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.

The chances of oral squamous cell carcinoma (OSCC) being diagnosed at an early stage are very low, and this leads to a poor prognosis. The presence of circulating miRNAs (miRNAs) in blood or saliva is now a potential non-invasive diagnostic biomarker, although the diagnostic accuracy of the studies reported remains vastly different due to differences in biofluids, miRNA panels, disease spectrum, and platforms.

Papillary thyroid carcinoma (PTC) represents the most common histological variant among differentiated thyroid cancers. N4-acetylcytidine (ac4C) is a modified nucleoside in mRNA, which is essential for the regulation of mRNA stability. N-acetyltransferase (NAT)10 is an enzyme responsible for ac4C modification, acting as an "ac4C writer." This study aimed to investigate the role of NAT10 in PTC and the underlying mechanisms involved. A total of forty-eight patients with PTC were recruited, and a nude mouse model was developed. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was employed to assess the expression levels of NAT10 and pyruvate kinase (PK) M2. Cell viability was evaluated using the cell counting kit-8 (CCK-8), while proliferation was determined through colony formation assay. Glycolysis indicators were measured using commercially available kits. Bioinformatics analysis was used to screen the target genes of NAT10. The interaction between NAT10 and PKM2 was analyzed via RNA immunoprecipitation (RIP) and dual luciferase reporter assays. NAT10 was increased in PTC tissues and cells. NAT10 inhibition suppressed cell proliferation and glycolysis in PTC cells and restrained tumor growth and tissue malignancy in xenograft tumor mice. Mechanistically, PKM2 has been identified as a downstream regulatory target influenced by NAT10-mediated ac4C acetylation. Additionally, rescue experiments indicated that the overexpression of PKM2 enhanced both cell viability and glycolysis activity in PTC cells. NAT10-mediated ac4C acetylation of PKM2 exacerbated the progression of PTC by promoting glycolysis, which might provide a new insight for PTC therapy.

Pediatric central nervous system tumors remain a leading cause of cancer-related mortality in children, while their diagnosis, risk stratification, and therapeutic management increasingly depend on integrated molecular characterization. However, representative tumor tissue is often difficult to obtain because of tumor location, surgical risk, limited biopsy material, and the impracticality of repeated sampling during disease evolution. Cerebrospinal fluid (CSF) has therefore emerged as a particularly informative liquid biopsy compartment for many CNS malignancies, enriched in tumor-derived cell-free DNA and, for tumors in contact with the CSF spaces, more directly reflective of intracranial tumor biology than plasma; its yield nonetheless varies with tumor biology and anatomical proximity to CSF pathways. Here, we review the evidence supporting CSF cell-free DNA sequencing as an emerging extension of molecular neuropathology in pediatric CNS tumors. Targeted next-generation sequencing, low-pass whole-genome sequencing, methylation-based classifiers, and nanopore sequencing now enable complementary assessment of somatic mutations, copy number alterations, epigenetic tumor class, and longitudinal tumor burden from low-input pediatric CSF samples. Recent studies have moved the field beyond analytical proof of concept towards defined clinical scenarios, including molecular diagnosis when biopsy is infeasible, molecular staging of high-CSF-shedding tumors, minimal residual disease monitoring in medulloblastoma and other embryonal tumors, and clarification of ambiguous radiological progression. CSF-based sequencing does not replace tissue neuropathology, but provides a liquid molecular layer that can complement, extend, or in selected situations partially substitute tissue-based diagnosis. Its broader adoption now depends on workflow standardization, assay-specific reporting standards, external quality assurance, and prospective evidence that CSF-guided decisions improve patient outcomes.

Mitochondria have emerged as key regulators of breast cancer stem cell (CSC) biology. Mitochondrial metabolic pathways, including oxidative phosphorylation (OXPHOS) and mitochondrial biogenesis, are frequently altered during tumorigenesis, highlighting their role in breast cancer pathogenesis. Since breast CSCs are highly dependent on mitochondrial metabolism, targeting mitochondrial DNA (mtDNA) replication may represent a strategy to impair CSC maintenance. Mitochondrial DNA polymerase-γ (POLG), composed of a catalytic subunit encoded by POLG1 and an accessory subunit encoded by POLG2, is essential for mtDNA replication and repair. In this pilot study, we investigated whether targeting POLG could modulate breast CSC activity. Genetic knockdown of POLG1 and POLG2 in MCF-7 cells resulted in mtDNA depletion, reduced mitochondrial protein expression, impaired energy production, and loss of stemness-related features. To pharmacologically target POLG, we tested Alovudine, a nucleoside reverse transcriptase inhibitor known to act as an off-target POLG inhibitor. In MCF-7 cells, Alovudine reduced clonogenic potential, decreased mitochondrial DNA-encoded protein levels, and lowered oxygen consumption. To further validate these findings, we employed the independent POLG inhibitor Zalcitabine (ddC) in additional breast cancer models. ddC impaired mitochondrial respiration, reduced mammosphere formation, and modulated SOX2 and NANOG expression. Preliminary Kaplan-Meier analyses in a cohort of 458 breast cancer patients showed that high POLG1 expression correlates with worse clinical outcomes, including relapse-free and overall survival. Taken together, these findings suggest that POLG supports mitochondrial function and CSC maintenance, highlighting its potential as a therapeutic target and prognostic biomarker in breast cancer.

Tumor-associated nerves have recently emerged as an understudied key regulator of cancer biology. However, its quantification using histological or transcriptomic approaches is challenging because their small diameters hinder reliable detection and their cell bodies that hold most mRNA reside outside the tumor. This study evaluated a Schwann cell (SC)-related transcriptomic score as a surrogate for tumor-associated nerves in tumors from triple-negative breast cancer (TNBC) patients.

Breast cancer is the most common malignancy among women, and metastatic cases have a significantly poorer prognosis than non-metastatic disease. Epithelial-mesenchymal transition (EMT), characterized by the acquisition of mesenchymal features and enhanced migratory capacity by epithelial cells, is a key mechanism underlying cancer metastasis. DHRS2 has recently gained attention for its role in proliferation, invasion, and apoptosis in breast cancer. This study aimed to investigate the relationship between DHRS2 and EMT-related genes in breast cancer.

Induction of programmed cancer cell death by selective aryl hydrocarbon receptor (AHR) ligands represents a promising strategy for developing novel anticancer therapeutics. In this study, we characterized the anticancer activity and underlying mechanism of the selective AHR ligand CGS-15943 in lung cancer cells. CGS-15943 potently inhibited the growth of lung cancer cell lines expressing high levels of AHR, whereas CRISPR-mediated knockout of AHR in H460 and H69AR cells markedly rescued cells from CGS-15943-induced cell death, demonstrating an essential role for AHR. To identify additional mediators of this response, we performed a genome-wide CRISPR knockout screen, which revealed eight enzymes involved in the heme biosynthesis pathway, three heme-containing enzymes, as well as AHR and its transcriptional partner ARNT, as critical determinants of CGS-15943-induced cell death. Transcriptomic analyses further showed that CGS-15943 induced AHR-dependent transcriptional programs enriched for oxidative stress and oxidized phospholipid response pathways. Together, these findings identify key components of the AHR signaling network that regulate a programmed heme-dependent cell death pathway and establish CGS-15943 as a promising lead compound for targeting AHR-positive lung cancers.

We investigated the potential of miR-640 to downregulate CDK4/6 inhibitor resistance-associated genes and evaluated its apoptotic, anti-metastatic and anti-proliferative effects, both alone and in combination with abemaciclib in breast cancer cells. miR-640 was identified via GSE126125 dataset analysis. Targets were predicted using miRDB, TargetScan and TargetMiner, filtering for resistance-associated genes. MTT assays determined IC50 values for abemaciclib and combinations. Functional effects were evaluated in MCF7 and MDA-MB-231 cells through Annexin V, cell cycle and wound healing assays. Target gene expression was quantified by RT-qPCR. Successful transfection significantly upregulated miR-640 (~50-fold). The miR-640/abemaciclib combination strongly inhibited migration, induced apoptosis and triggered cell line-specific phase arrests (S and G2/M in MCF7; G0/G1 in MDA-MB-231). Gene expression analysis showed significant downregulation of a comprehensive resistance network (including CDK4/6, CDKN2B, WNT7B, MAP3K1 and AURKA) in MCF7 cells. In MDA-MB-231 cells, PDK1, CDK6, CDKN2B, SMAD2, ZFP91, MAP3K1 and AURKA were significantly suppressed. This study identifies miR-640 as a potent tumour suppressor that resensitises breast cancer cells to CDK4/6 inhibition. By post-transcriptionally downregulating key resistance genes, miR-640-alone or additively with abemaciclib-suppresses proliferation and migration while inducing apoptosis, emerging as a promising combinatorial therapeutic strategy.

Autophagy is an evolutionarily conserved lysosomal degradation pathway that exerts context-dependent regulatory effects on tumorigenesis and development. Ubiquitin-specific protease 1 (USP1) has been identified as an oncogenic driver in multiple malignant tumors, yet its specific biological function in cervical cancer, especially its regulatory crosstalk with autophagy, remains largely unexplored. Immunohistochemistry, qRT-PCR, and Western blotting were used to examine USP1 expression in cervical cancer tissues and cell lines. A series of biological assays including CCK-8, colony formation, Transwell, and flow cytometry were conducted to explore the impacts of USP1 silencing on cell proliferation, migration, invasion, and apoptosis. Autophagic flux was monitored by LC3 immunofluorescence staining and Western blotting of autophagy-related markers. Co-immunoprecipitation and in vitro ubiquitination assays were used to clarify the interaction between USP1 and ATG13 and the deubiquitination effect of USP1 on ATG13. Rescue experiments with ATG13 overexpression combined with or without the USP1 inhibitor ML323 were performed to verify the functional regulatory axis of USP1-ATG13-autophagy. In addition, a xenograft mouse model was established by subcutaneously injecting SiHa cells stably expressing sh-USP1 and/or ATG13-overexpressing lentivirus into nude mice; tumor volume and weight were assessed 4 weeks post-injection. USP1 exhibited markedly elevated expression in both cervical cancer tissues and cell lines, and its overexpression was strongly associated with high pathological grades of cervical cancer. Functional assays revealed that silencing USP1 observably suppressed the proliferation, migration, and invasion of C33A and SiHa cells, and simultaneously promoted cellular apoptosis. Mechanistically, USP1 could directly bind to ATG13 and mediate its deubiquitination, thereby enhancing the protein stability of ATG13 and promoting the autophagic flux of cervical cancer cells. Notably, overexpression of ATG13 could reverse the inhibition of autophagy and the suppression of malignant phenotypes induced by USP1 knockdown, and this rescue effect was completely abrogated by ML323 treatment. In vivo xenograft experiments confirmed that USP1 knockdown significantly inhibited cervical cancer tumor growth, while ATG13 overexpression markedly rescued the tumor-suppressive effect induced by USP1 silencing. Our study reveals a novel molecular mechanism by which USP1 promotes the malignant progression of cervical cancer through stabilizing ATG13 and subsequently enhancing autophagic activity. USP1 may serve as a promising therapeutic target for cervical cancer, and modulation of autophagy holds clinical potential in cervical cancer intervention.

Cancer remains a major cause of global mortality, necessitating the identification of novel biomarkers to improve prognosis and guide therapy. ABCA1, an ATP-binding cassette transporter involved in cholesterol efflux, has been implicated in tumorigenesis, yet its pan-cancer roles and clinical relevance are not fully understood. We conducted a comprehensive multi-omics analysis of ABCA1 across diverse cancers, evaluating its expression, prognostic significance, genomic alterations, tumor immune microenvironment interactions, and regulatory mechanisms. ABCA1 expression was dysregulated in multiple malignancies and associated with poor prognosis in STAD, STES, and LGG, though favorable outcomes were observed in KIRC. It correlated with genomic instability markers (TMB, MSI, HRD), immune cell infiltration, and cancer stemness. Pathway analyses revealed enrichment in cholesterol metabolism and efferocytosis-related pathways. Among the cancer types examined, esophageal squamous cell carcinoma (ESCC) was selected for exploratory functional validation due to its prognostic relevance. In vitro, ABCA1 knockdown inhibited proliferation, invasion, and migration in ESCC cell lines. In silico drug sensitivity analysis suggested potential associations with dasatinib response and panobinostat resistance, warranting further experimental validation. Collectively, these findings highlight the context-dependent associations of ABCA1 with cancer progression, immune modulation, and genomic integrity, suggesting its potential utility as a prognostic biomarker that warrants further investigation for therapeutic targeting.

Extracellular vesicles (EVs) mediate intercellular communication within the tumour microenvironment by carrying cargoes from paracrine parent cells. EVs have attracted great research interest for their ability to carry nucleic acids into recipient cells and modulate cellular functions. However, previous studies have largely focused on RNA sequence information rather than RNA structure features. Here, we observed that EVs derived from colorectal cancer cells are enriched with endogenous double‑stranded RNA (dsRNA), a danger‑associated molecular pattern (DAMP) that leads to the activation of dsRNA‑sensing pathways in recipient cells. Crucially, we investigated the specific crosstalk between tumour-derived EVs and circulating platelets. As anucleate cells, platelets are uniquely suited models for isolating the effects of exogenous nucleic acids. Our analysis reveals that endogenous dsRNA from tumour EVs activates the platelet OAS-RNASEL innate immune ribonuclease cascade and the RNASEL/ABCE1/PELO axis, resulting in the decay of ribosomal protein mRNAs. This study, spanning from clinical observation to mechanistic validation, uncovers a novel pathway of tumour-platelet communication. We identify EV-enriched endogenous dsRNA as a functional mediator that enables tumour cells to directly reprogram platelet transcriptomes, revealing a new dimension of tumour-immune modulation.

PD-1 blockade has yet to achieve broad clinical success in colorectal cancer (CRC), with microsatellite-stable tumors proving especially resistant. At the same time, ferroptosis has emerged as a mechanistic link between redox control in tumor cells and the antitumor immune response. GPR39 is overexpressed in CRC, but its functional role in ferroptosis and immunotherapy resistance is currently unclear.

S-palmitoylation is a crucial post-translational modification that regulates diverse cellular processes, particularly signalling pathways. The ZDHHC family of enzymes catalyzes this modification, however, the role of ZDHHC16 in cancer warrants in-depth investigation. This study presents a comprehensive pan-cancer analysis of ZDHHC16, examining its expression patterns, clinical relevance, associations with immune responses, genomic characteristics, and potential as a therapeutic target. We further analysed single-cell and spatial transcriptomic data to identify specific cell populations associated with ZDHHC16 dysregulation. Our findings reveal that ZDHHC16 dysregulation is tissue-specific and promotes tumor progression and modulates immune responses, highlighting its potential as a therapeutic target in several cancers, including ACC and BRCA. In ACC and BRCA, high ZDHHC16 expression correlates with shorter overall survival (p < 0.001) and regulates PD-L1 expression.

Ovarian cancer (OC) remains a lethal gynecological malignancy with challenges in early diagnosis, treatment monitoring, and overcoming drug resistance. Liquid biopsy, a noninvasive approach analyzing tumor-derived components in bodily fluids, has emerged as a promising tool in OC management. This review summarizes advances in liquid biopsy technologies, focusing on circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs). ctDNA enables minimally invasive assessment for diagnosis, prognosis, treatment guidance (e.g., BRCA1/2-targeted therapy), minimal residual disease (MRD) detection, and monitoring of tumor evolution. CTCs, particularly clusters, provide insights into metastasis and therapeutic response. Emerging modalities such as tumor-educated platelets (TEPs), circular RNAs (circRNAs), and exosomes and protease activity-based liquid biopsy also show diagnostic and prognostic potential. Despite technical challenges like standardization and sensitivity, liquid biopsy holds significant promise for personalized OC care, with ongoing efforts to translate these technologies into clinical practice.

The incidence of breast cancer shows its largest peak around the age of 65 but also a peak around 45 indicating a bimodal distribution. While some potential explanations, such as age-related enrichment in specific breast cancer sub-types and BRCA1/2 mutations were proposed, they do not explain why the peaks are at 45 and 65, raising the possibility that the way the breast ages may play a role. Here using two mouse models, we show two distinct aging patterns of the mammary gland; one being progressive, the other bimodal. In the bimodal model, waves of overlapping genes and proteins associated with breast cancer pathways are observed at 11 and 19 months but are absent at 3 and 14 months. Further, in the bimodal model, the mammary glands at 11 and 19 months are more permissive to the growth of cancer cells but not at 14 or > 22 months, while in the progressive model, the growth of cancer cells increases starting at 14 months of age. Using scRNAseq, we established a bimodal aging signature. Since 11 and 19 months in mice correlate with 45 and 65 in humans, we tested the mammary gland-derived bimodal signature in two breast cancer databases and found that the signature is enriched in women diagnosed at 45 and 65. Therefore, our study raises the possibility that distinct patterns of aging of the breast exist and that they may contribute to the bimodal distribution of breast cancer. Further, our study adds to the growing evidence of non-linear aging.

Non-small cell lung cancer (NSCLC) is the most common form of lung cancer. Identifying novel molecular mechanisms underlying its progression and treatment resistance is crucial. MAGEA1, a cancer-testis antigen, exhibits oncogenic functions in multiple solid tumors; however, its expression profile and precise role in NSCLC remain poorly defined. MAGEA1 expression in NSCLC versus normal tissue was analyzed via TCGA bioinformatics, and differential expression was orthogonally validated by RT-qPCR and Western blot in normal lung epithelial and lung adenocarcinoma cell lines. Cellular proliferation, migration, and invasion were assessed by CCK-8 and Transwell assays. Apoptosis and radiosensitivity were evaluated using flow cytometry, colony formation, immunofluorescence, and comet assays. In vivo tumor growth and metastasis was examined in subcutaneous and lung metastasis mouse models. Downstream pathways were explored via RNA-seq. MAGEA1 was significantly upregulated in NSCLC tissues. Its overexpression promoted lung adenocarcinoma cell proliferation, migration, invasion, epithelial-mesenchymal transition (EMT), and in vivo tumor growth and metastasis, whereas MAGEA1 knockdown reversed these effects. Moreover, MAGEA1 overexpression increased irradiation-induced DNA damage and apoptosis and decreased clonogenic survival, indicating increased radiosensitivity. Mechanistically, MAGEA1 exerted its oncogenic effects primarily through activation of the AKT pathway. This study demonstrates that MAGEA1 drives lung adenocarcinoma progression by activating the PI3K/AKT pathway and correlates with elevated radiosensitivity, highlighting its potential as a therapeutic target in lung adenocarcinoma.

miR-210-3p is a well-established hypoxia-induced microRNA that is commonly upregulated in a wide range of solid tumors, traditionally linked to mitochondrial repression and hypoxia-inducible factor (HIF) signaling. However, its functional role in cancer remains complex and highly context dependent. Here we perform a comprehensive pan-cancer transcriptomic analysis together with functional assays, revealing that miR-210-3p not only mediates classical hypoxic responses but also amplifies mitotic gene expression through activation of FOXM1. Mechanistically, this effect is shown to be dependent on HIF1α but not on HIF2α and, importantly, it has not been recapitulated by hypoxia alone. Notably, activation of the mitotic program is observed in breast cancer cells but not in head and neck squamous carcinoma models, highlighting a strong degree of context dependency across tumor types. In breast cancer cells, miR-210-3p overexpression enhances FOXM1 phosphorylation, upregulates kinetochore regulators, and induces mitotic defects, correlating with poor prognosis in aggressive tumors. Together, these findings position miR-210-3p as a molecular integrator linking pseudohypoxia to mitotic dysregulation, contributing to tumor aggressiveness by sustaining HIF activity and promoting mitotic stress. This dual functionality reconciles its paradoxical effects on proliferation and highlights its potential as a therapeutic target in cancers characterized by pseudohypoxia and mitotic abnormalities.