Wiley最新文献

Lynch syndrome (LS) is a hereditary cancer predisposition syndrome caused by germline mutation of DNA mismatch repair (MMR) genes, most notably associated with colorectal cancer. Although LS patients face high risk of CRC, risk can vary even among those with the same pathogenic MMR germline mutations. We suggest a functional assay platform for assessing mutation risk using patient-derived organoid (PDOs). We measured organoid response to the cytotoxic effects of a methylating agent, N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) based on DNA damage-induced apoptosis. When normal (non-LS) colon organoids were used, treatment with MNNG and four passages of organoid culture led to decreased total growth (organoid area), but there was no significant change in number. To increase the effect of MNNG and induce apoptosis in normal colon organoids, we added O⁶BG (an MGMT inhibitor) and an ATR inhibitor. The cytotoxic effects of combined treatment with MNNG, O⁶BG and ATR inhibitor on non-LS-PDOs were significantly higher than in PDOs of LS patients. To detect the difference at an earlier phase, we examined DNA damage response by analyzing γH2AX expression after treatment with MNNG and O6BG for 24 h. Then, we found higher expression of γH2AX in non-LS-PDOs than in PDOs of LS patients, suggesting continued cell survival with mutation accumulation in LS-PDOs. In conclusion, treatment with MNNG and O6BG using PDOs and measurement of resulting DNA damage response could be used as a preclinical platform for risk stratification in LS patients.

MET is an actionable receptor tyrosine kinase, and MET-directed antibody-drug conjugates (ADCs) have recently entered clinical practice with FDA approval in non-small cell lung cancer and are now being evaluated across gastrointestinal malignancies, with patient selection based on MET immunohistochemistry (IHC) 3+ membranous staining at varying percentage thresholds. However, robust real-world data on MET protein expression and clinically relevant ADC-aligned thresholds in upper GI adenocarcinomas remain limited. We profiled 1532 upper GI adenocarcinomas using the clinically validated VENTANA MET (SP44) IHC assay. MET was stratified by (i) 3+ membranous staining fractions (any, ≥ 10%, ≥ 50%) reflecting contemporary ADC eligibility concepts and (ii) H-score (0-300; high ≥ 150). Overall survival analyses and multivariable Cox regression analyses were performed. High MET expression was uncommon (H-score ≥ 150: 2.3%; any 3+: 1.6%; ≥ 10% 3+: 1.3%; ≥ 50% 3+: 1.0%) and enriched in advanced T stage. MET IHC strongly predicted MET amplification (H-score ≥ 150: 63.6% amplified vs. 2.4% in negatives; any 3+: 75.0% vs. 2.6%; all p < 0.001). Any MET 3+ staining was independently associated with inferior overall survival (adjusted HR 2.22, 95% CI 1.29-3.83). Most MET 3+ tumors lacked concurrent HER2 positivity, Claudin-18.2 expression, or dMMR/MSI. In the largest real-world cohort to date, MET overexpression identifies a rare, biologically aggressive subset with poor outcomes. By applying the latest MET-ADC-relevant IHC criteria (including the ≥ 10% 3+ threshold), this study provides clinically translatable prevalence estimates and supports standardized MET testing to inform prospective MET-directed ADC trials in upper GI adenocarcinoma.

Esophageal adenocarcinoma (EAC) exhibits marked male predominance with male-to-female ratios reaching 8.5:1, yet the molecular basis underlying this sex disparity remains poorly characterized. We analyzed 92 EAC specimens using mass spectrometry-based proteomics, comprising 47 female and 45 male tumors from treatment-naïve patients. Differential expression, pathway enrichment, immunohistochemical, and survival analyses were used to identify sex-associated proteomic features and prognostic signatures. Proteomic profiling revealed focal yet biologically meaningful sex differences in EAC. After multiple testing correction, three proteins were differentially expressed: the autosomal protein pregnancy zone protein (PZP), enriched in female tumors, and the Y-chromosome-encoded proteins DDX3Y and RPS4Y1, which were overexpressed in male tumors. At nominal significance, proteins upregulated in female tumors showed marked enrichment of immune-related pathways. Proteins correlated with PZP expression formed a network dominated by complement cascade. Clinically, elevated PZP expression was associated with significantly poorer overall survival specifically in male patients, with no significant association detected in the combined or female-only cohort. Proteome-wide survival analyses further demonstrated distinct sex-specific prognostic landscapes. Our study provides the first comprehensive characterization of sex-associated proteomic differences in EAC. Sex shapes immune-related pathways, prognostic proteomic signatures, and survival associations. PZP emerges as a sex-differential, complement-associated protein with adverse prognostic significance in male patients, highlighting sex as a biologically and clinically relevant variable in EAC.

The incidence of human papillomavirus-positive (HPV+) oropharyngeal cancer (OPC) has increased rapidly, and HPV early antigen serology has been proposed as a scalable and cost-effective early detection test. HPV seropositivity can precede clinical presentation of OPC by several years, so additional surveillance procedures may be necessary to optimize early cancer detection. The potential for HPV circulating tumor DNA (ctDNA) to confirm a diagnosis of OPC in seropositive individuals is poorly understood. Here, we assess the relationship between HPV serology and HPV ctDNA with disease burden in a large cohort of HPV+ OPC. We analyzed baseline blood samples from 262 patients using a multiplex serology assay and an HPV-targeted deep sequencing assay (HPV-seq), and HPV-seq results were validated by an orthogonal droplet digital PCR assay. Both assays identified HPV16 as the most prevalent genotype (84%), with serology results indicating a total of 4 HPV genotypes and HPV ctDNA results indicating a total of 6 HPV genotypes. HPV ctDNA results demonstrated higher sensitivity and lower cross-reactivity between HPV types compared with HPV serology results. Furthermore, HPV ctDNA but not HPV16 E6 antibody levels were positively associated with disease burden as determined by N-category, overall stage, and by tumor volume (ctDNA vs. volume, r = 0.48 p = 6.4e-12; E6 vs. volume, r = -0.079 p = 0.26). Overall, this is the largest cohort to compare HPV serology and HPV ctDNA results in OPC, and these findings highlight the potential for ctDNA to augment future strategies for blood-based early detection of HPV+ OPC.

Mitochondrial activity must be tightly coordinated in plants to ensure that energy production is appropriately modulated in response to exogenous and endogenous signals. However, the underlying molecular mechanisms are largely unknown. Here, we investigated this issue by analysing the crosstalk between the nucleus and mitochondria mediated by pentatricopeptide repeat (PPR) proteins, which can regulate the proper function of mitochondrial electron transport chain complexes by affecting C-to-U editing of mitochondrial mRNA. More than 75% of PPR genes in maize (Zea mays) exhibited rhythmic expression, which changed in response to different light conditions. Analysis of mitochondrial RNA editing efficiency throughout the day identified editing sites displaying rhythmic variations, with many sites affecting protein function based on AlphaFold2 prediction. Notably, the peak phase of rhythmic RNA editing lagged behind that of PPR gene expression, suggesting that these two processes are tightly related. We also observed rhythmic expression of PPR genes and rhythmic editing of mitochondrial mRNA in rice (Oryza sativa). These findings suggest that PPR proteins might serve as integrators of environmental signals and transmit these signals to mitochondria by affecting RNA editing.

Angiosperm trees reorient their stems by producing tension wood (TW), a specialised xylem that generates contractile force. TW fibres develop a gelatinous (G) layer rich in cellulose, yet the molecular mechanisms governing G-layer formation remain poorly understood. COBRA-like genes encode glycosylphosphatidylinositol (GPI)-anchored proteins known to regulate cellulose deposition. Here, we functionally characterised PagCOBL5 in hybrid poplar (Populus alba × P. glandulosa) by identifying its upstream regulator and interaction partner. PagCOBL5 was preferentially expressed in mature xylem fibres, with high abundance in TW. Under mechanical stress, cobl5 knockout mutants exhibited impaired negative gravitropism and significantly thinner G-layer-phenotypes that were reversed in PagCOBL5-overexpressing lines. Furthermore, we found that the transcription factors PagLBD21 and PagLBD25 participate in the upstream negative regulation of PagCOBL5 expression, with the lbd21 lbd25/+ mutant exhibiting an enhanced gravitropic response and altered xylem cell differentiation. At the protein level, PagCOBL5 directly interacted with the cellulose synthase subunits PagCESA8b. This interaction positions PagCOBL5 as a key component recruited and spatially organised by the directionally moving cellulose synthase complex (CSC). Together, these results reveal a sophisticated regulatory and protein-interaction framework centred on PagCOBL5, providing pivotal molecular insights into how transcriptional modulation and cellulose synthase complexes coordinate G-layer formation and mechanical force generation during the gravitropic response.

Conifers exhibit distinct age-related transitions in wood development, yet the molecular mechanisms governing these changes remain poorly characterized. Here, we integrate multi-omics and functional analyses to unravel a transcriptional regulatory network underlying age-related wood formation in Chinese pine (Pinus tabuliformis). Cross-sectional and Raman microspectroscopy analyses revealed age-dependent enhancement of lignification and carbohydrate deposition in secondary xylem, coinciding with increased pith proportion. Temporal transcriptome profiling identified PtARN (AGE-RELATED NAC TRANSCRIPTION FACTOR) as a key age-correlated regulator, whose expression is directly activated by the conserved age timer PtDAL1 through promoter binding. We conducted a genome-wide identification of secondary cell wall biosynthesis pathway genes in P. tabuliformis, and genome-wide DNA affinity purification analysis uncovered that PtARN direct binding to promoters of 189 secondary cell wall biosynthesis genes. Strikingly, PtARN represses PtMYB162, a lignin biosynthesis suppressor, forming a regulatory cascade to fine-tune lignification. Collectively, our work establishes PtARN as a master regulator orchestrating age-dependent secondary cell wall deposition and lignification in the secondary xylem of Chinese pine, and delineates a previously uncharacterized PtDAL1-PtARN-mediated molecular regulatory network in P. tabuliformis. These findings significantly advance our understanding of the molecular regulatory network underlying wood formation in conifers, and bridging developmental timing with cell wall remodelling, and provide a robust framework for conifer-specific wood formation studies.