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Electrostatic spraying is considered an effective means to improve the efficacy of pesticide application and reduce pesticide consumption. However, the effectiveness of electrostatic spraying needs further validation in greenhouse environments, especially in long-range air-assisted spraying scenarios. A waist-shaped charging device has been improved to obtain a maximum charge-to-mass ratio of 4.4 mC/kg at an applied voltage of 6 kV in a laboratory setting, representing an increase of approximately 84.9% compared to a commercial circular charging electrode with a fan-shaped nozzle. A comparative air-assisted spray test between electrostatic deactivation (EDAS) and electrostatic activation (EAAS) was conducted on greenhouse tomato crops using a single hanging track autonomous sprayer equipped with a pair of waist-shaped charging devices. The results showed that EAAS yielded an overall average coverage of 28.4%, representing a significant 10.9% improvement over the 25.6% coverage achieved with EDAS. The overall coefficient of variation (CV) for EDAS and EAAS was 62.0% and 48.0%, respectively. Within these, the CV for the average coverage of the sample set reflecting axial distribution uniformity was 33.4% and 31.4%, respectively. Conversely, the CV for the average coverage of the sample group reflecting radial distribution uniformity was 33.7% and 17.9%, respectively. The results indicate that the waist-shaped charging device possesses remarkable charging capabilities, presenting favorable application prospects for long-range air-assisted spraying in greenhouses. The electrostatic application has a positive effect on enhancing the average coverage and improving the overall distribution uniformity. Notably, it significantly improves the radial distribution uniformity of the air-assisted spray at long range, albeit with limited improvement in the axial distribution uniformity. [ABSTRACT FROM AUTHOR]

As a highly productive rice, ratoon rice is widely planted worldwide, but the rolling of rice stubble in mechanical harvesting severely limits its total yield; based on this, some scholars have proposed rolled rice stubble righting machines. However, limited by the uncertainty of the field environment, the machine's localization accuracy of the target needs to be improved. To address this problem, real-time detection of rolled rice stubble rows is a prerequisite. Therefore, this paper introduces a deep learning method for the first time to achieve this. To this end, we presented a novel approach to improve a model that is used for the simplification of Mask R-CNN, which does not require any modules to be added or replaced on the original model. Firstly, two branches in the second stage were deleted, and the region proposals output from the stage was used directly as the mask generation region, and segmentation performance was substantially improved after a simple optimization of the region proposals. Further, the contribution of the feature map was counted, and the backbone network was simplified accordingly. The resulting SMR-RS model was still able to perform instance segmentation and has better segmentation performance than Mask R-CNN and other state-of-the-art models while significantly reducing the average image processing time and hardware consumption. [ABSTRACT FROM AUTHOR]

Simple Summary: Programmed death 1 (PD1)/programmed death ligand-1 (PD-L1) inhibitor is the standard therapy for advanced microsatellite instability (MSI)/mismatch repair-deficient (dMMR) gastrointestinal cancers. However, the suitable therapy after the progression of anti-PD1/PD-L1 for MSI/dMMR gastrointestinal cancer patients was unknown, until now. Here, we conducted a retrospective study to evaluate the efficacy of anti-PD1/PD-L1 plus other drug therapy versus chemotherapy with or without targeted therapy for patients who had progressed on prior anti-PD1/PD-L1 monotherapy. Our study found that anti-PD1/PD-L1 plus other drug therapy had significantly improved the disease control rate, progression-free survival, and overall survival, along with a numerically higher objective response rate versus chemotherapy with or without targeted therapy. The promising findings of our retrospective study need to be further confirmed in prospective trials. Background: In microsatellite instability (MSI)/mismatch repair-deficient (dMMR) gastrointestinal cancers, the optimum therapy after the progression of immune checkpoint inhibitors (ICIs) is yet unknown. Here, we compared the efficacy of programmed death 1 (PD1)/programmed death ligand-1 (PD-L1) inhibitors plus other therapy and chemotherapy with or without targeted therapy in MSI/dMMR gastrointestinal cancer patients after progression on anti-PD1/PD-L1 monotherapy. Methods: We retrospectively recruited MSI/dMMR gastrointestinal cancer patients who had progressed on anti-PD1/PD-L1 monotherapy. Objective response rate (ORR), disease control rate (DCR), progression-free survival (PFS), overall survival (OS), and PFS ratio (PFSr) were compared between patients who received anti-PD1/PD-L1 plus other therapy (ICI-plus group) and patients who received chemotherapy with or without targeted therapy (chemo-targeted group). Results: In total, 26 and 25 patients were recruited in the ICI-plus group and chemo-targeted group, respectively. Significantly better DCR (80.8% vs. 44.0%, p = 0.007), PFS (median PFS 6.9 months vs. 3.0 months, p = 0.001), OS (median OS NR vs. 14.1 months, p = 0.043), and PFSr (2.4 vs. 0.9, p = 0.021), along with a numerically higher ORR (23.1% vs. 12.0%, p = 0.503) were observed in the ICI-plus group compared with the chemo-targeted group. Multivariate analyses identified the therapy regimen as an important prognostic factor in gastrointestinal cancers. Conclusions: Compared to conventional chemotherapy with or without targeted therapy, continuing anti-PD1/PD-L1 in combination with other treatments showed better clinical outcomes in MSI/dMMR gastrointestinal cancer patients who progressed on PD1/PD-L1 blockade, which should be validated prospectively in clinical trials. [ABSTRACT FROM AUTHOR]

The cage-free system has gained a lot of interest in recent years because it can offer chickens more freedom and is easier to manage compared with free-range rearing systems, but few studies have focused on the effect of the cage-free rearing system on meat quality and flavor. In this study, 44 Jianghan chickens were reared in caged or cage-free systems to explore the effect of different rearing systems on meat-eating quality. Sensory evaluation of cooked muscles showed that the leg muscle aroma, juiciness, and flavor intensity significantly improved by the cage-free rearing. The cage-free hens had significantly lower body weight, abdominal fat percentage, and meat fat content, but higher meat moisture content. The cage-free group had brighter breast muscle and redder leg muscle color 24 h after slaughter. Transcriptomic and metabolomic profile analysis of the leg muscle samples showed that the cage-free rearing changed biosynthesis pathways associated with glycogen metabolism, lipid and fatty acid biosynthesis and transport, muscle cellular type, and cellular components, which were related to raw meat quality. Different rearing systems also resulted in differences in glycolipid metabolism, lipid metabolism, and altered levels of intramuscular fat content and other flavor precursors. Pathways such as glycerolipid metabolism, adipocytokine signaling, and metabonomic pathways such as linoleic acid, glycerophospholipid, arginine, proline, and β-alanine metabolism may be responsible for the meat quality and flavor change. [ABSTRACT FROM AUTHOR]

Summary: Liancheng white duck has two phenotypic traits: white feather and black beak–black foot, but the genes controlling these phenotypic traits are unknown. The objective of this study is to identify various candidate genes related to the plumage of Liancheng white duck. This study used F2 population construction generated between white Kaiya duck and Liancheng white duck and FST analysis between the dominant and recessive loci associated with the Liancheng white duck white feather in order to identify specific gene regions. As per the feather color statistics of the F2 population, it is estimated that there are about three or four genes controlling the white feather of Liancheng white ducks, and the FST results showed that four significant signals were found on chromosomes 4, 12, 13, and 21. Further annotation of these regions led to the identification of five genes involved in the melanin pathway, namely, KIT, CLOCK, MITF, CEBPA, and DOK5. Among them, CEBPA and DOK5 might be affecting the white feather traits of Liancheng white duck by regulating the melanin production and its transfer to the feather. The results provide insightful understanding into the genetic mechanisms of white feather in Liancheng white duck. [ABSTRACT FROM AUTHOR]

The development regulation of the uterine–vaginal junction (UVJ) epithelial folds during the sexual maturation of female birds played crucial roles in the adults' sperm storage duration and fertilization capability. However, there is a lack of studies on it in the breeding field of laying hens. In this study, White Leghorn was used for the morphological and developmental studies. According to the morphological characteristics, the development of the UVJ epithelial folds was classified into 4 stages (morphological stage T1–T4). Significant individual differences were observed simultaneously, which is one of the factors leading to the adults' UVJ morphological differences. Bulk RNA-seq suggested the different regulations of UVJ epithelial folds were classified into 3 stages (developmental stage S1–S3). Genes enriched in cell proliferation, differentiation, polarity, migration, adhesion and junction were supposed to regulate UVJ epithelial fold formation. Single-cell RNA-sequencing (scRNA-seq) showed significant differences between different types of cells within UVJ at the developmental stage S2. Immunohistochemical studies confirmed that the different proliferation rates between the epithelium and nonepithelium were one of the key factors leading to the formation of UVJ epithelial folds. Genes in the TGF-beta and WNT pathways may play roles in regulating the proliferation and differentiation of epithelium. Some factors, such as CHD2, CDC42 , and carbonic anhydrases, were important participants in forming UVJ epithelial folds. This study will provide new thoughts on the differential regulation of fertilization traits from the developmental biology perspective. [ABSTRACT FROM AUTHOR]

Chitosan- N -2-hydroxypropyl trimethyl ammonium chloride (QTS) was prepared by reaction of chitosan (CS) and glycidyl trimethylammonium chloride. Later, O -acetyl-chitosan- N -2-hydroxypropyl trimethyl ammonium chloride (AQTS) was synthesized by reaction of QTS with acetic acid in the presence of SOCl 2 . Both derivatives were characterized by FTIR, 1 H NMR, TGA, and XRD techniques. The degree of quaternization of QTS was 85.5%, and the degree of acetyl (DA) of AQTS was from 1.63 to 2.31. Compared with CS, the solubility of QTS and AQTS was improved at different levels, especially AQTS, it could be dissolved in many organic solvents, water, and aqueous solution. Notably, the solubility of AQTS in organic solvents increased as DA increased, while the solubility in water was reversed. The results of CS, QTS, and AQTS against Escherichia coli and Staphylococcus aureus showed that QTS and AQTS exhibited higher antibacterial activity than CS, and the antibacterial activity of AQTS decreased with increased DA. Moreover, the inhibition effect was AQTS1 (DA 1.63) > AQTS2 (DA 2.02) > QTS > AQTS3 (DA 2.31). On the basis of the results of the present study, it could be emphasized that hydrophobicity and positive charge density might strongly affect the antibacterial activity of quaternary ammonium chitosan derivatives. [ABSTRACT FROM AUTHOR]

A novel amphipathic chitosan derivative, N -benzoyl- O -acetyl-chitosan (BACS), was prepared by using the selective partial acylation of chitosan (CS), benzoyl chloride, and acetic acid under high-intensity ultrasound. The chemical structure and physical properties of BACS were characterized by FTIR, 1 H NMR, TGA, and XRD techniques. The degrees of substitution of benzoyl and acetyl for the chitosan derivatives were 0.26 and 1.15, respectively, which were calculated from the peak areas in NMR spectra by using the combined integral methods. The foaming properties of CS and BACS were determined and the results suggested BACS had better foam capacity and stability than those of chitosan. In addition, the antimicrobial activities of CS and BACS were also investigated against two species of bacteria ( Escherichia coli and Staphylococcus aureus ) and a fungus ( Aspergillus niger ), the results indicated that the antibacterial and antifungal activities of BACS were much stronger than those of the parent chitosan. These findings suggested that BACS was preferable for use as a food additive with a dual role of both foaming agent and food preservative. [ABSTRACT FROM AUTHOR]

Background: The Cancer Genome Atlas (TCGA) has identified four distinct molecular subtypes of gastric cancer (GC) with prognostic significance: Epstein-Barr virus (EBV)-positive, microsatellite instability (MSI)-high, genomically stable (GS), and chromosomal instability (CIN). Unfortunately, the complex analysis required for TCGA classification limits its practical use in clinical settings. Our study sought to devise a next-generation sequencing (NGS)-based method to classify GC more efficiently, serving as a promising biomarker for prognosis and immunotherapy efficacy., Methods: This study was a retrospective observation study, and we employed 2 independent GC cohorts. The 3DMed cohort (n=765), comprising data on 733 cancer-related genes along with 4 EBV-encoded genes, was utilized to develop the new NGS classification. Additionally, the secondary Korean cohort (n=55), which includes both genomic data and information on immune checkpoint inhibitor (ICI) treatment, was employed to establish a correlation between NGS subtypes and ICI responsiveness., Results: In the 3DMed cohort, we identified 5.2% EBV, 4.6% MSI, 30.6% GS, and 59.6% CIN subtypes. The MSI subtype exhibited the highest number of mutation events, along with the highest tumor mutational burden (TMB) and strong programmed cell death ligand 1 (PD-L1) expression. CIN tumors showed extensive copy number variations (CNVs) and genomic heterogeneity. The EBV subtype presented recurrent ARID1A and PIK3CA mutations and fewer TP53 mutations. GS tumors exhibited specific mutations in CDH1 and ARID1A . In the Korean cohort, ICIs were most effective in MSI and EBV cases, showing disease control rates of 100%, compared to 62.9% in GS and 12.5% in CIN subtypes., Conclusions: The NGS method successfully maps the mutational landscape of GC, providing a practical TCGA classification surrogate to optimize patient-specific treatment strategies., Competing Interests: Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://jgo.amegroups.com/article/view/10.21037/jgo-24-345/coif). B.Z. and J.C. are from 3D Medicines Inc. The other authors have no conflicts of interest to declare., (2024 AME Publishing Company. All rights reserved.)

Background: Emerging evidence has underscored the crucial role of infiltrating immune cells in the tumor immune microenvironment (TIME) of non-small cell lung cancer (NSCLC) development and progression. With the implementation of screening programs, the incidence of early-stage NSCLC is rising. However, the high risk of recurrence and poor survival rates associated with this disease necessitate a deeper understanding of the TIME and its relationship with driver alterations. The aim of this study was to provide an in-depth analysis of immune changes in early-stage NSCLC, highlighting the significant transitions in immune response during disease progression., Methods: Tumor tissues were collected from 105 patients with precancerous lesions or stage I-III NSCLC. Next-generation sequencing (NGS) was used to detect cancer driver alterations. Multiplex immunofluorescence (mIF) was performed to evaluate immune cell density, percentage, and spatial proximity to cancer cells in the TIME. Next Among these patients, 64 had NGS results, including three with adenocarcinoma in situ (AIS), 10 with minimally invasive adenocarcinoma (MIA), and 51 with stage I invasive cancers. Additionally, three patients underwent neoadjuvant immuno-chemotherapy and tumor tissue specimens before and after treatment were obtained., Results: Patients with stage I invasive cancer had significantly higher density (P=0.01) and percentage (P=0.02) of CD8 + T cells and higher percentages of M1 macrophages (P=0.04) and immature natural killer (NK) cells (P=0.041) in the tumor parenchyma compared to those with AIS/MIA. Patients with mutated epidermal growth factor receptor ( EGFR ) gene exhibited decreased NK cell infiltration, increased M2 macrophage infiltration, and decreased aggregation of CD4 + T cells near tumor cells compared to EGFR wild-type patients. As NSCLC progressed from stage I to III, CD8 + T cell density and proportion increased, while PD-L1 + tumor cells were in closer proximity to PD-1 + CD8 + T cells, potentially inhibiting CD8 + T cell function. Furthermore, M1 macrophages decreased in density and proportion, and the number of NK cells, macrophages, and B cells around tumor cells decreased. Additionally, patients with tertiary lymphoid structures (TLSs) had significantly higher proportion of M1 macrophages and lymphocytes near tumor cells, whereas those without TLS had PD-L1 + tumor cells more densely clustered around PD-1 + CD8 + T cells. Notably, neoadjuvant immuno-chemotherapy induced the development of TLS., Conclusions: This study offers an in-depth analysis of immune changes in NSCLC, demonstrating that the transition from AIS/MIA to invasive stage I NSCLC leads to immune activation, while the advancement from stage I to stage III cancer results in immune suppression. These findings contribute to our understanding of the molecular mechanisms underlying early-stage NSCLC progression and pave the way for the identification of potential treatment options., Competing Interests: Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://tlcr.amegroups.com/article/view/10.21037/tlcr-24-379/coif). Y.S. serves as an Editor-in-Chief of Translational Lung Cancer Research. D.Z., J.C., B.Z., Junling Zhang, and M.H. are from 3D Medicines Inc. The other authors have no other conflicts of interest to declare., (2024 AME Publishing Company. All rights reserved.)

Background: Peer victimization used to be considered as a crucial risk factor for children addicted to the internet. Whereas some victimized ones are function better than would be expected. Variability across individuals indicates that it is necessary to understand how children cope with being bullied and why they do not exhibit maladaptive outcomes., Objective: We explored the underlying mechanisms by testing whether subjective well-being was a mediator between peer victimization and Internet addiction and whether the mediation effects conditioned on the levels of parent-child relationship (PCR)., Methods: Data were collected from 65, 868 elementary school students in China (Mage = 9.56 years, SD = 0.62, 54.0% male) using four questionnaires., Results: We found that: (1) subjective well-being can partially mediate the relationship of the two variables; and (2) PCR can moderate direct path and second half of the intermediary process. These moderating effects were stronger for children with higher PCR vs. lower PCR, as a strong PCR can help children to deal with intense emotions and to access effective resources to obtain support., Conclusion: This study deepens our understanding of how peer victimization leads to internet addiction, identifies a supportive PCR as a crucial factor that strengthens the resilience of child victims, and highlights the value of focusing on improving the relationship between parents and children in intervening internet addiction related to peer victimization., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Zhou, Cai, Cui, Liu, He, Zhang, Chen and Wang.)

Background: Over 70% of the patients with hepatocellular carcinoma (HCC) are diagnosed at an advanced stage and lose the opportunity for radical surgery. Combination therapy of tyrosine kinase inhibitors (TKIs) and anti-programmed cell death protein-1 (PD-1) antibodies has achieved a high tumor response rate in both the first-line and second-line treatment of advanced HCC. However, few studies have prospectively evaluated whether TKIs plus anti-PD-1 antibodies could convert unresectable intermediate-advanced HCC into resectable disease., Methods: This single-arm, phase II study enrolled systemic therapy-naïve adult patients with unresectable Barcelona Clinic Liver Cancer stage B or C HCC. Patients received oral lenvatinib one time per day plus intravenous anti-PD-1 agents every 3 weeks (one cycle). Tumor response and resectability were evaluated before the fourth cycle, then every two cycles. The primary endpoint was conversion success rate by investigator assessment. Secondary endpoints included objective response rate (ORR) by independent imaging review (IIR) assessment per modified RECIST (mRECIST) and Response Evaluation Criteria in Solid Tumors, V.1.1 (RECIST 1.1), progression-free survival (PFS) and 12-month recurrence-free survival (RFS) rate by IIR per mRECIST, R0 resection rate, overall survival (OS), and safety. Biomarkers were assessed as exploratory objectives., Results: Of the 56 eligible patients enrolled, 53 (94.6%) had macrovascular invasion, and 16 (28.6%) had extrahepatic metastasis. The median follow-up was 23.5 months. The primary endpoint showed a conversion success rate of 55.4% (31/56). ORR was 53.6% per mRECIST and 44.6% per RECIST 1.1. Median PFS was 8.9 months, and median OS was 23.9 months. Among the 31 successful conversion patients, 21 underwent surgery with an R0 resection rate of 85.7%, a pathological complete response rate of 38.1%, and a 12-month RFS rate of 47.6%. Grade ≥3 treatment-related adverse events were observed in 42.9% of patients. Tumor immune microenvironment analysis of pretreatment samples displayed significant enrichment of CD8 + T cells (p=0.03) in responders versus non-responders., Conclusion: Lenvatinib plus anti-PD-1 antibodies demonstrate promising efficacy and tolerable safety as conversion therapy in unresectable HCC. Pre-existing CD8 + cells are identified as a promising biomarker for response to this regimen., Trial Registration Number: Chinese Clinical Trial Registry, ChiCTR1900023914., Competing Interests: Competing interests: ST, FZ, JC, SC, and XZ are employees of 3D Medicines Inc. Other authors declare no potential conflicts of interest., (© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background & Aims: Little is known about molecular biomarkers that predict the response and prognosis in unresectable hepatocellular carcinoma (HCC) treated with programmed death (PD)-1 inhibitors., Methods: A total of 62 HCC patients who underwent next-generation sequencing were retrospectively included in our department for this study. Patients with unresectable disease were subjected to systemic therapy. PD-1 inhibitors intervention (PD-1Ab) group and nonPD-1Ab group included 20 and 13 patients, respectively. Primary resistance was defined as initial on-treatment progression or progression with an initial stable disease of less than 6 months., Results: Chromosome 11q13 amplification (Amp11q13) was the most common copy number variation in our cohort. Fifteen (24.2%) patients harbored Amp11q13 in our dataset. Patients with Amp11q13 showed higher level of Des-γ-carboxy-prothrombin (DCP), tumor number and were more prone to be combined with portal vein tumor thrombosis (PVTT). In the PD-1Ab group, the proportion of progressive disease (PD) in patients with Amp11q13 was significantly higher than that in patients with nonAmp11q13 (100% vs 33.3%, P =0.03). In the nonPD-1Ab group, the proportion of PD in patients with Amp11q13 and nonAmp11q13 had no significant difference (0% vs 11.1%, P >0.99). In the PD-1Ab group, the median progression-free survival (PFS) was 1.5 months in Amp11q13 patients vs 16.2 months in non-Amp11q13 patients (HR, 0.05; 95% CI 0.01-0.45; P = 0.0003). No significant difference was observed in the nonPD-1Ab group. Notably, we found that hyperprogressive disease (HPD) might be associated with Amp11q13. The increased density of Foxp3+ Treg cells in HCC patients with Amp11q13 might be one of potential mechanisms., Conclusion: HCC patients with Amp11q13 are less likely to benefit from PD-1 blockade therapies. These findings may help guide the use of immunotherapy for HCC in routine clinical practice., Competing Interests: DZ, YC, MH, JC, SC, TB and YB were employed by the company 3D Medicines Shanghai Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Yan, Zhang, Chen, Lu, Huang, Cai, Chen, Bei, Bai, Lv, Fu and Zhang.)

Background: Minimal residual disease (MRD) is considered an essential factor leading to relapse within 2 years (early relapse) after radical surgery, which is challenging to be detected by conventional imaging. Circulating tumor DNA (ctDNA) provides a novel approach for detecting MRD and predicting clinical outcomes. Here, we tried to construct a fixed panel for plasma-only ctDNA NGS to enable tumor-uninformed MRD detection in hepatocellular carcinoma (HCC)., Methods: Here, we performed the followings: (i) profiling genomic alteration spectrum of ctDNA from the Chinese HCC cohort consisting of 493 individuals by NGS; (ii) screening of MRD monitoring genes; and (iii) performance evaluation of MRD monitoring genes in predicting early relapse in the ZJZS2020 cohort comprising 20 HCC patients who underwent curative resection., Results: A total of 493 plasma samples from the Chinese HCC cohort were detected using a 381/733-gene NGS panel to characterize the mutational spectrum of ctDNA. Most patients (94.1%, 464/493) had at least one mutation in ctDNA. The variants fell most frequently in TP53 (45.1%), LRP1B (20.2%), TERT (20.2%), FAT1 (16.2%), and CTNNB1 (13.4%). By customized filtering strategy, 13 MRD monitoring genes were identified, and any plasma sample with one or more MRD monitoring gene mutations was considered MRD-positive. In the ZJZS2020 cohort, MRD positivity presented a sensitivity of 75% (6/8) and a specificity of 100% (6/6) in identifying early postoperative relapse. The Kaplan-Meier analysis revealed a significantly short relapse-free survival (RFS; median RFS, 4.2 months vs . NR, P=0.002) in the MRD-positive patients versus those with MRD negativity. Cox regression analyses revealed MRD positivity as an independent predictor of poor RFS (HR 13.00, 95% CI 2.60-69.00, P=0.002)., Conclusions: We successfully developed a 13-gene panel for plasma-only MRD detection, which was effective and convenient for predicting the risk of early postoperative relapse in HCC., Competing Interests: TC, JinPC, XZ, CC, and MH are employees of 3D Medicines Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Xu, Cai, Zhong, Wen, Cai, He, Liao, Zhang, Fu, Chen, Cai, Zhong, Chen, Huang, Cheng and Pan.)

KRAS mutations lead to persistent activation of multiple downstream effectors that drive the cancer phenotype. Approximately 30%-50% of colorectal cancer (CRC) patients harbor KRAS mutations, which confer more aggressive tumor biology and shorter overall survival (OS), especially in microsatellite stable (MSS) metastatic CRC. Given that KRAS mutant protein has been proven difficult to target directly, identifying genes that function closely with KRAS and targeting these genes seems to be a promising therapeutic strategy for KRAS -mutated MSS CRC. Here, KRAS function-sensitive genes were identified by assessing the correlation between gene dependency scores from CRISPR knockout screens and KRAS mRNA expression in KRAS -mutated MSS CRC cell lines in the Cancer Cell Line Encyclopedia (CCLE) database. If the correlation coefficient was ≥ 0.6, the gene was considered a KRAS function-sensitive gene. Then KRAS function-sensitive genes related to prognosis were screened out in The Cancer Genome Atlas (TCGA) cohort, and the prognostic value was validated in the Gene Expression Omnibus (GEO) cohort. Single-sample gene set enrichment analysis (ssGSEA) was performed to investigate the potential mechanisms. PockDrug-Server was used to predict the druggability of candidate genes. The results showed that in 20 KRAS -mutated MSS CRC cell lines, 13 genes were identified as KRAS function-sensitive genes. Of these 13 genes, only BIK expression was significantly associated with progression-free survival (PFS) and OS, and the BIK-high patients had significantly poorer PFS (HR=3.18, P=0.020) and OS (HR=4.74, P=0.030) than the BIK-low patients. Multivariate Cox regression analysis revealed high BIK expression as an independent predictor for poorer prognosis in KRAS -mutated MSS CRC. The prognostic value of BIK was also successfully validated in a GEO cohort. The results of ssGSEA showed that the BIK-high group was more prone to strong metastasis activity than the BIK-low group. Pocket druggability prediction analysis presented that BIK had three druggable pockets, and their druggability scores were above 0.8. These findings suggested that BIK is a promising prognostic marker and therapeutic target in KRAS -mutated MSS CRC., Competing Interests: None., (AJCR Copyright © 2022.)

Liancheng white duck has two phenotypic traits: white feather and black beak-black foot, but the genes controlling these phenotypic traits are unknown. The objective of this study is to identify various candidate genes related to the plumage of Liancheng white duck. This study used F 2 population construction generated between white Kaiya duck and Liancheng white duck and F ST analysis between the dominant and recessive loci associated with the Liancheng white duck white feather in order to identify specific gene regions. As per the feather color statistics of the F 2 population, it is estimated that there are about three or four genes controlling the white feather of Liancheng white ducks, and the F ST results showed that four significant signals were found on chromosomes 4, 12, 13, and 21. Further annotation of these regions led to the identification of five genes involved in the melanin pathway, namely, KIT, CLOCK, MITF, CEBPA, and DOK5. Among them, CEBPA and DOK5 might be affecting the white feather traits of Liancheng white duck by regulating the melanin production and its transfer to the feather. The results provide insightful understanding into the genetic mechanisms of white feather in Liancheng white duck., (© 2022 Stichting International Foundation for Animal Genetics.)

Approximately 25% of prostate cancer (PCa) cases experience biochemical recurrence (BCR) following radical prostatectomy (RP). The patients with BCR, especially with BCR ≤2 year after RP (early BCR), are more likely to develop clinical metastasis and castration resistance. Now decision-making regarding BCR after RP relies solely on clinical parameters. We thus attempted to establish an early BCR-risk prediction model by combining a molecular signature with clinicopathological features for guiding clinical decision-making. In this study, an 8-gene signature was derived, and these eight genes were SPTBN2, LGI3, TGM3, LENG9, HAS3, SLC25A27, PCDHGA1, and ADPRHL1 . The Kaplan-Meier analysis revealed a significantly prolonged BCR-free survival in the patients with low-risk scores compared to those with high-risk scores in both training and validation datasets. Harrell's concordance index and time-dependent receiver operating characteristic analysis demonstrated that this gene signature tended to outperform three commercial panels at early BCR prediction. Moreover, this signature was also proven as an independent predictor of BCR-free survival. A nomogram, incorporating the gene signature and clinicopathologic features, was constructed and excellently predicted 1-, 2- and 3-year BCR-free survival of localized PCa patients after RP. Gene set enrichment analysis, tumor immunity, and mRNA expression profiling analysis showed that the high-risk group was more prone to the immunosuppressive microenvironment and impaired DNA damage response than the low-risk group. Collectively, we successfully developed a novel 8-gene signature as a powerful predictor for early BCR after RP and created a prognostic nomogram, which may help inform the clinical management of PCa., Competing Interests: None., (AJCR Copyright © 2022.)

Background: Gastrointestinal (GI) cancer is the second most common cancer type with mismatch repair-deficient (dMMR)/microsatellite instability-high (MSI-H) phenotype that is expected to respond to immune-checkpoint inhibitors (ICIs). However, approximately half of the patients with dMMR/MSI-H GI cancer derive no benefit from ICIs. We sought to identify the predictors of primary resistance to ICIs in dMMR/MSI-H GI cancer., Methods: Three independent cohorts were included: (1) the discovery cohort (65 patients with dMMR/MSI-H GI cancer) with ICI efficacy data and pre-ICIs tissue samples for genomic profile and tumor immune infiltration; (2) the validation cohort (22 patients with dMMR/MSI-H GI cancer) with ICI efficacy data and pre-ICIs plasma samples for genomic profile; and (3) the TCGA (The Cancer Genome Atlas) cohort not receiving ICIs (152 patients with MSI-H GI cancer) with genomic profile and survival data., Results: AKT1 and CDH1 mutations were identified as independent predictors of poor progression-free survival (PFS) and primary resistance to ICIs in dMMR/MSI-H GI cancer. We combined these two genes as an immuno-oncology therapy predictor (IOpred), which could recognize 52.4% (11/21) of dMMR/MSI-H patients with primary resistance to ICIs with a positive predictive value (PPV) of 91.7% (11/12). Receiver operating characteristic analysis demonstrated IOpred with a good performance in predicting primary resistance (area under the curve 0.751). Patients with IOpred-Mut (mutant AKT1 or CDH1) GI cancer had significantly shorter PFS (HR=8.36, p<0.001) and overall survival (OS, HR=5.17, p<0.001) than IOpred-WT (wild-type for both AKT1 and CDH1) cases upon ICI treatment. The validation cohort also confirmed the correlation between IOpred-mutation and poorer prognosis (PFS, HR=4.68, p=0.004; OS, HR=15.98, p<0.001) in dMMR/MSI-H patients after ICIs. The PPV of IOpred in identifying primary resistance to ICIs was 80% (4/5) in the validation cohort. Additionally, IOpred-WT patients could be further stratified by tumor mutational burden (TMB), wherein TMB-low patients (TMB ≤26.19 mutations per megabase (Mb)) had a significantly higher primary resistance rate to ICIs (34.8% vs 6.7%, p=0.014) and poorer PFS (HR=3.46, p=0.008) and OS (HR=4.42, p=0.047) than TMB-high patients (TMB >26.19 mutations/Mb)., Conclusions: IOpred was identified as a powerful predictor of primary resistance to ICIs in dMMR/MSI-H GI cancer, which might serve as a promising biomarker to help guide immunotherapy decision-making., Competing Interests: Competing interests: FZ, HC, JC, SC, and XZhao are employees of 3D Medicines. No other disclosures are reported., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: Epstein-Barr virus (EBV)-associated gastric cancer (GC) (EBVaGC) is a distinct molecular subtype of GC with a favorable prognosis. However, the exact effects and potential mechanisms of EBV infection on immune checkpoint blockade (ICB) efficacy in GC remain to be clarified. Additionally, EBV-encoded RNA (EBER) in situ hybridization (ISH), the traditional method to detect EBV, could cause false-positive/false-negative results and not allow for characterizing other molecular biomarkers recommended by standard treatment guidelines for GC. Herein, we sought to investigate the efficacy and potential biomarkers of ICB in EBVaGC identified by next-generation sequencing (NGS)., Design: An NGS-based algorithm for detecting EBV was established and validated using two independent GC cohorts (124 in the training cohort and 76 in the validation cohort). The value of EBV infection for predicting ICB efficacy was evaluated among 95 patients with advanced or metastatic GC receiving ICB. The molecular predictive biomarkers for ICB efficacy were identified to improve the prediction accuracy of ICB efficacy in 22 patients with EBVaGC., Results: Compared with orthogonal assay (EBER-ISH) results, the NGS-based algorithm achieved high performance with a sensitivity of 95.7% (22/23) and a specificity of 100% (53/53). EBV status was identified as an independent predictive factor for overall survival and progression-free survival in patients with DNA mismatch repair proficient (pMMR) GC following ICB. Moreover, the patients with EBV+/pMMR and EBV-/MMR deficient (dMMR) had comparable and favorable survival following ICB. Twenty-two patients with EBV+/pMMR achieved an objective response rate of 54.5% (12/22) on immunotherapy. Patients with EBVaGC with a high cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) level were less responsive to anti-programmed death-1/ligand 1 (PD-1/L1) monotherapy, and the combination of anti-CTLA-4 plus anti-PD-1/L1 checkpoint blockade benefited patients with EBVaGC more than anti-PD-1/L1 monotherapy with a trend close to significance (p=0.074). There were nearly significant differences in tumor mutational burden (TMB) level and SMARCA4 mutation frequency between the ICB response and non-response group., Conclusions: We developed an efficient NGS-based EBV detection strategy, and this strategy-identified EBV infection was as effective as dMMR in predicting ICB efficacy in GC. Additionally, we identified CTLA-4, TMB, and SMARCA4 mutation as potential predictive biomarkers of ICB efficacy in EBVaGC, which might better inform ICB treatment for EBVaGC., Competing Interests: Competing interests: ST, FZ, XZ, and JC are employees of 3D Medicines., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Colorectal cancer (CRC) is one of the most heritable cancers, and genetic factors play an important role in the increased CRC risk. However, the well-established CRC-risk genes were limited for explaining the increased risk of CRC individuals. Germline mutations in DNA damage repair (DDR) genes have also been reported to be implicated in CRC heritability. Here, we aimed to determine the prevalence and significance of germline DDR and well-established CRC-risk gene variants in CRCs with paired somatic analyses. Next-generation sequencing (NGS) was performed on tumor tissues and paired white blood cells collected from 2160 Chinese patients with CRC using well-designed 381- or 733-cancer gene panel. Germline/somatic variations were identified and assessed for pathogenicity and likely pathogenicity. Of 2160 CRCs, 136 pathogenic germline mutations in 133 patients (133/2160, 6.1%) were identified in 21 genes, including 19 out of 32 examined DDR genes. Compared with non-carriers, individuals with germline variants were prone to a higher level of microsatellite instability (MSI) and tumor mutational burden (TMB), and an earlier age of onset. Somatic sequencing identified second hits in 24/133 (18%) patients with germline variants. Among the mismatch repair (MMR) genes with germline mutations, the second hit significantly increased MSI and TMB, particularly apparent in MSH6 . All MMR germline variation carriers further with a second hit were all MSI-H and had an extraordinarily high level of TMB. Collectively, approximately 6.1% of CRC patients carried pathogenic germline variants, and additional somatic second hit increases the genomic instability in CRC, whereas the more clinical significance warrants further study., Competing Interests: Bei Zhang, Shuang Tong, Jinping Cai, Feilong Zhao, Xiaochen Zhao, and Shiqing Chen are employed by 3D Medicines Inc., (AJCR Copyright © 2021.)

The formin FHOD1 acts as a nucleating, capping and bundling protein of actin filaments. In cells, release from the C-terminal diaphanous autoregulatory domain (DAD) of FHOD1 stimulates the protein into the active form. However, the cellular physiological relevance of active form FHOD1 and the phenotypic regulation by FHOD1 depletion are not completely understood. Here, we show that in contrast with the cytosolic diffused expression of auto-inhibited FHOD1, active FHOD1 by C-terminal truncation was recruited into all three types of actin stress fibers in human osteosarcoma cells. Notably, the recruited active FHOD1 was more incorporated with myosin II than α-actinin, and associated with both naïve and mature focal adhesions. Active FHOD1 displayed faster turnover than actin molecules on ventral stress fibers. Moreover, we witnessed the emergence of active FHOD1 from the cell periphery, which subsequently moved centripetally together with transverse arcs. Furthermore, FHOD1 knockdown resulted in defective maturation of actomyosin bundles and subsequently longer non-contractile dorsal stress fibers, whereas the turnover of both actin and myosin II were maintained normally. Importantly, the loss of FHOD1 led to slower actin centripetal flow, resulting in abnormal cell spreading and migration defects. Taken together, these results reveal a critical role of FHOD1 in temporal- and spatial- control of the morphology and dynamics of functional actin stress fibers during variable cell behavior., (© 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.)