ORIGINAL RESEARCH article
Front. Immunol.
Sec. Molecular Innate Immunity
Volume 16 - 2025 | doi: 10.3389/fimmu.2025.1682637
Single-cell and Spatial Transcriptomics Integration Reveals FAM49B Promotes Tumor-associated Macrophages Polarization in Colorectal Cancer via the MK Pathway
Provisionally accepted
Tianyu Liu1,2Quchen Ding2Jin Gou1
Lei Liu3Xingming Lu1Jiatong Chen1Yiming E4Lianhong Li2Chongguo Zhang2Xiaojuan Zhu2*
Chunzhao Yu1,2*
Xiagang Luo2*- 1Sir Run Run Hospital Nanjing Medical University, Nanjing, China
- 2The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- 3Yixing People's Hospital, Yixing, China
- 4Suzhou Municipal Hospital, Suzhou, China
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Objectives: FAM49B has been shown to promote proliferation and metastasis of colorectal cancer (CRC) by stabilizing MYC through phosphorylation of NEK9; however, its role in shaping the immune suppressive tumor microenvironment (TME), particularly in macrophage polarization, remains unclear. Methods: We applied multi-omics approaches to study CRC by integrating 33 scRNA-seq samples from 16 CRC patients, 2 paired spatial transcriptomics (ST) samples, and bulk RNA data to characterize malignant epithelial cells (High_FAM49B_EP) and tumor-associated macrophages (TAMs). Functional validation of FAM49B was conducted via knockdown experiments and proteomics analysis. Results: A High_FAM49B_EP subpopulation was identified in primary tumors (PT) and liver metastases (LM), exhibiting elevated MYC signaling and association with poor prognosis. TAMs showed spatial heterogeneity: M1-like CXCL3⁺ TAMs predominated in PT, whereas M2-like SPP1⁺ TAMs were enriched in LM. CellChat analysis revealed that High_FAM49B_EP activated macrophage polarization through the MDK–NCL signaling axis. Pseudotime trajectory analysis confirmed differentiation from CXCL3⁺ to SPP1⁺ TAMs driven by upregulation of NCL. Spatial mapping showed co-localization of MDK⁺ epithelial cells with NCL⁺ TAMs in the immunosuppressive microenvironment. FAM49B knockdown significantly inhibited MDK expression and disrupted ECM–receptor interactions. Conclusions: FAM49B promotes immunosuppressive TME formation by mediating TAM polarization via the MDK–NCL axis, suggesting the FAM49B–MDK–NCL pathway as a potential therapeutic target for CRC metastasis.
Keywords: colorectal cacner, tumor environment (TME), FAM49B, MDK, Macrophage polarization, bioinformatics
Received: 09 Aug 2025; Accepted: 24 Sep 2025.
Copyright: © 2025 Liu, Ding, Gou, Liu, Lu, Chen, E, Li, Zhang, Zhu, Yu and Luo. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Xiaojuan Zhu, xjzhu1983@163.com
Chunzhao Yu, chunzhaoyu@njmu.edu.cn
Xiagang Luo, jssylxg2003@njmu.edu.cn
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