Rhabdomyosarcoma (RMS) is marked by a myogenesis differentiation blockade, and while the AKT/mTOR pathway is universally activated, its pharmacological inhibition has shown limited success. Here, we evaluate the activity of pan-AKT inhibitors Ipatasertib, ATP-competitive, and Miransertib, allosteric inhibitor, in RMS cell lines and fusion-positive/negative patient-derived xenografts (PDX). Unlike Miransertib, Ipatasertib show significant antitumor activity against a subset of RMS. Besides AKT, the other target of Ipatasertib, but not of Miransertib, is PRKG1, a cGMP-dependent protein kinase that shares the ATP binding pocket with AKT. We investigate the role of PRKG1 in PRKG1-depleted RMS cells and in xenograft models by transcriptomic approaches. PRKG1 silencing in RMS cells reduces tumor formation in xenograft models and induces a differentiated myogenic transcriptome. RMS show higher PRKG1 expression compared to any other developmental cancer, akin to fetal skeletal muscle. Importantly, PRKG1 expression in RMS correlates with mesodermal transcriptional signature and enhanced sensitivity to Ipatasertib, regardless of the fusion oncogene status. The antitumor activity of Ipatasertib is dose-dependent, reaching an effective intra-tumor concentration when administered at 25 mg/kg daily. This study unveils the role of PRKG1 in myogenesis and highlights the potential of PRKG1 as a clinical biomarker for Ipatasertib therapy in RMS.

RNA splicing dysregulation has emerged as a hallmark of cancer and a promising therapeutic target; however, its full landscape in human solid cancer remains poorly characterized. To address this, we perform alternative splicing analyses using RNA-sequencing data from 751 lung adenocarcinoma samples from our cohort integrated with 519 samples from The Cancer Genome Atlas. Visualization of splicing patterns using t-distributed stochastic neighbor embedding reveals substantial inter-tumor heterogeneity driven by distinct molecular subtypes and histological differentiation. We identify a unique molecular subtype associated with inactivating mutations in CMTR2, which encodes Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase 2. CMTR2 mutations are observed in 3.8% of cases and are predominantly truncating mutations, which form an isolated cluster within the splicing landscape. Intrinsic and CRISPR-Cas9-engineered CMTR2 mutations disrupt alternative splicing and sensitize cancer cells to sulfonamide-based RNA splicing modulators and immune checkpoint blockade therapy. Retrospective patient data confirm the increased sensitivity of CMTR2-deficient tumors to immune checkpoint blockade therapy. These findings uncover a previously unrecognized RNA splicing deficiency in human cancers and define a molecular subtype of lung adenocarcinoma driven by RNA splicing dysregulation, suggesting targets for therapeutic intervention in lung cancer.

Triple-negative breast cancer (TNBC) is one of the most aggressive subtypes of breast cancer, with limited targeted treatment options and poor clinical outcomes. HER3 has recently emerged as a promising therapeutic target, with HER3-directed antibody-drug conjugates advancing to Phase III clinical trials for non-small cell lung cancer. However, the downstream molecular mechanisms by which HER3 promotes TNBC progression remain poorly defined. In this study, we uncovered a previously unrecognized HER3/miR-34b-5p/PHF8 signaling axis that drives TNBC cell proliferation and tumor growth. Mechanistically, HER3 activation suppresses the tumor-suppressive microRNA miR-34b-5p, resulting in the upregulation of the histone demethylase PHF8 (KDM7B), which in turn represses the expression of the CDK inhibitor p27Kip1 and facilitates G1-S cell cycle progression. Functional studies using shRNA-mediated knockdown and overexpression systems demonstrate that PHF8 is a critical downstream effector of HER3. PHF8 depletion phenocopied HER3 knockdown, inducing G1 arrest and suppressing colony formation and proliferation in multiple TNBC cell lines, while PHF8 overexpression rescued the inhibitory effects of HER3 loss. Furthermore, orthotopic xenograft models revealed that enforced PHF8 expression restored tumor growth suppressed by HER3 silencing in vivo. Clinically, HER3 and PHF8 expression levels were positively correlated in TNBC tissue specimens, and TCGA dataset analyses indicated that the HER3/miR-34b-5p/PHF8 axis is significantly associated with poor survival outcomes in breast cancer patients. Collectively, our findings establish a novel epigenetic regulatory circuit through which HER3 drives TNBC progression and lay the groundwork for future therapeutic strategies aimed at disrupting HER3-epigenetic crosstalk in TNBC.

Therapies targeting BRAF can inhibit the development of melanoma with BRAF mutations and enhance survival rates, though acquired resistance inevitably arises. The non-receptor tyrosine kinase Fyn, recognized for its role in regulating tumor cell survival and drug resistance, has emerged as a promising therapeutic target in melanoma treatment. In this study, we conducted a virtual screening and identified TAE684 as a potent inhibitor of Fyn. Utilizing in vitro assays, including assessments of cell viability, reactive oxygen species (ROS) production and DNA damage, alongside an in vivo melanoma xenograft model, we demonstrated that either TAE684 treatment or Fyn knockdown resulted in increased ROS levels and DNA damage, ultimately inducing cell cycle arrest at the G2/M phase and apoptosis in melanoma cells. Significantly, the application of TAE684 in melanoma cells demonstrated a capacity to counteract vemurafenib resistance, presumably through the down-regulation of the AP-1 pathway. Furthermore, the combination of TAE684 with vemurafenib exhibits a synergistic effect, leading to decreased cell viability in melanoma cells resistant to vemurafenib treatment. These results highlight the potential of TAE684 as a dual-function agent that not only inhibits melanoma proliferation but also reverses resistance to vemurafenib by targeting Fyn, thereby establishing it as a promising candidate for melanoma therapy.

L-2-hydroxyglutarate (L-2-HG) functions as a metabolite implicated in the progression of various tumors. HIF1A, a central regulator of the hypoxic response, is known to be regulated by several metabolites. This study aims to elucidate whether L-2-HG regulates the function of HIF1A through histone lactylation modification, thereby contributing to brain metastasis in renal cell carcinoma (RCC). A mouse model of RCC brain metastasis was constructed, and high-throughput metabolomics, transcriptomics, and proteomics sequencing analyses were conducted. Bioinformatics analysis revealed that L-2-HG enhanced HIF1A expression by promoting histone lactylation modification, which suppressed ferroptosis and facilitated RCC brain metastasis. In vitro cellular experiments were conducted, including cell treatment, transfection, chromatin immunoprecipitation (ChIP), malignant phenotype detection assays, Western blotting, and RT-qPCR. The results showed that L-2-HG increased the lactylation modification of HIF1A and enhanced the resistance of renal cancer cells to ferroptosis, thereby increasing cell proliferation, migration, and invasion. In vivo experiments using a nude mouse lung metastasis model demonstrated the mechanism through which L-2-HG promoted RCC brain metastasis.

Group 3 (G3) is one of the most common and aggressive subtypes of the paediatric cerebellar tumour Medulloblastoma (MB), primarily driven by the MYC oncogene. The challenging targeting of MYC, coupled with gaps in understanding G3 MB molecular bases, has hindered the development of targeted therapies. The unconventional oncogenic roles of long noncoding RNAs (lncRNAs) offer opportunities to address this complexity, to provide insights and to identify novel targets. Using -omics approaches and molecular/cellular assays, we elucidate the mode-of-action of lncMB3, a MYC-dependent, anti-apoptotic lncRNA in G3 MB. LncMB3 regulates the TGF-β pathway, critically altered in G3 medulloblastomagenesis, via direct binding and translational inhibition of the mRNA for the epigenetic factor HMGN5. This regulatory axis affects apoptosis through photoreceptor lineage genes, including the G3 driver OTX2. The synergistic effects between lncMB3 targeting and cisplatin treatment underscore the relevance of this network. Additionally, we propose novel ferritin-based nanocarriers for the efficient delivery of antisense oligonucleotides against lncMB3. LncMB3 crucially links MYC amplification and apoptosis inhibition through a circuit involving RNA-based mechanisms, G3 MB key determinants and underexplored factors. This integrated framework deepens the understanding of G3 MB landscape and supports the potential for translating lncRNA research into future applications.

Family with sequence similarity 134, member B (FAM134B), known for its role as an ER-phagy receptor, has been implicated in the promotion of hepatocellular carcinoma (HCC) progression through the activation of the AKT signaling pathway. However, the precise mechanism underlying FAM134B's activation of AKT signaling remains to be elucidated. This study aimed to investigate the interaction between FAM134B and DEAD-box helicase 3 X-linked (DDX3X) and its implications for HCC. We found that FAM134B interacts with DDX3X, preventing its proteasomal degradation by reducing K48-linked polyubiquitination and enhancing K63-linked polyubiquitination. This stabilization of DDX3X is crucial for AKT signaling activation, as DDX3X is known to promote the transcription of Rac Family Small GTPase 1 (Rac1), a key activator of the AKT pathway. Our results confirmed that FAM134B activates AKT signaling through the DDX3X-Rac1-AKT axis in HCC. Furthermore, we observed that DDX3X is upregulated in HCC and contributes to tumor progression. Interestingly, DDX3X not only activates AKT signaling but also increases FAM134B expression by enhancing its transcriptional activity, suggesting a positive feedback loop between these two proteins in HCC. Lastly, we explored the therapeutic potential of combining the DDX3X inhibitor RK-33 with FAM134B knockdown in HCC treatment. Our findings indicate that this synergistic approach may offer a promising strategy for HCC therapy.

Posttranslational modification succinylation plays a pivotal role in tumorigenesis across malignancies, yet its mechanistic contributions to hepatocellular carcinoma (HCC) pathogenesis and therapeutic resistance remain poorly characterized. In this study, we systematically demonstrated that the splicing factor SRSF11 undergoes functional consequential succinylation in HCC progression. Mechanistically, lysine acetyltransferase 2 A (KAT2A) directly interacts with SRSF11 to catalyze its succinylation at lysine 419 (K419), thereby enhancing DNA damage repair capacity in both in vitro and in vivo HCC models. Structural and functional analyses revealed that K419 succinylation stabilizes SRSF11-spliceosome interactions, which promote the inclusion of exon 10 of RAD52 through enhanced pre-mRNAs binding. This exon-specific splicing event preserves the RAD51-binding domain essential for homologous recombination (HR) repair, ultimately facilitating RAD52-RAD51 dimer assembly and HR-mediated genomic stabilization. Clinically, elevated SRSF11 expression is correlated with increased HR activity, radioresistance, and reduced survival in HCC patients. Notably, genetic disruption of the KAT2A-SRSF11 axis sensitizes HCC cells to radiation-induced apoptosis. Our findings establish succinylation as a novel regulatory mechanism linking alternative splicing to DNA repair fidelity in HCC, while proposing therapeutic targeting of this pathway to overcome radioresistance in advanced HCC.

As a major contributor to cancer-associated deaths, advanced colorectal cancer (CRC) has a constrained range of effective treatment options. The short isoform of bromodomain-containing protein 4 (BRD4-S) has recently been implicated as a potential oncogenic driver; however, its regulatory mechanisms and functional role in CRC remain incompletely understood.

Osteosarcoma (OS) is a highly aggressive primary bone malignancy with a prominent propensity for metastasis. The identification of the key molecular drivers for OS progression is paramount to developing effective therapies. Although kinesin family member 18A (KIF18A) has previously been suggested to play a role as a potential oncogene in the development and metastatic progression of several types of cancer, little is known about its exact functional role in OS.

Since its introduction in 2008, sorafenib has remained the standard first-line systemic treatment for advanced hepatocellular carcinoma (HCC). Nevertheless, its clinical benefits are often compromised by the rapid emergence of drug resistance. This study explores the molecular mechanisms underlying sorafenib resistance, with particular emphasis on the involvement of connective tissue growth factor (CCN2/CTGF) in the regulation of c-Met signaling pathways.

Macrophage infiltration is prevalent in lung cancer tissues, significantly influencing disease progression and clinical outcomes. Lung squamous cell carcinoma (LUSC) is often diagnosed at advanced stages, resulting in poor prognosis. Identifying effective diagnostic biomarkers, particularly those associated with macrophage infiltration, is crucial for early detection and improved treatment outcomes. This study aims to identify diagnostic markers specifically linked to M1 macrophages in LUSC.

Ankyrin G (ANK3), belonging to the ankyrin family, contributes to cellular structural integrity by linking the cytoskeleton to the plasma membrane. Abnormal ANK3 expression has been reported across several human malignancies, yet the regulatory mechanisms involved are still poorly understood. The process of dividing introns into several steps is referred to as recursive splicing (RS). RS can control the quality of transcripts produced by regulating the retention of the RS-exon. Hundreds of annotated RS-exons in human mRNAs are attributed to the inhibition of RS by the exon junction complex (EJC).

Primary liver cancer (PLC) exhibits a high incidence and mortality rate. Early diagnosis and effective treatment are crucial for improving patient survival rates. This study aims to identify biomarkers of hepatitis B-related liver cancer and establish a new method for molecular subtype classification based on differential metabolite-related regulatory gene expression profiles.

Resistance to anoikis is a critical mechanism that enables metastatic dissemination. Abrogation of this cellular safeguard is therefore a hallmark of aggressive cancer progression. Despite the importance of anoikis, there are still few biomarkers among anoikis-related genes (ARGs) that could aid in the prognostication of bladder cancer (BC) patients and potentially serve as drug targets.

Research on the molecular progression of esophageal squamous dysplasia to cancer remains limited. The majority of prior studies have focused on morphological precancerous lesions sampled adjacent to tumors, and have relied primarily on the analysis of data from whole-exome sequencing.

Clonal hematopoiesis (CH) is characterized by the expansion of hematopoietic stem and progenitor cells harboring somatic mutations, which confers an increased risk of hematologic malignancies and cardiovascular disease. Among CH-associated mutations, mutations affecting splicing factors (SFs), including splicing factor 3b subunit 1 (SF3B1), serine/arginine-rich splicing factor 2 (SRSF2), U2 small nuclear RNA auxiliary factor 1 (U2AF1), and zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2 (ZRSR2), play a unique role in promoting clonal expansion and leukemogenesis. In this review, we summarize recent findings on the role of SF mutations in CH progression, their interplay with other mutations (e.g., DNA methyltransferase 3 alpha (DNMT3A), ten-eleven translocation methylcytosine dioxygenase 2 (TET2) and isocitrate dehydrogenase 2 (IDH2)), and their impact on hematopoietic homeostasis. Epidemiological studies have demonstrated that SF-mutant CH exhibits an accelerated clonal expansion compared to other CH clones. Furthermore, murine models suggest that SF mutations alone do not inherently confer a growth advantage for clonal expansion but rather enhance disease phenotypes when co-existing with epigenetic mutations, such as IDH2 and TET2. These findings suggest that SF mutations contribute to CH expansion and malignant transformation through a synergistic interplay with other mutations and external factors such as inflammation. Given the clinical significance of SF mutations, ongoing research is focused on developing targeted therapies that modulate aberrant RNA splicing and prevent CH-driven leukemogenesis. Understanding the mechanisms underlying mutant spliceosome-mediated CH expansion may provide novel insights into early detection, risk stratification, and therapeutic interventions in hematologic malignancies.

Pediatric high-grade gliomas (pHGGs) and diffuse midline gliomas (DMGs) represent some of the most aggressive and lethal childhood brain tumors. Recent molecular and epigenetic discoveries have redefined these entities as distinct from adult gliomas, with hallmark alterations such as H3K27M and H3G34R/V mutation driving unique biological behaviors. Advances in genomic, epigenomic, and transcriptomic profiling have enabled refined diagnostic classifications, improved our understanding of tumor heterogeneity, and revealed novel therapeutic targets. Despite these insights, standard of care approaches-primarily radiotherapy-remain palliative and conventional chemotherapy has shown limited efficacy. Emerging strategies, including targeted molecular therapies, immunotherapies, and innovative drug delivery techniques, offer promise but face significant challenges related to blood-brain barrier integrity, immune evasion, and intratumoral heterogeneity. Integration of DNA methylation profiling, enhancer landscape analysis, and liquid biopsy technologies are transforming diagnostic and monitoring capabilities. Future progress will depend on interdisciplinary collaboration, the development of predictive preclinical models, multi-omic integration, and adaptive clinical trial designs. Ultimately, tackling the biological complexity of pHGGs and DMGs through personalized, molecularly targeted approaches offers the best hope for improving outcomes in this devastating disease group.

Introduction Adamantinomatous craniopharyngioma (ACP) is a significant source of morbidity in the pediatric brain tumor population. It predominantly arises from the parasellar space. The tumors proximity to key vital structures often makes gross total surgical resection challenging and sometimes clinically inadvisable. Compounding the problem, adjunct therapies are not yet capable of providing a definitive cure. Recent preclinical research has made significant progress towards elucidating the mutagenic drivers of ACP, however much work remains to translate this into safe and effective treatments. Content Overview and Key Takeaways In the following chapter, we discuss the most up-to-date understanding of ACP biology and management. ACP is a histologically low grade tumor characterized by a mutation involving the beta-catenin protein, resulting in pathologic stability of the protein that impairs cell death or apoptosis. A subpopulation of tumor cells then enter a transcriptomic state characterized by cellular oncogenic senescence. It is unclear how this state leads to feed forward loops resulting in tumorigenesis. Despite its benign nature, the consistent anatomic origin of ACP in the sellar/suprasellar space, often abutting or involving the hypothalamus, the infundibulum, and the optic chiasm, contributes to multiple long-term complications such as endocrinopathies, obesity, vision loss, and obstructive hydrocephalus. Surgically, the current trend is towards conservative approaches with the goal of maximal safe resection without perturbing the hypothalamus. Adjunct radiotherapy is standard in cases of residual or recurrent disease. Close coordination with endocrinology colleagues is vital to appropriately care for these patients as they often suffer from lifelong endocrinopathies that remain a significant source of burden in this population.

Atypical teratoid rhabdoid tumors (ATRT) are rare, often lethal embryonal tumors of the central nervous system (CNS) that primarily affect very young children. Intensive multimodal approaches have resulted in improvements in survival albeit with significant associated toxicity. Recent molecular studies have led to the discovery of SMARCB1 inactivation and resultant BAF47/INI1 loss as the near-universal key genetic event that leads to widespread epigenetic dysregulation. Rarely, SMARCA4 encoding BRG1 is impacted. SMARCB1 and SMARCA4 are core subunits of the SWI/SNF chromatin remodeling complex, which is a fundamental epigenetic regulator of gene transcription. Up to a third of patients diagnosed with ATRT have Rhabdoid Tumor Predisposition Syndrome (RTPS) characterized by germline SMARCB1 (or SMARCA4) alterations. Patients with RTPS are at increased risk of developing synchronous or metachronous rhabdoid tumors outside the CNS. At least three molecular subgroups of ATRT (ATRT-TYR, ATRT-SHH, ATRT-MYC) have been identified through large-scale DNA methylation and transcriptomic studies, with each subgroup having distinct transcriptional, epigenomic and clinicopathologic features. In this book chapter, we will summarize key epidemiological and clinical features of ATRT, review current conventional multimodal regimens, summarize key findings from conducted prospective trials and recently concluded (2020 to present) meta-analyses, as well as discuss emerging targeted treatment approaches that exploit potential therapeutic vulnerabilities of this epigenetically influenced tumor.