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Zhu G, Zhang H, Xia M, Liu Y, Li M. EH domain-containing protein 2 (EHD2): Overview, biological function, and therapeutic potential. Cell Biochem Funct 2024; 42:e4016. [PMID: 38613224 DOI: 10.1002/cbf.4016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
EH domain-containing protein 2 (EHD2) is a member of the EHD protein family and is mainly located in the plasma membrane, but can also be found in the cytoplasm and endosomes. EHD2 is also a nuclear-cytoplasmic shuttle protein. After entering the cell nuclear, EHD2 acts as a corepressor of transcription to inhibit gene transcription. EHD2 regulates a series of biological processes. As a key regulator of endocytic transport, EHD2 is involved in the formation and maintenance of endosomal tubules and vesicles, which are critical for the intracellular transport of proteins and other substances. The N-terminal of EHD2 is attached to the cell membrane, while its C-terminal binds to the actin-binding protein. After binding, EHD2 connects with the actin cytoskeleton, forming the curvature of the membrane and promoting cell endocytosis. EHD2 is also associated with membrane protein trafficking and receptor signaling, as well as in glucose metabolism and lipid metabolism. In this review, we highlight the recent advances in the function of EHD2 in various cellular processes and its potential implications in human diseases such as cancer and metabolic disease. We also discussed the prospects for the future of EHD2. EHD2 has a broad prospect as a therapeutic target for a variety of diseases. Further research is needed to explore its mechanism, which could pave the way for the development of targeted treatments.
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Affiliation(s)
- Guoqiang Zhu
- Department of Urology, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Hu Zhang
- Department of Urology, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Min Xia
- Hengyang Medical School, Institute of Clinical Medicine, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
- Hengyang Medical School, Cancer Research Institute, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Yiqi Liu
- Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Mingyong Li
- Department of Urology, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
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Capoferri D, Mignani L, Manfredi M, Presta M. Proteomic Analysis Highlights the Impact of the Sphingolipid Metabolizing Enzyme β-Galactosylceramidase on Mitochondrial Plasticity in Human Melanoma. Int J Mol Sci 2024; 25:3062. [PMID: 38474307 DOI: 10.3390/ijms25053062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Mitochondrial plasticity, marked by a dynamism between glycolysis and oxidative phosphorylation due to adaptation to genetic and microenvironmental alterations, represents a characteristic feature of melanoma progression. Sphingolipids play a significant role in various aspects of cancer cell biology, including metabolic reprogramming. Previous observations have shown that the lysosomal sphingolipid-metabolizing enzyme β-galactosylceramidase (GALC) exerts pro-oncogenic functions in melanoma. Here, mining the cBioPortal for a Cancer Genomics data base identified the top 200 nuclear-encoded genes whose expression is negatively correlated with GALC expression in human melanoma. Their categorization indicated a significant enrichment in Gene Ontology terms and KEGG pathways related to mitochondrial proteins and function. In parallel, proteomic analysis by LC-MS/MS of two GALC overexpressing human melanoma cell lines identified 98 downregulated proteins when compared to control mock cells. Such downregulation was confirmed at a transcriptional level by a Gene Set Enrichment Analysis of the genome-wide expression profiling data obtained from the same cells. Among the GALC downregulated proteins, we identified a cluster of 42 proteins significantly associated with GO and KEGG categorizations related to mitochondrion and energetic metabolism. Overall, our data indicate that changes in GALC expression may exert a significant impact on mitochondrial plasticity in human melanoma cells.
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Affiliation(s)
- Davide Capoferri
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Luca Mignani
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Marcello Manfredi
- Department of Translational Medicine, University of Piemonte Orientale, 13100 Novara, Italy
| | - Marco Presta
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
- Consorzio Interuniversitario Biotecnologie (CIB), Unit of Brescia, 25123 Brescia, Italy
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3
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Gong C, Yang M, Long H, Liu X, Xu Q, Qiao L, Dong H, Liu Y, Li S. IL-6-Driven Autocrine Lactate Promotes Immune Escape of Uveal Melanoma. Invest Ophthalmol Vis Sci 2024; 65:37. [PMID: 38551584 PMCID: PMC10981435 DOI: 10.1167/iovs.65.3.37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 03/06/2024] [Indexed: 04/01/2024] Open
Abstract
Purpose Early metastasis, in which immune escape plays a crucial role, is the leading cause of death in patients with uveal melanoma (UM); however, the molecular mechanism underlying UM immune escape remains unclear, which greatly limits the clinical application of immunotherapy for metastatic UM. Methods Transcriptome profiles were revealed by RNA-seq analysis. TALL-104 and NK-92MI-mediated cell killing assays were used to examine the immune resistance of UM cells. The glycolysis rate was measured by extracellular acidification analysis. Protein stability was evaluated by CHX-chase assay. Immunofluorescence histochemistry was performed to detect protein levels in clinical UM specimens. Results Continuous exposure to IL-6 induced the expression of both PD-L1 and HLA-E in UM cells, which promoted UM immune escape. Transcriptome analysis revealed that the expression of most metabolic enzymes in the glycolysis pathway, especially the rate-limiting enzymes, PFKP and PKM, was upregulated, whereas enzymes involved in the acetyl-CoA synthesis pathway were downregulated after exposure to IL-6. Blocking the glycolytic pathway and lactate production by knocking down PKM and LDHA decreased PD-L1 and HLA-E protein, but not mRNA, levels in UM cells treated with IL-6. Notably, lactate secreted by IL-6-treated UM cells was crucial in influencing PD-L1 and HLA-E stability via the GPR81-cAMP-PKA signaling pathway. Conclusions Our data reveal a novel mechanism by which UM cells acquire an immune-escape phenotype by metabolic reprogramming and reinforce the importance of the link between inflammation and immune escape.
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Affiliation(s)
- Chaoju Gong
- Xuzhou Key Laboratory of Ophthalmology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Eye Institute of Xuzhou, Xuzhou, China
| | - Meiling Yang
- Xuzhou Key Laboratory of Ophthalmology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Eye Institute of Xuzhou, Xuzhou, China
| | - Huirong Long
- Xuzhou Key Laboratory of Ophthalmology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Eye Institute of Xuzhou, Xuzhou, China
- Department of Ophthalmology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Eye Institute of Xuzhou, Xuzhou, China
| | - Xia Liu
- Department of Pathology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Xuzhou, China
| | - Qing Xu
- Xuzhou Key Laboratory of Ophthalmology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Eye Institute of Xuzhou, Xuzhou, China
| | - Lei Qiao
- Xuzhou Key Laboratory of Ophthalmology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Eye Institute of Xuzhou, Xuzhou, China
| | - Haibei Dong
- Cancer Center, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Xuzhou, China
| | - Yalu Liu
- Department of Ophthalmology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Eye Institute of Xuzhou, Xuzhou, China
| | - Suyan Li
- Xuzhou Key Laboratory of Ophthalmology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Eye Institute of Xuzhou, Xuzhou, China
- Department of Ophthalmology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Eye Institute of Xuzhou, Xuzhou, China
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Tang H, Luo X, Shen X, Fan D, Rao J, Wan Y, Ma H, Guo X, Liu Z, Gao J. Lysosome-related biomarkers in preeclampsia and cancers: Machine learning and bioinformatics analysis. Comput Biol Med 2024; 171:108201. [PMID: 38428097 DOI: 10.1016/j.compbiomed.2024.108201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/21/2024] [Accepted: 02/18/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND Lysosomes serve as regulatory hubs, and play a pivotal role in human diseases. However, the precise functions and mechanisms of action of lysosome-related genes remain unclear in preeclampsia and cancers. This study aimed to identify lysosome-related biomarkers in preeclampsia, and further explore the biomarkers shared between preeclampsia and cancers. MATERIALS AND METHODS We obtained GSE60438 and GSE75010 datasets from the Gene Expression Omnibus database, pre-procesed them and merged them into a training cohort. The limma package in R was used to identify the differentially expressed mRNAs between the preeclampsia and normal control groups. Differentially expressed lysosome-related genes were identified by intersecting the differentially expressed mRNAs and lysosome-related genes obtained from Gene Ontology and GSEA databases. Gene Ontology annotations and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed using the DAVID database. The CIBERSORT method was used to analyze immune cell infiltration. Weighted gene co-expression analyses and three machine learning algorithm were used to identify lysosome-related diagnostic biomarkers. Lysosome-related diagnostic biomarkers were further validated in the testing cohort GSE25906. Nomogram diagnostic models for preeclampsia were constructed. In addition, pan-cancer analysis of lysosome-related diagnostic biomarkers were identified by was performed using the TIMER, Sangebox and TISIDB databases. Finally, the Drug-Gene Interaction, TheMarker and DSigDB Databases were used for drug-gene interactions analysis. RESULTS A total of 11 differentially expressed lysosome-related genes were identified between the preeclampsia and control groups. Three molecular clusters connected to lysosome were identified, and enrichment analysis demonstrated their strong relevance to the development and progression of preeclampsia. Immune infiltration analysis revealed significant immunity heterogeneity among different clusters. GBA, OCRL, TLR7 and HEXB were identified as lysosome-related diagnostic biomarkers with high AUC values, and validated in the testing cohort GSE25906. Nomogram, calibration curve, and decision curve analysis confirmed the accuracy of predicting the occurrence of preeclampsia based on OCRL and HEXB. Pan-cancer analysis showed that GBA, OCRL, TLR7 and HEXB were associated with the prognosis of patients with various tumors and tumor immune cell infiltration. Twelve drugs were identified as potential drugs for the treatment of preeclampsia and cancers. CONCLUSION This study identified GBA, OCRL, TLR7 and HEXB as potential lysosome-related diagnostic biomarkers shared between preeclampsia and cancers.
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Affiliation(s)
- Hai Tang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China; Foshan Institute of Fetal Medicine, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China; Department of Obstetrics, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China
| | - Xin Luo
- Foshan Institute of Fetal Medicine, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China; Department of Obstetrics, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China
| | - Xiuyin Shen
- Foshan Institute of Fetal Medicine, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China; Department of Obstetrics, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China
| | - Dazhi Fan
- Foshan Institute of Fetal Medicine, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China; Department of Obstetrics, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China
| | - Jiamin Rao
- Foshan Institute of Fetal Medicine, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China; Department of Obstetrics, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China
| | - Yingchun Wan
- Foshan Institute of Fetal Medicine, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China; Department of Obstetrics, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China
| | - Huiting Ma
- Foshan Institute of Fetal Medicine, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China; Department of Obstetrics, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China
| | - Xiaoling Guo
- Foshan Institute of Fetal Medicine, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China; Department of Obstetrics, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China
| | - Zhengping Liu
- Foshan Institute of Fetal Medicine, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China; Department of Obstetrics, Southern Medical University Affiliated Maternal and Child Health Hospital of Foshan, Foshan, Guangdong, 528000, China.
| | - Jie Gao
- Premarital Examination and Superior Examination Department, Jingzhou Gongan Maternal and Child Health Care Hospital, Jingzhou, Hubei, 434300, China.
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Just U, Burtscher H, Jeratsch S, Fischer M, Stocking C, Preussner J, Looso M, Schwanbeck R, Günther S, Huss R, Mullen L, Braun T. Proteomic and transcriptomic characterisation of FIA10, a novel murine leukemic cell line that metastasizes into the brain. PLoS One 2024; 19:e0295641. [PMID: 38215076 PMCID: PMC10786371 DOI: 10.1371/journal.pone.0295641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/27/2023] [Indexed: 01/14/2024] Open
Abstract
Brain metastasis leads to increased mortality and is a major site of relapse for several cancers, yet the molecular mechanisms of brain metastasis are not well understood. In this study, we established and characterized a new leukemic cell line, FIA10, that metastasizes into the central nervous system (CNS) following injection into the tail vein of syngeneic mice. Mice injected with FIA10 cells developed neurological symptoms such as loss of balance, tremor, ataxic gait and seizures, leading to death within 3 months. Histopathology coupled with PCR analysis clearly showed infiltration of leukemic FIA10 cells into the brain parenchyma of diseased mice, with little involvement of bone marrow, peripheral blood and other organs. To define pathways that contribute to CNS metastasis, global transcriptome and proteome analysis was performed on FIA10 cells and compared with that of the parental stem cell line FDCP-Mix and the related FIA18 cells, which give rise to myeloid leukemia without CNS involvement. 188 expressed genes (RNA level) and 189 proteins were upregulated (log2 ratio FIA10/FIA18 ≥ 1) and 120 mRNAs and 177 proteins were downregulated (log2 ratio FIA10/FIA18 ≤ 1) in FIA10 cells compared with FIA18 cells. Major upregulated pathways in FIA10 cells revealed by biofunctional analyses involved immune response components, adhesion molecules and enzymes implicated in extracellular matrix remodeling, opening and crossing the blood-brain barrier (BBB), molecules supporting migration within the brain parenchyma, alterations in metabolism necessary for growth within the brain microenvironment, and regulators for these functions. Downregulated RNA and protein included several tumor suppressors and DNA repair enzymes. In line with the function of FIA10 cells to specifically infiltrate the brain, FIA10 cells have acquired a phenotype that permits crossing the BBB and adapting to the brain microenvironment thereby escaping immune surveillance. These data and our model system FIA10 will be valuable resources to study the occurrence of brain metastases and may help in the development of potential therapies against brain invasion.
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Affiliation(s)
- Ursula Just
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Leibniz Institute for Virology, Hamburg, Germany
- Department of Biochemistry, Christian-Albrechts-University zu Kiel, Kiel, Germany
| | - Helmut Burtscher
- Pharma Research Penzberg, Roche Diagnostics GmbH, Penzberg, Germany
| | - Sylvia Jeratsch
- Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | | | | | - Jens Preussner
- Bioinformatics Core Unit, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- Bioinformatics Core Unit, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Ralf Schwanbeck
- Department of Biochemistry, Christian-Albrechts-University zu Kiel, Kiel, Germany
| | - Stefan Günther
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Ralf Huss
- Pharma Research Penzberg, Roche Diagnostics GmbH, Penzberg, Germany
| | - Lynne Mullen
- QIAGEN, Redwood City, California, United States of America
| | - Thomas Braun
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
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Cameron CM, Richardson B, Golden JB, Phoon YP, Tamilselvan B, Pfannenstiel L, Thapaliya S, Roversi G, Gao XH, Zagore LL, Cameron MJ, Gastman BR. A transcriptional evaluation of the melanoma and squamous cell carcinoma TIL compartment reveals an unexpected spectrum of exhausted and functional T cells. Front Oncol 2023; 13:1200387. [PMID: 38023136 PMCID: PMC10643547 DOI: 10.3389/fonc.2023.1200387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/27/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Significant heterogeneity exists within the tumor-infiltrating CD8 T cell population, and exhausted T cells harbor a subpopulation that may be replicating and may retain signatures of activation, with potential functional consequences in tumor progression. Dysfunctional immunity in the tumor microenvironment is associated with poor cancer outcomes, making exploration of these exhausted T cell subpopulations critical to the improvement of therapeutic approaches. Methods To investigate mechanisms associated with terminally exhausted T cells, we sorted and performed transcriptional profiling of CD8+ tumor-infiltrating lymphocytes (TILs) co-expressing the exhaustion markers PD-1 and TIM-3 from large-volume melanoma tumors. We additionally performed immunologic phenotyping and functional validation, including at the single-cell level, to identify potential mechanisms that underlie their dysfunctional phenotype. Results We identified novel dysregulated pathways in CD8+PD-1+TIM-3+ cells that have not been well studied in TILs; these include bile acid and peroxisome pathway-related metabolism and mammalian target of rapamycin (mTOR) signaling pathways, which are highly correlated with immune checkpoint receptor expression. Discussion Based on bioinformatic integration of immunophenotypic data and network analysis, we propose unexpected targets for therapies to rescue the immune response to tumors in melanoma.
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Affiliation(s)
- Cheryl M. Cameron
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, United States
| | - Brian Richardson
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, United States
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States
| | - Jackelyn B. Golden
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States
| | - Yee Peng Phoon
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH, United States
| | - Banumathi Tamilselvan
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, United States
| | - Lukas Pfannenstiel
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH, United States
| | - Samjhana Thapaliya
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH, United States
| | - Gustavo Roversi
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH, United States
| | - Xing-Huang Gao
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States
| | - Leah L. Zagore
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States
| | - Mark J. Cameron
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States
| | - Brian R. Gastman
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH, United States
- Department of Plastic Surgery, Cleveland Clinic, Cleveland, OH, United States
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Zheng SY, Hu XM, Huang K, Li ZH, Chen QN, Yang RH, Xiong K. Proteomics as a tool to improve novel insights into skin diseases: what we know and where we should be going. Front Surg 2022; 9:1025557. [PMID: 36338621 PMCID: PMC9633964 DOI: 10.3389/fsurg.2022.1025557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022] Open
Abstract
Background Biochemical processes involved in complex skin diseases (skin cancers, psoriasis, and wound) can be identified by combining proteomics analysis and bioinformatics tools, which gain a next-level insight into their pathogenesis, diagnosis, and therapeutic targets. Methods Articles were identified through a search of PubMed, Embase, and MEDLINE references dated to May 2022, to perform system data mining, and a search of the Web of Science (WoS) Core Collection was utilized to conduct a visual bibliometric analysis. Results An increased trend line revealed that the number of publications related to proteomics utilized in skin diseases has sharply increased recent years, reaching a peak in 2021. The hottest fields focused on are skin cancer (melanoma), inflammation skin disorder (psoriasis), and skin wounds. After deduplication and title, abstract, and full-text screening, a total of 486 of the 7,822 outcomes met the inclusion/exclusion criteria for detailed data mining in the field of skin disease tooling with proteomics, with regard to skin cancer. According to the data, cell death, metabolism, skeleton, immune, and inflammation enrichment pathways are likely the major part and hotspots of proteomic analysis found in skin diseases. Also, the focuses of proteomics in skin disease are from superficial presumption to depth mechanism exploration within more comprehensive validation, from basic study to a combination or guideline for clinical applications. Furthermore, we chose skin cancer as a typical example, compared with other skin disorders. In addition to finding key pathogenic proteins and differences between diseases, proteomic analysis is also used for therapeutic evaluation or can further obtain in-depth mechanisms in the field of skin diseases. Conclusion Proteomics has been regarded as an irreplaceable technology in the study of pathophysiological mechanism and/or therapeutic targets of skin diseases, which could provide candidate key proteins for the insight into the biological information after gene transcription. However, depth pathogenesis and potential clinical applications need further studies with stronger evidence within a wider range of skin diseases.
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Affiliation(s)
- Sheng-yuan Zheng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Xi-min Hu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, China
| | - Kun Huang
- Clinical Medicine Eight-Year Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Zi-han Li
- Clinical Medicine Eight-Year Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Qing-ning Chen
- Clinical Medicine Eight-Year Program, Xiangya School of Medicine, Central South University, Changsha, China
| | - Rong-hua Yang
- Department of Burn and Plastic Surgery, Guangzhou First People's Hospital, School of 173 Medicine, South China University of Technology, Guangzhou, China
- Correspondence: Rong-hua Yang Kun Xiong
| | - Kun Xiong
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Emergency and Trauma, Ministry of Education, College of Emergency and Trauma, Hainan Medical University, Haikou, China
- Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, China
- Correspondence: Rong-hua Yang Kun Xiong
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Martinez-Morales P, Morán Cruz I, Roa-de la Cruz L, Maycotte P, Reyes Salinas JS, Vazquez Zamora VJ, Gutierrez Quiroz CT, Montiel-Jarquin AJ, Vallejo-Ruiz V. Hallmarks of glycogene expression and glycosylation pathways in squamous and adenocarcinoma cervical cancer. PeerJ 2021; 9:e12081. [PMID: 34540372 PMCID: PMC8415283 DOI: 10.7717/peerj.12081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/06/2021] [Indexed: 12/18/2022] Open
Abstract
Background Dysregulation of glycogene expression in cancer can lead to aberrant glycan expression, which can promote tumorigenesis. Cervical cancer (CC) displays an increased expression of glycogenes involved in sialylation and sialylated glycans. Here, we show a comprehensive analysis of glycogene expression in CC to identify glycogene expression signatures and the possible glycosylation pathways altered. Methods First, we performed a microarray expression assay to compare glycogene expression changes between normal and cervical cancer tissues. Second, we used 401 glycogenes to analyze glycogene expression in adenocarcinoma and squamous carcinoma from RNA-seq data at the cBioPortal for Cancer Genomics. Results The analysis of the microarray expression assay indicated that CC displayed an increase in glycogenes related to GPI-anchored biosynthesis and a decrease in genes associated with chondroitin and dermatan sulfate with respect to normal tissue. Also, the glycogene analysis of CC samples by the RNA-seq showed that the glycogenes involved in the chondroitin and dermatan sulfate pathway were downregulated. Interestingly the adenocarcinoma tumors displayed a unique glycogene expression signature compared to squamous cancer that shows heterogeneous glycogene expression divided into six types. Squamous carcinoma type 5 (SCC-5) showed increased expression of genes implicated in keratan and heparan sulfate synthesis, glycosaminoglycan degradation, ganglio, and globo glycosphingolipid synthesis was related to poorly differentiated tumors and poor survival. Squamous carcinoma type 6 (SCC-6) displayed an increased expression of genes involved in chondroitin/dermatan sulfate synthesis and lacto and neolacto glycosphingolipid synthesis and was associated with nonkeratinizing squamous cancer and good survival. In summary, our study showed that CC tumors are not a uniform entity, and their glycome signatures could be related to different clinicopathological characteristics.
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Affiliation(s)
- Patricia Martinez-Morales
- CONACYT-Centro de Investigación Biomédica de Oriente, Mexican Institute of Social Security, Metepec, Puebla, México
| | - Irene Morán Cruz
- Centro de Investigación Biomédica de Oriente, Laboratory of Molecular Biology, Instituto Mexicano del Seguro Social, Metepec, Puebla, México
| | - Lorena Roa-de la Cruz
- Department of Biological Chemical Sciences, Universidad de las Américas-Puebla, San Andrés Cholula, Puebla, Mexico
| | - Paola Maycotte
- Centro de Investigación Biomédica de Oriente, Laboratory of Cell Biology, Instituto Mexicano del Seguro Social, Metepec, Puebla, México
| | - Juan Salvador Reyes Salinas
- Hospital de especialidades, General Manuel Ávila Camacho, Instituto Mexicano del Seguro Social, Puebla, Puebla, México
| | - Victor Javier Vazquez Zamora
- Hospital de especialidades, General Manuel Ávila Camacho, Instituto Mexicano del Seguro Social, Puebla, Puebla, México
| | | | - Alvaro Jose Montiel-Jarquin
- Hospital de especialidades, General Manuel Ávila Camacho, Instituto Mexicano del Seguro Social, Puebla, Puebla, México
| | - Verónica Vallejo-Ruiz
- Centro de Investigación Biomédica de Oriente, Laboratory of Molecular Biology, Instituto Mexicano del Seguro Social, Metepec, Puebla, México
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9
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Santos EC, Gomes RB, Fernandes PV, Ferreira MA, Abdelhay ESFW. The protein-protein interaction network of intestinal gastric cancer patients reveals hub proteins with potential prognostic value. Cancer Biomark 2021; 33:83-96. [PMID: 34366321 DOI: 10.3233/cbm-203225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Gastric cancer (GC) is the third leading cause of cancer worldwide. According to the Lauren classification, gastric adenocarcinoma is divided into two subtypes: diffuse and intestinal. The development of intestinal gastric cancer (IGC) can take years and involves multiple factors. OBJECTIVE To investigate the protein profile of tumor samples from patients with IGC in comparison with adjacent nontumor tissue samples. METHODS We used label-free nano-LC-MS/MS to identify proteins from the tissues samples. The results were analyzed using MetaCore™ software to access functional enrichment information. Protein-protein interactions (PPI) were predicted using STRING analysis. Hub proteins were determined using the Cytoscape plugin, CytoHubba. Survival analysis was performed using KM plotter. We identified 429 differentially expressed proteins whose pathways and processes were related to protein folding, apoptosis, and immune response. RESULTS The PPI network of these proteins showed enrichment modules related to the regulation of cell death, immune system, neutrophil degranulation, metabolism of RNA and chromatin DNA binding. From the PPI network, we identified 20 differentially expressed hub proteins, and assessed the prognostic value of the expression of genes that encode them. Among them, the expression of four hub genes was significantly associated with the overall survival of IGC patients. CONCLUSIONS This study reveals important findings that affect IGC development based on specific biological alterations in IGC patients. Bioinformatics analysis showed that the pathogenesis of IGC patients is complex and involves different interconnected biological processes. These findings may be useful in research on new targets to develop novel therapies to improve the overall survival of patients with IGC.
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Affiliation(s)
- Everton Cruz Santos
- Stem Cell Laboratory, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Ciência e Tecnologia Para o Controle do Câncer, Rio de Janeiro, RJ, Brazil
| | - Renata Binato Gomes
- Stem Cell Laboratory, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Ciência e Tecnologia Para o Controle do Câncer, Rio de Janeiro, RJ, Brazil
| | | | | | - Eliana Saul Furquim Werneck Abdelhay
- Stem Cell Laboratory, Bone Marrow Transplantation Unit, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Ciência e Tecnologia Para o Controle do Câncer, Rio de Janeiro, RJ, Brazil
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10
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Singh CK, George J, Chhabra G, Nihal M, Chang H, Ahmad N. Genetic Manipulation of Sirtuin 3 Causes Alterations of Key Metabolic Regulators in Melanoma. Front Oncol 2021; 11:676077. [PMID: 33937086 PMCID: PMC8085490 DOI: 10.3389/fonc.2021.676077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/29/2021] [Indexed: 12/29/2022] Open
Abstract
The mitochondrial sirtuin SIRT3 plays key roles in cellular metabolism and energy production, which makes it an obvious target for the management of cancer, including melanoma. Previously, we have demonstrated that SIRT3 was constitutively upregulated in human melanoma and its inhibition resulted in anti-proliferative effects in vitro in human melanoma cells and in vivo in human melanoma xenografts. In this study, we expanded our data employing knockdown and overexpression strategies in cell culture and mouse xenografts to further validate and establish the pro-proliferative function of SIRT3 in melanocytic cells, and its associated potential mechanisms, especially focusing on the metabolic regulation. We found that short-hairpin RNA (shRNA) mediated SIRT3 knockdown in G361 melanoma cells showed diminished tumorigenesis in immunodeficient Nu/Nu mice. Conversely, SIRT3 overexpressing Hs294T melanoma cells showed increased tumor growth. These effects were consistent with changes in markers of proliferation (PCNA), survival (Survivin) and angiogenesis (VEGF) in xenografted tissues. Further, in in vitro culture system, we determined the effect of SIRT3 knockdown on glucose metabolism in SK-MEL-2 cells, using a PCR array. SIRT3 knockdown caused alterations in a total of 37 genes involved in the regulation and enzymatic pathways of glucose (32 genes) and glycogen (5 genes) metabolism. Functions annotation of these identified genes, using the ingenuity pathway analysis (IPA), predicted cumulative actions of decreased cell viability/proliferation, tumor growth and reactive oxygen species (ROS), and increased apoptosis in response to SIRT3 knockdown. Further, IPA gene network analysis of SIRT3 modulated genes revealed the interactions among these genes in addition to several melanoma-associated genes. Sirtuin pathway was identified as one of the top canonical pathways showing the interaction of SIRT3 with metabolic regulatory genes along with other sirtuins. IPA analysis also predicted the inhibition of HIF1α, PKM, KDM8, PPARGC1A, mTOR, and activation of P53 and CLPP; the genes involved in major cancer/melanoma-associated signaling events. Collectively, these results suggest that SIRT3 inhibition affects cellular metabolism, to impart an anti-proliferative response against melanoma.
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Affiliation(s)
- Chandra K Singh
- Department of Dermatology, University of Wisconsin, Madison, WI, United States
| | - Jasmine George
- Department of Dermatology, University of Wisconsin, Madison, WI, United States
| | - Gagan Chhabra
- Department of Dermatology, University of Wisconsin, Madison, WI, United States
| | - Minakshi Nihal
- Department of Dermatology, University of Wisconsin, Madison, WI, United States
| | - Hao Chang
- Department of Dermatology, University of Wisconsin, Madison, WI, United States
| | - Nihal Ahmad
- Department of Dermatology, University of Wisconsin, Madison, WI, United States.,William S. Middleton VA Medical Center, Madison, WI, United States
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11
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Cisarova K, Folcher M, El Zaoui I, Pescini-Gobert R, Peter VG, Royer-Bertrand B, Zografos L, Schalenbourg A, Nicolas M, Rimoldi D, Leyvraz S, Riggi N, Moulin AP, Rivolta C. Genomic and transcriptomic landscape of conjunctival melanoma. PLoS Genet 2020; 16:e1009201. [PMID: 33383577 DOI: 10.1371/journal.pgen.1009201] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 10/14/2020] [Indexed: 02/07/2023] Open
Abstract
Conjunctival melanoma (CJM) is a rare but potentially lethal and highly-recurrent cancer of the eye. Similar to cutaneous melanoma (CM), it originates from melanocytes. Unlike CM, however, CJM is relatively poorly characterized from a genomic point of view. To fill this knowledge gap and gain insight into the genomic nature of CJM, we performed whole-exome (WES) or whole-genome sequencing (WGS) of tumor-normal tissue pairs in 14 affected individuals, as well as RNA sequencing in a subset of 11 tumor tissues. Our results show that, similarly to CM, CJM is also characterized by a very high mutation load, composed of approximately 500 somatic mutations in exonic regions. This, as well as the presence of a UV light-induced mutational signature, are clear signs of the role of sunlight in CJM tumorigenesis. In addition, the genomic classification of CM proposed by TCGA seems to be well-applicable to CJM, with the presence of four typical subclasses defined on the basis of the most frequently mutated genes: BRAF, NF1, RAS, and triple wild-type. In line with these results, transcriptomic analyses revealed similarities with CM as well, namely the presence of a transcriptomic subtype enriched for immune genes and a subtype enriched for genes associated with keratins and epithelial functions. Finally, in seven tumors we detected somatic mutations in ACSS3, a possible new candidate oncogene. Transfected conjunctival melanoma cells overexpressing mutant ACSS3 showed higher proliferative activity, supporting the direct involvement of this gene in the tumorigenesis of CJM. Altogether, our results provide the first unbiased and complete genomic and transcriptomic classification of CJM. Conjunctival melanoma is an extremely rare form of cancer of the eye that arises from melanocytes–the cells producing the protective pigment melanin–in the outmost layer of the eye: the conjunctiva. This tissue, similarly to the skin, can also be exposed to UV light radiation from the sun. We investigated the genetic background of this rare form of cancer in samples from fourteen patients, by global DNA and RNA sequencing. Our results showed that conjunctival melanoma is genetically very similar to cutaneous melanoma. More precisely, in tumor DNA we detected signs of damage caused by UV light, as well as mutations in the genes BRAF, NF1 and NRAS/HRAS, previously described to be involved in cutaneous melanoma. Analysis of tumor gene expression also revealed similarities between these two types of cancer, some of which could be used as prognostic factors or as indicators of a patients’ response to therapy. In addition, we identified frequent somatic mutations in ACSS3, a gene not yet associated with either conjunctival or cutaneous melanoma, which represents a potential key player in oncogenesis of conjunctival melanoma.
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12
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Hoefsmit EP, Rozeman EA, Van TM, Dimitriadis P, Krijgsman O, Conway JW, Pires da Silva I, van der Wal JE, Ketelaars SLC, Bresser K, Broeks A, Kerkhoven RM, Reeves JW, Warren S, Kvistborg P, Scolyer RA, Kapiteijn EW, Peeper DS, Long GV, Schumacher TNM, Blank CU. Comprehensive analysis of cutaneous and uveal melanoma liver metastases. J Immunother Cancer 2020; 8:e001501. [PMID: 33262254 PMCID: PMC7713183 DOI: 10.1136/jitc-2020-001501] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The profound disparity in response to immune checkpoint blockade (ICB) by cutaneous melanoma (CM) and uveal melanoma (UM) patients is not well understood. Therefore, we characterized metastases of CM and UM from the same metastatic site (liver), in order to dissect the potential underlying mechanism in differential response on ICB. METHODS Tumor liver samples from CM (n=38) and UM (n=28) patients were analyzed at the genomic (whole exome sequencing), transcriptional (RNA sequencing) and protein (immunohistochemistry and GeoMx Digital Spatial Profiling) level. RESULTS Comparison of CM and UM metastases from the same metastatic site revealed that, although originating from the same melanocyte lineage, CM and UM differed in somatic mutation profile, copy number profile, tumor mutational burden (TMB) and consequently predicted neoantigens. A higher melanin content and higher expression of the melanoma differentiation antigen MelanA was observed in liver metastases of UM patients. No difference in B2M and human leukocyte antigen-DR (HLA-DR) expression was observed. A higher expression of programmed cell death ligand 1 (PD-L1) was found in CM compared with UM liver metastases, although the majority of CM and UM liver metastases lacked PD-L1 expression. There was no difference in the extent of immune infiltration observed between CM and UM metastases, with the exception of a higher expression of CD163 (p<0.0001) in CM liver samples. While the extent of immune infiltration was similar for CM and UM metastases, the ratio of exhausted CD8 T cells to cytotoxic T cells, to total CD8 T cells and to Th1 cells, was significantly higher in UM metastases. CONCLUSIONS While TMB was different between CM and UM metastases, tumor immune infiltration was similar. The greater dependency on PD-L1 as an immune checkpoint in CM and the identification of higher exhaustion ratios in UM may both serve as explanations for the difference in response to ICB. Consequently, in order to improve current treatment for metastatic UM, reversal of T cell exhaustion beyond programmed cell death 1 blockade should be considered.
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Affiliation(s)
- Esmee P Hoefsmit
- Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Elisa A Rozeman
- Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Trieu My Van
- Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Petros Dimitriadis
- Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Oscar Krijgsman
- Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jordan W Conway
- Melanoma Institute Australia, North Sydney, New South Wales, Australia
| | | | | | - Steven L C Ketelaars
- Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kaspar Bresser
- Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Annegien Broeks
- Core Facility and Biobanking, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ron M Kerkhoven
- NKI Genomics Core Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Sarah Warren
- NanoString Technologies Inc, Seattle, Washington, USA
| | - Pia Kvistborg
- Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Richard A Scolyer
- Melanoma Institute Australia, North Sydney, New South Wales, Australia
- The University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - Ellen W Kapiteijn
- Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniel S Peeper
- Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Georgina V Long
- Melanoma Institute Australia, North Sydney, New South Wales, Australia
- Royal North Shore Hospital, Melanoma Institute Australia, and The University of Sydney, Wollstonecraft, New South Wales, Australia
| | - Ton N M Schumacher
- Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Christian U Blank
- Molecular Oncology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
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13
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Sanchez A, Kuras M, Murillo JR, Pla I, Pawlowski K, Szasz AM, Gil J, Nogueira FCS, Perez-Riverol Y, Eriksson J, Appelqvist R, Miliotis T, Kim Y, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Ekedahl H, Horvatovich P, Sugihara Y, Welinder C, Wieslander E, Kwon HJ, Domont GB, Malm J, Rezeli M, Betancourt LH, Marko-Varga G. Novel functional proteins coded by the human genome discovered in metastases of melanoma patients. Cell Biol Toxicol 2020; 36:261-272. [PMID: 31599373 PMCID: PMC7320927 DOI: 10.1007/s10565-019-09494-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/02/2019] [Indexed: 12/18/2022]
Abstract
In the advanced stages, malignant melanoma (MM) has a very poor prognosis. Due to tremendous efforts in cancer research over the last 10 years, and the introduction of novel therapies such as targeted therapies and immunomodulators, the rather dark horizon of the median survival has dramatically changed from under 1 year to several years. With the advent of proteomics, deep-mining studies can reach low-abundant expression levels. The complexity of the proteome, however, still surpasses the dynamic range capabilities of current analytical techniques. Consequently, many predicted protein products with potential biological functions have not yet been verified in experimental proteomic data. This category of 'missing proteins' (MP) is comprised of all proteins that have been predicted but are currently unverified. As part of the initiative launched in 2016 in the USA, the European Cancer Moonshot Center has performed numerous deep proteomics analyses on samples from MM patients. In this study, nine MPs were clearly identified by mass spectrometry in MM metastases. Some MPs significantly correlated with proteins that possess identical PFAM structural domains; and other MPs were significantly associated with cancer-related proteins. This is the first study to our knowledge, where unknown and novel proteins have been annotated in metastatic melanoma tumour tissue.
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Affiliation(s)
- Aniel Sanchez
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden.
| | - Magdalena Kuras
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Jimmy Rodriguez Murillo
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Indira Pla
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden
| | - Krzysztof Pawlowski
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden
- Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - A Marcell Szasz
- Cancer Center, Semmelweis University, Budapest, 1083, Hungary
| | - Jeovanis Gil
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Fábio C S Nogueira
- Proteomics Unit, Department of Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD Hinxton, Cambridge, UK
| | - Jonatan Eriksson
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Roger Appelqvist
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | | | - Yonghyo Kim
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Bo Baldetorp
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Skåne University Hospital, Lund University, Lund, Sweden
| | - Håkan Olsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Lotta Lundgren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Henrik Ekedahl
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Yutaka Sugihara
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Ho Jeong Kwon
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Gilberto B Domont
- Proteomics Unit, Department of Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Skåne University Hospital Malmö, Lund University, 205 02, Malmö, Sweden
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Lazaro Hiram Betancourt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
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14
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Shen WW, Bièche I, Fuhrmann L, Vacher S, Vincent-Salomon A, Torrino S, Lamaze C. EHD2 is a Predictive Biomarker of Chemotherapy Efficacy in Triple Negative Breast Carcinoma. Sci Rep 2020; 10:7998. [PMID: 32409676 DOI: 10.1038/s41598-020-65054-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 04/27/2020] [Indexed: 12/30/2022] Open
Abstract
EHD2 is a mechanotransducing ATPase localized in caveolae invaginations at the plasma membrane. EHD2 has recently been associated with several human cancers, however the significance of EHD2 transcript levels in cancer prognosis remains debated. Breast cancer is the most commonly occurring cancer in women and prognosis is variable depending on the subtypes. Triple negative breast cancer (TNBC) often has a poor therapeutic response. The aim of this study was to assess the prognostic significance of EHD2 transcripts and protein expression levels in breast carcinomas. We found that low EHD2 levels were associated with enhanced proliferation, migration and invasion of TNBC cells. EHD2 expression was significantly reduced in TNBC tissues and the loss of EHD2 led to higher expression of the pro-tumoral cytokine IL-8. In apparent contradiction with in vitro data, multivariate analysis of two independent cohorts of breast cancer patients revealed that low EHD2 was in fact associated with good prognosis in the highly proliferative TNBC subtype. Accordingly, TNBC low EHD2 expressers were found to benefit the most from chemotherapy when compared to all subtypes of breast cancers. Our study validates EHD2 expression level as an independent prognostic factor of metastasis-free survival and as a new predictive marker of chemotherapy efficacy in TNBC patients.
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15
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Betancourt LH, Szasz AM, Kuras M, Rodriguez Murillo J, Sugihara Y, Pla I, Horvath Z, Pawłowski K, Rezeli M, Miharada K, Gil J, Eriksson J, Appelqvist R, Miliotis T, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Horvatovich P, Welinder C, Wieslander E, Kwon HJ, Malm J, Nemeth IB, Jönsson G, Fenyö D, Sanchez A, Marko-Varga G. The Hidden Story of Heterogeneous B-raf V600E Mutation Quantitative Protein Expression in Metastatic Melanoma-Association with Clinical Outcome and Tumor Phenotypes. Cancers (Basel) 2019; 11:E1981. [PMID: 31835364 PMCID: PMC6966659 DOI: 10.3390/cancers11121981] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/23/2019] [Accepted: 12/03/2019] [Indexed: 02/07/2023] Open
Abstract
In comparison to other human cancer types, malignant melanoma exhibits the greatest amount of heterogeneity. After DNA-based detection of the BRAF V600E mutation in melanoma patients, targeted inhibitor treatment is the current recommendation. This approach, however, does not take the abundance of the therapeutic target, i.e., the B-raf V600E protein, into consideration. As shown by immunohistochemistry, the protein expression profiles of metastatic melanomas clearly reveal the existence of inter- and intra-tumor variability. Nevertheless, the technique is only semi-quantitative. To quantitate the mutant protein there is a fundamental need for more precise techniques that are aimed at defining the currently non-existent link between the levels of the target protein and subsequent drug efficacy. Using cutting-edge mass spectrometry combined with DNA and mRNA sequencing, the mutated B-raf protein within metastatic tumors was quantitated for the first time. B-raf V600E protein analysis revealed a subjacent layer of heterogeneity for mutation-positive metastatic melanomas. These were characterized into two distinct groups with different tumor morphologies, protein profiles and patient clinical outcomes. This study provides evidence that a higher level of expression in the mutated protein is associated with a more aggressive tumor progression. Our study design, comprised of surgical isolation of tumors, histopathological characterization, tissue biobanking, and protein analysis, may enable the eventual delineation of patient responders/non-responders and subsequent therapy for malignant melanoma.
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Affiliation(s)
- Lazaro Hiram Betancourt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - A. Marcell Szasz
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
- Cancer Center, Semmelweis University, Budapest 1083, Hungary
| | - Magdalena Kuras
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
| | - Jimmy Rodriguez Murillo
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden; (J.R.M.); (Y.S.)
| | - Yutaka Sugihara
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden; (J.R.M.); (Y.S.)
| | - Indira Pla
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
| | - Zsolt Horvath
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Krzysztof Pawłowski
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Kenichi Miharada
- Department of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, Sölvegatan 17, 221 84 Lund, Sweden;
| | - Jeovanis Gil
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Jonatan Eriksson
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Roger Appelqvist
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
| | - Tasso Miliotis
- Translational Science, Cardiovascular Renal and Metabolism, IMED Biotech Unit, AstraZeneca, 431 50 Gothenburg, Sweden;
| | - Bo Baldetorp
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Lund University, Skåne University Hospital, 222 42 Lund, Sweden;
| | - Håkan Olsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Lotta Lundgren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Faculty of Science and Engineering, University of Groningen, 9712 CP Groningen, The Netherlands;
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - Ho Jeong Kwon
- Department of Biotechnology, Yonsei University, Seoul 03722, Korea;
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
| | - Istvan Balazs Nemeth
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary;
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85 Lund, Sweden; (B.B.); (H.O.); (L.L.); (C.W.); (E.W.); (G.J.)
| | - David Fenyö
- Institute for Systems Genetics, NYU School of Medicine, 550 1st Ave, New York, NY 10016, USA;
| | - Aniel Sanchez
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden; (M.K.); (I.P.); (K.P.); (J.M.); (A.S.)
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical, Engineering, Lund University, BMC D13, 221 84 Lund, Sweden; (L.H.B.); (Z.H.); (M.R.); (J.G.); (J.E.); (R.A.); (G.M.-V.)
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16
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Gil J, Betancourt LH, Pla I, Sanchez A, Appelqvist R, Miliotis T, Kuras M, Oskolas H, Kim Y, Horvath Z, Eriksson J, Berge E, Burestedt E, Jönsson G, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Horvatovich P, Murillo JR, Sugihara Y, Welinder C, Wieslander E, Lee B, Lindberg H, Pawłowski K, Kwon HJ, Doma V, Timar J, Karpati S, Szasz AM, Németh IB, Nishimura T, Corthals G, Rezeli M, Knudsen B, Malm J, Marko-Varga G. Clinical protein science in translational medicine targeting malignant melanoma. Cell Biol Toxicol 2019; 35:293-332. [PMID: 30900145 PMCID: PMC6757020 DOI: 10.1007/s10565-019-09468-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/13/2019] [Indexed: 02/06/2023]
Abstract
Melanoma of the skin is the sixth most common type of cancer in Europe and accounts for 3.4% of all diagnosed cancers. More alarming is the degree of recurrence that occurs with approximately 20% of patients lethally relapsing following treatment. Malignant melanoma is a highly aggressive skin cancer and metastases rapidly extend to the regional lymph nodes (stage 3) and to distal organs (stage 4). Targeted oncotherapy is one of the standard treatment for progressive stage 4 melanoma, and BRAF inhibitors (e.g. vemurafenib, dabrafenib) combined with MEK inhibitor (e.g. trametinib) can effectively counter BRAFV600E-mutated melanomas. Compared to conventional chemotherapy, targeted BRAFV600E inhibition achieves a significantly higher response rate. After a period of cancer control, however, most responsive patients develop resistance to the therapy and lethal progression. The many underlying factors potentially causing resistance to BRAF inhibitors have been extensively studied. Nevertheless, the remaining unsolved clinical questions necessitate alternative research approaches to address the molecular mechanisms underlying metastatic and treatment-resistant melanoma. In broader terms, proteomics can address clinical questions far beyond the reach of genomics, by measuring, i.e. the relative abundance of protein products, post-translational modifications (PTMs), protein localisation, turnover, protein interactions and protein function. More specifically, proteomic analysis of body fluids and tissues in a given medical and clinical setting can aid in the identification of cancer biomarkers and novel therapeutic targets. Achieving this goal requires the development of a robust and reproducible clinical proteomic platform that encompasses automated biobanking of patient samples, tissue sectioning and histological examination, efficient protein extraction, enzymatic digestion, mass spectrometry-based quantitative protein analysis by label-free or labelling technologies and/or enrichment of peptides with specific PTMs. By combining data from, e.g. phosphoproteomics and acetylomics, the protein expression profiles of different melanoma stages can provide a solid framework for understanding the biology and progression of the disease. When complemented by proteogenomics, customised protein sequence databases generated from patient-specific genomic and transcriptomic data aid in interpreting clinical proteomic biomarker data to provide a deeper and more comprehensive molecular characterisation of cellular functions underlying disease progression. In parallel to a streamlined, patient-centric, clinical proteomic pipeline, mass spectrometry-based imaging can aid in interrogating the spatial distribution of drugs and drug metabolites within tissues at single-cell resolution. These developments are an important advancement in studying drug action and efficacy in vivo and will aid in the development of more effective and safer strategies for the treatment of melanoma. A collaborative effort of gargantuan proportions between academia and healthcare professionals has led to the initiation, establishment and development of a cutting-edge cancer research centre with a specialisation in melanoma and lung cancer. The primary research focus of the European Cancer Moonshot Lund Center is to understand the impact that drugs have on cancer at an individualised and personalised level. Simultaneously, the centre increases awareness of the relentless battle against cancer and attracts global interest in the exceptional research performed at the centre.
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Affiliation(s)
- Jeovanis Gil
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
| | - Lazaro Hiram Betancourt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
| | - Indira Pla
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - Aniel Sanchez
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - Roger Appelqvist
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Tasso Miliotis
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Translational Science, Cardiovascular Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Magdalena Kuras
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Henriette Oskolas
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Yonghyo Kim
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Zsolt Horvath
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Jonatan Eriksson
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Ethan Berge
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Elisabeth Burestedt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Bo Baldetorp
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Lund University, SUS, Lund, Sweden
| | - Håkan Olsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Lotta Lundgren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Jimmy Rodriguez Murillo
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Yutaka Sugihara
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Boram Lee
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Henrik Lindberg
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Krzysztof Pawłowski
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Ho Jeong Kwon
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Viktoria Doma
- Second Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Jozsef Timar
- Second Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Sarolta Karpati
- Department of Dermatology, Semmelweis University, Budapest, Hungary
| | - A Marcell Szasz
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Cancer Center, Semmelweis University, Budapest, 1083, Hungary
- MTA-TTK Momentum Oncology Biomarker Research Group, Hungarian Academy of Sciences, Budapest, 1117, Hungary
| | - István Balázs Németh
- Department of Dermatology and Allergology, University of Szeged, Szeged, H-6720, Hungary
| | - Toshihide Nishimura
- Clinical Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
- Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo, Japan
| | - Garry Corthals
- Van't Hoff Institute of Molecular Sciences, 1090 GS, Amsterdam, The Netherlands
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Beatrice Knudsen
- Biomedical Sciences and Pathology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
- Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo, Japan
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17
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Knol AC, Nguyen JM, Pandolfino MC, Denis MG, Khammari A, Dréno B. PD-L1 expression by tumor cell lines: A predictive marker in melanoma. Exp Dermatol 2019; 27:647-655. [PMID: 29505109 DOI: 10.1111/exd.13526] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2018] [Indexed: 12/24/2022]
Abstract
Prognostic biomarkers for patients with melanoma after lymph node resection are of clinical relevance and could thus enable the identification of patients who therefore would most benefit from adjuvant treatment. The aim of this work was to determine, using an in vitro model, whether immune-related biomarkers, such as MHC-class I and II, melanoma-associated antigens, IDO1 and PD-L1, could also be relevant to predict the risk of relapse of patients with stage III melanoma after lymph node resection. We established tumor cell lines from metastatic lymph nodes of 50 patients with melanoma. The expression of investigated biomarkers was determined on untreated and IFN-γ treated melanoma cell lines using flow cytometry. Among the selected biomarkers, the IFN-γ-induced expression of PD-L1 and IDO1 was associated with an increased risk of relapse (P = .0001 and P = .013, respectively) and was also associated with death for IDO1 (P = .0005). In the future, this immunologic signature could permit the identification of patients at higher risk of relapse and justifying an adjuvant treatment using immunotherapy.
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Affiliation(s)
- Anne C Knol
- Centre de recherche en Cancérologie et Immunologie Nantes-Angers [CRCINA], Institut National de la Santé et de la Recherche Médicale [INSERM] INSERM1232, Université de Nantes, Université d'Angers, CHU Nantes, Nantes, France
| | - Jean-Michel Nguyen
- Centre de recherche en Cancérologie et Immunologie Nantes-Angers [CRCINA], Institut National de la Santé et de la Recherche Médicale [INSERM] INSERM1232, Université de Nantes, Université d'Angers, CHU Nantes, Nantes, France.,Saint Jacques University Hospital, Service d'évaluation médicale et économique [SEME] Pôle Hospitalo-Universitaire 11 [PHU11], CHU Nantes, Nantes, France
| | - Marie-Christine Pandolfino
- Centre de recherche en Cancérologie et Immunologie Nantes-Angers [CRCINA], Institut National de la Santé et de la Recherche Médicale [INSERM] INSERM1232, Université de Nantes, Université d'Angers, CHU Nantes, Nantes, France.,Unité de Thérapie Cellulaire et Génique [UTCG], CHU Nantes, Nantes, France
| | - Marc G Denis
- Centre de recherche en Cancérologie et Immunologie Nantes-Angers [CRCINA], Institut National de la Santé et de la Recherche Médicale [INSERM] INSERM1232, Université de Nantes, Université d'Angers, CHU Nantes, Nantes, France.,Laboratoire de Biochimie et Plateforme de Génétique des Cancers, CHU Nantes, Nantes, France
| | - Amir Khammari
- Centre de recherche en Cancérologie et Immunologie Nantes-Angers [CRCINA], Institut National de la Santé et de la Recherche Médicale [INSERM] INSERM1232, Université de Nantes, Université d'Angers, CHU Nantes, Nantes, France.,Service de dermato-cancérologie, CHU Nantes, Nantes, France
| | - Brigitte Dréno
- Centre de recherche en Cancérologie et Immunologie Nantes-Angers [CRCINA], Institut National de la Santé et de la Recherche Médicale [INSERM] INSERM1232, Université de Nantes, Université d'Angers, CHU Nantes, Nantes, France.,Unité de Thérapie Cellulaire et Génique [UTCG], CHU Nantes, Nantes, France.,Service de dermato-cancérologie, CHU Nantes, Nantes, France
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18
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Betancourt LH, Pawłowski K, Eriksson J, Szasz AM, Mitra S, Pla I, Welinder C, Ekedahl H, Broberg P, Appelqvist R, Yakovleva M, Sugihara Y, Miharada K, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Wieslander E, Horvatovich P, Malm J, Jönsson G, Marko-Varga G. Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data. Sci Rep 2019; 9:5154. [PMID: 30914758 PMCID: PMC6435712 DOI: 10.1038/s41598-019-41625-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 03/13/2019] [Indexed: 12/18/2022] Open
Abstract
Metastatic melanoma is one of the most common deadly cancers, and robust biomarkers are still needed, e.g. to predict survival and treatment efficiency. Here, protein expression analysis of one hundred eleven melanoma lymph node metastases using high resolution mass spectrometry is coupled with in-depth histopathology analysis, clinical data and genomics profiles. This broad view of protein expression allowed to identify novel candidate protein markers that improved prediction of survival in melanoma patients. Some of the prognostic proteins have not been reported in the context of melanoma before, and few of them exhibit unexpected relationship to survival, which likely reflects the limitations of current knowledge on melanoma and shows the potential of proteomics in clinical cancer research.
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Affiliation(s)
| | - Krzysztof Pawłowski
- Lund University, Lund, Sweden.
- Warsaw University of Life Sciences SGGW, Warszawa, Poland.
| | | | - A Marcell Szasz
- Lund University, Lund, Sweden
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- Semmelweis University, Budapest, Hungary
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Peter Horvatovich
- Lund University, Lund, Sweden
- University of Groningen, Groningen, The Netherlands
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19
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Kuras M, Betancourt LH, Rezeli M, Rodriguez J, Szasz M, Zhou Q, Miliotis T, Andersson R, Marko-Varga G. Assessing Automated Sample Preparation Technologies for High-Throughput Proteomics of Frozen Well Characterized Tissues from Swedish Biobanks. J Proteome Res 2018; 18:548-556. [PMID: 30462917 DOI: 10.1021/acs.jproteome.8b00792] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Large cohorts of carefully collected clinical tissue materials play a central role in acquiring sufficient depth and statistical power to discover disease-related mechanisms and biomarkers of clinical significance. Manual preparation of such large sample cohorts requires experienced laboratory personnel. This carries other possible downsides such as low throughput, high risk of errors, and low reproducibility. In this work, three automated technologies for high-throughput proteomics of frozen sectioned tissues were compared. The instruments evaluated included the Bioruptor for tissue disruption and protein extraction; the Barocycler, which is able to disrupt tissues and digest the proteins; and the AssayMAP Bravo, a microchromatography platform for protein digestion, peptide desalting, and fractionation. Wide varieties of tissue samples from rat spleen, malignant melanoma, and pancreatic tumors were used for the assessment. The three instruments displayed reproducible and consistent results, as was proven by high correlations and low coefficients of variation between technical replicates and even more importantly, between replicates that were processed in different batches or at different time points. The results from this study allowed us to integrate these technologies into an automated sample preparation workflow for large-scale proteomic studies that are currently ongoing. Data are available via ProteomeXchange with identifiers PXD010296 and PXD011295.
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Affiliation(s)
- Magdalena Kuras
- Division of Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering , Lund University , 221 00 Lund , Sweden
| | - Lazaro Hiram Betancourt
- Division of Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering , Lund University , 221 00 Lund , Sweden
| | - Melinda Rezeli
- Division of Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering , Lund University , 221 00 Lund , Sweden
| | - Jimmy Rodriguez
- Division of Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering , Lund University , 221 00 Lund , Sweden
| | - Marcell Szasz
- Department of Pathology , Semmelweis University , Budapest 1085 , Hungary
| | - Qimin Zhou
- Department of Clinical Sciences Lund (Surgery) , Lund University, Lund, Sweden Skane University Hospital , 221 00 Lund , Sweden
| | - Tasso Miliotis
- Division of Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering , Lund University , 221 00 Lund , Sweden.,Translational Science, Cardiovascular Renal and Metabolism, IMED Biotech Unit , AstraZeneca , 431 50 Mölndal , Gothenburg , Sweden
| | - Roland Andersson
- Department of Clinical Sciences Lund (Surgery) , Lund University, Lund, Sweden Skane University Hospital , 221 00 Lund , Sweden
| | - Gyorgy Marko-Varga
- Division of Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering , Lund University , 221 00 Lund , Sweden.,First Department of Surgery , Tokyo Medical University , 160-8402 Tokyo , Japan
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20
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Marcell Szasz A, Malm J, Rezeli M, Sugihara Y, Betancourt LH, Rivas D, Gyorffy B, Marko-Varga G. Challenging the heterogeneity of disease presentation in malignant melanoma-impact on patient treatment. Cell Biol Toxicol 2018; 35:1-14. [PMID: 30357519 PMCID: PMC6514062 DOI: 10.1007/s10565-018-9446-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/29/2018] [Indexed: 11/27/2022]
Abstract
There is an increasing global interest to support research areas that can assist in understanding disease and improving patient care. The National Cancer Institute (NIH) has identified precision medicine-based approaches as key research strategies to expedite advances in cancer research. The Cancer Moonshot program ( https://www.cancer.gov/research/key-initiatives/moonshot-cancer-initiative ) is the largest cancer program of all time, and has been launched to accelerate cancer research that aims to increase the availability of therapies to more patients and, ultimately, to eradicate cancer. Mass spectrometry-based proteomics has been extensively used to study the molecular mechanisms of cancer, to define molecular subtypes of tumors, to map cancer-associated protein interaction networks and post-translational modifications, and to aid in the development of new therapeutics and new diagnostic and prognostic tests. To establish the basis for our melanoma studies, we have established the Southern Sweden Malignant Melanoma Biobank. Tissues collected over many years have been accurately characterized with respect to the tumor and patient information. The extreme variability displayed in the protein profiles and the detection of missense mutations has confirmed the complexity and heterogeneity of the disease. It is envisaged that the combined analysis of clinical, histological, and proteomic data will provide patients with a more personalized medical treatment. With respect to disease presentation, targeted treatment and medical mass spectrometry analysis and imaging, this overview report will outline and summarize the current achievements and status within malignant melanoma. We present data generated by our cancer research center in Lund, Sweden, where we have built extensive capabilities in biobanking, proteogenomics, and patient treatments over an extensive time period.
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Affiliation(s)
- A Marcell Szasz
- Center of Excellence in Biological and Medical Mass Spectrometry, Lund University, BMC D13, 221 84, Lund, Sweden
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Cancer Center, Semmelweis University, Budapest, 1083, Hungary
- MTA-TTK Momentum Oncology Biomarker Research Group, Hungarian Academy of Sciences, Budapest, 1117, Hungary
| | - Johan Malm
- Center of Excellence in Biological and Medical Mass Spectrometry, Lund University, BMC D13, 221 84, Lund, Sweden
- Department of Oncology, Lund University, Skåne University Hospital, 221 85, Lund, Sweden
- Department of Translational Medicine, Section for Clinical Chemistry, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - Melinda Rezeli
- Clinical Protein Science and Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Yutaka Sugihara
- Center of Excellence in Biological and Medical Mass Spectrometry, Lund University, BMC D13, 221 84, Lund, Sweden
- Clinical Protein Science and Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Lazaro H Betancourt
- Center of Excellence in Biological and Medical Mass Spectrometry, Lund University, BMC D13, 221 84, Lund, Sweden
- Clinical Protein Science and Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Daniel Rivas
- Institute of Environmental Sciences and Water Research, IDAEA, Spanish Research Council (CSIC), Barcelona, Spain
| | - Balázs Gyorffy
- MTA-TTK Momentum Oncology Biomarker Research Group, Hungarian Academy of Sciences, Budapest, 1117, Hungary
- 2nd Department of Pediatrics, Semmelweis University, Budapest, 1094, Hungary
| | - György Marko-Varga
- Center of Excellence in Biological and Medical Mass Spectrometry, Lund University, BMC D13, 221 84, Lund, Sweden.
- Clinical Protein Science and Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
- Division of Life Science and Biotechnology, Yonsei University, Soel, Korea.
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21
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Malm J, Sugihara Y, Szasz M, Kwon HJ, Lindberg H, Appelqvist R, Marko-Varga G. Biobank integration of large-scale clinical and histopathology melanoma studies within the European Cancer Moonshot Lund Center. Clin Transl Med 2018; 7:28. [PMID: 30123920 PMCID: PMC6098996 DOI: 10.1186/s40169-018-0203-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/06/2018] [Indexed: 02/08/2023] Open
Abstract
We present the Cancer Moonshot clinical project located at the European center in Lund. Here, tissue and blood samples have been collected and stored in a large-scale biobank. Multiple clinical centers around the world are participating and tissue and blood samples are sent to the European Cancer Moonshot Lund Center that acts as the clinical hub. Our center has been developed to generate and build large-scale biostorage archives of patient melanoma samples, which is then combined with a histopathological capability to characterize the patient tumours. Such a large-scale clinical sample processing initiative has begun with the aim of creating high-end histopathology indexing with database computational power and including proteogenomic analysis. The biobank at Lund has become an important resource in clinical research worldwide. Following suite, several national health programs are being initiated with the aim of also building large-scale biobank storages with a wealth of high-quality patient samples. In our Cancer Moonshot R&D activities, samples in the biobanks and the data derived from these samples are being used to build an understanding of disease presentation and using this information to move towards 'Big Data' proteogenomic and mass spectrometry imaging studies. Additionally, we report here a sample processing workflow that has been adapted to a fully-automated biobank processing strategy for large-scale studies.
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Affiliation(s)
- Johan Malm
- Department of Translational Medicine, Section for Clinical Chemistry, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden.
- Clinical Protein Science & Imaging, Biomedical Center, Dept. of Biomedical Engineering, Lund University, BMC C13, 221 84, Lund, Sweden.
- Centre of Excellence in Biological and Medical Mass Spectrometry, Lund University, BioMedical Centre D13, 221 85, Lund, Sweden.
| | - Yutaka Sugihara
- Clinical Protein Science & Imaging, Biomedical Center, Dept. of Biomedical Engineering, Lund University, BMC C13, 221 84, Lund, Sweden
- Department of Oncology, Clinical Sciences, Lund University, Skåne University Hospital, 221 85, Lund, Sweden
| | - Marcell Szasz
- Clinical Protein Science & Imaging, Biomedical Center, Dept. of Biomedical Engineering, Lund University, BMC C13, 221 84, Lund, Sweden
- 2nd Department of Pathology, Semmelweis University, Budapest, 1091, Hungary
| | - Ho Jeong Kwon
- Clinical Protein Science & Imaging, Biomedical Center, Dept. of Biomedical Engineering, Lund University, BMC C13, 221 84, Lund, Sweden
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749, Republic of Korea
| | - Henrik Lindberg
- Clinical Protein Science & Imaging, Biomedical Center, Dept. of Biomedical Engineering, Lund University, BMC C13, 221 84, Lund, Sweden
- Department of Oncology, Clinical Sciences, Lund University, Skåne University Hospital, 221 85, Lund, Sweden
| | - Roger Appelqvist
- Clinical Protein Science & Imaging, Biomedical Center, Dept. of Biomedical Engineering, Lund University, BMC C13, 221 84, Lund, Sweden
- Department of Oncology, Clinical Sciences, Lund University, Skåne University Hospital, 221 85, Lund, Sweden
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Center, Dept. of Biomedical Engineering, Lund University, BMC C13, 221 84, Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry, Lund University, BioMedical Centre D13, 221 85, Lund, Sweden
- Department of Oncology, Clinical Sciences, Lund University, Skåne University Hospital, 221 85, Lund, Sweden
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749, Republic of Korea
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22
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Sugihara Y, Rivas D, Malm J, Szasz M, Kwon H, Baldetorp B, Olsson H, Ingvar C, Rezeli M, Fehniger TE, Marko-Varga G. Endogenous expression mapping of malignant melanoma by mass spectrometry imaging. Clin Transl Med 2018; 7:22. [PMID: 30079437 PMCID: PMC6077138 DOI: 10.1186/s40169-018-0201-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/02/2018] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Currently, only a limited number of molecular biomarkers for malignant melanoma exist. This is the case for both diagnosing the disease, staging, and efficiently measuring the response to therapy by tracing the progression of disease development and drug impact. There is a great need to identify novel landmarks of disease progression and alterations. METHODS Matrix-assisted laser desorption ionisation mass spectrometry imaging (MALDI-MSI) has been developed within our group to study drug localisation within micro-environmental tissue compartments. Here, we expand further on this technology development and introduce for the first time melanoma tumour tissues to map metabolite localisation utilising high resolution mass spectrometry. MALDI-MSI can measure and localise the distribution pattern of a number of small molecule metabolites within tissue compartments of tumours isolated from melanoma patients. Data on direct measurements of metabolite identities attained at the local sites in tissue compartments has not been readily available as a measure of a clinical index for most cancer diseases. The current development on the mapping of endogenous molecular expression melanoma tumours by mass spectrometry imaging focuses on the establishment of a cancer tissue preparation process whereby a matrix crystal formation is homogenously built on the tissue surface, providing uniform molecular mapping. We apply this micro-preparation technology to disease presentation by mapping the molecular signatures from patient tumour sections. RESULTS We have automated the process with a micro-technological dispensing platform. This provides the basis for thin film generation of the cancer patient tissues prior to imaging screening. Compartmentalisation of the tumour regions are displayed within the image analysis interfaced with histopathological grading and characterisation. CONCLUSIONS This enables site localisation within the tumour with image mapping to disease target areas such as melanoma cells, macrophages, and lymphocytes.
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Affiliation(s)
- Yutaka Sugihara
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
- Department of Oncology, Clinical Sciences, Lund University, Skåne University Hospital, 221 85 Lund, Sweden
| | - Daniel Rivas
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
| | - Johan Malm
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry, BioMedical Centre D13, Lund University, 221 85 Lund, Sweden
| | - Marcell Szasz
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
- Cancer Center, Semmelweis University, Budapest, 1091 Hungary
- Department of Tumor Biology, National Koranyi Institute of Pulmonology, Budapest, 1121 Hungary
| | - HoJeong Kwon
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749 Republic of Korea
| | - Bo Baldetorp
- Department of Oncology, Clinical Sciences, Lund University, Skåne University Hospital, 221 85 Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry, BioMedical Centre D13, Lund University, 221 85 Lund, Sweden
| | - Håkan Olsson
- Department of Oncology, Clinical Sciences, Lund University, Skåne University Hospital, 221 85 Lund, Sweden
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Lund University, SUS, 221 85 Lund, Sweden
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
| | - Thomas E. Fehniger
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry, BioMedical Centre D13, Lund University, 221 85 Lund, Sweden
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University, BMC C13, 221 84 Lund, Sweden
- Department of Oncology, Clinical Sciences, Lund University, Skåne University Hospital, 221 85 Lund, Sweden
- Centre of Excellence in Biological and Medical Mass Spectrometry, BioMedical Centre D13, Lund University, 221 85 Lund, Sweden
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749 Republic of Korea
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23
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Huang YX, Song H, Tao Y, Shao XB, Zeng XS, Xu XL, Qi JL, Sun JF. Ovostatin 2 knockdown significantly inhibits the growth, migration, and tumorigenicity of cutaneous malignant melanoma cells. PLoS One 2018; 13:e0195610. [PMID: 29684087 PMCID: PMC5912766 DOI: 10.1371/journal.pone.0195610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 03/26/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND We previously identified ovostatin 2 (OVOS2) as a new candidate gene for cutaneous malignant melanoma (CMM) in a Chinese population. In this study, we aimed to investigate the exact role of OVOS2 in cell proliferation, invasion, and tumorigenesis of melanoma A375 cells. METHODS The downregulation of OVOS2 expression was performed using lentiviral vectors with specific shRNA. The effects of OVOS2 expression on cell proliferation, cell cycle, cell migration, cell invasion, and potential of tumorigenesis were further investigated. RESULTS The downregulation of OVOS2 significantly suppressed the proliferation of A375 cells and led to a G2/M phase block. The transwell cell migration assay showed that the reduced expression of OVOS2 also significantly inhibited the transmigration of A375 cells. The western blot results showed downregulated expression of p-FAK, p-AKT, and p-ERK. This was accompanied by the upregulated epithelial phenotypes E-cadherin and β-catenin, and downregulated expression of mesenchymal phenotype N-cadherin after OVOS2 knockdown. The transplantation tumor experiment in BALB/C nude mouse showed that after an observation period of 32 days, the growth speed and weight of the transplanted tumors were significantly suppressed in the BALB/c nude mice subcutaneously injected with OVOS2 knocked-down A375 cells. CONCLUSION The inhibition of OVOS2 had significant suppressive effects on the proliferation, motility, and migration capabilities of A375 cells, suggesting a crucial promotive role of OVOS2 in the pathogenesis and progression of CMM. The involved mechanisms are at least partly associated with the overactivation of FAK/MAPK/ERK and FAK/PI3K/AKT signals.
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Affiliation(s)
- Ying-Xue Huang
- Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, P. R. China
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, P. R. China
| | - Hao Song
- Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, P. R. China
| | - Yue Tao
- Drum Tower Hospital, Medical School of Nanjing University, Nanjing, P. R. China
| | - Xue-Bao Shao
- Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, P. R. China
| | - Xue-Si Zeng
- Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, P. R. China
| | - Xiu-Lian Xu
- Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, P. R. China
| | - Jin-Liang Qi
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, P. R. China
| | - Jian-Fang Sun
- Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, P. R. China
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24
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Hareza A, Bakun M, Świderska B, Dudkiewicz M, Koscielny A, Bajur A, Jaworski J, Dadlez M, Pawłowski K. Phosphoproteomic insights into processes influenced by the kinase-like protein DIA1/C3orf58. PeerJ 2018; 6:e4599. [PMID: 29666759 PMCID: PMC5896498 DOI: 10.7717/peerj.4599] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 03/21/2018] [Indexed: 12/27/2022] Open
Abstract
Many kinases are still ‘orphans,’ which means knowledge about their substrates, and often also about the processes they regulate, is lacking. Here, DIA1/C3orf58, a member of a novel predicted kinase-like family, is shown to be present in the endoplasmic reticulum and to influence trafficking via the secretory pathway. Subsequently, DIA1 is subjected to phosphoproteomics analysis to cast light on its signalling pathways. A liquid chromatography–tandem mass spectrometry proteomic approach with phosphopeptide enrichment is applied to membrane fractions of DIA1-overexpressing and control HEK293T cells, and phosphosites dependent on the presence of DIA1 are elucidated. Most of these phosphosites belonged to CK2- and proline-directed kinase types. In parallel, the proteomics of proteins immunoprecipitated with DIA1 reported its probable interactors. This pilot study provides the basis for deeper studies of DIA1 signalling.
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Affiliation(s)
- Agnieszka Hareza
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland.,International Institute of Molecular and Cellular Biology, Warszawa, Poland
| | - Magda Bakun
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Bianka Świderska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Małgorzata Dudkiewicz
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland
| | - Alicja Koscielny
- International Institute of Molecular and Cellular Biology, Warszawa, Poland
| | - Anna Bajur
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland.,International Institute of Molecular and Cellular Biology, Warszawa, Poland.,Current affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jacek Jaworski
- International Institute of Molecular and Cellular Biology, Warszawa, Poland
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Krzysztof Pawłowski
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warszawa, Poland.,Department of Translational Medicine, Clinical Sciences, Lund University, Lund, Sweden
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25
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Rodríguez-Cerdeira C, Molares-Vila A, Carnero-Gregorio M, Corbalán-Rivas A. Recent advances in melanoma research via "omics" platforms. J Proteomics 2017; 188:152-166. [PMID: 29138111 DOI: 10.1016/j.jprot.2017.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/25/2017] [Accepted: 11/08/2017] [Indexed: 02/09/2023]
Abstract
Melanoma has a high mortality rate and metastatic melanoma is highly resistant to conventional therapies. "Omics" fields such as proteomics and microRNA and exosome studies have provided new knowledge to complement the information generated by genomic studies. This work aimed to review the current status of biomarker discovery for melanoma through multi-"omics" platforms. A few sets of novel microRNAs and proteins are described, some of them with important implications in suppressing melanoma at different stages. Upregulation of genes involved in angiogenesis, immunosuppressive factors, modification of stroma, capture of melanoma cells in lymph nodes and factors responsible for tumour cell recruitment have been identified in exosomes, among molecules with other functions. A remarkable series of proteins involved in epithelial-mesenchymal/mesenchymal-epithelial transitions, inflammation, motility, proliferation and progression processes, centrosome amplification, aneuploidy, inhibition of CD8+ effector T-cells, and metastasis in general were identified. Genomic and protein-protein interactions or metabolome levels were not analysed. Proteomics tools such as Orbitrap shotgun mass spectrometry or deep mining proteomic analysis utilizing high-resolution reversed phase nanoseparation in combination with mass spectrometry are also discussed. The application of these tools together with bioinformatics approaches applied to the clinical setting will enable the implementation of personalized medicine in the near future.
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Affiliation(s)
- Carmen Rodríguez-Cerdeira
- Efficiency, Quality and Costs in Health Services Research Group (EFISALUD), Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain; Dermatology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo, Spain.
| | - Alberto Molares-Vila
- Efficiency, Quality and Costs in Health Services Research Group (EFISALUD), Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain; Department of Analytical & Food Chemistry, Universidade de Vigo (UVIGO), Spain
| | - Miguel Carnero-Gregorio
- Efficiency, Quality and Costs in Health Services Research Group (EFISALUD), Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain; Department of Biochemistry, Genetics & Immunology, Universidade de Vigo (UVIGO), Spain
| | - Alberte Corbalán-Rivas
- Nursery Department, Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, A Coruña, Spain
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