Spatial proteome profiling by immunohistochemistry-based laser capture microdissection and data-independent acquisition proteomics

Huang，Peiwu1,2; Kong，Qian1,2; Gao，Weina1; Chu，Bizhu1; Li，Hua2,3; Mao，Yiheng1; Cai，Zongwei2; Xu，Ruilian4; Tian，Ruijun1,5

2020-08-29

10.1016/j.aca.2020.06.049

ANALYTICA CHIMICA ACTA   影响因子和分区

0003-2670

1873-4324

Understanding the tumor heterogeneity through spatially resolved proteome profiling is important for biomedical research and clinical application. Laser capture microdissection (LCM) is a powerful technology for exploring local cell populations without losing spatial information. Conventionally, tissue sections are stained with hematoxylin and eosin (H&E) for cell-type identification before LCM. However, it generally requires experienced pathologists to distinguish different cell types, which limits the application of LCM to broad cancer research field. Here, we designed an immunohistochemistry (IHC)-based workflow for cell type-resolved proteome analysis of tissue samples. Firstly, targeted cell type was marked by IHC using antibody targeting cell-type specific marker to improve accuracy and efficiency of LCM. Secondly, to increase protein recovery from chemically crosslinked IHC tissues, we optimized a decrosslinking procedure to seamlessly combine with the integrated spintip-based sample preparation technology SISPROT. This newly developed approach, termed IHC-SISPROT, has comparable performance as H&E staining-based proteomic analysis. High sensitivity and reproducibility of IHC-SISPROT were achieved by combining with data independent acquisition proteomics. More than 3500 proteins were identified from only 0.2 mm and 12 μm thickness of hepatocellular carcinoma (HCC) tissue section. Furthermore, using 5 mm and 12 μm thickness of HCC tissue section, 6660 and 6052 protein groups were quantified from cancer cells and cancer-associated fibroblasts (CAFs) by the IHC-SISPROT workflow. Bioinformatic analysis revealed the enrichment of cell type-specific ligands and receptors and potentially new communications between cancer cells and CAFs by these signaling proteins. Therefore, IHC-SISPROT is a sensitive and accurate proteomic approach for spatial profiling of cell type-specific proteome from tissues.

Data-independent acquisition Immunohistochemistry Integrated sample preparation Laser capture microdissection Proteomics

SCI ; EI

英语

第一 ; 通讯

National Natural Science Foundation of China[91953118] ; China State Key Basic Research Program Grants[2016YFA0501403][2016YFA0501404] ; Guangdong Provincial Fund for Distinguished Young Scholars[2019B151502050] ; Guangdong Provincial Natural Science Grant[2016A030312016] ; Shenzhen Innovation of Science and Technology Commission[JCYJ20170412154126026]

Chemistry

Chemistry, Analytical

WOS:000561632900001

ELSEVIER

20202908938518

Cancer cells ; Cell culture ; Cell signaling ; Molecular biology ; Tissue ; Cell proliferation ; Histology ; Clinical research ; Diseases

Biomedical Engineering:461.1 ; Biological Materials and Tissue Engineering:461.2 ; Medicine and Pharmacology:461.6 ; Biology:461.9 ; Organic Compounds:804.1

CHEMISTRY

2-s2.0-85087761130

Scopus

1.Department of Chemistry,Southern University of Science and Technology,Shenzhen,518055,China
2.State Key Laboratory of Environmental and Biological Analysis,Department of Chemistry,Hong Kong Baptist University,China
3.SUSTech Core Research Facilities,Southern University of Science and Technology,Shenzhen,518055,China
4.Shenzhen People's Hospital,The First Affiliated Hospital of Southern University of Science and Technology,Shenzhen,518020,China
5.Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research,Shenzhen,518055,China

Huang，Peiwu,Kong，Qian,Gao，Weina,et al. Spatial proteome profiling by immunohistochemistry-based laser capture microdissection and data-independent acquisition proteomics[J]. ANALYTICA CHIMICA ACTA,2020,1127:140-148.

Huang，Peiwu.,Kong，Qian.,Gao，Weina.,Chu，Bizhu.,Li，Hua.,...&Tian，Ruijun.(2020).Spatial proteome profiling by immunohistochemistry-based laser capture microdissection and data-independent acquisition proteomics.ANALYTICA CHIMICA ACTA,1127,140-148.

Huang，Peiwu,et al."Spatial proteome profiling by immunohistochemistry-based laser capture microdissection and data-independent acquisition proteomics".ANALYTICA CHIMICA ACTA 1127(2020):140-148.