Multiomic analysis reveals conservation of cancer-associated fibroblast phenotypes across species and tissue of origin

A microfluidic co-culture platform for lung cancer cells electrotaxis study under the existence of stromal cells

Tumor metastasis is an important reason for the poor prognosis and high mortality in cancer patients. As major component of stromal cells in tumor microenvironment, cancer-associated fibroblasts (CAFs) secreted various factors to promote tumor metastasis. Studies have indicated that endogenous direct current electric field (dcEF) around tumor tissue induced directional migration of cancer cells. However, the regulatory effect of CAFs on cancer migration under dcEF stimulation is still unknown. In this study, a two-layers polydimethylsiloxane (PDMS)-based microfluidic chip was fabricated. The introduction of concave structures achieved the non-contacted co-culture of different cell types, and parallel channels in the chip provided stable and homogeneous dcEF. Cells electrotactic response was evaluated under co-culture circumstance. The results showed that CAFs exhibited directional migration towards anode under dcEF stimulation, while A549 cells had a trend of directional migration towards cathode. The co-existence of CAFs and dcEF significantly enhanced the motility and cathodal migration of A549 cells, suggesting synergistic influences of chemotaxis from CAFs and electrotaxis from dcEF stimulation. Moreover, we demonstrated that lung normal fibroblasts acquired CAFs properties after stimulated by dcEF, characterizing by increasing gene expression of α-SMA and IL-6. Overall, Our device and study provide new insight for tumor electrotaxis in complex microenvironment.

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.

Single-cell RNA sequencing and traditional RNA sequencing reveals the role of cancer-associated fibroblasts in head and neck squamous cell carcinomas cohort

BACKGROUND

Head and neck squamous cell carcinomas (HNSCs) are among the most common tumors worldwide. Despite the availability of various diagnostic and therapeutic strategies, the incidence and mortality rates of HNSC remain high. Cancer-associated fibroblasts (CAFs), as a major component of the tumor microenvironment, exhibit diverse biological characteristics in terms of origin, genetics, and phenotype, and have been increasingly recognized for their roles in tumor progression.

METHODS

To investigate the potential role of CAFs in HNSC, we performed a comprehensive bioinformatics analysis based on the TCGA HNSC cohort. We applied single-sample gene set enrichment analysis (ssGSEA), single-cell RNA sequencing (scRNA-seq) analysis, differential expression analysis, Cox regression, LASSO regression, and pathway enrichment analysis to identify CAF-related genes and assess their prognostic value.

RESULTS

We successfully identified a set of CAF-related genes and stratified the HNSC patients into high- and low-CAF groups. Based on the expression of these genes, we constructed a prognostic prediction model using LASSO and multivariate Cox regression analyses. A nomogram integrating the risk score and clinical characteristics was developed to improve individualized survival prediction. Enrichment analysis revealed that the type I interferon signaling pathway, cellular response to type I interferon, defense response to symbiont, and extracellular matrix organization were significantly associated with CAFs in HNSC.

CONCLUSION

Our study provides a novel CAF-based prognostic model and nomogram for predicting patient outcomes in HNSC. These findings highlight the importance of CAFs in the tumor microenvironment and their potential as therapeutic and prognostic biomarkers.

Conserved spatial subtypes and cellular neighborhoods of cancer-associated fibroblasts revealed by single-cell spatial multi-omics

Cancer-associated fibroblasts (CAFs) are a multifaceted cell population essential for shaping the tumor microenvironment (TME) and influencing therapy responses. Characterizing the spatial organization and interactions of CAFs within complex tissue environments provides critical insights into tumor biology and immunobiology. In this study, through integrative analyses of over 14 million cells from 10 cancer types across 7 spatial transcriptomics and proteomics platforms, we discover, validate, and characterize four distinct spatial CAF subtypes. These subtypes are conserved across cancer types and independent of spatial omics platforms. Notably, they exhibit distinct spatial organizational patterns, neighboring cell compositions, interaction networks, and transcriptomic profiles. Their abundance and composition vary across tissues, shaping TME characteristics, such as levels, distribution, and state composition of tumor-infiltrating immune cells, tumor immune phenotypes, and patient survival. This study enriches our understanding of CAF spatial heterogeneity in cancer and paves the way for novel approaches to target and modulate CAFs.

Tie2 activity in cancer associated myofibroblasts serves as novel target against reprogramming of cancer cells to embryonic-like cell state and associated poor prognosis in oral carcinoma patients

BACKGROUND

Myofibroblastic cancer-associated fibroblasts (CAF) in tumor stroma serves as an independent poor prognostic indicator, supporting higher stemness in oral cancer; however, the underlying biology is not fully comprehended. Here, we have explored the crucial role of Tunica Interna Endothelial Cell Kinase (Tie2/TEK) signaling in transition and maintenance of myofibroblastic phenotype of CAFs, and as possible link with the poor prognosis of head and neck squamous cell carcinoma (HNSCC) patients.

METHODS

Bulk and single cell RNA-sequencing (scRNAseq) methods and in-depth bioinformatic analysis were applied for CAF and cancer cells co-culture for studying molecular relationships. In vitro 3D-spheroid-forming ability, expression of stemness markers, in vivo tumor formation ability in zebrafish embryo and syngeneic mouse allografts formation was conducted to test stemness, upon targeting CAF-specific Tie2 activity by gene silencing or with small molecule inhibitor. Immunohistochemistry analysis was performed to locate the distribution of Tie2 and αSMA in primary tumors of oral carcinoma. Prognosis in HNSCC patient cohort from The Cancer Genome Atlas (TCGA) study was analysed based on single sample gene set enrichment score (ssGSEA) and Kaplan-Meier analysis.

RESULTS

Autocrine or exogenous TGFβ-induction in CAF led to the recruitment of histone deacetylase 2 (HDAC2) on the promoter of Tie2-antagonist, Angiopoietin-2 (ANGPT2), resulting in its downregulation, leading to phosphorylation of Tie2 (Y992) and subsequent activation of SRC (Y418). This led to SRC/ROCK mediated αSMA-positive stress-fiber formation with gain of myofibroblast phenotype. The CAF-specific Tie2-signaling was responsible for producing embryonic-like cell state in co-cultured cancer cells; with enhanced tumor initiating ability. Tie2 activity in CAF exerted the dynamic gene expression reprogramming, with the upregulation of 'cell migration' and downregulation of 'protein biosynthesis' related gene-regulatory-network modules in malignant cells. The AUCell scores calculated for gene signatures derived from these modules showed significant concordance in independently reported scRNAseq studies of HNSCC tumors and significant association with poor prognosis in HNSCC patient cohort.

CONCLUSIONS

CAF-specific Tie2 activity may serve as direct stromal-target against cancer cell plasticity leading to poor prognosis of oral cancer patients. Overall, our work has provided wider applicability of Tie2-specific functions in tumor biology, along with its known role in endothelial cell-specific function.

Spatial multi-omics reveals the potential involvement of SPP1+ fibroblasts in determining metabolic heterogeneity and promoting metastatic growth of colorectal cancer liver metastasis

This study investigates key microscopic regions involved in colorectal cancer liver metastasis (CRLM), focusing on the crucial role of cancer-associated fibroblasts (CAFs) in promoting tumor progression and providing molecular- and metabolism-level insights for its diagnosis and treatment using multi-omics. We followed 12 fresh surgical samples from 2 untreated CRLM patients. Among these, 4 samples were used for spatial transcriptomics (ST), 4 for spatial metabolomics, and 4 for single-cell RNA sequencing (scRNA-seq). Additionally, 92 frozen tissue samples from 40 patients were collected. Seven patients were used for immunofluorescence and RT-qPCR, while 33 patients were used for untargeted metabolomics. ST revealed that the spatial regions of CRLM consists of 7 major components, with fibroblast-dominated regions being the most prominent. These regions are characterized by diverse cell-cell interactions, and immunosuppressive and tumor growth-promoting environments. scRNA-seq identified that SPP1+ fibroblasts interact with CD44+ tumor cells, as confirmed through immunofluorescence. Spatial metabolomics revealed suberic acid and tetraethylene glycol as specific metabolic components of this structure, which was further validated by untargeted metabolomics. In conclusion, an SPP1+ fibroblast-rich spatial region with metabolic reprogramming capabilities and immunosuppressive properties was identified in CRLM, which potentially facilitates metastatic outgrowth through interactions with tumor cells.

B4GALT5 inhibits CD8+ T-cell response by downregulating MHC-I level through ERAD pathway in PDAC

BACKGROUND

Immune evasion is a crucial event in the progression of pancreatic ductal adenocarcinoma (PDAC). The identification of new immunotherapeutic targets may provide a promising platform for advancing PDAC treatment. This study aims to investigate the role of beta-1,4-galactosyltransferase-5 (B4GALT5) in immune evasion by pancreatic cancer cells and evaluate its potential as an immunotherapeutic target.

METHODS

We conducted a comprehensive analysis using RNA sequencing data and tissue microarrays from patients with PDAC to investigate the association between B4GALT5 expression and patient prognosis. Using animal models, we further explored the impact of B4GALT5 on the quantity and activity of tumor-infiltrating CD8+ T cells. RNA sequencing and co-immunoprecipitation were used to explore the mechanism by which B4GALT5 regulates major histocompatibility complex (MHC-I) levels.

RESULTS

Our study demonstrates that high expression of B4GALT5 in tumor cells is significantly associated with poor prognosis in patients with PDAC and reduced cytotoxic activity of tumor-infiltrating CD8+ T cells. Specifically, B4GALT5 suppresses MHC-I expression in tumor cells through the endoplasmic reticulum-associated degradation pathway, enabling them to evade immune surveillance by CD8+ T cells.

CONCLUSIONS

B4GALT5 impairs CD8+ T-cell recognition of tumor cells by regulating MHC-I levels, thereby promoting immune evasion. This makes B4GALT5 a highly promising immunotherapeutic target for improving the poor prognosis of patients with PDAC.

Multi-omic profiling in breast cancer: utility for advancing diagnostics and clinical care

INTRODUCTION

Breast cancer remains a major global health challenge. While advances in precision oncology have contributed to improvements in patient outcomes and provided a deeper understanding of the biological mechanisms that drive the disease, historically, research and patients' allocation to treatment have heavily relied on single-omic approaches, analyzing individual molecular dimensions such as genomics, transcriptomics, or proteomics. While these have provided deep insights into breast cancer biology, they often fail to offer a complete understanding of the disease's complex molecular landscape.

AREAS COVERED

In this review, the authors explore the recent advancements in multi-omic research in the realm of breast cancer and use clinical data to show how multi-omic integration can offer a more holistic understanding of the molecular alterations and their functional consequences underlying breast cancer.

EXPERT OPINION

The overall developments in multi-omic research and AI are expected to complement precision diagnostics through potentially refining prognostic models, and treatment selection. Overcoming challenges such as cost, data complexity, and lack of standardization is crucial for unlocking the full potential of multi-omics and AI in breast cancer patient care to enable the advancement of personalized treatments and improve patient outcomes.

Macrophages and fibroblasts as regulators of the immune response in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is one of the few cancers that has yet to benefit from immunotherapies. This is primarily a result of its characteristic 'cold' tumor microenvironment composed of cancer-associated fibroblasts (CAFs), a dense network of extracellular matrix and several immune cell types, the most abundant of which are the tumor-associated macrophages (TAMs). Advances in single-cell and spatial technologies have elucidated the vast functional heterogeneity of CAFs and TAMs, their symbiotic relationship and their cooperative role in the tumor microenvironment. In this Review, we provide an overview of the heterogeneity of CAFs and TAMs, how they establish an immunosuppressive microenvironment and their collaboration in the remodeling of the extracellular matrix. Finally, we examine why the impact of immunotherapy in PDAC has been limited and how a detailed molecular and spatial understanding of the combined role of CAFs and TAMs is paramount to the design of effective therapies.

Characterization of cancer-associated fibroblasts and their spatial architecture reveals heterogeneity and survival associations in classic Hodgkin lymphoma

Cancer-associated fibroblasts (CAFs) are a heterogeneous population of stromal cells, which modulate the immune system and can have both pro- and anti-tumorigenic effects. In classic Hodgkin lymphoma (cHL), the role of CAFs has remained largely undefined. We applied multiplexed immunofluorescence imaging and spatial analysis on tumor samples from two independent cHL patient cohorts (n = 131 and n = 148) to study CAFs and their interactions with Hodgkin Reed-Sternberg (HRS) and tumor microenvironment (TME) cells at the single-cell resolution. We show that higher proportions of CAFs are associated with favorable outcomes, independent of the clinical covariables. In contrast, a subset of CD45+ immune cells with strong fibroblast-activation protein positivity, classified as macrophages, was less abundant in nodular sclerosis subtype and associated with worse outcomes. Neighborhood analysis allowed for the identification of colocalization or regional exclusion of phenotypically defined cell types and recurrent cellular neighborhoods. Despite the positive impact of CAF proportions on survival, patients with enrichment of platelet-derived growth factor receptor beta (PDGFRB)-positive CAFs in the vicinity of HRS cells had worse survival in both cohorts, independent of the clinical determinants. Our findings distinguish various subsets of CAFs and macrophages impacting survival in cHL and underscore the importance of the spatial arrangements in the TME.

Cancer-associated fibroblasts promote EGFR-TKI resistance via the CTHRC1/glycolysis/H3K18la positive feedback loop

Acquired resistance to epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) remains a major challenge in the treatment of lung cancer. Cancer associated fibroblasts (CAFs) play a key role in promoting resistance to anti-cancer therapies. This study identified a subpopulation of CAFs characterized by the overexpression of collagen triple helix repeat-containing 1 (CTHRC1) through single-cell RNA sequencing of lung cancer patients undergoing EGFR-TKI treatment. These CTHRC1+ CAFs were enriched in drug-resistant tumors. Mechanistically, CTHRC1+ CAFs enhance the glycolytic activity of cancer cells by activating the TGF-β/Smad3 signaling pathway. Excess lactate produced in the process of glycolysis further upregulates CTHRC1 expression in CAFs through histone lactylation, creating a positive feedback loop that sustains EGFR-TKI resistance. The study also demonstrated that Gambogenic Acid, a natural compound, can disrupt this feedback loop, thereby improving the efficacy of EGFR-TKI therapy. Additionally, the presence of CTHRC1+ CAFs in tumor tissues could serve as a biomarker for predicting the response to EGFR-TKI therapy and patient prognosis. Overall, this study highlights the significant role of CAFs in EGFR-TKI resistance and suggests that targeting CTHRC1+ CAFs could be a promising strategy to overcome drug resistance in lung cancer.

Histological signatures map anti-fibrotic factors in mouse and human lungs

Fibrosis, the replacement of healthy tissue with collagen-rich matrix, can occur following injury in almost every organ1,2. Mouse lungs follow a stereotyped sequence of fibrogenesis-to-resolution after bleomycin injury3, and we reasoned that profiling post-injury histological stages could uncover pro-fibrotic versus anti-fibrotic features with functional value for human fibrosis. Here we quantified spatiotemporally resolved matrix transformations for integration with multi-omic data. First, we charted stepwise trajectories of matrix aberration versus resolution, derived from a high-dimensional set of histological fibre features, that denoted a reversible transition in uniform-to-disordered histological architecture. Single-cell sequencing along these trajectories identified temporally enriched 'ECM-secreting' (Csmd1-expressing) and 'pro-resolving' (Cd248-expressing) fibroblasts at the respective post-injury stages. Visium-based spatial analysis further suggested divergent matrix architectures and spatial-transcriptional neighbourhoods by fibroblast subtype, identifying distinct fibrotic versus non-fibrotic biomolecular milieu. Critically, pro-resolving fibroblast instillation helped to ameliorate fibrosis in vivo. Furthermore, the fibroblast neighbourhood-associated factors SERPINE2 and PI16 functionally modulated human lung fibrosis ex vivo. Spatial phenotyping of idiopathic pulmonary fibrosis at protein level additionally uncovered analogous fibroblast subtypes and neighbourhoods in human disease. Collectively, these findings establish an atlas of pro- and anti-fibrotic factors that underlie lung matrix architecture and implicate fibroblast-associated biological features in modulating fibrotic progression versus resolution.

Fibroblast hierarchy dynamics during mammary gland morphogenesis and tumorigenesis

Fibroblasts form a major component of the stroma in normal mammary tissue and breast tumors. Here, we have applied longitudinal single-cell transcriptome profiling of >45,000 fibroblasts in the mouse mammary gland across five different developmental stages and during oncogenesis. In the normal gland, diverse stromal populations were resolved, including lobular-like fibroblasts, committed preadipocytes and adipogenesis-regulatory, as well as cycling fibroblasts in puberty and pregnancy. These specialized cell types appear to emerge from CD34high mesenchymal progenitor cells, accompanied by elevated Hedgehog signaling. During late tumorigenesis, heterogeneous cancer-associated fibroblasts (CAFs) were identified in mouse models of breast cancer, including a population of CD34- myofibroblastic CAFs (myCAFs) that were transcriptionally and phenotypically similar to senescent CAFs. Moreover, Wnt9a was demonstrated to be a regulator of senescence in CD34- myCAFs. These findings reflect a diverse and hierarchically organized stromal compartment in the normal mammary gland that provides a framework to better understand fibroblasts in normal and cancerous states.

High antigen-presenting CAF levels correlate with reduced glycosaminoglycan biosynthesis-heparan sulfate/heparin metabolism in immune cells and poor prognosis in esophageal squamous cell carcinoma: Insights from bulk and single-cell transcriptome profiling

In esophageal squamous cell carcinoma (ESCC), the tumor microenvironment (TME) is characterized by a significant accumulation of cancer-associated fibroblasts (CAFs), which play a pivotal role in the host response against tumor cells. While fibroblasts are known to be crucial in the metabolic reprogramming of the TME, the specific metabolic alterations induced by these cells remain largely undefined. Utilizing single-cell RNA sequencing, we have identified a distinct subpopulation of antigen-presenting CAF (apCAF) within ESCC tumors. Our findings reveal that apCAF contribute to adverse patient outcomes by remodeling the tumor metabolic environment. Notably, apCAF modulate the glycosaminoglycan biosynthesis-heparan sulfate/heparin metabolism pathway in T cells, B cells, and macrophages. Disruption of this pathway may facilitate immune evasion by the tumor. These insights underscore the critical role of CAFs in shaping the metabolic landscape of the TME and lay the groundwork for developing therapeutic strategies aimed at enhancing anti-tumor immunity.

Postoperative adhesions are abrogated by a sustained-release anti-JUN therapeutic in preclinical models

Postoperative abdominal adhesions are the leading cause of bowel obstruction and a cause of chronic pain and infertility. Adhesion formation occurs after 50 to 90% of abdominal operations and has no proven preventative or treatment strategy. Abdominal adhesions derive primarily from the visceral peritoneum and are composed of polyclonally proliferating tissue-resident fibroblasts. We have previously shown that signaling of the transcription factor JUN regulates adhesiogenesis and that a small-molecule JUN inhibitor (T-5224) decreases adhesion formation. Here, we encapsulated T-5224 in a shear-thinning hydrogel with antiadhesion properties for intraperitoneal postoperative delivery and sustained release of a JUN inhibitor for adhesion prevention. The material properties of the T-5224-hydrogel support its use for open or minimally invasive surgical application. We found this therapeutic system to be safe, well tolerated, and efficacious in murine and porcine preclinical models. T-5224-hydrogel minimized adhesion quantity and also diminished adhesion fibrosis at an ultrastructural level. Moving toward clinical translation, we developed a large mammal adhesion model in pigs with bowel resection. Single-cell transcriptomic analysis showed that JUN and associated pathway signaling were diminished in adhesion-derived fibroblasts treated with T-5224-hydrogel. The JUN-inhibiting T-5224-hydrogel provided robust prevention of adhesion without deleterious effects on bowel anastomosis or abdominal wall healing. Adhesion biology is similar across surgical sites, and, therefore, this formulation has potential for applicability across the body. The development of therapeutics to prevent adhesions is of paramount importance with potential for high-impact translation to patient care to address a common, unmet clinical need.

Cross-Talk Between Cancer and Its Cellular Environment-A Role in Cancer Progression

The tumor microenvironment is a dynamic and complex three-dimensional network comprising the extracellular matrix and diverse non-cancerous cells, including fibroblasts, adipocytes, endothelial cells and various immune cells (lymphocytes T and B, NK cells, dendritic cells, monocytes/macrophages, myeloid-derived suppressor cells, and innate lymphoid cells). A constantly and rapidly growing number of studies highlight the critical role of these cells in shaping cancer survival, metastatic potential and therapy resistance. This review provides a synthesis of current knowledge on the modulating role of the cellular microenvironment in cancer progression and response to treatment.

Single-cell and spatial transcriptome profiling reveal CTHRC1+ fibroblasts promote EMT through WNT5A signaling in colorectal cancer

BACKGROUND

Cancer-associated fibroblasts (CAFs), known for facilitating the progression and metastasis of colorectal cancer (CRC), have become a promising therapeutic target. However, the significant heterogeneity of CAFs and their intricate crosstalk with tumor cells present substantial challenges in the development of precise and effective therapeutic strategies.

METHODS

Single-cell RNA sequencing (scRNA-seq) technology was used to identify various cell subtypes. Spatial transcriptomics (ST) was employed to map the spatial niches and colocalization patterns of these cell subtypes. Cell-cell interactions among these subtypes were analysed via CellChat and NicheNet software. Tumor cell invasion, migration, and proliferation were assessed through wound healing assays, transwell assays, colony formation assays, and xenograft mouse models.

RESULTS

We identified a significant spatial colocalization between CTHRC1+ CAFs and a distinct subtype of malignant epithelial cells, both residing within the EMT-active spatial niche. Our results demonstrate that CTHRC1+ CAFs, as a major source of WNT5A, promote epithelial-mesenchymal transition (EMT) and enhance tumor cell invasiveness by upregulating MSLN expression in adjacent malignant epithelial cells. This signaling axis contributes significantly to CRC progression and metastasis.

CONCLUSIONS

Targeting the CTHRC1+ CAF-WNT5A-MSLN signaling axis presents a promising therapeutic strategy for advanced CRC patients. Our study provides new insights into the role of CAFs in CRC progression and offers potential avenues for developing targeted therapies to disrupt this pathway.

Radiotherapy-Associated Cellular Senescence and EMT Alterations Contribute to Distinct Disease Relapse Patterns in Locally Advanced Cervical Cancer

A notable number of locally advanced cervical carcinoma (LACC) patients experience local or distant disease relapse following radiotherapy. The contribution of tumor microenvironment (TME) to tumor recurrence at different sites remains unclear. Here, single-nucleus RNA sequencing data from 28 pre- and on-treatment LACC samples from patients with different disease relapse patterns is analyzed. The findings revealed opposing alterations in the expression levels of the cellular senescence pathway after radiotherapy in patients with local and distant relapses. In contrast, an increase in the expression of the epithelial-mesenchymal transition module after radiotherapy in both relapse groups is observed. Cell-cell interactions, drug-target expression analyses in malignant cells after radiation, and multiplex immunofluorescence of tumor tissue identified interleukin-1 receptor type I (IL1R1) as a potential therapeutic target. It is demonstrated that combining the IL1R1 inhibitor anakinra with radiation can mitigate the effects of radiation on tumor cells. This study highlights the distinct roles of cellular senescence and EMT in tumor recurrence.

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.

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.

Advances in nanotechnology for targeting cancer-associated fibroblasts: A review of multi-strategy drug delivery and preclinical insights

Cancer-associated fibroblasts (CAFs) play a crucial role in the tumor microenvironment by promoting tumor growth, immune evasion, and metastasis. Recently, drug delivery systems targeting CAFs have emerged as a promising long-term and effective approach to cancer treatment. Advances in nanotechnology, in particular, have led to the development of nanomedicine delivery systems designed specifically to target CAFs, offering new possibilities for precise and personalized cancer therapies. This article reviews recent progress in drug delivery using nanocarriers that target CAFs. Additionally, we explore the potential of combining multiple therapies, such as chemotherapy and immunotherapy, with nanocarriers to enhance efficacy and overcome drug resistance. Although many preclinical studies show promise, the clinical application of nanomedicine still faces considerable challenges, especially in terms of drug penetration and large-scale production. Therefore, this review aims to provide a fresh perspective on CAF-targeted drug delivery systems and highlight potential future research directions and clinical applications.

Inhibiting mechanotransduction prevents scarring and yields regeneration in a large animal model

Modulating mechanotransduction by inhibiting yes-associated protein (YAP) in mice yields wound regeneration without scarring. However, rodents are loose-skinned and fail to recapitulate key aspects of human wound repair. We sought to elucidate the effects of YAP inhibition in red Duroc pig wounds, the most human-like model of scarring. We show that one-time treatment with verteporfin, a YAP inhibitor, immediately after wounding is sufficient to prevent scarring and to drive wound regeneration in pigs. By performing single-cell RNA sequencing (scRNA-seq) on porcine wounds in conjunction with spatial proteomic analysis, we found perturbations in fibroblast dynamics with verteporfin treatment and the presence of putative pro-regenerative/profibrotic fibroblasts enriched in regenerating/scarring pig wounds, respectively. We also identified differences in enriched myeloid cell subpopulations after treatment and linked this observation to increased elaboration of interleukin-33 (IL-33) in regenerating wounds. Finally, we validated our findings in a xenograft wound model containing human neonatal foreskin engrafted onto nude mice and used scRNA-seq of human wound cells to draw parallels with fibroblast subpopulation dynamics in porcine wounds. Collectively, our findings provide support for the clinical translation of local mechanotransduction inhibitors to prevent human skin scarring, and they clarify a YAP/IL-33 signaling axis in large animal wound regeneration.

Recent advancement in the spatial immuno-oncology

Recent advancements in spatial transcriptomics and spatial proteomics enabled the high-throughput profiling of single or multi-cell types and cell states with spatial information. They transformed our understanding of the higher-order architectures and paired cell-cell interactions within a tumor microenvironment (TME). Within less than a decade, this rapidly emerging field has discovered much crucial fundamental knowledge and significantly improved clinical diagnosis in the field of immuno-oncology. This review summarizes the conceptual frameworks to understand spatial omics data and highlights the updated knowledge of spatial immuno-oncology.

Stromal architecture and fibroblast subpopulations with opposing effects on outcomes in hepatocellular carcinoma

Dissecting the spatial heterogeneity of cancer-associated fibroblasts (CAFs) is vital for understanding tumor biology and therapeutic design. By combining pathological image analysis with spatial proteomics, we revealed two stromal archetypes in hepatocellular carcinoma (HCC) with different biological functions and extracellular matrix compositions. Using paired single-cell RNA and epigenomic sequencing with Stereo-seq, we revealed two fibroblast subsets CAF-FAP and CAF-C7, whose spatial enrichment strongly correlated with the two stromal archetypes and opposing patient prognosis. We discovered two functional units, one is the intratumor inflammatory hub featured by CAF-FAP plus CD8_PDCD1 proximity and the other is the marginal wound-healing hub with CAF-C7 plus Macrophage_SPP1 co-localization. Inhibiting CAF-FAP combined with anti-PD-1 in orthotopic HCC models led to improved tumor regression than either monotherapy. Collectively, our findings suggest stroma-targeted strategies for HCC based on defined stromal archetypes, raising the concept that CAFs change their transcriptional program and intercellular crosstalk according to the spatial context.

Drug Delivery System Targeting Cancer-Associated Fibroblast for Improving Immunotherapy

Cancer-associated fibroblasts (CAFs) are a heterogeneous population of non-malignant cells that play a crucial role in the tumor microenvironment, increasingly recognized as key contributors to cancer progression, metastasis, and treatment resistance. So, targeting CAFs has always been considered an important part of cancer immunotherapy. However, targeting CAFs to improve the efficacy of tumor therapy is currently a major challenge. Nanomaterials show their unique advantages in the whole process. At present, nanomaterials have achieved significant accomplishments in medical applications, particularly in the field of cancer-targeted therapy, showing enormous potential. It has been confirmed that nanomaterials can not only directly target CAFs, but also interact with the tumor microenvironment (TME) and immune cells to affect tumorigenesis. As for the cancer treatment, nanomaterials could enhance the therapeutic effect in many ways. Therefore, in this review, we first summarized the current understanding of the complex interactions between CAFs and TME, immune cells, and tumor cells. Next, we discussed common nanomaterials in modern medicine and their respective impacts on the TME, CAFs, and interactions with tumors. Finally, we focus on the application of nano drug delivery system targeting CAFs in cancer therapy.

Molecular and cellular dynamics of squamous cell carcinomas across tissues

Squamous cell carcinomas (SCCs), arising from the skin, head and neck, lungs, esophagus, and cervix, are collectively among the most common cancers and a frequent cause of cancer morbidity and mortality. Despite distinct stratified epithelial tissues of origin, converging evidence points toward shared biologic pathways across SCCs. With recent breakthroughs in molecular technologies have come novel SCC treatment paradigms, including immunotherapies and targeted therapy. This review compares commonalities and differences across SCCs from different anatomical sites, including risk factors and genetics, as well as cellular and molecular programs driving tumorigenesis. We review landmark discoveries of the "cancer stem cells" (CSCs) that initiate and propagate SCCs and their gene and translational regulation programs. This has led to an appreciation that interactions between CSCs and the immune system play key roles in invasion and therapeutic resistance. Here, we review the unifying principles of SCCs that have emerged from these exciting advances in our understanding of these epithelial cancers.

Epigenomic heterogeneity as a source of tumour evolution

In the past decade, remarkable progress in cancer medicine has been achieved by the development of treatments that target DNA sequence variants. However, a purely genetic approach to treatment selection is hampered by the fact that diverse cell states can emerge from the same genotype. In multicellular organisms, cell-state heterogeneity is driven by epigenetic processes that regulate DNA-based functions such as transcription; disruption of these processes is a hallmark of cancer that enables the emergence of defective cell states. Advances in single-cell technologies have unlocked our ability to quantify the epigenomic heterogeneity of tumours and understand its mechanisms, thereby transforming our appreciation of how epigenomic changes drive cancer evolution. This Review explores the idea that epigenomic heterogeneity and plasticity act as a reservoir of cell states and therefore as a source of tumour evolution. Best practices to quantify epigenomic heterogeneity and explore its various causes and consequences are discussed, including epigenomic reprogramming, stochastic changes and lasting memory. The design of new therapeutic approaches to restrict epigenomic heterogeneity, with the long-term objective of limiting cancer development and progression, is also addressed.

Single cell transcriptomics reveals the cellular heterogeneity of keloids and the mechanism of their aggressiveness

Keloid is a dermatofibrotic disease known for its aggressive nature and characterized by pathological scarring, which often leads to disfigurement and frequent recurrences. Effective therapies for keloids are still limited, presumably due to the inadequate comprehension of their aggressive mechanisms. In our study, we examined the unique scenario where both keloid and non-aggressive pathological scar originate from the same patient, providing a rare opportunity to explore the aggressive mechanisms of keloids through single-cell RNA sequencing. We found that the dominant fibroblast subgroup in keloids is mechanoresponsive group, which showed enhanced mechanotransduction and migration. This mechanoresponsive fibroblast subgroup is likely to be the key cell population and confer aggressive growth of keloids. The results also indicate that the endothelial cells and keratinocytes in keloid involve in endothelial-mesenchymal and epithelial-mesenchymal transitions. This study demonstrated the mechanoresponsive fibroblasts and multiple cellular mesenchymal processes could pave the way for further investigations into the keloid aggressiveness.

Heterogeneity and therapeutic implications of cancer-associated fibroblasts in lung cancer: Recent advances and future perspectives

Lung cancer is a leading cause of cancer-related mortality. The tumor microenvironment is a complex and heterogeneous cellular environment surrounding tumor cells, including cancer-associated fibroblasts (CAFs), blood vessels, immune cells, the extracellular matrix, and various cytokines secreted by cells. CAFs are highly heterogeneous and play crucial roles in lung cancer. This review highlights recent advances in the understanding of CAFs in lung cancer, focusing on their heterogeneity and functions in tumorigenesis, progression, angiogenesis, invasion, metastasis, therapy resistance, tumor immune suppression, and targeted therapy responses. Additionally, we explore the underlying mechanisms and the potential of CAFs as a target in the development of innovative therapies for lung cancer.

Dynamic Evolution of Fibroblasts Revealed by Single-Cell RNA Sequencing of Human Pancreatic Cancer

SIGNIFICANCE

Pancreatic cancer remains a high unmet medical need. Understanding the interactions between stroma and cancer cells in this disease may unveil new opportunities for therapeutic intervention.

Huaier-induced suppression of cancer-associated fibroblasts confers immunotherapeutic sensitivity in triple-negative breast cancer

BACKGROUND

Triple-negative breast cancer (TNBC) is the most intractable subgroup of breast neoplasms due to its aggressive nature. In recent years, immune checkpoint inhibitors (ICIs) have exhibited potential efficacy in TNBC treatment. However, only a limited fraction of patients benefit from ICI therapy, primarily because of the suppressive tumor immune microenvironment (TIME). Trametes robiniophila Murr (Huaier) is a traditional Chinese medicine (TCM) with potential immunoregulatory functions. However, the underlying mechanism remains unclear.

PURPOSE

The present study aimed to investigate the therapeutic role of Huaier in the TIME of TNBC patients.

METHODS

Single-cell RNA sequencing (scRNA-seq) was used to systematically analyze the influence of Huaier on the TNBC microenvironment for the first time. The mechanisms of the Huaier-induced suppression of cancer-associated fibroblasts (CAFs) were assessed via real-time quantitative polymerase chain reaction (qRT‒PCR) and western blotting. A tumor-bearing mouse model was established to verify the effects of the oral administration of Huaier on immune infiltration.

RESULTS

Unsupervised clustering of the transcriptional profiles suggested an increase in the number of apoptotic cancer cells in the Huaier group. Treatment with Huaier induced immunological alterations from a "cold" to a "hot" state, which was accompanied by phenotypic changes in CAFs. Mechanistic analysis revealed that Huaier considerably attenuated the formation of myofibroblastic CAFs (myoCAFs) by impairing transforming growth factor-beta (TGF-β)/SMAD signaling. In mouse xenograft models, Huaier dramatically modulated CAF differentiation, thus synergizing with the programmed cell death 1 (PD1) blockade to impede tumor progression.

CONCLUSIONS

Our findings demonstrate that Huaier regulates cancer immunity in TNBC by suppressing the transition of CAFs to myoCAFs and emphasize the crucial role of Huaier as an effective adjuvant agent in immunotherapy.

Ferroptosis and the tumor microenvironment

Ferroptosis is a type of regulated cell death characterized by its non-apoptotic, iron-dependent and oxidative nature. Since its discovery in 2012, extensive research has demonstrated its pivotal roles in tumorigenesis, metastasis and cancer therapy. The tumor microenvironment (TME) is a complex ecosystem comprising cancer cells, non-cancer cells, extracellular matrix, metabolites and cytokines. Recent studies have underscored a new paradigm in which non-cancer cells in the TME, such as immune and stromal cells, also play significant roles in regulating tumor progression and therapeutic resistance typically through complicated crosstalk with cancer cells. Notably, this crosstalk in the TME were partially mediated through ferrotopsis-related mechanisms. This review provides a comprehensive and systematic summary of the current findings concerning the roles of ferroptosis in the TME and how ferroptosis-mediated TME reprogramming impacts cancer therapeutic resistance and progression. Additionally, this review outlines various ferroptosis-related therapeutic strategies aimed at targeting the TME.

Cancer stem cells and their role in metastasis

Introduction

Cancer, next to cardiovascular diseases, remains the primary concern of modern medicine in developed countries. Despite the unprecedented progress in targeted therapies and personalised medicine, including immunotherapy and gene therapy, we are still unable to efficiently treat many malignancies. One of the major obstacles to treating cancer is its ability to metastasise. Hence, a better understanding of cancer biology with emphasis on the metastasis formation may hold the key to further ameliorating cancer treatment. Nowadays, there is a growing body of evidence for the common denominator of neoplasia, which seems to be universal - cancer stem cells which are being found in a growing number of cancers.

Material and methods

We conducted a Web of Science and Medline database search using the terms "cancer stem cells", "carcinogenesis", and "stem cells" in conjunction with "metastasis", without setting time limits.

Results

The existence of cancer stem cells was proven both in animal models and in humans. We know beyond doubt that cancer stem cells may be found in bladder cancer, breast cancer, and colon cancer, among others. The cancer stem cells in the aforementioned cancers may initiate tumour formation ex vivo and thus theoretically lead to tumour recurrence. Their role in the formation of metastases, however, is still under investigation.

Conclusions

Although their exact role is yet to be identified, it is now obvious that cancer stem cells give rise to primary mass in solid tumours and differentiated cancer cells in leukaemias. However, the role of cancer stem cells in metastasis is still obscure.

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.

Recent Advances of Small Extracellular Vesicles for the Regulation and Function of Cancer-Associated Fibroblasts

Cancer-associated fibroblasts (CAFs) are a heterogeneous cell population in the tumor microenvironment (TME) that critically affect cancer progression. Small extracellular vesicles (sEVs) act as information messengers by transmitting a wide spectrum of biological molecules, including proteins, nucleic acids, and metabolites, from donor cells to recipient cells. Previous studies have demonstrated that CAFs play important roles in tumor progression by regulating tumor cell proliferation, metastasis, therapeutic resistance, and metabolism via sEVs. In turn, tumor-derived sEVs can also regulate the activation and phenotype switch of CAFs. The dynamic crosstalk between CAFs and cancer cells via sEVs could ultimately determine cancer progression. In this review, we summarized the recent advance of the biological roles and underlying mechanisms of sEVs in mediating CAF-tumor cell interaction and its impact on cancer progression. We also reviewed the clinical applications of tumor- and CAF-derived sEVs, which could identify novel potential targets and biomarkers for cancer diagnosis, therapy, and prognosis.

Single-cell resolution spatial analysis of antigen-presenting cancer-associated fibroblast niches

Recent studies have identified a unique subtype of cancer-associated fibroblasts (CAFs) termed antigen-presenting CAFs (apCAFs), which remain the least understood CAF subtype. To gain a comprehensive understanding of the origin and function apCAFs, we construct a fibroblast molecular atlas across 14 types of solid tumors. Our integration study unexpectedly reveals two distinct apCAF lineages present in most cancer types: one associated with mesothelial-like cells and the other with fibrocytes. Using a high-resolution single-cell spatial imaging platform, we characterize the spatial niches of these apCAF lineages. We find that mesothelial-like apCAFs are located near cancer cells, while fibrocyte-like apCAFs are associated with tertiary lymphoid structures. Additionally, we discover that both apCAF lineages can up-regulate the secreted protein SPP1, which facilitates primary tumor formation and peritoneal metastasis. Taken together, this study offers an unprecedented resolution in analyzing apCAF lineages and their spatial niches.

YAP1 Inhibition Induces Phenotype Switching of Cancer-Associated Fibroblasts to Tumor Suppressive in Prostate Cancer

Prostate cancer rarely responds to immune-checkpoint blockade (ICB) therapies. Cancer-associated fibroblasts (CAF) are critical components of the immunologically "cold" tumor microenvironment and are considered a promising target to enhance the immunotherapy response. In this study, we aimed to reveal the mechanisms regulating CAF plasticity to identify potential strategies to switch CAFs from protumorigenic to antitumor phenotypes and to enhance ICB efficacy in prostate cancer. Integration of four prostate cancer single-cell RNA sequencing datasets defined protumorigenic and antitumor CAFs, and RNA-seq, flow cytometry, and a prostate cancer organoid model demonstrated the functions of two CAF subtypes. Extracellular matrix-associated CAFs (ECM-CAF) promoted collagen deposition and cancer cell progression, and lymphocyte-associated CAFs (Lym-CAF) exhibited an antitumor phenotype and induced the infiltration and activation of CD8+ T cells. YAP1 activity regulated the ECM-CAF phenotype, and YAP1 silencing promoted switching to Lym-CAFs. NF-κB p65 was the core transcription factor in the Lym-CAF subset, and YAP1 inhibited nuclear translocation of p65. Selective depletion of YAP1 in ECM-CAFs in vivo promoted CD8+ T-cell infiltration and activation and enhanced the therapeutic effects of anti-PD-1 treatment on prostate cancer. Overall, this study revealed a mechanism regulating CAF identity in prostate cancer and highlighted a therapeutic strategy for altering the CAF subtype to suppress tumor growth and increase sensitivity to ICB. Significance: YAP1 regulates cancer-associated fibroblast phenotypes and can be targeted to switch cancer-associated fibroblasts from a protumorigenic subtype that promotes extracellular matrix deposition to a tumor-suppressive subtype that stimulates antitumor immunity and immunotherapy efficacy.

Understanding and measuring mechanical signals in the tumor stroma

The tumor microenvironment (TME) is well known for its immune suppressive role, especially in solid tumors which are characterized by a thick, dense stroma. Apart from cell-cell interactions and biochemical signals, the tumor stroma is also characterized by its distinct mechanical properties, which are dictated by the composition and architecture of its extracellular matrix (ECM). Cancer-associated fibroblasts (CAFs) are the main producers and remodelers of the stromal ECM, and their heterogeneity has recently become a focus of intense research. This review describes recent findings highlighting CAF subtypes and their specific functions, as well as the development of 3D models to study tumor stroma mechanics in vitro. Finally, we discuss the quantitative techniques used to measure tissue mechanical properties at different scales. Given the diagnostic and prognostic value of stroma stiffness and composition, and the recent development of anti-tumor therapeutic strategies targeting the stroma, understanding and measuring tumor stroma mechanical properties has never been more timely or relevant.

Single-cell RNA sequencing elucidated the landscape of breast cancer brain metastases and identified ILF2 as a potential therapeutic target

Distant metastasis remains the primary cause of morbidity in patients with breast cancer. Hence, the development of more efficacious strategies and the exploration of potential targets for patients with metastatic breast cancer are urgently needed. The data of six patients with breast cancer brain metastases (BCBrM) from two centres were collected, and a comprehensive landscape of the entire tumour ecosystem was generated through the utilisation of single-cell RNA sequencing. We utilised the Monocle2 and CellChat algorithms to investigate the interrelationships among each subcluster. In addition, multiple signatures were collected to evaluate key components of the subclusters through multi-omics methodologies. Finally, we elucidated common expression programs of malignant cells, and experiments were conducted in vitro and in vivo to determine the functions of interleukin enhancer-binding factor 2 (ILF2), which is a key gene in the metastasis module, in BCBrM progression. We found that subclusters in each major cell type exhibited diverse characteristics. Besides, our study indicated that ILF2 was specifically associated with BCBrM, and experimental validations further demonstrated that ILF2 deficiency hindered BCBrM progression. Our study offers novel perspectives on the heterogeneity of BCBrM and suggests that ILF2 could serve as a promising biomarker or therapeutic target for BCBrM.

Mimicking and analyzing the tumor microenvironment

The tumor microenvironment (TME) is increasingly appreciated to play a decisive role in cancer development and response to therapy in all solid tumors. Hypoxia, acidosis, high interstitial pressure, nutrient-poor conditions, and high cellular heterogeneity of the TME arise from interactions between cancer cells and their environment. These properties, in turn, play key roles in the aggressiveness and therapy resistance of the disease, through complex reciprocal interactions between the cancer cell genotype and phenotype, and the physicochemical and cellular environment. Understanding this complexity requires the combination of sophisticated cancer models and high-resolution analysis tools. Models must allow both control and analysis of cellular and acellular TME properties, and analyses must be able to capture the complexity at high depth and spatial resolution. Here, we review the advantages and limitations of key models and methods in order to guide further TME research and outline future challenges.

Hippo pathway in cancer cells induces NCAM1+αSMA+ fibroblasts to modulate tumor microenvironment

Cancer cells adeptly manipulate the tumor microenvironment (TME) to evade host antitumor immunity. However, the role of cancer cell-intrinsic signaling in shaping the immunosuppressive TME remains unclear. Here, we found that the Hippo pathway in cancer cells orchestrates the TME by influencing the composition of cancer-associated fibroblasts (CAFs). In a 4T1 mouse breast cancer model, Hippo pathway kinases, large tumor suppressor 1 and 2 (LATS1/2), promoted the formation of neural cell adhesion molecule 1 (NCAM1)+alpha-smooth muscle actin (αSMA)+ CAFs expressing the transforming growth factor-β, which is associated with T cell inactivation and dysfunction. Depletion of LATS1/2 in cancer cells resulted in a less immunosuppressive TME, indicated by the reduced proportions of NCAM1+αSMA+ CAFs and dysfunctional T cells. Notably, similar Hippo pathway-induced NCAM1+αSMA+ CAFs were observed in human breast cancer, highlighting the potential of TME-manipulating strategies to reduce immunosuppression in cancer immunotherapy.

Cancer Stemness Online: A Resource for Investigating Cancer Stemness and Associations with Immune Response

Cancer progression involves the gradual loss of a differentiated phenotype and the acquisition of progenitor and stem cell-like features, which are potential culprits of immunotherapy resistance. Although the state-of-the-art predictive computational methods have facilitated the prediction of cancer stemness, there remains a lack of efficient resources to accommodate various usage requirements. Here, we present the Cancer Stemness Online, an integrated resource for efficiently scoring cancer stemness potential at both bulk and single-cell levels. This resource integrates eight robust predictive algorithms as well as 27 signature gene sets associated with cancer stemness for predicting stemness scores. Downstream analyses were performed from five distinct aspects: identifying the signature genes of cancer stemness; exploring the associations with cancer hallmarks and cellular states; exploring the associations with immune response and the communications with immune cells; investigating the contributions to patient survival; and performing a robustness analysis of cancer stemness among different methods. Moreover, the pre-calculated cancer stemness atlas for more than 40 cancer types can be accessed by users. Both the tables and diverse visualizations of the analytical results are available for download. Together, Cancer Stemness Online is a powerful resource for scoring cancer stemness and expanding downstream functional interpretation, including immune response and cancer hallmarks. Cancer Stemness Online is freely accessible at http://bio-bigdata.hrbmu.edu.cn/CancerStemnessOnline.

Cross-tissue human fibroblast atlas reveals myofibroblast subtypes with distinct roles in immune modulation

Fibroblasts, known for their functional diversity, play crucial roles in inflammation and cancer. In this study, we conduct comprehensive single-cell RNA sequencing analyses on fibroblast cells from 517 human samples, spanning 11 tissue types and diverse pathological states. We identify distinct fibroblast subpopulations with universal and tissue-specific characteristics. Pathological conditions lead to significant shifts in fibroblast compositions, including the expansion of immune-modulating fibroblasts during inflammation and tissue-remodeling myofibroblasts in cancer. Within the myofibroblast category, we identify four transcriptionally distinct subpopulations originating from different developmental origins, with LRRC15+ myofibroblasts displaying terminally differentiated features. Both LRRC15+ and MMP1+ myofibroblasts demonstrate pro-tumor potential that contribute to the immune-excluded and immune-suppressive tumor microenvironments (TMEs), whereas PI16+ fibroblasts show potential anti-tumor functions in adjacent non-cancerous regions. Fibroblast-subtype compositions define patient subtypes with distinct clinical outcomes. This study advances our understanding of fibroblast biology and suggests potential therapeutic strategies for targeting specific fibroblast subsets in cancer treatment.

Universal and tissue-specific fibroblasts in chronic inflammation and cancer

In this issue of Cancer Cell, Gao et al. map fibroblast diversity across tumors and chronic inflammatory tissues. The authors uncover universal fibroblast subtypes such as LRRC15+ and MMP1+ myofibroblasts along with specialized tissue-specific subtypes. They reveal cellular roles of fibroblasts in immunosuppression through stromal niches and cell-cell interactions.

Spatial oncology: Translating contextual biology to the clinic

Microscopic examination of cells in their tissue context has been the driving force behind diagnostic histopathology over the past two centuries. Recently, the rise of advanced molecular biomarkers identified through single cell profiling has increased our understanding of cellular heterogeneity in cancer but have yet to significantly impact clinical care. Spatial technologies integrating molecular profiling with microenvironmental features are poised to bridge this translational gap by providing critical in situ context for understanding cellular interactions and organization. Here, we review how spatial tools have been used to study tumor ecosystems and their clinical applications. We detail findings in cell-cell interactions, microenvironment composition, and tissue remodeling for immune evasion and therapeutic resistance. Additionally, we highlight the emerging role of multi-omic spatial profiling for characterizing clinically relevant features including perineural invasion, tertiary lymphoid structures, and the tumor-stroma interface. Finally, we explore strategies for clinical integration and their augmentation of therapeutic and diagnostic approaches.

Hematoxylin and Eosin Architecture Uncovers Clinically Divergent Niches in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) represents one of the only cancers with an increasing incidence rate and is often associated with intra- and peri-tumoral scarring, referred to as desmoplasia. This scarring is highly heterogeneous in extracellular matrix (ECM) architecture and plays complex roles in both tumor biology and clinical outcomes that are not yet fully understood. Using hematoxylin and eosin (H&E), a routine histological stain utilized in existing clinical workflows, we quantified ECM architecture in 85 patient samples to assess relationships between desmoplastic architecture and clinical outcomes such as survival time and disease recurrence. By utilizing unsupervised machine learning to summarize a latent space across 147 local (e.g., fiber length, solidity) and global (e.g., fiber branching, porosity) H&E-based features, we identified a continuum of histological architectures that were associated with differences in both survival and recurrence. Furthermore, we mapped H&E architectures to a CO-Detection by indEXing (CODEX) reference atlas, revealing localized cell- and protein-based niches associated with outcome-positive versus outcome-negative scarring in the tumor microenvironment. Overall, our study utilizes standard H&E staining to uncover clinically relevant associations between desmoplastic organization and PDAC outcomes, offering a translatable pipeline to support prognostic decision-making and a blueprint of spatial-biological factors for modeling by tissue engineering methods.

Panoramic tumor microenvironment in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is notorious for its resistance to various treatment modalities. The genetic heterogeneity of PDAC, coupled with the presence of a desmoplastic stroma within the tumor microenvironment (TME), contributes to an unfavorable prognosis. The mechanisms and consequences of interactions among different cell types, along with spatial variations influencing cellular function, potentially play a role in the pathogenesis of PDAC. Understanding the diverse compositions of the TME and elucidating the functions of microscopic neighborhoods may contribute to understanding the immune microenvironment status in pancreatic cancer. As we delve into the spatial biology of the microscopic neighborhoods within the TME, aiding in deciphering the factors that orchestrate this intricate ecosystem. This overview delineates the fundamental constituents and the structural arrangement of the PDAC microenvironment, highlighting their impact on cancer cell biology.

Single-cell characterization of differentiation trajectories and drug resistance features in gastric cancer with peritoneal metastasis

BACKGROUND

Gastric cancer patients with peritoneal metastasis (GCPM) experience a rapidly deteriorating clinical trajectory characterized by therapeutic resistance and dismal survival, particularly following the development of malignant ascites. However, the intricate dynamics within the peritoneal microenvironment (PME) during the treatment process remain largely unknown.

METHODS

Matched samples from primary tumours (PT), peritoneal metastases (PM), and paired pre-treatment and post-chemo/immunotherapy (anti-PD-1/PD-L1) progression malignant ascites samples, were collected from 48 patients. These samples were subjected to single-cell RNA sequencing (n = 30), multiplex immunofluorescence (n = 30), and spatial transcriptomics (n = 3). Furthermore, post hoc analyses of a phase 1 clinical trial (n = 20, NCT03710265) and an in-house immunotherapy cohort (n = 499) were conducted to validate the findings.

RESULTS

Tracing the evolutionary trajectory of epithelial cells unveiled the terminally differentially MUC1+ cancer cells with a high epithelial-to-mesenchymal transition potential, and they demonstrated spatial proximity with fibroblasts and endothelial cells, correlating with poor prognosis. A significant expansion of macrophage infiltrates, which exhibited the highest proangiogenic activity, was observed in the ascites compared with PT and PM. Besides, higher C1Q+ macrophage infiltrates correlated with significantly lower GZMA+ T-lymphocyte infiltrates in therapeutic failure cases, potentially mediated by the LGALS9-CD45 and SPP1-CD44 ligand-receptor interactions. In the chemoresistant group, intimate interactions between C1Q+ macrophages and fibroblasts through the complement activation pathway were found. In the group demonstrating immunoresistance, heightened TGF-β production activity was detected in MUC1+ cancer cells, and they were skewed to interplay with C1Q+ macrophages through the GDF15-TGF-βR2 axis. Ultimately, post hoc analyses indicated that co-targeting TGF-β and PDL1 pathways may confer superior clinical benefits than sole anti-PD-1/PD-L1 therapy for patients presenting with GCPM at the time of diagnosis.

CONCLUSIONS

Our findings elucidated the cellular differentiation trajectories and crucial drug resistance features within PME, facilitating the exploration of effective targets for GCPM treatment.

HIGHLIGHTS

MUC1+ cancer cells with a high epithelial-to-mesenchymal transition potential and exhibiting spatial proximity to fibroblasts and endothelial cells constitute the driving force of gastric cancer peritoneal metastasis (GCPM). Higher C1Q+ macrophage infiltrates correlated with significantly lower GZMA+ T-lymphocyte infiltrates within the peritoneal microenvironment in therapeutic failure cases. Co-targeting TGF-β and PDL1 pathways may confer superior clinical benefits than sole anti-PD-1/PD-L1 therapy for patients presenting with GCPM at diagnosis.

Functional heterogeneity of cancer-associated fibroblasts with distinct neoadjuvant immunotherapy plus chemotherapy response in esophageal squamous cell carcinoma

Novel neoadjuvant immunotherapy combined with chemotherapy (neoICT) has improved outcomes for patients with esophageal squamous-cell carcinoma (ESCC), but challenges persist in low response rates and therapy resistance. Little is known about the intra-tumoral heterogeneity in the ESCC tumor microenvironment (TME) that underlies differential responses to neoadjuvant therapy. We applied single-cell RNA sequencing (scRNA-seq) profiling and multiplexed immunofluorescence staining to thoroughly decipher the TME in ESCC specimens from a neoadjuvant anti-PD1 combination therapy clinical trial. The cancer-associated fibroblasts (CAFs) population showed the significant alteration in abundance following neoadjuvant therapy. Specifically, IL6 + CCL2 + immunomodulatory CAFs and a novel CD248 + mechanoresponsive CAFs subset exhibited increasing infiltration. Mechanistically, CD248 + mechanoresponsive CAFs approached and lined the tumor nest to physically block the infiltration of CD8 + T cells and drug delivery, while IL6 + CCL2 + immunomodulatory CAFs induced therapeutic resistance with distinct IL-6 expression. Among patients treated with neoICT, we observed prominent CAF-T cell interactions. In particular, the NECTIN2-TIGIT ligand-receptor pair was enriched in treated samples, and TIGIT was identified as the major inhibitory checkpoint of T cells. Our findings demonstrate distinct alterations in TME constituent responses to neoadjuvant immunotherapy and identify functional phenotypes of CAFs associated with unfavorable therapeutic responses in patients. This provides potential targets to enhance responses to neoadjuvant therapy in ESCC.

Single-cell sequencing to multi-omics: technologies and applications

Cells, as the fundamental units of life, contain multidimensional spatiotemporal information. Single-cell RNA sequencing (scRNA-seq) is revolutionizing biomedical science by analyzing cellular state and intercellular heterogeneity. Undoubtedly, single-cell transcriptomics has emerged as one of the most vibrant research fields today. With the optimization and innovation of single-cell sequencing technologies, the intricate multidimensional details concealed within cells are gradually unveiled. The combination of scRNA-seq and other multi-omics is at the forefront of the single-cell field. This involves simultaneously measuring various omics data within individual cells, expanding our understanding across a broader spectrum of dimensions. Single-cell multi-omics precisely captures the multidimensional aspects of single-cell transcriptomes, immune repertoire, spatial information, temporal information, epitopes, and other omics in diverse spatiotemporal contexts. In addition to depicting the cell atlas of normal or diseased tissues, it also provides a cornerstone for studying cell differentiation and development patterns, disease heterogeneity, drug resistance mechanisms, and treatment strategies. Herein, we review traditional single-cell sequencing technologies and outline the latest advancements in single-cell multi-omics. We summarize the current status and challenges of applying single-cell multi-omics technologies to biological research and clinical applications. Finally, we discuss the limitations and challenges of single-cell multi-omics and potential strategies to address them.