Cross-Organ Human Fibroblast Atlas Reveals Unique Roles of Different Myofibroblast Subtypes in Immune Regulation

Research Background and Motivation

Fibroblasts play critical roles in maintaining tissue homeostasis, inflammatory responses, fibrosis, and cancer progression. In recent years, the diversity of fibroblasts in the tumor microenvironment (TME) has garnered significant academic attention. Studies have shown that fibroblasts perform complex functions in cancer by regulating the extracellular matrix (ECM), signaling with cancer cells and immune cells, among other mechanisms. However, the heterogeneity and plasticity of fibroblasts make them difficult to manipulate in treatment. Therefore, clarifying the states of disease-associated fibroblasts, their interactions with immune cells, and their impact on clinical outcomes will provide new insights for optimizing cancer treatment strategies.

To this end, Gao and colleagues systematically analyzed fibroblast heterogeneity across tissues and disease states using single-cell RNA sequencing (scRNA-seq). The core objective of the study was to construct a cross-organ fibroblast atlas to reveal the distribution characteristics, functional attributes, and dynamic changes of fibroblast subtypes in different pathological states.

Research Origin

This paper was completed by researchers such as Yang Gao, Jianan Li, and Wenfeng Cheng, from renowned research institutions including Peking University, Shenzhen Bay Laboratory, and the Chinese Academy of Medical Sciences. The paper was published in the October 14, 2024, issue of the journal “Cancer Cell,” further expanding the functional analysis of cancer fibroblasts and providing new targets for cancer therapy.

Research Process

The entire research process was divided into multiple steps, covering data integration, fibroblast subtype identification, functional analysis, and clinical relevance analysis.

Data Collection and Processing

The research team integrated scRNA-seq data from 517 human samples, including 11 types of tissues and various pathological states (such as chronic inflammation, fibrosis, precancerous lesions, and cancer), totaling transcriptomic data from 269,899 fibroblasts. To ensure data quality, the team conducted rigorous quality control on each dataset, removing non-fibroblast cells, ultimately obtaining a complete cross-organ fibroblast atlas.

Identification of Fibroblast Subtypes

Using the Batch Balanced K Nearest Neighbors (BBKNN) clustering algorithm, the study identified 20 transcriptionally distinct fibroblast subtypes. By conducting integrated analyses, the team categorized these fibroblast subtypes into different functional groups, including tissue-specific fibroblasts, myofibroblasts, and primary fibroblasts.

Functional Characterization of Fibroblast Subtypes

Through regulatory network analysis and transcription factor activity analysis, the study found that each fibroblast subtype possesses unique gene expression patterns and signal pathway activation characteristics. For example, LRRC15+ myofibroblasts exhibited immune suppression traits, while MMP1+ fibroblasts might be related to immune evasion in the tumor microenvironment. Based on these characteristics, the study further linked each fibroblast subtype with the immune cell distribution in disease states, revealing distinct roles in tumors and inflammation.

Main Findings

Reprogramming of Fibroblasts in Pathological States

The composition of fibroblast subtypes underwent significant changes under different pathological states. The study found that both chronic inflammation and cancer promoted the expansion of immune-regulatory fibroblasts, while myofibroblasts exhibited tissue remodeling functions in cancer. In the tumor microenvironment, different myofibroblast subtypes had unique functional attributes, such as LRRC15+ fibroblasts showing immune exclusion in cancer tissues, whereas PI16+ fibroblasts displayed potential anti-tumor effects in adjacent non-cancer tissues.

Impact of Fibroblast Subtypes on the Tumor Immune Microenvironment

In cancer patients, the study identified multiple cell modules co-present with fibroblasts. For instance, PI16+ fibroblasts mainly coexisted with CD8+ T cells and CD14+ macrophages, forming an anti-tumor immune environment. In contrast, LRRC15+ myofibroblasts coexisted with Spp1+ macrophages, constituting an immune exclusion cell module, which exhibited lower T cell infiltration in tumor samples.

Heterogeneity of Myofibroblasts

Within the myofibroblast category, the study identified four main subtypes: LRRC15+, MMP1+, HOPX+, and SFRP2+. Among them, LRRC15+ fibroblasts had potential tumor-promoting capabilities and were closely associated with immune exclusion in the tumor microenvironment. MMP1+ fibroblasts exhibited immune suppression traits, forming an immune-suppressive cell module through interactions with Tregs and LAMP3+ dendritic cells.

Interactions Between Fibroblasts and Immune Cells

Through cell co-occurrence analysis, the study revealed complex interaction mechanisms between fibroblasts and different immune cells. For example, MMP1+ fibroblasts promoted the formation of an immunosuppressive environment by interacting with Tregs through ligand-receptor pairs such as CCL2-CCR4 and CXCL16-CXCR6. LRRC15+ fibroblasts influenced immune exclusion in the tumor microenvironment through interactions with Spp1+ macrophages.

Conclusion and Significance

This study deeply revealed the heterogeneity of fibroblasts and their functional characteristics in the tumor microenvironment through a cross-organ and pathological state human fibroblast atlas. The results indicate that different fibroblast subtypes have a significant impact on shaping the tumor microenvironment, with their immune regulatory roles being reprogrammed in response to pathological state changes. These findings not only offer new perspectives for understanding the role of fibroblasts in cancer progression but also provide potential targets and strategies for future cancer therapies targeting fibroblasts.

Research Highlights

1. Cross-Organ Atlas Construction: This study integrated single-cell data from multiple tissues and pathological states, unveiling the heterogeneity of fibroblasts and providing distribution characteristics of fibroblasts in healthy and diseased tissues.
2. Functional Analysis of Fibroblast Subtypes: Identified distinct roles of specific fibroblast subtypes in cancer and inflammation, including immune suppression, immune exclusion, and anti-tumor functions.
3. Interaction Network Between Fibroblasts and Immune Cells: Identified ligand-receptor interactions between fibroblast subtypes and specific immune cells, providing important evidence for further understanding the mechanisms of fibroblast function in the tumor microenvironment.
4. Clinical Prognosis Relevance: The study indicates that the composition of different fibroblast subtypes can significantly affect clinical prognosis, providing a reference for precise stratification and personalized treatment of cancer patients.

Limitations of the Study

Despite creating a detailed human fibroblast atlas, several limitations remain. Firstly, the lack of comprehensive clinical data limits further exploration of the clinical relevance of fibroblast phenotypes. Secondly, the study mainly focused on interactions between fibroblasts and immune cells; future research should further explore interactions between fibroblasts and tumor cells. Additionally, future studies should employ three-dimensional culture techniques and in vivo experiments to further validate the functional characteristics of fibroblast subtypes.

Conclusion

By constructing a cross-organ fibroblast atlas, this study reveals the transcriptional heterogeneity of fibroblasts in healthy and pathological states and their interaction with immune cells, providing a new basis for exploring fibroblast functions in cancer progression and potential targets for therapy.