Promotion of cholangiocarcinoma growth by diverse cancer-associated fibroblast subpopulations

Bile acids produced by gut microbiota activate TGR5 to promote colorectal liver metastasis progression by inducing MDSCs infiltration in liver

BACKGROUND

CRLM (Colorectal liver metastasis), a prevalent form of distant metastasis in colorectal cancer, is a leading cause of mortality in affected patients. Despite advancements in immunotherapy for colorectal cancer, clinical benefits in CRLM patients remain limited. The immunosuppressive liver microenvironment plays a pivotal role in facilitating metastatic colonization and disease progression.

METHODS

We performed fecal metabolomics in ABX (antibiotic-treated) mice and single-cell RNA sequencing on hepatic tissues from four cohorts: CRC (colorectal cancer) , CRLM, LCA-fed CRC, and LCA-fed CRLM mice, to delineate intergroup immune heterogeneity. Cellular and molecular profiling across groups was conducted via Luminex multiplex assays, flow cytometry, and immunofluorescence. Integrated multi-omics analyses elucidated LCA-driven pathways modulating metastatic progression RESULTS: We demonstrated that LCA (lithocholic acid), a gut microbiota-derived metabolite, activates TGR5 in hepatic CAFs (cancer-associated fibroblasts) to upregulate CCL3 secretion. Elevated CCL3 levels subsequently recruit MDSCs (myeloid-derived suppressor cells) into metastatic niches. While MDSCs primarily suppress T-cell activation, we identified a paradoxical role of MDSC-derived CCL2 in attenuating immunosuppression via CCR2 signaling, suggesting a compensatory pro-inflammatory axis within the tumor microenvironment CONCLUSIONS: These findings suggest new immunotherapeutic strategies for the treatment of CRLM.

The fibroinflammatory response in cancer

Fibroinflammation refers to the highly integrated fibrogenic and inflammatory responses mediated by the concerted function of fibroblasts and innate immune cells in response to tissue perturbation. This process underlies the desmoplastic remodelling of the tumour microenvironment and thus plays an important role in tumour initiation, growth and metastasis. More specifically, fibroinflammation alters the biochemical and biomechanical signalling in malignant cells to promote their proliferation and survival and further supports an immunosuppressive microenvironment by polarizing the immune status of tumours. Additionally, the presence of fibroinflammation is often associated with therapeutic resistance. As such, there is increasing interest in targeting this process to normalize the tumour microenvironment and thus enhance the treatment of solid tumours. Herein, we review advances made in unravelling the complexity of cancer-associated fibroinflammation that can inform the rational design of therapies targeting this.

Fufang-Biejia-Ruangan tablet targeting both cancer-associated fibroblasts and tumor cells by HIPPO-PI3K/AKT cascades in intrahepatic cholangiocarcinoma treatment

BACKGROUND

Intrahepatic cholangiocarcinoma (ICC) ranks second among primary liver cancers in terms of prevalence, characterized by poor prognosis and scarce therapeutic interventions. Fufang-Biejia-Ruangan tablet (BJRG), a traditional Chinese herbal remedy, has been widely used for liver diseases. However, its therapeutic efficacy and underlying mechanisms in ICC remain poorly understood.

AIM OF THE STUDY

This study aims to systematically investigate the anti-ICC effects of BJRG, focusing on tumor progression and microenvironment modulation, through experimental and transcriptomic analyses.

METHODS

The chemical composition of BJRG was analyzed employing ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). In vitro assays were performed with QBC939 and LX-2 cell lines. Two primary ICC models (AKT/YAP and sgP53/KRAS) were established via hydrodynamic tail-vein injection of corresponding plasmids. A co-culture system for subcutaneous tumor formation was developed using cancer-associated fibroblasts (CAFs) derived from the AKT/YAP model and primary tumor cells derived from the sgP53/KRAS model.

RESULTS

UPLC-MS analysis identified 1091 chemical components, primarily terpenoids, sugars, glycosides, and phenylpropanoids. The therapeutic efficacy of BJRG was evaluated for the treatment of ICC. BJRG treatment slowed down the growth of both human ICC cell lines and AKT/YAP ICC mouse model. Mechanistically, BJRG inhibited HIPPO-PI3K/AKT signaling pathway in ICC tumor cells. Importantly, BJRG significantly inhibited the growth of CAFs via HIPPO-PI3K/AKT cascades. Of note, co-culture CAFs with ICC cell lines substantially sensitized the efficacy of BJRG in sgP53/KRAS syngeneic tumor model. Furthermore, BJRG therapy not only affected CAFs but also induced alterations in vascular structures and hypoxic conditions within lesions in the AKT/YAP model. This intervention promoted the infiltration of T lymphocytes and macrophages into the tumor microenvironment, which may further augment the anti-proliferative effects of BJRG by enhancing the immune response within ICC tumor tissues.

CONCLUSION

Our research demonstrates BJRG's anti-ICC efficacy via diverse pathways, including the suppression of tumor cell proliferation, regulation of CAFs activity, and promotion of immune cell infiltration. These findings underscore BJRG as a promising therapeutic candidate for ICC, offering novel mechanistic insights and highlighting its potential for clinical translation.

Hepatic iNKT cells facilitate colorectal cancer metastasis by inducing a fibrotic niche in the liver

The liver is an important metastatic organ that contains many innate immune cells, yet little is known about their role in anti-metastatic defense. We investigated how invariant natural killer T (iNKT) cells influence colorectal cancer-derived liver metastasis using different models in immunocompetent mice. We found that hepatic iNKT cells promote metastasis by creating a supportive niche for disseminated cancer cells. Mechanistically, iNKT cells respond to disseminating cancer cells by producing the fibrogenic cytokines interleukin-4 (IL-4) and IL-13 in a T cell receptor-independent manner. Selective abrogation of IL-4 and IL-13 sensing in hepatic stellate cells prevented their transdifferentiation into extracellular matrix-producing myofibroblasts, which hindered metastatic outgrowth of disseminated cancer cells. This study highlights a novel tumor-promoting axis driven by iNKT cells in the initial stages of metastasis.

Palmitic Acid Accumulation Activates Fibroblasts and Promotes Matrix Stiffness in Colorectal Cancer

Obstructions can occur during any stage of colorectal cancer and correspond with poor prognosis. Obstructive colorectal cancer (OCRC) is harder and exhibits increased tumor budding and proliferation of myofibroblasts compared with nonobstructive colorectal cancer, suggesting that the occurrence of obstruction may be related to extracellular matrix (ECM) remodeling. In this study, we found that colorectal cancer and OCRC samples differed substantially in ECM composition, specifically in collagen (newly formed and mature) and proteoglycans (including glycosaminoglycan, hyaluronic acid, and chondroitin sulfate). OCRC also exhibited considerable changes in ECM biomechanics and collagen arrangement. Interestingly, OCRC samples presented a notable increase in matrix cancer-associated fibroblasts (mCAF). The abundance of mCAFs correlated with the accumulation of palmitic acid (PA), and high concentrations of PA increased the secretion of ECM-related proteins by mCAFs. Additionally, PA did not directly affect normal fibroblasts but rather activated the NF-κB pathway in tumor cells to stimulate secretion of CSF1, TGFβ1, and CXCL8, which promoted the activation of normal fibroblasts into mCAFs and exacerbated ECM stiffening. Drug screening with a natural compound library identified vanillylacetone as a potential inhibitor of PA-induced cytokine secretion and ECM stiffening. These findings highlight intratumoral PA accumulation as a key mechanism driving ECM alterations and OCRC progression and suggest that targeting this axis may be useful for treating patients with colorectal cancer with risk of obstruction. Significance: Palmitic acid accumulation activates the NF-κB pathway in colorectal cancer cells to promote cytokine secretion that facilitates the generation of matrix cancer-associated fibroblasts, driving extracellular matrix remodeling and development of obstructions.

Cancer-associated fibroblasts (CAFs) and plaque-associated fibroblasts (PAFs): Unraveling the cellular crossroads of atherosclerosis and cancer

Atherosclerosis is a complex process involving various cells and molecules within the atherosclerotic plaque. Recent evidence suggests that plaque-associated fibroblasts (PAFs), also known as atherosclerosis-associated fibroblasts (AAFs), might play a significant role in the development and progression of the disease. The microenvironment of the atherosclerotic plaque, resembling the tumor microenvironment (TME), includes various cellular populations like plaque-associated macrophages (PAMs), plaque-associated neutrophils (PANs), vascular smooth muscle cells (VSMCs), myeloid-derived suppressor cells (MDSCs), and PAFs. Similar to cancer-associated fibroblasts (CAFs) in tumors, PAFs exhibits a wide range of characteristics and functions. Their interactions with endothelial cells, smooth muscle cells, and other stromal cells, including adventitial fibroblast precursors, significantly influence atherosclerosis progression. Moreover, the ability of PAFs to express various markers such as alpha-SMA, Desmin, VEGF, and GFAP, highlights their diverse origins from different precursor cells, including vascular smooth muscle cells, endothelial cells, glial cells of the enteric nervous system, adventitial fibroblast precursors, as well as resident and circulating fibrocytes. This article explores the molecular interactions between PAFs, cells associated with atherosclerosis, and other stromal cells. It further examines the role of PAFs in the development and progression of atherosclerosis, and compares their features with those of CAFs. The research suggests that studying tumor-associated fibroblasts can help understand fibroblast subpopulations in atherosclerotic plaque. Identifying specific subpopulations could provide new insight into atherosclerosis complexity and lead to the development of innovative drugs for medical intervention.

Comprehensive analysis of SQOR involvement in ferroptosis resistance of pancreatic ductal adenocarcinoma in hypoxic environments

Introduction

Pancreatic ductal adenocarcinoma (PDAC) exhibits higher hypoxia level than most solid tumors, and the presence of intratumoral hypoxia is associated with a poor prognosis. However, the identification of hypoxia levels based on pathological images, and the mechanisms regulating ferroptosis resistance, remain to be elucidated. The objective of this study was to construct a deep learning model to evaluate the hypoxia characteristics of PDAC and to explore the role of Sulfide quinone oxidoreductase (SQOR) in hypoxia-mediated ferroptosis resistance.

Methods

Multi-omics data were integrated to analyze the correlation between hypoxia score of PDAC, SQOR expression and prognosis, and ferroptosis resistance level. A deep learning model of Whole Slide Images (WSIs) were constructed to predict the hypoxia level of patients. In vitro hypoxia cell models, SQOR knockdown experiments and nude mouse xenograft models were used to verify the regulatory function of SQOR on ferroptosis.

Results

PDAC exhibited significantly higher hypoxia levels than normal tissues, correlating with reduced overall survival in patients. In slide level, our deep learning model can effectively identify PDAC hypoxia levels with good performance. SQOR was upregulated in tumor tissues and positively associated with both hypoxia score and ferroptosis resistance. SQOR promotes the malignant progression of PDAC in hypoxic environment by enhancing the resistance of tumor cells to ferroptosis. SQOR knockdown resulted in decreased cell viability, decreased migration ability and increased MDA level under hypoxic Ersatin induced conditions. Furthermore, SQOR inhibitor in combination with ferroptosis inducer has the potential to inhibit tumor growth in vivo in a synergistic manner.

Discussion

This study has established a hypoxia detection model of PDAC based on WSIs, providing a new tool for clinical evaluation. The study revealed a new mechanism of SQOR mediating ferroptosis resistance under hypoxia and provided a basis for targeted therapy.

SCGB3A1-Epi and KLK10-Epi Crosstalk With Fibroblasts Promotes Liver Metastasis of Breast Cancer and Pancreatic Ductal Adenocarcinoma

BACKGROUND

The liver often serves as the principal site for metastatic spread from a variety of solid tumors, and metastasis to the liver markedly diminishes patient survival. Single-cell RNA sequencing (scRNA-seq) has helped uncover the complexity of liver tumor metastasis. However, the key cellular subtypes of breast cancer and pancreatic ductal adenocarcinoma (PDAC) with liver metastasis and their mechanisms of action are unclear, making treatment difficult.

METHODS

We used integrated scRNA-seq data to dissect liver metastasis-specific epithelial cell subtypes in breast cancer and PDAC, and elucidated their mechanisms through functional analyses and intercellular interactions with fibroblasts.

RESULTS

Interestingly, our results show that SCGB3A1-Epi and KLK10-Epi are key drivers of liver metastasis in breast cancer and PDAC, respectively. These subtypes are associated with high malignancy rates and involved in oxidative phosphorylation and other critical pathways. Specific ligand-receptor interactions were observed between these epithelial subtypes and fibroblasts, with significant interactions between CD74-APP receptors in SCGB3A1-Epi and Fib-11 in breast cancer and between SPP1-CD44 receptors in KLK10-Epi and Fib-11 in PDAC. High expression levels of Fib-11 and CD74 were correlated with improved survival in breast cancer, whereas high SPP1 and CD44 expression predicted worse PDAC outcomes. Fib-11 is implicated in signaling pathways associated with tumor metastasis, particularly those involving cell adhesion molecules.

CONCLUSIONS

We revealed the cellular heterogeneity of liver metastasis and provided a crucial research foundation for developing novel therapeutic strategies to specifically target metastatic cell subtypes, thereby enhancing patient prognosis.

The malignant signature gene of cancer-associated fibroblasts serves as a potential prognostic biomarker for colon adenocarcinoma patients

Background

Colon adenocarcinoma (COAD) is the most frequently occurring type of colon cancer. Cancer-associated fibroblasts (CAFs) are pivotal in facilitating tumor growth and metastasis; however, their specific role in COAD is not yet fully understood. This research utilizes single-cell RNA sequencing (scRNA-seq) to identify and validate gene markers linked to the malignancy of CAFs.

Methods

ScRNA-seq data was downloaded from a database and subjected to quality control, dimensionality reduction, clustering, cell annotation, cell communication analysis, and enrichment analysis, specifically focusing on fibroblasts in tumor tissues compared to normal tissues. Fibroblast subsets were isolated, dimensionally reduced, and clustered, then combined with copy number variation (CNV) inference and pseudotime trajectory analysis to identify genes related to malignancy. A Cox regression model was constructed based on these genes, incorporating LASSO analysis, nomogram construction, and validation.Subsequently, we established two FNDC5-knockdown cell lines and utilized colony formation and transwell assays to investigate the impact of FNDC5 on cellular biological behaviors.

Results

Using scRNA-seq data, we analyzed 8,911 cells from normal and tumor samples, identifying six distinct cell types. Cell communication analysis highlighted interactions between these cell types mediated by ligands and receptors. CNV analysis classified CAFs into three groups based on malignancy levels. Pseudo-time analysis identified 622 pseudotime-related genes and generated a forest plot using univariate Cox regression. Lasso regression identified the independent prognostic gene FNDC5, which was visualized in a nomogram. Kaplan-Meier survival analysis confirmed the prognostic value of FNDC5, showing associations with T stage and distant metastasis. In vitro experiment results demonstrated a strong association between FNDC5 expression levels and the proliferative, migratory, and invasive abilities of colon cancer cells.

Conclusion

We developed a risk model for genes related to the malignancy of CAFs and identified FNDC5 as a potential therapeutic target for COAD.

Fibroblast atlas: Shared and specific cell types across tissues

Understanding the heterogeneity of fibroblasts depends on decoding the complexity of cell subtypes, their origin, distribution, and interactions with other cells. Here, we integrated 249,156 fibroblasts from 73 studies across 10 tissues to present a single-cell atlas of fibroblasts. We provided a high-resolution classification of 18 fibroblast subtypes. In particular, we revealed a previously undescribed cell population, TSPAN8+ chromatin remodeling fibroblasts, characterized by high expression of genes with functions related to histone modification and chromatin remodeling. Moreover, TSPAN8+ chromatin remodeling fibroblasts were detectable in spatial transcriptome data and multiplexed immunofluorescence assays. Compared with other fibroblast subtypes, TSPAN8+ chromatin remodeling fibroblasts exhibited higher scores in cell differentiation and resident fibroblast, mainly interacting with endothelial cells and T cells through ligand VEGFA and receptor F2R, and their presence was associated with poor prognosis. Our analyses comprehensively defined the shared and specific characteristics of fibroblast subtypes across tissues and provided a user-friendly data portal, Fibroblast Atlas.

Benign non-immune cells in tumor microenvironment

The tumor microenvironment (TME) is a highly complex and continuous evolving ecosystem, consisting of a diverse array of cellular and non-cellular components. Among these, benign non-immune cells, including cancer-associated fibroblasts (CAFs), adipocytes, endothelial cells (ECs), pericytes (PCs), Schwann cells (SCs) and others, are crucial factors for tumor development. Benign non-immune cells within the TME interact with both tumor cells and immune cells. These interactions contribute to tumor progression through both direct contact and indirect communication. Numerous studies have highlighted the role that benign non-immune cells exert on tumor progression and potential tumor-promoting mechanisms via multiple signaling pathways and factors. However, these benign non-immune cells may play different roles across cancer types. Therefore, it is important to understand the potential roles of benign non-immune cells within the TME based on tumor heterogeneity. A deep understanding allows us to develop novel cancer therapies by targeting these cells. In this review, we will introduce several types of benign non-immune cells that exert on different cancer types according to tumor heterogeneity and their roles in the TME.

Mutant KRAS and CK2 Cooperatively Stimulate SLC16A3 Activity to Drive Intrahepatic Cholangiocarcinoma Progression

Intrahepatic cholangiocarcinoma (iCCA) is a lethal malignancy affecting the liver and biliary system. Enhanced understanding of the pathogenic mechanisms underlying iCCA tumorigenesis and the discovery of appropriate therapeutic targets are imperative to improve patient outcomes. In this study, we investigated the functions and regulations of solute carrier family 16 member 3 (SLC16A3), which has been reported to be a biomarker of poor prognosis in iCCA. High SLC16A3 expression was enriched in KRAS viral oncogene homolog-mutated iCCA tumors, and mutant KRAS elevated SLC16A3 expression via the PI3K-AKT-mTORC1-HIF1α pathway. SLC16A3 not only enhanced glycolysis but also induced epigenetic reprogramming to regulate iCCA progression. Phosphorylation of SLC16A3 at S436 was vital for its oncogenic function and was linked to iCCA progression. Casein kinase 2 (CK2) directly phosphorylated SLC16A3 at S436, and CK2 inhibition with CX-4945 (silmitasertib) reduced the growth of KRAS-mutated iCCA tumor xenografts and patient-derived organoids. Together, this study provides valuable insights into the diverse functions of SLC16A3 in iCCA and comprehensively elucidates the upstream regulatory mechanisms, providing potential therapeutic strategies for patients with iCCA with KRAS mutations. Significance: Characterization of the oncogenic function and regulators of SLC16A3 in intrahepatic cholangiocarcinogenesis revealed the potential of CK2 inhibitors as a promising treatment for KRAS-mutated tumors.

Hepatic stellate cells control liver zonation, size and functions via R-spondin 3

Hepatic stellate cells (HSCs) have a central pathogenetic role in the development of liver fibrosis. However, their fibrosis-independent and homeostatic functions remain poorly understood1-5. Here we demonstrate that genetic depletion of HSCs changes WNT activity and zonation of hepatocytes, leading to marked alterations in liver regeneration, cytochrome P450 metabolism and injury. We identify R-spondin 3 (RSPO3), an HSC-enriched modulator of WNT signalling, as responsible for these hepatocyte-regulatory effects of HSCs. HSC-selective deletion of Rspo3 phenocopies the effects of HSC depletion on hepatocyte gene expression, zonation, liver size, regeneration and cytochrome P450-mediated detoxification, and exacerbates alcohol-associated and metabolic dysfunction-associated steatotic liver disease. RSPO3 expression decreases with HSC activation and is inversely associated with outcomes in patients with alcohol-associated and metabolic dysfunction-associated steatotic liver disease. These protective and hepatocyte-regulating functions of HSCs via RSPO3 resemble the R-spondin-expressing stromal niche in other organs and should be integrated into current therapeutic concepts.

High-Efficiency Cell-Type Proteomics Strategy Deciphers Cholangiocarcinoma Fibrosis-Associated Pathological Heterogeneity

Cholangiocarcinoma (CCA) is the second most common primary liver cancer and is characterized by huge heterogeneity, difficult diagnosis, and poor prognosis. Fibrosis-associated heterogeneity in CCA serves as an indicator of the malignant progression of cancer; however, a precise approach to deciphering fibrosis heterogeneity is still lacking. Typically, the tissue proteome is profiled by analyzing bulk tissues, which gives average results of different cell types, especially for CCA tissues in which cancer cells occupy a very small proportion. Laser microdissection (LMD) can precisely dissect CCA cell clusters, but the required manual, time-consuming annotation limits its efficiency. Herein, we develop π-CellSeg-CCA, a pathological image analysis algorithm based on Mask R-CNN and ResNet-18, to enable automated annotation of CCA and normal bile duct regions for LMD and achieve an enhanced recognition accuracy of ∼90%. Driven by π-CellSeg-CCA, we develop a new strategy by integrating a machine learning algorithm, LMD, simple and integrated spintip-based proteomics technology (SISPROT), and high-sensitivity mass spectrometry to decipher CCA fibrosis-associated pathological heterogeneity. We identify over 8000 proteins, including marker proteins specifically expressed in CCA from only 1 mm2 samples. A protein specifically upregulated in fibrosis CCA, MUC16, is further investigated to reveal its association with worse prognosis and its contribution to the progression of CCA. We expect that the algorithm-assisted cell-type proteomics strategy is promising for studying the tumor microenvironment with limited clinical materials.

Combined Therapy Targeting MET and Pro-HGF Activation Shows Significant Therapeutic Effect Against Liver Metastasis of CRPC

The liver is the most lethal metastatic site in castration-resistant prostate cancer (CRPC). Overexpression of MET protein has been reported in CRPC, and MET is an important driver gene in androgen-independent CRPC cells. Mouse CRPC cell line CRTC2 was established by subcutaneous injection of hormone-sensitive PC cells (TRAMP-C2) in castrated nude mice. CRCT2/luc2 cells were injected into the spleen of castrated nude mice, and liver metastasis was confirmed at 2 weeks post-injection. We administered MET inhibitor (MET-I) and HGF activator inhibitor (HGFA-I) to this liver metastasis model and assessed the therapeutic effect. After intrasplenic injection, CRTC2 showed a higher incidence of liver metastasis whereas no metastasis was observed in TRAMP-C2. Microarray analysis revealed increased expression of HGF, MET, and HPN, HGFAC (encoding HGF activating proteases) in liver metastasis. Proliferation of CRCT2 was significantly inhibited by co-administration of MET-I and HGFA-I by in vitro analysis with HGF-enriched condition. In an analysis of the mouse model, the combination-therapy group showed the strongest reduction for liver metastasis. Immunohistochemical staining also revealed the strongest decrease in phosphorylation of MET in the combination-therapy group. Co-culture with HGF-expressed mouse fibroblasts showed attenuation of the inhibitory effect of MET-I; however, additional HGFA-I overcame the resistance. We established an androgen-independent CRPC cell line, CRTC2, and liver metastasis model in mice. Significant effect was confirmed by combined treatment of MET-I and HGFA-I by in vitro and in vivo analysis. The results suggested the importance of combined treatment with both MET- and HGF-targeting agents in the treatment of HGF-enriched conditions including liver metastasis.

Cancer-Associated Fibroblasts in Intrahepatic Cholangiocarcinoma: Insights into Origins, Heterogeneity, Lymphangiogenesis, and Peritoneal Metastasis

Intrahepatic cholangiocarcinoma (iCCA) denotes a rare, highly malignant, and heterogeneous class of primary liver adenocarcinomas exhibiting phenotypic characteristics of cholangiocyte differentiation. Among the distinctive pathological features of iCCA, one that differentiates the most common macroscopic subtype (eg, mass-forming type) of this hepatic tumor from conventional hepatocellular carcinoma is a prominent desmoplastic reaction manifested as a dense fibro-collagenous-enriched tumor stroma. Cancer-associated fibroblasts (CAFs) represent the most abundant mesenchymal cell type in the desmoplastic reaction. Although the protumor effects of CAFs in iCCA have been increasingly recognized, more recent cell lineage tracing studies, advanced single-cell RNA sequencing, and expanded biomarker analyses have provided new awareness into their ontogeny, as well as underscored their biological complexity as reflected by the presence of multiple subtypes. In addition, evidence supports CAFs' potential to display cancer-restrictive roles, including immunosuppression. However, CAFs also play important roles in facilitating metastasis, as exemplified by lymph node metastasis and peritoneal carcinomatosis, which are common in iCCA. Herein, the authors provide a timely appraisal of the origins and phenotypic and functional complexity of CAFs in iCCA, together with providing mechanistic insights into lymphangiogenesis and peritoneal metastasis relevant to this lethal human cancer.

Genetic, Epigenetic, and Microenvironmental Drivers of Cholangiocarcinoma

Cholangiocarcinoma (CCA) is an aggressive and heterogeneous malignancy of the biliary tree that carries a poor prognosis. Multiple features at the genetic, epigenetic, and microenvironmental levels have been identified to better characterize CCA carcinogenesis. Genetic alterations, such as mutations in IDH1/2, BAP1, ARID1A, and FGFR2, play significant roles in CCA pathogenesis, with variations across different subtypes, races/ethnicities, and causes. Epigenetic dysregulation, characterized by DNA methylation and histone modifications, further contributes to the complexity of CCA, influencing gene expression and tumor behavior. Furthermore, CCA cells exchange autocrine and paracrine signals with other cancer cells and the infiltrating cell types that populate the microenvironment, including cancer-associated fibroblasts and tumor-associated macrophages, further contributing to an immunosuppressive niche that supports tumorigenesis. This review explores the multifaceted genetic, epigenetic, and microenvironmental drivers of CCA. Understanding these diverse mechanisms is essential for characterizing the complex pathways of CCA carcinogenesis and developing targeted therapies to improve patient outcomes.

Single-cell transcriptomics reveals intratumor heterogeneity and the potential roles of cancer stem cells and myCAFs in colorectal cancer liver metastasis and recurrence

Metastasis and recurrence are the primary obstacles to long-term survival in colorectal cancer (CRC) patients. In this study, we employed single-cell RNA sequencing (scRNA-seq) to comprehensively delineate the transcriptomic landscape of primary and liver metastatic CRCs, and revealed novel cellular crosstalk between cancer cell subpopulation and myofibroblastic CAFs (myCAFs) at single-cell resolution. We identified a cancer cell subpopulation termed stem/transient amplifying-like (stem/TA-like) cells, which expressed genes associated with stem cell-like characteristics and metastatic potential. MyCAFs in their microenvironment showed the potential to remodel the extracellular matrix (ECM), regulate angiogenesis, and support a pro-metastatic microenvironment through paracrine signaling involving FN1, BGN, and other ECM components. Notably, we found that they may communicate through the ligand-receptor pairs FN1-CD44 and GDF15-TGFBR2, which may be linked to the liver metastatic process. Additionally, our findings suggest that both stem/TA-like cells and myCAFs could be involved in CRC recurrence following chemotherapy. A unique gene signature generated using the gene expression characteristics of stem/TA-like cells and myCAFs (SM signature) can be used to assess recurrence risk in CRC patients. Collectively, these findings highlight the intratumor heterogeneity and the potential roles of cancer stem cells and myCAFs in CRC liver metastasis and recurrence, providing new targets and insights for the prognostic assessment of CRC patients and the improved selection of effective treatment options.

Single-cell analyses reveal metastasis mechanism and microenvironment remodeling of lymph node in intrahepatic cholangiocarcinoma

Background & Aims

Lymph node metastasis (LNM) is a major determinant of recurrence and prognosis in intrahepatic cholangiocarcinoma (iCCA). LNM disrupts T cell-mediated cytotoxicity, promotes tumor-specific immune tolerance, and facilitates distant metastasis. Despite its importance, extensive research on LMN in iCCA is lacking. This study aimed to systematically explore the heterogeneity of the LNM-associated microenvironment in iCCA by integrating single-cell and multi-omics analyses, identifying metastasis-associated cell subgroups, and validating these findings through multiple cohorts.

Methods

We analyzed single-cell transcriptomics data from primary tumors, cancer-adjacent liver tissues, and tumor-draining lymph nodes of four patients with iCCA who underwent radical surgery. Additionally, we collected 81 tumor and matched lymph node tissue sections from patients with iCCA. We performed single-cell RNA sequencing and multiplex immunohistochemistry, followed by differential gene expression analysis, functional enrichment analysis, single-cell copy number variation assessment, and pseudotime analysis.

Results

Our analysis revealed the complex heterogeneity of the iCCA LNM-associated microenvironment. We found a significant increase in stromal and mature immune cells in the metastatic lymph nodes. T cells constitute the predominant component, with diverse functional subtypes. We identified CD36+ macrophages and SAA1+ tumor cells as key players in the metastatic process. The SAA1-CD36 receptor‒ligand pair may be crucial in forming the LNM-associated microenvironment.

Conclusions

We identified several metastasis-associated cell subgroups. These findings provide new insights into the mechanisms underlying LNM in iCCA and lay the groundwork for the development of novel therapeutic strategies. Our study highlights the importance of single-cell technologies in understanding tumor microenvironment complexity and offers valuable resources for future research.

Impact and implications

The lack of single-cell transcriptome analysis of intrahepatic cholangiocarcinoma (iCCA) lymph node metastases has prevented us from understanding the underlying mechanisms of disease progression. To fill this knowledge gap, we elucidated the unique ecosystem of iCCA lymph node metastases, which is an important advance in clarifying the impact of the immune environment on the development of this disease. The results of this study identified several LNM-related therapeutic targets, which will not only be helpful to basic researchers, but also provide potential diagnostic and treatment ideas for physicians, thereby helping patients and their caregivers develop more personalized treatment plans. This finding is highly important for improving the prognosis of patients with advanced iCCA in the future.

Dickkopf-1 promotes tumor progression of gefitinib- resistant non-small cell lung cancer through cancer cell-fibroblast interactions

BACKGROUND

Cancer cell-secreted proteins play a critical role in tumor progression and chemoresistance by influencing intercellular interactions within the tumor microenvironment. Investigating the intratumoral functions of these secretory proteins may provide insights into understanding and treating chemoresistant cancers. This study aims to identify potential anticancer target(s) in gefitinib-resistant non-small cell lung cancer (NSCLC), with a focus on secretory proteins and their effects on intercellular interactions.

METHODS

Differentially expressed secretory proteins were identified in gefitinib-resistant human NSCLC cell lines (PC9-GR and HCC827-GR), revealing an elevation in Dickkopf-1 (DKK1) expression and secretion. To elucidate the role of DKK1 in gefitinib-resistant cancer, the anticancer effects of a neutralizing antibody against DKK1 were evaluated in tumors comprising either cancer cells alone or cancer cells co-injected with human lung fibroblasts (MRC-5). Following the confirmation of the importance of cancer cell-fibroblast interactions in the protumorigenic activity of DKK1, the fibroblast traits modulated by DKK1 were further analyzed.

RESULTS

Gefitinib-resistant NSCLC cells exhibited increased DKK1 protein expression. Although elevated DKK1 levels were linked to poor prognosis, DKK1 did not directly affect cancer cell proliferation. However, DKK1 blockade showed significant anticancer effects in gefitinib-resistant tumors containing lung fibroblasts, suggesting that DKK1's pro-tumorigenic roles are mediated through cancer cell-fibroblast interactions. DKK1 altered fibroblast characteristics, enhancing inflammatory fibroblast traits while diminishing myofibroblast traits in tumor microenvironment. These DKK1-induced changes were mediated via activation of the c-JUN pathway in fibroblasts. Moreover, DKK1 was identified as a potential anticancer target across various cancer types beyond gefitinib-resistant lung cancer.

CONCLUSIONS

This study clarifies that DKK1 mediates interactions between cancer cells and fibroblasts in gefitinib-resistant lung cancer, contributing to tumor progression. Therefore, we propose DKK1 as a promising anticancer target for the treatment of gefitinib-resistant NSCLC.

Association between cancer-associated fibroblasts and prognosis of neoadjuvant chemoradiotherapy in esophageal squamous cell carcinoma: a bioinformatics analysis based on single-cell RNA sequencing

BACKGROUND

Esophageal squamous cell carcinoma (ESCC) is a prevalent and aggressive subtype of esophageal cancer, posing a significant mortality and economic burden, especially in East and Southeast Asia. Current therapeutic strategies have limitations in improving patient survival, particularly regarding disease progression and resistance. This study aimed to investigate the impact of neoadjuvant chemoradiotherapy (NCRT) on the ESCC microenvironment.

METHODS

We utilized single-cell RNA sequencing to systematically characterize the tumor and cancer-associated fibroblasts (CAFs) subtypes. Marker genes of myofibroblastic CAFs (myCAFs) were employed to establish a prognostic model and verify its application in other datasets. Other experiments were conducted on clinical samples to explore potential ESCC risk-related genes.

RESULTS

Our bioinformatics and statistical analyses revealed an increased proportion of fibroblasts and epithelial cells in NCRT and identified the Ep_c1 subtype associated with a better prognosis. Further results indicated a complex communication network between Ep_c1 and myCAFs. The top 30 marker genes of myCAFs were used to construct a prognostic signature with a significant response to immunotherapy. Finally, experiments identified Complement C1s subcomponent (C1S), Decorin (DCN), and Neuroblastoma suppression of tumorigenicity 1 (NBL1) as potential ESCC risk-related genes.

CONCLUSION

Our findings highlight the dynamic alterations in the post-NCRT ESCC microenvironment and provide a foundation for the development of personalized treatment and immunotherapeutic approaches. Future studies are warranted to further validate these findings and explore their clinical implications.

A Novel 167-Amino Acid Protein Encoded by CircPCSK6 Inhibits Intrahepatic Cholangiocarcinoma Progression via IKBα Ubiquitination

Intrahepatic cholangiocarcinoma (ICC), a formidable challenge in oncology, demands innovative biomarkers and therapeutic targets. This research highlights the importance of the circular RNA (circRNA) circPCSK6 and its peptide derivative circPCSK6-167aa in ICC. CircPCSK6 is significantly downregulated in both ICC patients and mouse primary ICC models, and its lower expression is linked to adverse prognosis, highlighting its pivotal role in ICC pathogenesis. Functionally, this study elucidates the regulatory effect of circPCSK6-167aa on IκBα ubiquitination within the NF-κB pathway, which is mediated by its competitive binding to the E3 ligase RBBP6. This complex interaction leads to reduced activation of the NF-κB pathway, thereby curbing tumor cell proliferation, migration, invasion, stemness, and hepatic-lung metastasis in vivo. This groundbreaking discovery expands the understanding of circRNA-driven tumorigenesis through atypical signaling pathways. Additionally, this investigation identified EIF4A3 as a detrimental regulator of circPCSK6, exacerbating ICC malignancy. Importantly, by leveraging patient-derived xenograft (PDX), organoids, and organoid-derived PDX models, higher levels of circPCSK6-167aa enhance sensitivity to gemcitabine, indicating its potential to improve the effectiveness of chemotherapy. These insights emphasize the therapeutic promise of targeting circPCSK6-167aa, offering vital biological insights and clinical directions for developing cutting-edge therapeutic approaches, thus revealing innovative strategies and targets for future treatments.

Hepatic Stellate Cells Functional Heterogeneity in Liver Cancer

Hepatic stellate cells (HSCs) are the liver's pericytes, and play key roles in liver homeostasis, regeneration, fibrosis, and cancer. Upon injury, HSCs activate and are the main origin of myofibroblasts and cancer-associated fibroblasts (CAFs) in liver fibrosis and cancer. Primary liver cancer has a grim prognosis, ranking as the third leading cause of cancer-related deaths worldwide, with hepatocellular carcinoma (HCC) being the predominant type, followed by intrahepatic cholangiocarcinoma (iCCA). Moreover, the liver hosts 35% of all metastatic lesions. The distinct spatial distribution and functional roles of HSCs across these malignancies represent a significant challenge for universal therapeutic strategies, requiring a nuanced and tailored understanding of their contributions. This review examines the heterogeneous roles of HSCs in liver cancer, focusing on their spatial localization, dynamic interactions within the tumor microenvironment (TME), and emerging therapeutic opportunities, including strategies to modulate their activity, and harness their potential as targets for antifibrotic and antitumor interventions.

Deciphering Colorectal Cancer-Hepatocyte Interactions: A Multiomics Platform for Interrogation of Metabolic Crosstalk in the Liver-Tumor Microenvironment

Metabolic reprogramming is a hallmark of cancer, enabling tumor cells to adapt to and exploit their microenvironment for sustained growth. The liver is a common site of metastasis, but the interactions between tumor cells and hepatocytes remain poorly understood. In the context of liver metastasis, these interactions play a crucial role in promoting tumor survival and progression. This study leverages multiomics coverage of the microenvironment via liquid chromatography and high-resolution, high-mass-accuracy mass spectrometry-based untargeted metabolomics, 13C-stable isotope tracing, and RNA sequencing to uncover the metabolic impact of co-localized primary hepatocytes and a colon adenocarcinoma cell line, SW480, using a 2D co-culture model. Metabolic profiling revealed disrupted Warburg metabolism with an 80% decrease in glucose consumption and 94% decrease in lactate production by hepatocyte-SW480 co-cultures relative to SW480 control cultures. Decreased glucose consumption was coupled with alterations in glutamine and ketone body metabolism, suggesting a possible fuel switch upon co-culturing. Further, integrated multiomics analysis indicates that disruptions in metabolic pathways, including nucleoside biosynthesis, amino acids, and TCA cycle, correlate with altered SW480 transcriptional profiles and highlight the importance of redox homeostasis in tumor adaptation. Finally, these findings were replicated in three-dimensional microtissue organoids. Taken together, these studies support a bioinformatic approach to study metabolic crosstalk and discovery of potential therapeutic targets in preclinical models of the tumor microenvironment.

Antigen-presenting fibroblasts: emerging players in immune modulation and therapeutic targets

Antigen-presenting fibroblasts are a newly recognized subset that challenges the traditional view of these cells as mere structural components. Under pathological or environmental stimuli, fibroblasts acquire antigen-presenting capabilities through the expression of MHC-II molecules and co-stimulatory factors, enabling them to interact with T cells and modulate immune responses. These specialized fibroblasts have been identified across various tissues and diseases, where they play context-dependent roles, either amplifying immune dysregulation or contributing to immune homeostasis. This review synthesizes recent advances in understanding the origins, activation, and functions of antigen-presenting fibroblasts. It highlights their role in promoting pathogenic immune responses and offering therapeutic opportunities through targeted modulation. Advancing our understanding of antigen-presenting fibroblasts holds great promise for developing innovative approaches to immune modulation and therapy across a range of diseases.

Metastatic tumor growth in steatotic liver is promoted by HAS2-mediated fibrotic tumor microenvironment

Steatotic liver enhances liver metastasis of colorectal cancer (CRC), but this process is not fully understood. Steatotic liver induced by a high-fat diet increases cancer-associated fibroblast (CAF) infiltration and collagen and hyaluronic acid (HA) production. We investigated the role of HA synthase 2 (HAS2) in the fibrotic tumor microenvironment in steatotic liver using Has2ΔHSC mice, in which Has2 is deleted from hepatic stellate cells. Has2ΔHSC mice had reduced steatotic liver-associated metastatic tumor growth of MC38 CRC cells, collagen and HA deposition, and CAF and M2 macrophage infiltration. We found that low-molecular weight HA activates Yes-associated protein (YAP) in cancer cells, which then releases connective tissue growth factor to further activate CAFs for HAS2 expression. Single-cell analyses revealed a link between CAF-derived HAS2 and M2 macrophages and CRC cells through CD44; these cells were associated with exhausted CD8+ T cells via programmed death-ligand 1 and programmed cell death protein 1 (PD-1). HA synthesis inhibitors reduced steatotic liver-associated metastasis of CRC, YAP expression, and CAF and M2 macrophage infiltration, and improved response to anti-PD-1 antibody. In conclusion, steatotic liver modulates a fibrotic tumor microenvironment to enhance metastatic cancer activity through a bidirectional regulation between CAFs and metastatic tumors, enhancing the metastatic potential of CRC in the liver.

Advancing biliary tract malignancy treatment: emerging frontiers in cell-based therapies

Biliary tract malignancies, including intrahepatic cholangiocarcinoma, extrahepatic cholangiocarcinoma, and gallbladder cancer, represent a group of aggressive cancers with poor prognosis due to late-stage diagnosis, limited treatment options, and resistance to conventional therapies like chemotherapy and radiotherapy. These challenges emphasize the urgent need for innovative therapeutic approaches. In recent years, cell-based therapies have emerged as a promising avenue, offering potential solutions through immune modulation, genetic engineering, and targeted intervention in the tumor microenvironment. This Mini-review provides an overview of current advancements in cell-based therapies for biliary malignancies, encompassing immune cell-based strategies such as CAR-T cells, NK cells, dendritic cell vaccines, and tumor-infiltrating lymphocytes. We also examine strategies to overcome the immunosuppressive tumor microenvironment and discuss the integration of cell therapies into multimodal treatment regimens. By synthesizing preclinical and clinical findings, this review highlights key insights and future directions, aiming to assist researchers and clinicians in translating these approaches into effective treatments. The transformative potential of cell-based therapies discussed here makes this review a valuable resource for advancing biliary malignancy research and clinical applications.

Single-cell and spatial-resolved profiling reveals cancer-associated fibroblast heterogeneity in colorectal cancer metabolic subtypes

BACKGROUND

Colorectal cancer (CRC) presents significant treatment challenges due to its high heterogeneity and complex intercellular interactions. Further exploration of CRC subtypes and interactions among tumor-specific clusters will facilitate the development of personalized treatment strategies.

METHODS

Single-cell RNA sequencing and bulk RNA sequencing datasets were integrated to determine CRC metabolic subtypes by hierarchical clustering. The analysis was further extended to cellchat, pseudotime, immune infiltration, and clinicopathological relevance to explore the characteristics of secreted frizzled related protein 2 (SFRP2) + cancer-associated fibroblast (CAF) clusters, and validated by spatial transcriptomics (ST), in vivo experiments, and multiple immunohistochemistry (mIHC).

RESULTS

CRC samples were stably classified into three heterogeneous metabolic subtypes, each exhibiting different microenvironment and CAF heterogeneity, particularly in the distribution of SFRP2 + CAF, which was aligned with metabolic activity. SFRP2 + CAF exhibits high extracellular matrix (ECM) activity and is closely involved in cellular communication, not only promoting the malignant progression of cancer cells but also inducing the differentiation of Tregs. Compared to responders of chemotherapy, the proportion of SFRP2 + CAFs is significantly increased in non-responders. Importantly, mIHC and ST analyses confirm that cancer cells with low expression of agmatinase (AGMAT) can recruit SFRP2 + CAFs, and Treg infiltration surrounding SFRP2 + CAFs was observed. AGMAT combined with oxaliplatin showed the best efficacy in vivo, which may be associated with the inhibition of SFRP2 + CAF infiltration.

CONCLUSIONS

Our study identified and described the potential protumor biological properties of SFRP2 + CAFs, and AGMAT may be a valuable target for disrupting their properties.

Functional heterogeneity of fibroblasts in primary tumors and metastases

Cancer-associated fibroblasts (CAFs) are abundant components of the tumor microenvironment (TME) of most solid malignancies and have emerged as key regulators of cancer progression and therapy response. Although recent technological advances have uncovered substantial CAF molecular heterogeneity at the single-cell level, defining functional roles for most described CAF populations remains challenging. With the aim of bridging CAF molecular and functional heterogeneity, this review focuses on recently identified functional interactions of CAF subtypes with malignant cells, immune cells, and other stromal cells in primary tumors and metastases. Dissecting the heterogeneous functional crosstalk of specific CAF populations with other components is starting to uncover candidate combinatorial strategies for therapeutically targeting the TME and cancer progression.

Myeloid cell-derived apCAFs promote HNSCC progression by regulating proportion of CD4+ and CD8+ T cells

It is well-known that cancer-associated fibroblasts (CAFs) are involved in the desmoplastic responses in Head and Neck Squamous Cell Carcinoma (HNSCC). CAFs are pivotal in the tumor microenvironment (TME) molding, and exert a profound influence on tumor development. The origin and roles of CAFs, however, are still unclear in the HNSCC, especially antigen-presenting cancer-associated fibroblasts (apCAFs). Our current study tried to explore the origin, mechanism, and function of the apCAFs in the HNSCC. Data from single-cell transcriptomics elucidated the presence of apCAFs in the HNSCC. Leveraging cell trajectory and Cellchat analysis along with robust lineage-tracing assays revealed that apCAFs were primarily derived from myeloid cells. This transdifferentiation was propelled by the macrophage migration inhibitory factor (MIF), which was secreted by tumor cells and activated the JAK/STAT3 signaling pathway. Analysis of the TCGA database has revealed that markers of apCAFs were inversely correlated with survival rates in patients with HNSCC. In vivo experiments have demonstrated that apCAFs could facilitate tumor progression. Furthermore, apCAFs could modulate ratio of CD4+ T cells/CD8+ T cells, such as higher ratio of CD4+ T cells/CD8+ T cells could promote tumor progression. Most importantly, data from in vivo assays revealed that inhibitors of MIF and p-STAT3 could significantly inhibit the OSCC growth. Therefore, our findings show potential innovative therapeutic approaches for the HNSCC.Significance: ApCAFs derived from myeloid cells promote the progression of HNSCC by increasing the ratio of CD4+/CD8+ cells, indicating potential novel targets to be used to treat the human HNSCC.

The Immune-Genomics of Cholangiocarcinoma: A Biological Footprint to Develop Novel Immunotherapies

Cholangiocarcinoma (CCA) represents approximately 3% of all gastrointestinal cancers and is a highly heterogeneous and aggressive malignancy originating from the epithelial cells of the biliary tree. CCA is classified by anatomical location into intrahepatic (iCCA), extrahepatic (eCCA), gallbladder cancer (GBC), and ampullary cancers. Although considered a rare tumor, CCA incidence has risen globally, particularly due to the increased diagnosis of iCCA. Genomic and immune profiling studies have revealed significant heterogeneity within CCA, leading to the identification of molecular subtypes and actionable genetic alterations in 40-60% of cases, particularly in iCCA. Among these, FGFR2 rearrangements or fusions (7-15%) and IDH1 mutations (10-20%) are common in iCCA, while HER2 amplifications/overexpression are more frequent in eCCA and GBC. The tumor-immune microenvironment (TIME) of CCAs plays an active role in the pathogenesis and progression of the disease, creating a complex and plastic environment dominated by immune-suppressive populations. Among these, cancer-associated fibroblasts (CAFs) are a key component of the TIME and are associated with worse survival due to their role in maintaining a poorly immunogenic landscape through the deposition of stiff extracellular matrix and release of pro-tumor soluble factors. Improved understanding of CCA tumor biology has driven the development of novel treatments. Combination therapies of cisplatin and gemcitabine with immune checkpoint inhibitors (ICIs) have replaced the decade-long standard doublet chemotherapy, becoming the new standard of care in patients with advanced CCA. However, the survival improvements remain modest prompting research into more effective ways to target the TIME of CCAs. As key mechanisms of immune evasion in CCA are uncovered, novel immune molecules emerge as potential therapeutic targets. Current studies are exploring strategies targeting multiple immune checkpoints, angiogenesis, and tumor-specific antigens that contribute to immune escape. Additionally, the success of ICIs in advanced CCA has led to interest in their application in earlier stages of the disease, such as in adjuvant and neoadjuvant settings. This review offers a comprehensive overview of the immune biology of CCAs and examines how this knowledge has guided clinical drug development, with a focus on both approved and emergent treatment strategies.

Cancer-associated fibroblasts as therapeutic targets for cancer: advances, challenges, and future prospects

Research into cancer treatment has been mainly focused on developing therapies to directly target cancer cells. Over the past decade, extensive studies have revealed critical roles of the tumour microenvironment (TME) in cancer initiation, progression, and drug resistance. Notably, cancer-associated fibroblasts (CAFs) have emerged as one of the primary contributors in shaping TME, creating a favourable environment for cancer development. Many preclinical studies have identified promising targets on CAFs, demonstrating remarkable efficacy of some CAF-targeted treatments in preclinical models. Encouraged by these compelling findings, therapeutic strategies have now advanced into clinical evaluation. We aim to provide a comprehensive review of relevant subjects on CAFs, including CAF-related markers and targets, their multifaceted roles, and current landscape of ongoing clinical trials. This knowledge can guide future research on CAFs and advocate for clinical investigations targeting CAFs.

Hepatic stellate cell single cell atlas reveals a highly similar activation process across liver disease aetiologies

Background & Aims

The progression of chronic liver disease (CLD) is characterized by excessive extracellular matrix deposition, disrupting hepatic architecture and function. Upon liver injury, hepatic stellate cells (HSCs) differentiate towards myofibroblasts and become inflammatory, proliferative and fibrogenic. To date, it is still unclear whether HSC activation is driven by similar mechanisms in different aetiologies.

Methods

HSCs from multiple publicly available single-cell RNA-sequencing datasets were annotated and merged into a single-cell HSC activation atlas. Spheroid co-cultures of primary mouse hepatocytes/HSCs (n = 5) and ELISAs on patient plasma samples (n = 80) were performed to validate the mechanistic insight obtained from the HSC atlas.

Results

We established an HSC activation atlas in which HSCs are clearly divided into three distinct transcriptomic profiles: quiescent HSCs, initiatory HSCs and myofibroblasts. These transcriptomic profiles are present in each of the investigated mouse liver injury models as well as in human CLDs, indicating that HSC activation is a conserved process. This activation process is driven by a core set of transcription factors independent of liver injury or species. Furthermore, we reveal novel ligands associated with activation of HSCs in multiple liver injury models and validate the profibrotic effect of parathyroid hormone. Finally, we identify COLEC10 as a conserved marker for quiescent HSCs and a biomarker of liver fibrosis in patients with different CLDs (p <0.0001).

Conclusions

We reveal unexpected similarities in the regulatory mechanisms of HSCs across diverse liver injury settings and species. The HSC activation atlas has the potential to provide novel insights into liver fibrosis and steer novel treatment options.

Impact and implications

This study establishes a single-cell atlas of hepatic stellate cells across various liver injuries, highlighting a conserved activation process between different injuries and across species. The discovery of novel activating ligands and the biomarker COLEC10 in human plasma could be used to enhance diagnostic and therapeutic strategies. Additionally, the conserved activation process supports the use of any mouse model for mechanistic studies and testing of new anti-fibrotic compounds, streamlining preclinical research efforts.

Multi-omics analysis unveils the role of inflammatory cancer-associated fibroblasts in chordoma progression

Cancer-associated fibroblasts (CAFs) constitute the primary cellular component of the stroma in chordomas, characterized by an abundance of mucinous stromal elements, potentially facilitating their initiation and progression; however, this inference has yet to be fully confirmed. In this study, single-cell RNA sequencing (scRNA-seq), spatial transcriptomics (ST), bulk RNA-seq, multiplexed quantitative immunofluorescence (QIF), and in vivo and in vitro experiments were performed to determine the heterogeneity, spatial distribution, and clinical significance of CAFs in chordoma. ScRNA-seq was performed on 87,693 single cells derived from seven tumor samples and four control nucleus pulposus samples. A distinct CAF cluster distinguished by the upregulated expression of inflammatory genes and enriched functionality in activating inflammation-associated cells was identified. Pseudotime trajectory and cell communication analyses suggested that this inflammatory CAF (iCAF) subset originated from normal fibroblasts and interacted extensively with tumors and various other cell types. By integrating the scRNA-seq results with ST, the presence of iCAF in chordoma tissue was further confirmed, indicating their positioning at a distance from the tumor cells. Bulk RNA-seq data analysis from 126 patients revealed a correlation between iCAF signature scores, chordoma invasiveness, and poor prognosis. QIF validation involving an additional 116 patients found that although iCAFs were not in close proximity to tumor cells compared with other CAF subsets, their density correlated with malignant tumor phenotypes and adverse outcomes. In vivo and in vitro experiments further confirmed that iCAFs accelerate the malignant progression of chordomas. These findings could provide insights into the development of novel therapeutic strategies. © 2024 The Pathological Society of Great Britain and Ireland.

The Immune Landscape and Its Potential for Immunotherapy in Advanced Biliary Tract Cancer

Biliary tract cancers (BTC) are a highly heterogeneous group of cancers at the genomic, epigenetic and molecular levels. The vast majority of patients initially present at an advanced (unresectable) disease stage due to a lack of symptoms and an aggressive tumour biology. Chemotherapy has been the mainstay of treatment in patients with advanced BTC but the survival outcomes and prognosis remain poor. The addition of immune checkpoint inhibitors (ICI) to chemotherapy have shown only a marginal benefit over chemotherapy alone due to the complex tumour immune microenvironment of these cancers. This review appraises our current understanding of the immune landscape of advanced BTC, including emerging transcriptome-based classifications, highlighting the mechanisms of immune evasion and resistance to ICI and their therapeutic implications. It describes the shifting treatment paradigm from traditional chemotherapy to immunotherapy combinations as well as the potential biomarkers for predicting response to ICI.

C3+ cancer-associated fibroblasts promote tumor growth and therapeutic resistance in gastric cancer via activation of the NF-κB signaling pathway

BACKGROUND

Gastric cancer (GC) remains one of the most lethal malignancies globally, with limited therapeutic options. Cancer-associated fibroblasts (CAFs), a diverse population of stromal cells within the tumor microenvironment (TME), play a central role in tumor progression and therapeutic resistance. However, the specific markers identifying tumor-promoting CAF subsets in GC have yet to be fully characterized.

METHODS

Through animal studies and RNA sequencing, complement C3 (C3) emerged as a key marker linked to tumor-promoting CAF subsets. Single-cell sequencing and multiplex immunofluorescence staining confirmed that C3 expression is predominantly localized within CAFs. Independent cohort analyses demonstrated a strong association between elevated levels of C3+ CAFs and poor clinical outcomes in GC patients. To further investigate, small interfering RNA (siRNA)-mediated knockdown of C3 in CAFs was employed in vitro, with subsequent experiments, including cell migration assays, cell viability assays, and immunofluorescence, revealing significant functional impacts.

RESULTS

C3 secreted by CAFs promoted Epithelial-mesenchymal transition (EMT) and accelerated cancer cell migration. Patients with minimal C3+ CAF infiltration exhibited a higher probability of deriving therapeutic benefit from adjuvant treatments. Furthermore, C3+ CAFs were associated with immunosuppressive effects and an immune-evasive microenvironment marked by CD8 + T cell dysfunction. A lower prevalence of C3+ CAFs correlated with improved responsiveness to immunotherapy in GC patients. Enrichment analysis highlighted pronounced activation of the NF-κB signaling pathway in C3+ CAFs relative to their C3- counterparts, supported by elevated phosphorylation levels of IKK, IκBα, and p65 in C3+ CAFs compared to both C3- CAFs and normal fibroblasts (NFs). Silencing p65 nuclear translocation in CAFs through siRNA significantly suppressed C3 secretion.

CONCLUSIONS

The study suggests that NF-κB pathway-mediated CAF activation enhances C3 secretion, driving EMT, migration, chemoresistance, and immune evasion in GC progression. Targeting the NF-κB/C3 signaling axis in CAFs may offer a viable therapeutic strategy for GC management.

New Relevant Evidence in Cholangiocarcinoma Biology and Characterization

Among solid tumors, cholangiocarcinoma (CCA) emerges as one of the most difficult to eradicate. The silent and asymptomatic nature of this tumor, particularly in its early stages, as well as the high heterogeneity at genomic, epigenetic, and molecular levels delay the diagnosis, significantly compromising the efficacy of current therapeutic options and thus contributing to a dismal prognosis. Extensive research has been conducted on the molecular pathobiology of CCA, and recent advances have been made in the classification and characterization of new molecular targets. Both targeted therapy and immunotherapy have emerged as effective and safe strategies for various types of cancers, demonstrating potential benefits in advanced CCA. Furthermore, the deeper comprehension of the cellular and molecular components in the tumor microenvironment (TME) has opened up possibilities for new innovative treatment methods. This review discusses recent evidence in the characterization and molecular biology of CCA, highlighting novel possible druggable targets.

Unraveling the role of cancer-associated fibroblasts in colorectal cancer

Within the intricate milieu of colorectal cancer (CRC) tissues, cancer-associated fibroblasts (CAFs) act as pivotal orchestrators, wielding considerable influence over tumor progression. This review endeavors to dissect the multifaceted functions of CAFs within the realm of CRC, thereby highlighting their indispensability in fostering CRC malignant microenvironment and indicating the development of CAFs-targeted therapeutic interventions. Through a comprehensive synthesis of current knowledge, this review delineates insights into CAFs-mediated modulation of cancer cell proliferation, invasiveness, immune evasion, and neovascularization, elucidating the intricate web of interactions that sustain the pro-tumor metabolism and secretion of multiple factors. Additionally, recognizing the high level of heterogeneity within CAFs is crucial, as they encompass a range of subtypes, including myofibroblastic CAFs, inflammatory CAFs, antigen-presenting CAFs, and vessel-associated CAFs. Innovatively, the symbiotic relationship between CAFs and the intestinal microbiota is explored, shedding light on a novel dimension of CRC pathogenesis. Despite remarkable progress, the orchestrated dynamic functions of CAFs remain incompletely deciphered, underscoring the need for continued research endeavors for therapeutic advancements in CRC management.

Dynamics of liver cancer cellular taxa revealed through single-cell RNA sequencing: Advances and challenges

Liver cancer is a leading cause of death worldwide, representing a substantial public health challenge. The advent of single-cell RNA sequencing has significantly advanced our understanding of cellular dynamics from the onset of liver cancer to therapeutic intervention. This technology has unveiled profound insights into cancer heterogeneity and the tumor microenvironment (TME), enabling the identification of key molecular drivers and phenotypic landscapes of liver cancer at a single-cell resolution. This review highlights recent advancements in mapping functional cell subsets, phenotypic alterations, and the diversity of the TME. These insights are pivotal for advancing targeted therapies and developing prognostic tools. Moreover, this review covers the ongoing challenges and advances from tumor initiation to progression, offering a detailed perspective on advancing personalized treatment.

The histological growth patterns in liver metastases from colorectal cancer display differences in lymphoid, myeloid, and mesenchymal cells

Colorectal liver metastases grow following different histologic growth patterns (HGPs), classified as desmoplastic and nondesmoplastic (dHGP, non-dHGP), being the latter associated with worst prognosis. This study aimed to investigate the tumor microenvironment (TME) between HGPs supporting different survival. Multiplexed immunohistochemical staining was performed with the Opal7 system in a 100-patients cohort to evaluate the tumor-liver interface with three different cell panels: lymphoid, myeloid, and carcinoma-associated fibroblasts. Differences between HGPs were assessed by Mann-Whitney U test with Pratt correction and Holm-Bonferroni multitest adjustment. Cytotoxic T-cells were more abundant in tumoral areas of dHGP, while non-dHGP had higher macrophages infiltration, Th2, CD163+, and Calprotectin+ cells as well as higher pSMAD2 expression. Regarding carcinoma-associated fibroblasts, several subsets expressing COL1A1 were enriched in dHGP, while αSMAlow_single cells were present at higher densities in non-dHGP. Interestingly, Calprotectin+ cells confer better prognoses in non-dHGP, identifying a subgroup of good outcome patients that unexpectedly also show an enrichment in other myeloid cells. In summary, our results illustrate different TME landscapes with respect to HGPs. dHGP presents a higher degree of immunocompetence, higher amounts of Collagen 1 as well as lesser presence of myeloid cell populations, features that might be influencing on the better prognosis of encapsulated metastases.

Single-cell multi-omics in the study of digestive system cancers

Digestive system cancers are prevalent diseases with a high mortality rate, posing a significant threat to public health and economic burden. The diagnosis and treatment of digestive system cancer confront conventional cancer problems, such as tumor heterogeneity and drug resistance. Single-cell sequencing (SCS) emerged at times required and has developed from single-cell RNA-seq (scRNA-seq) to the single-cell multi-omics era represented by single-cell spatial transcriptomics (ST). This article comprehensively reviews the advances of single-cell omics technology in the study of digestive system tumors. While analyzing and summarizing the research cases, vital details on the sequencing platform, sample information, sampling method, and key findings are provided. Meanwhile, we summarize the commonly used SCS platforms and their features, as well as the advantages of multi-omics technologies in combination. Finally, the development trends and prospects of the application of single-cell multi-omics technology in digestive system cancer research are prospected.

Immunogenic cell death-related cancer-associated fibroblast clusters and prognostic risk model in cervical cancer

Cervical cancer (CC) remains a leading cause of female cancer mortality globally. Immunogenic cell death (ICD) influences the tumor microenvironment (TME) and adaptive immune responses. Cancer-associated fibroblasts (CAFs) within the TME suppress anti-tumor immunity and contribute to CC progression. This study identified three ICD-related CAF clusters linked to patient survival, including IL6+CAF and ILR1+CAF, which were associated with clinical outcomes. Using a nine-gene risk model, patients were stratified into risk groups, with high-risk individuals showing worse survival and correlations with pathways such as hypoxia and TGFβ. The model also predicted immunotherapy responses, highlighting immune infiltration differences across risk groups. These findings provide insights into the role of CAF clusters in CC and present a risk model that supports prognosis prediction and personalized therapy.

The role of mesenchymal cells in cholangiocarcinoma

The tumour microenvironment (TME) significantly influences tumour formation and progression through dynamic interactions. Cholangiocarcinoma (CCA), a highly desmoplastic tumour, lacks early diagnostic biomarkers and has limited effective treatments owing to incomplete understanding of its molecular pathogenesis. Investigating the role of the TME in CCA progression could lead to better therapies. RNA sequencing was performed on seven CCA patient-derived xenografts (PDXs) and their corresponding patient samples. Differential expression analysis was conducted, and Qiagen Ingenuity Pathway Analysis was used to predict dysregulated pathways and upstream regulators. PDX- and cell line-derived spheroids, with and without immortalised mesenchymal stem cells, were grown and analysed for morphology, growth and viability. Histological analysis confirmed biliary phenotypes. RNA sequencing indicated upregulation of extracellular matrix-receptor interaction and PI3K-AKT pathways in the presence of mesenchymal cells, with several genes linked to poor survival. Mesenchymal cells restored the activity of inhibited cancer-associated kinases. Thus, adding mesenchymal cells to CCA spheroid models restored key paracrine signalling pathways lost in PDXs, enhancing tumour growth and viability. These findings highlight the importance of including stromal components in cancer models to improve pre-clinical studies.

Clinical significances of liver fibrotic markers in patients with cholangiocarcinoma after radical resections

Objectives

We examined the relation between several fibrotic markers reflecting liver parenchymal injury and conventional liver function or surgical outcomes in 67 patients with cholangiocarcinoma who underwent biliary drainage for obstructive jaundice followed by surgical resection.

Material and Methods

We examined conventional clinicopathological factors, six hepatic fibrosis parameters, including platelet count, hyaluronic acid, Mac-2 binding protein glycosylation isomer (M2BPGi), type IV collagen 7S, aspartate aminotransferase-to-platelet ratio index (APRI), and FIB-4 index before hepatectomy, and surgical outcomes or long-term prognosis.

Results

Obstructive jaundice was observed in 57% of the patients, a history of biliary diseases in 7.5%, and chronic hepatic injuries in 17.9%. M2BPGi was significantly higher in patients with obstructive jaundice as the primary sign (p <0.05), the FIB-4 index was significantly correlated with patient age (p <0.01), and serum hyaluronic acid and T4C7 levels were significantly increased in distal cholangiocarcinoma (CC). No markers were associated with the histological hepatic fibrotic index, tumor-related factors, or postoperative morbidities. Tumor relapse was observed in 37% of patients, and cancer-related death was observed in 25%. A higher FIB-4 index was significantly associated with shorter cancer-free survival (p <0.05). Cox multivariate analysis showed that bilirubin levels, poor histological cancer differentiation, and absence of fibrotic markers were associated with cancer-free, cancer-specific overall, and overall survival.

Conclusion

Although a sufficient relation exists between these markers and elastographic or histological fibrotic indexes, the clinical significance of measuring conventional fibrotic markers might no longer be necessary in future studies.

Exosomal linc00152 intensifies the crosstalk between cholangiocarcinoma cells and cancer-associated fibroblasts

INTRODUCTION AND OBJECTIVES

Cholangiocarcinoma is a highly lethal carcinoma. Exosomes derived from cancer-associated fibroblasts (CAFs) serve key roles in the crosstalk between CAFs and cancer cells. Exploring the roles of CAF-derived exosomes and the mechanisms contribute to a better understanding of the development of cholangiocarcinoma.

MATERIALS AND METHODS

Carcinoma and para-carcinoma tissues were collected from patients. Exosomes were isolated from CAFs and characterized by transmission electron microscopy, dynamic light scattering and western blot. Cholangiocarcinoma cells were cocultured with CAF-derived exosomes, and its proliferation, migration and invasion were evaluated with CCK-8, EdU incorporation and transwell assays, respectively. The interaction between a long non-coding RNA linc00152 and an RNA-binding protein hnRNPA2B1 was determined with RNA immunoprecipitation and RNA pull-down. The ubiquitination of hnRNPA2B1 was examined with western blot.

RESULTS

Linc00152 was highly expressed in cholangiocarcinoma tissues and cells, and its increased expression was associated with advanced tumor stage and poor prognosis. Linc00152 was highly enriched in CAFs and CAF-derived exosomes. CAF-derived exosomes promoted cholangiocarcinoma cell proliferation, migration, and invasion by delivering linc00152. Further analysis showed that hnRNPA2B1 recruited linc00152 and enhanced its loading into exosomes. The interaction between hnRNPA2B1 and linc00152 was identified, and linc00152 repressed the proteasome-dependent degradation of hnRNPA2B1 in cholangiocarcinoma cells. The oncogenic activities of linc00152 in cholangiocarcinoma cells were dependent on hnRNPA2B1 upregulation.

CONCLUSIONS

CAF-derived exosomes harboring linc00152 enhance malignancy in cholangiocarcinoma, identifying a novel role of exosomal linc00152 for intensifying the crosstalk between CAFs and cholangiocarcinoma cells.

Single-cell analysis defines LGALS1+ fibroblasts that promote proliferation and migration of intrahepatic cholangiocarcinoma

The incidence rate of intrahepatic cholangiocarcinoma (ICC), which has a poor prognosis, is rapidly increasing. To investigate the intratumor heterogeneity in ICC, we analyzed single-cell RNA sequencing data from the primary tumor and adjacent normal tissues of 14 treatment-naïve patients. We identified 10 major cell types, along with 45 subclusters of cells. Notably, we identified a fibroblast cluster, Fibroblast_LUM+, which was preferably enriched in tumor tissues and actively interacted with cholangiocytes. LGALS1 was verified as a marker gene of Fibroblast_LUM+, contributing to the malignant phenotype of ICC. Higher amount of LGALS1+ fibroblasts was associated with poorer overall survival of ICC patients. Mechanistically, LGALS1+ fibroblasts activated the proliferation and migration of tumor cells by upregulating the expression levels of CCR2, ADAM15, and β-integrin. Silencing LGALS1 in cancer-associated fibroblasts (CAFs) suppressed CAF-augmented tumor cell migration and invasion in vitro as well as tumor formation in vivo, suggesting that blockade of LGALS1 serves as a potential therapeutic approach for ICC. Taken together, our single-cell analysis provides insight into the interaction between malignant cells and specific subtypes of fibroblasts, which contributes to better understanding of the intratumor heterogeneity in ICC and the development of novel strategies for the treatment of ICC by targeting fibroblasts in the tumor microenvironment.

Preexisting senescent fibroblasts in the aged bladder create a tumor-permissive niche through CXCL12 secretion

Aging is a major risk factor for cancer, but the precise mechanism by which aging promotes carcinogenesis remains largely unknown. Here, using genetically modified mouse models, we show that p16high senescent (p16h-sn) fibroblasts accumulate with age, constitute inflammatory cancer-associated fibroblasts (CAFs) and promote tumor growth in bladder cancer models. Single-cell RNA sequencing of fibroblasts from aged mice revealed higher expression of the C-X-C motif chemokine 12 gene (Cxcl12) in p16h-sn fibroblasts than in p16low fibroblasts. Elimination of p16h-sn cells or inhibition of CXCL12 signaling notebly suppressed bladder tumor growth in vivo. We identified high expression levels of SMOC2, GUCY1A1 (GUCY1A3), CXCL12, CRISPLD2, GAS1 and LUM as a signature of p16h-sn CAFs in humans and mice, which was associated with age and poor prognosis in patients with advanced and nonadvanced bladder cancer. Here we show that p16h-sn fibroblasts in the aged bladder create a cancer-permissive niche and promote tumor growth by secreting CXCL12.

Feedback loop LINC00511-YTHDF2-SOX2 regulatory network drives cholangiocarcinoma progression and stemness

Cholangiocarcinoma (CCA) was identified as a malignant tumor with rising incidence and mortality rates, and the roles of long noncoding RNA (lncRNA) in CCA remained not entirely clear. In this study, LINC00511 had high expression in CCA, which was closely related to poor prognosis. Knockdown of LINC00511 significantly inhibited cell malignant biological behaviors. It also affected the stemness of CCA, evidenced by decreased SOX2 protein expression. Moreover, the study revealed the interaction of LINC00511, YTHDF2, and SOX2 in CCA. Specifically, LINC00511 facilitated the formation of a complex with YTHDF2 on SOX2 mRNA, which uniquely enhances the mRNA's stability through m6A methylation sites. This stabilization appears crucial for maintaining malignant behaviors in CCA cells. Additionally, LINC00511 modulated SOX2 expression via the PI3K/AKT signaling pathway. Meanwhile, SOX2 can also promote LINC00511 expression as an upstream transcription factor, thereby confirming a positive feedback loop formed by LINC00511, YTHDF2, and SOX2, which plays a significant role in the occurrence and development of CCA. Finally, the study successfully constructed two patient-derived xenograft models, revealing the vital role of LINC00511 in CCA development. In summary, this research provides a comprehensive understanding of the role of LINC00511 in the pathogenesis of CCA.

Tryptophan 2,3-dioxygenase-positive matrix fibroblasts fuel breast cancer lung metastasis via kynurenine-mediated ferroptosis resistance of metastatic cells and T cell dysfunction

BACKGROUND

Tumor metastasis is a major threat to cancer patient survival. The organ-specific niche plays a pivotal role in tumor organotropic metastasis. Fibroblasts serve as a vital component of the metastatic microenvironment, but how heterogeneous metastasis-associated fibroblasts (MAFs) promote organotropic metastasis is poorly characterized. Here, we aimed to decipher the heterogeneity of MAFs and elucidate the distinct roles of these fibroblasts in pulmonary metastasis formation in breast cancer.

METHODS

Mouse models of breast cancer pulmonary metastasis were established using an in vivo selection method of repeated injections of metastatic cells purified from the mouse lung. Single-cell RNA-sequencing (scRNA-seq) was employed to investigate the heterogeneity of MAFs. Transgenic mice were used to examine the contribution of tryptophan 2,3-dioxygenase-positive matrix fibroblasts (TDO2+ MFs) in lung metastasis.

RESULTS

We uncovered 3 subtypes of MAFs in the lung metastatic microenvironment, and their transcriptome profiles changed dynamically as lung metastasis evolved. As the predominant subtype, MFs were exclusively marked by platelet-derived growth factor receptor alpha (PDGFRA) and mainly located on the edge of the metastasis, and T cells were enriched around MFs. Notably, high MF signatures were significantly associated with poor survival in breast cancer patients. Lung metastases were markedly diminished, and the suppression of T cells was dramatically attenuated in MF-depleted experimental metastatic mouse models. We found that TDO2+ MFs controlled pulmonary metastasis by producing kynurenine (KYN), which upregulated ferritin heavy chain 1 (FTH1) level in disseminated tumor cells (DTCs), enabling DTCs to resist ferroptosis. Moreover, TDO2+ MF-secreted chemokines C-C motif chemokine ligand 8 (CCL8) and C-C motif chemokine ligand 11 (CCL11) recruited T cells. TDO2+ MF-derived KYN induced T cell dysfunction. Conditional knockout of Tdo2 in MFs diminished lung metastasis and enhanced immune activation.

CONCLUSIONS

Our study reveals crucial roles of TDO2+ MFs in promoting lung metastasis and DTCs' immune evasion in the metastatic niche. It suggests that targeting the metabolism of lung-specific stromal cells may be an effective treatment strategy for breast cancer patients with lung metastasis.