OLFM4 Expression in Ductal Carcinoma In Situ and in Invasive Breast Cancer Cohorts by a SWATH‐Based Proteomic Approach

Valo, Isabelle; Raro, Pédro; Boissard, Alice; Maarouf, Amine; Jézéquel, Pascal; Verriele, Véronique; Campone, Mario; Coqueret, Olivier; Guette, Catherine

doi:10.1002/pmic.201800446

Cited by 20 publications

(17 citation statements)

References 42 publications

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“…Subsequently, this list of 130 candidates was crossed with experimental data collected on rat malignant mesotheliomas (MMs) differing by their invasiveness (21), and then with clinical data from cohorts of patients with colon adenocarcinoma (22) or breast cancer (23). As a result of technological improvements that occurred between these two studies, the number of specific biomarkers identified in breast cancer was higher than that in colon cancer.…”

Section: Data Collection Methodsmentioning

confidence: 99%

Biomarkers of tumor invasiveness in proteomics (Review)

et al. 2020

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Over the past two decades, quantitative proteomics has emerged as an important tool for deciphering the complex molecular events involved in cancers. The number of references involving studies on the cancer metastatic process has doubled since 2010, while the last 5 years have seen the development of novel technologies combining deep proteome coverage capabilities with quantitative consistency and accuracy. To highlight key findings within this huge amount of information, the present review identified a list of tumor invasive biomarkers based on both the literature and data collected on a biocollection of experimental cell lines, tumor models of increasing invasiveness and tumor samples from patients with colorectal or breast cancer. Crossing these different data sources led to 76 proteins of interest out of 1,245 mentioned in the literature. Information on these proteins can potentially be translated into clinical prospects, since they represent potential targets for the development and evaluation of innovative therapies, alone or in combination. Herein, a systematical review of the biology of each of these proteins, including their specific subcellular/extracellular or multiple localizations is presented. Finally, as an important advantage of quantitative proteomics is the ability to provide data on all these molecules simultaneously in cell pellets, body fluids or paraffin-embedded sections of tumors/invaded tissues, the significance of some of their interconnections is discussed.

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Section: Data Collection Methodsmentioning

confidence: 99%

Biomarkers of tumor invasiveness in proteomics (Review)

et al. 2020

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“…For treatment with trypsin, desalting, and peptide analysis, ultrapure water (Purelab Option-Q, 18.2 MΩ.cm, VWR International S.A.S., Fontenay-sous-Bois, France) was used during all procedures. See legends to Supplementary Table S1 and reference [68] for additional informations on sample preparation of human tumor samples.…”

Section: Sample Preparation For Swath-ms Analysismentioning

confidence: 99%

S100A4 Is a Biomarker of Tumorigenesis, EMT, Invasion, and Colonization of Host Organs in Experimental Malignant Mesothelioma

Nader

Guillon

Petit

et al. 2020

Cancers

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Recent findings suggest that S100A4, a protein involved in communication between stromal cells and cancer cells, could be more involved than previously expected in cancer invasiveness. To investigate its cumulative value in the multistep process of the pathogenesis of malignant mesothelioma (MM), SWATH-MS (sequential window acquisition of all theoretical fragmentation spectra), an advanced and robust technique of quantitative proteomics, was used to analyze a collection of 26 preneoplastic and neoplastic rat mesothelial cell lines and models of MM with increasing invasiveness. Secondly, proteomic and histological analyses were conducted on formalin-fixed paraffin-embedded sections of liver metastases vs. primary tumor, and spleen from tumor-bearing rats vs. controls in the most invasive MM model. We found that S100A4, along with 12 other biomarkers, differentiated neoplastic from preneoplastic mesothelial cell lines, and invasive vs. non-invasive tumor cells in vitro, and MM tumors in vivo. Additionally, S100A4 was the only protein differentiating preneoplastic mesothelial cell lines with sarcomatoid vs. epithelioid morphology in relation to EMT (epithelial-to-mesenchymal transition). Finally, S100A4 was the most significantly increased biomarker in liver metastases vs. primary tumor, and in the spleen colonized by MM cells. Overall, we showed that S100A4 was the only protein that showed increased abundance in all situations, highlighting its crucial role in all stages of MM pathogenesis.

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“…We then used mass spectrometry analysis to understand how p21 maintains senescence besides its well-known function as a cdk inhibitor. To this end, this protein was inactivated in senescent cells, extracts were collected after 48 hr and analyzed by SWATH-MS approaches as we recently described (20). GSEA analysis indicated that Myc and E2Fs proliferative pathways were reactivated as expected.…”

Section: Mtor Inhibition Prevents Cis Escapementioning

confidence: 98%

tRNA Biogenesis and Specific Aminoacyl-tRNA Synthetases Regulate Senescence Stability Under the Control of mTOR

Guillon

Toutain

Boissard

et al. 2020

Preprint

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Running title: tRNA deregulation during senescence ABSTRACT Senescence normally prevents the propagation of abnormal cells but is also associated with cancer progression and chemotherapy resistance. These contradictory effects are related to the stability of epigenetic marks and to the senescence-associated secretory phenotype (SASP). The SASP reinforces the proliferative arrest but also induces tumor growth and inflammation during aging. S e n e s c e n c e i s t h e r e f o r e m u c h m o r e heterogeneous than initially thought. How this response varies is not really understood.Using experimental models of senescence escape, we now described that the deregulation of tRNA biogenesis affects the stability of this suppression, leading to chemotherapy resistance. Proteomic analyses showed that several aminoacyl-tRNA synthetases were down-regulated in senescent cells. tRNA transcription was also inhibited as a consequence of a reduced DNA binding of the type III RNA polymerase. Reducing RNA Pol III activity by BRF1 depletion maintained senescence and blocked cell persistence. Results showed that the YA R S 1 a n d L A R S 1 a m i n o a c y l -t R N A synthetases were necessary for cell emergence and that their corresponding tRNA-Leu-CAA and tRNA-Tyr-GTA were up-regulated in persistent cells. On the contrary, the CARS1 ligase had no effect on persistence and the expression of the corresponding tRNA-Cys was not modified. Results also showed that these tRNAs were regulated by mTOR and that this abnormal tRNA biogenesis induced an ER stress which was resolved by the kinase during chemotherapy escape.Overall, these findings highlight a new regulation of tRNA biology during senescence and suggest that specific tRNAs and ligases contribute to the strength and heterogeneity of this suppression and to chemotherapy resistance.

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OLFM4 Expression in Ductal Carcinoma In Situ and in Invasive Breast Cancer Cohorts by a SWATH‐Based Proteomic Approach

Cited by 20 publications

References 42 publications

Biomarkers of tumor invasiveness in proteomics (Review)

Biomarkers of tumor invasiveness in proteomics (Review)

S100A4 Is a Biomarker of Tumorigenesis, EMT, Invasion, and Colonization of Host Organs in Experimental Malignant Mesothelioma

tRNA Biogenesis and Specific Aminoacyl-tRNA Synthetases Regulate Senescence Stability Under the Control of mTOR

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