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Elshoeibi AM, Elsayed B, Kaleem MZ, Elhadary MR, Abu-Haweeleh MN, Haithm Y, Krzyslak H, Vranic S, Pedersen S. Proteomic Profiling of Small-Cell Lung Cancer: A Systematic Review. Cancers (Basel) 2023; 15:5005. [PMID: 37894372 PMCID: PMC10605593 DOI: 10.3390/cancers15205005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/24/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
The accurate diagnosis of small-cell lung cancer (SCLC) is crucial, as treatment strategies differ from those of other lung cancers. This systematic review aims to identify proteins differentially expressed in SCLC compared to normal lung tissue, evaluating their potential utility in diagnosing and prognosing the disease. Additionally, the study identifies proteins differentially expressed between SCLC and large cell neuroendocrine carcinoma (LCNEC), aiming to discover biomarkers distinguishing between these two subtypes of neuroendocrine lung cancers. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, a comprehensive search was conducted across PubMed/MEDLINE, Scopus, Embase, and Web of Science databases. Studies reporting proteomics information and confirming SCLC and/or LCNEC through histopathological and/or cytopathological examination were included, while review articles, non-original articles, and studies based on animal samples or cell lines were excluded. The initial search yielded 1705 articles, and after deduplication and screening, 16 articles were deemed eligible. These studies revealed 117 unique proteins significantly differentially expressed in SCLC compared to normal lung tissue, along with 37 unique proteins differentially expressed between SCLC and LCNEC. In conclusion, this review highlights the potential of proteomics technology in identifying novel biomarkers for diagnosing SCLC, predicting its prognosis, and distinguishing it from LCNEC.
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Affiliation(s)
| | - Basel Elsayed
- College of Medicine, QU Health, Qatar University, Doha 2713, Qatar (M.N.A.-H.); (S.V.)
| | - Muhammad Zain Kaleem
- College of Medicine, QU Health, Qatar University, Doha 2713, Qatar (M.N.A.-H.); (S.V.)
| | | | | | - Yunes Haithm
- College of Medicine, QU Health, Qatar University, Doha 2713, Qatar (M.N.A.-H.); (S.V.)
| | - Hubert Krzyslak
- Department of Clinical Biochemistry, Aalborg University Hospital, 9000 Aalborg, Denmark
| | - Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha 2713, Qatar (M.N.A.-H.); (S.V.)
| | - Shona Pedersen
- College of Medicine, QU Health, Qatar University, Doha 2713, Qatar (M.N.A.-H.); (S.V.)
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2
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Guo JH, Ma YS, Lin JW, Jiang GX, He J, Lu HM, Wu W, Diao X, Fan QY, Wu CY, Liu JB, Fu D, Hou LK. Whole-exome and targeted gene sequencing of large-cell lung carcinoma reveals recurrent mutations in the PI3K pathway. Br J Cancer 2023; 129:366-373. [PMID: 37179440 PMCID: PMC10338432 DOI: 10.1038/s41416-023-02301-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/25/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Large cell lung carcinoma (LCLC) is an exceptionally aggressive disease with a poor prognosis. At present, little is known about the molecular pathology of LCLC. METHODS Ultra-deep sequencing of cancer-related genes and exome sequencing were used to detect the LCLC mutational in 118 tumor-normal pairs. The cell function test was employed to confirm the potential carcinogenic mutation of PI3K pathway. RESULTS The mutation pattern is determined by the predominance of A > C mutations. Genes with a significant non-silent mutation frequency (FDR) < 0.05) include TP53 (47.5%), EGFR (13.6%) and PTEN (12.1%). Moreover, PI3K signaling (including EGFR, FGRG4, ITGA1, ITGA5, and ITGA2B) is the most mutated pathway, influencing 61.9% (73/118) of the LCLC samples. The cell function test confirmed that the potential carcinogenic mutation of PI3K pathway had a more malignant cell function phenotype. Multivariate analysis further revealed that patients with the PI3K signaling pathway mutations have a poor prognosis (P = 0.007). CONCLUSIONS These results initially identified frequent mutation of PI3K signaling pathways in LCLC and indicate potential targets for the treatment of this fatal type of LCLC.
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Affiliation(s)
- Jun-Hong Guo
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Yu-Shui Ma
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China
| | - Jie-Wei Lin
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Geng-Xi Jiang
- Department of Thoracic Surgery, Navy Military Medical University Affiliated Changhai Hospital, Shanghai, 200433, China
| | - Juan He
- Pharmacy Department, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Hai-Min Lu
- Department of Thoracic Surgery, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China
| | - Wei Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Xun Diao
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China
| | - Qi-Yu Fan
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China
| | - Chun-Yan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China.
| | - Ji-Bin Liu
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China.
| | - Da Fu
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China.
| | - Li-Kun Hou
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China.
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Klaila G, Vutov V, Stefanou A. Supervised topological data analysis for MALDI mass spectrometry imaging applications. BMC Bioinformatics 2023; 24:279. [PMID: 37430224 DOI: 10.1186/s12859-023-05402-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) displays significant potential for applications in cancer research, especially in tumor typing and subtyping. Lung cancer is the primary cause of tumor-related deaths, where the most lethal entities are adenocarcinoma (ADC) and squamous cell carcinoma (SqCC). Distinguishing between these two common subtypes is crucial for therapy decisions and successful patient management. RESULTS We propose a new algebraic topological framework, which obtains intrinsic information from MALDI data and transforms it to reflect topological persistence. Our framework offers two main advantages. Firstly, topological persistence aids in distinguishing the signal from noise. Secondly, it compresses the MALDI data, saving storage space and optimizes computational time for subsequent classification tasks. We present an algorithm that efficiently implements our topological framework, relying on a single tuning parameter. Afterwards, logistic regression and random forest classifiers are employed on the extracted persistence features, thereby accomplishing an automated tumor (sub-)typing process. To demonstrate the competitiveness of our proposed framework, we conduct experiments on a real-world MALDI dataset using cross-validation. Furthermore, we showcase the effectiveness of the single denoising parameter by evaluating its performance on synthetic MALDI images with varying levels of noise. CONCLUSION Our empirical experiments demonstrate that the proposed algebraic topological framework successfully captures and leverages the intrinsic spectral information from MALDI data, leading to competitive results in classifying lung cancer subtypes. Moreover, the framework's ability to be fine-tuned for denoising highlights its versatility and potential for enhancing data analysis in MALDI applications.
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Affiliation(s)
- Gideon Klaila
- Institute for Algebra, Geometry, Topology and their Applications (ALTA), University of Bremen, 28359, Bremen, Germany.
| | - Vladimir Vutov
- Institute for Statistics, University of Bremen, 28359, Bremen, Germany
| | - Anastasios Stefanou
- Institute for Algebra, Geometry, Topology and their Applications (ALTA), University of Bremen, 28359, Bremen, Germany
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Balbisi M, Sugár S, Schlosser G, Szeitz B, Fillinger J, Moldvay J, Drahos L, Szász AM, Tóth G, Turiák L. Inter- and intratumoral proteomics and glycosaminoglycan characterization of ALK rearranged lung adenocarcinoma tissues: a pilot study. Sci Rep 2023; 13:6268. [PMID: 37069213 PMCID: PMC10110559 DOI: 10.1038/s41598-023-33435-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/12/2023] [Indexed: 04/19/2023] Open
Abstract
Lung cancer is one of the most common types of cancer with limited therapeutic options, therefore a detailed understanding of the underlying molecular changes is of utmost importance. In this pilot study, we investigated the proteomic and glycosaminoglycan (GAG) profile of ALK rearranged lung tumor tissue regions based on the morphological classification, mucin and stromal content. Principal component analysis and hierarchical clustering revealed that both the proteomic and GAG-omic profiles are highly dependent on mucin content and to a lesser extent on morphology. We found that differentially expressed proteins between morphologically different tumor types are primarily involved in the regulation of protein synthesis, whereas those between adjacent normal and different tumor regions take part in several other biological processes (e.g. extracellular matrix organization, oxidation-reduction processes, protein folding) as well. The total amount and the sulfation profile of heparan sulfate and chondroitin sulfate showed small differences based on morphology and larger differences based on mucin content of the tumor, while an increase was observed in both the total amount and the average rate of sulfation in tumors compared to adjacent normal regions.
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Affiliation(s)
- Mirjam Balbisi
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest, 1117, Hungary
- Doctoral School of Pharmaceutical Sciences, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary
| | - Simon Sugár
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest, 1117, Hungary
- Doctoral School of Pharmaceutical Sciences, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Eötvös Loránd University, Pázmány Péter sétány 1, Budapest, 1117, Hungary
| | - Beáta Szeitz
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary
| | - János Fillinger
- Department of Pathology, National Korányi Institute of Pulmonology, Korányi Frigyes út 1., Budapest, 1121, Hungary
| | - Judit Moldvay
- 1st Department of Pulmonology, National Korányi Institute of Pulmonology, Korányi Frigyes út 1., Budapest, 1121, Hungary
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest, 1117, Hungary
| | - A Marcell Szász
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary
| | - Gábor Tóth
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest, 1117, Hungary.
| | - Lilla Turiák
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest, 1117, Hungary.
- Doctoral School of Pharmaceutical Sciences, Semmelweis University, Üllői út 26., Budapest, 1085, Hungary.
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Pál D, Tóth G, Sugár S, Fügedi KD, Szabó D, Kovalszky I, Papp D, Schlosser G, Tóth C, Tornóczky T, Drahos L, Turiák L. Compositional Analysis of Glycosaminoglycans in Different Lung Cancer Types-A Pilot Study. Int J Mol Sci 2023; 24:ijms24087050. [PMID: 37108213 PMCID: PMC10138872 DOI: 10.3390/ijms24087050] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/26/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Lung cancer is one of the most commonly diagnosed cancer types. Studying the molecular changes that occur in lung cancer is important to understand tumor formation and identify new therapeutic targets and early markers of the disease to decrease mortality. Glycosaminoglycan chains play important roles in various signaling events in the tumor microenvironment. Therefore, we have determined the quantity and sulfation characteristics of chondroitin sulfate and heparan sulfate in formalin-fixed paraffin-embedded human lung tissue samples belonging to different lung cancer types as well as tumor adjacent normal areas. Glycosaminoglycan disaccharide analysis was performed using HPLC-MS following on-surface lyase digestion. Significant changes were identified predominantly in the case of chondroitin sulfate; for example, the total amount was higher in tumor tissue compared to the adjacent normal tissue. We also observed differences in the degree of sulfation and relative proportions of individual chondroitin sulfate disaccharides between lung cancer types and adjacent normal tissue. Furthermore, the differences in the 6-O-/4-O-sulfation ratio of chondroitin sulfate were different between the lung cancer types. Our pilot study revealed that further investigation of the role of chondroitin sulfate chains and enzymes involved in their biosynthesis is an important aspect of lung cancer research.
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Affiliation(s)
- Domonkos Pál
- MS Proteomics Research Group, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Doctoral School of Pharmaceutical Sciences, Semmelweis University, H-1085 Budapest, Hungary
| | - Gábor Tóth
- MS Proteomics Research Group, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Simon Sugár
- MS Proteomics Research Group, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Doctoral School of Pharmaceutical Sciences, Semmelweis University, H-1085 Budapest, Hungary
| | - Kata Dorina Fügedi
- MS Proteomics Research Group, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
- Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, H-1111 Budapest, Hungary
| | - Dániel Szabó
- MS Proteomics Research Group, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Ilona Kovalszky
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, H-1085 Budapest, Hungary
| | - Dávid Papp
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Csaba Tóth
- Teaching Hospital Markusovszky, University of Pécs, H-9700 Szombathely, Hungary
| | - Tamás Tornóczky
- Department of Pathology, Faculty of Medicine and Clinical Center, University of Pécs, H-7624 Pécs, Hungary
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Research Centre for Natural Sciences, H-1117 Budapest, Hungary
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Speciation Analysis Highlights the Interactions of Auranofin with the Cytoskeleton Proteins of Lung Cancer Cells. Pharmaceuticals (Basel) 2022; 15:ph15101285. [PMID: 36297397 PMCID: PMC9610265 DOI: 10.3390/ph15101285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 12/01/2022] Open
Abstract
Two types of lung cells (epithelial cancer lung cells, A-549 and lung fibroblasts MRC-5) were exposed to the clinically established gold drug auranofin at concentrations close to the half-maximal inhibitory drug concentrations (IC50). Collected cells were subjected to speciation analysis using inductively coupled plasma mass spectrometry (ICP-MS). Auranofin showed better affinity toward proteins than DNA, RNA, and hydrophilic small molecular weight compounds. It can bind to proteins that vary in size (~20 kDa, ~75 kDa, and ≥200 kDa) and pI. However, the possibility of dimerization and protein–protein complex formation should also be taken into account. µRPLC/CZE-ESI-MS/MS studies on trypsinized proteins allowed the indication of 76 peptides for which signal intensity was influenced by auranofin presence in cells. Based on it, identity was proposed for 20 proteins. Except for thioredoxin reductase (TrxR), which is directly targeted by gold complex, the proteins were found to be transformed. Five indicated proteins: myosin, plectin, talin, two annexins, and kinase M3K5, are responsible for cell–cell, cell–protein interactions, and cell motility. A wound healing test confirmed their regulation by auranofin as cell migration decreased by 40% while the cell cycle was not interrupted.
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Tóth G, Sugár S, Balbisi M, Molnár BA, Bugyi F, Fügedi KD, Drahos L, Turiák L. Optimized Sample Preparation and Microscale Separation Methods for High-Sensitivity Analysis of Hydrophilic Peptides. Molecules 2022; 27:molecules27196645. [PMID: 36235181 PMCID: PMC9573374 DOI: 10.3390/molecules27196645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
The optimization of solid-phase extraction (SPE) purification and chromatographic separation is usually neglected during proteomics studies. However, the effects on detection performance are not negligible, especially when working with highly glycosylated samples. We performed a comparative study of different SPE setups, including an in-house optimized method and reversed-phase chromatographic gradients for the analysis of highly glycosylated plasma fractions as a model sample for glycopeptide analysis. The in-house-developed SPE method outperformed the graphite-based and hydrophilic interaction liquid chromatography (HILIC) purification methods in detection performance, recovery, and repeatability. During optimization of the chromatography, peak distribution was maximized to increase the peptide detection rate. As a result, we present sample purification and chromatographic separation methods optimized for the analysis of hydrophilic samples, the most important of which is heavily N-glycosylated protein mixtures.
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Affiliation(s)
- Gábor Tóth
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
| | - Simon Sugár
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
- Doctoral School of Pharmaceutical Sciences, Semmelweis University, Üllői út 26, H-1085 Budapest, Hungary
| | - Mirjam Balbisi
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
| | - Balázs András Molnár
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellért tér 4, H-1111 Budapest, Hungary
| | - Fanni Bugyi
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117 Budapest, Hungary
| | - Kata Dorina Fügedi
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szt. Gellért tér 4, H-1111 Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
- Correspondence: ; Tel.: +36-13-82-6548
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