Proteomic analysis of FFPE tissue: barriers to clinical impact

Mason, Jeffrey T.

doi:10.1080/14789450.2016.1221346

Cited by 18 publications

(12 citation statements)

References 19 publications

(23 reference statements)

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“…Data analysis was performed using MaxQuant (v1.5.2.8) [21]. For peptide identification, the Andromeda search engine and the reviewed human database without isoforms downloaded from Uniprot on 25th July, 2016 (20,193 entries) were used.…”

Section: Methodsmentioning

confidence: 99%

“…The availability of formalin fixed paraffin embedded (FFPE) tissues provides a retrospective source of proteomic information, especially in conjunction with clinicopathological annotation and follow-up data [20], [21]. Coupled with label-free shotgun proteomics and immunohistochemistry, these FFPE tissues have been widely used to identify biomarkers and drug targets in different disease settings [22], [23], [24], [25].…”

Section: Introductionmentioning

confidence: 99%

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Proteome Profiling of Primary Pancreatic Ductal Adenocarcinomas Undergoing Additive Chemoradiation Link ALDH1A1 to Early Local Recurrence and Chemoradiation Resistance

Oria

Bronsert

Thomsen

et al. 2018

Translational Oncology

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Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis with frequent post-surgical local recurrence. The combination of adjuvant chemotherapy with radiotherapy is under consideration to achieve a prolonged progression-free survival (PFS). To date, few studies have determined the proteome profiles associated with response to adjuvant chemoradiation. We herein analyzed the proteomes of primary PDAC tumors subjected to additive chemoradiation after surgical resection and achieving short PFS (median 6 months) versus prolonged PFS (median 28 months). Proteomic analysis revealed the overexpression of Aldehyde Dehydrogenase 1 Family Member A1 (ALDH1A1) and Monoamine Oxidase A (MAOA) in the short PFS cohort, which were corroborated by immunohistochemistry. In vitro, specific inhibition of ALDH1A1 by A37 in combination with gemcitabine, radiation, and chemoradiation lowered cell viability and augmented cell death in MiaPaCa-2 and Panc 05.04 cells. ALDH1A1 silencing in both cell lines dampened cell proliferation, cell metabolism, and colony formation. In MiaPaCa-2 cells, ALDH1A1 silencing sensitized cells towards treatment with gemcitabine, radiation or chemoradiation. In Panc 05.04, increased cell death was observed upon gemcitabine treatment only. These findings are in line with previous studies that have suggested a role of ALDH1A1 chemoradiation resistance, e.g., in esophageal cancer. In summary, we present one of the first proteome studies to investigate the responsiveness of PDAC to chemoradiation and provide further evidence for a role of ALDH1A1 in therapy resistance.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Proteome Profiling of Primary Pancreatic Ductal Adenocarcinomas Undergoing Additive Chemoradiation Link ALDH1A1 to Early Local Recurrence and Chemoradiation Resistance

Oria

Bronsert

Thomsen

et al. 2018

Translational Oncology

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“…In addition, laser‐based tissue microdissection has enabled the molecular analysis of specifically defined populations of cells captured directly from their tissue microenvironment. By virtue of such technological developments, retrospective proteomic studies using FFPE tissues have successfully explored the identification of disease‐related proteins to elucidate the molecular mechanisms underlying diseases . We have also demonstrated proteomic profiling of tumor cells laser‐microdissected from FFPE tissues of non‐small cell lung carcinoma (NSCLC) as part of our study on biomarker discovery .…”

Section: Introductionmentioning

confidence: 99%

Differential Proteomic Analysis between Small Cell Lung Carcinoma (SCLC) and Pulmonary Carcinoid Tumors Reveals Molecular Signatures for Malignancy in Lung Cancer

Fujii

Miyata

Takahashi

et al. 2018

Proteomics Clinical Apps

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“…Multiple comparative proteomic reports showed that the retrieved molecular information varied by extraction method, tissue type, and instrument, and made comparison of results between studies difficult (Hood et al, ; Geoui et al, ; Kojima et al, ; Mason, ). Because the lysine side chains are mostly involved in the reaction with formaldehyde, some studies reported the lysine (K) to arginine (R) terminal peptide ratio (K/R), as a way to evaluate and classify chemical variations found in FFPE tissues.…”

Section: Methods To Preserve and Store Tissuesmentioning

confidence: 99%

Proteome analysis of tissues by mass spectrometry

Đapić

Baljeu‐Neuman

Uwugiaren

et al. 2019

Mass Spectrometry Reviews

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Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh‐frozen and formalin‐fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue‐sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom‐up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys‐C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue‐specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.

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Proteomic analysis of FFPE tissue: barriers to clinical impact

Cited by 18 publications

References 19 publications

Proteome Profiling of Primary Pancreatic Ductal Adenocarcinomas Undergoing Additive Chemoradiation Link ALDH1A1 to Early Local Recurrence and Chemoradiation Resistance

Proteome Profiling of Primary Pancreatic Ductal Adenocarcinomas Undergoing Additive Chemoradiation Link ALDH1A1 to Early Local Recurrence and Chemoradiation Resistance

Differential Proteomic Analysis between Small Cell Lung Carcinoma (SCLC) and Pulmonary Carcinoid Tumors Reveals Molecular Signatures for Malignancy in Lung Cancer

Proteome analysis of tissues by mass spectrometry

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