genes and investigated their potential impact on selected epigenetic modulators. KEY FINDINGS We found that EEF1 complex proteins were deregulated in several types of cancer. Lower EEF1A1, EEF1B2, EEF1D and EEF1G levels were correlated with poor survival in glioma, while lower EEF1B2, EEF1D and EEF1E1 levels were correlated with better survival in hepatocellular carcinoma. We detected genetic alterations within EEF1 genes in up to 35% of the patients and showed that these alterations resulted in down-regulation of histone modifying enzymes KMT2C, KMT2D, KMT2E, KAT6A and EP300. SIGNIFICANCE Here in this study, we showed that EEF1 deregulations might result in differential epigenomic landscapes, which affect the overall transcriptional profile, contributing to carcinogenesis. Identification of these molecular distinctions might be useful in developing targeted drug therapies and personalized medicine.
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Affiliation(s)
- Burcu Biterge-Sut
- Nigde Omer Halisdemir University, Faculty of Medicine, Department of Medical Biology, Nigde, Turkey.
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19
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Nascimento-Filho CHV, Webber LP, Borgato GB, Goloni-Bertollo EM, Squarize CH, Castilho RM. Hypoxic niches are endowed with a protumorigenic mechanism that supersedes the protective function of PTEN. FASEB J 2019; 33:13435-13449. [PMID: 31560860 DOI: 10.1096/fj.201900722r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide and is characterized by a fast-paced growth. Like other solid tumors, the HNSCC growth rate results in the development of hypoxic regions identified by the expression of hypoxia-inducible factor 1α (HIF-1α). Interestingly, clinical data have shown that pharmacological induction of intratumoral hypoxia caused an unexpected rise in tumor metastasis and the accumulation of cancer stem cells (CSCs). However, little is known on the molecular circuitries involved in the presence of intratumoral hypoxia and the augmented population of CSCs. Here we explore the impact of hypoxia on the behavior of HNSCC and define that the controlling function of phosphatase and tensin homolog (PTEN) over HIF-1α expression and CSC accumulation are de-regulated during hypoxic events. Our findings indicate that hypoxic niches are poised to accumulate CSCs in a molecular process driven by the loss of PTEN activity. Furthermore, our data suggest that targeted therapies aiming at the PTEN/PI3K signaling may constitute an effective strategy to counteract the development of intratumoral hypoxia and the accumulation of CSCs.-Nascimento-Filho, C. H. V., Webber, L. P., Borgato, G. B., Goloni-Bertollo, E. M., Squarize, C. H., Castilho, R. M. Hypoxic niches are endowed with a protumorigenic mechanism that supersedes the protective function of PTEN.
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Affiliation(s)
- Carlos H V Nascimento-Filho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, Michigan, USA.,Genetics and Molecular Biology Research Unit, Department of Molecular Biology, School of Medicine of São José do Rio Preto, São Paulo, Brazil
| | - Liana P Webber
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, Michigan, USA.,Department of Oral Pathology, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Gabriell B Borgato
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, Michigan, USA.,Department of Oral Biology, School of Dentistry, State University of Campinas, Piracicaba, São Paulo, Brazil
| | - Eny M Goloni-Bertollo
- Genetics and Molecular Biology Research Unit, Department of Molecular Biology, School of Medicine of São José do Rio Preto, São Paulo, Brazil
| | - Cristiane H Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, Michigan, USA.,University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan, USA
| | - Rogerio M Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, Michigan, USA.,University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan, USA
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20
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Fonseca FP, Macedo CCS, Dos Santos Costa SF, Leme AFP, Rodrigues RR, Pontes HAR, Altemani A, van Heerden WFP, Martins MD, de Almeida OP, Santos-Silva AR, Lopes MA, Vargas PA. Mass spectrometry-based proteome profile may be useful to differentiate adenoid cystic carcinoma from polymorphous adenocarcinoma of salivary glands. Oral Surg Oral Med Oral Pathol Oral Radiol 2019; 128:639-650. [PMID: 31494112 DOI: 10.1016/j.oooo.2019.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 06/12/2019] [Accepted: 07/24/2019] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The aim of this study was to determine the proteome of adenoid cystic carcinoma (AdCC) and polymorphous adenocarcinoma (PAc) and to identify a protein signature useful in distinguishing these two neoplasms. STUDY DESIGN Ten cases of AdCC and 10 cases of PAc were microdissected for enrichment of neoplastic tissue. The samples were submitted to liquid chromatography-tandem mass spectrometry (LC-MS/MS), and the proteomics data were analyzed by using the MaxQuant software. LC-MS/MS spectra were searched against the Human UniProt database, and statistical analyses were performed with Perseus software. Bioinformatic analyses were performed by using discovery-based proteomic data on both tumors. RESULTS LC-MS/MS analysis identified 1957 proteins. The tumors shared 1590 proteins, and 261 were exclusively identified in AdCC and 106 in PAc. Clustering analysis of the statistically significant proteins clearly separated AdCC from PAc. Protein expression 10 times higher in one group than in the other led to a signature of 16 proteins-6 upregulated in AdCC and 10 in PAc. A new clustering analysis showed reverse regulation and also differentiated both tumors. CONCLUSIONS Global proteomics may be useful in discriminating these two malignant salivary neoplasms that frequently show clinical and microscopic overlaps, but additional validation studies are still necessary to determine the diagnostic potential of the protein signature obtained.
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Affiliation(s)
- Felipe Paiva Fonseca
- Department of Oral Diagnosis, Oral Pathology Division, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil; Department of Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Carolina Carneiro Soares Macedo
- Department of Oral Diagnosis, Oral Pathology Division, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil
| | | | - Adriana Franco Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, Brazil
| | - Romênia Ramos Rodrigues
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, Brazil
| | - Hélder Antônio Rebelo Pontes
- Service of Oral Pathology, João de Barros Barreto University Hospital, Federal University of Pará, Belém, Brazil
| | - Albina Altemani
- Department of Pathology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Willie F P van Heerden
- Department of Oral Pathology and Oral Biology, School of Dentistry, University of Pretoria, Pretoria, South Africa
| | - Manoela Domingues Martins
- Department of Oral Diagnosis, Oral Pathology Division, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil; Department of Pathology, School of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Oslei Paes de Almeida
- Department of Oral Diagnosis, Oral Pathology Division, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil
| | - Alan Roger Santos-Silva
- Department of Oral Diagnosis, Oral Pathology Division, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil
| | - Márcio Ajudarte Lopes
- Department of Oral Diagnosis, Oral Pathology Division, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil
| | - Pablo Agustin Vargas
- Department of Oral Diagnosis, Oral Pathology Division, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba, Brazil; Department of Oral Pathology and Oral Biology, School of Dentistry, University of Pretoria, Pretoria, South Africa.
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21
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Chen X, Li A, Sun BF, Yang Y, Han YN, Yuan X, Chen RX, Wei WS, Liu Y, Gao CC, Chen YS, Zhang M, Ma XD, Liu ZW, Luo JH, Lyu C, Wang HL, Ma J, Zhao YL, Zhou FJ, Huang Y, Xie D, Yang YG. 5-methylcytosine promotes pathogenesis of bladder cancer through stabilizing mRNAs. Nat Cell Biol 2019; 21:978-990. [PMID: 31358969 DOI: 10.1038/s41556-019-0361-y] [Citation(s) in RCA: 408] [Impact Index Per Article: 81.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 06/12/2019] [Indexed: 01/16/2023]
Abstract
Although 5-methylcytosine (m5C) is a widespread modification in RNAs, its regulation and biological role in pathological conditions (such as cancer) remain unknown. Here, we provide the single-nucleotide resolution landscape of messenger RNA m5C modifications in human urothelial carcinoma of the bladder (UCB). We identify numerous oncogene RNAs with hypermethylated m5C sites causally linked to their upregulation in UCBs and further demonstrate YBX1 as an m5C 'reader' recognizing m5C-modified mRNAs through the indole ring of W65 in its cold-shock domain. YBX1 maintains the stability of its target mRNA by recruiting ELAVL1. Moreover, NSUN2 and YBX1 are demonstrated to drive UCB pathogenesis by targeting the m5C methylation site in the HDGF 3' untranslated region. Clinically, a high coexpression of NUSN2, YBX1 and HDGF predicts the poorest survival. Our findings reveal an unprecedented mechanism of RNA m5C-regulated oncogene activation, providing a potential therapeutic strategy for UCB.
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Affiliation(s)
- Xin Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ang Li
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bao-Fa Sun
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Ya-Nan Han
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xun Yuan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ri-Xin Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wen-Su Wei
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yanchao Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Chun-Chun Gao
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Sheng Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mengmeng Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Multiscale Research Institute for Complex Systems, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiao-Dan Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhuo-Wei Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jun-Hang Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Cong Lyu
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Hai-Lin Wang
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Multiscale Research Institute for Complex Systems, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, China
| | - Yong-Liang Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Fang-Jian Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ying Huang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
| | - Dan Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China. .,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
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22
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Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer. Nat Commun 2018; 9:3598. [PMID: 30185791 PMCID: PMC6125363 DOI: 10.1038/s41467-018-05696-2] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 07/13/2018] [Indexed: 01/13/2023] Open
Abstract
Different regions of oral squamous cell carcinoma (OSCC) have particular histopathological and molecular characteristics limiting the standard tumor−node−metastasis prognosis classification. Therefore, defining biological signatures that allow assessing the prognostic outcomes for OSCC patients would be of great clinical significance. Using histopathology-guided discovery proteomics, we analyze neoplastic islands and stroma from the invasive tumor front (ITF) and inner tumor to identify differentially expressed proteins. Potential signature proteins are prioritized and further investigated by immunohistochemistry (IHC) and targeted proteomics. IHC indicates low expression of cystatin-B in neoplastic islands from the ITF as an independent marker for local recurrence. Targeted proteomics analysis of the prioritized proteins in saliva, combined with machine-learning methods, highlights a peptide-based signature as the most powerful predictor to distinguish patients with and without lymph node metastasis. In summary, we identify a robust signature, which may enhance prognostic decisions in OSCC and better guide treatment to reduce tumor recurrence or lymph node metastasis. Oral cancer has region-specific histopathological and molecular characteristics, complicating its classification by the standard tumor-node-metastasis system. Here, the authors combine discovery and targeted proteomics with IHC to identify region-specific and saliva biomarkers for oral cancer prognosis.
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23
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Choudhary I, Lee H, Pyo MJ, Heo Y, Chae J, Yum SS, Kang C, Kim E. Proteomic Investigation to Identify Anticancer Targets of Nemopilema nomurai Jellyfish Venom in Human Hepatocarcinoma HepG2 Cells. Toxins (Basel) 2018; 10:E194. [PMID: 29748501 PMCID: PMC5983250 DOI: 10.3390/toxins10050194] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 04/24/2018] [Accepted: 04/27/2018] [Indexed: 12/30/2022] Open
Abstract
Nemopilema nomurai is a giant jellyfish that blooms in East Asian seas. Recently, N. nomurai venom (NnV) was characterized from a toxicological and pharmacological point of view. A mild dose of NnV inhibits the growth of various kinds of cancer cells, mainly hepatic cancer cells. The present study aims to identify the potential therapeutic targets and mechanism of NnV in the growth inhibition of cancer cells. Human hepatocellular carcinoma (HepG2) cells were treated with NnV, and its proteome was analyzed using two-dimensional gel electrophoresis, followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI/TOF/MS). The quantity of twenty four proteins in NnV-treated HepG2 cells varied compared to non-treated control cells. Among them, the amounts of fourteen proteins decreased and ten proteins showed elevated levels. We also found that the amounts of several cancer biomarkers and oncoproteins, which usually increase in various types of cancer cells, decreased after NnV treatment. The representative proteins included proliferating cell nuclear antigen (PCNA), glucose-regulated protein 78 (GRP78), glucose-6-phosphate dehydrogenase (G6PD), elongation factor 1γ (EF1γ), nucleolar and spindle-associated protein (NuSAP), and activator of 90 kDa heat shock protein ATPase homolog 1 (AHSA1). Western blotting also confirmed altered levels of PCNA, GRP78, and G6PD in NnV-treated HepG2 cells. In summary, the proteomic approach explains the mode of action of NnV as an anticancer agent. Further characterization of NnV may help to unveil novel therapeutic agents in cancer treatment.
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Affiliation(s)
- Indu Choudhary
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea.
| | - Hyunkyoung Lee
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea.
| | - Min Jung Pyo
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea.
| | - Yunwi Heo
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea.
| | - Jinho Chae
- Marine Environmental Research and Information Laboratory, Gunpo 15850, Korea.
| | - Seung Shic Yum
- South Sea Environmental Research Center, Korea Institute of Ocean Science and Technology (KIOST), Geoje 53201, Korea.
- Faculty of Marine Environmental Science, University of Science and technology (UST), Geoje 53201, Korea.
| | - Changkeun Kang
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea.
- Institutes of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea.
| | - Euikyung Kim
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea.
- Institute of Animal Medicine, Gyeongsang National University, Jinju 52828, Korea.
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24
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Cheng DD, Li SJ, Zhu B, Zhou SM, Yang QC. EEF1D overexpression promotes osteosarcoma cell proliferation by facilitating Akt-mTOR and Akt-bad signaling. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:50. [PMID: 29510727 PMCID: PMC5839064 DOI: 10.1186/s13046-018-0715-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/21/2018] [Indexed: 11/17/2022]
Abstract
Background Dysregulation of eukaryotic translation elongation factor 1 delta (EEF1D) in cancers has been reported; however, the role and mechanisms of EEF1D in osteosarcoma remain poorly understood. The aim of this study is to investigate the expression and role of EEF1D in osteosarcoma and to elucidate its underlying mechanisms. Methods The expression of EEF1D in osteosarcomas and cell lines was evaluated by qRT-PCR, Western blotting and immunohistochemistry. EEF1D knockdown using small interfering RNA (siRNA) was employed to analyze the role of EEF1D in osteosarcoma cell proliferation and cell cycle progression. The host signaling pathways affected by EEF1D knockdown were detected using PathScan® intracellular signaling array kit. Results The expression of EEF1D was found to be up-regulated in human osteosarcoma tissues and cell lines. Its expression was positively correlated with Enneking stage and the tumor recurrence. EEF1D knockdown inhibited osteosarcoma cell proliferation, colony-forming ability, and cell cycle G2/M transition in vitro. In addition, EEF1D knockdown decreased the levels of phospho-Akt, phospho-mTOR, and phospho-Bad proteins. Conclusions EEF1D is upregulated in osteosarcoma and plays a tumor promoting role by facilitating Akt-mTOR and Akt-Bad signaling pathways. Accordingly, EEF1D is a potential target for cancer therapy. Electronic supplementary material The online version of this article (10.1186/s13046-018-0715-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dong-Dong Cheng
- Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600, Yishan Road, Shanghai, 200233, China
| | - Shi-Jie Li
- Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600, Yishan Road, Shanghai, 200233, China
| | - Bin Zhu
- Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600, Yishan Road, Shanghai, 200233, China
| | - Shu-Min Zhou
- Institution of microsurgery for limbs, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600, Yishan Road, Shanghai, 200233, China.
| | - Qing-Cheng Yang
- Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, No. 600, Yishan Road, Shanghai, 200233, China.
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25
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Foster BL, Ao M, Salmon CR, Chavez MB, Kolli TN, Tran AB, Chu EY, Kantovitz KR, Yadav M, Narisawa S, Millán JL, Nociti FH, Somerman MJ. Osteopontin regulates dentin and alveolar bone development and mineralization. Bone 2018; 107:196-207. [PMID: 29313816 PMCID: PMC5803363 DOI: 10.1016/j.bone.2017.12.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 11/09/2017] [Accepted: 12/03/2017] [Indexed: 01/09/2023]
Abstract
The periodontal complex is essential for tooth attachment and function and includes the mineralized tissues, cementum and alveolar bone, separated by the unmineralized periodontal ligament (PDL). To gain insights into factors regulating cementum-PDL and bone-PDL borders and protecting against ectopic calcification within the PDL, we employed a proteomic approach to analyze PDL tissue from progressive ankylosis knock-out (Ank-/-) mice, featuring reduced PPi, rapid cementogenesis, and excessive acellular cementum. Using this approach, we identified the matrix protein osteopontin (Spp1/OPN) as an elevated factor of interest in Ank-/- mouse molar PDL. We studied the role of OPN in dental and periodontal development and function. During tooth development in wild-type (WT) mice, Spp1 mRNA was transiently expressed by cementoblasts and strongly by alveolar bone osteoblasts. Developmental analysis from 14 to 240days postnatal (dpn) indicated normal histological structures in Spp1-/- comparable to WT control mice. Microcomputed tomography (micro-CT) analysis at 30 and 90dpn revealed significantly increased volumes and tissue mineral densities of Spp1-/- mouse dentin and alveolar bone, while pulp and PDL volumes were decreased and tissue densities were increased. However, acellular cementum growth was unaltered in Spp1-/- mice. Quantitative PCR of periodontal-derived mRNA failed to identify potential local compensators influencing cementum in Spp1-/- vs. WT mice at 26dpn. We genetically deleted Spp1 on the Ank-/- mouse background to determine whether increased Spp1/OPN was regulating periodontal tissues when the PDL space is challenged by hypercementosis in Ank-/- mice. Ank-/-; Spp1-/- double deficient mice did not exhibit greater hypercementosis than that in Ank-/- mice. Based on these data, we conclude that OPN has a non-redundant role regulating formation and mineralization of dentin and bone, influences tissue properties of PDL and pulp, but does not control acellular cementum apposition. These findings may inform therapies targeted at controlling soft tissue calcification.
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Affiliation(s)
- B L Foster
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, USA.
| | - M Ao
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - C R Salmon
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, University of Campinas, São Paulo, Brazil
| | - M B Chavez
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - T N Kolli
- Division of Biosciences, College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - A B Tran
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - E Y Chu
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - K R Kantovitz
- Department of Dental Materials, São Leopoldo Mandic Research Center, Campinas, São Paulo, Brazil
| | - M Yadav
- Sanford Children's Health Research Center, Sanford Burnham Prebys Medical Research Institute, La Jolla, CA, USA
| | - S Narisawa
- Sanford Children's Health Research Center, Sanford Burnham Prebys Medical Research Institute, La Jolla, CA, USA
| | - J L Millán
- Sanford Children's Health Research Center, Sanford Burnham Prebys Medical Research Institute, La Jolla, CA, USA
| | - F H Nociti
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, University of Campinas, São Paulo, Brazil
| | - M J Somerman
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
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26
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Hassan MK, Kumar D, Naik M, Dixit M. The expression profile and prognostic significance of eukaryotic translation elongation factors in different cancers. PLoS One 2018; 13:e0191377. [PMID: 29342219 PMCID: PMC5771626 DOI: 10.1371/journal.pone.0191377] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/03/2018] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic translation factors, especially initiation factors have garnered much attention with regards to their role in the onset and progression of different cancers. However, the expression levels and prognostic significance of translation elongation factors remain poorly explored in different cancers. In this study, we have investigated the mRNA transcript levels of seven translation elongation factors in different cancer types using Oncomine and TCGA databases. Furthermore, we have identified the prognostic significance of these factors using Kaplan-Meier Plotter and SurvExpress databases. We observed altered expression levels of all the elongation factors in different cancers. Higher expression of EEF1A2, EEF1B2, EEF1G, EEF1D, EEF1E1 and EEF2 was observed in most of the cancer types, whereas reverse trend was observed for EEF1A1. Overexpression of many factors predicted poor prognosis in breast (EEF1D, EEF1E1, EEF2) and lung cancer (EEF1A2, EEF1B2, EEF1G, EEF1E1). However, we didn’t see any common correlation of expression levels of elongation factors with survival outcomes across cancer types. Cancer subtype stratification showed association of survival outcomes and expression levels of elongation factors in specific sub-types of breast, lung and gastric cancer. Most interestingly, we observed a reciprocal relationship between the expression levels of the two EEF1A isoforms viz. EEF1A1 and EEF1A2, in most of the cancer types. Our results suggest that translation elongation factors can have a role in tumorigenesis and affect survival in cancer specific manner. Elongation factors have potential to serve as biomarkers and therapeutic drug targets, yet further study is required. Reciprocal relationship of differential expression between EEF1A isoforms observed in multiple cancer types indicates opposing roles in cancer and needs further investigation.
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Affiliation(s)
- Md. Khurshidul Hassan
- School of Biological Sciences, National Institute of Science Education and Research, HBNI, Bhimpur- Padanpur, Jatni, Khurda, Odisha, India
| | - Dinesh Kumar
- School of Biological Sciences, National Institute of Science Education and Research, HBNI, Bhimpur- Padanpur, Jatni, Khurda, Odisha, India
| | - Monali Naik
- School of Biological Sciences, National Institute of Science Education and Research, HBNI, Bhimpur- Padanpur, Jatni, Khurda, Odisha, India
| | - Manjusha Dixit
- School of Biological Sciences, National Institute of Science Education and Research, HBNI, Bhimpur- Padanpur, Jatni, Khurda, Odisha, India
- * E-mail:
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27
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Sridharan GV, D'Alessandro M, Bale SS, Bhagat V, Gagnon H, Asara JM, Uygun K, Yarmush ML, Saeidi N. Multi-omic network-based interrogation of rat liver metabolism following gastric bypass surgery featuring SWATH proteomics. TECHNOLOGY 2017; 5:139-184. [PMID: 29780857 PMCID: PMC5956888 DOI: 10.1142/s233954781750008x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Morbidly obese patients often elect for Roux-en-Y gastric bypass (RYGB), a form of bariatric surgery that triggers a remarkable 30% reduction in excess body weight and reversal of insulin resistance for those who are type II diabetic. A more complete understanding of the underlying molecular mechanisms that drive the complex metabolic reprogramming post-RYGB could lead to innovative non-invasive therapeutics that mimic the beneficial effects of the surgery, namely weight loss, achievement of glycemic control, or reversal of non-alcoholic steatohepatitis (NASH). To facilitate these discoveries, we hereby demonstrate the first multi-omic interrogation of a rodent RYGB model to reveal tissue-specific pathway modules implicated in the control of body weight regulation and energy homeostasis. In this study, we focus on and evaluate liver metabolism three months following RYGB in rats using both SWATH proteomics, a burgeoning label free approach using high resolution mass spectrometry to quantify protein levels in biological samples, as well as MRM metabolomics. The SWATH analysis enabled the quantification of 1378 proteins in liver tissue extracts, of which we report the significant down-regulation of Thrsp and Acot13 in RYGB as putative targets of lipid metabolism for weight loss. Furthermore, we develop a computational graph-based metabolic network module detection algorithm for the discovery of non-canonical pathways, or sub-networks, enriched with significantly elevated or depleted metabolites and proteins in RYGB-treated rat livers. The analysis revealed a network connection between the depleted protein Baat and the depleted metabolite taurine, corroborating the clinical observation that taurine-conjugated bile acid levels are perturbed post-RYGB.
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Affiliation(s)
- Gautham Vivek Sridharan
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
| | - Matthew D'Alessandro
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
| | - Shyam Sundhar Bale
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
| | - Vicky Bhagat
- Warren Alpert Medical School of Brown University, 222 Richmond St., Providence, RI 02903, USA
| | - Hugo Gagnon
- Phenoswitch Bioscience, 3001 12e Avenue N, Sherbrooke, QC J1H 5N4, Canada
| | - John M Asara
- Beth Israel Deaconness Medical Center, 3 Blackfan Circle Rm 425, Boston, MA 02115, USA
| | - Korkut Uygun
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
| | - Martin L Yarmush
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
| | - Nima Saeidi
- Center for Engineering in Medicine, Harvard Medical School - Massachusetts General Hospital, 51 Blossom Street, Boston, MA 02114, USA
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28
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Rodrigues PC, Sawazaki-Calone I, Ervolino de Oliveira C, Soares Macedo CC, Dourado MR, Cervigne NK, Miguel MC, Ferreira do Carmo A, Lambert DW, Graner E, Daniela da Silva S, Alaoui-Jamali MA, Paes Leme AF, Salo TA, Coletta RD. Fascin promotes migration and invasion and is a prognostic marker for oral squamous cell carcinoma. Oncotarget 2017; 8:74736-74754. [PMID: 29088820 PMCID: PMC5650375 DOI: 10.18632/oncotarget.20360] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/12/2017] [Indexed: 01/06/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) prognosis is related to clinical stage and histological grade. However, this stratification needs to be refined. We conducted a comparative proteome study in microdissected samples from normal oral mucosa and OSCC to identify biomarkers for malignancy. Fascin and plectin were identified as differently expressed and both are implicated in several malignancies, but the clinical impacts of aberrant fascin and plectin expression in OSCCs remains largely unknown. Immunohistochemistry and real-time quantitative PCR were carried out in ex vivo OSCC samples and cell lines. A loss-of-function strategy using shRNA targeting fascin was employed to investigate in vitro and in vivo the fascin role on oral tumorigenesis. Transfections of microRNA mimics were performed to determine whether the fascin overexpression is regulated by miR-138 and miR-145. We found that fascin and plectin are frequently upregulated in OSCC samples and cell lines, but only fascin overexpression is an independent unfavorable prognostic indicator of disease-specific survival. In combination with advanced T stage, high fascin level is also an independent factor of disease-free survival. Knockdown of fascin in OSCC cells promoted cell adhesion and inhibited migration, invasion and EMT, and forced expression of miR-138 in OSCC cells significantly decreased the expression of fascin. In addition, fascin downregulation leads to reduced filopodia formation and decrease on paxillin expression. The subcutaneous xenograft model showed that tumors formed in the presence of low levels of fascin were significantly smaller compared to those formed with high fascin levels. Collectively, our findings suggest that fascin expression correlates with disease progression and may serve as a prognostic marker and therapeutic target for patients with OSCC.
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Affiliation(s)
- Priscila Campioni Rodrigues
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, SP, Brazil.,Unit of Cancer Research and Translational Medicine, Faculty of Medicine and Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Iris Sawazaki-Calone
- Oral Pathology and Oral Medicine, Dentistry School, Western Paraná State University, Cascavel, PR, Brazil
| | | | | | - Mauricio Rocha Dourado
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, SP, Brazil.,Unit of Cancer Research and Translational Medicine, Faculty of Medicine and Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Nilva K Cervigne
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, SP, Brazil.,Current/Present address: Clinical Department, Faculty of Medicine of Jundiai, Jundiai, SP, Brazil
| | - Marcia Costa Miguel
- Department of Dentistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Andreia Ferreira do Carmo
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, SP, Brazil.,Department of Dentistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Daniel W Lambert
- Integrated Biosciences, School of Clinical Dentistry and Sheffield Cancer Centre, University of Sheffield, Sheffield, United Kingdom
| | - Edgard Graner
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, SP, Brazil
| | - Sabrina Daniela da Silva
- Departments of Medicine, Oncology, Pharmacology and Therapeutics, Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, Quebec, Canada.,Otolaryngology-Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Moulay A Alaoui-Jamali
- Departments of Medicine, Oncology, Pharmacology and Therapeutics, Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, Quebec, Canada.,Otolaryngology-Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | | | - Tuula A Salo
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, SP, Brazil.,Unit of Cancer Research and Translational Medicine, Faculty of Medicine and Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland.,Institute of Oral and Maxillofacial Disease, University of Helsinki, and HUSLAB, Department of Pathology, Helsinki University Hospital, Helsinki, Finland
| | - Ricardo D Coletta
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, SP, Brazil
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29
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Salmon CR, Giorgetti APO, Paes Leme AF, Domingues RR, Kolli TN, Foster BL, Nociti FH. Microproteome of dentoalveolar tissues. Bone 2017; 101:219-229. [PMID: 28527949 DOI: 10.1016/j.bone.2017.05.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/12/2017] [Accepted: 05/15/2017] [Indexed: 01/18/2023]
Abstract
Proteomic analysis of extracellular matrices (ECM) of dentoalveolar tissues can provide insights into developmental, pathological, and reparative processes. However, targeted dissection of mineralized tissues, dental cementum (DC), alveolar bone (AB), and dentin (DE), presents technical difficulties. We demonstrate an approach combining EDTA decalcification and laser capture microdissection (LCM), followed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), to analyze proteome profiles of these tissues. Using the LCM-LC-MS/MS approach, a total of 243 proteins was identified from all tissues, 193 proteins in DC, 147 in AB, and 135 proteins DE. Ninety proteins (37% of total) were common to all tissues, whereas 52 proteins (21%) were overlapping in only two. Also, 101 (42%) proteins were exclusively detected in DC (60), AB (15), or DE (26). Identification in all tissues of expected ECM proteins including collagen alpha-1(I) chain (COL1A1), collagen alpha-1(XII) chain (COL12A1), biglycan (BGN), asporin (ASPN), lumican (LUM), and fibromodulin (FMOD), served to validate the approach. Principal component analysis (PCA) and hierarchical clustering identified a high degree of similarity in DC and AB proteomes, whereas DE presented a distinct dataset. Exclusively and differentially identified proteins were detected from all three tissues. The protein-protein interaction network (interactome) of DC was notable for its inclusion of several indicators of metabolic function (e.g. mitochondrial proteins, protein synthesis, and calcium transport), possibly reflecting cementocyte activity. The DE proteome included known and novel mineralization regulators, including matrix metalloproteinase 20 (MMP-20), 5' nucleotidase (NT5E), and secreted phosphoprotein 24 (SPP-24 or SPP-2). Application of the LCM-LC-MS/MS approach to dentoalveolar tissues would be of value in many experimental designs, including developmental studies of transgenic animals, investigation of treatment effects, and identification of novel regenerative factors.
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Affiliation(s)
- Cristiane R Salmon
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, State University of Campinas, São Paulo, Brazil
| | - Ana Paula O Giorgetti
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, State University of Campinas, São Paulo, Brazil
| | - Adriana F Paes Leme
- National Biosciences Laboratory, Brazilian Synchrotron Light Laboratory, Campinas, SP, Brazil
| | - Romênia R Domingues
- National Biosciences Laboratory, Brazilian Synchrotron Light Laboratory, Campinas, SP, Brazil
| | - Tamara N Kolli
- Biosciences Division, College of Dentistry, Ohio State University, Columbus, OH, United States
| | - Brian L Foster
- Biosciences Division, College of Dentistry, Ohio State University, Columbus, OH, United States
| | - Francisco H Nociti
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, State University of Campinas, São Paulo, Brazil.
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Ramos-García P, Gil-Montoya JA, Scully C, Ayén A, González-Ruiz L, Navarro-Triviño FJ, González-Moles MA. An update on the implications of cyclin D1 in oral carcinogenesis. Oral Dis 2017; 23:897-912. [DOI: 10.1111/odi.12620] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/07/2016] [Accepted: 12/01/2016] [Indexed: 12/11/2022]
Affiliation(s)
- P Ramos-García
- School of Dentistry; University of Granada; Granada Spain
| | - JA Gil-Montoya
- School of Dentistry; University of Granada; Granada Spain
- Instituto de Biomedicina; University of Granada; Granada Spain
| | - C Scully
- University College of London; London UK
| | - A Ayén
- School of Medicine; University of Granada; Granada Spain
| | - L González-Ruiz
- Servicio de Dermatología; Hospital General Universitario de Ciudad Real; Ciudad Real Spain
| | - FJ Navarro-Triviño
- Servicio de Dermatología; Complejo Hospitalario San Cecilio; Granada Spain
| | - MA González-Moles
- School of Dentistry; University of Granada; Granada Spain
- Instituto de Biomedicina; University of Granada; Granada Spain
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31
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Klepikova AV, Kasianov AS, Chesnokov MS, Lazarevich NL, Penin AA, Logacheva M. Effect of method of deduplication on estimation of differential gene expression using RNA-seq. PeerJ 2017; 5:e3091. [PMID: 28321364 PMCID: PMC5357343 DOI: 10.7717/peerj.3091] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/14/2017] [Indexed: 12/11/2022] Open
Abstract
Background RNA-seq is a useful tool for analysis of gene expression. However, its robustness is greatly affected by a number of artifacts. One of them is the presence of duplicated reads. Results To infer the influence of different methods of removal of duplicated reads on estimation of gene expression in cancer genomics, we analyzed paired samples of hepatocellular carcinoma (HCC) and non-tumor liver tissue. Four protocols of data analysis were applied to each sample: processing without deduplication, deduplication using a method implemented in SAMtools, and deduplication based on one or two molecular indices (MI). We also analyzed the influence of sequencing layout (single read or paired end) and read length. We found that deduplication without MI greatly affects estimated expression values; this effect is the most pronounced for highly expressed genes. Conclusion The use of unique molecular identifiers greatly improves accuracy of RNA-seq analysis, especially for highly expressed genes. We developed a set of scripts that enable handling of MI and their incorporation into RNA-seq analysis pipelines. Deduplication without MI affects results of differential gene expression analysis, producing a high proportion of false negative results. The absence of duplicate read removal is biased towards false positives. In those cases where using MI is not possible, we recommend using paired-end sequencing layout.
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Affiliation(s)
- Anna V Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.,A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Artem S Kasianov
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,N. I. Vavilov Institute for General Genetics, Moscow, Russia
| | - Mikhail S Chesnokov
- N.N. Blokhin Russian Cancer Research Center of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Natalia L Lazarevich
- N.N. Blokhin Russian Cancer Research Center of the Ministry of Health of the Russian Federation, Moscow, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.,A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.,A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan
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32
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Flores IL, Santos-Silva AR, Coletta RD, Leme AFP, Lopes MA. Low expression of angiotensinogen and dipeptidyl peptidase 1 in saliva of patients with proliferative verrucous leukoplakia. World J Clin Cases 2016; 4:356-363. [PMID: 27900324 PMCID: PMC5112355 DOI: 10.12998/wjcc.v4.i11.356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 06/14/2016] [Accepted: 09/18/2016] [Indexed: 02/05/2023] Open
Abstract
AIM To elucidate the profile of the salivary proteome.
METHODS Unstimulated whole mouth saliva was collected from 30 volunteers [15 proliferative verrucous leukoplakia (PVL) patients and 15 controls] and proteins were submitted for mass spectrometry-based proteomics using the discovery approach, followed by analyses of variance and logistic regression tests.
RESULTS A total of two hundred and eighty-three proteins were confidently identified in saliva. By combining two low abundance proteins from the PVL group, angiotensinogen (AGT) and dipeptidyl peptidase 1 (DPP1), a model for group differentiation was built with a concordance index of 94.2%, identifying both proteins as potential etiologic biomarkers for PVL.
CONCLUSION This study suggests that both AGT and DPP1 may be involved in developmental mechanisms of PVL.
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