Application of two-dimensional difference gel electrophoresis to identify protein changes between center, margin, and adjacent non-tumor tissues obtained from non-small-cell lung cancer with adenocarcinoma or squamous cell carcinoma subtype

Ciereszko, Andrzej; Dietrich, Mariola A.; Słowińska, Mariola; Nynca, Joanna; Ciborowski, Michał; Kaczmarek, Monika M.; Myszczyński, Kamil; Kiśluk, Joanna; Majewska, Anna; Michalska-Falkowska, Anna; Kodzik, Natalia; Reszeć, Joanna; Sierko, Ewa; Nikliński, Jacek

doi:10.1371/journal.pone.0268073

Cited by 8 publications

(4 citation statements)

References 199 publications

(185 reference statements)

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“…Tissue samples were histologically reviewed and classified. After lung tumor resection, the whole specimen was examined macroscopically by a pathologist following previously published methods ( Ciereszko et al, 2022 ) to determine the exact tumor localization, identify macroscopic tumor residuals, search for macroscopic infiltration of pulmonary pleura, and evaluate necrosis in the tumor center. The pathologist cut the tissue samples into tumor center and periphery subsamples.…”

Section: Methodsmentioning

confidence: 99%

Exploration of oxidized phosphocholine profile in non-small-cell lung cancer

Godzien,

Lopez-Lopez,

Sieminska

et al. 2024

Front. Mol. Biosci.

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Introduction: Lung cancer is one of the most frequently studied types of cancer and represents the most common and lethal neoplasm. Our previous research on non-small cell lung cancer (NSCLC) has revealed deep lipid profile reprogramming and redox status disruption in cancer patients. Lung cell membranes are rich in phospholipids that are susceptible to oxidation, leading to the formation of bioactive oxidized phosphatidylcholines (oxPCs). Persistent and elevated levels of oxPCs have been shown to induce chronic inflammation, leading to detrimental effects. However, recent reports suggest that certain oxPCs possess anti-inflammatory, pro-survival, and endothelial barrier-protective properties. Thus, we aimed to measure the levels of oxPCs in NSCLC patients and investigate their potential role in lung cancer.Methods: To explore the oxPCs profiles in lung cancer, we performed in-depth, multi-level metabolomic analyses of nearly 350 plasma and lung tissue samples from 200 patients with NSCLC, including adenocarcinoma (ADC) and squamous cell carcinoma (SCC), the two most prevalent NSCLC subtypes and COPD patients as a control group. First, we performed oxPC profiling of plasma samples. Second, we analyzed tumor and non-cancerous lung tissues collected during the surgical removal of NSCLC tumors. Because of tumor tissue heterogeneity, subsequent analyses covered the surrounding healthy tissue and peripheral and central tumors. To assess whether the observed phenotypic changes in the patients were associated with measured oxPC levels, metabolomics data were augmented with data from medical records.Results: We observed a predominance of long-chain oxPCs in plasma samples and of short-chain oxPCs in tissue samples from patients with NSCLC. The highest concentration of oxPCs was observed in the central tumor region. ADC patients showed higher levels of oxPCs compared to the control group, than patients with SCC.Conclusion: The detrimental effects associated with the accumulation of short-chain oxPCs suggest that these molecules may have greater therapeutic utility than diagnostic value, especially given that elevated oxPC levels are a hallmark of multiple types of cancer.

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Section: Methodsmentioning

confidence: 99%

Exploration of oxidized phosphocholine profile in non-small-cell lung cancer

Godzien,

Lopez-Lopez,

Sieminska

et al. 2024

Front. Mol. Biosci.

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“…The exact time of resection start, vessel ligation, resection end, and tissue sample preservation were recorded and documented. The details of tissue samples collection in the clinical setting–macroscopic evaluation resected specimens were described previously ( Ciereszko et al, 2022 ), together with the biobanking conditions and Standard Operating Procedures ( Niklinski et al, 2017 ; Michalska-Falkowska et al, 2023 ). Cancer stages were determined following pathological tumour-node-metastasis (pTNM) staging.…”

Section: Methodsmentioning

confidence: 99%

First insight about the ability of specific glycerophospholipids to discriminate non-small cell lung cancer subtypes

Sieminska,

Miniewska,

Mroz

et al. 2024

Front. Mol. Biosci.

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Introduction: Discrimination between adenocarcinoma (ADC) and squamous cell carcinoma (SCC) subtypes in non-small cell lung cancer (NSCLC) patients is a significant challenge in oncology. Lipidomics analysis provides a promising approach for this differentiation.Methods: In an accompanying paper, we explored oxPCs levels in a cohort of 200 NSCLC patients. In this research, we utilized liquid chromatography coupled with mass spectrometry (LC-MS) to analyze the lipidomics profile of matching tissue and plasma samples from 25 NSCLC patients, comprising 11 ADC and 14 SCC cases. This study builds upon our previous findings, which highlighted the elevation of oxidised phosphatidylcholines (oxPCs) in NSCLC patients.Results: We identified eight lipid biomarkers that effectively differentiate between ADC and SCC subtypes using an untargeted approach. Notably, we observed a significant increase in plasma LPA 20:4, LPA 18:1, and LPA 18:2 levels in the ADC group compared to the SCC group. Conversely, tumour PC 16:0/18:2, PC 16:0/4:0; CHO, and plasma PC 16:0/18:2; OH, PC 18:0/20:4; OH, PC 16:0/20:4; OOH levels were significantly higher in the ADC group.Discussion: Our study is the first to report that plasma LPA levels can distinguish between ADC and SCC patients in NSCLC, suggesting a potential role for LPAs in NSCLC subtyping. This finding warrants further investigation into the mechanisms underlying these differences and their clinical implications.

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“…We used a Western blot procedure using stain-free gels (V3 stain-free workflow, Bio-Rad, Hercules, CA, USA) to validate the mass spectrometry results, as previously described [ 68 ], with some modifications. This method eliminates the need for the use of housekeeping proteins as loading controls for Western blots [ 69 ].…”

Section: Methodsmentioning

confidence: 99%

Comparative proteomic analysis of the ovarian fluid and eggs of Siberian sturgeon

Kodzik,

Ciereszko,

Szczepkowska

et al. 2024

BMC Genomics

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Background Sturgeon species are living fossils that exhibit unique reproductive characteristics, and elucidation of the molecular processes governing the formation and quality of sturgeon eggs is crucial. However, comprehensive data on the protein composition of sturgeon ovarian fluid (OF) and eggs and their functional significance are lacking. To address this knowledge gap, the aim of the present study was to conduct a comprehensive comparative proteomic analysis of Siberian sturgeon OF and eggs using liquid chromatography–mass spectrometry (LC–MS/MS). Results A total of 617 proteins were identified in OF, and 565 proteins were identified in eggs. A total of 772 proteins showed differential abundance. Among the differentially abundant proteins, 365 were more abundant in OFs, while 407 were more abundant in eggs. We identified 339 proteins unique to OFs and 287 proteins specific to eggs, and further investigated the top 10 most abundant proteins in each. The functional annotation of the OF proteins highlighted their predominant association with immune system processes, including the complement and coagulation cascade, neutrophil and leukocyte-mediated immunity, cholesterol metabolism, and regulation of the actin cytoskeleton. Analysis of egg proteins revealed enrichment in metabolic pathways, such as oxidative phosphorylation and fatty acid metabolism, and protein ubiquitination and translation. OF-specific proteins included extracellular matrix and secretory vesicles, and eggs were enriched in proteins localized to mitochondria and ribosome components. Conclusions This study presents the first comprehensive characterization of the protein composition of sturgeon OF and eggs and elucidates their distinct functional roles. These findings advance our understanding of sturgeon reproduction, OF-egg signaling and the origin of OF proteins. The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium with the dataset identifier PXD044168 to ensure accessibility for further research.

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Application of two-dimensional difference gel electrophoresis to identify protein changes between center, margin, and adjacent non-tumor tissues obtained from non-small-cell lung cancer with adenocarcinoma or squamous cell carcinoma subtype

Cited by 8 publications

References 199 publications

Exploration of oxidized phosphocholine profile in non-small-cell lung cancer

Exploration of oxidized phosphocholine profile in non-small-cell lung cancer

First insight about the ability of specific glycerophospholipids to discriminate non-small cell lung cancer subtypes

Comparative proteomic analysis of the ovarian fluid and eggs of Siberian sturgeon

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