Orthogonal proteomic platforms and their implications for the stable classification of high-grade serous ovarian cancer subtypes

SummaryThe National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) has established a two-dimensional liquid chromatography-tandem mass spectrometry (2DLC-MS/MS) workflow using isobaric tagging to compare protein abundance across samples. The workflow has been used for large-scale clinical proteomic studies with deep proteomic coverage within and outside of CPTAC. SWATH-MS, an instance of data-independent acquisition (DIA) proteomic methods, was recently developed as an alternate proteomic approach. In this study, we analyzed remaining aliquots of peptides using SWATH-MS from the original retrospective TCGA samples generated for the CPTAC ovarian cancer proteogenomic study (Zhang et al., 2016). The SWATH-MS results indicated that both methods confidently identified differentially expressed proteins in enriched pathways associated with the robust Mesenchymal subtype of high-grade serous ovarian cancer (HGSOC) and the homologous recombination deficient tumors also present in the original study. The results demonstrated that SWATH/DIA-MS presents a promising complementary or orthogonal alternative to the CPTAC harmonized proteomic method, with the advantages of simpler, faster, and cheaper workflows, as well as lower sample consumption. However, the SWATH/DIA-MS workflow resulted in shallower proteome coverage. Overall, we concluded that both analytical methods are suitable to characterize clinical samples such as in the high-grade serous ovarian cancer study, providing proteomic workflow alternatives for cancer researchers depending on the specific goals and context of the studies.

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Oncogenic Role of miR-200c-3p in High-Grade Serous Ovarian Cancer Progression via Targeting the 3′-Untranslated Region of DLC1

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18115741 ◽

2021 ◽

Vol 18 (11) ◽

pp. 5741

Author(s):

Sheril June Ankasha ◽

Mohamad Nasir Shafiee ◽

Norhazlina Abdul Wahab ◽

Raja Affendi Raja Ali ◽

Norfilza Mohd Mokhtar

Keyword(s):

Ovarian Cancer ◽

Cancer Progression ◽

Untranslated Region ◽

Luciferase Reporter ◽

Clinical Samples ◽

Binding Motif ◽

Skov3 Cell ◽

High Grade ◽

Serous Ovarian Cancer ◽

Dlc1 Expression

High-grade serous ovarian cancer (HGSC) is the most common ovarian cancer with highly metastatic properties. A small non-coding RNA, microRNA (miRNA) was discovered to be a major regulator in many types of cancers through binding at the 3′-untranslated region (3′UTR), leading to degradation of the mRNA. In this study, we sought to investigate the underlying mechanisms involved in the dysregulation of miR-200c-3p in HGSC progression and metastasis. We identified the upregulation of miR-200c-3p expression in different stages of HGSC clinical samples and the downregulation of the tumor suppressor gene, Deleted in Liver Cancer 1 (DLC1), expression. Over expression of miR-200c-3p in HGSC cell lines downregulated DLC1 but upregulated the epithelial marker, E-cadherin (CDH1). Based on in silico analysis, two putative binding sites were found within the 3′UTR of DLC1, and we confirmed the direct binding of miR-200c-3p to the target binding motif at position 1488–1495 bp of 3′UTR of DLC1 by luciferase reporter assay in a SKOV3 cell line co-transfected with vectors and miR-200c-3p mimic. These data showed that miR-200c-3p regulated the progression of HGSC by regulating DLC1 expression post-transcription and can be considered as a promising target for therapeutic purposes.

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