title: MicroRNA paraffin-based studies in osteosarcoma reveal reproducible independent prognostic profiles at 14q32.
abstract: BACKGROUND
  Although microRNAs (miRNAs) are implicated in osteosarcoma biology and chemoresponse, miRNA prognostic models are still needed, particularly because prognosis is imperfectly correlated with chemoresponse. Formalin-fixed, paraffin-embedded tissue is a necessary resource for biomarker studies in this malignancy with limited frozen tissue availability.
  
  
  METHODS
  We performed miRNA and mRNA microarray formalin-fixed, paraffin-embedded assays in 65 osteosarcoma biopsy and 26 paired post-chemotherapy resection specimens and used the only publicly available miRNA dataset, generated independently by another group, to externally validate our strongest findings (n = 29). We used supervised principal components analysis and logistic regression for survival and chemoresponse, and miRNA activity and target gene set analysis to study miRNA regulatory activity.
  
  
  RESULTS
  Several miRNA-based models with as few as five miRNAs were prognostic independently of pathologically assessed chemoresponse (median recurrence-free survival: 59 months versus not-yet-reached; adjusted hazards ratio = 2.90; P = 0.036). The independent dataset supported the reproducibility of recurrence and survival findings. The prognostic value of the profile was independent of confounding by known prognostic variables, including chemoresponse, tumor location and metastasis at diagnosis. Model performance improved when chemoresponse was added as a covariate (median recurrence-free survival: 59 months versus not-yet-reached; hazard ratio = 3.91; P = 0.002). Most prognostic miRNAs were located at 14q32 - a locus already linked to osteosarcoma - and their gene targets display deregulation patterns associated with outcome. We also identified miRNA profiles predictive of chemoresponse (75% to 80% accuracy), which did not overlap with prognostic profiles.
  
  
  CONCLUSIONS
  Formalin-fixed, paraffin-embedded tissue-derived miRNA patterns are a powerful prognostic tool for risk-stratified osteosarcoma management strategies. Combined miRNA and mRNA analysis supports a possible role of the 14q32 locus in osteosarcoma progression and outcome. Our study creates a paradigm for formalin-fixed, paraffin-embedded-based miRNA biomarker studies in cancer.
authors: Division of Hematology/Oncology, Sarcoma Program, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA.
authors: Andrew D
authors: AD
authors: Kelly
authors: Center for Cancer Computational Biology, Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA ; Bioinformatics and Computational Genomics, Institut de Recherches Cliniques de Montréal, 110 Avenue Des Pins O, Montreal, Quebec H2W 1R7, Canada.
authors: Benjamin
authors: B
authors: Haibe-Kains
authors: Division of Hematology/Oncology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02215, USA.
authors: Katherine A
authors: KA
authors: Janeway
authors: Division of Hematology/Oncology, Sarcoma Program, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA.
authors: Katherine E
authors: KE
authors: Hill
authors: Center for Cancer Computational Biology, Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA.
authors: Eleanor
authors: E
authors: Howe
authors: Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA.
authors: Jeffrey
authors: J
authors: Goldsmith
authors: Department of Pathology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02215, USA.
authors: Kyle
authors: K
authors: Kurek
authors: Department of Pathology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02215, USA.
authors: Antonio R
authors: AR
authors: Perez-Atayde
authors: Division of Hematology/Oncology, Sarcoma Program, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA.
authors: Nancy
authors: N
authors: Francoeur
authors: Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
authors: Jian-Bing
authors: JB
authors: Fan
authors: Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA.
authors: Craig
authors: C
authors: April
authors: Molecular Genetics Core Facility, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02215, USA.
authors: Hal
authors: H
authors: Schneider
authors: Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA.
authors: Mark C
authors: MC
authors: Gebhardt
authors: Center for Cancer Computational Biology, Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA.
authors: Aedin
authors: A
authors: Culhane
authors: Center for Cancer Computational Biology, Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA.
authors: John
authors: J
authors: Quackenbush
authors: Division of Hematology/Oncology, Sarcoma Program, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA.
authors: Dimitrios
authors: D
authors: Spentzos