Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer

Stromal fibrin shapes immune infiltration landscape of pancreatic ductal adenocarcinoma

In pancreatic ductal adenocarcinoma (PDAC), in-situ coagulation creates a thrombotic, crosslinked fibrin (x-fibrin)-rich tumor stroma (FibTS), whose impact on immune cell behavior remains unclear. We aimed to elucidate how FibTS in PDAC regulates immune cell infiltration, polarization, and crosstalk that favors immunosuppressive microenvironment and tumor growth. We assessed the spatial distribution of immune cells by multiplex immunostaining of human PDAC tissues, along with novel bioengineering and mouse tumor models. We investigated how FibTS influences the infiltration of tumor-associated macrophage (TAM) and T-cell subtypes and identified two distinct variants of PDAC, fibrin-high (Fibhi) and fibrin-low (Fiblow). Our findings reveal that PDAC cells secrete fibrinogen and thrombin to form FibTS, which acts as a physical barrier and biochemical niche that restricts CD8+ T-cell and TAM penetration into the tumor. The FibTS impeded immune cell penetration from the tumor stroma into the tumor parenchyma. Selective inhibition of FibTS formation by genetic and pharmacological tools altered the infiltration patterns of CD8+ T-cells and TAMs, decelerating PDAC growth. This study demonstrates that the barrier function of FibTS is crucial for immune evasion, particularly against macrophage and T-cell activity, presenting a potential therapeutic strategy to reshape the immune landscape within PDAC and slow tumor progression.

Cutting-edge technologies illuminate the neural landscape of cancer: Insights into tumor development

Neurogenesis constitutes a pivotal facet of malignant tumors, wherein cancer and its therapeutic interventions possess the ability to reconfigure the nervous system, establishing a pathologic feedback loop that exacerbates tumor progression. Recent strides in high-resolution imaging, single-cell analysis, multi-omics technologies, and experimental models have opened unprecedented avenues in cancer neuroscience. This comprehensive review summarizes the latest advancements of these emerging technologies in elucidating the biological mechanisms underlying tumor initiation, invasion, metastasis, and the dynamic heterogeneity of the tumor microenvironment(TME), with a specific focus on neuron-glial-tumor interactions in glioblastoma(GBM) and other neurophilic cancers. Moreover, we innovatively propose target screening processes based on sequencing technologies and database frameworks. It rigorously evaluates ongoing clinical trial drugs and efficacy while spotlighting characteristic cells in the central and peripheral TME, consolidating cancer biomarkers pivotal for future targeted therapies and management strategies. By integrating these cutting-edge findings, this review aims to offer fresh insights into tumor-nervous system interactions, establishing a robust foundation for forthcoming clinical advancements.

VCPIP1 facilitates pancreatic adenocarcinoma progression via Hippo/YAP signaling

Dysregulation of Hippo signaling is observed in pancreatic adenocarcinoma (PAAD). Moreover, overactivation of YAP is crucial for tumor progression. Although the inhibitory phospho-cascade is functional, the reason for YAP hyperactivation in PAAD remains unclear. Recent studies have revealed that the ubiquitin modification of YAP also plays an important role in the Hippo/YAP axis and cancer progression. To gain a better understanding of the potential mechanisms underlying the ubiquitination and deubiquitination of YAP, we carried out siRNA screening for critical deubiquitinases in PAAD. By using a deubiquitinase (DUB) library, we identified valosin-containing protein-interacting protein 1 (VCPIP1) as an important effector of YAP function and PAAD progression. Inhibition of VCPIP1 hampered PAAD progression via Hippo signaling. Clinical data revealed that VCPIP1 was elevated in PAAD and correlated with poor survival in PAAD patients. Biochemical assays demonstrated that VCPIP1 interacted with YAP, inhibiting K48-linked polyubiquitination and thereby increasing YAP stability. YAP directly binds to the VCPIP1 promoter region, enhancing its transcription in PAAD. Our study revealed a forward feedback loop between VCPIP1 and Hippo signaling in PAAD, indicating that VCPIP1 is a potential therapeutic drug target in PAAD.

Phosphorylation of USP32 by CDK5 regulates Rap1 stability and therapeutic resistance in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal human cancer. Gemcitabine-based chemotherapy remains the cornerstone for advanced PDAC. However, resistance to chemotherapy greatly limits its clinical therapeutic efficacy. Accordingly, the identification of novel therapeutic targets to overcome chemoresistance and improve prognosis is urgently needed. Screening of deubiquitinase family members, tandem affinity purification, mass spectrometry, and RNA sequencing (RNA-Seq) analysis were performed to predict the interactions and function of the CDK5-USP32-Rap1 axis in PDAC. In vitro and in vivo experiments were performed to elucidate the regulatory mechanism and biological roles of this axis in glycolytic reprogramming and chemoresistance in PDAC. Finally, TCGA database analysis and immunohistochemistry were performed to determine the expression and clinical significance of CDK5, USP32, and Rap1 in PDAC tissues. USP32 was identified as a bona fide deubiquitinase of Rap1. USP32 deubiquitinates and stabilizes Rap1, thereby promoting glycolytic reprogramming and chemoresistance in PDAC cells. Moreover, we unexpectedly found that CDK5-mediated phosphorylation of USP32 is required for its deubiquitinase activity toward Rap1 and drives malignant phenotypes of PDAC. Additionally, these functions can be significantly inhibited by pharmacological inhibition (roscovitine) or genetic ablation of CDK5. Importantly, combining a CDK5 inhibitor with gemcitabine has a synergetic anticancer effect. Indeed, the effectiveness of targeting CDK5 to sensitize PDAC cells to gemcitabine was confirmed in a patient-derived xenograft (PDX) model. CDK5 and USP32 expression is markedly elevated in PDAC samples and positively associated with Rap1 expression. Increased expression of CDK5, USP32, and Rap1 is significantly associated with poorer prognosis in PDAC. We identified the previously unrecognized oncogenic function and clinical importance of the CDK5-USP32-Rap1 axis, providing preclinical evidence for potential new combination strategies for PDAC therapy.

CellHit: a web server to predict and analyze cancer patients' drug responsiveness

We present the CellHit web server (https://cellhit.bioinfolab.sns.it/), a web-based platform designed to predict and analyze cancer patients' responsiveness to drugs using transcriptomic data. By leveraging extensive pharmacogenomics datasets from the Genomics of Drug Sensitivity in Cancer v1 and v2 (GDSC) and Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) and transcriptomic data from the Cancer Cell Line Encyclopedia (CCLE) and The Cancer Genome Atlas Program (TCGA). CellHit integrates a computational pipeline for preprocessing, gene imputation, and robust alignment between patient and cell line transcriptomic data with pre-trained SOTA models for drug sensitivity prediction. The pipeline employs batch correction, enhanced Celligner methodology, and Parametric UMAP for stable and actionable alignment. The intuitive interface requires no programming expertise, offering interactive visualizations, including low-dimensional embeddings and drug sensitivity heatmaps for the input transcriptomic samples. Results feature contextual metadata, SHAP-based feature importance, and transcriptomic neighbors from reference datasets, simplifying interpretation and hypothesis generation. CellHit provides precomputed predictions across TCGA samples and offers the ability to run custom analyses online on input samples, democratizing precision oncology by enabling rapid, interpretable predictions accessible the research community.

SRSF12 deficiency enhances tumor innervation and accelerates pancreatic tumorigenesis

The peripheral nervous system significantly determines the fate of solid tumors and their microenvironment. In neurotropic malignancies such as pancreatic and prostate cancer, denervation in animal models demonstrate significantly delays in tumor initiation and progression, underscoring the critical neural dependency of these cancers. While tumor innervation establishes a structural basis for the neuromodulatory effects, the degree of innervation exhibits marked heterogeneity across tumor types, and its regulatory mechanisms remain poorly characterized. In this study, we screened genes associated with innervation status in pancreatic cancer and identified the splicing factor SRSF12 as a critical gene related to tumor innervation. In clinical samples, SRSF12 was expressed at low levels in pancreatic cancer tissues, and its downregulation was linked to poor prognosis in patients. Then we crossed Kras mutation and Srsf12 knockout mice (KrasG12DSrsf12 fl/fl) together with Srsf12 fl/flPdx1cre mice and found that depletion of Srsf12 accelerated Kras-driven pancreatic tumorigenesis and enhanced tumor innervation. Furthermore, we demonstrated that SRSF12 inhibits neurite outgrowth primarily by generating a LAMA3 splice isoform that lacks the fourth and fifth LG (G45) domains. Mechanistically, G45 promotes tumor innervation by activating ITGB1 and FAK in neurons. Together, our findings delineate SRSF12 as a novel suppressor of tumor innervation and pancreatic tumorigenesis, while also identifying a tumor-specific target for SRSF12-deficient pancreatic cancer.

Exploring the biological mechanism and clinical value of perineural invasion in pancreatic cancer

Pancreatic cancer (PC) is an extremely aggressive malignancy, with a 5-year survival rate of only 13 %. Perineural invasion (PNI) is a hallmark pathological feature of PC and is observed in almost all cases. Accordingly, PC ranks highly among solid tumors in terms of PNI incidence. The interaction between PC and the nervous system plays a pivotal role in tumor growth and metastasis. In PC, PNI is a key driver of local tumor progression, distant metastasis, and poor prognosis. Clarification of tumor-nerve crosstalk and the underlying molecular mechanisms is needed to facilitate the development of new therapeutic strategies to slow PC progression and alleviate PNI-associated symptoms. In this review, we present a comprehensive overview of the manifestations and characteristics of PNI in PC, summarize the molecular networks that regulate PNI, examine the relationship between PNI and the tumor microenvironment, and discuss the current research challenges and future directions in this critical area.

Integrated spatial morpho-transcriptomics predicts functional traits in pancreatic cancer

Analyses of patient-derived cell lines have greatly enhanced discovery of molecular biomarkers and therapeutic targets. However, characterization of cellular morphological properties is limited. We studied cell morphologies of human pancreatic adenocarcinoma (PDAC) cell lines and their associations with drug sensitivity, gene expression, and functional properties. By integrating live cell and spatial mRNA imaging, we identified KRAS inhibitor-induced morphological changes specific for drug-resistant cells that correlated with gene expression changes. We then categorized a large panel of patient-derived PDAC cell lines into morphological (e.g., polygonal, irregular, spheroid) and organizational (e.g., tightly aggregated, multilayered, dispersed) subtypes and found differences in gene expression, therapeutic targeting potential, and metastatic proclivity. In human PDAC tissues, we identified prognostic expression signatures associated with distinct cancer cell organization patterns. In summary, we highlight the potential of cell morphological information in rapid, cost-effective assays to aid precision oncology efforts leveraging patient-derived in vitro models and tissues.

Quantifying and interpreting biologically meaningful spatial signatures within tumor microenvironments

The tumor microenvironment (TME) plays a crucial role in orchestrating tumor cell behavior and cancer progression. Recent advances in spatial profiling technologies have uncovered novel spatial signatures, including univariate distribution patterns, bivariate spatial relationships, and higher-order structures. These signatures have the potential to revolutionize tumor mechanism and treatment. In this review, we summarize the current state of spatial signature research, highlighting computational methods to uncover spatially relevant biological significance. We discuss the impact of these advances on fundamental cancer biology and translational research, address current challenges and future research directions.

Spatial Transcriptomics Reveals Novel Mechanisms Involved in Perineural Invasion in Pancreatic Ductal Adenocarcinomas

BACKGROUND

Pancreatic ductal adenocarcinoma (PDAC) has a high incidence of perineural invasion (PNI), a pathological feature of the cancer invasion of nerves. PNI is associated with a poor prognosis, local recurrence and cancer pain. It has been suggested that interactions between nerves and the tumor microenvironment (TME) play a role in PDAC tumorigenesis.

METHODS

Here, we used Nanostring GeoMx Digital Spatial Profiler to analyze the whole transcriptome of both cancer and nerve cells in the microenvironment of PNI and non-PNI foci from 13 PDAC patients.

CONCLUSIONS

We identified previously reported pathways involved in PNI, including Axonal Guidance and ROBO-SLIT Signaling. Spatial transcriptomics highlighted the role of PNI foci in influencing the immune landscape of the TME and similarities between PNI and nerve injury response. This study revealed that endocannabinoid and polyamine metabolism may contribute to PNI, cancer growth and cancer pain. Key members of these pathways can be targeted, offering potential novel research avenues for exploring new cancer treatment and/or pain management options in PDAC.

Central nervous system and immune cells interactions in cancer: unveiling new therapeutic avenues

Cancer remains a leading cause of mortality worldwide. Despite significant advancements in cancer research, our understanding of its complex developmental pathways remains inadequate. Recent research has clarified the intricate relationship between the central nervous system (CNS) and cancer, particularly how the CNS influences tumor growth and metastasis via regulating immune cell activity. The interactions between the central nervous system and immune cells regulate the tumor microenvironment via various signaling pathways, cytokines, neuropeptides, and neurotransmitters, while also incorporating processes that alter the tumor immunological landscape. Furthermore, therapeutic strategies targeting neuro-immune cell interactions, such as immune checkpoint inhibitors, alongside advanced technologies like brain-computer interfaces and nanodelivery systems, exhibit promise in improving treatment efficacy. This complex bidirectional regulatory network significantly affects tumor development, metastasis, patient immune status, and therapy responses. Therefore, understanding the mechanisms regulating CNS-immune cell interactions is crucial for developing innovative therapeutic strategies. This work consolidates advancements in CNS-immune cell interactions, evaluates their potential in cancer treatment strategies, and provides innovative insights for future research and therapeutic approaches.

Intratumor heterogeneity in KRAS signaling shapes treatment resistance

KRAS mutations are linked to some of the deadliest forms of cancer. Pharmacological studies suggest that co-targeting KRAS with feedback/bypass pathways could lead to enhanced anti-tumor activity. The underlying premise is that cancers display a deep-rooted hypersensitivity to KRAS inactivation. Here, we investigate the role of intratumor heterogeneity in pancreatic ductal adenocarcinoma, focusing on oncogenic KRAS addiction and treatment resistance. Integrated analysis of single-cell and bulk RNA sequencing data reveals that most tumors display a mixture of cells with vastly different degrees of KRAS dependency. We identify distinct cell populations that vary in their gene expression patterns pertaining to the predicted level of KRAS signaling activity, cell growth, and differentiation commitment within each tumor. Selective targeting of mutant KRAS suppresses the growth of tumor cells with high RAS/mitogen-activated protein kinase (MAPK) activity while sparing pre-existing subsets with low RAS signaling activity, necessitating alternative treatments. Combination immunotherapy leads to durable tumor regression in preclinical models.

Comprehensive analysis of mitochondrial-related gene signature for prognosis, tumor immune microenvironment evaluation, and candidate drug development in colon cancer

Colon adenocarcinoma (COAD), a common digestive system malignancy, involves crucial alterations in mitochondria-related genes influencing tumor growth, metastasis, and immune evasion. Despite limited studies on prognostic models for these genes in COAD, we established a mitochondrial-related risk prognostic model, including nine genes based on available TCGA and MitoCarta 3.0 databases, and validated its predictive power. We investigated the tumor microenvironment (TME), immune cell infiltration, complex cell communication, tumor mutation burden, and drug sensitivity of COAD patients using R language, CellChat, and additional bioinformatic tools from single-cell and bulk-tissue sequencing data. The risk model revealed significant differences in immune cell infiltration between high-risk and low-risk groups, with the strongest correlation found between tissue stem cells and macrophages in COAD. The risk score exhibited a robust correlation with TME signature genes and immune checkpoint molecules. Integrating the risk score with the immune score, microsatellite status, or TMB through TIDE analysis enhanced the accuracy of predicting immunotherapy benefits. Predicted drug efficacy offered options for both high- and low-risk group patients. Our study established a novel mitochondrial-related nine-gene prognostic signature, providing insights for prognostic assessment and clinical decision-making in COAD patients.

Learning and actioning general principles of cancer cell drug sensitivity

High-throughput screening of drug sensitivity of cancer cell lines (CCLs) holds the potential to unlock anti-tumor therapies. In this study, we leverage such datasets to predict drug response using cell line transcriptomics, focusing on models' interpretability and deployment on patients' data. We use large language models (LLMs) to match drug to mechanisms of action (MOA)-related pathways. Genes crucial for prediction are enriched in drug-MOAs, suggesting that our models learn the molecular determinants of response. Furthermore, by using only LLM-curated, MOA-genes, we enhance the predictive accuracy of our models. To enhance translatability, we align RNAseq data from CCLs, used for training, to those from patient samples, used for inference. We validated our approach on TCGA samples, where patients' best scoring drugs match those prescribed for their cancer type. We further predict and experimentally validate effective drugs for the patients of two highly lethal solid tumors, i.e., pancreatic cancer and glioblastoma.

Peripheral, central, and chemotherapy-induced neuropathic changes in pancreatic cancer

In pancreatic cancer, significant alterations occur in the local nervous system, including axonogenesis, neural remodeling, perineural invasion, and perineural neuritis. Pancreatic cancer can impact the central nervous system (CNS) through cancer cell-intrinsic factors or systemic factors, particularly in the context of cancer cachexia. These peripheral and central neuropathic changes exert substantial influence on cancer initiation and progression. Moreover, chemotherapy-induced neuropathy is common in pancreatic cancer, causing peripheral nerve damage and cognitive dysfunction. Targeting the crosstalk between pancreatic cancer and the nervous system, either peripherally or centrally, holds promise in cancer treatment, pain relief, and improved quality of life. Here, we summarize recent findings on the molecular mechanisms behind these neuropathic changes in pancreatic cancer and discuss potential intervention strategies.

Extracellular matrix stiffness regulates colorectal cancer progression via HSF4

BACKGROUND

Colorectal cancer (CRC) has high incidence and mortality rates, with severe prognoses during invasion and metastasis stages. Despite advancements in diagnostic and therapeutic technologies, the impact of the tumour microenvironment, particularly extracellular matrix (ECM) stiffness, on CRC progression and metastasis is not fully understood.

METHODS

This study included 107 CRC patients. Tumour stiffness was assessed using magnetic resonance elastography (MRE), and collagen ratio was analysed with Masson staining. CRC cell lines were cultured on matrices of varying stiffness, followed by transcriptome sequencing to identify stiffness-related genes. An HSF4 knockout CRC cell model was cultured in different ECM stiffness to evaluate the effects of HSF4 on cell proliferation, migration, and invasion in vitro and in vivo.

RESULTS

CRC tumour stiffness was significantly higher than normal tissue and positively correlated with collagen content and TNM staging. High-stiffness matrices significantly regulated cell functions and signalling pathways. High HSF4 (heat shock transcriptional factor 4) expression was strongly associated with tumour stiffness and poor prognosis. HSF4 expression increased with higher TNM stages, and its knockout significantly inhibited cell proliferation, migration, and invasion, especially on high-stiffness matrices. In vivo experiments confirmed that HSF4 promoted tumour growth and metastasis, independent of collagen protein increase.

CONCLUSIONS

This study reveals that tumour stiffness promotes the proliferation and metastasis of CRC by regulating EMT-related signalling pathways through HSF4. Tumour stiffness and HSF4 could be valuable targets for prognostic assessment and therapeutic intervention in CRC.

Deciphering mechanical cues in the microenvironment: from non-malignant settings to tumor progression

The tumor microenvironment functions as a dynamic and intricate ecosystem, comprising a diverse array of cellular and non-cellular components that precisely orchestrate pivotal tumor behaviors, including invasion, metastasis, and drug resistance. While unraveling the intricate interplay between the tumor microenvironment and tumor behaviors represents a tremendous challenge, recent research illuminates a crucial biological phenomenon known as cellular mechanotransduction. Within the microenvironment, mechanical cues like tensile stress, shear stress, and stiffness play a pivotal role by activating mechanosensitive effectors such as PIEZO proteins, integrins, and Yes-associated protein. This activation initiates cascades of intrinsic signaling pathways, effectively linking the physical properties of tissues to their physiological and pathophysiological processes like morphogenesis, regeneration, and immunity. This mechanistic insight offers a novel perspective on how the mechanical cues within the tumor microenvironment impact tumor behaviors. While the intricacies of the mechanical tumor microenvironment are yet to be fully elucidated, it exhibits distinct physical attributes from non-malignant tissues, including elevated solid stresses, interstitial hypertension, augmented matrix stiffness, and enhanced viscoelasticity. These traits exert notable influences on tumor progression and treatment responses, enriching our comprehension of the multifaceted nature of the microenvironment. Through this innovative review, we aim to provide a new lens to decipher the mechanical attributes within the tumor microenvironment from non-malignant contexts, broadening our knowledge on how these factors promote or inhibit tumor behaviors, and thus offering valuable insights to identify potential targets for anti-tumor strategies.

Sympathetic nerve signaling rewires the tumor microenvironment: a shift in "microenvironmental-ity"

Nerve signaling within the tumor microenvironment (TME) plays a critical role in the initiation, progression, and metastasis of solid tumors. Due to their highly responsive behavior and activation upon injury and cancer onset, this review specifically focuses on how sympathetic nerves rewire the TME. Within tumors, sympathetic nerves closely interact with various TME components, and their combined signaling often shifts tumor-intrinsic physiology toward tumor-supportive phenotypes. In turn, the TME components, such as myeloid cells, lymphoid cells, extracellular matrix (ECM), endothelial cells, cancer associated fibroblasts (CAFs), and Schwann cells, secrete neurotrophic and axon guidance factors that influence both sympathetic outgrowth and tumor cell behavior, further exacerbating tumor progression and metastasis. Here, we review the current evidence on the multidirectional impacts of sympathetic nerves and both immune and non-immune TME components, the nature of these communication processes, and how exploring these interactions may inform future therapeutics to impair cancer progression and metastasis.

The Safety and Suitability of DNA Sequencing of Tissue Biopsies Performed on Patients Referred to a Phase I Unit

BACKGROUND

Early-phase clinical trials offer a unique opportunity for patients with cancer. These trials often mandate biopsies to collect tumor tissue for research purposes, requiring patients to undergo invasive procedures. Some trials mandate molecular prescreening, but the success of these analyses relies on the quality and quantity of the tested materials. Additionally, bioptic procedures may result in complications.

METHODS

We retrospectively examined the records of patients referred to the Early Drug Development (EDD) Unit of the European Institute of Oncology who underwent biopsies for research purposes between January 2014 and December 2022. Our objective was to assess the safety of biopsy procedures and adequacy of the samples for NGS testing.

RESULTS

In total, 355 out of 731 patients (48.6%) underwent protocol-mandated biopsies. The most frequent sites of biopsy were the liver, lymph nodes, skin, and breast. Histological diagnosis was achieved in 349 (98%) patients, and NGS testing was successfully conducted in 111/127 (88.4%) cases. Of the 16 unsuccessful NGS attempts, 9 were performed on liver tissue. Unsuccessful NGS testing was attributed to poor sample quality and/or quantity, and the success rate varied significantly based on the specific tests attempted. Complications occurred in a small proportion of patients (4.8%), and none were serious.

CONCLUSIONS

The non-negligible failure rate of NGS testing highlights the crucial need for implementing specific guidelines and Standard Operating Procedures for samples intended for NGS. With the use of a risk-based biopsy framework to guide clinical decisions, procedure-related complications may be minimized.

NGF-mediated crosstalk: unraveling the influence of metabolic deregulation on the interplay between neural and pancreatic cancer cells and its impact on patient outcomes

Neural invasion is one of the most common routes of invasion in pancreatic cancer and it is responsible for the high rate of tumor recurrence after surgery and the pain generation associated with pancreatic cancer. Several molecules implicated in neural invasion are also responsible for pain onset including NGF belonging to the family of neutrophins. NGF released by cancer cells can sensitize sensory nerves which in turn results in severe pain. NGF receptors, TrkA and P75NTR, are expressed on both PDAC cells and nerves, strongly suggesting their role in neural invasion. The crosstalk between the nervous system and cancer cells has emerged as an important regulator of pancreatic cancer and its microenvironment. Nerve cells influence the pancreatic tumor microenvironment and these interactions are important for cancer metabolism reprogramming and tumor progression. In this review, we summarized the current knowledge on the interaction between nerves and pancreatic cancer cells and its impact on cancer metabolism.

Depicting the cellular complexity of pancreatic adenocarcinoma by Imaging Mass Cytometry: focus on cancer-associated fibroblasts

Introduction

Pancreatic ductal adenocarcinoma (PDAC) represents the complexity of interaction between cancer and cells of the tumor microenvironment (TME). Immune cells affect tumor cell behavior, thus driving cancer progression. Cancer-associated fibroblasts (CAFs) are responsible of the desmoplastic and fibrotic reaction by regulating deposition and remodeling of extracellular matrix (ECM). As tumor-promoting cells abundant in PDAC ECM, CAFs represent promising targets for novel anticancer interventions. However, relevant clinical trials are hampered by the lack of specific markers and elusive differences among CAF subtypes. Indeed, while single-cell transcriptomic analyses have provided important information on the cellular constituents of PDACs and related molecular pathways, studies based on the identification of protein markers in tissues aimed at identifying CAF subtypes and new molecular targets result incomplete.

Methods

Herein, we applied multiplexed Imaging Mass Cytometry (IMC) at single-cell resolution on 8 human PDAC tissues to depict the PDAC composing cells, and profiling immune cells, endothelial cells (ECs), as well as endocrine cells and tumor cells.

Results

We focused on CAFs by characterizing up to 19 clusters distinguished by phenotype, spatiality, and interaction with immune and tumor cells. We report evidence that specific subtypes of CAFs (CAFs 10 and 11) predominantly are enriched at the tumor-stroma interface and closely associated with tumor cells. CAFs expressing different combinations of FAP, podoplanin and cadherin-11, were associated with a higher level of CA19-9. Moreover, we identified specific subsets of FAP+ and podoplanin+/cadherin-11+ CAFs enriched in patients with negative prognosis.

Discussion

The present study provides new general insights into the complexity of the PDAC microenvironment by defining phenotypic heterogeneities and spatial distributions of CAFs, thus suggesting different functions of their subtypes in the PDAC microenvironment.

Macrophage diversity in cancer dissemination and metastasis

Invasion and metastasis are hallmarks of cancer. In addition to the well-recognized hematogenous and lymphatic pathways of metastasis, cancer cell dissemination can occur via the transcoelomic and perineural routes, which are typical of ovarian and pancreatic cancer, respectively. Macrophages are a universal major component of the tumor microenvironment and, in established tumors, promote growth and dissemination to secondary sites. Here, we review the role of tumor-associated macrophages (TAMs) in cancer cell dissemination and metastasis, emphasizing the diversity of myeloid cells in different tissue contexts (lungs, liver, brain, bone, peritoneal cavity, nerves). The generally used models of lung metastasis fail to capture the diversity of pathways and tissue microenvironments. A better understanding of TAM diversity in different tissue contexts may pave the way for tailored diagnostic and therapeutic approaches.

Pancreatic ductal adenocarcinoma microenvironment: Soluble factors and cancer associated fibroblasts as modulators of NK cell functions

Pancreatic Ductal Adenocarcinoma (PDAC) is the most frequent pancreatic cancer and represents one of the most aggressive human neoplasms. Typically identified at advance stage disease, most PDAC tumors are unresectable and resistant to standard therapies. The immunosuppressive microenvironment in PDAC impedes tumor control but a greater understanding of the complex stromal interactions within the tumor microenvironment (TME) and the development of strategies capable of restoring antitumor effector immune responses could be crucial to fight this aggressive tumor and its spread. Natural Killer (NK) cells play a crucial role in cancer immunosurveillance and represent an attractive target for immunotherapies, both as cell therapy and as a pharmaceutical target. This review describes some crucial components of the PDAC TME (collagens, soluble factors and fibroblasts) that can influence the presence, phenotype and function of NK cells in PDAC patients tumor tissue. This focused overview highlights the therapeutic relevance of dissecting the complex stromal composition to define new strategies for NK cell-based immunotherapies to improve the treatment of PDAC.

The role of BUD31 in clear cell renal cell carcinoma: prognostic significance, alternative splicing, and tumor immune environment

BUD31, a splicing factor, is linked to various cancers. This study examines BUD31's expression, prognostic value, mutation profile, genomic instability, tumor immune environment, and role in clear cell renal cell carcinoma (ccRCC), focusing on cell cycle regulation via alternative splicing. BUD31 expression was analyzed using TCGA and GTEx databases across 33 cancers. Techniques included IHC staining, survival analysis, Cox regression, and nomogram construction. Mutation landscape, genomic instability, and tumor immune microenvironment were evaluated. Functional assays on ccRCC cell lines involved BUD31 knockdown, RNA sequencing, and alternative splicing analysis. BUD31 was upregulated in multiple tumors, including ccRCC. High BUD31 expression correlated with worse survival outcomes and was identified as an independent predictor of poor prognosis in ccRCC. High BUD31 expression also correlated with increased genomic instability and a less active immune microenvironment. BUD31 knockdown inhibited cell proliferation, migration, and invasion in vitro and reduced tumor growth in vivo. RNA sequencing identified 390 alternative splicing events regulated by BUD31, including 17 cell cycle-related genes. KEGG analysis highlighted pathways involved in cell cycle regulation, indicating BUD31's role in promoting cell cycle progression through alternative splicing. BUD31 is upregulated in various tumors and is associated with poor outcomes, increased genomic instability, and a suppressed immune microenvironment in ccRCC. BUD31 promotes cell cycle progression via alternative splicing, suggesting it as a prognostic biomarker and potential therapeutic target in ccRCC.

The landscape of cancer-rewired GPCR signaling axes

We explored the dysregulation of G-protein-coupled receptor (GPCR) ligand systems in cancer transcriptomics datasets to uncover new therapeutics opportunities in oncology. We derived an interaction network of receptors with ligands and their biosynthetic enzymes. Multiple GPCRs are differentially regulated together with their upstream partners across cancer subtypes and are associated to specific transcriptional programs and to patient survival patterns. The expression of both receptor-ligand (or enzymes) partners improved patient stratification, suggesting a synergistic role for the activation of GPCR networks in modulating cancer phenotypes. Remarkably, we identified many such axes across several cancer molecular subtypes, including many involving receptor-biosynthetic enzymes for neurotransmitters. We found that GPCRs from these actionable axes, including, e.g., muscarinic, adenosine, 5-hydroxytryptamine, and chemokine receptors, are the targets of multiple drugs displaying anti-growth effects in large-scale, cancer cell drug screens, which we further validated. We have made the results generated in this study freely available through a webapp (gpcrcanceraxes.bioinfolab.sns.it).