A methodological study of genome-wide DNA methylation analyses using matched archival formalin-fixed paraffin embedded and fresh frozen breast tumors

Espinal, Allyson C.; Wang, Dan; Yan, Li; Liu, Song; Tang, Li; Hu, Qiang; Morrison, Carl; Ambrosone, Christine B.; Higgins, Michael J.; Sucheston‐Campbell, Lara E.

doi:10.18632/oncotarget.14739

Cited by 10 publications

(6 citation statements)

References 23 publications

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“…This was not only true for the 6 HGSC tumors but also for the benign and borderline tumors included in our study, indicating that this could be the general case for ovarian tumors despite disease severity. Similar correlations between fresh frozen tissue and FFPE tissue have been recently reported for brain tumors and breast tumors [ 28 , 29 ]. Noteworthy, one report has shown that the EPIC platform performs well in fresh frozen and FFPE tissue.…”

Section: Discussionsupporting

confidence: 81%

DNA Methylation in Ovarian Tumors—a Comparison Between Fresh Tissue and FFPE Samples

et al. 2021

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Among women, ovarian cancer (OC) is one of the most severe forms of malignancy, accounting for a low 5-year survival rate, of approximately 52%. Early symptoms are unspecific and hence hard to detect. The origin of OC and its subtypes are still unclear, underlying the need for efficient diagnostic biomarkers. In that regard, epigenetics studies are emerging in cancer diagnostics, with encouraging outcomes. Among them, DNA methylation profiling has shown that the origins of the cancer epigenome are associated with molecular factors that are crucial to carcinogenesis, such as regulation of oncogenes and tumor suppressors. Furthermore, those events have been detected in abnormal cell morphology before neoplastic formation, indicating its potential crucial use in the OC diagnostics in the future. Nonetheless, studies are limited, and whether methylation analysis can be performed optimally in formalin-fixed paraffin-embedded (FFPE) preparations of OC cases is still elusive. In the present report, we investigated the performance of DNA methylation analysis in FFPE samples, compared to their matched fresh frozen tissue in a small cohort of OC samples. We found that the overall DNA methylation profile in FFPE tissue showed high concordance to that found in fresh frozen tissue, and accounting for the small cohort size, the differentially methylated sites found primarily in frozen tissue, compared to benign samples, were also reproducible in FFPE. Overall, by using samples from our current clinical setting of tissue preservation, these preliminary observations might provide insights into the clinical use of FFPE tissues in methylation studies without critically compromising the outcome.

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Section: Discussionsupporting

confidence: 81%

DNA Methylation in Ovarian Tumors—a Comparison Between Fresh Tissue and FFPE Samples

et al. 2021

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“…Formalin-fixed paraffin embedded (FFPE) samples (punches, curls, or sections) [12] were deparaffinized, lysed, incubated until completely digested, and heated to inactivate the Proteinase K. Following bisulfite treatment, FFPE lysates were restored using the Infinium HD DNA Restoration Kit (Illumina). DNA was purified using the DNA Clean & Concentrator-5 kit (Zymo Research) for quantification by Quant-iT Picogreen (Invitrogen) and block randomized across plates with respect to self-reported race, sample type (slide, punch, or curl), patient age, and ER status using the OSAT program [13].…”

Section: Methodsmentioning

confidence: 99%

FOXA1 hypermethylation: link between parity and ER-negative breast cancer in African American women?

Espinal

Buas

Wang

et al. 2017

Breast Cancer Res Treat

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Background Reproductive factors, particularly parity, have differential effects on breast cancer risk according to estrogen receptor (ER) status, especially among African American (AA) women. One mechanism could be through DNA methylation, leading to altered expression levels of genes important in cell fate decisions. Methods Using the Illumina 450K BeadChip, we compared DNA methylation levels in paraffin-archived tumor samples from 383 AA and 350 European American (EA) women in the Women’s Circle of Health Study (WCHS). We combined 450K profiles with RNA-seq data and prioritized genes based on differential methylation by race, correlation between methylation and gene expression, and biological function. We measured tumor protein expression and assessed its relationship to DNA methylation. We evaluated associations between reproductive characteristics and DNA methylation using linear regression. Results 410 loci were differentially methylated by race, with the majority unique to ER− tumors. FOXA1 was hypermethylated in tumors from AA versus EA women with ER− cancer, and increased DNA methylation correlated with reduced RNA and protein expression. Importantly, parity was positively associated with FOXA1 methylation among AA women with ER− tumors (P = 0.022), as was number of births (P = 0.026), particularly among those who did not breastfeed (P = 0.008). These same relationships were not observed among EA women, although statistical power was more limited. Conclusions Methylation and expression of FOXA1 is likely impacted by parity and breastfeeding. Because FOXA1 regulates a luminal gene expression signature in progenitor cells and represses the basal phenotype, this could be a mechanism that links these reproductive exposures with ER− breast cancer.

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“…or differing preparation protocols (e.g. addition of the DNA restoration step for FFPE, ( 46–48 )). Enriched labels also varied by storage condition among low-signal samples (binomial test, BH-adjusted P < 1e-3), where ‘colorectal,’ ‘intestine,’ and ‘mucosa’ were enriched among FFPE, while ‘nasal,’ ‘pancreas,’ and ‘epithelial’ were enriched among FF samples.…”

Section: Resultsmentioning

confidence: 99%

Human methylome variation across Infinium 450K data on the Gene Expression Omnibus

Maden

Thompson

Hansen

et al. 2021

NAR Genomics and Bioinformatics

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While DNA methylation (DNAm) is the most-studied epigenetic mark, few recent studies probe the breadth of publicly available DNAm array samples. We collectively analyzed 35 360 Illumina Infinium HumanMethylation450K DNAm array samples published on the Gene Expression Omnibus. We learned a controlled vocabulary of sample labels by applying regular expressions to metadata and used existing models to predict various sample properties including epigenetic age. We found approximately two-thirds of samples were from blood, one-quarter were from brain and one-third were from cancer patients. About 19% of samples failed at least one of Illumina’s 17 prescribed quality assessments; signal distributions across samples suggest modifying manufacturer-recommended thresholds for failure would make these assessments more informative. We further analyzed DNAm variances in seven tissues (adipose, nasal, blood, brain, buccal, sperm and liver) and characterized specific probes distinguishing them. Finally, we compiled DNAm array data and metadata, including our learned and predicted sample labels, into database files accessible via the recountmethylation R/Bioconductor companion package. Its vignettes walk the user through some analyses contained in this paper.

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A methodological study of genome-wide DNA methylation analyses using matched archival formalin-fixed paraffin embedded and fresh frozen breast tumors

Cited by 10 publications

References 23 publications

DNA Methylation in Ovarian Tumors—a Comparison Between Fresh Tissue and FFPE Samples

DNA Methylation in Ovarian Tumors—a Comparison Between Fresh Tissue and FFPE Samples

FOXA1 hypermethylation: link between parity and ER-negative breast cancer in African American women?

Human methylome variation across Infinium 450K data on the Gene Expression Omnibus

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