Tumor-informed deep sequencing of ctDNA detects minimal residual disease and predicts relapse in osteosarcoma

Yiwei Fu; Yu Xu; Weihai Liu; Jiajun Zhang; Fen Wang; Qijie Jian; Gang Huang; Changye Zou; Xianbiao Xie; Albert H Kim; Dimitrios Mathios; Fei Pang; Feng Li; Kai Wang; Jingnan Shen; Junqiang Yin

doi:10.1016/j.eclinm.2024.102697

Tumor-informed deep sequencing of ctDNA detects minimal residual disease and predicts relapse in osteosarcoma

EClinicalMedicine. 2024 Jun 20:73:102697. doi: 10.1016/j.eclinm.2024.102697. eCollection 2024 Jul.

Authors

Yiwei Fu^{1

2}, Yu Xu^{1

2}, Weihai Liu^{1

2}, Jiajun Zhang^{1

2}, Fen Wang³, Qijie Jian⁴, Gang Huang^{1

2}, Changye Zou^{1

2}, Xianbiao Xie^{1

2}, Albert H Kim^{5

6}, Dimitrios Mathios^{5

6}, Fei Pang⁴, Feng Li⁴, Kai Wang⁴, Jingnan Shen^{1

2}, Junqiang Yin^{1

2}

Affiliations

¹ Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China.
² Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China.
³ Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China.
⁴ OrigiMed, Shanghai, 201124, China.
⁵ Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA.
⁶ The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA.

Abstract

Background: Current surveillance modalities of osteosarcoma relapse exhibit limited sensitivity and specificity. Although circulating tumor DNA (ctDNA) has been established as a biomarker of minimal residual disease (MRD) in many solid tumors, a sensitive ctDNA detection technique has not been thoroughly explored for longitudinal MRD detection in osteosarcoma.

Methods: From August 2019 to June 2023, 59 patients diagnosed with osteosarcoma at the First Affiliated Hospital of Sun Yat-sen University were evaluated in this study. Tumor-informed MRD panels were developed through whole exome sequencing (WES) of tumor tissues. Longitudinal blood samples were collected during treatment and subjected to multiplex PCR-based next-generation sequencing (NGS). Kaplan-Meier curves and Log-rank tests were used to compare outcomes, and Cox regression analysis was performed to identify prognostic factors.

Findings: WES analysis of 83 patients revealed substantial mutational heterogeneity, with non-recurrent mutated genes accounting for 58.1%. Tumor-informed MRD panels were successfully obtained for 85.5% of patients (71/83). Among 59 patients with successful MRD panel customization and available blood samples, 13 patients exhibited positive ctDNA detection after surgery. Patients with negative post-operative ctDNA had better event-free survival (EFS) compared to those with positive ctDNA, at 1-6 months after surgery, after adjuvant chemotherapy, and more than 6 months after surgery (p < 0.05). In both univariate and multivariate Cox regression analysis, ctDNA results emerged as a significant predictor of EFS (p < 0.05). ctDNA detection preceded positive imaging in 5 patients, with an average lead time of 92.6 days. Thirty-nine patients remained disease-free, with ctDNA results consistently negative or turning negative during follow-up.

Interpretation: Our study underscores the applicability of tumor-informed deep sequencing of ctDNA in osteosarcoma MRD surveillance and, to our knowledge, represents the largest cohort to date. ctDNA detection is a significant prognostic factor, enabling the early identification of tumor relapse and progression compared to standard imaging, thus offering valuable insights in guiding osteosarcoma patient management.

Funding: The Grants of National Natural Science Foundation of China (No. 82072964, 82072965, 82203798, 82203026), the Natural Science Foundation of Guangdong (No. 2023A1515012659, 2023A1515010302), and the Regional Combination Project of Basic and Applied Basic Research Foundation of Guangdong (No. 2020A1515110010).

Keywords: Circulating tumor DNA (ctDNA); Minimal residual disease (MRD); Next-generation sequencing (NGS); Osteosarcoma relapse; Tumor-informed MRD panel.