Article
Applications of formalin fixed paraffin-embedded tissue proteomics in the study of cancer
Registro en:
FISCHER, Juliana de Saldanha da Gama et al. Applications of formalin fixed paraffin-embedded tissue proteomics in the study of cancer. Austin Proteomics, v. 1, n. 1, p. 1-7, 2014.
2471-0164
Autor
Fischer, Juliana de Saldanha da Gama
Carvalho, Paulo Costa
Canedo, Nathalie H. S.
Gonçalves, Katia Maria da S.
Aquino, Priscila Ferreira de
Almeida, Barbara
Pannain, Vera L. N.
Carvalho, Maria da Gloria da Costa
Resumen
CNPq, FAPERJ, Fundação do Câncer Among the many challenges in identifying novel tumoral diagnostic, prognostic, and personal therapy biomarkers we highlight the challenge of dealing with a single tumor’s molecular complexity and heterogeneity. Formalin-fixed paraffin-embedded (FFPE) tissue specimens are commonly used by pathologists for diagnosing cancer; this material comprises a valuable resource for molecular studies addressing tumoral molecular profiles. Here we demonstrate the effectiveness of shotgun proteomics in assessing the cellular heterogeneity using FFPE tissues slides under three different scenarios: 1)
Comparing astrocytoma grade I versus glioblastoma, 2) Assessing different morphological areas from the same histological slide of a glioblastoma and comparing the identifications with those from a fresh tissue, 3) Comparing two different histopathological profiles in the same patient’s liver: cirrhosis and cancer.
Briefly, contents of FFPE slides were scraped, washed three times with xylene and then rehydrated in a grade ethanol series [100%, 90%(v/v), 70 % (v/v)]. A total of 100 µL of 0.2% (w/v) RapiGestTM in 50mM ammonium bicarbonate was then added to each sample. Tryptic digests were separated by reversed-phase
capillary liquid chromatography coupled to nano-electrospray high-resolution mass spectrometry for identification. The samples were analyzed in technical replicates by LC-MS/MS on an Orbitrap XL. Our datasets enabled elucidating key tumoral regions allowing a better comprehension of such specific tumor
areas; the identifications and raw data are available at http://max.ioc.fiocruz.br/julif/ffpecases.