Histology-guided Protein Digestion/extraction from Formalin-fixed and Paraffin-embedded Pressure Ulcer Biopsies

Overview

Journal Exp Dermatol

Specialty Dermatology

Date 2015 Oct 7

PMID 26440596

Citations 7

Authors

Domenico Taverna

Alonda C Pollins

Lillian B Nanney

Giovanni Sindona

Richard M Caprioli

Affiliations

Soon will be listed here.

Abstract

Herein we present a simple, reproducible and versatile approach for in situ protein digestion and identification on formalin-fixed and paraffin-embedded (FFPE) tissues. This adaptation is based on the use of an enzyme delivery platform (hydrogel discs) that can be positioned on the surface of a tissue section. By simultaneous deposition of multiple hydrogels over select regions of interest within the same tissue section, multiple peptide extracts can be obtained from discrete histological areas. After enzymatic digestion, the hydrogel extracts are submitted for LC-MS/MS analysis followed by database inquiry for protein identification. Further, imaging mass spectrometry (IMS) is used to reveal the spatial distribution of the identified peptides within a serial tissue section. Optimization was achieved using cutaneous tissue from surgically excised pressure ulcers that were subdivided into two prime regions of interest: the wound bed and the adjacent dermal area. The robust display of tryptic peptides within these spectral analyses of histologically defined tissue regions suggests that LC-MS/MS in combination with IMS can serve as useful exploratory tools.

Citing Articles

A Fast-Tracking Sample Preparation Protocol for Proteomics of Formalin-Fixed Paraffin-Embedded Tumor Tissues.

Darville L, Lockhart J, Reddy S, Fang B, Izumi V, Boyle T Methods Mol Biol. 2024; 2823:193-223.

PMID: 39052222 PMC: 11648944. DOI: 10.1007/978-1-0716-3922-1_13.

Hanging drop sample preparation improves sensitivity of spatial proteomics.

Kwon Y, Piehowski P, Zhao R, Sontag R, Moore R, Burnum-Johnson K Lab Chip. 2022; 22(15):2869-2877.

PMID: 35838077 PMC: 9320080. DOI: 10.1039/d2lc00384h.

Towards Precision Dermatology: Emerging Role of Proteomic Analysis of the Skin.

Fredman G, Skov L, Mann M, Dyring-Andersen B Dermatology. 2021; 238(2):185-194.

PMID: 34062531 PMC: 8984998. DOI: 10.1159/000516764.

Mapping and Identification of Native Proteins of Developing Teeth in Mouse Mandibles.

Colley M, Liang S, Tan C, Trobough K, Bach S, Chun Y Anal Chem. 2020; 92(11):7630-7637.

PMID: 32362116 PMC: 7898936. DOI: 10.1021/acs.analchem.0c00359.

Hierarchical Cluster and Region of Interest Analyses Based on Mass Spectrometry Imaging of Human Brain Tumours.

Hiratsuka T, Arakawa Y, Yajima Y, Kakimoto Y, Shima K, Yamazaki Y Sci Rep. 2020; 10(1):5757.

PMID: 32238824 PMC: 7113320. DOI: 10.1038/s41598-020-62176-8.

References

Seeley E, Caprioli R . Molecular imaging of proteins in tissues by mass spectrometry. Proc Natl Acad Sci U S A. 2008; 105(47):18126-31. PMC: 2587620. DOI: 10.1073/pnas.0801374105. View

Roy S, Sen C . Study of the human chronic wound tissue: addressing logistic barriers and productive use of laser capture microdissection. Methods Mol Biol. 2013; 1037:233-43. PMC: 4380270. DOI: 10.1007/978-1-62703-505-7_12. View

Moussai D, Mitsui H, Pettersen J, Pierson K, Shah K, Suarez-Farinas M . The human cutaneous squamous cell carcinoma microenvironment is characterized by increased lymphatic density and enhanced expression of macrophage-derived VEGF-C. J Invest Dermatol. 2010; 131(1):229-36. DOI: 10.1038/jid.2010.266. View

Luk V, Fiddes L, Luk V, Kumacheva E, Wheeler A . Digital microfluidic hydrogel microreactors for proteomics. Proteomics. 2012; 12(9):1310-8. DOI: 10.1002/pmic.201100608. View

Sen C, Gordillo G, Roy S, Kirsner R, Lambert L, Hunt T . Human skin wounds: a major and snowballing threat to public health and the economy. Wound Repair Regen. 2009; 17(6):763-71. PMC: 2810192. DOI: 10.1111/j.1524-475X.2009.00543.x. View

Harris G, Nicklay J, Caprioli R . Localized in situ hydrogel-mediated protein digestion and extraction technique for on-tissue analysis. Anal Chem. 2013; 85(5):2717-23. PMC: 3595595. DOI: 10.1021/ac3031493. View

Langenkamp E, Kamps J, Mrug M, Verpoorte E, Niyaz Y, Horvatovich P . Innovations in studying in vivo cell behavior and pharmacology in complex tissues--microvascular endothelial cells in the spotlight. Cell Tissue Res. 2013; 354(3):647-69. DOI: 10.1007/s00441-013-1714-7. View

Schwartz S, Caprioli R . Imaging mass spectrometry: viewing the future. Methods Mol Biol. 2010; 656:3-19. DOI: 10.1007/978-1-60761-746-4_1. View

Edsberg L, Wyffels J, Brogan M, Fries K . Analysis of the proteomic profile of chronic pressure ulcers. Wound Repair Regen. 2012; 20(3):378-401. DOI: 10.1111/j.1524-475X.2012.00791.x. View

10.

Taverna D, Boraldi F, De Santis G, Caprioli R, Quaglino D . Histology-directed and imaging mass spectrometry: An emerging technology in ectopic calcification. Bone. 2015; 74:83-94. PMC: 4355241. DOI: 10.1016/j.bone.2015.01.004. View

11.

Krizman D, Burrows J . Use of formalin-fixed, paraffin-embedded tissue for proteomic biomarker discovery. Methods Mol Biol. 2013; 1002:85-92. DOI: 10.1007/978-1-62703-360-2_7. View

12.

Taverna D, Norris J, Caprioli R . Histology-directed microwave assisted enzymatic protein digestion for MALDI MS analysis of mammalian tissue. Anal Chem. 2014; 87(1):670-6. PMC: 4287167. DOI: 10.1021/ac503479a. View

13.

Taverna D, Nanney L, Pollins A, Sindona G, Caprioli R . Spatial mapping by imaging mass spectrometry offers advancements for rapid definition of human skin proteomic signatures. Exp Dermatol. 2011; 20(8):642-7. PMC: 3135742. DOI: 10.1111/j.1600-0625.2011.01289.x. View

14.

Pollins A, Friedman D, Nanney L . Proteomic investigation of human burn wounds by 2D-difference gel electrophoresis and mass spectrometry. J Surg Res. 2007; 142(1):143-52. PMC: 2696121. DOI: 10.1016/j.jss.2007.01.001. View

15.

McDonnell L, Heeren R . Imaging mass spectrometry. Mass Spectrom Rev. 2007; 26(4):606-43. DOI: 10.1002/mas.20124. View

16.

Zhou J, Jones D, Duong D, Levey A, Lah J, Peng J . Proteomic analysis of postsynaptic density in Alzheimer's disease. Clin Chim Acta. 2013; 420:62-8. PMC: 3714371. DOI: 10.1016/j.cca.2013.03.016. View

17.

Yates 3rd J, Eng J, McCormack A, Schieltz D . Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal Chem. 1995; 67(8):1426-36. DOI: 10.1021/ac00104a020. View

18.

Mannello F, Ligi D, Canale M, Raffetto J . Omics profiles in chronic venous ulcer wound fluid: innovative applications for translational medicine. Expert Rev Mol Diagn. 2014; 14(6):737-62. DOI: 10.1586/14737159.2014.927312. View

19.

Mukherjee S, Rodriguez-Canales J, Hanson J, Emmert-Buck M, Tangrea M, Prieto D . Proteomic analysis of frozen tissue samples using laser capture microdissection. Methods Mol Biol. 2013; 1002:71-83. DOI: 10.1007/978-1-62703-360-2_6. View

20.

Gentil B, Delphin C, Mbele G, Deloulme J, Ferro M, Garin J . The giant protein AHNAK is a specific target for the calcium- and zinc-binding S100B protein: potential implications for Ca2+ homeostasis regulation by S100B. J Biol Chem. 2001; 276(26):23253-61. DOI: 10.1074/jbc.M010655200. View