Stratification of follicular thyroid tumours using data-independent acquisition proteomics and a comprehensive thyroid tissue spectral library

被引：25

作者：

Sun, Yaoting ^{[1
,2
,3
]}

Li, Lu ^{[1
,2
,3
]}

Zhou, Yan ^{[1
,2
,3
]}

Ge, Weigang ^{[4
]}

Wang, He ^{[4
]}

Wu, Runxin ^{[2
,3
,5
]}

Liu, Wei ^{[4
]}

Chen, Hao ^{[4
]}

Xiao, Qi ^{[1
,2
,3
]}

Cai, Xue ^{[1
,2
,3
]}

Dong, Zhen ^{[2
,3
]}

Zhang, Fangfei ^{[2
,3
]}

Xiao, Junhong ^{[6
]}

Wang, Guangzhi ^{[6
]}

He, Yi ^{[7
]}

Gao, Jinlong ^{[2
,3
]}

Kon, Oi Lian ^{[8
]}

Iyer, Narayanan Gopalakrishna ^{[8
,9
]}

Guan, Haixia ^{[10
]}

Teng, Xiaodong ^{[11
]}

Zhu, Yi ^{[2
,3
]}

Zhao, Yongfu ^{[6
]}

Guo, Tiannan ^{[1
,2
,3
]}

机构：

[1] Zhejiang Univ, 866 Yuhangtang Rd, Hangzhou 310058, Peoples R China

[2] Westlake Univ, Sch Life Sci, Westlake Lab Life Sci & Biomed, Key Lab Struct Biol Zhejiang Prov, Hangzhou, Peoples R China

[3] Westlake Inst Adv Study, Inst Basic Med Sci, Hangzhou, Zhejiang, Peoples R China

[4] Westlake Omics Hangzhou Biotechnol Co Ltd, Hangzhou, Peoples R China

[5] Johns Hopkins Univ, Dept Biomed Engn, Whiting Sch Engn, Baltimore, MD USA

[6] Dalian Med Univ, Hosp 2, Dept Gen Surg, Dalian 116023, Peoples R China

[7] Dalian Med Univ, Hosp 2, Dept Urol, Dalian, Peoples R China

[8] Natl Canc Ctr Singapore, Div Med Sci, Singapore, Singapore

[9] Natl Canc Ctr Singapore, Dept Head & Neck Surg, Singapore, Singapore

[10] Guangdong Prov Peoples Hosp, Guangdong Acad Med Sci, Dept Endocrinol, Guangzhou, Peoples R China

[11] Zhejiang Univ, Affiliated Hosp 1, Sch Med, Dept Pathol, Hangzhou, Peoples R China

来源：

MOLECULAR ONCOLOGY | 2022年 / 16卷 / 08期

基金：

国家重点研发计划; 英国医学研究理事会; 中国国家自然科学基金;

关键词：

data-independent acquisition; mass spectrometry; proteomics; spectral library; thyroid nodules; CANCER INCIDENCE; EXPRESSION; NODULES; BENIGN; TRENDS;

D O I：

10.1002/1878-0261.13198

中图分类号：

R73 [肿瘤学];

学科分类号：

100214 ;

摘要：

Thyroid nodules occur in about 60% of the population. A major challenge in thyroid nodule diagnosis is to distinguish between follicular adenoma (FA) and carcinoma (FTC). Here, we present a comprehensive thyroid spectral library covering five types of thyroid tissues. This library includes 121 960 peptides and 9941 protein groups. This spectral library can be used to quantify up to 7863 proteins from thyroid tissues, and can also be used to develop parallel reaction monitoring (PRM) assays for targeted protein quantification. Next, to stratify follicular thyroid tumours, we compared the proteomes of 24 FA and 22 FTC samples, and identified 204 differentially expressed proteins (DEPs). Our data suggest altered ferroptosis pathways in malignant follicular carcinoma. In all, 31 selected proteins effectively distinguished follicular tumours. Of those DEPs, nine proteins were further verified by PRM in an independent cohort of 18 FA and 19 FTC. Together, we present a comprehensive spectral library for DIA and targeted proteomics analysis of thyroid tissue specimens, and identified nine proteins that could potentially distinguish FA and FTC.

引用

页码：1611 / 1624

页数：14

共 42 条

[1] Analyse multiple disease subtypes and build associated gene networks using genome-wide expression profiles [J].

Aibar, Sara ;

Fontanillo, Celia ;

Droste, Conrad ;

Roson-Burgo, Beatriz ;

Campos-Laborie, Francisco J. ;

Hernandez-Rivas, Jesus M. ;

Rivas, Javier De Las .

BMC GENOMICS, 2015, 16

[2] Preoperative Diagnosis of Benign Thyroid Nodules with Indeterminate Cytology [J].

Alexander, Erik K. ;

Kennedy, Giulia C. ;

Baloch, Zubair W. ;

Cibas, Edmund S. ;

Chudova, Darya ;

Diggans, James ;

Friedman, Lyssa ;

Kloos, Richard T. ;

LiVolsi, Virginia A. ;

Mandel, Susan J. ;

Raab, Stephen S. ;

Rosai, Juan ;

Steward, David L. ;

Walsh, P. Sean ;

Wilde, Jonathan I. ;

Zeiger, Martha A. ;

Lanman, Richard B. ;

Haugen, Bryan R. .

NEW ENGLAND JOURNAL OF MEDICINE, 2012, 367 (08) :705-715

[3] Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins [J].

Blattmann, Peter ;

Stutz, Vivienne ;

Lizzo, Giulia ;

Richard, Joy ;

Gut, Philipp ;

Aebersold, Ruedi .

SCIENTIFIC DATA, 2019, 6 (1)

[4] Thyroid Nodules [J].

Burman, Kenneth D. ;

Wartofsky, Leonard .

NEW ENGLAND JOURNAL OF MEDICINE, 2015, 373 (24) :2347-2356

[5] PulseDIA: Data-Independent Acquisition Mass Spectrometry Using Multi-Injection Pulsed Gas-Phase Fractionation [J].

Cai, Xue ;

Ge, Weigang ;

Yi, Xiao ;

Sun, Rui ;

Zhu, Jiang ;

Lu, Cong ;

Sun, Ping ;

Zhu, Tiansheng ;

Ruan, Guan ;

Yuan, Chunhui ;

Liang, Shuang ;

Lyu, Mengge ;

Huang, Shiang ;

Zhu, Yi ;

Guo, Tiannan .

JOURNAL OF PROTEOME RESEARCH, 2021, 20 (01) :279-288

[6] Molecular markers of endometrial carcinoma detected in uterine aspirates [J].

Colas, Eva ;

Perez, Cristina ;

Cabrera, Silvia ;

Pedrola, Nuria ;

Monge, Marta ;

Castellvi, Josep ;

Eyzaguirre, Fernando ;

Gregorio, Jesus ;

Ruiz, Anna ;

Llaurado, Marta ;

Rigau, Marina ;

Garcia, Marta ;

Ertekin, Tugce ;

Montes, Melania ;

Lopez-Lopez, Rafael ;

Carreras, Ramon ;

Xercavins, Jordi ;

Ortega, Alicia ;

Maes, Tamara ;

Rosell, Elisabet ;

Doll, Andreas ;

Abal, Miguel ;

Reventos, Jaume ;

Gil-Moreno, Antonio .

INTERNATIONAL JOURNAL OF CANCER, 2011, 129 (10) :2435-2444

[7] Follicular Thyroid Carcinoma: A Perspective [J].

Daniels, Gilbert H. .

THYROID, 2018, 28 (10) :1229-1242

[8] Carbonic anhydrase 4 and crystallin alpha-B immunoreactivity may distinguish benign from malignant thyroid nodules in patients with indeterminate thyroid cytology [J].

Davidov, Tomer ;

Nagar, Michael ;

Kierson, Malca ;

Chekmareva, Marina ;

Chen, Chunxia ;

Lu, Shou-en ;

Lin, Yong ;

Chernyavsky, Victoriya ;

Potdevin, Lindsay ;

Arumugam, Dena ;

Barnard, Nicola ;

Trooskin, Stanley .

JOURNAL OF SURGICAL RESEARCH, 2014, 190 (02) :565-574

[9] DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput [J].

Demichev, Vadim ;

Messner, Christoph B. ;

Vernardis, Spyros I. ;

Lilley, Kathryn S. ;

Ralser, Markus .

NATURE METHODS, 2020, 17 (01) :41-+

[10] KinMap: a web-based tool for interactive navigation through human kinome data [J].

Eid, Sameh ;

Turk, Samo ;

Volkamer, Andrea ;

Rippmann, Friedrich ;

Fulle, Simone .

BMC BIOINFORMATICS, 2017, 18

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