A cell's fate is shaped by its inherited state, or lineage, and the ever-shifting context of its environment. CRISPR-based recording technologies are a promising solution for mapping the lineage of a developing system; however, challenges remain regarding single-cell recovery, engineering complexity, and scale. Here, we introduce BASELINE, which uses base editing to generate high-resolution lineage trees in conjunction with single-cell profiling. BASELINE uses the Cas12a adenine base editor to irreversibly edit nucleotides across target arrays built from 50 synthetic target sites, which are integrated multiple times into a cell's genome. We demonstrate that BASELINE accumulates lineage-specific marks over a wide range of biologically relevant intervals, recording more than 4300 bits of information in a model of pancreatic cancer, a 50-fold increase over existing technologies. Single-cell sequencing reveals high-fidelity capture of these recorders, averaging 29 cell divisions captured per lineage, within the estimated range of mammalian development. We expect BASELINE to apply to a wide range of lineage-tracing projects in development and disease, especially those in which cellular engineering makes small, more distributed systems challenging.

Ferroptosis is an iron-dependent form of programmed cell death driven by lipid peroxidation, distinct from apoptosis and necrosis. It has been confirmed as a key regulator in hepatocellular carcinoma (HCC). This study systematically elucidates three interconnected regulatory networks of ferroptosis-metabolic, epigenetic, and microenvironmental-and proposes a closed-loop regulatory model integrating these dimensions. By integrating metabolic biomarkers, epigenetic indicators, and microenvironmental features, we also summarize emerging strategies to enhance ferroptosis sensitivity. By summarizing the regulatory nodes as well as clinical translation progress, this work provides a comprehensive roadmap for overcoming therapeutic bottlenecks in HCC and realizing ferroptosis-based precision medicine.

The fat mass and obesity-associated protein (FTO), an RNA demethylase acting on both internal m6;A and cap-proximal m6;Am, functions in cancer as a context-dependent epitranscriptomic regulator whose net effect cannot be reduced to an oncogene-tumor-suppressor dichotomy. Its biological output is shaped by tumor lineage, subcellular localization, upstream signaling, and competing m6;A reader activities, predominantly YTHDF2-mediated decay and IGF2BP-mediated stabilization, although both reader families display additional non-canonical functions and are themselves modulated by post-translational modifications. Building on the now well-established context-dependence of FTO biology, which we do not claim as a novel observation, this review synthesizes current evidence on FTO's roles at the intersection of tumor immune contexture, immune checkpoint regulation, metabolic reprogramming, and therapeutic resistance. We examine how FTO may contribute to immune exclusion through metabolic competition, exosomal signaling, and stromal reprogramming; modulate PD-L1 expression through direct and indirect mechanisms; and influence response to chemotherapy, targeted therapy, radiotherapy, and CNS-directed treatment. Emerging FTO inhibitors, FTO-degraders, and combination strategies with immune checkpoint blockade, ferroptosis inducers, or glycolytic inhibitors are evaluated against their underlying preclinical evidence base. The contribution of this review lies less in proposing a new framework than in three forms of integration typically addressed in isolation: explicit calibration of mechanistic claims to evidence tier, systematic separation of tumor-intrinsic from immune-cell-intrinsic FTO functions across lymphoid and myeloid compartments, and translation of reader-network biology into biomarker-stratified trial design. Technical limitations of epitranscriptomic methods are addressed as constraints on inference. To our knowledge, no FTO-targeted strategy has yet entered Phase I oncology evaluation; current combination rationales therefore remain preclinically supported rather than clinically established.

Glioblastoma (GBM) is the most common and aggressive primary malignant tumor of the adult central nervous system, with nearly 90% of cases recurring within two years despite standard surgery, radiotherapy, and chemotherapy. Tumor-associated macrophages (TAMs) play critical roles in GBM recurrence, but their characteristics in recurrent GBM remain insufficiently defined. Krüppel-like factor 10 (KLF10) regulates metabolism, mitochondrial function, proliferation, and apoptosis; however, its role in GBM-associated TAMs remains unclear.

Recent studies have shown that while chemotherapy kills tumor cells, it may also induce adaptive changes in cells within the tumor microenvironment, particularly cancer-associated fibroblasts (CAFs), which could paradoxically promote tumor progression. This study aimed to investigate the role of CAFs exposed to paclitaxel (PTX) or doxorubicin (DOX) in tumor progression and explore the underlying mechanisms.

Oral cancer (OC) remains a therapeutic challenge due to limited validated targets. Cis-pQTLs from the deCODE cohort (n = 35,559) were harmonized with OC-GWAS (3547 cases and 691,466 controls) meta-data through a two-sample Mendelian randomization (MR) framework. Robust Validation included replication in the UKB-PPP dataset, colocalization analysis, SMR (Summary-based MR), HEIDI (Heterogeneity in Dependent Instruments) tests, and eQTL evidence. Additional analyses encompassed protein-protein interaction (PPI) networks, Kyoto Encyclopedia of Genes and Genomes annotation (KEGG)/Gene Ontology (GO) pathway enrichment, mediation, Druggability and side effects analysis. Oral cancer (OC) remains a therapeutic challenge due to limited validated targets. Cis-pQTLs from the deCODE cohort (n = 35,559) were harmonized with OC-GWAS (3547 cases and 691,466 controls) meta-data through a two-sample Mendelian randomization (MR) framework. Robust Validation included replication in the UKB-PPP dataset, colocalization analysis, SMR (Summary-based MR), HEIDI (Heterogeneity in Dependent Instruments) tests, and eQTL evidence. Additional analyses encompassed protein-protein interaction (PPI) networks, Kyoto Encyclopedia of Genes and Genomes annotation (KEGG)/Gene Ontology (GO) pathway enrichment, mediation, Druggability and side effects analysis. To experimentally corroborate the MR findings, the quantitative real-time PCR (qRT-PCR) was performed to examine the mRNA expression levels of selected genes in oral squamous cell carcinoma (OSCC) cell lines (SCC-9 and SCC-25) and normal human oral epithelial cells (HOEC). Multi-omics MR identified TNFSF8 (p = 2.49 × 10-8, OR = 1.24) as a Tier 1 target. XXYLT1 (p = 1.41 × 10-4, OR = 1.34) and HSD17B14 (p = 0.04, OR = 2.00) achieved Tier 2. eQTLs-pQTLs Relationship revealed XXYLT1 expression explained 24.65% of risk through elevated plasma protein levels, TNFSF8 eQTLs mediated 72.80% via protein upregulation. Mediation analyses on CD4 on HLA DR+ CD4+ T cells (7.18%) contributed to the risk of OC by upregulating plasma HSD17B14, while daily cigarette consumption (20.63%) and CD8+ T cell percentage leukocytes (12.06%) contributed to the risk of OC by upregulating plasma TNFSF8. Drug safety assessments highlighted systemic TNFSF8 inhibition may elevate skin cancer risk. Multi-omics MR prioritizes TNFSF8 as a therapeutic target for oral cancer. Multi-omics MR identified TNFSF8 (p = 2.49 × 10-8, OR = 1.24) as a Tier 1 target. XXYLT1 (p = 1.41 × 10-4, OR = 1.34) and HSD17B14 (p = 0.04, OR = 2.00) achieved Tier 2. eQTLs-pQTLs Relationship revealed XXYLT1 expression explained 24.65% of risk through elevated plasma protein levels, TNFSF8 eQTLs mediated 72.80% via protein upregulation. Mediation analyses on CD4 on HLA DR+ CD4+ T cells (7.18%) contributed to the risk of OC by upregulating plasma HSD17B14, while daily cigarette consumption (20.63%) and CD8+ T cell percentage leukocytes (12.06%) contributed to the risk of OC by upregulating plasma TNFSF8. Drug safety assessments highlighted systemic TNFSF8 inhibition may elevate skin cancer risk. qRT-PCR confirmed significant upregulation of XXYLT1 and HSD17B14 in both SCC-9 and SCC-25 cell lines (p < 0.001), which is consistent with MR predictions. TNFSF8 was not reliably detected in these cancer cells, aligning with its proposed immune-mediated mechanism. Multi-omics MR prioritizes TNFSF8 as a therapeutic target for oral cancer. qPCR validation confirms the dysregulation of XXYLT1 and HSD17B14, while findings regarding TNFSF8 underscore its immune origin. These findings warrant further functional studies.

Androgen receptor splice variant 7 (AR-V7) is associated with resistance to androgen receptor-targeting therapies in prostate cancer, but its prevalence and clinical relevance in non-prostatic cancers remain incompletely characterized. A systematic review was conducted in accordance with PRISMA guidelines. Thirty-four studies, including 4855 clinical cases and 60 cell lines, were included. Overall, AR-V7 positivity was reported in 948/4855 clinical cases (19.5%); however, this represents a descriptive estimate across heterogeneous tumor types, study designs, and detection methods. Breast cancer accounted for 4057 of 4855 clinical cases (83.6%) and 815 of 948 AR-V7-positive cases (86.0%), with a within-cancer prevalence of 20.1%. However, after excluding the TCGA cohort in which AR-V7 was inferred through splice-junction analysis, the prevalence of AR-V7-positive breast cancer decreased to 9%. Higher tumor-specific proportions were observed in salivary duct carcinoma (55.2%), hepatocellular carcinoma (57.1%), and non-muscle-invasive bladder cancer (82.6%), but these estimates were based on smaller cohorts and should be interpreted cautiously. AR-V7 was present in several treatment-naive non-prostatic cancers, suggesting that it may represent a preexisting molecular feature in selected contexts. Current evidence suggests that AR-V7 warrants further investigation as a candidate biomarker. Standardized detection methods and prospective studies are needed before its clinical utility can be established.

Kidney renal clear cell carcinoma (KIRC) is the most common and aggressive subtype of renal cell carcinoma and is characterized by poor prognosis and high molecular heterogeneity. Long noncoding RNAs (lncRNAs) have emerged as crucial regulators in cancer, yet the functional role of SNHG11 in KIRC remains unclear. In this study, we perform integrated multiomics analysis using data from the TCGA and ICGC cohorts and reveal that SNHG11, a methylation-associated lncRNA, is significantly correlated with poor clinical outcomes. In vitro and in vivo assays demonstrate that SNHG11 promotes tumor proliferation and progression. Mechanistically, SNHG11 enhances oxidative phosphorylation, as evidenced by increased ATP production, disrupted mitochondrial membrane potential, and altered NAD +/NADH ratios. Furthermore, SNHG11 expression is associated with somatic mutation patterns, particularly those involving BAP1 and PBRM1, indicating potential crosstalk between epigenetic regulation and genetic alterations. These findings reveal that SNHG11 is a novel biomarker in KIRC and a potential therapeutic target.

Lung cancer remains a major global health challenge, and the oncogenic function of KDM1B (Lysine-specific Demethylase 1B) is still poorly characterized. This study employed integrated bioinformatics and experimental approaches to investigate KDM1B's function in lung cancer. Pan-cancer analysis using databases such as TIMER revealed notably elevated KDM1B mRNA expression in LUAD datasets, suggesting its potential as a diagnostic biomarker. A strong association was also found between increased KDM1B levels and immune cell infiltration in LUAD datasets. Protein interaction networks constructed using STRING and Cytoscape revealed close associations between KDM1B and key regulatory genes in NSCLC. KEGG enrichment analysis linked KDM1B to the mTOR signaling, which is critical for cell proliferation and survival. RT-PCR and western blotting for experimental validation showed KDM1B expression was significantly increased in A549 and NCI-H460 lung cancer cells. The deletion of KDM1B inhibits cell growth, induces G0/G1 phase cell cycle arrest, and promotes apoptosis in A54 cells. Moreover, cell proliferation was significantly inhibited by the KDM1B inhibitor, tranylcypromine, and induced G0/G1 phase cell cycle arrest, increased apoptosis, ROS, and glycolytic activity in A549 cells. Collectively, these findings highlight KDM1B as a valuable therapeutic target in lung adenocarcinoma and emphasize its key role in lung cancer development.

BACKGROUND Neurofibromatosis type 1 (NF1) and Marfan syndrome (MFS) are genetically determined systemic disorders. Their simultaneous occurrence is exceptionally rare, with only a few cases reported in the literature. CASE REPORT A 13-year-old boy was admitted to a cardiology clinic due to mitral and tricuspid valve prolapse. He was tall, with severe scoliosis and distinctive dysmorphic features typical of MFS. More than 20 cafe-au-lait spots, characteristic of NF1, were present on his skin. The family history included NF1 in his twin brother, mother, maternal uncle, and maternal grandmother. The maternal uncle also exhibited phenotypic features of MFS and died at a young age from a suspected ruptured intracranial aneurysm. Genetic testing in our patient revealed an NF1 mutation, as well as a 16p13.11 microduplication that could explain his developmental delay and speech difficulties. The diagnosis of MFS was based on characteristic dysmorphic features and the presence of aortic root dilation, despite negative findings concerning the fibrillin-1 (FBN1) mutation typically associated with MFS. CONCLUSIONS A thorough assessment of physical features is essential to detect atypical phenotypes and recognize potential coexistence of multiple genetic syndromes. This case highlights the clinical importance of systematic cardiac evaluation, given that cardiac abnormalities typical of MFS may be critical for its recognition. Reporting such an unusual coexistence of NF1 and MFS underscores the need for multidisciplinary care to improve long-term outcomes in patients with overlapping genetic disorders.

Tyrosine kinase inhibitor (TKI) resistance severely limits clinical outcomes in hepatocellular carcinoma (HCC), highlighting the urgent need to elucidate its underlying molecular mechanisms. In this study, an unbiased genome-wide CRISPR/Cas9 screening identified novel key factors related to the therapeutic responsiveness of TKI in HCC. By integrating data from 20 datasets encompassing 322 samples, a comprehensive TKI therapeutic response landscape for HCC was constructed. GO and Reactome enrichment analyses revealed that dysregulated RNA splicing, ubiquitination, endocytosis/exocytosis, and cell cycle pathways modulate TKI sensitivity, with close links to antitumor immunity. This study identified GPATCH4, CCT3, C19orf53, UACA, PPM1M, and LIN37 as key genes mediating TKI resistance in HCC. These six genes were found to be highly expressed in HCC and significantly associated with HCC patient prognosis. Drug sensitivity assays identified a significant association between their expression and responsiveness to TKI agents. In-house quantitative real-time PCR validated their differential expression levels in normal hepatocytes, parental HCC cells, and TKI-resistant HCC sublines. ssGSEA, TIMER2, and ESTIMATE analysis revealed that their expression modulates HCC immune infiltration. Bibliometric analysis revealed a growing focus on immunotherapy-based combination regimens to overcome TKI resistance. Ferroptosis, epithelial-mesenchymal transition and hypoxia were new research directions, which were closely related to the pathways investigated in this study. In conclusion, this study identified RNA splicing, ubiquitination, endocytosis/exocytosis, and cell cycle pathways, as well as GPATCH4, CCT3, C19orf53, UACA, PPM1M, and LIN37, as novel directions and targets for TKI-immunotherapy combination strategies, providing new insights for overcoming TKI resistance in HCC.

Acute myeloid leukemia (AML) is an aggressive and molecularly heterogeneous hematologic malignancy associated with poor clinical outcomes, particularly in elderly and high-risk patients. Increasing evidence suggests that metabolic reprogramming plays a critical role in leukemia progression, immune dysregulation, and therapeutic resistance. However, the prognostic value of metabolism-associated molecular networks in AML remains insufficiently understood.

To investigate the role of histone deacetylase 2 (HDAC2) in cisplatin resistance in ovarian cancer (OC). Cisplatin-resistant OC cell lines were employed to construct HDAC2 overexpression and knockdown models, and their effects on cell proliferation and apoptosis were examined. Chromatin immunoprecipitation, immunoprecipitation, and dual-luciferase reporter assays were performed to investigate the regulation of SMAD7 protein stability and promoter activity by HDAC2. Expression of DNA damage repair-related genes was detected by qRT-PCR. A xenograft mouse model was established for in vivo validation. HDAC2 was highly expressed in cisplatin-resistant OC cells. Overexpression of HDAC2 enhanced drug resistance and inhibited apoptosis and DNA damage, whereas knockdown of HDAC2 exhibited the opposite effects. Mechanistically, HDAC2 directly deacetylated the SMAD7 protein to prevent its degradation rather than suppressing its transcription via H3K27 deacetylation. The HDAC2/SMAD7 axis promoted drug resistance by activating the Wnt/β-catenin signalling pathway and modulating DNA damage repair-related genes. In vivo experiments confirmed that HDAC2 knockdown significantly inhibited tumour growth and enhanced the sensitivity. HDAC2 enhances cisplatin resistance in OC by deacetylating and stabilising SMAD7 protein, thereby activating the Wnt/β-catenin signalling pathway and promoting DNA damage repair.

Liquid biopsy has emerged as a transformative development in oncology, enabling the minimally invasive detection and monitoring of cancer through the analysis of tumor-derived material in blood. Moving beyond single-variable analysis, multifeature sequencing-based liquid biopsy (MSLB) integrates diverse classes of data from a single blood sample to provide deep multifactorial insight into tumor biology. In this review, MSLB is defined as the extraction of multiple biological signals from a single sequencing dataset and is put in the context of other layers of multimodal diagnostics. We focus on how recent advances in patient-, and potentially microbe-derived, cell-free nucleic acid analysis expand the biological information that can be extracted from a single blood sample. MSLB enables this by allowing the concurrent assessment of, for example, DNA methylation, copy number, fragmentation, and, in exploratory workflows, microbe-associated signals. This provides a broader view of tumor, immune, and microenvironment states. When combined with emerging bioinformatic and machine-learning frameworks, these complementary signals may improve early detection, disease monitoring, and treatment selection. Addressing challenges in standardization, validation, and regulatory alignment will be essential to determine how MSLB can be integrated into routine oncologic practice.

Glioblastoma (GBM) is an aggressive and highly lethal brain tumor. Secondary glioblastoma (sGBM), which arises through malignant progression from lower-grade diffuse glioma, represents a clinically and biologically distinct subset of GBM. In this disease context, the protein tyrosine phosphatase receptor type Z1-mesenchymal-epithelial transition factor (PTPRZ1-MET; ZM) fusion has emerged as a recurrent oncogenic driver associated with adverse clinical outcomes. In this study, we analyzed 159 patients with sGBM, including 15 ZM-positive and 144 ZM-negative cases, and confirmed that ZM-positive tumors were associated with significantly shorter overall and progression-free survival. Transcriptomic profiling identified 359 genes upregulated in ZM-positive tumors, with enrichment in cell-cycle regulation and mitotic spindle-related pathways. To explore surrogate biomarkers associated with ZM fusion status, we benchmarked eight machine-learning classifiers and retained XGBoost as the primary feature-prioritization model. MET, PCDHGA3, and FAM3C emerged as the most informative biomarkers, and the fixed three-gene panel showed stable discriminative performance across cross-validation, nested evaluation, feature-pool sensitivity analyses, repeated random seeds, and class-weighted modeling. Protein-level validation in an independent formalin-fixed, paraffin-embedded (FFPE) cohort using multiplex and conventional chromogenic immunohistochemistry supported the pathology-compatible detection of elevated MET, PCDHGA3, and FAM3C expression in ZM-positive tumors. Collectively, these findings support a robust three-gene molecular signature that may facilitate the identification and stratification of ZM fusion-positive sGBM and provide biological insights with potential translational relevance for precision glioma diagnosis.

Homeodomain-interacting protein kinase 2 (HIPK2) can function either as a tumour suppressor or promoter in cancer. Understanding key features of HIPK2 context dependent effects in cancer could lead to novel therapeutic strategies. Our investigation of HIPK2 expression in gastric cancer (GC) showed it to be down regulated.HIPK2 manifested context dependent anti- and pro-tumorigenic effects as demonstrated in GC cell lines SNU638 and NUGC-3 (β-Cateninlow, CD44Hi) and AGS (β-CateninHi, CD44low). The dualistic effects could be plausible due to HIPK2's differential impacts on the Akt-mTOR pathway. The HIPK2 inhibitor TBID further supported this context-dependent regulation of mTOR markers. Gene expression combined with protein-protein interactions analysis was used to identify the HIPK2-NLK-MAPK11 axis linked by their interaction with transcription factor MYB in GC. Validation of the axis was shown by increased NLK and MAPK11 expression in GC cell lines concordant with lower HIPK2 expression. Similarly, HIPK2 ectopically expressing cells showed lower levels of NLK and MAPK11 expression. Combinatorial targeting of HIPK2-NLK/MAPK11 axis with (HIPK2i + NLKi) or (HIPK2i + MAPK11i) resulted in a synergistic effect suppressing GC cell proliferation and mTOR markers. Targeting HIPK2 in combination with NLK or MAPK11 can be a promising strategy to overcome context dependent effects of HIPK2.

To determine whether quantitative molecular parameters derived from saturation transfer MR fingerprinting (ST-MRF) can differentiate tumor progression from treatment-related change and provide prognostic information in IDH-wildtype glioblastoma.

T/B cell receptors (T/BCR), coordinating antigen-targeting immune response, play crucial roles in anti-tumor immune response. Tracking T and B cell clonal evolution in situ at single-cell resolution is essential for understanding the adaptive immune responses. To address the lack of tools for in situ single-cell T/BCR (XCR) sequencing, we develop Stereo-XCR-seq, an efficient method for retrieving and sequencing TCR and BCR from spatial transcriptome cDNA libraries at subcellular resolution. Stereo-XCR-seq enables high-fidelity, unbiased recovery of XCR sequences alongside spatial transcriptomics in extensive tissues, facilitating the identification of heterogeneous lymphoid aggregates with distinct clonal activities in situ. Using Stereo-XCR-seq, we uncover that IgG+ plasma cell aggregates display features of ectopic germinal center-like (GC-like) niches to select tumor-reactive clones from distal immature tertiary lymphoid structures in 11 lung adenocarcinoma (LUAD) tumors. The presence of these IgG+ plasma cell aggregates in LUAD indicates an improved anti-tumor immune surveillance and sensitivity towards immune checkpoint blockade (ICB) therapy. Collectively, Stereo-XCR-seq enables in situ single-cell profiling of T and B cell clonal activities and their interactions with local microenvironment, links tumor reactivity to intratumoral distribution of lymphocytes, and thus offers a versatile tool for dissecting lymphocyte clonal dynamics across human diseases.

Polycythaemia vera (PV) may rarely evolve into acute erythroid leukaemia (AEL). We herein report a known case of JAK2 p. V617F mutated PV presenting with progressive hepatosplenomegaly, abdominothoracic lymphadenopathy, ascites and various haematological derangements. Rapid diagnostic work-up revealed extensive marrow, hepatic and ascitic fluid infiltration by many CD71+, LMO2+ and p53+ proerythroblasts. Next generation sequencing showed TP53, ASXL1 and TET2 gene mutations. A chemotherapeutic regimen of ruxolitinib, azacitidine and venetoclax was initiated. A comprehensive review of the English literature emphasises clinical, morphologic, immunophenotypic and genetic characteristics of AEL transformation in PV.

Canine mammary tumours (CMTs) are one of the most frequently observed malignancies in female dogs. Many studies have investigated epigenetic changes in CMT at the nuclear level, yet the role of mtDNA methylation, particularly in the D-loop region, remains largely unexplored. Given the significant importance of the D-loop region in mtDNA replication and transcription, and the previous identification of CpG enrichment there, this preliminary study aimed to assess apparent methylation signals in the mitochondrial D-loop region. We examined CpG, CHG and CHH methylation contexts in matched tumour and normal tissues from six German Shepherd dogs with histologically classified mammary carcinomas using enzymatic methyl-sequencing and high-throughput amplicon sequencing. Overall, CpG and CHH contexts exhibited greater variability between tumour and normal tissues than CHG, which remained relatively stable. Correlation analyses revealed a putative positive relationship between differences in CpG and CHH methylation (Spearman's r = 0.829, p = 0.042). This might suggest a coordinated epigenetic modulation of these two methylation patterns in the carcinogenesis process, yet due to the limited study group (n = 6) the hypothesis should be verified on a larger cohort. These findings demonstrate a plausible existence of intra-individual epigenetic divergence at the mitochondrial level. To our knowledge, this is the first study to assess the influence of mtDNA methylation on CMT, and it supports further investigation of mitochondrial epigenetics in canine oncology.