Colorectal cancer (CRC) is a heterogeneous disease shaped by genetic and epigenetic alterations. Approximately 20% of CRCs exhibit widespread CpG island hypermethylation, termed the CpG Island Methylator Phenotype (CIMP), frequently accompanied by MLH1 promoter hypermethylation, deficient mismatch repair (dMMR) and microsatellite instability (MSI). However, methylation patterns associated with MSI, independent of CIMP and MLH1 silencing, and the influence of anatomical location and patient age on the CRC methylome remain incompletely defined. We performed epigenome-wide DNA methylation profiling of 259 sporadic CRCs using the Illumina EPICv2 array. Differential methylation between MSI and microsatellite stable (MSS) CRCs was assessed after adjustment for tumour purity and anatomical location, then MLH1 promoter methylation and CIMP status, to delineate MSI-associated methylation changes. Additionally, we evaluated the effects of anatomical location and age on methylation patterns. While differential methylation between MSS and MSI CRCs was dominated by MLH1 promoter hypermethylation, additional adjustment for MLH1 hypermethylation and CIMP identified 656 CpG sites associated with MSI, beyond the global methylator phenotype. These included hypermethylation at LRP6, GSK3β, and CDK12, identifying differential methylation of genes involved in WNT signalling and transcriptional regulation. Within MSI CRCs, we observed the co-occurrence of MLH1 hypermethylation with promoter hypermethylation at TXNRD1. Anatomical location was strongly associated with methylation, whereas age had more modest effects. These results identify methylation changes associated with sporadic MSI beyond CIMP status and MLH1 hypermethylation, reveal heterogeneity within MSI CRCs, and indicate that anatomical location is a major determinant of the CRC methylome, advancing molecular stratification of CRC.

Glioblastoma is profoundly heterogeneous, and single-modality analyses often miss prognostically relevant structure. We introduce a transparent, end-to-end workflow that fuses available whole-slide histology and RNA-seq to discover clinically meaningful glioblastoma subgroups using an unsupervised learning model after feature extraction. Haematoxylin-eosin slides are tiled, tissue-screened and stain-normalised; tiles are embedded with a pretrained ResNet-50 to yield 2048-dimensional features, averaged per patient and compressed to 30-D by an autoencoder. In parallel, RNA-seq (~48 k genes) undergoes low-variance filtering and normalisation, then a second autoencoder produces a 30-D transcriptomic embedding. The two 30-D representations are concatenated into a 60-D fused vector, robustly scaled and refined with PCA (≈98% variance retained). Across K-means, Gaussian mixture models and Agglomerative clustering (k = 2-20), Agglomerative k = 2 was decisively best (mean silhouette ≈0.53), yielding clusters of 150 and 8 patients (survival subset 147 and 8). Survival separation was substantial (median 454 vs. 138 days; log-rank p = 0.0096). In Cox models, the poorer-prognosis cluster showed increased risk (HR ≈ 2.70), which remained significant after age adjustment (HR = 2.15, 95% CI 1.04-4.46; age per year HR = 1.02, 95% CI 1.01-1.04). Attribution and consensus analyses yielded compact, interpretable gene sets (22 shared; 8 per cluster), including markers associated with NOTCH/γ-secretase and oxidative phosphorylation. These findings nominate biologically plausible hypotheses for future validation rather than immediate treatment-selection rules. Overall, this study demonstrates that auditable late fusion of histology and transcriptomics, built from routine data, can identify survival-associated glioblastoma subgroups and provides a hypothesis-generating framework for prospective, harmonised, multi-centre validation.

Hepatocellular carcinoma (HCC) is characterized by pronounced metabolic reprogramming and is frequently accompanied by the development of an immunosuppressive microenvironment. However, the key molecular mediators linking tumour metabolic dysregulation to immune microenvironment remodelling remain insufficiently defined. This study aimed to identify critical metabolic genes in HCC and to investigate their roles in lipid metabolic reprogramming and immunosuppression.

Anti-PD-1 therapy resistance remains a critical barrier in non-small cell lung cancer (NSCLC) management, and the underlying mechanisms are incompletely defined.

Clonal hematopoiesis (CH) arises from the expansion of hematopoietic stem and progenitor cells bearing somatic mutations, often in genes linked to epigenetic regulation and inflammation. Once considered a benign age-related phenomenon, CH has gained increasing attention for its potential to influence cancer biology beyond hematologic malignancies. Recent studies have uncovered an unexpectedly high prevalence of CH in patients with colorectal cancer (CRC), raising important questions about its origin, context-specific drivers, and pathological consequences. While cytotoxic therapies are known contributors, accumulating evidence suggests that the chronic inflammatory and metabolic alterations intrinsic to CRC may also shape hematopoietic clonality. In turn, CH-derived myeloid cells harboring mutations such as DNMT3A or TET2 can modulate the tumor microenvironment, promote inflammation, and impair antitumor immunity. In this review, we synthesize emerging findings on the bidirectional relationship between CH and CRC, highlighting the mechanistic underpinnings and potential implications for disease progression, therapeutic resistance, and immune modulation. Understanding this evolving interface may open new avenues for risk stratification and treatment personalization in CRC.

Bevacizumab is widely used as an anti-angiogenic maintenance therapy in ovarian cancer; however, there are currently no validated clinical criteria to guide patient selection for its use.

Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer with limited treatment options. Although PARP inhibitor (PARPi) offers great promise in treating TNBC with deficiency in homologous recombination (HR), most TNBC patients are HR-proficient. Furthermore, acquired resistance to PARPi remains as a challenge. Thus, there is an unmet need to identify new therapeutic target for developing advanced TNBC treatment strategy.

Ferroptosis, an iron-dependent form of cell death driven by lipid peroxidation, has emerged as a potential therapeutic strategy for therapy-resistant cancers. Glutathione peroxidase 4 and the selenoprotein biosynthesis pathway essential for its translation are key regulators of ferroptosis but lack effective therapeutic targeting. In a drug screening using a selenoprotein translation reporter, here we identify FMS-like tyrosine kinase 3 (FLT3) inhibitors as suppressors of selenoprotein translation that induce ferroptosis in FLT3-mutant acute myeloid leukaemia. Mechanistically, FLT3 inhibition disrupts selenocysteine recoding, in which a UGA stop codon is recoded as selenocysteine via the SECIS element and associated binding proteins. Notably, the antileukemic efficacy of the FLT3 inhibitor gilteritinib was markedly reduced by dietary vitamin E, which attenuated ferroptosis. This study highlights ferroptosis as a vulnerability in FLT3-mutant acute myeloid leukaemia and suggests that high vitamin E intake may compromise tyrosine kinase inhibitor efficacy partly by suppressing ferroptosis.

The high incidence and mortality rates of tumors have resulted in significant social and economic burdens, posing a major global threat to human life and societal development. In recent years, molecular targeted therapy for tumors has become a research hotspot. C-MET, the receptor for hepatocyte growth factor (HGF), plays a crucial role in the HGF/C-MET signaling pathway, which is involved in various processes such as tumor cell growth, invasion, migration, angiogenesis, epithelial-mesenchymal transition, tumor microenvironment remodeling and therapeutic resistance. Several C-MET-targeting strategies have been developed, including small-molecule tyrosine kinase inhibitors (TKIs), monoclonal antibodies (mAbs) against C-MET or HGF, antibody-drug conjugates (ADCs), nucleic acid aptamers, soluble receptors, natural compounds, and proteolysis targeting chimeras (PROTACs) targeting MET. These inhibitors have demonstrated encouraging anti-tumor effects in both preclinical and clinical studies, with several already available on the market. However, further research is still needed on the activation mechanisms of the HGF/C-MET signaling pathway and its interactions with other receptor tyrosine kinases, which will aid in identifying suitable patients for these treatments. This review provides a comprehensive overview of the structure, regulation, signaling pathways, and functions of C-MET, along with recent advances in C-MET inhibitors, offering valuable insights for cancer therapy.

Chimeric antigen receptor (CAR) T-cell therapy has revolutionized oncology, and its foundational logic-precise antigen recognition coupled with durable effector activity-extends naturally to chronic non-malignant diseases sustained by long-lived pathological cells. These include viral reservoirs, autoreactive B and plasma cells, activated fibroblasts, alloimmune clones, and senescent cells that remodel tissue niches and evade clearance by conventional therapies. This review highlights how CAR-based strategies can be adapted across diverse disease settings by redirecting engineered immune responses toward disease-sustaining cellular compartments. Co-stimulatory domains such as CD28, 4-1BB, and OX40 enhance persistence and effector function; programmed cell death protein 1 (PD-1)-CD28 switch receptors reverse inhibitory signaling; and cytokine-resistant CARs incorporating dominant-negative transforming growth factor-β (TGF-β) receptors maintain activity within suppressive microenvironments. We discuss these approaches across infections, including human immunodeficiency virus (HIV) and Epstein-Barr virus (EBV); autoimmunity involving CD19- and B-cell maturation antigen (BCMA)-directed depletion strategies and CAR-engineered regulatory T cells (CAR-Tregs); fibrosis targeting fibroblast activation protein (FAP); hemophilia using B-cell antibody receptor (BAR)-CARs against factor VIII and factor IX inhibitors; transplantation employing human leukocyte antigen (HLA)-specific CAR-Tregs; and senescence-associated pathologies targeting urokinase plasminogen activator receptor (uPAR) and natural killer group 2D ligands (NKG2DLs). Early clinical experiences in systemic lupus erythematosus, systemic sclerosis, myositis, and multiple sclerosis, together with preclinical successes in chronic infections and fibrotic disease, demonstrate both feasibility and durable disease modification. By extending CAR-T therapy beyond oncology, these applications position programmable cellular immunotherapy as a broadly adaptable platform for eliminating persistent pathological cells, remodeling diseased tissue environments, and restoring long-term immune homeostasis.

Hypoxia, a hallmark of solid tumors, poses a significant challenge in cancer therapy due to its association with poor prognosis and resistance to conventional treatments. Oncolytic viruses represent a promising treatment strategy, as they selectively replicate within cancer cells and lyse them, potentially including those in hypoxic tumor regions. Here, we examined how hypoxic conditions influence the activity of enadenotucirev (EnAd), a clinically relevant group B oncolytic adenovirus previously detected in hypoxic areas of xenograft tumors. We demonstrated that hypoxia enhances virus production by boosting transcription and translation of immediate-early, early, and late adenoviral genes. The immediate-early gene E1A was upregulated within 2 h (17-fold) after virus entry under hypoxia, driven by a conserved hypoxia-response element (HRE) in its promoter. Mechanistic studies revealed that the hypoxia-inducible factor (HIF)-2α and HIF-1β heterodimers bind to this HRE, transactivating E1A. By inducing E1A expression, hypoxia also elevated viral genome synthesis, structural protein production, and therapeutic transgene expression, underscoring the potential of EnAd to target the hypoxic tumor microenvironment. This is the first report of a functional HRE in a human adenovirus, conserved across 59 adenovirus genotypes, and identifies hypoxia as a driver of enhanced oncolytic activity with implications for adenovirus-based therapies in solid tumors.

Myeloproliferative neoplasms (MPNs) are broadly classified into BCR::ABL1-positive chronic myeloid leukaemia (CML) and BCR::ABL1-negative subtypes such as polycythaemia vera (PV), essential thrombocythaemia and primary myelofibrosis. Although traditionally considered mutually exclusive, rare cases of coexisting BCR::ABL1 rearrangement and Janus kinase 2 (JAK2) mutation have increasingly been recognised.We report the first Philippine case series of three patients with concurrent CML and JAK2-positive MPNs. Two patients developed PV 6-9 years after the initial diagnosis of CML despite ongoing tyrosine kinase inhibitor (TKI) therapy and molecular response, while a third patient had persistent thrombocytosis and was later found to have a concomitant JAK2-mutated MPN with fibrotic marrow features after 4 years.Compared with previously reported cases, our series demonstrates similarly delayed emergence of JAK2-mutated clones while highlighting real-world challenges in TKI intolerance, sequential TKI use and the need for combined cytoreductive strategies in a resource-limited setting.

The ABO blood group system is one of the most clinically significant human blood group systems and is closely associated with pathogenesis, progression, and prognosis of numerous diseases. This narrative review synthesizes recent epidemiological evidence and explores potential mechanisms linking ABO to cardiovascular diseases, malignancies, diabetes, Plasmodium falciparum malaria, COVID‑19, and rheumatic diseases.

Immunotherapy resistance remains a major barrier to achieving sustained patient improvement in non-small cell lung cancer (NSCLCs). Here, through integrating CODEX, metabolomics, CyTOF, ATAC-seq, and single-cell spatial transcriptomics from NSCLC tumors, we uncover an unrecognized role of ALDH9A1 in promoting resistance to anti-PD-1 therapy. In immunocompetent, but not immunocompromised mouse models, loss of ALDH9A1 markedly restrains tumor growth. This effect is accompanied by increased maturation of tertiary lymphoid structures and reduced accumulation of protumorigenic MDSCs within tumor immune microenvironment. Mechanistically, ALDH9A1-driven carnitine production elevates acetyl-CoA levels, remodels chromatin accessibility, and activates Il1b superenhancers in tumor cells, thereby promoting MDSC polarization and CD8+ T cell exhaustion. In vivo, genetic or pharmacological inhibition of ALDH9A1, or antibody-mediated IL-1β neutralization, suppresses tumor progression and restores sensitivity to anti-PD-1 therapy. IL-1β further activates NF-κB and upregulates ALDH9A1, establishing a feedback ALDH9A1-IL-1β loop. Importantly, the ALDH9A1/IL-1β axis is frequently hyperactivated in NSCLC patients and correlates with inferior responses to anti-PD-1 immunotherapy. Together, this study reveals a previously unappreciated NSCLC-specific immunoregulatory pathway and identifies ALDH9A1 as a promising therapeutic target for improving immunotherapy efficacy.

Regulation of cancer cells by their environment contributes to tumorigenesis and drug response, though the extent to which the oncogenic state can alter a cell's perception of its environment is not clear. EML4-ALK is a receptor tyrosine kinase (RTK) fusion oncoprotein that suppresses transmembrane EGFR signaling in cancer cells. ALK inhibition restores signaling through EGFR, thereby promoting survival and drug tolerance. Here, we tested whether such modulation of EGFR activity was common among other RTK fusions, which collectively are found in ~5% of all cancers. Using live- and fixed-cell microscopy in isogenic and patient-derived cell lines, we found that a wide variety of RTK fusions suppress transmembrane EGFR, through mechanisms that include the sequestration of the adaptor protein Grb2. Targeted therapies rapidly released Grb2 from sequestration and potentiated EGFR. Synthetic optogenetic analogs of RTK fusions confirmed that cytoplasmic sequestration of Grb2 was sufficient to suppress perception of extracellular EGF and could do so without driving signaling from the synthetic fusion itself, demonstrating that fusion signaling and suppression of EGFR signaling could be functionally decoupled. Our study uncovers that a large number of RTK fusions simultaneously act as both activators and suppressors of signaling, the mechanisms of which could be exploited for biomimetic therapies that enhance cell killing and suppress drug tolerance.

Chemotherapy resistance remains a major challenge in cancer treatment, driven by cancer cells' ability to acquire adaptive properties, rewire signaling pathways, and alter chromatin structure to evade drug-induced cytotoxicity. Because these processes rely heavily on epigenetic mechanisms that regulate chromatin organization and transcriptional plasticity, epigenetic regulators have emerged as key contributors to chemotherapy resistance. To investigate resistance to paclitaxel, one of the most widely used chemotherapeutic agents in triple-negative breast cancer (TNBC), we employed an epigenome-focused knockout library (EPIKOL), a CRISPR-Cas9-based library, designed to systematically disrupt genes involved in chromatin regulation. Chemoresistant cell lines were generated through a stepwise dose-escalation protocol that recapitulates clinically relevant drug adaptation. However, these resistant cells exhibit a multidrug-resistant (MDR) phenotype, posing significant challenges for efficient viral transduction and the selection of stable cell populations. In this study, we describe key methodological steps for achieving high-efficiency lentiviral transduction and selection, enabling the successful application of EPIKOL CRISPR screens in chemoresistant TNBC models. Following the described protocol, an epigenome-wide CRISPR screen was conducted on chemoresistant TNBC cells, and novel epigenetic regulators of chemoresistance were identified. This protocol provides a robust framework for identifying epigenetic regulators that contribute to acquired paclitaxel resistance using a CRISPR-based loss-of-function approach.

BACKGROUND Multiple endocrine neoplasia type 2A (MEN 2A) is a rare autosomal-dominant genetic syndrome characterized by mutations in the RET gene and tumors of endocrine glands, including pheochromocytomas. Pheochromocytoma is a benign primary endocrine tumor of the adrenal glands that produces catecholamines and in rare cases is complicated by pheochromocytoma multisystem crisis (PMC), a life-threatening endocrine emergency caused by severe catecholamine overproduction. This report describes a 42-year-old woman presenting with PMC associated with bilateral pheochromocytomas and MEN2A. CASE REPORT The patient presented with a sudden onset of back pain and dyspnea with severe shock. An enhanced computed tomography examination revealed bilateral adrenal gland tumors, and she was diagnosed with PMC complicated by multiple organ failure and catecholamine-induced cardiomyopathy. We introduced simultaneous veno-venous extracorporeal membrane oxygenation and continuous hemodiafiltration. A definitive operation for PMC was performed on hospital day 12, with the intent of complete resection of bilateral pheochromocytomas. The patient was weaned from continuous hemodiafiltration on hospital day 21st day and was finally weaned from artificial ventilation on hospital day 30. Genetic examination revealed a pathogenic RET mutation (Cys634Arg, C634R), leading to the diagnosis of MEN2A. She is now undergoing rehabilitation, with intensive surveillance for thyroid medullary carcinoma and hyperparathyroidism. CONCLUSIONS PMC can easily lead to multiple organ failure within a few days. A multidisciplinary approach to PMC can rescue these patients by making surgical pheochromocytoma resection possible. If synchronous bilateral pheochromocytomas are detected, MEN2A should be suspected.

Although sequencing costs have steadily decreased with advances in technology, they remain high for large scale studies. The design of traditional individual-disease sequencing studies is either case only or cases with relatively few controls, resulting in potential loss of statistical power for discovery of disease associated genes. Here we show that for a given number of sequenced cases, a large control sample size is critical to maximize power for rare variant burden analysis. Furthermore, we have developed an end-to-end workflow based tool (CoCoRV-nf) to facilitate the use of external biobank sequence resources as controls. The modules include consistent variant QC, variant annotation, ancestry population prediction, and gene based burden analysis using summary genotype information, and combined analysis from multiple independent results. The tool supports exomes and genomes from gnomAD and All of Us as controls with preprocessed datasets. We apply the tool in two rare neurological diseases: amyotrophic lateral sclerosis and neuroblastoma. For each disease, two case cohorts are paired with gnomAD and All of Us data, respectively, followed by a combined analysis. Not only did we recapture known genes, but also, we identified new candidate genes for both diseases. By leveraging multiple large external biobank sequence data, we demonstrate the feasibility of using our tool to maximize statistical power to identify new disease predisposition genes.

Breast cancer is one of the leading causes of cancer-related deaths among women worldwide, with estrogen receptor-positive (ER+) breast cancer being the most common subtype. Cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) have become a crucial therapeutic approach for this type of cancer. However, ER+ breast cancer frequently develops resistance to CDK4/6i, limiting therapeutic efficacy. Alternative splicing is a key post-transcriptional regulatory mechanism that may drive such resistance. In this review, we comprehensively analyzed the literature on the molecular mechanisms and key signaling pathways associated with CDK4/6i resistance in ER+ breast cancer and introduced the role of alternative splicing, with a particular focus on its function in tumor drug resistance. Available evidence suggests that splicing dysregulation may influence resistance through multiple pathways, including cell-cycle control, epithelial-mesenchymal transition, growth factor and RAS/MAPK signaling, and immune-related programs. Recent work has also suggested that reduced expression of the splicing regulator NSRP1 may be associated with CDK4/6i resistance through altered NSD2 splicing and activation of interferon signaling, although this mechanism currently requires further independent validation. Collectively, these findings support alternative splicing as a promising but still evolving area of investigation in CDK4/6i resistance. This work provides deeper insights into the role of alternative splicing in CDK4/6i resistance and offers a theoretical foundation for developing novel therapeutic approaches. Future research may focus on developing drugs that precisely modulate specific splicing events or combining CDK4/6i with splicing modulators to reverse or delay resistance.

Radioresistance remains a major obstacle in the treatment of non-small cell lung cancer (NSCLC). Transcription factor AP-2α (TFAP2A) has been implicated in tumor progression, but its role in NSCLC radioresistance and translational therapeutic relevance remain unclear.