Abstract
Introduction: Fine-needle aspiration cytology (FNAC) specimens are widely utilized for the diagnosis and molecular testing of various cancers. We performed a comparative proteomic analysis of three different sample types, including breast FNAC, core needle biopsy (CNB), and surgical resection tissues. Our goal was to evaluate the suitability of FNAC for in-depth proteomic analysis and for identifying potential therapeutic biomarkers in breast cancer. Methods: High-throughput proteomic analysis was conducted on matched FNAC, CNB, and surgical resection tissue samples obtained from breast cancer patients. The protein identification, including currently established or promising therapeutic targets, was compared among the three different sample types. Gene Ontology (GO) enrichment analysis was also performed on all matched samples. Results: Compared to tissue samples, FNAC testing revealed a comparable number of proteins (7,179 in FNAC; 7,196 in CNB; and 7,190 in resection samples). Around 85% of proteins were mutually identified in all sample types. FNAC, along with CNB, showed a positive correlation between the number of enrolled tumor cells and identified proteins. In the GO analysis, the FNAC samples demonstrated a higher number of genes for each pathway and GO terms than tissue samples. CCND1, CDK6, HER2, and IGF1R were found in higher quantities in the FNAC compared to tissue samples, while TUBB2A was only detected in the former. Conclusion: FNAC is suitable for high-throughput proteomic analysis, in addition to an emerging source that could be used to identify and quantify novel cancer biomarkers.
Journal Section:
Research Article
References
1.
Early Breast Cancer Trialists' Collaborative Group
; Davies
C
, Godwin
J
, Gray
R
, Clarke
M
, Cutter
D
. Relevance of breast cancer hormone receptors and other factors to the efficacy of adjuvant tamoxifen: patient-level meta-analysis of randomised trials
. Lancet
. 2011
;378
(9793
):771
–84
. 2.
Moasser
MM
, Krop
IE
. The evolving landscape of HER2 targeting in breast cancer
. JAMA Oncol
. 2015
;1
(8
):1154
–61
. 3.
Slamon
D
, Eiermann
W
, Robert
N
, Pienkowski
T
, Martin
M
, Press
M
, et al. Adjuvant trastuzumab in HER2-positive breast cancer
. N Engl J Med
. 2011
;365
(14
):1273
–83
. 4.
Wolff
AC
, Hammond
MEH
, Allison
KH
, Harvey
BE
, Mangu
PB
, Bartlett
JMS
, et al. Human epidermal growth factor receptor 2 testing in breast cancer: American society of clinical oncology/college of American pathologists clinical practice guideline focused update
. Arch Pathol Lab Med
. 2018
;142
(11
):1364
–82
. 5.
Abraham
J
, Coleman
R
, Elias
A
, Holmes
FA
, Kalinsky
K
, Kittaneh
M
, et al. Use of cyclin-dependent kinase (CDK) 4/6 inhibitors for hormone receptor-positive, human epidermal growth factor receptor 2-negative, metastatic breast cancer: a roundtable discussion by the Breast Cancer Therapy Expert Group (BCTEG)
. Breast Cancer Res Treat
. 2018
;171
(1
):11
–20
. 6.
Mayer
EL
. Targeting breast cancer with CDK inhibitors
. Curr Oncol Rep
. 2015
;17
(5
):443
. 7.
Gupta
DK
, Mooney
EE
, Layfield
LJ
. Fine-needle aspiration cytology: a survey of current utilization in relationship to hospital size, surgical pathology volume, and institution type
. Diagn Cytopathol
. 2000
;23
(1
):59
–65
. 8.
Ernst
LM
, Rimm
DL
. Quantitative examination of mechanophysical tumor cell enrichment in fine-needle aspiration specimens
. Cancer
. 2002
;96
(5
):275
–9
. 9.
Symmans
WF
, Ayers
M
, Clark
EA
, Stec
J
, Hess
KR
, Sneige
N
, et al. Total RNA yield and microarray gene expression profiles from fine-needle aspiration biopsy and core-needle biopsy samples of breast carcinoma
. Cancer
. 2003
;97
(12
):2960
–71
. 10.
Lee
HB
, Joung
JG
, Kim
J
, Lee
KM
, Ryu
HS
, Lee
HO
, et al. The use of FNA samples for whole-exome sequencing and detection of somatic mutations in breast cancer surgical specimens
. Cancer Cytopathol
. 2015
;123
(11
):669
–77
. 11.
Roy-Chowdhuri
S
, Chen
H
, Singh
RR
, Krishnamurthy
S
, Patel
KP
, Routbort
MJ
, et al. Concurrent fine needle aspirations and core needle biopsies: a comparative study of substrates for next-generation sequencing in solid organ malignancies
. Mod Pathol
. 2017
;30
(4
):499
–508
. 12.
Treece
AL
, Montgomery
ND
, Patel
NM
, Civalier
CJ
, Dodd
LG
, Gulley
ML
, et al. FNA smears as a potential source of DNA for targeted next-generation sequencing of lung adenocarcinomas
. Cancer Cytopathol
. 2016
;124
(6
):406
–14
. 13.
Valero
V
3rd, Saunders
TJ
, He
J
, Weiss
MJ
, Cameron
JL
, Dholakia
A
, et al. Reliable detection of somatic mutations in fine needle aspirates of pancreatic cancer with next-generation sequencing: implications for surgical management
. Ann Surg
. 2016
;263
(1
):153
–61
. 14.
Jung
M
, Lee
C
, Han
D
, Kim
K
, Yang
S
, Nikas
IP
, et al. Proteomic-based machine learning analysis reveals PYGB as a novel immunohistochemical biomarker to distinguish inverted urothelial papilloma from low-grade papillary urothelial carcinoma with inverted growth
. Front Oncol
. 2022
;12
:841398
. 15.
Tyanova
S
, Albrechtsen
R
, Kronqvist
P
, Cox
J
, Mann
M
, Geiger
T
. Proteomic maps of breast cancer subtypes
. Nat Commun
. 2016
;7
:10259
. 16.
Harel
M
, Ortenberg
R
, Varanasi
SK
, Mangalhara
KC
, Mardamshina
M
, Markovits
E
, et al. Proteomics of melanoma response to immunotherapy reveals mitochondrial dependence
. Cell
. 2019
;179
(1
):236
–50.e18
. 17.
Do
M
, Kim
H
, Yeo
I
, Lee
J
, Park
IA
, Ryu
HS
, et al. Clinical application of multiple reaction monitoring-mass spectrometry to human epidermal growth factor receptor 2 measurements as a potential diagnostic tool for breast cancer therapy
. Clin Chem
. 2020
;66
(10
):1339
–48
. 18.
Park
J
, Oh
HJ
, Han
D
, Wang
JI
, Park
IA
, Ryu
HS
, et al. Parallel reaction monitoring-mass spectrometry (PRM-MS)-Based targeted proteomic surrogates for intrinsic subtypes in breast cancer: comparative analysis with immunohistochemical phenotypes
. J Proteome Res
. 2020
;19
(7
):2643
–53
. 19.
Lee
H
, Kim
K
, Woo
J
, Park
J
, Kim
H
, Lee
KE
, et al. Quantitative proteomic analysis identifies AHNAK (neuroblast differentiation-associated protein AHNAK) as a novel candidate biomarker for bladder urothelial carcinoma diagnosis by liquid-based cytology
. Mol Cel Proteomics
. 2018
;17
(9
):1788
–802
. 20.
Park
JH
, Lee
C
, Han
D
, Lee
JS
, Lee
KM
, Song
MJ
, et al. Moesin (MSN) as a novel proteome-based diagnostic marker for early detection of invasive bladder urothelial carcinoma in liquid-based cytology
. Cancers
. 2020
;12
(4
):1018
. 21.
Lee
CH
, Chung
SY
, Moon
KC
, Park
IA
, Chung
YR
, Ryu
HS
. A pilot study evaluating fine-needle aspiration cytology of clear-cell renal cell carcinoma: comparison of ancillary immunocytochemistry and cytomorphological characteristics of SurePath liquid-based preparations with conventional smears
. Acta Cytol
. 2015
;59
(3
):239
–47
. 22.
Lee
KM
, Lee
H
, Han
D
, Moon
WK
, Kim
K
, Oh
HJ
, et al. Combined the SMAC mimetic and BCL2 inhibitor sensitizes neoadjuvant chemotherapy by targeting necrosome complexes in tyrosine aminoacyl-tRNA synthase-positive breast cancer
. Breast Cancer Res
. 2020
;22
(1
):130
. 23.
Tyanova
S
, Temu
T
, Cox
J
. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics
. Nat Protoc
. 2016
;11
(12
):2301
–19
. 24.
Cox
J
, Neuhauser
N
, Michalski
A
, Scheltema
RA
, Olsen
JV
, Mann
M
. Andromeda: a peptide search engine integrated into the MaxQuant environment
. J Proteome Res
. 2011
;10
(4
):1794
–805
. 25.
Vizcaino
JA
, Deutsch
EW
, Wang
R
, Csordas
A
, Reisinger
F
, Rios
D
, et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination
. Nat Biotechnol
. 2014
;32
(3
):223
–6
. 26.
Chen
J
, Bardes
EE
, Aronow
BJ
, Jegga
AG
. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
. Nucleic Acids Res
. 2009
;37
(suppl 2
):W305
–11
. 27.
Tyanova
S
, Temu
T
, Sinitcyn
P
, Carlson
A
, Hein
MY
, Geiger
T
, et al. The Perseus computational platform for comprehensive analysis of (prote)omics data
. Nat Methods
. 2016
;13
(9
):731
–40
. 28.
Guo
R
, Luo
J
, Chang
J
, Rekhtman
N
, Arcila
M
, Drilon
A
. MET-dependent solid tumours - molecular diagnosis and targeted therapy
. Nat Rev Clin Oncol
. 2020
;17
(9
):569
–87
. 29.
Masoud
V
, Pages
G
. Targeted therapies in breast cancer: new challenges to fight against resistance
. World J Clin Oncol
. 2017
;8
(2
):120
–34
. 30.
Shi
J
, Liu
F
, Song
Y
. Progress: targeted therapy, immunotherapy, and new chemotherapy strategies in advanced triple-negative breast cancer
. Cancer Manag Res
. 2020
;12
:9375
–87
. 31.
Voutsadakis
IA
. 8p11.23 amplification in breast cancer: molecular characteristics, prognosis and targeted therapy
. J Clin Med
. 2020
;9
(10
):3079
. 32.
Shin
D
, Park
J
, Han
D
, Moon
JH
, Ryu
HS
, Kim
Y
. Identification of TUBB2A by quantitative proteomic analysis as a novel biomarker for the prediction of distant metastatic breast cancer
. Clin Proteomics
. 2020
;17
:16
. 33.
Lindeman
NI
, Cagle
PT
, Aisner
DL
, Arcila
ME
, Beasley
MB
, Bernicker
EH
, et al. Updated molecular testing guideline for the selection of lung cancer patients for treatment with targeted tyrosine kinase inhibitors: guideline from the College of American pathologists, the international association for the study of lung cancer, and the association for molecular pathology
. J Thorac Oncol
. 2018
;13
(3
):323
–58
. 34.
Groelz
D
, Sobin
L
, Branton
P
, Compton
C
, Wyrich
R
, Rainen
L
. Non-formalin fixative versus formalin-fixed tissue: a comparison of histology and RNA quality
. Exp Mol Pathol
. 2013
;94
(1
):188
–94
. 35.
von Ahlfen
S
, Missel
A
, Bendrat
K
, Schlumpberger
M
. Determinants of RNA quality from FFPE samples
. PLoS One
. 2007
;2
(12
):e1261
. 36.
Zhang
Y
, Muller
M
, Xu
B
, Yoshida
Y
, Horlacher
O
, Nikitin
F
, et al. Unrestricted modification search reveals lysine methylation as major modification induced by tissue formalin fixation and paraffin embedding
. Proteomics
. 2015
;15
(15
):2568
–79
. 37.
Gustafsson
OJ
, Arentz
G
, Hoffmann
P
. Proteomic developments in the analysis of formalin-fixed tissue
. Biochim Biophys Acta
. 2015
;1854
(6
):559
–80
. 38.
Dupain
C
, Masliah-Planchon
J
, Gu
C
, Girard
E
, Gestraud
P
, Du Rusquec
P
, et al. Fine-needle aspiration as an alternative to core needle biopsy for tumour molecular profiling in precision oncology: prospective comparative study of next-generation sequencing in cancer patients included in the SHIVA02 trial
. Mol Oncol
. 2021
;15
(1
):104
–15
. 39.
Hartley
CP
, Mahajan
AM
, Selvaggi
SM
, Rehrauer
WM
. FNA smears of pancreatic ductal adenocarcinoma are superior to formalin-fixed paraffin-embedded tissue as a source of DNA: comparison of targeted KRAS amplification and genotyping in matched preresection and postresection samples
. Cancer Cytopathol
. 2017
;125
(11
):838
–47
. 40.
Ulivi
P
, Romagnoli
M
, Chiadini
E
, Casoni
GL
, Capelli
L
, Gurioli
C
, et al. Assessment of EGFR and K-ras mutations in fixed and fresh specimens from transesophageal ultrasound-guided fine needle aspiration in non-small cell lung cancer patients
. Int J Oncol
. 2012
;41
(1
):147
–52
. 41.
Gleeson
FC
, Kipp
BR
, Kerr
SE
, Voss
JS
, Graham
RP
, Campion
MB
, et al. Kinase genotype analysis of gastric gastrointestinal stromal tumor cytology samples using targeted next-generation sequencing
. Clin Gastroenterol Hepatol
. 2015
;13
(1
):202
–6
. 42.
Wisniewski
JR
, Zougman
A
, Nagaraj
N
, Mann
M
. Universal sample preparation method for proteome analysis
. Nat Methods
. 2009
;6
(5
):359
–62
. 43.
Lüönd
F
, Tiede
S
, Christofori
G
. Breast cancer as an example of tumour heterogeneity and tumour cell plasticity during malignant progression
. Br J Cancer
. 2021
;125
(2
):164
–75
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