Single-cell transcriptomic architecture and intercellular crosstalk of human intrahepatic cholangiocarcinoma

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.

Tumor-colonizing Pseudoalteromonas elyakovii metabolically reprograms the tumor microenvironment and promotes breast ductal carcinoma

The correlation between the microbiota found in tumors and tumor development is being progressively understood, specifically regarding its involvement in the initiation and advancement of tumors. We examined a total of 102 samples, examining the microbial composition at the species level in each person unveiled significant variations in both the microbial makeup and tumor proportions among individuals, examining the fluctuating alterations in the microbial profile during breast cancer advancement and progression. The levels of expression for Pseudoalteromonas elyakovii were notably elevated in the tumor groups when compared to the para-cancer normal group, aligning with the results obtained from qRT-PCR analysis. The relationship between tumor immunity and microorganisms within the tumor was investigated using double immunofluorescence staining combined with SweAMI probe in situ hybridization and scRNA-seq, allowing for an in-depth analysis of intratumoral microorganisms. Experiments have demonstrated that the supernatant derived from P. elyakovii displayed a significant ability to promote tumor growth and stimulation. In summary, we describe the characteristics of the intratumoral microbiota and the tumor-promoting effects of P. elyakovii supernatant within a small dose range in ductal carcinoma of the breast and characterize the potential clinical application value of intratumoural microorganisms in the progression of cancer and immunotherapy.

IMPORTANCE

Despite the existing studies, the specific microbial factors that influence the occurrence and progression of breast cancer still remain unclear. Researchers have clarified the distinctive microbial profile related to ductal carcinoma, a common histological type of breast cancer, in order to identify tumor-specific microbes and their roles in tumorigenesis. With the tumor microbiome as the focus, the enrichment of Pseudoalteromonas elyakovii features accelerates the disease progression in patients with ductal carcinoma of the breast. This study reveals the initial role relationship and innovative findings between Pseudoalteromonas elyakovii and ductal carcinoma in the breast.

Integrated transcriptomics profile reveals the role of Gal-1 and miR-21 in intrahepatic cholangiocarcinoma progression

Intrahepatic cholangiocarcinoma (ICC) is a highly invasive liver tumor with a poor prognosis, arises from the intrahepatic bile ducts. It is the second most common type of liver cancer. Understanding the mechanisms driving ICC progression is crucial for identification of biomarkers and therapeutic targets. Galectin-1 (Gal-1), encoded by the LGALS1 gene, is known to be upregulated in various malignancies and plays a significant role in cancer progression. However, its underlying mechanisms in ICC have yet to be fully elucidated. The study employed RNA-seq analysis, western blot, cell migration, colony forming, EdU assay, qRT-PCR, luciferase assay and mIHC to investigate the expression pattern of Gal-1 in ICC and its role in the progression of the disease. Our findings revealed a significant upregulation of Gal-1 in ICC tissues. Notably, downregulation of Gal-1inhibited ICC cell proliferation and migration. Further, Gal-1 appears to promote ICC progression through miR-21/STAT3-related pathways, playing a critical role to the tumor microenvironment. These results suggest that Gal-1 may serve as a promising molecular diagnostic marker and therapeutic target for ICC.

Dissecting the Spatial and Single-Cell Transcriptomic Architecture of Cancer Stem Cell Niche Driving Tumor Progression in Gastric Cancer

Despite significant advancements in identifying novel therapeutic targets and compounds, cancer stem cells (CSCs) remain pivotal in driving therapeutic resistance and tumor progression in gastric cancer (GC). High-resolution knowledge of the transcriptional programs underlying the role of CSC niche in driving tumor stemness and progression is still lacking. Herein, spatial and single-cell RNA sequencing of 32 human gastric mucosa tissues at various stages of malignancy, illuminating the phenotypic plasticity of tumor epithelium and transcriptional trajectory from mature gastric chief cells to the CSC state, which is associated with activation of EGFR and WNT signaling pathways, is conducted. Moreover, the CSCs interact with not only the immunosuppressive CXCL13+ T cells and CCL18+ M2 macrophages to evade immune surveillance, but also the inflammatory cancer-associated fibroblasts (iCAFs) to promote tumorigenesis and maintain stemness, which construct the CSC niche leading to inferior prognosis. Notably, it is uncovered that amphiregulin (AREG) derived from iCAFs promotes tumor stemness by upregulating the expression of SOX9 in tumor cells, and contributes to drug resistance via the AREG-ERBB2 axis. This study provides valuable insight into the characteristics of CSC niche in driving tumor stemness and progression, offering novel perspective for designing effective strategies to overcome GC therapy resistance.

Single-Cell Transcriptomic Analysis Reveals an Aggressive Basal-Like Tumor Cell Subpopulation Associated With Poor Prognosis in Intrahepatic Cholangiocarcinoma

BACKGROUND AND AIM

Intrahepatic cholangiocarcinoma (ICC) is the second most common primary liver cancer whose incidence is increasing globally. However, the high tumor heterogeneity of ICC restricts the efficacy of available systematic therapies. We aim to dissect the tumor heterogeneity of ICC utilizing high-resolution single-cell RNA sequencing to identify novel therapeutic targets.

METHODS

We performed single-cell RNA sequencing (scRNA-seq) of 26 tumor samples from 23 ICC patients and spatial transcriptomic sequencing of six tumor sections from six ICC patients. Bulk RNA-seq data from two public datasets were used for validation. Additionally, immunohistochemical staining and multiplex immunofluorescence staining were conducted to validate the infiltration and distribution of cells in the tumor microenvironment.

RESULTS

We discovered that malignant cells in ICC samples exhibited a remarkably high degree of tumor heterogeneity. We identified a basal-like tumor cell subpopulation characterized by the expression of basal epithelial related genes including KRT5, KRT6A, and KRT17. The basal-like tumor subpopulation was characterized by activation of MET signaling and extracellular matrix organization associated with tumor invasion and correlated with poor prognosis. Cell-cell communication analysis further showed significant HGF-MET interaction between inflammatory cancer-associated fibroblasts (iCAFs) and basal-like tumor cells. We found that iCAFs were the major source of HGF in tumor environment and contributed to the basal-like phenotype formation of tumor cells by HGF-MET axis.

CONCLUSIONS

We identified an aggressive basal-like tumor cell subpopulation, which correlated with poor prognosis in ICC. The MET pathway contributes to the aggressiveness of basal-like tumor cells and serves as a novel therapeutic target for ICC.

LAMA4+ CD90+ eCAFs provide immunosuppressive microenvironment for liver cancer through induction of CD8+ T cell senescence

Despite significant advances in cancer biology research and treatment, clinical outcomes for patients with liver cancer remain unsatisfactory. The biological and molecular mechanisms underlying the bidirectional signaling between tumor cells and the tumor microenvironment (TME), which promotes tumor progression in the liver, remain to be elucidated. Fibroblasts are crucial regulators of tumor progression and response to therapy; however, our understanding of their roles remains limited. Here, we integrated single-cell RNA sequencing and spatial transcriptomic data of pan-liver cancers to characterize the different subtypes of cancer-associated fibroblasts (CAFs). siRNA transfection was used for knockdown the expression of LAMA4. Western blot assay was used for gene expression analysis. Flow cytometry was used to detect proliferation, toxicity and cytolytic capacity of CD8+ T cells. To establish a spontaneous murine hepatocellular carcinoma (HCC) model, a combined DEN and CCL4 approach was performed. Notably, we identified CD90+ extracellular matrix CAFs (eCAFs) associated with poor prognosis. These CD90+ eCAFs, located distal to the tumor nest, overlapped with the distribution of CD8+ T cells. Functional experiments demonstrated that CD90+ eCAFs recruited CD8+ T cells and inhibited their function through secretion of LAMA4. Further investigation revealed that LAMA4 induced the CD8+ T cell senescence through a DNA damage signaling pathway mediated by the receptor ITGA6. In a mouse model of spontaneous HCC, targeting LAMA4 can inhibit the progression of malignant transformation and synergize with anti-PD-1 therapy. Our study reveals the function of specific CAFs subtypes and highlights the importance of interactions with the immune system.

CAF-mediated tumor vascularization: From mechanistic insights to targeted therapies

Cancer-associated fibroblasts (CAFs) are a major component of the tumor microenvironment (TME) and play a crucial role in tumor progression. The biological properties of tumors, such as drug resistance, vascularization, immunosuppression, and metastasis are closely associated with CAFs. During tumor development, CAFs contribute to tumor progression by remodeling the extracellular matrix (ECM), inhibiting immune cell function, promoting angiogenesis, and facilitating tumor cell growth, invasion, and metastasis. Studies have shown that CAFs can promote endothelial cell proliferation by directly secreting cytokines such as vascular endothelial growth factor (VEGF) and fibroblast Growth Factor (FGF), as well as through exosomes. CAFs also secrete the chemokine stromal cell-derived factor 1 (SDF-1) to recruit endothelial progenitor cells (EPCs) into the peripheral blood and guide their migration to the tumor periphery. Additionally, CAFs can induce tumor cells to transform into "endothelial cells" that participate in vascular wall formation. However, the precise mechanisms remain to be further investigated. Due to their widespread presence in various solid tumors and their tumor-promoting function, CAFs are emerging as therapeutic targets. In this review, we summarize the specific mechanisms through which CAFs promote angiogenesis and outline current therapeutic strategies targeting CAF-induced vascularization, ongoing clinical trials targeting CAFs, and discuss potential future treatment approaches. We hope this will contribute to the advancement of CAF-targeted tumor treatment strategies.

Extracellular vesicle-derived miRNA-mediated cell-cell communication inference for single-cell transcriptomic data with miRTalk

MicroRNAs are released from cells in extracellular vesicles (EVs), representing an essential mode of cell-cell communication (CCC) via a regulatory effect on gene expression. Single-cell RNA-sequencing technologies have ushered in an era of elucidating CCC at single-cell resolution. Herein, we present miRTalk, a pioneering approach for inferring CCC mediated by EV-derived miRNA-target interactions (MiTIs). The benchmarking against simulated and real-world datasets demonstrates the superior performance of miRTalk, and the application to four disease scenarios reveals the in-depth MiTI-mediated CCC mechanisms. Collectively, miRTalk can infer EV-derived MiTI-mediated CCC with scRNA-seq data, providing new insights into the intercellular dynamics of biological processes.

Gene expression profile of anoikis reveals new subtypes of liver cancer and discovery of therapeutic targets and biomarkers

Hepatocellular carcinoma and cholangiocarcinoma, the two predominant histological subtypes of primary liver cancer, are characterized by a high global incidence and poor prognosis. Moreover, the therapeutic options are still limited, with surgical intervention being the predominant approach. Anchorage-Dependent Cell Death (Anoikis) is a form of regulated cell death triggered by the detachment of cells from their extracellular matrix, is crucial for maintaining tissue homeostasis. However, tumor cells often evade anoikis, a capability that is essential for their survival in the bloodstream and subsequent metastasis. Our study classified liver cancer into two distinct subtypes, C1 and C2, based on the differential expression of anoikis-related genes. Subtype C1 patients exhibited elevated expression of BRMS1, PTK2, and CASP8, which could serve as potential therapeutic targets for anoikis-based treatments. Conversely, subtype C2 patients showed higher expression of NTRK2, STAT3, SIK1, AKT1, and EGFR, suggesting these genes as promising therapeutic targets for C2 subtype liver cancer. Furthermore, employing Weighted Correlation Network analysis, machine learning models, and experimental validation, we identified NPY1R and HGF as potential biomarkers for the diagnosis and treatment of liver cancer.

Single-cell transcriptomic analysis reveals prognosis-related stromal signatures that potentiate stratification of patients with extrahepatic cholangiocarcinoma

BACKGROUND

Extrahepatic cholangiocarcinoma (eCCA) is a rare but refractory cancer with dense desmoplasia. Prognosis-associated stromal cells in eCCA remain poorly characterized. Here, we profiled the tumor cellular composition and identified prognosis-related stromal signatures by single-cell RNA sequencing (scRNA-seq) in eCCA. ECCA patients were further stratified into different categories based on identified stromal signatures.

METHODS

Using scRNA-seq, we profiled the transcriptomes of 37,498 individual cells from eight eCCA biopsies, including five tumor tissues and three paired adjacent normal tissues. Bulk RNA sequencing (bRNA-seq) was also performed on 43 eCCA tumor tissues. Stromal cell composition and heterogeneity were examined through differential gene expression and gene set enrichment analyses. By assessing the expression levels of marker genes in bRNA-seq data, the correlation of stromal cell clusters with survival was explored. The GSVA scores of the cell-specific signature genes of the prognosis-related stromal cell subtypes were calculated and used to stratify eCCA patients.

RESULTS

The results revealed that tumor stroma in eCCA were composed of hematopoietic progenitor-like cells (HPLCs), fibroblasts (Fb), Schwann cells (Sch), endothelial cells and immune cells. Prognosis-associated stromal cell subpopulations included MKI67 + HPLC, TMEM158 + C3-Fb, FOXP3 + regulatory T cells (Treg), SLIT2 + Sch, TPSD1 + C2-mast cells (MC) and CTSG + C3-MC. Based on these stromal signatures, the eCCA tumors were categorized into three classes: proliferative Group 1 with enrichment of MKI67 + HPLC, inflammatory and fibrotic Group 2 with enrichment of TPSD1 + C2- MC, FOXP3 + Treg and TMEM158 + C3-Fb, and neuronal Group 3 with enrichment of SLIT2 + Sch and CTSG + C3-MC. ECCA patients in Group 3 had a better prognosis when compared to Group 1 and 2, reflecting different impact of stromal subtypes on tumor progression.

CONCLUSION

Single-cell transcriptomic analysis reveals prognosis-related stromal signatures that potentiate the stratification of eCCA into proliferative, inflammatory and fibrotic, and neuronal phenotypes, which has important implications on molecular classification and exploring therapeutic targets in eCCA.

Multimodal sequencing of neoadjuvant nivolumab treatment in hepatocellular carcinoma reveals cellular and molecular immune landscape for drug response

A striking characteristic of liver cancer is its extensive heterogeneity, particularly with regard to its varied response to immunotherapy. In this study, we employed multimodal sequencing approaches to explore the various aspects of neoadjuvant nivolumab treatment in liver cancer patients. We used spatially-resolved transcriptomics, single- and bulk-cell transcriptomics, and TCR clonotype analyses to examine the spatiotemporal dynamics of the effects of nivolumab. We observed a significantly higher clonal expansion of T cells in the tumors of patients who responded to the treatment, while lipid accumulation was detected in those of non-responders, likely due to inherent differences in lipid metabolic processes. Furthermore, we found a preferential enrichment of T cells, which was associated with a better drug response. Our results also indicate a functional antagonism between tumor-associated macrophages (TAMs) and CD8 cells and their spatial separation. Notably, we identified a UBASH3B/NR1I2/CEACAM1/HAVCR2 signaling axis, highlighting the intense communication among TAMs, tumor cells, and T-cells that leads to pro-tumorigenic outcomes resulting in poorer nivolumab response. In summary, using integrative multimodal sequencing investigations, combined with the multi-faceted exploration of pre- and post-treatment samples of neoadjuvant nivolumab-treated HCC patients, we identified useful mechanistic determinants of therapeutic response. We also reconstructed the spatiotemporal model that recapitulates the physiological restoration of T cell cytotoxicity by anti-PD1 blockade. Our findings could provide important biomarkers and explain the mechanistic basis differentiating the responders and non-responders.

Cancer-associated fibroblasts: multidimensional players in liver cancer

Cancer-associated fibroblasts (CAFs), the most abundant stromal cells in the tumor microenvironment (TME), control tumor growth through production and organization of the extracellular matrix (ECM) for a long time. However, the results from different studies that have focused on targeting CAFs to disturb tumor progression are extremely controversial. Recent studies using advanced single-cell RNA sequencing technology (scRNAseq) combined with multiple genetically engineered mouse models have identified diverse CAF subpopulations in the premalignant liver microenvironment (PME) of hepatocellular carcinoma (HCC) and TME of intrahepatic cholangiocarcinoma (ICC), providing a deeper understanding of the exact roles of each CAF subpopulation in cancer development. This review focuses on the specific protein markers, signaling pathways, and functions of various emerging CAF subclusters that contribute to the development of ICC and HCC. Elucidating the role and regulation of CAF subpopulations under different pathophysiological conditions will facilitate the discovery of new therapeutics that modulate CAF activity.

Multiple-omics analysis reveals a dedifferentiation-immune loop in intrahepatic cholangiocarcinoma

Intrahepatic cholangiocarcinoma (ICC) is known for its diverse cell types and resistance to standard treatments, highlighting the importance of understanding its tumor microenvironment (TME) for improved prognostic accuracy and therapeutic innovation. Our study used a multi-omics approach to analyze the ICC TME in both human and mouse samples, linking survival outcomes to the complex cellular interactions within the TME. We discovered a dedifferentiation phenomenon in ICC cells driven by the Yes-associated protein (YAP) pathway, influenced by tumor-associated macrophages (TAMs). Conversely, ICC cells promoted an immunosuppressive environment in TAMs. Targeting TAMs in a transgenic mouse model disrupted this loop, enhancing T cell responses and suggesting a novel immunotherapy avenue for ICC. Our findings reveal a reciprocal dedifferentiation-immunosuppression loop between ICC cells and TAMs, advocating TAM targeting as a promising therapy and highlighting the potential of macrophage modulation in ICC treatment.

Cancer-associated fibroblasts in breast cancer in the single-cell era: Opportunities and challenges

Breast cancer is a leading cause of morbidity and mortality in women, and its progression is closely linked to the tumor microenvironment (TME). Cancer-associated fibroblasts (CAFs), key components of the TME, play a crucial role in promoting tumor growth by driving cancer cell proliferation, invasion, extracellular matrix (ECM) remodeling, inflammation, chemoresistance, and immunosuppression. CAFs exhibit considerable heterogeneity and are classified into subgroups based on different combinations of biomarkers. Single-cell RNA sequencing (scRNA-seq) enables high-throughput and high-resolution analysis of individual cells. Relying on this technology, it is possible to cluster complex CAFs according to different biomarkers to analyze the specific phenotypes and functions of different subpopulations. This review explores CAF clusters in breast cancer and their associated biomarkers, highlighting their roles in disease progression and potential for targeted therapies.

Prognostic implications and therapeutic opportunities related to CAF subtypes in CMS4 colorectal cancer: insights from single-cell and bulk transcriptomics

Cancer-associated fibroblasts (CAFs) significantly influence tumor progression and therapeutic resistance in colorectal cancer (CRC). However, the distributions and functions of CAF subpopulations vary across the four consensus molecular subtypes (CMSs) of CRC. This study performed single-cell RNA and bulk RNA sequencing and revealed that myofibroblast-like CAFs (myCAFs), tumor-like CAFs (tCAFs), inflammatory CAFs (iCAFs), CXCL14+CAFs, and MT+CAFs are notably enriched in CMS4 compared with other CMSs of CRC. Multiplex immunohistochemistry was used to validate the distribution of CAF subtypes in patients with different CMSs. Prognosis-related CAF subtypes were identified, leading to the selection of four key genes (COL3A1, COL1A2, GEM, and TMEM47). Through machine learning, we developed a CAF poor-prognosis gene (CAFPRG) model to predict outcomes of patients with CMS4. High levels of CAFPRGs were identified as independent poor-risk factors for prognosis (p < 0.001). Tumors with elevated CAFPRGs exhibited increased infiltration of immune-suppressive cells and resistance to chemotherapy. The expression of these key genes was confirmed to be significantly higher in CAFs than in normal fibroblasts (NFs). Therefore, CAFPRGs may be valuable for precisely predicting patient survival and may present potential therapeutic opportunities for CMS4 CRC.

The solid tumor microenvironment and related targeting strategies: a concise review

The malignant tumor is a serious disease threatening human life. Increasing studies have confirmed that the tumor microenvironment (TME) is composed of a variety of complex components that precisely regulate the interaction of tumor cells with other components, allowing tumor cells to continue to proliferate, resist apoptosis, evade immune surveillance and clearance, and metastasis. However, the characteristics of each component and their interrelationships remain to be deeply understood. To target TME, it is necessary to deeply understand the role of various components of TME in tumor growth and search for potential therapeutic targets. Herein, we innovatively classify the TME into physical microenvironment (such as oxygen, pH, etc.), mechanical microenvironment (such as extracellular matrix, blood vessels, etc.), metabolic microenvironment (such as glucose, lipids, etc.), inflammatory microenvironment and immune microenvironment. We introduce a concise but comprehensive classification of the TME; depict the characteristics of each component in TME; summarize the existing methods for detecting each component in TME; highlight the current strategies and potential therapeutic targets for TME; discuss current challenges in presenting TME and its clinical applications; and provide our prospect on the future research direction and clinical benefits of TME.

Dissecting endothelial cell heterogeneity with new tools

The formation of a blood vessel network is crucial for organ development and regeneration. Over the past three decades, the central molecular mechanisms governing blood vessel growth have been extensively studied. Recent evidence indicates that vascular endothelial cells-the specialized cells lining the inner surface of blood vessels-exhibit significant heterogeneity to meet the specific needs of different organs. This review focuses on the current understanding of endothelial cell heterogeneity, which includes both intra-organ and inter-organ heterogeneity. Intra-organ heterogeneity encompasses arterio-venous and tip-stalk endothelial cell specialization, while inter-organ heterogeneity refers to organ-specific transcriptomic profiles and functions. Advances in single-cell RNA sequencing (scRNA-seq) have enabled the identification of new endothelial subpopulations and the comparison of gene expression patterns across different subsets of endothelial cells. Integrating scRNA-seq with other high-throughput sequencing technologies promises to deepen our understanding of endothelial cell heterogeneity at the epigenetic level and in a spatially resolved context. To further explore human endothelial cell heterogeneity, vascular organoids offer powerful tools for studying gene function in three-dimensional culture systems and for investigating endothelial-tissue interactions using human cells. Developing organ-specific vascular organoids presents unique opportunities to unravel inter-organ endothelial cell heterogeneity and its implications for human disease. Emerging technologies, such as scRNA-seq and vascular organoids, are poised to transform our understanding of endothelial cell heterogeneity and pave the way for innovative therapeutic strategies to address human vascular diseases.

Cancer‑associated fibroblasts: a pivotal regulator of tumor microenvironment in the context of radiotherapy

BACKGROUND

In the course of tumor treatment, radiation therapy (RT) not only kills cancer cells, but also induces complex biological effects in non-malignant cells around cancer cells. These biological effects such as angiogenesis, changes in stromal composition and immune cell infiltration remodel the tumor microenvironment (TME). As one of the major components of the TME, Cancer‑associated fibroblasts (CAFs) are not only involved in tumorigenesis, progression, recurrence, and metastasis but also regulate the tumor-associated immune microenvironment. CAFs and tumor cells or immune cells have complex intercellular communication in the context of tumor radiation.

MAIN CONTENT

Different cellular precursors, spatial location differences, absence of specific markers, and advances in single-cell sequencing technology have gradually made the abundant heterogeneity of CAFs well known. Due to unique radioresistance properties, CAFs can survive under high doses of ionizing radiation. However, radiation can induce phenotypic and functional changes in CAFs and further act on tumor cells and immune cells to promote or inhibit tumor progression. To date, the effect of RT on CAFs and the effect of irradiated CAFs on tumor progression and TME are still not well defined.

CONCLUSION

In this review, we review the origin, phenotypic, and functional heterogeneity of CAFs and describe the effects of RT on CAFs, focusing on the mutual crosstalk between CAFs and tumor or immune cells after radiation. We also discuss emerging strategies for targeted CAFs therapy.

Periplakin Attenuates Liver Fibrosis via Reprogramming CD44Low Cells into CD44High Liver Progenitor Cells

BACKGROUND & AIMS

Liver progenitor cells (LPCs) contribute significantly to the restoration of injured liver parenchyma and promote liver regeneration, thereby ameliorating liver fibrosis. However, the mechanism of the derivation of LPCs remains poorly understood.

METHODS

We first examined the expression of periplakin (PPL) in patients and mouse models with liver fibrosis. Adenovirus overexpressing PPL was injected into the tail vein of mouse models to detect the regulatory effect of PPL on liver fibrosis. Single-cell sequencing explored how PPL influences liver fibrosis progression. Additionally, PPL+CD44Low cells and PPL+CD44High LPCs were transplanted into 3,5-diethoxycarbonyl-1,4-dihydrocollidine-induced mouse models to assess their therapeutic efficacy in treating liver fibrosis.

RESULTS

The expression of PPL is upregulated in fibrotic livers in human and mouse models of liver fibrosis. Functionally, we found that PPL overexpression significantly attenuated liver fibrosis. Mechanistically, PPL was specifically expressed in LPCs and promoted LPC expansion. Moreover, we observed that PPL+ cells could be categorized into PPL+CD44Low and PPL+CD44High subsets, and PPL+CD44Low cells were found to redifferentiate into PPL+CD44High LPCs during liver fibrosis. Furthermore, transplantation of PPL+CD44High LPCs notably suppressed liver fibrosis.

CONCLUSIONS

These findings demonstrate that PPL+CD44Low cells can be reprogrammed into PPL+CD44High LPCs, which ameliorate liver fibrosis, suggesting a potential application of PPL for the treatment of liver fibrosis.

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.

Pan-cancer analysis predicts MBOAT2 as a potential new ferroptosis related gene immune checkpoint

BACKGROUND

The phospholipid-modifying enzyme MBOAT2 plays a crucial role in iron homeostasis by inhibiting iron sequestration, thus preventing iron-induced cell death. It achieves this by remodeling the phospholipid composition of cell membranes through phospholipid metabolism. Although multiple studies have highlighted the significance of MBOAT2 in tumorigenesis, a comprehensive pan-cancer analysis has not been conducted to date.

METHODS

In this study, we analyzed the expression levels of MBOAT2 using RNA sequencing data from the TCGA and GTEx databases. We also investigated MBOAT2 protein information using resources such as the Human Protein Atlas (HPA), GeneCards, and String databases. To assess the prognostic value of MBOAT2, we conducted survival analysis based on clinical data from TCGA. Additionally, we performed enrichment analysis using the R package "clusterProfiler" and explored the relationship between MBOAT2 expression and immune cell infiltration, as well as immune checkpoint interactions in TCGA datasets. Furthermore, we examined the correlation between MBOAT2 expression and clinical pathology through immunohistochemical analysis of breast, prostate, lung, and liver cancer tissues in the HPA database. Finally, western blotting was used to validate MBOAT2 protein expression in breast and prostate cancer cell lines.

RESULTS

Our analysis revealed that MBOAT2 was highly expressed in a wide range of cancer types, with its expression correlating with improved survival outcomes in the TCGA dataset. Moreover, we found a significant association between MBOAT2 expression and immune regulation, particularly in relation to immune cell infiltration and immune checkpoint interactions.

CONCLUSION

MBOAT2 holds promise as a prognostic biomarker and may serve as a target for immunotherapy in various malignancies. Further investigation into its role in cancer immunity could offer new insights into potential therapeutic strategies.

Tumor cell villages define the co-dependency of tumor and microenvironment in liver cancer

Spatial cellular context is crucial in shaping intratumor heterogeneity. However, understanding how each tumor establishes its unique spatial landscape and what factors drive the landscape for tumor fitness remains significantly challenging. Here, we analyzed over 2 million cells from 50 tumor biospecimens using spatial single-cell imaging and single-cell RNA sequencing. We developed a deep learning-based strategy to spatially map tumor cell states and the architecture surrounding them, which we referred to as Spatial Dynamics Network (SDN). We found that different tumor cell states may be organized into distinct clusters, or 'villages', each supported by unique SDNs. Notably, tumor cell villages exhibited village-specific molecular co-dependencies between tumor cells and their microenvironment and were associated with patient outcomes. Perturbation of molecular co-dependencies via random spatial shuffling of the microenvironment resulted in destabilization of the corresponding villages. This study provides new insights into understanding tumor spatial landscape and its impact on tumor aggressiveness.

Exosomal RNAs and EZH2: unraveling the molecular dialogue driving tumor progression

The EZH2 gene encodes an enzyme that is part of the epigenetic factor Polycomb Repressive Complex 2 (PRC2). In order to control gene expression, PRC2 mainly modifies chromatin structure. In this complex process, EZH2 methylates histone proteins, which in turn suppresses further RNA transcriptions. As a result, EZH2 dysregulations can occasionally induce abnormal gene expression patterns, which can aid in the development and progression of cancer. Non-coding RNAs significantly impact the expression of EZH2 through epigenetic mechanisms. Meanwhile, normal and cancerous cells frequently release vesicles into the extracellular matrix, also known as exosomes, that occasionally carry RNA molecules from their origin cells, including messenger RNAs, microRNAs, and other non-coding RNAs. Thus exosomes are granted the ability to regulate numerous physiological functions and act as crucial messengers between cells by influencing gene expression in the recipient cell. We conducted this review to focus on EZH2's substantial biological role and the mechanisms that regulate it, driven by the desire to understand the possible impact of exosomal RNAs on EZH2 expression.

LiverSCA 2.0: An Enhanced Comprehensive Cell Atlas for Human Hepatocellular Carcinoma and Intrahepatic Cholangiocarcinoma

BACKGROUND

Hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) are two distinct types of primary liver cancer (PLC) characterized by considerable extents of cellular and molecular heterogeneities. We recently developed a web-based cell atlas called LiverSCA that possesses a user-friendly interface and comprehensive functionalities. It facilitates the exploration of gene expression patterns, cellular compositions, and intercellular communication within the microenvironments of liver and PLC tumors.

METHODS

To further enhance the documentation of data pinpointing different phenotypes/subtypes of liver and PLC, we extended the catalog of LiverSCA with additional datasets, e.g., ICC and metabolic dysfunction-associated steatotic liver disease/steatosis (MASLD/MASH).

RESULTS

The current enhanced version of the LiverSCA cell atlas encompasses six phenotypes (normal, HBV-HCC, HCV-HCC, non-viral HCC, ICC, and MASH), 63 patients, and over 248,000 cells. Furthermore, we have incorporated comparative visualization methods that allow users to simultaneously examine and compare gene expression levels between two different phenotypes.

CONCLUSIONS

We are committed to the continuous development of LiverSCA and envision that it will serve as a valuable resource to support researchers in convenient investigations into the cellular and molecular landscapes of liver and PLC.

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.

Single-cell multi-omics deciphers hepatocyte dedifferentiation and illuminates maintenance strategies

Due to the similarity to human hepatocytes, porcine hepatocytes play an important role in hepatic research and drug evaluation. However, once hepatocytes were cultured in vitro, it was often prone to dedifferentiate, resulting in the loss of their characteristic features and normal functions, which impede their application in liver transplantation and hepatotoxic drugs evaluation. Up to now, this process has yet to be thoroughly investigated from the single-cell resolution and multi-omics perspective. In this study, we utilized 10× multiome technology to dissect the heterogeneity of porcine hepatocytes at different time points (Days 0, 1, 3, 5 and 7) during dedifferentiation. We comprehensively investigated cell heterogeneity, cellular dynamics, signalling pathways, potential gene targets, enhancer-driven gene regulatory networks, cell-cell communications of these cells and the conservation of mechanisms across species. We found that a series of critical signalling pathways driven by ERK, PI3K, Src and TGF-β were activated during this process, especially in the early stage of dedifferentiation. Based on these discoveries, we constructed a chemical combination targeting these pathways, which effectively inhibited the dedifferentiation of porcine hepatocytes in vitro. To validate the effectiveness of this combination, we transplanted such treated hepatocytes into FRGN mice, and the results demonstrated that these cells could effectively repopulate the liver and improve the survival of mice.

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.

Analyze the Diversity and Function of Immune Cells in the Tumor Microenvironment From the Perspective of Single-Cell RNA Sequencing

BACKGROUND

Cancer development is closely associated with complex alterations in the tumor microenvironment (TME). Among these, immune cells within the TME play a huge role in personalized tumor diagnosis and treatment.

OBJECTIVES

This review aims to summarize the diversity of immune cells in the TME, their impact on patient prognosis and treatment response, and the contributions of single-cell RNA sequencing (scRNA-seq) in understanding their functional heterogeneity.

METHODS

We analyzed recent studies utilizing scRNA-seq to investigate immune cell populations in the TME, focusing on their interactions and regulatory mechanisms.

RESULTS

ScRNA-seq reveals the functional heterogeneity of immune cells, enhances our understanding of their role in tumor antibody responses, and facilitates the construction of immune cell interaction networks. These insights provide guidance for the development of cancer immunotherapies and personalized treatment approaches.

CONCLUSION

Applying scRNA-seq to immune cell analysis in the TME offers a novel pathway for personalized cancer treatment. Despite its promise, several challenges remain, highlighting the need for further advancements to fully integrate scRNA-seq into clinical applications.

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.

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.

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.

Uncovering immune cell heterogeneity in hepatocellular carcinoma by combining single-cell RNA sequencing with T-cell receptor sequencing

BACKGROUND

Understanding the status and function of tumor-infiltrating immune cells is essential for improving immunotherapeutic effects and predicting the clinical response in human patients with carcinoma. However, little is known about tumor-infiltrating immune cells, and the corresponding research results in hepatocellular carcinoma (HCC) are limited.

AIM

To investigate potential biomarker genes that are important for the development of HCC and to understand how immune cell subsets react throughout this process.

METHODS

Using single-cell RNA sequencing and T-cell receptor sequencing, the heterogeneity and potential functions of immune cell subpopulations from HCC tissue and normal tissue adjacent to carcinoma, as well as their possible interactions, were analyzed.

RESULTS

Eight T-cell clusters from patients were analyzed and identified using bioinformatics, including six typical major T-cell clusters and two newly identified T-cell clusters, among which Fc epsilon receptor 1G+ T cells were characterized by the upregulation of Fc epsilon receptor 1G, tyrosine kinase binding protein, and T cell receptor delta constant, whereas metallothionein 1E+ T cells proliferated significantly in tumors. Differentially expressed genes, such as regulator of cell cycle, cysteine and serine rich nuclear protein 1, SMAD7 and metallothionein 1E, were identified as significantly upregulated in tumors and have potential as biomarkers. In association with T-cell receptor analysis, we inferred the clonal expansion characteristics of each T-cell cluster in HCC patients.

CONCLUSION

We identified lymphocyte subpopulations and potential biomarker genes critical for HCC development and revealed the clonal amplification of infiltrating T cells. These data provide valuable resources for understanding the response of immune cell subsets in HCC.

Hamid SS. Multiomics in silico analysis identifies TM4SF4 as a cell surface target in hepatocellular carcinoma

The clinical application of cellular immunotherapy in hepatocellular carcinoma (HCC) is impeded by the lack of a cell surface target frequently expressed in HCC cells and with minimal presence in normal tissues to reduce on-target, off-tumor toxicity. To address this, an in silico multomics analysis was conducted to identify an optimal therapeutic target in HCC. A longlist of genes (n = 12,948) expressed in HCCs according to The Human Protein Atlas database were examined. Eight genes were shortlisted to identify one with the highest expression in HCCs, without being shed into circulation, and with restrictive expression profile in other normal human tissues. A total of eight genes were shortlisted and subsequently ranked according to the combination of their transcript and protein expression levels in HCC cases (n = 791) derived from four independent datasets. TM4SF4 was the top-ranked target with the highest expression in HCCs. TM4SF4 showed more favorable expression profile with significantly lower expression in normal human tissues but more highly expressed in HCC compared with seven other common HCC therapeutic targets. Furthermore, scRNA-seq and immunohistochemistry datasets showed that TM4SF4 was absent in immune cell populations but highly expressed in the bile duct canaliculi of hepatocytes, regions inaccessible to immune cells. In scRNA-seq dataset of HCCs, TM4SF4 expression was positively associated with mitochondrial components and oxidative phosphorylation Gene Ontologies in HCC cells (n = 15,787 cells), suggesting its potential roles in mitochondrial-mediated oncogenic effects in HCC. Taken together, TM4SF4 is proposed as a promising cell surface target in HCC due to its high expression in HCC cells with restricted expression profile in non-cancerous tissues, and association with HCC oncogenic pathways.

Mapping of the T-cell Landscape of Biliary Tract Cancer Unravels Anatomic Subtype-Specific Heterogeneity

Biliary tract cancer (BTC), encompassing diseases such as intrahepatic (ICC), extrahepatic cholangiocarcinoma (ECC), and gallbladder cancer, is not only increasing but also poses a significant and urgent health threat due to its high malignancy. Genomic differences point to the possibility that these subtypes represent distinct diseases. Elucidation of the specific distribution of T-cell subsets, critical to cancer immunity, across these diseases could provide better insights into the unique biology of BTC subtypes and help identify potential precision medicine strategies. To address this, we conducted single-cell RNA sequencing and T-cell receptor sequencing on CD3+ T cells from 36 samples from 16 patients with BTC across all subtypes and analyzed 355 pathologic slides to examine the spatial distribution of T cells and tertiary lymphoid structures. Compared with ICC and gallbladder cancer, ECC possessed a unique immune profile characterized by T-cell exhaustion, elevated CXCL13 expression in CD4+ T helper-like and CD8+CXCL13+ exhausted T cells, more mature tertiary lymphoid structures, and fewer desert immunophenotypes. Conversely, ICC displayed an inflamed immunophenotype with an enrichment of IFN-related pathways and high expression of LGALS1 in activated regulatory T cells, associated with immunosuppression. Inhibition of LGALS1 reduced tumor growth and regulatory T-cell prevalence in ICC mouse models. Overall, this study unveils T-cell diversity across BTC subtypes at the single-cell and spatial level that could open paths for tailored immunotherapies. Significance: Single-cell and spatial analyses detailed the T-cell characteristics specific to anatomic subtypes of biliary tract cancer, identifying unique immunologic features that could potentially be harnessed to improve patient outcomes.

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.

Prognostic implications of tumor histology and microenvironment in surgically resected intrahepatic cholangiocarcinoma: a single institutional experience

Intrahepatic cholangiocarcinoma (ICC) is a highly aggressive malignant neoplasm. Certain histologic features and the tumor microenvironment may impact disease progression. We aim to characterize the clinicopathologic features of ICC to identify prognostic factors. A total of 50 surgically resected ICC (partial or transplant) cases were analyzed. The cohort included 26 men and 24 women with a median age of 62 years. Eighteen (36%) cases were multifocal ICC with a mean largest tumor size of 6.5 cm. Neoadjuvant and adjuvant chemotherapy was done in eight (16%) and 33 (66%) patients, respectively. Histologically, 42 (84%) were small duct type, seven (14%) large duct type, and one mixed (2%). Thirty (60%) cases showed lymphovascular invasion (LVI) and 11 (22%) with perineural invasion (PNI). Twenty-eight (56%) cases demonstrated dense intratumoral hyaline fibrosis and 18 (36%) with tumor necrosis, each ≥ 10% tumor volume. On follow-up, 35 (70%) patients died of disease after a median disease-specific survival (DSS) of 21 months. Univariate analysis revealed that hyaline fibrosis and adjuvant chemotherapy were associated with better DSS, while tumor size, multifocality, necrosis, and peritumoral neutrophil to lymphocyte ratio were associated with worse DSS. In contrast, age, sex, small vs. large duct types, LVI, and individual inflammatory cell counts were not significant prognostic factors. In summary, ICC is a heterogeneous malignancy with variable clinical courses associated with tumor burden, histology, and microenvironment. Targeting specific components within the tumor microenvironments may be a promising approach for treatment in the future.

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.

The importance of preclinical models for cholangiocarcinoma drug discovery

INTRODUCTION

Biliary tract cancer (BTC) comprises a clinically diverse and genetically heterogeneous group of tumors along the intra- and extrahepatic biliary system (intrahepatic and extrahepatic cholangiocarcinoma) and gallbladder cancer with the common feature of a poor prognosis, despite increasing molecular knowledge of associated genetic aberrations and possible targeted therapies. Therefore, the search for even more precise and individualized therapies is ongoing and preclinical tumor models are central to the development of such new approaches.

AREAS COVERED

The models described in the current review include simple and advanced in vitro and in vivo models, including cell lines, 2D monolayer, spheroid and organoid cultures, 3D bioprinting, patient-derived xenografts, and more recently, machine-perfusion platform-based models of resected liver specimens. All these models have individual advantages, disadvantages and limitations that need to be considered depending on the desired application.

EXPERT OPINION

In addition to potential cost limitations, availability of BTC cell types, time required for model establishment and growth success rate, the individual models differently reflect relevant characteristics such as tumor heterogeneity, spatial tumor-stroma microenvironment interactions, metabolic and nutritional gradients and immunological interactions. Therefore, a consequent combination of different models may be required to improve clinical study outcomes by strengthening the preclinical data basis.

Single-Cell and Spatial Transcriptomics Delineate the Microstructure and Immune Landscape of Intrahepatic Cholangiocarcinoma in the Leading-Edge Area

Intrahepatic cholangiocarcinoma (ICC) tumor cells and their interactions with the immune microenvironment, particularly at the leading-edge area, have been underexplored. This study employs single-cell RNA sequencing (scRNA-seq) and spatial transcriptome (ST) analysis on samples from the tumor core, adjacent non-tumorous tissue, and the leading-edge area of nine ICC patients. These findings indicate that tumor cells at the leading-edge area demonstrate enhanced proliferation and are tightly associated with the stroma, including endothelial cells and POSTN+ FAP+ fibroblasts. Notably, CD8+ T cells in this region exhibit a naive phenotype with low cytotoxicity and signs of exhaustion, likely due to compromised antigen presentation by antigen-presenting cells (APCs). The predominant CD8+ T cell subset, mucosal-associated invariant T (MAIT) cells, recruits SPP1+ macrophages within the stroma. This interaction, along with the presence of POSTN+ cancer-associated fibroblasts (CAFs) and endothelial cells, forms a unique "triad structure" that fosters tumor growth and ICC progression. The research highlights the intricate characteristics and interactions of ICC tumor cells in the leading-edge area, offering insights into potential therapeutic targets for intervention.

Single-Cell Sequencing Reveals Heterogeneity and Interactions Between Epithelial Cells and Fibroblasts in Post-ESD Oesophageal Stricture

Oesophageal stricture, especially circumferential lesions, is a common complication of endoscopic submucosal dissection (ESD). However, the exact mechanisms underlying its development remain unclear. Consequently, understanding tissue microenvironment changes is crucial for identifying therapeutic targets. To address this, single-cell RNA sequencing (scRNA-seq) was performed on oesophageal stricture samples and normal controls. Alterations in cellular composition were observed, particularly in epithelial, endothelial, fibroblast and immune cells. A notable increase was observed in the number of differentiating suprabasal cell_2 (DFSC_2), which displayed pro-keratinizing traits. Detailed investigations revealed augmentation in a subset of these cells, characterised by elevated FTH1 and ECM1 expression, indicating their role in epithelial remodelling. Furthermore, fibroblast heterogeneity was demonstrated, with significant activation of myofibroblasts within stricture tissues. MDK-NCL, CXCL5/6-CXCR2, and TGFA-EGFR ligand-receptor pairs were enhanced in stricture tissues, mediating epithelial-stromal interactions. This study dissected the transcriptional landscape of postoperative oesophageal stricture tissues, providing valuable insights into stricture mechanisms and potential preventive strategies.

uniLIVER: a human liver cell atlas for data-driven cellular state mapping

The liver performs several vital functions such as metabolism, toxin removal, and glucose storage through the coordination of various cell types. With the recent breakthrough of the single-cell/single-nucleus RNA-seq (sc/snRNA-seq) techniques, there is a great opportunity to establish a reference cell map of the liver at single-cell resolution with transcriptome-wise features. In this study, we build a unified liver cell atlas uniLIVER (http://lifeome.net/database/uniliver) by integrative analysis of a large-scale sc/snRNA-seq data collection of normal human liver with 331,125 cells and 79 samples from 6 datasets. Moreover, we introduce LiverCT, a novel machine learning based method for mapping any query dataset to the liver reference map by introducing the definition of "variant" cellular states analogy to the sequence variants in genomic analysis. Applying LiverCT on liver cancer datasets, we find that the "deviated" states of T cells are highly correlated with the stress pathway activities in hepatocellular carcinoma, and the enrichments of tumor cells with the hepatocyte-cholangiocyte "intermediate" states significantly indicate poor prognosis. Besides, we find that the tumor cells of different patients have different zonation tendencies and this zonation tendency is also significantly associated with the prognosis. This reference atlas mapping framework can also be extended to any other tissues.

Utilizing sc-linker to integrate single-cell RNA sequencing and human genetics to identify cell types and driver genes associated with non-small cell lung cancer

BACKGROUND

Genome-wide association studies (GWAS) provide a powerful method for identifying the loci and genes that contribute to disease. However, in many cases, the specific cell types and states that confer disease risk through these genes remain unknown. Determining this relationship is crucial for identifying pathogenic processes and developing therapeutic strategies.

METHODS

In this study, we utilized the sc-linker framework developed by Jagadeesh, which is an integrated framework that combines single-cell RNA sequencing (scRNA-seq), epigenomic single nucleotide polymorphism (SNP)-to-gene mapping, and GWAS summary statistics to infer potential cell types and diseases affected by genetic variations.

RESULTS

Using normal cell type programs in the sc-linker, we identified type 2 alveolar cells in normal lung tissues that are closely associated with non-small cell lung cancer (NSCLC). Additionally, we identified cancer-associated fibroblasts (CAFs) associated with lung cancer using disease-dependent programs. By integrating extensive single-cell data from NSCLC, we discerned heterogeneity among CAFs subgroups. Finally, using MAGMA, we identified RAB31 as a driver gene in disease-related fibroblasts. Proteins from the RAB family are involved in the dynamic regulation of cell membrane compartments and are dysregulated in various tumor types, potentially altering biological properties such as the proliferation, migration, and invasion of cancer cells. We found that the Ras-related protein Rab-31 (RAB31) was significantly overexpressed in tumor-associated fibroblasts compared to that in normal fibroblasts and was closely associated with poor prognosis in patients with NSCLC.

CONCLUSIONS

By integrating scRNA-seq, epigenomic, and GWAS datasets, we found that ACT2 and CAFs have specific disease heritability in lung cancer and identified the driver gene RAB31 as a potential therapeutic target.

Single-Cell RNA-Seq Uncovers Cellular Heterogeneity from Deep Fascia in Necrotizing Fasciitis Patients

PURPOSE

Necrotizing fasciitis (NF) is a scarce but potentially life-threatening infection. However, no research has reported the cellular heterogeneity in patients with NF. We aim to investigate the change of cells from deep fascia in response to NF by single-cell RNA-seq.

METHODS

Fascia samples from NF patients (NF group, NG, n = 3) and volunteer (control group, CG, n = 4) were obtained and we utilized scRNA-seq to observe the variation of cells and differentially expressed genes. Then, multiplex staining and multispectral imaging and immunohistochemistry were used to be further verified.

RESULTS

Our findings showed that three fibroblast subclusters (antigen-presenting Fib, mesenchymal Fib, and myoFib) and three macrophage subclusters (SPP1+ Mac0, IL1B+ Mac1, and SPP1+M2) were found to have increased proportions with distinct roles in NF patients. The balance of M1/M2 polarization may be the key therapeutic target to determine the outcome of NF. Furthermore, the levels of SAA1, PTX3, S100 family, MARCO, and STAB1 were up-regulated in different subclusters with anti-infection roles against NF, which were proven by immunohistochemistry. These proteins may act as a biomarker or even as a candidate therapy for NF.

CONCLUSION

Our findings revealed the potential anti-infection role of deep fascia during the procession of NF, helping us understand the immunologic function of fascia and provide novel insights for its therapeutic strategies for NF.

Profiling signaling mediators for cell-cell interactions and communications with microfluidics-based single-cell analysis tools

Cell-cell interactions and communication represent the fundamental cornerstone of cells' collaborative efforts in executing diverse biological processes. A profound understanding of how cells interface through various mediators is pivotal across a spectrum of biological systems. Recent strides in microfluidic technologies have significantly bolstered the precision and prowess in capturing and manipulating cells with exceptional spatial and temporal resolution. These advanced methodologies converge with multi-signal mediator detection systems, furnishing potent, high-throughput platforms for dissecting cell-cell interactions at the single-cell level. This approach empowers researchers to delve into intricate cellular dynamics with unprecedented accuracy and efficiency. Here, we present a critical evaluation of the latest advancements in microfluidics-driven techniques for detecting signal mediators involved in cell-cell interactions and communication at the single-cell level. We underscore notable biological applications that have benefited from these technologies and identify pressing challenges that must be addressed in future endeavors leveraging microfluidic tools for single-cell interaction studies.

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.

Spatial analyses revealed CXCL5 and SLC6A14 as the markers of microvascular invasion in intrahepatic cholangiocarcinoma

BACKGROUND

Microvascular invasion (MVI) is a critical prognostic factor in intrahepatic cholangiocarcinoma (ICC), strongly associated with postoperative recurrence. However, the phenotypic features and spatial organization of MVI remain inadequately understood.

METHODS

We performed a spatial transcriptomic analysis on 29,632 spots from six ICC samples, manually delineating MVI clusters using the cloupe software. Key biomarkers were identified and validated in an independent cohort of 135 ICC patients. Functional and survival analyses were conducted to assess clinical relevance, and cell-cell communication pathways were investigated.

RESULTS

MVI regions exhibited heightened proliferation, angiogenesis, and epithelial-mesenchymal transition, driven by increased expression of transcription factors SOX10, ZEB1, and SNAI2. CXCL5 and SLC6A14 were identified as potential MVI biomarkers and showed high expression in tumor-invasive areas. Serum CXCL5 demonstrated strong predictive power for vascular invasion (AUC = 0.92) and intrahepatic metastasis (AUC = 0.96). High expression of both CXCL5 and SLC6A14 was associated with the worst survival outcomes. MVI regions were enriched with immunosuppressive MRC1+ macrophages and exhibited elevated immune checkpoint expression, including HAVCR2 and TIGHT, indicative of immune resistance. Cell-cell communication analysis revealed CXCL5-CXCR2 and LGALS9-HAVCR2 as key ligand-receptor pairs contributing to the immunosuppressive microenvironment.

CONCLUSIONS

This study identifies CXCL5 and SLC6A14 as key biomarkers of MVI, highlighting their roles in tumor proliferation, immune resistance, and poor clinical outcomes. These findings provide valuable insights into the spatial organization of MVI and its contribution to ICC progression, offering potential therapeutic targets.

Roles of Cellular Neighborhoods in Hepatocellular Carcinoma Pathogenesis

The development of hepatocellular carcinoma (HCC) involves an intricate interplay among various cell types within the liver. Unraveling the orchestration of these cells, particularly in the context of various etiologies, may hold the key to deciphering the underlying mechanisms of this complex disease. The advancement of single-cell and spatial technologies has revolutionized our ability to determine cellular neighborhoods and understand their crucial roles in disease pathogenesis. In this review, we highlight the current research landscape on cellular neighborhoods in chronic liver disease and HCC, as well as the emerging computational approaches applicable to delineate disease-associated cellular neighborhoods, which may offer insights into the molecular mechanisms underlying HCC pathogenesis and pave the way for effective disease interventions.

Advances and applications in single-cell and spatial genomics

The applications of single-cell and spatial technologies in recent times have revolutionized the present understanding of cellular states and the cellular heterogeneity inherent in complex biological systems. These advancements offer unprecedented resolution in the examination of the functional genomics of individual cells and their spatial context within tissues. In this review, we have comprehensively discussed the historical development and recent progress in the field of single-cell and spatial genomics. We have reviewed the breakthroughs in single-cell multi-omics technologies, spatial genomics methods, and the computational strategies employed toward the analyses of single-cell atlas data. Furthermore, we have highlighted the advances made in constructing cellular atlases and their clinical applications, particularly in the context of disease. Finally, we have discussed the emerging trends, challenges, and opportunities in this rapidly evolving field.

Integrative analysis of single-Cell RNA sequencing and experimental validation in the study of abdominal aortic aneurysm progression

BACKGROUND

Abdominal aortic aneurysm (AAA) is a complex vascular disorder characterized by the progressive dilation of the abdominal aorta, with a high risk of rupture and mortality. Understanding the cellular interactions and molecular mechanisms underlying AAA development is critical for identifying potential therapeutic targets.

METHODS

This study utilized datasets GSE197748, GSE164678 and GSE183464 from the GEO database, encompassing bulk and single-cell RNA sequencing data from AAA and control samples. We performed principal component analysis, differential expression analysis, and functional enrichment analysis to identify key pathways involved in AAA. Cell-cell interactions were investigated using CellPhoneDB, focusing on fibroblasts, vascular smooth muscle cells (VSMCs), and macrophages. We further validated our findings using a mouse model of AAA induced by porcine pancreatic enzyme infusion, followed by gene expression analysis and co-immunoprecipitation experiments.

RESULTS

Our analysis revealed significant alterations in gene expression profiles between AAA and control samples, with a pronounced immune response and cell adhesion pathways being implicated. Single-cell RNA sequencing data highlighted an increased proportion of pro-inflammatory macrophages, along with changes in the composition of fibroblasts and VSMCs in AAA. CellPhoneDB analysis identified critical ligand-receptor interactions, notably collagen type I alpha 1 chain (COL1A1)/COL1A2-CD18 and thrombospondin 1 (THBS1)-CD3, suggesting complex communication networks between fibroblasts and VSMCs. In vivo experiments confirmed the upregulation of these genes in AAA mice and demonstrated the functional interaction between COL1A1/COL1A2 and CD18.

CONCLUSION

The interaction between fibroblasts and VSMCs, mediated by specific ligand-receptor pairs such as COL1A1/COL1A2-CD18 and THBS1-CD3, plays a pivotal role in AAA pathogenesis.