Dataset Information

Overcoming intra-tumoral heterogeneity for biomarker discovery in the High-Grade Serous Ovarian Cancer proteome

ABSTRACT: High-grade serous ovarian cancer (HGSC) has a disproportionate impact on cancer-related mortality in women. There is an urgent need to improve treatment options for HGSC. This includes better selection of patients who will benefit from existing treatments, including HRD targeted therapy, and discovery of new targeted therapeutic options. Reliable tissue-based biomarkers that can guide treatment selection are key to progress in this area. A challenge for their definition is the large volume of disease that is characteristically present at HGSC diagnosis and that can show considerable heterogeneity within and between anatomical sites. In order to address this issue, we carried out a detailed study of the HGSC proteome in eleven individuals by comparing genomic and gene-expression features with multiple independent proteomic results derived from fresh frozen (FF) and formalin fixed paraffin embedded (FFPE) samples from both ovary and a common metastatic site, omentum. Our findings gave emphasis to the influence of sample site of origin on biomarker expression, and revealed opportunities to detect mechanisms shaping the HGSC tumour immune microenvironment from tissue proteomics. The dataset also forms a useful resource to investigate molecular heterogeneity in HGSC.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Ovarian Serous Carcinoma Cell, Ovarian Epithelial Cell

DISEASE(S): Ovarian Serous Carcinoma

SUBMITTER: Srinivas Srikanth Manda

LAB HEAD: Rosemary Balleine

PROVIDER: PXD042150 | Pride | 2025-06-13

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	171016_E0006_P02_106_S_M04_1.wiff	Wiff
	171016_E0006_P02_106_S_M04_1.wiff.scan	Wiff
	171016_E0006_P02_157_S_M04_1.wiff	Wiff
	171016_E0006_P02_157_S_M04_1.wiff.scan	Wiff
	171016_E0006_P02_158_S_M04_1.wiff	Wiff

Items per page:

1 - 5 of 2714

Publications

Overcoming intra-tumoral heterogeneity for biomarker discovery in the high-grade serous ovarian cancer proteome.

Manda Srikanth S SS Espersen Maiken M MM Mapagu Cristina C Bouantoun Natalie N Boros Jessica J Chiew Yoke-Eng YE Srirangan Sivatharsny S Pattnaik Swetansu S Kennedy Catherine J CJ Brand Alison H AH Garsed Dale W DW Pandey Ahwan A Bowtell David D L DDL Lucas Natasha N Xavier Dylan D Mahboob Sadia S Bucio-Noble Daniel D Tully Brett B Hains Peter G PG Robinson Phillip J PJ Zhong Qing Q Reddel Roger R DeFazio Anna A Balleine Rosemary L RL

NPJ precision oncology 20250611 1

Improved biomarkers of treatment response are needed for patients with high-grade serous ovarian cancer (HGSC). A challenge is substantial anatomical site-to-site variation in expression. We completed data-independent acquisition-mass spectrometry (DIA-MS) analysis of 404 fresh frozen and 78 formalin-fixed, paraffin-embedded HGSC tissue samples from the ovary (adnexal) and a common secondary site (omentum) in 11 patients. This was compared with mutation testing, gene expression, and whole-genome ...[more]

PMID: 40500315

Similar Datasets

Project description:Clinical proteomics on solid tissue samples from human tumour biopsies present multiple challenges. These include limited sample availability, reducing endogenous protease activity and challenges with efficiently solubilising and digesting proteins for high throughput mass spectrometry while achieving comprehensive proteome coverage. Protocols for cancer biopsy proteomics involves three sample preparation steps: tissue washing, lysis and digestion, followed by peptide clean-up by SPE. Our team have reported improvements in all three steps that greatly reduce processing time, enabling greater automation and higher sample throughput. Our aim was to develop a universal protocol for tissue sample preparation that is quick and simple while improving protein solubilization, proteome coverage and reproducibility. Sample preparation with small (<2 mg) biopsies pose additional limitations including the risk of sample loss and introducing variability with multiple reagent additions steps. We now report a one-pot method called heat and beat (HnB). By identifying the limitations and challenges of the existing protocols, we were able to develop a new protocol with fewer steps by achieving lysis, reduction, alkylation and digestion in essentially a single step which was preceded by a 7 min sample heat treatment step. This was achieved by several changes to the existing protocol including the combined use of a beadbeater for tissue homogenisation followed by pressure cycling technology (PCT) using a Barocycler to further lyse and digest the sample. The procedure requires 38 minutes and was tested on 6 tissue types, across three tissue embedding techniques, fresh frozen, OCT embedded (FF-OCT), and FFPE. Our results show that HnB is an efficient new one-pot procedure. The protocol significantly reduced endogenous protease activity, improves peptide yield by up to 3-fold and delivers digestion efficiency of 85-90% from each sample source. We obtained an increase in the number of proteins identified of up to two-fold while reducing variability and processing time.

Project description:This study was performed to evaluated RNA extraction and gene expression analysis of FFPE specimen stored for more than 20 years. Using long time stored FFPE material; large retrospective studies correlating molecular features with therapeutic response and clinical outcome, can be performed. Quantitative PCR (qPCR) was used to evaluate RNA extraction methods and to compare gene expression profiles of FFPE and fresh frozen (FF) tissue. Extracted RNA was subsequently subjected to microarray analysis and compared to qPCR data. The Ambion RecoverAll kit appears to be particularly suited for RNA extraction of long time stored FFPE tissues. Gene expression analysis using Affymetrix platform displayed a high degree of correlation for endogenous control genes comparing FF and FFPE tissues. We conclude that high quality gene expression signatures can be recognized using Affymetrix gene expression platform on FFPE tissue stored for more than 20 years. However, a general interpretation must be done with caution as different FFPE procedures have varying effects on RNA quality. Three RNA extraction methods from Roche (Basel, Switzerland), Ambion (Austin, TX, USA) and Qiagen (Hilden, Germany), designed for FFPE material was used. The methods were compared using qPCR. For the qPCR analysis, two different concentrations of input cDNA were used (20ng and 100ng) and 32 human endogenous control genes were examined. RNA from the Ambion FFPE kit was further analyzed by using microarray. Amplification of RNA prior to microarray analysis was performed using Nugen technologies (San Carlos, CA, USA). Nugen has developed amplification kits both for FFPE and FF materials: WT- ovation FFPE RNA amplification System V2 (Nugen FFPE), Ovation FF RNA Amplification System V2 (Nugen V2 FF) and Ovation FF Pico RNA Amplification System (Nugen PICO FF). The Nugen FFPE kit, designed for FFPE material was only used for FFPE tissue. The Nugen Pico FF kit, designed to target small amounts of FF RNA (>500 pg) and the Nugen V2 FF kit designed to target total FF RNA, were only used for FF tissue. Affymetrix standard amplification protocol (Affy FF) designed for FF RNA was also included as the standard method for amplification.