Single-cell and spatial analyses of the GDF family in tumors, with a focus on the prognostic and biological role of GDF15 in hepatocellular carcinoma

Xiaoqian Feng; Qian Huai; Fumin Zhang; Wenkang Yuan; Xingyu Li; Zhuo Yu; Hao Zhang; Yaoling Zhu; Xu Zhang; Baole Tao; Ying Dai; Yishan Du

doi:10.1186/s13578-025-01431-9

Single-cell and spatial analyses of the GDF family in tumors, with a focus on the prognostic and biological role of GDF15 in hepatocellular carcinoma

Cell Biosci. 2025 Jun 27;15(1):92. doi: 10.1186/s13578-025-01431-9.

Authors

Xiaoqian Feng^#¹, Qian Huai^#², Fumin Zhang^#³, Wenkang Yuan^#⁴, Xingyu Li², Zhuo Yu⁵, Hao Zhang⁶, Yaoling Zhu⁷, Xu Zhang², Baole Tao⁸, Ying Dai⁹, Yishan Du¹⁰

Affiliations

¹ Department of Laboratory Medicine, the First Medical Centre, Chinese PLA General Hospital, Beijing, 100853, China.
² Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.
³ Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.
⁴ Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.
⁵ Department of Radiology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China.
⁶ Department of Anesthesiology, The Chinese People's Armed Police Forces Anhui Provincial Corps Hospital, Hefei, 230041, China.
⁷ Chaohu Clinical Medical College, Anhui Medical University, Hefei, 230601, China.
⁸ The Affiliated High School of Peking University, Beijing, 100080, China.
⁹ Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China. dabora20051@hotmail.com.
¹⁰ The First Affiliated Hospital of Ningbo University, Ningbo, 117881, China. duysh95@163.com.

^# Contributed equally.

Abstract

Growth differentiation factors (GDFs) are a subfamily of the TGF-β superfamily whose expression increases in response to cellular stress and disease. Despite emerging cell- or animal-based evidence supporting an association between the GDF subfamily and cancer, systematic pan-cancer analyses of the GDF subfamily based on single-cell and spatial transcriptomes remains unavailable. In this study, we performed a comprehensive analysis of the GDF subfamily in 33 cancers, including expression, diagnosis, methylation, prognostic value, immune infiltration analysis, and potential biological pathways. We focused on the analysis of multi-group scRNA-seq and spatial data in hepatocellular carcinoma (HCC) to determine the role of the GDF family in the tumor microenvironment and its applicability in immunotherapy. Moreover, both the gain and loss of function strategies were used to assess the function of Growth differentiation factor 15 (GDF15) in cell lines of HCC. The GDF subfamily is expressed to varying degrees in most tumors and is significantly correlated with the prognosis of cancer patients. Subsequent scRNA-seq analysis depicted the heterogeneous cellular ecosystems of normal liver and HCC. Hepatocytes expressing GDF15 were less differentiated in HCC, and GDF15 promoted proliferation and invasion of HCC cell lines. Compared to normal liver, the strength of crosstalk between GDF15-positive Hepatocytes and other cells was enhanced in tumors, especially cancer-associated fibroblasts (CAFs)-derived Periostin and GDF15-positive Hepatocytes both regulate each other and jointly promote hepatocarcinogenesis. Further spatial transcriptomic data showed that GDF15 expression was negatively correlated with immune infiltration, especially in M1-type macrophages. Notably, validation analyses in bulk RNA-seq consistently emphasized the clinical significance of these findings. This study provides a comprehensive overview of the oncogenic role of the GDF subfamily in a wide range of tumors, highlights the important role of GDF15 in HCC ecosystem, and provides important biomarkers and potential therapeutic targets for future research.

Keywords: Clinical significance; Diagnosis; Growth differentiation factor15; Growth differentiation factors subfamily; Immune infiltration; Prognostic biomarker.