Quantitative proteomics identifies and validates urinary biomarkers of rhabdomyosarcoma in children

Na Xu; Yuncui Yu; Chao Duan; Jing Wei; Wei Sun; Chiyi Jiang; Binglin Jian; Wang Cao; Lulu Jia; Xiaoli Ma

doi:10.1186/s12014-023-09401-4

Quantitative proteomics identifies and validates urinary biomarkers of rhabdomyosarcoma in children

Clin Proteomics. 2023 Mar 14;20(1):10. doi: 10.1186/s12014-023-09401-4.

Authors

Na Xu^#^{1

2}, Yuncui Yu^#³, Chao Duan¹, Jing Wei³, Wei Sun⁴, Chiyi Jiang¹, Binglin Jian¹, Wang Cao³, Lulu Jia^#⁵, Xiaoli Ma^#⁶

Affiliations

¹ Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China.
² Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, China.
³ Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China.
⁴ Proteomics Research Center, Core Facility of Instruments, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
⁵ Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China. jluyu@126.com.
⁶ Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China. mxl1232022@126.com.

^# Contributed equally.

Abstract

Background: Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma with poor prognosis in children. The 5-year survival rate for early RMS has improved, whereas it remains unsatisfactory for advanced patients. Urine can rapidly reflect changes in the body and identify low-abundance proteins. Early screening of tumor markers through urine in RMS allows for earlier treatment, which is associated with better outcomes.

Methods: RMS patients under 18 years old, including those newly diagnosed and after surgery, were enrolled. Urine samples were collected at the time points of admission and after four cycles of chemotherapy during follow-up. Then, a two-stage workflow was established. (1) In the discovery stage, differential proteins (DPs) were initially identified in 43 RMS patients and 12 healthy controls (HCs) using a data-independent acquisition method. (2) In the verification stage, DPs were further verified as biomarkers in 54 RMS patients and 25 HCs using parallel reaction monitoring analysis. Furthermore, a receiver operating characteristic (ROC) curve was used to construct the protein panels for the diagnosis of RMS. Gene Ontology (GO) and Ingenuity Pathway Analysis (IPA) software were used to perform bioinformatics analysis.

Results: A total of 251 proteins were significantly altered in the discovery stage, most of which were enriched in the head, neck and urogenital tract, consistent with the most common sites of RMS. The most overrepresented biological processes from GO analysis included immunity, inflammation, tumor invasion and neuronal damage. Pathways engaging the identified proteins revealed 33 common pathways, including WNT/β-catenin signaling and PI3K/AKT signaling. Finally, 39 proteins were confirmed as urinary biomarkers for RMS, and a diagnostic panel composed of 5 candidate proteins (EPS8L2, SPARC, HLA-DRB1, ACAN, and CILP) was constructed for the early screening of RMS (AUC: 0.79, 95%CI = 0.66 ~ 0.92).

Conclusions: These findings provide novel biomarkers in urine that are easy to translate into clinical diagnosis of RMS and illustrate the value of global and targeted urine proteomics to identify and qualify candidate biomarkers for noninvasive molecular diagnosis.

Keywords: Biomarker; Mass spectrometry; Pediatric; Rhabdomyosarcoma; Urinary proteomics.

Abstract

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