NAR cancer最新文献

Lynch syndrome (LS) is a colorectal cancer predisposition caused by an inherited heterozygous defect in any of four DNA mismatch repair (MMR) genes. MMR prevents nucleotide substitution mutations by correcting errors of replication opposite undamaged or subtly altered nucleotides. Here, we investigated whether dietary mutagens, which generally induce helix-distorting nucleotide lesions, affect LS-associated carcinogenesis. To this aim, we exposed mouse models of LS to 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), a food-derived heterocyclic amine that selectively adducts guanines. PhIP exposure induced loss of the wild-type MMR allele in heterozygous intestinal stem cells, leading to MMR deficiency and to impaired DNA damage signalling associated with the clonal expansion of MMR-deficient intestinal stem cells. Whole-genome sequencing revealed that PhIP becomes significantly more mutagenic in intestinal stem cells when MMR is lost, inducing not only PhIP-guanine adduct-mediated C:G>A:T transversions but also a broader substitution spectrum that resembles the spontaneous mutational signature of LS-associated colorectal cancer. Thus, MMR corrects PhIP-induced misincorporations outside of adducted guanines. Chronic PhIP exposure of intestine-specific MMR-deficient mice induced adenocarcinomas with histopathological features of LS-associated CRC. This study implicates food-derived mutagens in multiple stages of LS-associated carcinogenesis, including allelic loss, and defective DNA damage signalling and compound hypermutagenesis in the resulting MMR-deficient cells.

Chemoresistance represents a significant challenge in the chemotherapy of colorectal cancer (CRC), limiting the effectiveness. In this regard, gene expression heterogeneity plays a critical role, influencing cancer cell adaptability and survival under chemotherapy. Our previous data revealed that ribosomal protein uL3 positively correlates with both chemoresistance and poor prognosis in CRC patients. This study explores the combination of 5-fluorouracil (5-FU), the first-line treatment of CRC, with G-quadruplex (G4) ligands, which have recently emerged as promising candidates for cancer therapy, to overcome uL3-mediated chemoresistance. We found that resistant p53-deficient and uL3-silenced CRC cells showed increased levels of G4 structures compared to both sensitive p53-deficient and p53-proficient cells, thereby exhibiting vulnerability to the cytotoxic effects of two well-established G4 ligands, pyridostatin (PDS) and RHPS4. The combination of 5-FU with PDS or RHPS4 exhibited a synergistic effect, selectively targeting tumor cells. This approach enabled a >10-fold reduction in the 5-FU dose, improving treatment efficacy. The effectiveness of this combination was further validated in vivo using uL3-silenced CRC cell-derived xenografts in a chicken embryo model. Overall, our findings highlight a novel and promising combination strategy that targets chemoresistance in CRCs characterized by non-functional p53 and reduced levels of uL3.

Epitranscriptomic modifications regulate gene expression and have been implicated in cancer, including breast cancer. Using the SCAN-B cohort, we analyzed 49 messenger RNA modification regulators (mRMPs) across breast cancer subtypes. In the basal subtype, we found significant overexpression of m⁶A readers (IGF2BP1-3), m⁵C regulators (NSUN5, ALYREF, YBX1, YBX2), pseudouridine [PUS1, MARS (or MetRS), RPUSD2], and RNA editing enzymes [APOBEC3A (A3A), A3G, ADAR1], all linked to poor survival. Conversely, the m⁶A writer METTL14 was downregulated. Our findings highlight key mRMPs as potential biomarkers and therapeutic targets, underscoring the role of RNA modifications in breast cancer progression.

Personalized treatment selection is crucial for cancer patients due to the high variability in drug response. While actionable mutations can increasingly inform treatment decisions, most therapies still rely on population-based approaches. Here, we introduce neural interaction explainable AI (NeurixAI), an explainable and highly scalable deep learning framework that models drug-gene interactions and identifies transcriptomic patterns linked with drug response. Trained on data from 546 646 drug perturbation experiments involving 1135 drugs and molecular profiles from 476 tumors, NeurixAI accurately predicted treatment responses for 272 targeted and 30 chemotherapeutic drugs in unseen tumor samples (Spearman's rho >0.2), maintaining high performance on an external validation set. Additionally, NeurixAI identified the anticancer potential of 160 repurposed non-cancer drugs. Using explainable artificial intelligence (xAI), our framework uncovered key genes influencing drug response at the individual tumor level and revealed both known and novel mechanisms of drug resistance. These findings demonstrate the potential of integrating transcriptomics with xAI to optimize cancer treatment, enable drug repurposing, and identify new therapeutic targets.

Treatment of patients with platinum-resistant ovarian cancer is a major clinical challenge. We found that high expression of a meiotic protein, Synaptonemal Complex Protein 2 (SYCP2), is associated with platinum resistance and tyrosine kinase ABL1 inhibitor sensitivity in ovarian cancer. We demonstrate that tyrosine kinase ABL1 inhibitors inhibit cancer cell proliferation more efficiently in ovarian cancer cell lines with SYCP2 overexpression. Moreover, ABL1 inhibition effectively prevents tumor growth in vivo. Mechanistically, we identified a phosphorylation motif [RK]-x(2,3)-[DE]-x(2,3)-Y in SYCP2 and found that abolishing ABL1-mediated phosphorylation of SYCP2 at its tyrosine (Y) 739 within this motif renders ABL1 sensitivity of cancer cells. Importantly, ABL1 and SYCP2 colocalize at sites of R-loops after damage and promote transcription-coupled homologous recombination. Moreover, ABL1-mediated Y739 phosphorylation of SYCP2 promotes function of SYCP2 at sites of R-loops by facilitating RAD51 localization and repair, contributing to ovarian cancer cell survival. Overall, these findings highlight a novel therapeutic mechanism where ABL1 inhibitors induce cell death in platinum-resistant ovarian cancer by impairing transcription-coupled homologous recombination repair.

The mycotoxin, aflatoxin B₁ (AFB₁), is a potent mutagen that contaminates agricultural food supplies. After ingestion, AFB₁ is oxidized into a reactive electrophile that alkylates DNA, forming bulky lesions such as the genotoxic formamidopyrimidine lesion, AFB₁-Fapy dG. This lesion is mainly repaired by nucleotide excision repair (NER) in bacteria; however, in humans the picture is less clear. We report a plasmid-based host cell reactivation assay containing a site-specific AFB₁-Fapy dG lesion and present evidence that this lesion is mainly repaired by transcription-coupled NER (TC-NER) in human cells. Using a combination of isogenic knockout cell lines and immortalized fibroblasts from xeroderma pigmentosum and Cockayne syndrome patients, we show that the TC-NER factors CSA, CSB, and UVSSA are required for efficient AFB₁-Fapy dG repair, while the global-genome NER protein, XPC, is dispensable. Furthermore, knockout of CSB or UVSSA impairs AFB₁-Fapy dG repair to a similar degree as knockout of the core NER nuclease, XPF. Our data indicate that TC-NER is the major repair pathway for AFB₁-Fapy dG adducts in human cells.

The presentation of peptides on HLA molecules is essential to CD8⁺ T cell responses. Here, we show that loss of uL14 significantly downregulates the expression of antigen processing and presentation (APP) components in melanoma cell lines. Peptides generated following knockdown show different characteristics, with altered peptide charge, and differences in anchor residue positions. These peptides also have lower predicted binding to the HLA alleles and a shorter predicted HLA-peptide complex half-life. These result in a functional difference in APP, and knockdown of uL14 causes a reduction in the ability of CD8⁺ T cells to recognize and kill melanoma cells in a co-culture assay. Together, our data suggest that loss of uL14 alters the peptide pool available for presentation and thus may act as an escape mechanism from tumor immune surveillance.

Noncoding RNAs play pivotal roles in tumorigenesis and cancer progression. Recent evidence has identified vault RNAs (vtRNAs) as critical regulators of cellular homeostasis. The human genome encodes four vtRNA paralogs, which are differentially expressed in cancer tissues and contribute to tumor development. The best studied vtRNA1-1 is involved in regulating apoptosis resistance, autophagy, lysosomal biogenesis, and drug resistance. Here, we present the first comprehensive characterization of vtRNA1-2 using a knockout hepatocellular carcinoma (HCC) cell line. Loss of vtRNA1-2 impaired cancer cell viability and proliferation by modulating mitogen-activated protein kinase signaling. Additionally, vtRNA1-2-deficient cells exhibited reduced motility and a decreased invasive potential. Unlike vtRNA1-1, vtRNA1-2 did not influence autophagy or lysosomal activity. Instead, vtRNA1-2 is implicated in the regulation of angiogenesis, a key process in tumor progression. VTRNA1-2-promoter hypomethylation is correlated with chromatin accessibility in liver cancer samples and we uncovered an association between promoter methylation and key patient clinical conditions as registered in the TCGA metadata. These findings highlight a distinct oncogenic role for vtRNA1-2 in HCC and suggest that it may serve as a potential therapeutic target. Our study underscores the functional divergence among vtRNA paralogs, supporting the concept that each exerts unique biological effects rather than acting as redundant molecular entities.

Germline mutations in the DNA repair helicase XPD can cause the diseases xeroderma pigmentosum (XP) and trichothiodystrophy (TTD). XP patients bear an increased risk of skin cancer including melanoma. This is not observed for TTD patients despite DNA repair defects. To examine whether TTD cells harbor features counteracting tumorigenesis, we developed a TTD melanoma cell model containing the XPD variant R722W. Intriguingly, TTD melanoma cells exhibited reduced proliferation and an increased signature of the melanocyte lineage factor MITF, along with a strong basal upregulation of REDD2, an inhibitor of the mTOR/S6K/4EBP1-dependent messenger RNA (mRNA) translation machinery. REDD2 levels were partially driven by MITF and contributed to reduced melanoma proliferation. In a TTD model for melanocytes-the progenitor cells of melanoma-the MITF gene signature was also increased, but here without affecting REDD2 expression. However, ribosomal protein synthesis was reduced particularly in R722W melanocytes after UV stress, indicating a compromised mRNA translation machinery. Impaired translation was also demonstrated for the TTD XPD variant A725P, but not for an XP variant. Concludingly, the impaired translation and reduced fitness observed in TTD melanocytes and melanoma cells, particularly after UV stress, offer a possible explanation why TTD patients do not develop melanomas.

Hypoxia-inducible factor (HIF) is a master regulator of cancer cell adaptation to tumor hypoxia and is involved in cancer progression. Single-cell (sc) differences in the HIF response allow for tumor evolution and cause therapy resistance. These sc-differences are usually ascribed to tumor microenvironmental differences and/or clonal (epi)genetic variability. However, the sc-heterogeneity of the HIF response in otherwise identical cells cultured under defined in vitro conditions has not yet been addressed. Therefore, we analyzed the sc-response to hypoxia in nonclonal cell lines and multiple clonal derivatives, including HIF-1α or HIF-2α knockouts. While HIF-1α and HIF-1 target mRNA sc-heterogeneity was slightly higher than global transcription or specific housekeeping messenger RNAs (mRNAs), HIF-2α and especially HIF-2 target mRNA sc-heterogeneity was extraordinary, and remained in independent clones following HIFα knockouts. Unexpectedly, neither HIF-2α mRNA nor nuclear protein levels correlated with target mRNA levels. Unsupervised but not supervised HIF target gene dimensionality reduction revealed the initial sample composition after scRNA-seq, demonstrating that, owing to sc-heterogeneity, individual HIF target genes are not sufficient to unequivocally identify hypoxic cancer cells. In conclusion, the pronounced intrinsic sc-heterogeneity of the HIF response represents a hitherto unrecognized feature of cancer cells that impairs clinical HIF pathway-dependent cancer cell identification and targeting.