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PubMed2024

Cost-effectiveness of population-wide genomic screening for Lynch Syndrome and polygenic risk scores to inform colorectal cancer screening.

PURPOSE: Genomic screening to identify individuals with Lynch Syndrome (LS) and those with a high polygenic risk score (PRS) promises to personalize colorectal cancer (CRC) screening. Understanding its clinical and economic impact is needed to inform screening guidelines and reimbursement policies. METHODS: We developed a Markov model to simulate individuals over a lifetime. We compared LS+PRS genomic screening with standard of care (SOC) for a cohort of US adults at age 30. The Markov model included health states of no CRC, CRC stages (A-D), and death. We estimated incidence, mortality, and discounted economic outcomes of the population under different interventions. RESULTS: Screening 1000 individuals for LS+PRS resulted in 1.36 fewer CRC cases and 0.65 fewer deaths compared with SOC. The incremental cost-effectiveness ratio was $124,415 per quality-adjusted life year; screening had a 69% probability of being cost-effective using a willingness-to-pay threshold of $150,000/quality-adjusted life year . Setting the PRS threshold at the 90th percentile of the LS+PRS screening program to define individuals at high risk was most likely to be cost-effective compared with 95th, 85th, and 80th percentiles. CONCLUSION: Population-level LS+PRS screening is marginally cost-effective, and a threshold of 90th percentile is more likely to be cost-effective than other thresholds.

Humans↗

PubMed2025

Primary Care Provider Perspectives on Expanded Genomic Screening in Children.

OBJECTIVES: Expanding pediatric genomic screening beyond current newborn screening presents both opportunities and challenges to primary care providers. We are developing a novel paradigm called Age-Based Genomic Screening (ABGS), which will incorporate targeted genomic sequencing for select, highly actionable genetic conditions into routine care at relevant time-points throughout childhood. We surveyed pediatric primary care providers in North Carolina to identify potential ABGS implementation determinants and strategies to address them. STUDY DESIGN: We disseminated an electronic survey to family medicine and pediatric primary care clinicians. Survey items were modeled on constructs previously identified as important to genomic medicine and assessed perceived utility, benefits, barriers, and facilitators of implementing targeted genomic screening in pediatric primary care. Data were analyzed using descriptive statistics and content analysis, as appropriate. RESULTS: A total of 93 individuals completed the survey. Over 85% of respondents agreed that genomic screening was important and impactful in their patient care but about 30% lacked confidence in their ability to implement it in their practice. The most cited benefits of the ABGS program were related to readiness for implementation and the evidence, strength, and quality of the intervention. The most concerning barriers included cost for patients and available resources, with 87% and 75% of respondents having extreme or moderate concern for these barriers, respectively. CONCLUSIONS: Our findings have implications both for the design of the ABGS pilot program and directions for future research in genomic implementation. In particular, the blueprint for the pilot program must include specific plans for ensuring primary care providers have the time and resources available for shared decision making with their patients about engaging in genomic screening.

Journal Article↗

PubMed2024

Offering complex genomic screening in acute pediatric settings: Family decision-making and outcomes.

PURPOSE: Families of children in pediatric acute care who are offered ultrarapid genomic sequencing are making complex decisions during a high-stress period. To reduce complexity for families and clinicians, we offered genomic screening for the child and parents after the completion of diagnostic testing. We evaluated uptake, understanding, and service delivery preferences. METHODS: A cohort of 235 families who had completed ultrarapid diagnostic genomic sequencing at 17 Australian hospitals were offered up to 3 screens on their genomic data: pediatric-onset, adult-onset, and expanded couple carrier screening. We investigated decision making, understanding, and service delivery preferences using surveys at 3 time points (pre counseling, post counseling, and post result) and performed inductive content analysis of pretest genetic counseling transcripts. RESULTS: A total of 119 families (51%) attended genetic counseling with 115 (49%) accepting genomic screening. Survey respondents were more likely to find decisions about couple carrier screening easy (87%) compared with adult (68%; P = .002) or pediatric (71%; P = .01) screening decisions. All respondents with newly detected pathogenic variants accurately recalled this 1 month later. A delayed offer of screening was acceptable to most respondents (78%). CONCLUSION: Separating genomic screening from the stressful diagnostic period is supported by families who demonstrate good knowledge and recall. Our results suggest delaying genomic screening should be trialed more widely.

Humans↗

PubMed2026

Genomic Screening for Infants and Reproductive Adults.

Recent progress in genomic sequencing, bioinformatics, cloud computation, and artificial intelligence is advancing a more mature understanding of the architecture of childhood genetic diseases. This knowledge and these technologies are enabling expanded genomic screening of infant and reproductive adult populations. With many new disease-modifying and curative therapies in development and approval processes, there exists unparalleled opportunity to identify, treat, and decrease the population burden of genetic disease and transform medical genetics. Broad implementation of genomic population screening, however, requires investments for overcoming remaining evidence gaps and operational challenges, and for delivery in a sustainable manner that is acceptable to parents, prospective parents, and physicians.

Journal Article↗

PubMed2026

Uncertainty and information management for Lynch syndrome in a genomic screening cohort: Connections to clinical engagement.

OBJECTIVE: Lynch syndrome (LS) is a common hereditary cancer predisposition syndrome. This study explores how individuals learning about LS-related cancer risk through a population genomic screening program appraise, reappraise, and manage uncertainty and engage in medical management. METHODS: We recruited participants with an LS result from a population genomic screening study, purposively sampling based on the characteristics of sex, age, LS gene, and family history of cancer. Semi-structured interviews and chart reviews focused on participants' experiences of learning about the LS result and making management decisions. Thematic analysis and heatmapping were used to explore participant characteristics related to uncertainty management and clinical engagement. RESULTS: Seventeen participants completed interviews, describing uncertainty discrepancies or ambivalent appraisals. Most participants who appraised their LS risk as a threat had high clinical engagement. All participants who had lower clinical engagement received misinformation, had little support from clinicians, or had misunderstandings about LS. CONCLUSION: Accurate information from trusted sources is critical to support uncertainty management and subsequent engagement in clinical risk management choices. PRACTICE IMPLICATIONS: Ensuring primary care providers have the information and tools to provide patients with accurate information may support recommended clinical engagement, thereby improving health outcomes for this population.

Clinical Engagement↗

PubMed2025

Efficacy of EGFR tyrosine kinase inhibitors in patients with non-small cell lung cancer with EGFR exon 19 insertions: clinical-genomic, preclinical analysis through LC-SCRUM-Asia (multi-institutional genomic screening registry).

BACKGROUND: EGFR exon 19 insertions (EGFRex19ins) are rare EGFR mutations. Their clinical-genomic characteristics and outcomes with EGFR-tyrosine kinase inhibitors (TKIs) remain uncertain. METHODS: We evaluated the clinical-genomic characteristics and outcomes of EGFR-TKIs for EGFRex19ins in the multi-institutional prospective lung cancer genomic screening project (LC-SCRUM-Asia). We also studied preclinical Ba/F3 models expressing EGFR-K745_E746insIPVAIK (Ba/F3-IPVAIK) to investigate their sensitivity to 1st-, 2nd-, 3rd-generation, and EGFR exon 20 insertion-active TKIs. RESULTS: In LC-SCRUM-Asia, 16,204 NSCLC patients were enrolled from March 2015 to December 2023. EGFRex19ins were detected in 13 samples (0.1 % of NSCLC). The median age was 72 years (range, 38-80); most patients were female (77 %), had adenocarcinoma (92 %), and were never-smokers (62 %). Twelve patients (93 %) had EGFR-K745_E746insIPVAIK, while one (7 %) had EGFR-K745_E746insVPVAIK. The most frequent co-mutation was TP53 (62 %); no patients had other driver alterations. Six patients (46 %) tested positive for EGFR exon 19 deletions with PCR-based Cobas EGFR test, likely due to cross-reactivity arising from sequence homology. Twelve patients received EGFR-TKIs; five (42 %) experienced partial response. In the preclinical study, Ba/F3-IPVAIK showed the highest sensitivity to 2nd-generation EGFR-TKIs compared to other EGFR-TKIs. Structural studies supported these consistent results. When broken down by EGFR-TKI generations, response rates for 1st-, 2nd-, and 3rd-generation TKIs were 50 % (1/2), 80 % (4/5), and 0 % (0/5), respectively. The median PFS for 1st-, 2nd-, and 3rd-generation TKIs were 8.7 (95 % CI, 7.4-NR), 14.7 (95 % CI, 8.0-NR), and 4.4 (95 % CI, 3.4-NR) months, respectively. CONCLUSION: Our preclinical, structural, and clinical findings indicate 2nd-generation EGFR-TKIs are more effective for EGFRex19ins compared to other TKIs.

Adult↗

PubMed2024

Opportunistic genomic screening has clinical utility: An interventional cohort study.

PURPOSE: Practice is shifting toward genome-first approaches, such as opportunistic screening for secondary findings (SFs). Analysis of SFs could be extended beyond medically actionable results to include non-medically actionable monogenic disease risks, carrier status, pharmacogenomic variants, and risk variants for common complex disease. However, evidence on the clinical utility of returning these results is lacking. We assessed the outcomes of opportunistic screening for a broad spectrum of SFs by evaluating the yield, impact on clinical management, and consistency between SFs and participants' clinical features and family history. METHODS: Adult cancer patients had exome sequencing with the option to learn multiple categories of SFs. Outcomes data were collected through chart review and participant-reported measures up to one year after return of results. RESULTS: All participants (n = 139, 85.6% female, average 54.6 years old) who elected to learn SFs had ≥1 variant reported (100% [139/139]). The yield of reportable findings was highest for pharmacogenomic variants (97.8% [135/138] of participants), followed by common disease risk variants (89.4% [118/132]), carrier status (89.3% [117/131]), and variants related to Mendelian (27.2% [34/125]), medically actionable (15.2% [21/138]), and early-onset neurodegenerative (2.6% [3/117]) disease risks. SFs from the American College of Medical Genetics and Genomics list (v3.2, noncancer genes) were reported in 1.4% (2/138) of participants. SFs across all categories demonstrated clinical utility by prompting management changes in 28.1% (39/139) of participants. Moreover, a considerable proportion of participants had suggestive clinical features (49.0% (24/49)]) or family history (21.8% (27/124)) potentially related to their SFs. CONCLUSION: Our findings indicate there are potential benefits from opportunistic screening for a broad range of SFs.

Humans↗

PubMed2025

Comparative Genomic Screening Identifies Developmental Constraint Loci Underscoring the Phenotypic Evolution of Syngnathids.

Seahorses and their relatives (syngnathids) exhibit remarkable diversity in morphology and function, characterized by their distinctive body shapes and specialized feeding mechanisms. Despite recent advances in uncovering the genetic basis of some traits, the genotype-phenotype map in syngnathids remains incomplete. In this study, we employed forward-genomic approaches and developed a method to enrich for human disease amino acid loci at a genomic scale. Our aim was to identify genetic loci associated with fin size reduction, tooth loss, and spinal curvature in syngnathids. Intriguingly, we identified a convergent amino acid change in the lat4a gene shared by syngnathids and some flying fishes, with in vitro analysis confirming its role in fin size evolution in both lineages. While genes critical for tooth development are conserved in syngnathids, the absence of key regulatory elements, such as pitx2, likely contributes to tooth loss. Additionally, we implicated col6a3 in spinal curvature development in seadragons. These findings reveal novel genetic signatures and developmental constraints underlying syngnathid diversity, demonstrating the utility of comparative genomics and targeted gene enrichment in exploring vertebrate evolution.

Animals↗

PubMed2026

Functional genomic screens uncover FERMT2 as a critical regulator of YAP/TAZ-driven tumorigenicity.

YAP and TAZ are transcriptional regulators essential for mechanotransduction, development, and tissue homeostasis, whose dysregulation is implicated in multiple diseases, including cancer. To identify key regulators of YAP/TAZ signaling required for breast cancer cell fitness, we performed CRISPR/Cas9-based loss-of-function genetic screens both in vitro and in vivo. A custom sgRNA library targeting 216 candidate YAP/TAZ modulators was screened across three breast cancer cell lines. Among these, FERMT2, a component of the integrin signaling pathway, consistently emerged as a strong drop-out hit, highlighting its essential role in sustaining YAP/TAZ-dependent fitness. Bioinformatic analysis of large-scale cancer datasets further revealed genetic co-dependency between FERMT2, YAP, and TAZ, particularly in tumors with high YAP/TAZ expression. Functional validation through FERMT2 knockout and silencing demonstrated its requirement for proliferation, anchorage-independent growth, and tumorigenicity in triple-negative breast cancer cells. FERMT2 loss impaired YAP/TAZ nuclear accumulation, reduced the expression of YAP/TAZ target genes, and decreased phosphorylation at key tyrosine residues. Mechanistically, FERMT2 regulates YAP/TAZ independently of the canonical Hippo pathway through integrin-mediated activation of FAK. Consistent with this, glucocorticoid-driven FAK activation restored YAP/TAZ signaling in FERMT2-depleted cells. Partial epistasis analyses also indicate that FERMT2 modulates actin-dependent regulation of YAP/TAZ. Together, these findings identify FERMT2 as a pivotal upstream regulator of YAP/TAZ via FAK signaling, demonstrate that YAP/TAZ are principal effectors of integrin activity, and suggest that FERMT2 may represent a selective vulnerability in cancers with elevated YAP/TAZ signaling.

Humans↗

PubMed2025

The acceptability of blood spot screening and genome sequencing in newborn screening: a systematic review examining evidence and frameworks.

BACKGROUND: Population-wide newborn blood spot screening programmes are a successful public health intervention used to detect whether the baby is at risk of certain rare conditions, with the aim of earlier diagnosis and provision of optimal care and treatment. Evaluating candidate conditions to include in newborn blood spot and genetic sequencing raises questions regarding acceptability to parents/carers. METHODS: In the context of the possible expansion of the newborn blood spot screening programme in the United Kingdom, this review aimed to systematically review research on the acceptability to parents of newborn blood spot screening and genetic sequencing. A protocol was developed prior to commencing the review and was registered on the PROSPERO database. A team of researchers carried out the review, with checking at all stages carried out by at least two individuals. We included research published after 2013 with participants who were pregnant or a recent parent of a newborn and were resident in a high-income country. We included quantitative and qualitative studies that investigated the acceptability to parents/carers of newborn blood spot screening or genetic sequencing. Quantitative studies were narratively synthesised, and theories/frameworks identified and evaluated. Qualitative studies were analysed for recurring themes, and a meta-synthesis was carried out to compare and contrast these two types of data. We quality appraised included articles using tools appropriate for their study design. RESULTS: Searches were carried out in September to November 2023 and screening identified 25 relevant research articles. Just over half were from North America, with four existing reviews and nine qualitative studies. Domains of acceptability described in the literature were: support for screening; level of anxiety, information and knowledge; consent; views of the procedure; and support after screening. The research indicated consensus support for blood spot screening, and for expanding to some other conditions, although some parental anxiety was reported. Parents/carers mostly perceived that they had received sufficient information, but the timing of this could be improved. While parents indicated interest in genomic screening, studies highlighted the need for clearer consent procedures and greater support for parents following genomic screening than for blood spot screening. Only three included studies reported using any kind of theoretical framework. DISCUSSION: Most parents/carers found newborn blood spot screening programmes to be acceptable and favoured their large-scale implementation. A minority of parents/carers expressed concerns regarding the acceptability of processes underpinning newborn blood spot screening, such as consent, the timing of receiving information and support available after testing. More research is needed regarding the acceptability of newborn genomic sequencing screening programmes, which are less established compared with newborn blood spot screening programmes. LIMITATIONS: The over-representation of studies conducted in the United States has implications for the applicability of findings to other countries where testing is not typically mandatory and health systems differ considerably. Most studies were of cross-sectional design and there was limited representation of people from lower incomes and non-white ethnicity. While the inclusion of studies only in populations of future or very recent parents provided coherence to the findings, unclear reporting of participants may have resulted in under- or overinclusion of some studies. FUNDING: This article presents independent research funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme as award number NIHR159927.

ACCEPTABILITY↗

PubMed2026

Development of a low-coverage whole genome sequencing screen for apomixis using a diverse set of Malus germplasm.

In the past decade, plant biologists have made several major discoveries pertaining to the genetic basis of apomixis (clonal propagation by seed) that have shown promise in preserving high-value hybrid rice and sorghum genotypes. This progress was made possible by foundational gene discovery efforts in model species and natural apomicts, but pleiotropic obstacles still limit its broad agricultural adoption, especially in eudicots. Thus, it follows that investigations of novel apomicts should lead to the development of new molecular tools for plant breeding. The two most common ways to identify clonal seed production are flow-cytometry seed screens and genome sequencing to compare the DNA sequences of the maternal parent and progeny, traditionally using low-throughput markers. While flow-cytometry has been the dominant method for more than two decades, it provides indirect information on the genetics of a resulting embryo and can be ineffective in certain species. Here we developed a method using short-read whole-genome sequencing at moderately low coverage (averaging 3X and 6X) to screen diverse Malus genotypes maintained in a USDA germplasm collection for clonal seed production. In total, we sequenced 55 genotypes, 1,216 of their embryos, and identified 17 previously undescribed apomictic genotypes. Several more were detected with the flow cytometry seed screen, which helped resolve certain types of reproduction and sources of noise in low-coverage datasets. This low-pass screening-by-sequencing method is a relatively low-cost, rapid method for detecting apomictic genotypes in diverse plant germplasm and when used thoughtfully in conjunction with flow cytometry, provides a new way to visualize the genetic outcomes of sexual and asexual reproduction in plants.

Apomixis↗

PubMed2024

Estimating the sensitivity of genomic newborn screening for treatable inherited metabolic disorders.

PURPOSE: Over 30 research groups and companies are exploring newborn screening using genomic sequencing (NBSeq), but the sensitivity of this approach is not well understood. METHODS: We identified individuals with treatable inherited metabolic disorders (IMDs) and ascertained the proportion whose DNA analysis revealed explanatory deleterious variants (EDVs). We examined variables associated with EDV detection and estimated the sensitivity of DNA-first NBSeq. We further predicted the annual rate of true-positive and false-negative NBSeq results in the United States for several conditions on the Recommended Uniform Screening Panel. RESULTS: We identified 635 individuals with 80 unique IMDs. In univariate analyses, Black race (OR = 0.37, 95% CI: 0.16-0.89, P = .02) and public insurance (OR = 0.60, 95% CI: 0.39-0.91, P = .02) were less likely to be associated with finding EDVs. Had all individuals been screened with NBSeq, the sensitivity would have been 80.3%. We estimated that between 0 and 649.9 cases of Recommended Uniform Screening Panel IMDs would be missed annually by NBSeq in the United States. CONCLUSION: The overall sensitivity of NBSeq for treatable IMDs is estimated at 80.3%. That sensitivity will likely be lower for Black infants and those who are on public insurance.

Humans↗

PubMed2025

Assessment of the variant prioritization strategy for genomic newborn screening in the Generation Study.

PURPOSE: Genomic sequencing offers the opportunity to screen for hundreds of rare genetic conditions. To minimize potential negative impact on families and clinical services, it is crucial to reduce false-positive results while prioritizing clinical utility. We present an automated variant prioritization approach in the Generation Study, a research study investigating genomic sequencing in 100,000 newborns in England. Prioritized variants will subsequently undergo manual review by a registered clinical scientist and a specialist clinician before being reported back to parents. METHODS: We assessed specificity of our automated variant prioritization approach in 34,410 samples not enriched for rare diseases and sensitivity in 546 samples from patients with diagnostic variants in genes relevant to newborn screening. We used coverage and copy-number variants callability metrics to evaluate variant detection. RESULTS: We estimated that 3% to 5% of samples will have prioritized variants that require manual review and that <1% of cases will have reportable variants requiring further confirmation of the condition. Sensitivity in genes included in the Generation Study was estimated to be approximately 80%. Gene-level specificity results led to changes in variant prioritization rules and conditions that are included. CONCLUSION: Gene-specific assessment of variant prioritization is crucial to establish analytical validity prior to inclusion in genomic newborn screening.

Humans↗

PubMed2026

The costs of genomic newborn screening in England: A micro-costing analysis from the Generation Study.

PURPOSE: This study estimates the total cost per newborn of delivering genomic newborn screening (gNBS) within the Genomics England-led Generation Study. METHODS: A time-driven activity-based costing approach was used to estimate gNBS costs from recruitment to confirmatory testing. Resource use data were obtained through document review, semi-structured interviews with study staff, and direct observation across six English National Health Service Trusts. Inputs were categorized as labor, consumables, or equipment, with unit costs sourced from published pay scales, catalogs, or literature. Equipment costs were annualized at a discount rate of 3.5%. All costs were estimated in 2025 Great British Pounds (£) from the healthcare providers perspective, including overheads and data storage. A one-way deterministic sensitivity analysis was conducted, varying key cost parameters (±20%) and testing alternative delivery scenarios. RESULTS: gNBS costs £1208 per newborn, with sequencing comprising 58% of the total costs, mainly consumables. The cost was reduced by 20% to £963 when excluding research-specific recruitment and consent activities to reflect the delivery of gNBS as part of routine clinical care. CONCLUSION: This study provides an estimate of gNBS costs, highlighting sequencing as the main cost driver. Combined with evidence on outcomes and health care utilization, these findings will inform future cost-effectiveness analyses, supporting policy decisions regarding national implementation in England.

Neonatal Screening↗

PubMed2026

Druggable genome CRISPRi screen in hydrogels reveals regulators of cortactin-driven actin remodeling promoting glioblastoma invasion.

To identify therapeutic targets limiting glioblastoma invasion, we applied druggable genome CRISPRi screens and multiomic analysis to patient-derived glioblastoma cells in micro-dissectible biomimetic 3D hydrogels that permitted separation and analysis of core versus invasive fractions. Of 2,550 genes screened, 12 encoded druggable targets whose suppression limited invasion, of which AURKB (encoding aurora kinase B) and ACP1 (encoding low molecular weight protein tyrosine phosphatase, LMW-PTP) were validated in neurosphere assays and in vivo. Proximity labeling identified cortactin as a link between LMW-PTP and aurora B, and we observed that cortactin underwent serine phosphorylation by aurora B and tyrosine dephosphorylation by LMW-PTP. Targeting ACP1 or AURKB via CRISPRi or inhibitors in culture and in vivo shifted the cortactin phosphorylation balance in glioblastoma, reducing levels of cortactin and the actin-related protein 2/3 (Arp2/3) complex that mediates cortactin-induced actin stabilization, thereby reducing actin-cortactin-Arp2/3 colocalization and subsequent actin polymerization. AURKB or ACP1 targeting shifted actin from cytoplasm to the nucleus, reducing mesenchymal gene expression. Biophysical analysis implicated AURKB in glioblastoma cell adhesion and stiffness needed for initial migration and ACP1 in mechanical stress resistance required for later migration. These findings revealed a targetable axis balancing kinase and phosphatase activities to regulate actin polymerization during glioblastoma invasion.

Humans↗

PubMed2025

Druggable genome CRISPRi screen in 3D hydrogels reveals regulators of cortactin-driven actin remodeling in invading glioblastoma cells.

To identify new therapeutic targets that limit glioblastoma (GBM) invasion, we applied druggable-genome CRISPR screens to patient-derived GBM cells in micro-dissectible biomimetic 3D hydrogel platforms that permit separation and independent analysis of core vs. invasive fractions. We identified 12 targets whose suppression limited invasion, of which ACP1 (LMW-PTP) and Aurora Kinase B (AURKB) were validated in neurosphere assays. Proximity labeling analysis identified cortactin as an ACP1-AURKB link, as cortactin undergoes serine phosphorylation by AURKB and tyrosine dephosphorylation by ACP1. Suppression of ACP1 or AURKB in culture and in vivo shifted the balance of cortactin phosphorylation in GBM and reduced actin polymerization and actin-cortactin co-localization. Additional biophysical analysis implicated AURKB in GBM cell adhesion and cortical stiffness, and ACP1 in resistance to mechanical stress and shape plasticity needed for 3D migration. These findings reveal a novel targetable axis that balances kinase and phosphatase activities to regulate actin polymerization during GBM invasion.

CRISPR↗

PubMed2026

Genome-wide screening and functional analysis of protein glycosylation-related genes involved in tomato fruit ripening.

Protein glycosylation, an essential co- and post-translational modification, plays critical roles in plant growth, development, and stress responses. However, its functional role in tomato fruit ripening has not been extensively investigated. Here, key protein glycosylation-related genes involved in tomato fruit ripening were identified by genome-wide screen and subsequently functional characterization. First, a dataset comprising 242 glycosylation-related proteins was established based on Gene Ontology annotations in tomato, combined with sequence homology to protein glycosylation-related proteins from Arabidopsis thaliana and Homo sapiens. Then, Subsequently, 28 genes encoding highly expressed glycosylation-related proteins (RPKM > 30) at the breaker (BR) stage were selected for functional screening, and subsequently 6 genes were identified as regulators of fruit ripening by method of virus-induced gene silencing (VIGS). Among them, Solyc03g098600 (STT3B), Solyc01g109410 (OST48), Solyc04g082670 (RPN1), and Solyc08g076460 (DAD1) functioned as positive regulators of tomato fruit ripening, whereas Solyc04g005340 (UAM2) and Solyc08g075340 (XEG113), acted as negative regulators. The expression of these genes responded dynamically to multiple ripening-related cues, including temperature, light, ethylene, and transcription factors. Furthermore, silencing of these genes individually affected the expression of genes involved in fruit ripening, including ethylene biosynthesis genes (ACS2, ACS4, ACO1, and ACO3), ripening-associated transcription factors (RIN, NOR, NOR-LIKE1, FUL1, and FUL2), and the key gene (PSY1) of lycopene biosynthesis pathway. Collectively, these findings demonstrate that protein glycosylation plays an important role in tomato fruit ripening by modulating ethylene signaling, ripening-associated transcriptional regulation, and lycopene biosynthesis.

Fruit ripening↗

PubMed2026

A multicenter survey on BRAF screening for the implementation of perioperative cancer genomic medicine for resectable colorectal oligometastases.

BACKGROUND: Genomic screening is an essential, but potentially time-consuming procedure, especially in neoadjuvant settings. We evaluated the preoperative screening of the BRAF V600E mutation for recruitment to a clinical trial among patients with resectable colorectal oligometastases (CRM). METHODS: In April 2022, an investigator-initiated trial was launched to investigate the efficacy and safety of perioperative use of the BEACON triplet regimen for BRAF V600E mutant resectable CRM. BRAF screening was retrospectively conducted in patients with resected colorectal liver metastases in 2019 for planning the trial and prospectively conducted in preoperative patients with resectable CRM from January 2022 to June 2025 for patient recruitment to the trial. RESULTS: BRAF V600E mutation was detected in 12 (3.2%) of 379 postoperative patients retrospectively and in 36 (1.7%) of 2140 preoperative patients prospectively, with 1840 patients (86.0%) carrying the wild-type and 264 patients (12.3%) classified as untested. The detection rate of the BRAF V600E mutation was significantly lower when the screening was performed prospectively in preoperative patients (P < 0.001). The untested rates varied across metastatic organs, with 10.3% in the liver, 18.1% in the lungs, 12.0% in the lymph nodes, 16.7% in the peritoneum, and 7.8% in other organs. The untested rates decreased consistently across semiannual comparisons: 28.5% in the first evaluation, followed by 15.0%, 12.0%, 8.4%, 9.1%, 7.3%, and 7.1% (P < 0.01 when compared with the first period). CONCLUSION: Raising physician awareness, as reflected by the untested rate, is a crucial factor in conducting clinical trials to implement perioperative cancer genomic medicine.

Humans↗