PMID- 36228107
OWN - NLM
STAT- MEDLINE
DCOM- 20230412
LR  - 20240305
IS  - 1615-9861 (Electronic)
IS  - 1615-9853 (Print)
IS  - 1615-9853 (Linking)
VI  - 23
IP  - 7-8
DP  - 2023 Apr
TI  - Data-independent acquisition and quantification of extracellular matrix from 
      human lung in chronic inflammation-associated carcinomas.
PG  - e2200021
LID - 10.1002/pmic.202200021 [doi]
LID - 2200021
AB  - Early events associated with chronic inflammation and cancer involve significant 
      remodeling of the extracellular matrix (ECM), which greatly affects its 
      composition and functional properties. Using lung squamous cell carcinoma (LSCC), 
      a chronic inflammation-associated cancer (CIAC), we optimized a robust proteomic 
      pipeline to discover potential biomarker signatures and protein changes 
      specifically in the stroma. We combined ECM enrichment from fresh human tissues, 
      data-independent acquisition (DIA) strategies, and stringent statistical 
      processing to analyze "Tumor" and matched adjacent histologically normal 
      ("Matched Normal") tissues from patients with LSCC. Overall, 1802 protein groups 
      were quantified with at least two unique peptides, and 56% of those proteins were 
      annotated as "extracellular." Confirming dramatic ECM remodeling during CIAC 
      progression, 529 proteins were significantly altered in the "Tumor" compared to 
      "Matched Normal" tissues. The signature was typified by a coordinated loss of 
      basement membrane proteins and small leucine-rich proteins. The dramatic increase 
      in the stromal levels of SERPINH1/heat shock protein 47, that was discovered 
      using our ECM proteomic pipeline, was validated by immunohistochemistry (IHC) of 
      "Tumor" and "Matched Normal" tissues, obtained from an independent cohort of LSCC 
      patients. This integrated workflow provided novel insights into ECM remodeling 
      during CIAC progression, and identified potential biomarker signatures and future 
      therapeutic targets.
CI  - (c) 2022 The Authors. Proteomics published by Wiley-VCH GmbH.
FAU - Bons, Joanna
AU  - Bons J
AD  - Buck Institute for Research on Aging, Novato, California, USA.
FAU - Pan, Deng
AU  - Pan D
AD  - Department of Pathology, University of California, San Francisco, California, 
      USA.
FAU - Shah, Samah
AU  - Shah S
AD  - Buck Institute for Research on Aging, Novato, California, USA.
FAU - Bai, Rosemary
AU  - Bai R
AD  - Department of Pathology, University of California, San Francisco, California, 
      USA.
FAU - Chen-Tanyolac, Chira
AU  - Chen-Tanyolac C
AD  - Department of Pathology, University of California, San Francisco, California, 
      USA.
FAU - Wang, Xianhong
AU  - Wang X
AD  - Department of Pathology, University of California, San Francisco, California, 
      USA.
FAU - Elliott, Daffolyn R Fels
AU  - Elliott DRF
AD  - Department of Pathology, University of California, San Francisco, California, 
      USA.
FAU - Urisman, Anatoly
AU  - Urisman A
AD  - Department of Pathology, University of California, San Francisco, California, 
      USA.
FAU - O'Broin, Amy
AU  - O'Broin A
AD  - Buck Institute for Research on Aging, Novato, California, USA.
FAU - Basisty, Nathan
AU  - Basisty N
AUID- ORCID: 0000-0001-6173-1139
AD  - Buck Institute for Research on Aging, Novato, California, USA.
FAU - Rose, Jacob
AU  - Rose J
AD  - Buck Institute for Research on Aging, Novato, California, USA.
FAU - Sangwan, Veena
AU  - Sangwan V
AD  - Division of Thoracic and Upper Gastrointestinal Surgery, Montreal General 
      Hospital, McGill University Health Centre, Montreal, Quebec, Canada.
FAU - Camilleri-Broet, Sophie
AU  - Camilleri-Broet S
AD  - Department of Pathology, McGill University, Montreal, Quebec, Canada.
FAU - Tankel, James
AU  - Tankel J
AD  - Division of Thoracic and Upper Gastrointestinal Surgery, Montreal General 
      Hospital, McGill University Health Centre, Montreal, Quebec, Canada.
FAU - Gascard, Philippe
AU  - Gascard P
AD  - Department of Pathology, University of California, San Francisco, California, 
      USA.
FAU - Ferri, Lorenzo
AU  - Ferri L
AD  - Division of Thoracic and Upper Gastrointestinal Surgery, Montreal General 
      Hospital, McGill University Health Centre, Montreal, Quebec, Canada.
FAU - Tlsty, Thea D
AU  - Tlsty TD
AD  - Department of Pathology, University of California, San Francisco, California, 
      USA.
FAU - Schilling, Birgit
AU  - Schilling B
AUID- ORCID: 0000-0001-9907-2749
AD  - Buck Institute for Research on Aging, Novato, California, USA.
LA  - eng
GR  - 27145/CRUK_/Cancer Research UK/United Kingdom
GR  - S10 OD016281/OD/NIH HHS/United States
GR  - A29071/CRUK_/Cancer Research UK/United Kingdom
GR  - A27145/CRUK_/Cancer Research UK/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20221013
PL  - Germany
TA  - Proteomics
JT  - Proteomics
JID - 101092707
RN  - 0 (Extracellular Matrix Proteins)
SB  - IM
MH  - Humans
MH  - *Proteomics
MH  - Extracellular Matrix/metabolism
MH  - Lung/metabolism
MH  - *Carcinoma, Squamous Cell/pathology
MH  - Inflammation/metabolism
MH  - Extracellular Matrix Proteins/metabolism
PMC - PMC10391693
MID - NIHMS1898790
OTO - NOTNLM
OT  - data-independent acquisition
OT  - extracellular matrix
OT  - lung squamous cell carcinoma
OT  - quantification
OT  - serpins
COIS- The authors declare no conflict of interest.
EDAT- 2022/10/14 06:00
MHDA- 2023/04/12 06:42
PMCR- 2024/03/03
CRDT- 2022/10/13 14:54
PHST- 2022/09/17 00:00 [revised]
PHST- 2022/07/29 00:00 [received]
PHST- 2022/09/21 00:00 [accepted]
PHST- 2023/04/12 06:42 [medline]
PHST- 2022/10/14 06:00 [pubmed]
PHST- 2022/10/13 14:54 [entrez]
PHST- 2024/03/03 00:00 [pmc-release]
AID - PMIC13591 [pii]
AID - 10.1002/pmic.202200021 [doi]
PST - ppublish
SO  - Proteomics. 2023 Apr;23(7-8):e2200021. doi: 10.1002/pmic.202200021. Epub 2022 Oct 
      13.