A TCF4-dependent gene regulatory network confers resistance to immunotherapy in melanoma

Mapping the rapid growth of multi-omics in tumor immunotherapy: Bibliometric evidence of technology convergence and paradigm shifts

This study aims to fill the knowledge gap in systematically mapping the evolution of omics-driven tumor immunotherapy research through a bibliometric lens. While omics technologies (genomics, transcriptomics, proteomics, metabolomics)provide multidimensional molecular profiling, their synergistic potential with immunotherapy remains underexplored in large-scale trend analyses. A comprehensive search was conducted using the Web of Science Core Collection for literature related to omics in tumor immunotherapy, up to August 2024. Bibliometric analyses, conducted using R version 4.3.3, VOSviewer 1.6.20, and Citespace 6.2, examined publication trends, country and institutional contributions, journal distributions, keyword co-occurrence, and citation bursts. This analysis of 9,494 publications demonstrates rapid growth in omics-driven tumor immunotherapy research since 2019, with China leading in output (63% of articles) yet exhibiting limited multinational collaboration (7.9% vs. the UK's 61.8%). Keyword co-occurrence and citation burst analyses reveal evolving frontiers: early emphasis on "PD-1/CTLA-4 blockade" has transitioned toward "machine learning," "multi-omics," and "lncRNA," reflecting a shift to predictive modeling and biomarker discovery. Multi-omics integration has facilitated the development of immune infiltration-based prognostic models, such as TIME subtypes, which have been validated across multiple tumor types, which inform clinical trial design (e.g. NCT06833723). Additionally, proteomic analysis of melanoma patients suggests that metabolic biomarkers, particularly oxidative phosphorylation and lipid metabolism, may stratify responders to PD-1 blockade therapy. Moreover, spatial omics has confirmed ENPP1 as a potential novel therapeutic target in Ewing sarcoma. Citation trends underscore clinical translation, particularly mutation-guided therapies. Omics technologies are transforming tumor immunotherapy by enhancing biomarker discovery and improving therapeutic predictions. Future advancements will necessitate longitudinal omics monitoring, AI-driven multi-omics integration, and international collaboration to accelerate clinical translation. This study presents a systematic framework for exploring emerging research frontiers and offers insights for optimizing precision-driven immunotherapy.

Modeling a mesenchymal cell state by bioprinting for the molecular analysis of dormancy in melanoma

Malignant melanoma is a highly aggressive tumor originating from the pigment producing cells, the melanocytes. It accounts for the majority of skin cancer related deaths worldwide. This is often due to the development of therapy resistance or tumor dormancy, eventually resulting in tumor relapse by yet undefined mechanisms. Tumor dormancy is thought to be mediated by the cellular microenvironment and models taking this factor into account are urgently needed. We 3D bioprinted melanoma cells in the hydrogels Cellink Bioink (CIB) or Matrigel (MG), each as a substitute of the extracellular matrix, and, thereby, induced a quiescent or a proliferative phenotype of the melanoma cell lines, respectively. RNA-Seq with subsequent comprehensive bioinformatical and molecular analyses assigned CIB-cultured cells to a predominantly mesenchymal and Matrigel-cultured cells to a more mitotic phenotype, emphasizing the CIB model as a suitable platform for the investigation of dormancy under consideration of the microenvironment. Melanoma cells in CIB 3D culture reflect a quiescent and migratory active cell state e.g. by revealing significant downregulation of genes associated with replication and cell cycle progression in this setting. Using this model system, we identified the mechanosensory gene FHL2 as one early sensor of changes in the ECM and suggest a FHL2-p21/AP-1 axis contributing to the dormant phenotype of melanoma cells in CIB.

Interpretable Differential Abundance Signature (iDAS)

Single-cell technologies have revolutionized the understanding of cellular dynamics by allowing researchers to investigate individual cell responses under various conditions, such as comparing diseased versus healthy states. Many differential abundance methods have been developed in this field, however, the understanding of the gene signatures obtained from those methods is often incomplete, requiring the integration of cell type information and other biological factors to yield interpretable and meaningful results. To better interpret the gene signatures generated in the differential abundance analysis, iDAS is developed to classify the gene signatures into multiple categories. When applied to melanoma single-cell data with multiple cell states and treatment phenotypes, iDAS identified cell state- and treatment phenotype-specific gene signatures, as well as interaction effect-related gene signatures with meaningful biological interpretations. The iDAS model is further applied to a longitudinal study and spatially resolved omics data to demonstrate its versatility in different analytical contexts. These results demonstrate that the iDAS framework can effectively identify robust, cell-state specific gene signatures and is versatile enough to accommodate various study designs, including multi-factor longitudinal and spatially resolved data.

Double-sided niche regulation in skin stem cell and cancer: mechanisms and clinical applications

The niche microenvironment plays a crucial role in regulating the fate of normal skin stem cells (SSCs) and cancer stem cells (CSCs). Therapeutically targeting the CSC niche holds promise as an effective strategy; however, the dual effects of shared SSC niche signaling in CSCs have contributed to the aggressive characteristics of tumors and poor survival rates in skin cancer patients. The lack of a clear underlying mechanism has significantly hindered drug development for effective treatment. This article explores recent advances in understanding how niche factors regulate cell fate determination between skin stem cells and skin CSCs, along with their clinical implications. The dual roles of key components of the adhesive niche, including the dermo-epidermal junction and adherens junction, various cell types-especially immune cells and fibroblasts-as well as major signaling pathways such as Sonic hedgehog (Shh), Wingless-related integration site (Wnt)/β-catenin, YAP (Yes-associated protein)/TAZ (transcriptional coactivator with PDZ-binding motif), and Notch, are highlighted. Additionally, recent advances in clinical trials and drug development targeting these pathways are discussed. Overall, this review provides valuable insights into the complex interactions between skin cancer stem cells and their microenvironment, laying the groundwork for future research and clinical strategies.

MCSP+ metastasis founder cells activate immunosuppression early in human melanoma metastatic colonization

To investigate the early, poorly understood events driving metastatic progression, we searched for the earliest detectable disseminated cancer cells (DCCs), also often referred to as disseminated tumor cells (DTCs), in sentinel lymph node (SLN) biopsies of 492 patients with stage I-III melanoma. Using micromanipulator-assisted isolation of rare DCCs, single-cell mRNA and DNA sequencing, codetection by indexing immunofluorescence imaging and survival analysis, we identified melanoma-associated chondroitin sulfate proteoglycan (MCSP)+ melanoma cells as metastasis founder cells (MFCs). We found that DCCs entering SLNs predominantly exhibited a transitory phenotype that, upon interferon-γ exposure triggered by CD8 T cells, dedifferentiated into a neural-crest-like phenotype. This was accompanied by increased production of small extracellular vesicles (sEVs) carrying the immunomodulatory proteins CD155 and CD276 but rarely programmed cell death protein 1 ligand 1. The sEVs suppressed CD8 T cell proliferation and function, facilitating colony formation. Targeting MCSP+ MFCs or their immune escape mechanisms could be key to curing melanoma early by preventing manifestation of metastasis.

Death-ision: the link between cellular resilience and cancer resistance to treatments

One of the key challenges in defeating advanced tumors is the ability of cancer cells to evade the selective pressure imposed by chemotherapy, targeted therapies, immunotherapy and cellular therapies. Both genetic and epigenetic alterations contribute to the development of resistance, allowing cancer cells to survive initially effective treatments. In this narration, we explore how genetic and epigenetic regulatory mechanisms influence the state of tumor cells and their responsiveness to different therapeutic strategies. We further propose that an altered balance between cell growth and cell death is a fundamental driver of drug resistance. Cell death programs exist in various forms, shaped by cell type, triggering factors, and microenvironmental conditions. These processes are governed by temporal and spatial constraints and appear to be more heterogeneous than previously understood. To capture the intricate interplay between death-inducing signals and survival mechanisms, we introduce the concept of Death-ision. This framework highlights the dynamic nature of cell death regulation, determining whether specific cancer cell clones evade or succumb to therapy. Building on this understanding offers promising strategies to counteract resistant clones and enhance therapeutic efficacy. For instance, combining DNMT inhibitors with immune checkpoint blockade may counteract YAP1-driven resistance or the use of transcriptional CDK inhibitors could prevent or overcome chemotherapy resistance. Death-ision aims to provide a deeper understanding of the diversity and evolution of cell death programs, not only at diagnosis but also throughout disease progression and treatment adaptation.

Epigenetic mechanisms in melanoma development and progression

Knowledge of cancer development and progression gained over the last few decades has enabled mapping of genetic and epigenetic changes unique to different phases of tumor evolution. Here we focus on epigenetic changes that drive melanoma development and progression. We highlight the importance of epigenetic mechanisms which encompass crosstalk with melanoma microenvironment that affect metastasis and therapy resistance. This review summarizes recent advances and describes potential strategies to leverage this knowledge to devise new therapies.

GLI2 Facilitates Tumor Immune Evasion and Immunotherapeutic Resistance by Coordinating WNT and Prostaglandin Signaling

Therapeutic resistance to immune checkpoint blockade has been commonly linked to the process of mesenchymal transformation (MT) and remains a prevalent obstacle across many cancer types. An improved mechanistic understanding for MT-mediated immune evasion promises to lead to more effective combination therapeutic regimens. Herein, we identified the hedgehog transcription factor, GLI2, as a key node of tumor-mediated immune evasion and immunotherapy resistance during MT. GLI2 generated an immunotolerant tumor microenvironment through the upregulation of WNT ligand production and increased prostaglandin synthesis. This pathway drove the recruitment, viability, and function of granulocytic myeloid-derived suppressor cells while also impairing type I conventional dendritic cell, CD8+ T-cell, and NK cell functionality. Pharmacologic inhibition of EP2/EP4 prostaglandin receptor signaling or WNT ligand secretion each reversed a subset of the immunomodulatory effects of GLI2 and prevented primary and adaptive resistance to anti-PD-1 immunotherapy, respectively. A transcriptional GLI2 signature correlated with resistance to anti-PD-1 immunotherapy in patients with stage IV melanoma. Together, these findings provide a translational roadmap to direct combination immunotherapies in the clinic. Significance: WNT and prostaglandin signaling generate an immunotolerant environment in GLI2-active tumors and can be targeted as a component of immunotherapeutic combination strategies to overcome resistance in tumors exhibiting mesenchymal plasticity.

CRKL silencing inhibits melanoma growth and enhances its chemotherapy sensitivity through the PI3K/AKT and NLRP3/GSDMD pathways

Great advances have been made in malignant melanoma treatments, whereas drug resistance still limits many drug applications. CRKL has been reported to be overexpressed in various tumors and showed poor prognosis. However, its specific function and mechanism in melanoma remain unclear. In the present study, we investigated the expression of CRKL and its clinical association by bioinformatics and clinical analysis, and then performed a series of in vitro and in vivo experiments to demonstrate its function and mechanism. Results showed that CRKL increased during melanoma progression and was strongly associated with poor prognosis. CRKL silencing effectively inhibited melanoma cell growth and invasion via ERK/MMP9 and PI3K/AKT signaling pathways both in vitro and in vivo. Moreover, CRKL silencing induced pyroptosis in melanoma cells by upregulating the levels of pyroptosis-associated proteins, such as NLRP3, cleaved Caspase-1, and GSDMD-N. Importantly, our study demonstrated that interfering with CRKL expression enhanced the chemotherapy sensitivity of melanoma cells to cisplatin by regulating PI3K/AKT and NLRP3/GSDMD signaling pathways. In conclusion, our study uncovers a novel molecular mechanism by which CRKL functions in melanoma and highlights potential therapeutic strategies for improving chemotherapy sensitivity in melanoma patients.

Current Progress and Future Directions of Immunotherapy in Head and Neck Squamous Cell Carcinoma: A Narrative Review

Importance

For decades, the 3 therapeutic pillars for head and neck squamous cell carcinoma (HNSCC) have been radiation therapy, chemotherapy, and surgery. In recent years, a fourth pillar, immunotherapy, has shifted the existing paradigm of oncologic care by improving survival outcomes. This narrative review highlights key completed and ongoing clinical trials that have led to new therapeutic approaches and are aiming to further alter the current standard of care.

Observations

Immunotherapy in HNSCC first saw success in phase 3 clinical trials with immune checkpoint inhibitors (ICIs) for programmed cell death 1 protein in patients with recurrent or metastatic (R/M) disease. However, only approximately 15% to 20% of patients with R/M HNSCC achieve durable responses. Subsequent trials aimed to broaden ICIs to the definitive or curative setting, in combination with established chemoradiation modalities. These studies have yielded disappointing results, raising concerns that concurrent administration of ICI with chemoradiation- or radiation-induced attenuation of immune responses may contribute to lack of efficacy. Therefore, recent studies have attempted to introduce ICI sequentially, either prior to standard of care surgery in the neoadjuvant setting or following definitive treatment in the adjuvant or maintenance setting. These trials have demonstrated mixed results but with promising initial results from early phase neoadjuvant trials demonstrating early signals of response. Further trials are currently underway with various combinatorial approaches in the neoadjuvant and adjuvant settings to assess response rates and survival.

Conclusions and Relevance

The introduction of ICIs has brought a dramatic shift in the treatment landscape of HNSCC. Completed trials have provided new hope for patients, but failures in several settings suggest that further studies based on a biologic understanding of immune responses are required to expand immunotherapeutic approaches.

Management of metastatic melanoma with combinations including PD-1 inhibitors

INTRODUCTION

Melanoma is among the most immunogenic malignancies. The advent of immune checkpoint inhibitors (ICIs) has revolutionized the landscape of melanoma treatment. Long-term durable cancer control is possible in nearly 50% of non-resectable, metastatic melanoma patients with anti-CTLA4 and anti-PD-1 antibodies.

AREAS COVERED

This review provides a critical overview of the current data and future research directions on the management of metastatic melanoma with ICIs. We reviewed the efficacy and safety of combinations with PD-1 inhibitors through PubMed database research (Nov 2024-Mar 2025).

EXPERT OPINION

A decade after ipilimumab's approval, challenges remain. To cure more patients, the development of combinations is warranted. Combinations with a limited number of ipilimumab applications improve the overall survival outcome by approximately 10%, with a dramatic increase in adverse events including fatal events. Anti-LAG3/nivolumab is a promising alternative, offering similar efficacy to ipilimumab/nivolumab with better tolerability. In our opinion, ipilimumab/nivolumab combination should be the first-line therapy for high-risk patients (high LDH, brain or liver metastasis), while nivolumab/relatlimab or PD-1 monotherapy may be preferable for lower-risk cases. However, treatment decisions are increasingly complex, since most patients nowadays are pretreated in the (neo)-adjuvant setting. The key limitation today is the lack of biomarkers to guide individualized treatment strategies.

KLF12 transcriptional activation by a novel LncRNA A930015D03Rik enhances melanoma metastasis

Melanoma metastasis remains a poorly understood yet fatal hallmark of cancer progression, with limited therapeutic strategies targeting its underlying mechanisms. While the transcription factor KLF12 shows paradoxical roles across malignancies, its context-dependent functions in melanoma-particularly its regulatory interplay with extracellular vesicle (EV)-driven intercellular communication-have not been systematically explored. To address this gap, we investigated how metastatic melanoma cells exploit KLF12-mediated pathways through EV cargo transfer to propagate aggressive phenotypes. Our research results indicate that highly metastatic cells transfer lncRNA A930015D03Rik through exosomes, acting as a sponge for miR-204-5p, which promotes the expression of KLF12. The transcriptional activation of KLF12 facilitates the activation of critical pro-cancer pathways such as inflammation and NF-κB, while inhibiting the tumor-suppressive mechanisms of P53 and oxidative phosphorylation. This ultimately enhances the migration and invasion capabilities of low-metastatic tumor cells, driving the malignant progression of melanoma. In this study, we identified a novel tumor-derived EVs lncRNA, A930015D03Rik, which can enhance the expression of KLF12 through a ceRNA mechanism and influence the post-translational regulation of KLF12, thereby modulating the plasticity of tumor metastasis. This exosome-genome feedforward circuit explains KLF12's microenvironment-contingent pro-metastatic function, offering significant insights for the development of future therapeutic strategies targeting tumor metastasis.

Safely Targeting Cancer, the Wound That Never Heals, Utilizing CBP/Beta-Catenin Antagonists

Stem cells, both normal somatic (SSC) and cancer stem cells (CSC) exist in minimally two states, i.e., quiescent and activated. Regulation of these two states, including their reliance on different metabolic processes, i.e., FAO and glycolysis in quiescent versus activated stem cells respectively, involves the analysis of a complex array of factors (nutrient and oxygen levels, adhesion molecules, cytokines, etc.) to initiate the epigenetic changes to either depart or enter quiescence. Quiescence is a critical feature of SSC that is required to maintain the genomic integrity of the stem cell pool, particularly in long lived complex organisms. Quiescence in CSC, whether they are derived from mutations arising in SSC, aberrant microenvironmental regulation, or via dedifferentiation of more committed progenitors, is a critical component of therapy resistance and disease latency and relapse. At the beginning of vertebrate evolution, approximately 450 million years ago, a gene duplication generated the two members of the Kat3 family, CREBBP (CBP) and EP300 (p300). Despite their very high degree of homology, these two Kat3 coactivators play critical and non-redundant roles at enhancers and super-enhancers via acetylation of H3K27, thereby controlling stem cell quiescence versus activation and the cells metabolic requirements. In this review/perspective, we discuss the unique regulatory roles of CBP and p300 and how specifically targeting the CBP/β-catenin interaction utilizing small molecule antagonists, can correct lineage infidelity and safely eliminate quiescent CSC.

Stromal lipid species dictate melanoma metastasis and tropism

Cancer cells adapt to signals in the tumor microenvironment (TME), but the TME cues that impact metastasis and tropism are still incompletely understood. We show that abundant stromal lipids from young subcutaneous adipocytes, including phosphatidylcholines, are taken up by melanoma cells, where they upregulate melanoma PI3K-AKT signaling, fatty acid oxidation, oxidative phosphorylation (OXPHOS) leading to oxidative stress, resulting in decreased metastatic burden. High OXPHOS melanoma cells predominantly seed the lung and brain; decreasing oxidative stress with antioxidants shifts tropism from the lung to the liver. By contrast, the aged TME provides fewer total lipids but is rich in ceramides, leading to lower OXPHOS and high metastatic burden. Aged TME ceramides taken up by melanoma cells activate the S1P-STAT3-IL-6 signaling axis and promote liver tropism. Inhibiting OXPHOS in the young TME or blocking the IL-6 receptor in the aged TME reduces the age-specific patterns of metastasis imposed by lipid availability.

Deubiquitination by USP7 Stabilizes JunD and Activates AIFM2 (FSP1) to Inhibit Ferroptosis in Melanoma

Ferroptosis resistance in melanoma cells is a key factor in melanoma progression, influenced by the tumor microenvironment. This study investigates the regulatory mechanisms of the USP7-JunD-AIFM2 pathway, which contributes to ferroptosis resistance in melanoma cells. We identified USP7 as a critical deubiquitinase that stabilizes the transcription factor JunD. Stabilized JunD, in turn, promotes the expression of AIFM2 (also known as FSP1), enhancing ferroptosis resistance in melanoma. Inhibition of USP7 led to JunD degradation and reduced AIFM2 levels, effectively sensitizing melanoma cells to ferroptosis both in vitro and in murine xenograft models. These findings underscore the role of the USP7-JunD-AIFM2 pathway in ferroptosis resistance and suggest that targeting USP7 could provide a potential therapeutic strategy against resistant melanoma.

Dual role of interferon-gamma in the response of melanoma patients to immunotherapy with immune checkpoint inhibitors

Interferon-gamma (IFN-γ) is a cytokine produced mainly by immune cells and can affect cancer cells by modulating the activity of multiple signaling pathways, including the canonical Janus-activated kinase/signal transducer and activator of transcription (JAK/STAT) cascade. In melanoma, IFN-γ can exert both anticancer effects associated with cell-cycle arrest and cell death induction and protumorigenic activity related to immune evasion leading to melanoma progression. Notably, IFN-γ plays a crucial role in the response of melanoma patients to immunotherapy with immune checkpoint inhibitors (ICIs), which are currently used in the clinic. As these agents target programmed death-1 (PD-1) and its ligand (PD-L1), cytotoxic T-lymphocyte-associated protein-4 (CTLA-4) and lymphocyte-activation gene 3 (LAG-3), they are designed to restore the antimelanoma immune response. In this respect, IFN-γ produced by cells in the tumor microenvironment in response to ICIs has a beneficial influence on both immune and melanoma cells by increasing antigen presentation, recruiting additional T-cells to the tumor site, and inducing direct antiproliferative effects and apoptosis in melanoma cells. Therefore, IFN-γ itself and IFN-γ-related gene signatures during the response to ICIs can constitute biomarkers or predictors of the clinical outcome of melanoma patients treated with ICIs. However, owing to its multifaceted roles, IFN-γ can also contribute to developing mechanisms associated with the acquisition of resistance to ICIs. These mechanisms can be associated with either decreased IFN-γ levels in the tumor microenvironment or diminished responsiveness to IFN-γ due to changes in the melanoma phenotypes associated with affected activity of other signaling pathways or genetic alterations e.g., in JAK, which restricts the ability of melanoma cells to respond to IFN-γ. In this respect, the influence of IFN-γ on melanoma-specific regulators of the dynamic plasticity of the cell phenotype, including microphthalmia-associated transcription factor (MITF) and nerve growth factor receptor (NGFR)/CD271 can affect the clinical efficacy of ICIs. This review comprehensively discusses the role of IFN-γ in the response of melanoma patients to ICIs with respect to its positive influence and role in IFN-γ-related mechanisms of resistance to ICIs as well as the potential use of predictive markers on the basis of IFN-γ levels and signatures of IFN-γ-dependent genes.

Antigenic cancer persister cells survive direct T cell attack

Drug-tolerant persister cancer cells were first reported fifteen years ago as a quiescent, reversible cell state which tolerates unattenuated cytotoxic drug stress. It remains unknown whether a similar phenomenon contributes to immune evasion. Here we report a persister state which survives weeks of direct cytotoxic T lymphocyte (CTL) attack. In contrast to previously known immune evasion mechanisms that avoid immune attack, antigenic persister cells robustly activate CTLs which deliver Granzyme B, secrete IFNγ, and induce tryptophan starvation resulting in apoptosis initiation. Instead of dying, persister cells paradoxically leverage apoptotic caspase activity to avoid inflammatory death. Furthermore, persister cells acquire mutations and epigenetic changes which enable outgrowth of CTL-resistant cells. Persister cell features are enriched in inflamed tumors which regressed during immunotherapy in vivo and in surgically resected human melanoma tissue under immune stress ex vivo. These findings reveal a persister cell state which is a barrier to immune-mediated tumor clearance.

Single-Cell Multi-Omics: Insights into Therapeutic Innovations to Advance Treatment in Cancer

Advances in single-cell multi-omics technologies have deepened our understanding of cancer biology by integrating genomic, transcriptomic, epigenomic, and proteomic data at single-cell resolution. These single-cell multi-omics technologies provide unprecedented insights into tumour heterogeneity, tumour microenvironment, and mechanisms of therapeutic resistance, enabling the development of precision medicine strategies. The emerging field of single-cell multi-omics in genomic medicine has improved patient outcomes. However, most clinical applications still depend on bulk genomic approaches, which fail to directly capture the genomic variations driving cellular heterogeneity. In this review, we explore the common single-cell multi-omics platforms and discuss key analytical steps for data integration. Furthermore, we highlight emerging knowledge in therapeutic resistance and immune evasion, and the potential of new therapeutic innovations informed by single-cell multi-omics. Finally, we discuss the future directions of the application of single-cell multi-omics technologies. By bridging the gap between technological advancements and clinical implementation, this review provides a roadmap for leveraging single-cell multi-omics to improve cancer treatment and patient outcomes.

Intratumoral Collagen Deposition Supports Angiogenesis Suggesting Anti-angiogenic Therapy in Armored and Cold Tumors

A previous study classifies solid tumors based on collagen deposition and immune infiltration abundance, identifying a refractory subtype termed armored & cold tumors, characterized by elevated collagen deposition and diminished immune infiltration. Beyond its impact on immune infiltration, collagen deposition also influences tumor angiogenesis. This study systematically analyzes the association between immuno-collagenic subtypes and angiogenesis across diverse cancer types. As a result, armored & cold tumors exhibit the highest angiogenic activity in lung adenocarcinoma (LUAD). Single-cell and spatial transcriptomics reveal close interactions and spatial co-localization of fibroblasts and endothelial cells. In vitro experiments demonstrate that collagen stimulates tumor cells to express vascular endothelial growth factor A (VEGFA) and directly enhances vessel formation and endothelial cell proliferation through sex determining region Y box 18 (SOX18) upregulation. Collagen inhibition via multiple approaches effectively suppresses tumor angiogenesis in vivo. In addition, armored & cold tumors display superior responsiveness to anti-angiogenic therapy in advanced LUAD cohorts. Post-immunotherapy resistance, the transformation into armored & cold tumors emerges as a potential biomarker for selecting anti-angiogenic therapy. In summary, collagen deposition is shown to drive angiogenesis across various cancers, providing a novel and actionable framework to refine therapeutic strategies combining chemotherapy with anti-angiogenic treatments.

The long non-coding RNA ROSALIND protects the mitochondrial translational machinery from oxidative damage

Upregulation of mitochondrial respiration coupled with high ROS-scavenging capacity is a characteristic shared by drug-tolerant cells in several cancers. As translational fidelity is essential for cell fitness, protection of the mitochondrial and cytosolic ribosomes from oxidative damage is pivotal. While mechanisms for recognising and repairing such damage exist in the cytoplasm, the corresponding process in the mitochondria remains unclear.By performing Ascorbate PEroXidase (APEX)-proximity ligation assay directed to the mitochondrial matrix followed by isolation and sequencing of RNA associated to mitochondrial proteins, we identified the nuclear-encoded lncRNA ROSALIND as an interacting partner of ribosomes. ROSALIND is upregulated in recurrent tumours and its expression can discriminate between responders and non-responders to immune checkpoint blockade in a melanoma cohort of patients. Featuring an unusually high G content, ROSALIND serves as a substrate for oxidation. Consequently, inhibiting ROSALIND leads to an increase in ROS and protein oxidation, resulting in severe mitochondrial respiration defects. This, in turn, impairs melanoma cell viability and increases immunogenicity both in vitro and ex vivo in preclinical humanised cancer models. These findings underscore the role of ROSALIND as a novel ROS buffering system, safeguarding mitochondrial translation from oxidative stress, and shed light on potential therapeutic strategies for overcoming cancer therapy resistance.

Decoding melanoma's cellular mosaic to unlock immunotherapy potential

Cancer evolution is driven by molecular events within cancer cells and their complex interactions with surrounding cells. Intra-tumor heterogeneity - driven by somatic genetic mutations, epigenetic dysregulation, immune cell infiltration, and microenvironmental factors - complicates the identification of reliable biomarkers and therapeutic targets. Single-cell sequencing and spatial multiomics technologies are revolutionizing our comprehension of how each component of the cellular machinery and tissue architecture collaborates to propel cancer progression. Much like how the restoration and interpretation of Pompeii mosaics have enriched our understanding of ancient Roman life, unraveling the intricate mosaic of cancer will transform the way this disease is diagnosed and treated. This review describes how the advent of single-cell multiomics has provided crucial insights into cutaneous melanoma biology and the mechanisms underlying resistance to immunotherapy.

Metabolism of Tryptophan, Glutamine, and Asparagine in Cancer Immunotherapy-Synergism or Mechanism of Resistance?

Amino acids are crucial components of proteins, key molecules in cellular physiology and homeostasis. However, they are also involved in a variety of other mechanisms, such as energy homeostasis, nitrogen exchange, further synthesis of bioactive compounds, production of nucleotides, or activation of signaling pathways. Moreover, amino acids and their metabolites have immunoregulatory properties, significantly affecting the behavior of immune cells. Immunotherapy is one of the oncological treatment methods that improves cytotoxic properties of one's own immune system. Thus, enzymes catalyzing amino acid metabolism, together with metabolites themselves, can affect immune antitumor properties and responses to immunotherapy. In this review, we will discuss the involvement of tryptophan, glutamine, and asparagine metabolism in the behavior of immune cells targeted by immunotherapy and summarize results of the most recent investigations on the impact of amino acid metabolites on immunotherapy.

DNA methylation status classifies pleural mesothelioma cells according to their immune profile: implication for precision epigenetic therapy

BACKGROUND

Co-targeting of immune checkpoint inhibitors (ICI) CTLA-4 and PD-1 has recently become the new first-line standard of care therapy of pleural mesothelioma (PM) patients, with a significant improvement of overall survival (OS) over conventional chemotherapy. The analysis by tumor histotype demonstrated greater efficacy of ICI therapy compared to standard chemotherapy in non-epithelioid (non-E) vs. epithelioid (E) PM, although some E PM patients also benefit from ICI treatment. This evidence suggests that molecular tumor features, beyond histotype, could be relevant to improve the efficacy of ICI therapy in PM. Among these, tumor DNA methylation emerges as a promising factor to explore, due to its potential role in driving the immune phenotype of cancer cells. Therefore, we utilized a panel of cultured PM cells of different histotype to provide preclinical evidence supporting the role of the tumor methylation landscape, along with its pharmacologic modulation, to prospectively improve the efficacy of ICI therapy of PM patients.

METHODS

The methylome profile (EPIC array) of distinct E (n = 5) and non-E (n = 9) PM cell lines was analyzed, followed by integrated analysis with their associated transcriptomic profile (Clariom S array), before and after in vitro treatment with the DNA hypomethylating agent (DHA) guadecitabine. The most variable methylated probes were selected to calculate the methylation score (CIMP index) for each cell line at baseline. Genes that were differentially expressed (DE) and differentially methylated (DM) were then selected for gene ontology analysis.

RESULTS

The CIMP index stratified PM cell lines into two distinct classes, CIMP (hyper-methylated; n = 7) and LOW (hypo-methylated; n = 7), regardless of their E or non-E histotype. Integrated methylome and transcriptome analyses revealed that CIMP PM cells exhibited a substantial number of hyper-methylated, silenced genes, which negatively impacted their immune phenotype compared to LOW PM cells. Treatment with DHA reverted the methylation-driven immune-compromised profile of CIMP PM cells and enhanced the constitutive immune-favorable profile of LOW PM cells.

CONCLUSION

The study highlighted the relevance of DNA methylation in shaping the constitutive immune classification of PM cells, independent of their histological subtypes. The identified role of DHA in shifting the phenotype of PM cells towards an immune-favorable state highlights its potential for evaluation in phase I/II clinical trials investigating the efficacy of epigenetic-based ICI combinations to reverse cancer immune resistance mechanisms.

The UBA1-STUB1 Axis Mediates Cancer Immune Escape and Resistance to Checkpoint Blockade

SIGNIFICANCE

Our study reveals UBA1 as a predictive biomarker for clinical outcomes in ICB cohorts, mediating cancer immune evasion and ICB resistance. We further highlight JAK1 stabilization as a key mechanism of UBA1 inhibition and nominate the UBA1-STUB1 axis as an immuno-oncology therapeutic target to improve the efficacy of ICB.

Integrated cancer cell-specific single-cell RNA-seq datasets of immune checkpoint blockade-treated patients

Immune checkpoint blockade (ICB) therapies have emerged as a promising avenue for the treatment of various cancers. Despite their success, the efficacy of these treatments is variable across patients and cancer types. Numerous single-cell RNA-sequencing (scRNA-seq) studies have been conducted to unravel cell-specific responses to ICB treatment. However, these studies are limited in their sample sizes and require advanced coding skills for exploration. Here, we have compiled eight scRNA-seq datasets from nine cancer types, encompassing 223 patients, 90,270 cancer cells, and 265,671 other cell types. This compilation forms a unique resource tailored to investigate how cancer cells respond to ICB treatment across cancer types. We meticulously curated, quality-checked, pre-processed, and analyzed the data, ensuring easy access for researchers. Moreover, we designed a user-friendly interface for seamless exploration. By sharing the code and data for creating these interfaces, we aim to assist fellow researchers. These resources offer valuable support to those interested in leveraging and exploring single-cell datasets across diverse cancer types, facilitating a comprehensive understanding of ICB responses.

Integrative multi-omics analysis for identifying novel therapeutic targets and predicting immunotherapy efficacy in lung adenocarcinoma

Aim: Lung adenocarcinoma (LUAD), the most prevalent subtype of non-small cell lung cancer (NSCLC), presents significant clinical challenges due to its high mortality and limited therapeutic options. The molecular heterogeneity and the development of therapeutic resistance further complicate treatment, underscoring the need for a more comprehensive understanding of its cellular and molecular characteristics. This study sought to delineate novel cellular subpopulations and molecular subtypes of LUAD, identify critical biomarkers, and explore potential therapeutic targets to enhance treatment efficacy and patient prognosis. Methods: An integrative multi-omics approach was employed to incorporate single-cell RNA sequencing (scRNA-seq), bulk transcriptomic analysis, and genome-wide association study (GWAS) data from multiple LUAD patient cohorts. Advanced computational approaches, including Bayesian deconvolution and machine learning algorithms, were used to comprehensively characterize the tumor microenvironment, classify LUAD subtypes, and develop a robust prognostic model. Results: Our analysis identified eleven distinct cellular subpopulations within LUAD, with epithelial cells predominating and exhibiting high mutation frequencies in Tumor Protein 53 (TP53) and Titin (TTN) genes. Two molecular subtypes of LUAD [consensus subtype (CS)1 and CS2] were identified, each showing distinct immune landscapes and clinical outcomes. The CS2 subtype, characterized by increased immune cell infiltration, demonstrated a more favorable prognosis and higher sensitivity to immunotherapy. Furthermore, a multi-omics-driven machine learning signature (MOMLS) identified ribonucleotide reductase M1 (RRM1) as a critical biomarker associated with chemotherapy response. Based on this model, several potential therapeutic agents targeting different subtypes were proposed. Conclusion: This study presents a comprehensive multi-omics framework for understanding the molecular complexity of LUAD, providing insights into cellular heterogeneity, molecular subtypes, and potential therapeutic targets. Differential sensitivity to immunotherapy among various cellular subpopulations was identified, paving the way for future immunotherapy-focused research.

Pan-inhibition of super-enhancer-driven oncogenic transcription by next-generation synthetic ecteinascidins yields potent anti-cancer activity

The plasticity of cancer cells facilitates their ability to adopt heterogeneous differentiation states, posing a significant challenge to therapeutic interventions. Specific gene expression programs, driven in part by super-enhancers (SEs), underlie cancer cell states. Here we successfully inhibit SE-driven transcription in phenotypically distinct metastatic melanoma cells using next-generation synthetic ecteinascidins. Through functional genomic methodologies, we demonstrate that these compounds inhibit the expression of genes encoding lineage-specific or ubiquitous transcription factors/coactivators by selectively targeting the CpG-rich sequences within their promoters and/or enhancers. This prevents the formation of transcription factor/coactivator condensates necessary for SE-dependent gene expression. Consequently, these compounds exhibit cytotoxic activity across distinct subpopulations of metastatic melanoma cells and inhibit tumor proliferation, including those resistant to current therapies. These findings extend to other cancers, like small cell lung cancer, recently approved for ecteinascidin-based treatment. Overall, our study provides preclinical proof that pan-inhibition of SE-dependent genes with synthetic ecteinascidins is a promising therapeutic approach for tumors with heterogeneous transcriptional landscapes.

Anti-Tumor Effects of Sheep Umbilical Cord Mesenchymal Stem Cells on Melanoma Cells

Melanoma is among the most common malignancies and has recently exhibited increased resistance to treatments, resulting in a more aggressive disease course. Mesenchymal stem cells (MSCs) secrete cytokines both in vivo and in vitro, which regulate tumor cell signaling pathways and the tumor microenvironment, thereby influencing tumor progression. This study investigates the anti-melanogenesis effects of sheep umbilical cord mesenchymal stem cells (SUCMSCs) to assess their potential application in melanoma treatment. Our findings indicate that, in vitro, SUCMSCs reduce melanin content and tyrosinase activity, inhibit melanoma cell viability, proliferation, migration, and invasion, and promote melanoma cell apoptosis. Subsequent in vivo experiments confirmed that SUCMSCs effectively suppress tumor growth, and histological analysis via HE staining revealed notable differences. Additionally, transcriptome sequencing analysis indicated that the anti-tumor effects were primarily mediated through autophagy, apoptosis, and the TGF-β and NF-κB signaling pathways. The RT-qPCR validation results aligned with the transcriptome data. In summary, SUCMSCs exert anti-melanogenesis effects through the interaction of multiple signaling pathways and cytokines, demonstrating significant potential for melanoma treatment.

LnCeCell 2.0: an updated resource for lncRNA-associated ceRNA networks and web tools based on single-cell and spatial transcriptomics sequencing data

We describe LnCeCell 2.0 (http://bio-bigdata.hrbmu.edu.cn/LnCeCell), an updated resource for lncRNA-associated competing endogenous RNA (ceRNA) networks and web tools based on single-cell and spatial transcriptomics sequencing (stRNA-seq) data. We have updated the LnCeCell 2.0 database with significantly expanded data and improved features, including (i) 257 single-cell RNA sequencing and stRNA-seq datasets across 86 diseases/phenotypes and 80 human normal tissues, (ii) 836 581 cell-specific and spatial spot-specific ceRNA interactions and functional networks for 1 002 988 cells and 367 971 spatial spots, (iii) 15 489 experimentally supported lncRNA biomarkers related to disease pathology, diagnosis and treatment, (iv) detailed annotation of cell type, cell state, subcellular and extracellular locations of ceRNAs through manual curation and (v) ceRNA expression profiles and follow-up clinical information of 20 326 cancer patients. Further, a panel of 24 flexible tools (including 8 comprehensive and 16 mini-analysis tools) was developed to investigate ceRNA-regulated mechanisms at single-cell/spot resolution. The CeCellTraject tool, for example, illustrates the detailed ceRNA distribution of different cell populations and explores the dynamic change of the ceRNA network along the developmental trajectory. LnCeCell 2.0 will facilitate the study of fine-tuned lncRNA-ceRNA networks with single-cell and spatial spot resolution, helping us to understand the regulatory mechanisms behind complex microbial ecosystems.

TCTN1 Induces Fatty Acid Oxidation to Promote Melanoma Metastasis

Metabolic reprogramming promotes and sustains multiple steps of melanoma metastasis. Identification of key regulators of metabolic reprogramming could lead to the development of treatments for preventing and treating metastatic melanoma. In this study, we identified that tectonic family member 1 (TCTN1) promotes melanoma metastasis by increasing fatty acid oxidation (FAO). In clinical melanoma samples, high expression of TCTN1 correlated with increased metastasis and shorter patient survival. Functionally, TCTN1 promoted melanoma invasion and migration in vitro and distant metastasis in vivo and induced a mesenchymal-like phenotype switch. Mechanistically, TCTN1 acted as a protein scaffold to promote the binding of HADHA and HADHB, subunits of the mitochondrial trifunctional protein complex, thus leading to FAO activation. TCTN1-mediated FAO activated the p38/MAPK signaling pathway in melanoma cells, promoting tumor epithelial-mesenchymal transition and stemness. Molecular docking indicated that the prostaglandin F receptor agonist fluprostenol can block HADHA/HADHB binding, which was confirmed experimentally. Treatment with fluprostenol was able to inhibit TCTN1-induced melanoma invasion and metastasis. Taken together, these findings elucidate the mechanism of TCTN1-mediated promotion of melanoma metastasis and support the potential application of fluprostenol for targeted therapy of metastatic melanoma. Significance: TCTN1 activates fatty acid oxidation to induce melanoma mesenchymal phenotype switching and invasion by promoting the binding of the subunits of MTP, which can be targeted with fluprostenol to inhibit melanoma metastasis.

Characterization of human melanoma skin cancer models: A step towards model-based melanoma research

Advancing 3D in vitro human tissue models is crucial for biomedical research and drug development to address the ethical and biological limitations of animal testing. Recently, 3D skin models have proven to be effective for studying serious skin conditions, such as melanoma. For these advanced models to be applicable in preclinical studies, thorough characterization is essential to understand their applicability and limitations. In this study, we used bioimaging and RNA sequencing to assess the architecture and transcriptomic profiles of skin models, including models with melanoma. Our results indicated that these models closely mimicked skin morphology and gene expression patterns. The full-thickness (FT) model shows a superior resemblance to the human skin, particularly in basement membrane formation and cellular interactions. The integrity of the skin-like properties and gene expression signatures of both skin and melanoma cells were preserved upon the integration of melanoma cells, establishing these models as robust platforms for cancer research. The responsiveness of the FT melanoma models to vemurafenib treatment was successfully monitored, demonstrating their validity as a reliable, reproducible, and humane tool for pharmacological testing and drug development. Furthermore, the transcriptomic data showed that skin models with cancer spheroids had upregulated genes linked to aggressive and resilient cancer behavior compared to spheroids alone. This emphasizes the importance of the microenvironment in cancer progression and suggests that 3D skin models can serve to uncover mechanisms and therapeutic targets that are not detectable in simpler systems. STATEMENT OF SIGNIFICANCE: This study introduces advanced, ethically sound skin and melanoma models as alternatives to animal testing in drug discovery. By thoroughly characterizing these models using bioimaging and RNA sequencing, we demonstrate their close resemblance to human skin, particularly in full-thickness models. These models not only replicate the complex cellular interactions and gene expression patterns of human tissue but also maintain robustness after melanoma integration. Our findings highlight the potential of these models in revealing cancer mechanisms and therapeutic targets, offering a significant impact on melanoma research and preclinical testing.

A pan-cancer analysis of the oncogenic role of N-acetyltransferase 8 like in human cancer

BACKGROUND

N-Acetyltransferase 8 Like (NAT8L) inhibits natural killer (NK)/T-cell cytotoxicity by impairing the formation of the immunological synapse via N-acetylaspartate (NAA). Existing research has predominantly focused on the metabolic functions of NAT8L, particularly in adipose tissues and myelination in the brain. However, in contrast to other N-acetyltransferases such as NAT1 and NAT2, the role of NAT8L in cancer has been less extensively studied. In this study, we conducted a comprehensive pan-cancer analysis to investigate the carcinogenic role of NAT8L in human cancers.

METHODS

We utilized the standardized TCGA pan-cancer dataset to analyze differential expression, clinical prognosis, gene mutation, immune infiltration, epigenetic modification, tumor stemness, and heterogeneity. Additionally, we evaluated the sensitivity of NAT8L to small molecule drugs using the GDSC and CTRP databases.

RESULTS

In this study, we identified that NAT8L expression was upregulated in 6 cancers and downregulated in 12 compared to normal tissues. We analyzed its prognostic value in 5 tumor types (KIRP, COAD, COADREAD, GBMLGG, LUSC) and found correlations with overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI). Furthermore, NAT8L expression was significantly correlated with levels of most immune checkpoints, immunomodulators, and immune cell infiltration. The mutation frequencies for bladder cancer (BLCA), glioblastoma multiforme and glioma (GBMLGG), lower-grade glioma (LGG), and KIRP were 1.2%, 0.9%, 0.8%, and 0.4%, respectively.

CONCLUSION

Our findings suggest that NAT8L may serve as a potential prognostic marker and therapeutic target across a variety of cancers, particularly in KIRP, COAD, COADREAD, GBMLGG, and lung squamous cell carcinoma (LUSC).

IFNγ-dependent metabolic reprogramming restrains an immature, pro-metastatic lymphatic state in melanoma

Lymphatic vessels play a crucial role in activating anti-tumor immune surveillance but also contribute to metastasis and systemic tumor progression. Whether distinct lymphatic phenotypes exist that govern the switch between immunity and metastasis remains unclear. Here we reveal that cytotoxic immunity normalizes lymphatic function and uncouples immune and metastatic potential. We find that in mice and humans, intratumoral lymphatic vessel density negatively correlates with productive cytotoxic immune responses and identify IFNγ as an intrinsic inhibitor of lymphangiogenesis. Specific deletion of the Ifngr1 in lymphatic endothelial cells (LECs) greatly expanded the intratumoral lymphatic network and drove the emergence of a tip-like endothelial state, promoting lymph node metastasis but not dendritic cell migration. IFNγ inhibits oxidative phosphorylation, which is required for proliferation and acquisition of the pathologic transcriptional state. Our data indicate that IFNγ induces a phenotypic switch in tumor-associated lymphatic vessels to reinforce canonical immune surveillance and block metastasis.

Changes in AXL and/or MITF melanoma subpopulations in patients receiving immunotherapy

Background

Tumor heterogeneity is a hurdle to effective therapy, as illustrated by the 'mixed responses' frequently seen in immunotherapy-treated patients. Previously, AXL+ tumor cells were identified to be highly resistant to targeted therapy, whereas more differentiated MITF+ tumor cells do respond to RAF and MEK inhibitors.

Patients and methods

In this study, we analyzed tumor heterogeneity and explored the presence of the previously described AXL+ or MITF+ melanoma subpopulations in metastatic tissues by NanoString gene expression analysis, single-cell RNA sequencing and in situ multiplex immunofluorescence. Furthermore, we analyzed how these subpopulations correlate with immunological pressure and response to immunotherapy by immunomodulating antibodies or autologous tumor lysate-loaded dendritic cell vaccination.

Results

Our data demonstrate large interpatient variability and variable therapy-induced changes independent of the type of therapy. We identify the presence of previously described AXL+ and MITF+ subpopulations in metastatic tissues both at the mRNA level and in situ at the protein level, and demonstrate that MITF+ melanoma cells are significantly decreased upon immunotherapy, while AXL+ melanoma cell numbers are stable. MITF+ tumor cells showed the most significant inverse correlation with CD8+ T cells. Our patient cohort also shows that immunotherapy-induced changes in the abundance of AXL+ or MITF+ tumor cells did not correlate with improved survival.

Conclusions

Overall, this study suggests that more differentiated MITF+ tumors are efficiently targeted by immunotherapy, while AXL+ tumor cells may be more resistant, analogous to their response to targeted therapy.

NRF1-induced mmu_circ_0001388/hsa_circ_0029470 confers ferroptosis resistance in ischemic acute kidney injury via the miR-193b-3p/TCF4/GPX4 axis

AIMS

Circular RNAs (circRNAs) are critical in the progression of ischemic acute kidney injury (AKI). Nevertheless, the specific functions and regulatory pathways of mmu_circ_0001388 and hsa_circ_0029470 remain elusive.

METHODS

Real-time quantitative polymerase chain reaction (RT-qPCR) was utilized to assess the expression patterns of mmu_circ_0001388, hsa_circ_0029470, and miR-139b-3p. Protein expressions of nuclear respiratory factor 1 (NRF1), transcription factor 4 (TCF4), glutathione peroxidase 4 (GPX4), and Acyl-CoA synthetase long-chain family member 4 (ACSL4) were identified via immunoblotting. Furthermore, the functions and control mechanisms of mmu_circ_003062 and hsa_circ_0075663 were examined via diverse cell and animal studies, encompassing bioinformatics prediction, dual-luciferase reporter (DLR), chromatin immunoprecipitation (ChIP), fluorescence in situ hybridization (FISH), flow cytometry (FCM), hematoxylin and eosin (H&E) staining, dihydroethidium (DHE), TUNEL, immunohistochemistry, and transmission electron microscopy (TEM), and Fe2+ assay.

KEY FINDINGS

Initially, the induction of mmu_circ_0001388 by NRF1 was observed in vitro and in vivo following ischemia/reperfusion (I/R) injury. Subsequently, knockdown or overexpression of mmu_circ_0001388 was found to either promote or inhibit ferroptosis caused by I/R in Boston University mouse proximal tubule (BUMPT) cells, respectively. From a mechanistic standpoint, mmu_circ_0001388 was found to function as a sponge for miR-193b-3p, which promoted TCF4 and subsequently enhanced GPX4, thereby suppressing ferroptosis. Finally, the overexpression of mmu_circ_0001388 was shown to ameliorate I/R-induced AKI in mice. In parallel, hsa_circ_0029470, homologous to mmu_circ_0001388, demonstrated an identical control pathway in human renal tubular epithelial (HK-2) cells.

SIGNIFICANCE

The NRF1/mmu_circ_0001388, hsa_circ_0029470/miR-193b-3p/TCF4/GPX4 axis is pivotal in regulating ferroptosis induced by ischemic AKI and holds potential as a therapeutic target.

BRD4 Degradation Enhanced Glioma Sensitivity to Temozolomide by Regulating Notch1 via Glu-Modified GSH-Responsive Nanoparticles

Temozolomide (TMZ) serves as the principal chemotherapeutic agent for glioma; nonetheless, its therapeutic efficacy is compromised by the rapid emergence of drug resistance, the inadequate targeting of glioma cells, and significant systemic toxicity. ARV-825 may play a role in modulating drug resistance by degrading the BRD4 protein, thereby exerting anti-glioma effects. Therefore, to surmount TMZ resistance and achieve efficient and specific drug delivery, a dual-targeted glutathione (GSH)-responsive nanoparticle system (T+A@Glu-NP) is designed and synthesized for the co-delivery of ARV-825 and TMZ. As anticipated, T+A@Glu-NPs significantly enhanced penetration of the blood-brain barrier (BBB), facilitated drug uptake by glioma cells, and exhibited efficient accumulation in brain tissue. Additionally, T+A@Glu-NPs exhibited augmented efficacy against glioma both in vitro and in vivo through the induction of apoptosis, inhibition of proliferation, and cell cycle arrest. Furthermore, mechanistic exploration revealed that T+A@Glu-NPs degraded the BRD4 protein, leading to the downregulation of Notch1 gene transcription and the inhibition of the Notch1 signaling pathway, thereby augmenting the therapeutic efficacy of glioma chemotherapy. Taken together, the findings suggest that T+A@Glu-NPs represents a novel and promising therapeutic strategy for glioma chemotherapy.

Genomic heterogeneity and ploidy identify patients with intrinsic resistance to PD-1 blockade in metastatic melanoma

The introduction of immune checkpoint blockade (ICB) has markedly improved outcomes for advanced melanoma. However, many patients develop resistance through unknown mechanisms. While combination ICB has improved response rate and progression-free survival, it substantially increases toxicity. Biomarkers to distinguish patients who would benefit from combination therapy versus aPD-1 remain elusive. We analyzed whole-exome sequencing of pretreatment tumors from four cohorts (n = 140) of ICB-naïve patients treated with aPD-1. High genomic heterogeneity and low ploidy robustly identified patients intrinsically resistant to aPD-1. To establish clinically actionable predictions, we optimized and validated a predictive model using ploidy and heterogeneity to confidently identify (90% PPV) patients with intrinsic resistance to and worse survival on aPD-1. We further observed that three of seven (43%) patients predicted to be intrinsically resistant to single-agent PD-1 ICB responded to combination ICB, suggesting that these patients may benefit disproportionately from combination ICB. These findings highlight the importance of heterogeneity and ploidy, nominating an approach toward clinical actionability.

Pharmacological targeting of casein kinase 1δ suppresses oncogenic NRAS-driven melanoma

Activating mutations in NRAS account for 15-20% of melanoma, yet effective anti-NRAS therapies are still lacking. In this study, we unveil the casein kinase 1δ (CK1δ) as an uncharacterized regulator of oncogenic NRAS mutations, specifically Q61R and Q61K, which are the most prevalent NRAS mutations in melanoma. The genetic ablation or pharmacological inhibition of CK1δ markedly destabilizes NRAS mutants and suppresses their oncogenic functions. Moreover, we identify USP46 as a bona fide deubiquitinase of NRAS mutants. Mechanistically, CK1δ directly phosphorylates USP46 and activates its deubiquitinase activity towards NRAS mutants, thus promoting oncogenic NRAS-driven melanocyte malignant transformation and melanoma progression in vitro and in vivo. Our findings underscore the significance of the CK1δ-USP46 axis in stabilizing oncogenic NRAS mutants and provide preclinical evidence that targeting this axis holds promise as a therapeutic strategy for human melanoma harboring NRAS mutations.

Single-cell and bulk transcriptome analysis reveals tumor cell heterogeneity and underlying molecular program in uveal melanoma

BACKGROUND

Uveal melanoma (UM) is a rare and deadly eye cancer with high metastatic potential. Despite the predominance of malignant cells within the tumor microenvironment, the heterogeneity and underlying molecular features remain to be fully characterized.

METHODS

We analyzed single-cell transcriptomic profiling of 37,660 malignant cells from 17 UM tumors. A consensus non-negative factorization algorithm was used to decipher transcriptional programs underlying tumor cell-intrinsic heterogeneity. Tumor-infiltrated immune cells were computationally estimated from bulk transcriptomes and bioinformatics methods. A gene signature was derived for subtyping and prognostic stratification and validated in multicenter cohorts.

RESULTS

ScRNA-seq analysis revealed the existence of diverse subpopulations and transcriptional variability among malignant cells within and between tumors. Furthermore, we observed that the heterogeneity of malignant cell states and compositions correlated with genomic, immunological, and clinical characteristics. By identifying gene expression programs associated with malignant cell heterogeneity at the single cell level, UM samples were classified into two distinct intra-tumoral subtypes (ITMHlo and ITMHhi) with different prognoses and immune microenvironments. Finally, a machine learning-derived 9-gene signature was developed to translate single-cell information into bulk tissue transcriptomes for patient stratification and was validated in multicenter cohorts.

CONCLUSIONS

Our study provides insight into understanding the intra-tumoral heterogeneity of UM and its potential impact on patient stratification.

The hallmarks of cancer immune evasion

According to the widely accepted "three Es" model, the host immune system eliminates malignant cell precursors and contains microscopic neoplasms in a dynamic equilibrium, preventing cancer outgrowth until neoplastic cells acquire genetic or epigenetic alterations that enable immune escape. This immunoevasive phenotype originates from various mechanisms that can be classified under a novel "three Cs" conceptual framework: (1) camouflage, which hides cancer cells from immune recognition, (2) coercion, which directly or indirectly interferes with immune effector cells, and (3) cytoprotection, which shields malignant cells from immune cytotoxicity. Blocking the ability of neoplastic cells to evade the host immune system is crucial for increasing the efficacy of modern immunotherapy and conventional therapeutic strategies that ultimately activate anticancer immunosurveillance. Here, we review key hallmarks of cancer immune evasion under the "three Cs" framework and discuss promising strategies targeting such immunoevasive mechanisms.

The classification of melanocytic gene signatures

Gene expression profiling technologies have revolutionized cell biology, enabling researchers to identify gene signatures linked to various biological attributes of melanomas, such as pigmentation status, differentiation state, proliferative versus invasive capacity, and disease progression. Although the discovery of gene signatures has significantly enhanced our understanding of melanocytic phenotypes, reconciling the numerous signatures reported across independent studies and different profiling platforms remains a challenge. Current methods for classifying melanocytic gene signatures depend on exact gene overlap and comparison with unstandardized baseline transcriptomes. In this study, we aimed to categorize published gene signatures into clusters based on their similar patterns of expression across clinical cutaneous melanoma specimens. We analyzed nearly 800 melanoma samples from six gene expression repositories and developed a classification framework for gene signatures that is resilient against biases in gene identification across profiling platforms and inconsistencies in baseline standards. Using 39 frequently cited published gene signatures, our analysis revealed seven principal classes of gene signatures that correlate with previously identified phenotypes: Differentiated, Mitotic/MYC, AXL, Amelanotic, Neuro, Hypometabolic, and Invasive. Each class is consistent with the phenotypes that the constituent gene signatures represent, and our classification method does not rely on overlapping genes between signatures. To facilitate broader application, we created WIMMS (what is my melanocytic signature, available at https://wimms.tanlab.org/), a user-friendly web application. WIMMS allows users to categorize any gene signature, determining its relationship to predominantly cited signatures and its representation within the seven principal classes.

NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors

Neuroblastoma, a rare embryonic tumor arising from neural crest development, is responsible for 15% of pediatric cancer-related deaths. Recently, several single-cell transcriptome studies were performed on neuroblastoma patient samples to investigate the cell of origin and tumor heterogeneity. However, these individual studies involved a small number of tumors and cells, limiting the conclusions that could be drawn. To overcome this limitation, we integrated seven single-cell or single-nucleus datasets into a harmonized cell atlas covering 362,991 cells across 61 patients. We use this atlas to decipher the transcriptional landscape of neuroblastoma at single-cell resolution, revealing associations between transcriptomic profiles and clinical outcomes within the tumor compartment. In addition, we characterize the complex immune-cell landscape and uncover considerable heterogeneity among tumor-associated macrophages. Finally, we showcase the utility of our atlas as a resource by expanding it with additional data and using it as a reference for data-driven cell-type annotation.

Characterization of cell states in biliary tract cancers identifies mechanisms of therapeutic resistance in a phase II trial of DKN-01/nivolumab

Biliary tract cancers demonstrate profound therapeutic resistance, and broadly effective therapies for refractory disease are lacking. We conducted a single-arm, second-line phase II trial combining DKN-01, a humanized monoclonal antibody targeting Dickkopf-1 (DKK-1), and nivolumab to treat patients with advanced biliary tract cancer (NCT04057365). No objective responses were seen. To identify mechanisms of treatment failure, we analyzed paired pre-treatment and on-treatment biopsies using scRNA-seq and constructed a detailed molecular classification of malignant and immune cells. We annotated five biliary tract cancer malignant cell states: classical, basal, mesenchymal, neural-like, and endothelial-like. Neural-like and endothelial-like states, which drive therapeutic resistance in other cancers, have not previously been described in BTC. Malignant cell states co-varied with distinct immune cell states, revealing diverse mechanisms of myeloid and T-cell mediated immune suppression, including M2 myeloid and terminally exhausted T cell programs that were induced by DKN-01/nivolumab. Here, we provide the first systematic classification of functionally annotated cell states in biliary tract cancer and provide new insight into resistance mechanisms to an immunotherapy combination that can inform the next generation of trials.

Cancer drug-tolerant persister cells: from biological questions to clinical opportunities

The emergence of drug resistance is the most substantial challenge to the effectiveness of anticancer therapies. Orthogonal approaches have revealed that a subset of cells, known as drug-tolerant 'persister' (DTP) cells, have a prominent role in drug resistance. Although long recognized in bacterial populations which have acquired resistance to antibiotics, the presence of DTPs in various cancer types has come to light only in the past two decades, yet several aspects of their biology remain enigmatic. Here, we delve into the biological characteristics of DTPs and explore potential strategies for tracking and targeting them. Recent findings suggest that DTPs exhibit remarkable plasticity, being capable of transitioning between different cellular states, resulting in distinct DTP phenotypes within a single tumour. However, defining the biological features of DTPs has been challenging, partly due to the complex interplay between clonal dynamics and tissue-specific factors influencing their phenotype. Moreover, the interactions between DTPs and the tumour microenvironment, including their potential to evade immune surveillance, remain to be discovered. Finally, the mechanisms underlying DTP-derived drug resistance and their correlation with clinical outcomes remain poorly understood. This Roadmap aims to provide a comprehensive overview of the field of DTPs, encompassing past achievements and current endeavours in elucidating their biology. We also discuss the prospect of future advancements in technologies in helping to unveil the features of DTPs and propose novel therapeutic strategies that could lead to their eradication.

Ferroptosis-related oxaliplatin resistance in multiple cancers: Potential roles and therapeutic Implications

Oxaliplatin (OXA)-based therapy is effective in the treatment of multiple cancers. However, primary or acquired OXA resistance remains an emerging challenge for its clinical application. Ferroptosis is an iron-dependent mode of cell death that has been demonstrated to play an essential role in the chemoresistance of many drugs, including OXA. In particular, dysregulation of SLC7A11-GPX4, one of the major antioxidant systems of ferroptosis, was found in the OXA resistance of colorectal cancer (CRC) and hepatocellular carcinoma (HCC). In addition, Nrf2, the upstream regulator of GPX4 and many other antioxidant factors, is also involved in the OXA resistance of CRC and HCC. Inhibition of SLC7A11-GPX4 or Nrf2 by genetic deletion of pharmaceutical inhibition could significantly reverse OXA resistance. Long noncoding RNA (lncRNA) also participates in chemoresistance and ferroptosis of cancer cells. Specifically, LINC01134 promotes the recruitment of Nrf2 to the promoter of GPX4, thereby exerting transcriptional regulation of GPX4, which eventually increases the OXA sensitivity of HCC through upregulation of ferroptosis. On the other hand, a novel lncRNA DACT3-AS1 sensitizes gastric cancer cells to OXA through miR-181a-5p/sirtuin 1(SIRT1)-mediated ferroptosis. Therapies based on ferroptosis or a combination of OXA and ferroptosis enhancers could provide new therapeutic insights to overcome OXA resistance. In the present review, we present the current understanding of ferroptosis-related OXA resistance, highlight ferroptosis pathogenesis in OXA chemoresistance, and summarize available therapies that target OXA resistance by enhancing ferroptosis.

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.

Advancements and Challenges in Personalized Therapy for BRAF-Mutant Melanoma: A Comprehensive Review

Over the past several decades, advancements in the treatment of BRAF-mutant melanoma have led to the development of BRAF inhibitors, BRAF/MEK inhibitor combinations, anti-PD-1 therapy, and anti-CTLA4 therapy. Although these therapies have shown substantial efficacy in clinical trials, their sustained effectiveness is often challenged by the tumor microenvironment, which is a highly heterogeneous and complex milieu of immunosuppressive cells that affect tumor progression. The era of personalized medicine holds substantial promise for the tailoring of treatments to individual genetic profiles. However, tumor heterogeneity and immune evasion mechanisms contribute to the resistance to immunotherapy. Despite these challenges, tumor-infiltrating lymphocyte (TIL) therapy, as exemplified by lifileucel, has demonstrated notable efficacy against BRAF V600-mutant melanoma. Additionally, early response biomarkers, such as COX-2 and MMP2, along with FDG-PET imaging, offer the potential to improve personalized immunotherapy by predicting patient responses and determining the optimal treatment duration. Future efforts should focus on reducing the T-cell harvesting periods and costs associated with TIL therapy to enhance efficiency and accessibility.

Cancer cell states: Lessons from ten years of single-cell RNA-sequencing of human tumors

Human tumors are intricate ecosystems composed of diverse genetic clones and malignant cell states that evolve in a complex tumor micro-environment. Single-cell RNA-sequencing (scRNA-seq) provides a compelling strategy to dissect this intricate biology and has enabled a revolution in our ability to understand tumor biology over the last ten years. Here we reflect on this first decade of scRNA-seq in human tumors and highlight some of the powerful insights gleaned from these studies. We first focus on computational approaches for robustly defining cancer cell states and their diversity and highlight some of the most common patterns of gene expression intra-tumor heterogeneity (eITH) observed across cancer types. We then discuss ambiguities in the field in defining and naming such eITH programs. Finally, we highlight critical developments that will facilitate future research and the broader implementation of these technologies in clinical settings.

The small MAF transcription factor MAFG co-opts MITF to promote melanoma progression

Transcription factor deregulation potently drives melanoma progression by dynamically and reversibly controlling gene expression programs. We previously identified the small MAF family transcription factor MAFG as a putative driver of melanoma progression, prompting an in-depth evaluation of its role in melanoma. MAFG expression increases with human melanoma stages and ectopic MAFG expression enhances the malignant behavior of human melanoma cells in vitro, xenograft models, and genetic mouse models of spontaneous melanoma. Moreover, MAFG induces a melanoma phenotype switch from a melanocytic state to a more dedifferentiated state. Mechanistically, MAFG interacts with the lineage transcription factor MITF which is required for the pro-tumorigenic effects of MAFG. MAFG and MITF co-occupy numerous genomic sites and MAFG overexpression influences the expression of genes harboring binding sites for the MAFG~MITF complex. These results establish MAFG as a potent driver of melanomagenesis through dimerization with MITF and uncover an unappreciated mechanism of MITF regulation.