title: Diagnostic and prognostic value of SHOX2 and SEPT9 DNA methylation and cytology in benign, paramalignant and malignant pleural effusions.
abstract: Pleural effusions (PE) are a common clinical problem. The discrimination between benign (BPE), malignant (MPE) and paramalignant (PPE) pleural effusions is highly important to ensure appropriate patient treatment. Today, cytology is the gold standard for diagnosing malignant pleural effusions. However, its sensitivity is limited due to the sometimes low abundance of tumor cells and the challenging assessment of cell morphology in cytological samples. This study aimed to develop and validate a diagnostic test, which allows for the highly specific detection of malignant cells in pleural effusions based on the DNA methylation biomarkers SHOX2 and SEPT9. A quantitative real-time PCR assay was developed which enabled the accurate and sensitive detection of SHOX2 and SEPT9 in PEs. Cytological and DNA methylation analyses were conducted in a case control study comprised of PEs from 114 patients (58 cases, 56 controls). Cytological analysis as well as SHOX2 and SEPT9 methylation resulted in 100% specificity. 21% of the cases were cytologically positive and 26% were SHOX2 or SEPT9 methylation positive. The combined analysis of cytology and DNA methylation resulted in an increase of 71% positively classified PEs from cancer patients as compared to cytological analysis alone. The absolute sensitivity of cytology and DNA methylation was not determinable due to the lack of an appropriate gold standard diagnostic for distinguishing between MPEs and PPEs. Therefore, it was unclear which PEs from cancer patients were malignant (containing tumor cells) and which PEs were paramalignant and resulted from benign conditions in cancer patients, respectively. Furthermore, DNA methylation analysis in PEs allowed the prognosis of the overall survival in cancer patients (Kaplan-Meier analysis, log rank test, p=0.02 (SHOX2), p=0.02 (SEPT9)). The developed test may be used as a diagnostic and prognostic adjunct to existing clinical and cytopathological investigations in patients with PEs of unclear etiology.
authors.affiliation: University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany.
authors.forename: Dimo
authors.initials: D
authors.lastname: Dietrich
authors.affiliation: University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany.
authors.forename: Maria
authors.initials: M
authors.lastname: Jung
authors.affiliation: University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany.
authors.forename: Svenja
authors.initials: S
authors.lastname: Puetzer
authors.affiliation: University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany.
authors.forename: Annette
authors.initials: A
authors.lastname: Leisse
authors.affiliation: University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany.
authors.forename: Emily Eva
authors.initials: EE
authors.lastname: Holmes
authors.affiliation: University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Meller
authors.affiliation: University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany.
authors.forename: Barbara
authors.initials: B
authors.lastname: Uhl
authors.affiliation: Metanomics Health GmbH, Berlin, Germany.
authors.forename: Philipp
authors.initials: P
authors.lastname: Schatz
authors.affiliation: Roche Pharma AG, Hematology/Oncology, Grenzach-Wyhlen, Germany.
authors.forename: Claudia
authors.initials: C
authors.lastname: Ivascu
authors.affiliation: University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany.
authors.forename: Glen
authors.initials: G
authors.lastname: Kristiansen
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000235:genetics; D019175:DNA Methylation; D005260:Female; D018398:Homeodomain Proteins / Q000235:genetics*; D006801:Humans; D053208:Kaplan-Meier Estimate; D008297:Male; D008875:Middle Aged; D016066:Pleural Effusion, Malignant / Q000175:diagnosis* / Q000235:genetics / Q000473:pathology*; D011379:Prognosis; D015203:Reproducibility of Results; D058112:Septins / Q000235:genetics*; D055815:Young Adult
chemical_list: D014408:Biomarkers, Tumor; D018398:Homeodomain Proteins; C484664:SHOX2 protein, human; C474315:SEPTIN9 protein, human; D058112:Septins