Integrating cfDNA liquid biopsy and organoid-based drug screening reveals PI3K signaling as a promising therapeutic target in colorectal cancer

Sep 22, 2026

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Precision medicine often depends on biomarkers obtained mainly through next-generation sequencing, yet this approach has not reliably identified effective drugs for most cancer patients. This study combines cfDNA liquid biopsy with organoid-based functional drug testing to identify candidate therapies for colorectal cancer. Prospective CRC enrollment enabled cfDNA deep sequencing and organoid evaluation of PI3K/mTOR inhibition, revealing clinically relevant mutation patterns and targetable responses, supporting PI3K pathway targeting.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages13

Reading Time33 min

AccessFree to download

Abstract

Background

Methods

Results

Conclusion

Introduction

Liquid biopsy overview

cfDNA and ctDNA concepts

Clinical rationale and heterogeneity

Yang et al. Journal of Translational Medicine (2024) 22:132 [https://doi.org/10.1186/s12967-023-04675-6](https://doi.org/10.1186/s12967-023-04675-6) Journal of Translational Medicine RESEARCH Open Access Integrating cfDNA liquid biopsy and organoid-based drug screening reveals PI3K signaling as a promising therapeutic target in colorectal cancer HuanYang1,2†, Xing Xiao2†, Leli Zeng3, Haiteng Zeng2, Yueyuan Zheng4, Jingshu Wang5, Guanghua Li 1, Weigang Dai1, Yulong He2,6, Suihai Wang7*, Jianjun Peng1* and Wei Chen2,6* Abstract Background The current precision medicine relies on biomarkers, which are mainly obtained through nextgeneration sequencing (NGS) . However, this model failed to find effective drugs for most cancer patients. This study tried to combine liquid biopsy with functional drug tests using organoid models to find potential drugs for cancer patients. Methods Colorectal cancer (CRC) patients were prospectively enrolled and blood samples were collected from patients before the start of treatment. Targeted deep sequencing of cfDNA samples was performed using a 14-gene panel. Gastrointestinal (GI) cancer organoids were established and PI3K and mTOR inhibitors were evaluated on organoid models. Results A total of 195 mutations were detected across 58 cfDNA samples. The most frequently mutated genes were KRAS, TP53, PIK3CA, and BRAF, all of which exhibited higher mutation rates than tissue biopsy. Although 81% of variants had an allele frequency of less than 1%, certain mutations in KRAS, TP53, and SMAD4 had high allele frequencies exceeding 10% . Notably, among the seven patients with high allele frequency mutations, six had metastatic tumors, indicating that a high allele frequency of ctDNA could potentially serve as a biomarker of later-stage cancer. A high rate of PIK3CA mutation (31 out of 67, or 46. 3%) was discovered in CRC patients, suggesting possible tumor progression mechanisms and targeted therapy opportunities. To evaluate the value of anti PI3K strategy in GI cancer, different lines of GI cancer organoids were established. The organoids recapitulated the morphologies ofthe original tumors. Organoids were generally insensitive to PI3K inhibitors. However, CRC-3 and GC-4 showed response to mTOR inhibitor Everolimus, and GC-3 was sensitive to PI3Kδ inhibitor Idelalisib. The CRC organoid with a PIK3CA mutation showed greater sensitivity to the PI3K inhibitor Alpelisib than wildtype organoids, suggesting potential treatment options for the corresponding patients. †HuanYang and Xing Xiao contributed equally to this work. *Correspondence: Suihai Wang [suihaiw65@163.com](suihaiw65@163.com)[ ](suihaiw65@163.com)Jianjun Peng[pjianj@mail.sysu.edu.cn](pjianj@mail.sysu.edu.cn)[ ](pjianj@mail.sysu.edu.cn)Wei Chen[chenw296@mail.sysu.edu.cn](chenw296@mail.sysu.edu.cn) Full list of author information is available at the end of the article © The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit [http://creativecommons.org/licenses/by/4.0/](http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ()[. The Creative Commons Public Domain Dedication waiver (](http://creativecommons.org/license

FAQs

Why does the study combine cfDNA liquid biopsy with organoid-based drug testing?

The study addresses the limitation of relying on biomarker models from sequencing alone to find effective drugs. It uses functional tests in patient-derived organoids alongside cfDNA-derived biomarker information to better match therapy to tumor biology.

How were cfDNA mutations characterized in the research?

Blood samples collected before treatment underwent targeted deep sequencing using a 14-gene panel. Across 58 cfDNA samples, 195 mutations were detected, with common alterations including KRAS, TP53, PIK3CA, and BRAF.

What PI3K/mTOR-related therapeutic responses were observed in organoid models?

Organoids were largely insensitive to PI3K inhibitors overall, but CRC-3 and GC-4 responded to the mTOR inhibitor Everolimus, and GC-3 showed sensitivity to the PI3Kδ inhibitor Idelalisib. The CRC organoid with a PIK3CA mutation showed greater sensitivity to the PI3K inhibitor Alpelisib than wildtype organoids.

Sep 22, 2026

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