Objective This finite element study aimed to compare the effects of different canine traction auxiliaries on the biomechanical responses during en-masse retraction of mandibular anterior teeth with clear aligners. Materials and Methods Based on patient CBCT data, bilateral mandibular first premolar extraction was simulated, with 0.2 mm en-masse retraction of lower anterior teeth. Miniscrew implants were simulated in all experimental groups except the control. Six conditions were tested: (1) control—no auxiliary; (2) lingual button at canine neck; (3) precision cut on aligner at canine region; (4) 4 mm power arm at canine neck; (5) 6 mm power arm; (6) 8 mm power arm. All groups received 150 g retraction force. Results Anterior teeth exhibited tipping movement in all groups. Maximum principal stress on periodontal ligament was concentrated mainly at the labial apical region and lingual cervical region. Group 3 showed the minimum extrusion of central and lateral incisors (0.003305 mm and 0.005997 mm, respectively), with the smallest crown-to-root displacement ratio (0.277 and 0.254), and relatively lower maximum principal stress on periodontal ligament. All experimental groups demonstrated smaller canine extrusion and crown-to-root displacement ratio compared to the control. Group 2 exhibited the minimum canine extrusion (0.01088 mm). Group 6 showed the minimum von Mises stress on canine root (0.6836 MPa). Conclusions When clear aligners were used for mandibular anterior retraction, traction applied via precision cuts at the canine region of the aligner achieved favorable torque and vertical control of the incisors, with lower von Mises stress. All traction auxiliaries demonstrated notable effectiveness in controlling canine torque and vertical position. However, none of the three power arm groups showed a clear advantage over the precision cut or lingual button designs.

Abstract To systematically define tumor-intrinsic mechanisms driving immune resistance in ovarian cancer (OC), we integrated an in vitro genome-wide CRISPR immune screen, in vivo targeted immune screens, and analysis of 16 published ICB patient cohorts. From this pipeline, 693 candidate genes were shortlisted, and METTL5 emerged as a key regulator of tumor-intrinsic immune evasion. Pan-cancer TCGA analysis revealed significant METTL5 upregulation across multiple cancer types, with OC showing the second-highest expression among 34 malignancies. Although METTL5 expression did not correlate with OC stage or overall survival, higher expression was strongly associated with reduced cytolytic activity scores, suggesting suppressed antitumor immunity. In the MDACC HGSOC cohort (NCT03026062), patients with elevated METTL5 expression in baseline tumor samples exhibited significantly poorer responses and shorter overall survival after ICB therapy, supporting its clinical relevance. Mechanistically, METTL5 loss in OC models specifically reduced m6A methylation at A1832 of 18S rRNA, disrupting helix 44 structure and impairing ribosomal scanning and translation. RiboLace-based active ribosome profiling demonstrated that METTL5 knockout reprograms translation, notably downregulating genes enriched in the “Response of EIF2AK1 to Heme Deficiency” pathway, consistent with defective integrated stress response (ISR). Translation of ATF4 was markedly reduced, accompanied by decreased expression of downstream targets SLC7A11 and SLC3A2, key components of the cystine/glutamate antiporter that suppress lipid peroxidation and ferroptosis. As a result, METTL5-deficient OC cells displayed increased lipid peroxidation and heightened sensitivity to T cell-mediated ferroptosis in vitro and in vivo. Reintroduction of ATF4 restored SLC7A11/SLC3A2 expression and reversed ferroptosis sensitivity, while pharmacologic inhibition of ferroptosis produced similar effects. These findings identify METTL5 as a central regulator of ATF4 translation, oxidative stress control, and immune resistance in OC. Elevated METTL5 expression may serve as a biomarker for poor ICB response. Therapeutically, METTL5 inhibition, ATF4 translation suppression or ferroptosis induction represent potential strategies to enhance immunotherapy efficacy. This study establishes the METTL5-ATF4-ferroptosis axis as a critical tumor-intrinsic mechanism of immune evasion and provides a generalizable framework for decoding cancer-immune interactions. Citation Format: Jiakai Hou, Cheng-wei Ju, Nicholas A. Egan, Yanjun Wei, Yunfei Wang, Minghao Dang, Tianyi Zhou, Leilei Shi, Ningbo Zheng, Si Chen, Ashley Guerrero, Xiaofang Liang, Wanfu Wu, Areej Akhtar, Chitra Dhiman, Debanwita Roy Burman, Andro Gerges, Mason D. Flores, Han Li, Li-Sheng Zhang, Marleen Kok, Xiaobo Mao, Linghua Wang, Qin Feng, Yiwen Chen, Sanghoon Lee, Daniel McGrail, Nidhi Sahni, Chuan He, Amir A. Jazaeri, Weiyi Peng. Tumor-intrinsic METTL5 restricts T cell-induced ferroptosis by impairing ATF4 translation in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 2915.

Poor clinical responses to immune checkpoint blockade (ICB) observed in ovarian cancer (OC) highlight an unmet need to understand the mechanisms driving immune evasion in this disease. To address this, an integrative analysis is conducted by combining in vitro genome-wide immune screens, in vivo ICB screens, and clinical data mining, and METTL5 is identified as a crucial OC-intrinsic factor that promotes immune resistance. Immunologically "cold" OC tumors and poor responders to ICB exhibit elevated METTL5 expression. Mechanistically, knocking out (KO) METTL5 in OC disrupts ATF4 translation by altering 18S rRNA m6A levels, leading to the downregulation of SLC7A11 and SLC3A2, whose function is to suppress ferroptosis activity. Consequently, METTL5 KO enhances tumor sensitivity to T cell-mediated antitumor immunity. Notably, the immune-sensitive phenotypes seen in METTL5-KO tumors can be reversed by either ATF4 overexpression or ferroptosis inhibition. These findings underscore the central role of the METTL5/ATF4/ferroptosis axis in controlling OC responses to immunotherapy.

Host anti-viral factors are essential for controlling SARS-CoV-2 infection but remain largely unknown due to the biases of previous large-scale studies toward pro-viral host factors. To fill in this knowledge gap, we perform a genome-wide CRISPR dropout screen and integrate analyses of the multi-omics data of the CRISPR screen, genome-wide association studies, single-cell RNA-Seq, and host-virus proteins or protein/RNA interactome. This study uncovers many host factors that are currently underappreciated, including the components of V-ATPases, ESCRT, and N-glycosylation pathways that modulate viral entry and/or replication. The cohesin complex is also identified as an anti-viral pathway, suggesting an important role of three-dimensional chromatin organization in mediating host-viral interaction. Furthermore, we discover another anti-viral regulator KLF5, a transcriptional factor involved in sphingolipid metabolism, which is up-regulated, and harbors genetic variations linked to COVID-19 patients with severe symptoms. Anti-viral effects of three identified candidates (DAZAP2/VTA1/KLF5) are confirmed individually. Molecular characterization of DAZAP2/VTA1/KLF5-knockout cells highlights the involvement of genes related to the coagulation system in determining the severity of COVID-19. Together, our results provide further resources for understanding the host anti-viral network during SARS-CoV-2 infection and may help develop new countermeasure strategies.

Esophageal squamous cell carcinoma (ESCC) is a prevalent malignant tumor of the digestive system that poses a significant threat to human life and health. It is crucial to thoroughly investigate the mechanisms of esophageal carcinogenesis and identify potential key molecular events in its carcinogenesis. Single-cell transcriptome sequencing is an emerging technology that has gained prominence in recent years for studying molecular mechanisms, which may help to further explore the underlying mechanisms of the ESCC tumor microenvironment in depth. The single-cell dataset was obtained from GSE160269 in the Gene Expression Omnibus database, including 60 tumor samples and four paracancer samples. The single-cell data underwent dimensional reduction clustering analysis to identify clusters and annotate expression profiles. Subcluster analysis was conducted for each cellular taxon. Copy number variation analysis of tumor cell subpopulations was performed to primarily identify malignant cells within them. A proposed chronological analysis was performed to obtain the process of cell differentiation. In addition, cell communication, transcription factor analysis, and tumor pathway analysis were also performed. Relevant risk models and key genes were established by univariate COX regression and LASSO analysis. The key genes obtained from the screen were subjected to appropriate silencing and cellular assays, including CCK-8, 5-ethynyl-2'-deoxyuridine, colony formation, and western blot. Single-cell analysis revealed that normal samples contained a large number of fibroblasts, T cells, and B cells, with fewer other cell types, whereas tumor samples exhibited a relatively balanced distribution of cell types. Subclassification analysis of immune cells, fibroblasts, endothelial cells, and epithelial cells revealed their specific spatial characteristics. The prognostic risk model, we constructed successfully, achieved accurate prognostic stratification for ESCC patients. The screened key gene, UPF3A, was found to be significantly associated with the development of ESCC by cellular assays. This process might be linked to the phosphorylation of ERK and P38. Single-cell transcriptome analysis successfully revealed the distribution of cell types and major expressed factors in ESCC patients, which could facilitate future in-depth studies on the therapeutic mechanisms of ESCC.

In this study, by constructing a rat model of orthodontic recurrence and intervening with coptisine, the IL-6, IL-8, TNF- α and soluble intercellular adhesion molecule-1 (sICAM-1) content were analyzed to assess the regulatory mechanism of coptisine on the health status of recurrent periodontal tissue after orthodontics and the occurrence of periodontal tissue inflammation. Male rats were assigned into three groups by constructing coptisine liposome nano-objects: blank group (Blank, 10 rats), orthodontic tooth movement model group (50 rats). The orthodontic tooth movement model group was randomly divided into model group (module), model control group (control-free), model coptisine treatment group (treatment-free), model blank functional liposome group (control-lip) and model functional coptisine liposome group (treatment-lip). Rats in model group were killed on the day after device was removed. Rats in other groups received equal doses of normal saline, coptisine, blank functional liposomes, and functional coptisine liposomes by intragastric administration on the day of device removal and then were killed after 7 days of continuous treatment. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, we found that Fas/FasL signaling pathway was enriched in pathways related to apoptosis, disease infection and inflammation. Western blot experiments confirmed that coptisine could inhibit Fas/FasL signaling activation in the process of relapse after orthodontics. Lipopolysaccharides (LPS) treatment significantly increased inflammatory cytokines and sICAM-1, as well as the level of Fas and FasL. Coptisine treatment inhibited LPS-induced Fas/FasL signaling pathway in periodontal ligament cells. Coptisine attenuated the relapsed inflammation after orthodontics by inhibiting Fas/FasL signaling.

Background: Breast invasive carcinoma (BRCA) is a malignant tumor with high morbidity and mortality, and the prognosis is still unsatisfactory. Both ferroptosis and cuproptosis are apoptosis-independent cell deaths caused by the imbalance of corresponding metal components in cells and can affect the proliferation rate of cancer cells. The aim in this study was to develop a prognostic model of cuproptosis/ferroptosis-related genes (CFRGs) to predict survival in BRCA patients. Methods: Transcriptomic and clinical data for breast cancer patients were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Cuproptosis and ferroptosis scores were determined for the BRCA samples from the TCGA cohort using Gene Set Variation Analysis (GSVA), followed by weighted gene coexpression network analysis (WGCNA) to screen out the CFRGs. The intersection of the differentially expressed genes grouped by high and low was determined using X-tile. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) were used in the TGCA cohort to identify the CFRG-related signature. In addition, the relationship between risk scores and immune infiltration levels was investigated using various algorithms, and model genes were analyzed in terms of single-cell sequencing. Finally, the expression of the signature genes was validated with quantitative real-time PCR (qRT‒PCR) and immunohistochemistry (IHC). Results: A total of 5 CFRGs (ANKRD52, HOXC10, KNOP1, SGPP1, TRIM45) were identified and were used to construct proportional hazards regression models. The high-risk groups in the training and validation sets had significantly worse survival rates. Tumor mutational burden (TMB) was positively correlated with the risk score. Conversely, Tumor Immune Dysfunction and Exclusion (TIDE) and tumor purity were inversely associated with risk scores. In addition, the infiltration degree of antitumor immune cells and the expression of immune checkpoints were lower in the high-risk group. In addition, risk scores and mTOR, Hif-1, ErbB, MAPK, PI3K/AKT, TGF-β and other pathway signals were correlated with progression. Conclusion: We can accurately predict the survival of patients through the constructed CFRG-related prognostic model. In addition, we can also predict patient immunotherapy and immune cell infiltration.

Abstract Background The resistance to radiationtherapy is responsible for the poor prognosis of ESCC(esophageal squamous cell carcinoma). Our previous clinical study confirmed that YAP1 gene amplification is one of the poor prognostic indicators of radical chemoradiotherapy for ESCC. However, the underlying mechanism by which YAP1 mediates radio-resistance still remained poorly understood. Here we aim to explore the combined guiding value and related action mechanism of YAP1 and its downstream target gene Dickkopf-related protein 1(DKK1) in the treatment of ESCC. Methods We collected the clinical information and tissues of 94 ESCC patients and histodochemistry and survival analysis were performed.Using Western, co-IP, CHIP and luciferase experiments to verify the expression and regulatory relationship of YAP1 and DKK1. We also performed cell viability, transwell, Immunofluorescence of γ-H2AX and clonogenic assay to investigate the proliferation capacity and radiation sensitivity of KYSE510 cells and KYSE150 cells after lentiviral-transfected cell lines were constructed. Finally, Tumor growth curves of mices were used to verify the relationship between cell viability and radiation sensitivity. Results Cell experiments demonstrated that YAP1 overexpression promoted the malignant phenotype of ESCC cells and DNA damage repair to mediate radioresistance. In our present study, YAP1 and DKK1 were firstly found to have a synergistic predictive value for ESCC prognosis. Both knockdown YAP1 and application of YAP1 inhibitor repressed transcriptional activation of DKK1. The CHIP experiment and luciferase reporter showed that YAP1 activated DKK1 directly through its transcription factor TEAD4, which both affected the proliferation and migration ability of esophageal cancer cells. Moreover, the application of the YAP1 inhibitor CA3 combined with X-rays could significantly suppressed the xenograft tumor formation. Conclusion In conclusion, our study uncovers the role and mechanisms through which YAP1 and DKK1 as key regulators of radiotherapy resitance. YAP1/TEAD4 directly regulated the expression of DKK1, both participated in cell radioresistance, proliferation, migration and invasion and may be a potential joint predictor of ESCC.

BackgroundCuproptosis is a novel form of programmed cell death that differs from other types such as pyroptosis, ferroptosis, and autophagy. It is a promising new target for cancer therapy. Additionally, immune-related genes play a crucial role in cancer progression and patient prognosis. Therefore, our study aimed to create a survival prediction model for lung adenocarcinoma patients based on cuproptosis and immune-related genes. This model can be utilized to enhance personalized treatment for patients. MethodsRNA sequencing (RNA-seq) data of lung adenocarcinoma (LUAD) patients were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The levels of immune cell infiltration in the GSE68465 cohort were determined using gene set variation analysis (GSVA), and immune-related genes (IRGs) were identified using weighted gene coexpression network analysis (WGCNA). Additionally, cuproptosis-related genes (CRGs) were identified using unsupervised clustering. Univariate COX regression analysis and least absolute shrinkage selection operator (LASSO) regression analysis were performed to develop a risk prognostic model for cuproptosis and immune-related genes (CIRGs), which was subsequently validated. Various algorithms were utilized to explore the relationship between risk scores and immune infiltration levels, and model genes were analyzed based on single-cell sequencing. Finally, the expression of signature genes was confirmed through quantitative real-time PCR (qRT-PCR), immunohistochemistry (IHC), and Western blotting (WB). ResultsWe have identified 5 Oncogenic Driver Genes namely CD79B, PEBP1, PTK2B, STXBP1, and ZNF671, and developed proportional hazards regression models. The results of the study indicate significantly reduced survival rates in both the training and validation sets among the high-risk group. Additionally, the high-risk group displayed lower levels of immune cell infiltration and expression of immune checkpoint compared to the low-risk group.

The glioblastoma (GBM) stem cell–like cells (GSCs) are critical for tumorigenesis/therapeutic resistance of GBM. Mounting evidence supports tumor-promoting function of long noncoding RNAs (lncRNAs), but their role in GSCs remains poorly understood. By combining CRISPRi screen with orthogonal multiomics approaches, we identified a lncRNA DARS1-AS1 –controlled posttranscriptional circuitry that promoted the malignant properties of GBM cells/GSCs. Depleting DARS1-AS1 inhibited the proliferation of GBM cells/GSCs and self-renewal of GSCs, prolonging survival in orthotopic GBM models. DARS1-AS1 depletion also impaired the homologous recombination (HR)–mediated double-strand break (DSB) repair and enhanced the radiosensitivity of GBM cells/GSCs. Mechanistically, DARS1-AS1 interacted with YBX1 to promote target mRNA binding and stabilization, forming a mixed transcriptional/posttranscriptional feed-forward loop to up-regulate expression of the key regulators of G 1 -S transition, including E2F1 and CCND1. DARS1-AS1 /YBX1 also stabilized the mRNA of FOXM1 , a master transcription factor regulating GSC self-renewal and DSB repair. Our findings suggest DARS1-AS1 /YBX1 axis as a potential therapeutic target for sensitizing GBM to radiation/HR deficiency–targeted therapy.

Emerging evidence suggests that cryptic translation beyond the annotated translatome produces proteins with developmental or physiological functions. However, functions of cryptic non-canonical open reading frames (ORFs) in cancer remain largely unknown. To fill this gap and systematically identify colorectal cancer (CRC) dependency on non-canonical ORFs, we apply an integrative multiomic strategy, combining ribosome profiling and a CRISPR–Cas9 knockout screen with large-scale analysis of molecular and clinical data. Many such ORFs are upregulated in CRC compared to normal tissues and are associated with clinically relevant molecular subtypes. We confirm the in vivo tumor-promoting function of the microprotein SMIMP, encoded by a primate-specific, long noncoding RNA, the expression of which is associated with poor prognosis in CRC, is low in normal tissues and is specifically elevated in CRC and several other cancer types. Mechanistically, SMIMP interacts with the ATPase-forming domains of SMC1A, the core subunit of the cohesin complex, and facilitates SMC1A binding to cis -regulatory elements to promote epigenetic repression of the tumor-suppressive cell cycle regulators encoded by CDKN1A and CDKN2B . Thus, our study reveals a cryptic microprotein as an important component of cohesin-mediated gene regulation and suggests that the ‘dark’ proteome, encoded by cryptic non-canonical ORFs, may contain potential therapeutic or diagnostic targets.

Emerging evidence suggests that cryptic translation within long noncoding RNAs (lncRNAs) may produce novel proteins with important developmental/physiological functions. However, the role of this cryptic translation in complex diseases (e.g., cancer) remains elusive. Here, we applied an integrative strategy combining ribosome profiling and CRISPR/Cas9 screening with large-scale analysis of molecular/clinical data for breast cancer (BC) and identified estrogen receptor α–positive (ER+) BC dependency on the cryptic ORFs encoded by lncRNA genes that were upregulated in luminal tumors. We confirmed the in vivo tumor-promoting function of an unannotated protein, GATA3-interacting cryptic protein (GT3-INCP) encoded by LINC00992, the expression of which was associated with poor prognosis in luminal tumors. GTE-INCP was upregulated by estrogen/ER and regulated estrogen-dependent cell growth. Mechanistically, GT3-INCP interacted with GATA3, a master transcription factor key to mammary gland development/BC cell proliferation, and coregulated a gene expression program that involved many BC susceptibility/risk genes and impacted estrogen response/cell proliferation. GT3-INCP/GATA3 bound to common cis regulatory elements and upregulated the expression of the tumor-promoting and estrogen-regulated BC susceptibility/risk genes MYB and PDZK1. Our study indicates that cryptic lncRNA-encoded proteins can be an important integrated component of the master transcriptional regulatory network driving aberrant transcription in cancer, and suggests that the “hidden” lncRNA-encoded proteome might be a new space for therapeutic target discovery.

BACKGROUND:Disulfidptosis is a recently discovered programmed cell death pathway. However, the exact molecular mechanism of disulfidptosis in cutaneous melanoma remains unclear.METHODS:In this study, clustering analysis was performed using data from public databases to construct a prognostic model, which was subsequently externally validated. The biological functions of the model genes were then investigated through various experimental techniques, including qRT-PCR, Western blotting, CCK-8 assay, wound healing assay, and Transwell assay.RESULTS:We constructed a signature using cutaneous melanoma (CM) data, which accurately predicts the overall survival (OS) of patients. The predictive value of this signature for prognosis and immune therapy response was validated using multiple external datasets. High-risk CM subgroups may exhibit decreased survival rates, alterations in the tumor microenvironment (TME), and increased tumor mutation burden. We initially verified the expression levels of five optimum disulfidptosis-related genes (ODRGs) in normal tissues and CM. The expression levels of these genes were further confirmed in HaCaT cells and three melanoma cell lines using qPCR and protein blotting analysis. HLA-DQA1 emerged as the gene with the highest regression coefficient in our risk model, highlighting its role in CM. Mechanistically, HLA-DQA1 demonstrated the ability to suppress CM cell growth, proliferation, and migration.CONCLUSION:In this study, a novel signature related to disulfidptosis was constructed, which accurately predicts the survival rate and treatment sensitivity of CM patients. Additionally, HLA-DQA1 is expected to be a feasible therapeutic target for effective clinical treatment of CM.

Histone 2A (H2A) monoubiquitination is a fundamental epigenetics mechanism of gene expression, which plays a critical role in regulating cell fate. However, it is unknown if H2A ubiquitination is involved in EGFR-driven tumorigenesis. In the current study, we have characterized a previously unidentified oncogenic lncRNA (lncEPAT) that mediates the integration of the dysregulated EGFR pathway with H2A deubiquitination in tumorigenesis. LncEPAT was induced by the EGFR pathway, and high-level lncEPAT expression positively correlated with the glioma grade and predicted poor survival of glioma patients. Mass spectrometry analyses revealed that lncEPAT specifically interacted with deubiquitinase USP16. LncEPAT inhibited USP16's recruitment to chromatin, thereby blocking USP16-mediated H2A deubiquitination and repressing target gene expression, including CDKN1A and CLUSTERIN. Depletion of lncEPAT promoted USP16-induced cell cycle arrest and cellular senescence, and then repressed GBM cell tumorigenesis. Thus, the EGFR-lncEPAT-ubH2A coupling represents a previously unidentified mechanism for epigenetic gene regulation and senescence resistance during GBM tumorigenesis.

Genetic screens are widely exploited to develop novel therapeutic approaches for cancer treatment. With recent advances in single-cell technology, single-cell CRISPR screen (scCRISPR) platforms provide opportunities for target validation and mechanistic studies in a high-throughput manner. Here, we aim to establish scCRISPR platforms which are suitable for immune-related screens involving multiple cell types. We integrated two scCRISPR platforms, namely Perturb-seq and CROP-seq, with both in vitro and in vivo immune screens. By leveraging previously generated resources, we optimized experimental conditions and data analysis pipelines to achieve better consistency between results from high-throughput and individual validations. Furthermore, we evaluated the performance of scCRISPR immune screens in determining underlying mechanisms of tumor intrinsic immune regulation. Our results showed that scCRISPR platforms can simultaneously characterize gene expression profiles and perturbation effects present in individual cells in different immune screen conditions. Results from scCRISPR immune screens also predict transcriptional phenotype associated with clinical responses to cancer immunotherapy. More importantly, scCRISPR screen platforms reveal the interactive relationship between targeting tumor intrinsic factors and T cell-mediated antitumor immune response which cannot be easily assessed by bulk RNA-seq. Collectively, scCRISPR immune screens provide scalable and reliable platforms to elucidate molecular determinants of tumor immune resistance.

Defective cholesterol biosynthesis in eye lens cells is often associated with cataracts; however, how genes involved in cholesterol biosynthesis are regulated in lens cells remains unclear. Here, we show that Quaking (Qki) is required for the transcriptional activation of genes involved in cholesterol biosynthesis in the eye lens. At the transcriptome level, lens-specific Qki-deficient mice present downregulation of genes associated with the cholesterol biosynthesis pathway, resulting in a significant reduction of total cholesterol level in the eye lens. Mice with Qki depletion in lens epithelium display progressive accumulation of protein aggregates, eventually leading to cataracts. Notably, these defects are attenuated by topical sterol administration. Mechanistically, we demonstrate that Qki enhances cholesterol biosynthesis by recruiting Srebp2 and Pol II in the promoter regions of cholesterol biosynthesis genes. Supporting its function as a transcription co-activator, we show that Qki directly interacts with single-stranded DNA. In conclusion, we propose that Qki-Srebp2-mediated cholesterol biosynthesis is essential for maintaining the cholesterol level that protects lens from cataract development.

BACKGROUND:The human genome encodes over 14,000 pseudogenes that are evolutionary relics of protein-coding genes and commonly considered as nonfunctional. Emerging evidence suggests that some pseudogenes may exert important functions. However, to what extent human pseudogenes are functionally relevant remains unclear. There has been no large-scale characterization of pseudogene function because of technical challenges, including high sequence similarity between pseudogene and parent genes, and poor annotation of transcription start sites.RESULTS:To overcome these technical obstacles, we develop an integrated computational pipeline to design the first genome-wide library of CRISPR interference (CRISPRi) single-guide RNAs (sgRNAs) that target human pseudogene promoter-proximal regions. We perform the first pseudogene-focused CRISPRi screen in luminal A breast cancer cells and reveal approximately 70 pseudogenes that affect breast cancer cell fitness. Among the top hits, we identify a cancer-testis unitary pseudogene, MGAT4EP, that is predominantly localized in the nucleus and interacts with FOXA1, a key regulator in luminal A breast cancer. By enhancing the promoter binding of FOXA1, MGAT4EP upregulates the expression of oncogenic transcription factor FOXM1. Integrative analyses of multi-omic data from the Cancer Genome Atlas (TCGA) reveal many unitary pseudogenes whose expressions are significantly dysregulated and/or associated with overall/relapse-free survival of patients in diverse cancer types.CONCLUSIONS:Our study represents the first large-scale study characterizing pseudogene function. Our findings suggest the importance of nuclear function of unitary pseudogenes and underscore their underappreciated roles in human diseases. The functional genomic resources developed here will greatly facilitate the study of human pseudogene function.

The efficiency of CRISPR/Cas9-mediated protein knockout is determined by three factors: sequence-specific sgRNA activity, frameshift probability, and the characteristics of targeted amino acids. A number of computational methods have been developed for predicting sgRNA efficiency from different perspectives. We propose GuidePro, a two-layer ensemble predictor that enables the integration of multiple predictive methods and feature sets. GuidePro leverages information from DNA sequences, amino acids, and protein structures, and reduces the impact of dataset-specific biases. Tested on independent datasets, GuidePro demonstrated consistent superior performance in predicting phenotypes caused by protein loss-of-function. GuidePro is implemented as a web application for prioritizing sgRNAs that target protein-coding genes in human, monkey and mouse genomes, available at https://bioinformatics.mdanderson.org/apps/GuidePro .

目的:在正畸复发过程中,探究miR-146a对大鼠牙周组织中炎症相关基因的表达情况及相关信号通路的影响.方法:24只雄性SD大鼠,分为空白组(C组)和正畸牙齿移动模型组,模型组加力14 d后去除装置,并将其随机分为模型组(N组)、模型对照组(P组)、模型治疗组(T组);去除装置后,N组即刻处死取材,T组注射agomiR-146a,P组注射等量的阴性对照agomiR-control;连续注射7 d后取各组牙周组织,使用RT-PCR检测组织中miR-146a的表达情况,用RT-PCR和Western blot检测IRAK-1和TRAF6基因和蛋白的表达情况,用ELISA法检测牙周组织中IL-6、IL-1β、TNF-α的表达变化,用HE染色观察各组牙周组织形态学变化.结果:与C组比较,P组miR-146a的表达量明显下降(P<0.01),IRAK-1、TRAF6及炎症指标的表达均显著增加(P<0.01),且炎性细胞浸润增多,牙槽骨吸收;T组注射miR-146a激动剂后,miR-146a的表达量有所升高,IRAK-1、TRAF6及炎症指标的表达均显著降低(P<0.05),炎性细胞浸润减少,牙槽骨吸收减轻;而N组各个指标的表达没有明显变化(P>0.05).结论:miR-146a激动剂可通过降低TRAF6和IRAK1的表达缓解由正畸复发导致的牙周组织炎症.

目的 评价依据Andrews六要素制定的不同治疗方案对骨性Ⅱ类患者侧貌美观的影响,并研究正畸医生与非专业人员审美评价的差异.方法 选取一名符合实验标准的骨性Ⅱ类患者作为研究对象,使用Dolphin Imaging导入试验对象头颅侧位片,与侧貌照片进行重叠,以Andrews六要素理论为指导制定正畸掩饰性治疗方案、正畸代偿结合颏成形方案及正畸-正颌方案,得到相应的侧貌彩图后用Photoshop转变成侧貌剪影图,选取正畸医生和非专业人员根据Likert量表对6张剪影图进行评分.结果 两组评分者均认为根据Andrews六要素制定的正畸正颌双颌手术方案侧貌最美观,正畸代偿结合颏成形方案中颏部前移8 mm次之.在专业组中,原始侧貌得分明显低于非专业组,而双颌手术侧貌得分明显高于非专业组.结论 对于下颌后缩的骨性Ⅱ类患者,根据Andrews六要素制定的正畸正颌双颌手术方案是最佳治疗方式,而在正畸代偿辅以颏成形术方案中,通过Andrews六要素制定的颏部前移量最有利于患者改善侧貌美观.专业组与非专业组之间存在审美差异.