RNA-Seq-based toxicogenomic assessment of fresh frozen and formalin-fixed tissues yields similar mechanistic insights.
Formalin-fixed, paraffin-embedded (FFPE) pathology specimens represent a potentially vast resource for transcriptomic-based biomarker discovery. We present here a comparison of results from a whole transcriptome RNA-Seq analysis of RNA extracted from fresh frozen and FFPE livers. The samples were derived from rats exposed to aflatoxin B1 (AFB1 ) and a corresponding set of control animals. Principal components analysis indicated that samples were separated in the two groups representing presence or absence of chemical exposure, both in fresh frozen and FFPE sample types. Sixty-five percent of the differentially expressed transcripts (AFB1 vs. controls) in fresh frozen samples were also differentially expressed in FFPE samples (overlap significance: P < 0.0001). Genomic signature and gene set analysis of AFB1 differentially expressed transcript lists indicated highly similar results between fresh frozen and FFPE at the level of chemogenomic signatures (i.e., single chemical/dose/duration elicited transcriptomic signatures), mechanistic and pathology signatures, biological processes, canonical pathways and transcription factor networks. Overall, our results suggest that similar hypotheses about the biological mechanism of toxicity would be formulated from fresh frozen and FFPE samples. These results indicate that phenotypically anchored archival specimens represent a potentially informative resource for signature-based biomarker discovery and mechanistic characterization of toxicity.
Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.
Scott S
SS
Auerbach
SRA International, Durham, NC, USA.
Dhiral P
DP
Phadke
SRA International, Durham, NC, USA.
Deepak
D
Mav
Library & Information Services Branch, Office of the Deputy Director, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.
Stephanie
S
Holmgren
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.
Yuan
Y
Gao
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.
Bin
B
Xie
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.
Joo Heon
JH
Shin
SRA International, Durham, NC, USA.
Ruchir R
RR
Shah
Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.
B Alex
BA
Merrick
Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.
Raymond R
RR
Tice
D016604:Aflatoxin B1 / Q000633:toxicity; D000818:Animals; D054316:Biomarkers, Pharmacological / Q000032:analysis; D005557:Formaldehyde; D005615:Freezing; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000187:drug effects; D008099:Liver / Q000187:drug effects* / Q000473:pathology; D008297:Male; D051381:Rats; D011916:Rats, Inbred F344; D017423:Sequence Analysis, RNA / Q000379:methods*; D043922:Toxicogenetics / Q000379:methods*
D054316:Biomarkers, Pharmacological; D005557:Formaldehyde; D016604:Aflatoxin B1
Aflatoxin B1; FFPE; Mechanism; RNA-Seq; Toxicogenomics