Dataset Information

Intra-tumor heterogeneity revealed by mass spectrometry im-aging is associated with the prognosis of breast cancer

ABSTRACT: Intra-tumor heterogeneity (ITH) results from coexistence of genetically distinct cancer cell (sub)populations, their phenotypic plasticity, and the presence of heterotypic components of the tumor microenvironment (TME). Here we addressed potential association between phenotypic ITH revealed by mass spectrometry imaging (MSI) and the prognosis of breast cancer. Tissue specimens resected from 59 patients treated radically due to the locally advanced HER2-positive invasive ductal carcinoma were included in the study. After on-tissue trypsin digestion of cellu-lar proteins, peptide maps of all cancer regions (about 380,000 spectra in total) were segmented by an unsupervised approach to reveal their intrinsic heterogeneity. A high degree of similarity between spectra was observed, which indicated relative homogeneity of cancer regions. How-ever, when the number and diversity of the detected clusters of spectra were analyzed, differ-ences between patient groups were observed. It is noteworthy that a higher degree of heteroge-neity was found in tumors from patients who remained disease-free during a 5-year follow-up (n=38) compared to tumors from patients with progressive disease (distant metastases detected during follow-up, n=21). Interestingly, such differences were not observed between patients with different status of regional lymph nodes, cancer grade, or expression of estrogen receptor at the time of the primary treatment. Subsequently, spectral components with different abundance in cancer regions were detected in patients with different outcomes, and their hypothetical identity was established by assignment to measured masses of tryptic peptides identified in correspond-ing tissue lysates. Such differentiating components were associated with proteins involved in immune regulation and hemostasis. We postulate that a higher heterogeneity of tumors with a better prognosis could reflect the presence of heterotypic components including the microvas-culature and infiltrating immune cells, that facilitated response to treatment.

INSTRUMENT(S): ultraflex

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Breast Cancer Cell

DISEASE(S): Breast Cancer

SUBMITTER: Monika Pietrowska

LAB HEAD: Piotr Widłak

PROVIDER: PXD027878 | Pride | 2022-02-17

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	BC-ITH-PT_20210811.mgf	Mgf
	MS-MS-combined_spectra_BC.dat	Other

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Publications

Intra-Tumor Heterogeneity Revealed by Mass Spectrometry Imaging Is Associated with the Prognosis of Breast Cancer.

Gawin Marta M Kurczyk Agata A Niemiec Joanna J Stanek-Widera Agata A Grela-Wojewoda Aleksandra A Adamczyk Agnieszka A Biskup-Frużyńska Magdalena M Polańska Joanna J Widłak Piotr P

Cancers 20210827 17

Intra-tumor heterogeneity (ITH) results from the coexistence of genetically distinct cancer cell (sub)populations, their phenotypic plasticity, and the presence of heterotypic components of the tumor microenvironment (TME). Here we addressed the potential association between phenotypic ITH revealed by mass spectrometry imaging (MSI) and the prognosis of breast cancer. Tissue specimens resected from 59 patients treated radically due to the locally advanced HER2-positive invasive ductal carcinoma ...[more]

PMID: 34503159

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Project description:Intra-individual tumoral heterogeneity (ITH) is a hallmark of solid tumors and impedes accurate genomic diagnosis and selection of proper therapy. The purpose of this study was to identify ITH of ovarian serous adenocarcinomas (OSAs) and to determine the utility of ascitic cancer cells as a resource for mutation profiling in spite of ITH. We performed whole-exome sequencing, copy number profiling, and DNA methylation profiling of four OSA genomes using multiregional biopsies from 13 intraovarian lesions, 12 extraovarian tumor lesions (omentum/peritoneum), and ascitic cells. We observed substantial levels of heterogeneity in mutations and copy number alterations (CNAs) of the OSAs. We categorized the mutations into 'common', 'shared' and 'private' according to the regional distribution. Six common, 8 shared, and 24 private mutations were observed in known cancer-related genes,. but common mutations had a higher mutant allele frequency and included TP53 mutations in all four OSAs. Region-specific chromosomal amplifications and deletions involving BRCA1, PIK3CA, and RB1 were also identified. Of note, the mutations detected in ascitic cancer cells represented 92.3-100% of overall somatic mutations in the given case. Phylogenetic analyses of ascitic genomes predicted a polyseeding origin of somatic mutations in ascitic cells. Our results demonstrate that despite ITH, somatic mutations, CNAs, and DNA methylations in both âcommonâ category and cancer-related genes were highly conserved in ascitic cells of OSAs, highlighting the clinical relevance of genome analysis of ascitic cells. Ascitic tumor cells may serve as a potential resource to discover somatic mutations of primary OSA with diagnostic and therapeutic relevance. The purpose of this study was to identify intra-individual tumor heterogenety of ovarian serous adenocarcinomas Four to nine different ovarian cancer areas from intraovarian and extra-ovarian lesions that were at least 1cm apart as well as 50 ml ascites were collected from the four OSA patients. Genomic DNA from tumor and matched normal samples were simultaneously hybridized onto the array. Total 29 array experiments were conducted.

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