RNA trafficking and subcellular localization-a review of mechanisms, experimental and predictive methodologies.

RNA localization is essential for regulating spatial translation, where RNAs are trafficked to their target locations via various biological mechanisms. In this review, we discuss RNA localization in the context of molecular mechanisms, experimental techniques and machine learning-based prediction tools. Three main types of molecular mechanisms that control the localization of RNA to distinct cellular compartments are reviewed, including directed transport, protection from mRNA degradation, as well as diffusion and local entrapment. Advances in experimental methods, both image and sequence based, provide substantial data resources, which allow for the design of powerful machine learning models to predict RNA localizations. We review the publicly available predictive tools to serve as a guide for users and inspire developers to build more effective prediction models. Finally, we provide an overview of multimodal learning, which may provide a new avenue for the prediction of RNA localization.

MrGPS: an m6A-related gene pair signature to predict the prognosis and immunological impact of glioma patients.

N6-methyladenosine (m6A) RNA methylation is the predominant epigenetic modification for mRNAs that regulates various cancer-related pathways. However, the prognostic significance of m6A modification regulators remains unclear in glioma. By integrating the TCGA lower-grade glioma (LGG) and glioblastoma multiforme (GBM) gene expression data, we demonstrated that both the m6A regulators and m6A-target genes were associated with glioma prognosis and activated various cancer-related pathways. Then, we paired m6A regulators and their target genes as m6A-related gene pairs (MGPs) using the iPAGE algorithm, among which 122 MGPs were significantly reversed in expression between LGG and GBM. Subsequently, we employed LASSO Cox regression analysis to construct an MGP signature (MrGPS) to evaluate glioma prognosis. MrGPS was independently validated in CGGA and GEO glioma cohorts with high accuracy in predicting overall survival. The average area under the receiver operating characteristic curve (AUC) at 1-, 3- and 5-year intervals were 0.752, 0.853 and 0.831, respectively. Combining clinical factors of age and radiotherapy, the AUC of MrGPS was much improved to around 0.90. Furthermore, CIBERSORT and TIDE algorithms revealed that MrGPS is indicative for the immune infiltration level and the response to immune checkpoint inhibitor therapy in glioma patients. In conclusion, our study demonstrated that m6A methylation is a prognostic factor for glioma and the developed prognostic model MrGPS holds potential as a valuable tool for enhancing patient management and facilitating accurate prognosis assessment in cases of glioma.

Diagnostic Prediction of portal vein thrombosis in chronic cirrhosis patients using data-driven precision medicine model.

BACKGROUND: Portal vein thrombosis (PVT) is a significant issue in cirrhotic patients, necessitating early detection. This study aims to develop a data-driven predictive model for PVT diagnosis in chronic hepatitis liver cirrhosis patients. METHODS: We employed data from a total of 816 chronic cirrhosis patients with PVT, divided into the Lanzhou cohort (n = 468) for training and the Jilin cohort (n = 348) for validation. This dataset encompassed a wide range of variables, including general characteristics, blood parameters, ultrasonography findings and cirrhosis grading. To build our predictive model, we employed a sophisticated stacking approach, which included Support Vector Machine (SVM), Naïve Bayes and Quadratic Discriminant Analysis (QDA). RESULTS: In the Lanzhou cohort, SVM and Naïve Bayes classifiers effectively classified PVT cases from non-PVT cases, among the top features of which seven were shared: Portal Velocity (PV), Prothrombin Time (PT), Portal Vein Diameter (PVD), Prothrombin Time Activity (PTA), Activated Partial Thromboplastin Time (APTT), age and Child-Pugh score (CPS). The QDA model, trained based on the seven shared features on the Lanzhou cohort and validated on the Jilin cohort, demonstrated significant differentiation between PVT and non-PVT cases (AUROC = 0.73 and AUROC = 0.86, respectively). Subsequently, comparative analysis showed that our QDA model outperformed several other machine learning methods. CONCLUSION: Our study presents a comprehensive data-driven model for PVT diagnosis in cirrhotic patients, enhancing clinical decision-making. The SVM-Naïve Bayes-QDA model offers a precise approach to managing PVT in this population.

Accurate identification of structural variations from cancer samples.

Structural variations (SVs) are commonly found in cancer genomes. They can cause gene amplification, deletion and fusion, among other functional consequences. With an average read length of hundreds of kilobases, nano-channel-based optical DNA mapping is powerful in detecting large SVs. However, existing SV calling methods are not tailored for cancer samples, which have special properties such as mixed cell types and sub-clones. Here we propose the Cancer Optical Mapping for detecting Structural Variations (COMSV) method that is specifically designed for cancer samples. It shows high sensitivity and specificity in benchmark comparisons. Applying to cancer cell lines and patient samples, COMSV identifies hundreds of novel SVs per sample.

DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning.

MOTIVATION: Accurate prediction of RNA subcellular localization plays an important role in understanding cellular processes and functions. Although post-transcriptional processes are governed by trans-acting RNA binding proteins (RBPs) through interaction with cis-regulatory RNA motifs, current methods do not incorporate RBP-binding information. RESULTS: In this article, we propose DeepLocRNA, an interpretable deep-learning model that leverages a pre-trained multi-task RBP-binding prediction model to predict the subcellular localization of RNA molecules via fine-tuning. We constructed DeepLocRNA using a comprehensive dataset with variant RNA types and evaluated it on the held-out dataset. Our model achieved state-of-the-art performance in predicting RNA subcellular localization in mRNA and miRNA. It has also demonstrated great generalization capabilities, performing well on both human and mouse RNA. Additionally, a motif analysis was performed to enhance the interpretability of the model, highlighting signal factors that contributed to the predictions. The proposed model provides general and powerful prediction abilities for different RNA types and species, offering valuable insights into the localization patterns of RNA molecules and contributing to our understanding of cellular processes at the molecular level. A user-friendly web server is available at: https://biolib.com/KU/DeepLocRNA/.

Improving bulk RNA-seq classification by transferring gene signature from single cells in acute myeloid leukemia.

The advances in single-cell RNA sequencing (scRNA-seq) technologies enable the characterization of transcriptomic profiles at the cellular level and demonstrate great promise in bulk sample analysis thereby offering opportunities to transfer gene signature from scRNA-seq to bulk data. However, the gene expression signatures identified from single cells are typically inapplicable to bulk RNA-seq data due to the profiling differences of distinct sequencing technologies. Here, we propose single-cell pair-wise gene expression (scPAGE), a novel method to develop single-cell gene pair signatures (scGPSs) that were beneficial to bulk RNA-seq classification to transfer knowledge across platforms. PAGE was adopted to tackle the challenge of profiling differences. We applied the method to acute myeloid leukemia (AML) and identified the scGPS from mouse scRNA-seq that allowed discriminating between AML and control cells. The scGPS was validated in bulk RNA-seq datasets and demonstrated better performance (average area under the curve [AUC] = 0.96) than the conventional gene expression strategies (average AUC$\le$ 0.88) suggesting its potential in disclosing the molecular mechanism of AML. The scGPS also outperformed its bulk counterpart, which highlighted the benefit of gene signature transfer. Furthermore, we confirmed the utility of scPAGE in sepsis as an example of other disease scenarios. scPAGE leveraged the advantages of single-cell profiles to enhance the analysis of bulk samples revealing great potential of transferring knowledge from single-cell to bulk transcriptome studies.

Deciphering associations between gut microbiota and clinical factors using microbial modules.

MOTIVATION: Human gut microbiota plays a vital role in maintaining body health. The dysbiosis of gut microbiota is associated with a variety of diseases. It is critical to uncover the associations between gut microbiota and disease states as well as other intrinsic or environmental factors. However, inferring alterations of individual microbial taxa based on relative abundance data likely leads to false associations and conflicting discoveries in different studies. Moreover, the effects of underlying factors and microbe-microbe interactions could lead to the alteration of larger sets of taxa. It might be more robust to investigate gut microbiota using groups of related taxa instead of the composition of individual taxa. RESULTS: We proposed a novel method to identify underlying microbial modules, i.e. groups of taxa with similar abundance patterns affected by a common latent factor, from longitudinal gut microbiota and applied it to inflammatory bowel disease (IBD). The identified modules demonstrated closer intragroup relationships, indicating potential microbe-microbe interactions and influences of underlying factors. Associations between the modules and several clinical factors were investigated, especially disease states. The IBD-associated modules performed better in stratifying the subjects compared with the relative abundance of individual taxa. The modules were further validated in external cohorts, demonstrating the efficacy of the proposed method in identifying general and robust microbial modules. The study reveals the benefit of considering the ecological effects in gut microbiota analysis and the great promise of linking clinical factors with underlying microbial modules. AVAILABILITY AND IMPLEMENTATION: https://github.com/rwang-z/microbial_module.git.

bvnGPS: a generalizable diagnostic model for acute bacterial and viral infection using integrative host transcriptomics and pretrained neural networks.

MOTIVATION: The confusion of acute inflammation infected by virus and bacteria or noninfectious inflammation will lead to missing the best therapy occasion resulting in poor prognoses. The diagnostic model based on host gene expression has been widely used to diagnose acute infections, but the clinical usage was hindered by the capability across different samples and cohorts due to the small sample size for signature training and discovery. RESULTS: Here, we construct a large-scale dataset integrating multiple host transcriptomic data and analyze it using a sophisticated strategy which removes batch effect and extracts the common information from different cohorts based on the relative expression alteration of gene pairs. We assemble 2680 samples across 16 cohorts and separately build gene pair signature (GPS) for bacterial, viral, and noninfected patients. The three GPSs are further assembled into an antibiotic decision model (bacterial-viral-noninfected GPS, bvnGPS) using multiclass neural networks, which is able to determine whether a patient is bacterial infected, viral infected, or noninfected. bvnGPS can distinguish bacterial infection with area under the receiver operating characteristic curve (AUC) of 0.953 (95% confidence interval, 0.948-0.958) and viral infection with AUC of 0.956 (0.951-0.961) in the test set (N = 760). In the validation set (N = 147), bvnGPS also shows strong performance by attaining an AUC of 0.988 (0.978-0.998) on bacterial-versus-other and an AUC of 0.994 (0.984-1.000) on viral-versus-other. bvnGPS has the potential to be used in clinical practice and the proposed procedure provides insight into data integration, feature selection and multiclass classification for host transcriptomics data. AVAILABILITY AND IMPLEMENTATION: The codes implementing bvnGPS are available at https://github.com/Ritchiegit/bvnGPS. The construction of iPAGE algorithm and the training of neural network was conducted on Python 3.7 with Scikit-learn 0.24.1 and PyTorch 1.7. The visualization of the results was implemented on R 4.2, Python 3.7, and Matplotlib 3.3.4.

GPGPS: a robust prognostic gene pair signature of glioma ensembling IDH mutation and 1p/19q co-deletion.

MOTIVATION: Many studies have shown that IDH mutation and 1p/19q co-deletion can serve as prognostic signatures of glioma. Although these genetic variations affect the expression of one or more genes, the prognostic value of gene expression related to IDH and 1p/19q status is still unclear. RESULTS: We constructed an ensemble gene pair signature for the risk evaluation and survival prediction of glioma based on the prior knowledge of the IDH and 1p/19q status. First, we separately built two gene pair signatures IDH-GPS and 1p/19q-GPS and elucidated that they were useful transcriptome markers projecting from corresponding genome variations. Then, the gene pairs in these two models were assembled to develop an integrated model named Glioma Prognostic Gene Pair Signature (GPGPS), which demonstrated high area under the curves (AUCs) to predict 1-, 3- and 5-year overall survival (0.92, 0.88 and 0.80) of glioma. GPGPS was superior to the single GPSs and other existing prognostic signatures (avg AUC = 0.70, concordance index = 0.74). In conclusion, the ensemble prognostic signature with 10 gene pairs could serve as an independent predictor for risk stratification and survival prediction in glioma. This study shed light on transferring knowledge from genetic alterations to expression changes to facilitate prognostic studies. AVAILABILITY AND IMPLEMENTATION: Codes are available at https://github.com/Kimxbzheng/GPGPS.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Deregulation of immune response contributing to fulminant hepatitis in HEV infected pregnant women.

Hepatitis E virus (HEV) infection in pregnant women is associated with a wide spectrum of adverse consequences for both mother and fetus. The high mortality in this population appears to be associated with hormonal changes and consequent immunological changes. This study conducted an analysis of immune responses in pregnant women infected with HEV manifesting varying severity. Data mining analysis of the GSE79197 was utilized to examine differentially biological functions in pregnant women with HEV infection (P-HEV) versus without HEV infection (P-nHEV), P-HEV progressing to ALF (P-ALF) versus P-HEV, and P-HEV versus non-pregnant women with HEV infection (nP-HEV). We found cellular response to interleukin and immune response-regulating signalings were activated in P-HEV compared with P-nHEV. However, there was a significant decrease of immune responses, such as T cell activation, leukocyte cell-cell adhesion, regulation of lymphocyte activation, and immune response-regulating signaling pathway in P-ALF patient than P-HEV patient. Compared with nP-HEV, MHC protein complex binding function was inhibited in P-HEV. Further microRNA enrichment analysis showed that MAPK and T cell receptor signaling pathways were inhibited in P-HEV compared with nP-HEV. In summary, immune responses were activated during HEV infection while being suppressed when developing ALF during pregnancy, heightening the importance of immune mediation in the pathogenesis of severe outcome in HEV infected pregnant women.

Analysis of differential metabolites in serum metabolomics of patients with aortic dissection.

BACKGROUND: Pathogenesis and diagnostic biomarkers of aortic dissection (AD) can be categorized through the analysis of differential metabolites in serum. Analysis of differential metabolites in serum provides new methods for exploring the early diagnosis and treatment of aortic dissection. OBJECTIVES: This study examined affected metabolic pathways to assess the diagnostic value of metabolomics biomarkers in clients with AD. METHOD: The serum from 30 patients with AD and 30 healthy people was collected. The most diagnostic metabolite markers were determined using metabolomic analysis and related metabolic pathways were explored. RESULTS: In total, 71 differential metabolites were identified. The altered metabolic pathways included reduced phospholipid catabolism and four different metabolites considered of most diagnostic value including N2-gamma-glutamylglutamine, PC(phocholines) (20:4(5Z,8Z,11Z,14Z)/15:0), propionyl carnitine, and taurine. These four predictive metabolic biomarkers accurately classified AD patient and healthy control (HC) samples with an area under the curve (AUC) of 0.9875. Based on the value of the four different metabolites, a formula was created to calculate the risk of aortic dissection. Risk score = (N2-gamma-glutamylglutamine × -0.684) + (PC (20:4(5Z,8Z,11Z,14Z)/15:0) × 0.427) + (propionyl carnitine × 0.523) + (taurine × -1.242). An additional metabolic pathways model related to aortic dissection was explored. CONCLUSION: Metabolomics can assist in investigating the metabolic disorders associated with AD and facilitate a more in-depth search for potential metabolic biomarkers.

Integrative machine learning and neural networks for identifying PANoptosis-related lncRNA molecular subtypes and constructing a predictive model for head and neck squamous cell carcinoma.

PURPOSE: PANoptosis is considered a novel type of cell death that plays important roles in tumor progression. In this study, we applied machine learning algorithms to explore the relationships between PANoptosis-related lncRNAs (PRLs) and head and neck squamous cell carcinoma (HNSCC) and established a neural network model for prognostic prediction. METHODS: Information about the HNSCC cohort was downloaded from the TCGA database, and the differentially expressed prognostic PRLs between tumor and normal samples were assessed in patients with different tumor subtypes via nonnegative matrix factorization (NMF) analysis. Subsequently, five kinds of machine-learning algorithms were used to select the core PRLs across the subtypes, and the interactive features were pooled into a neural network model to establish a PRL-related risk score (PLRS) system. Survival differences were compared via Kaplan‒Meier analysis, and the predictive effects were assessed with the areas under the ROCs. Moreover, functional enrichment analysis, immune infiltration, tumor mutation burden (TMB) and clinical therapeutic response were also conducted to further evaluate the novel predictive model. RESULTS: A total of 347 PRLs were identified, 225 of which were differentially expressed between tumor and normal samples. Patients were divided into two clusters via NMF analysis, in which cluster 1 had a better prognosis and more immune cells and functional infiltrates. With the application of five machine learning algorithms, we selected 13 interactive PRLs to construct the predictive model. The AUCs for the ROCs in the entire set were 0.735, 0.740 and 0.723, respectively. Patients in the low-PLRS group exhibited a better prognosis, greater immune cell enrichment, greater immune function activation, lower TMB and greater sensitivity to immunotherapy. CONCLUSION: In this study, we established a novel neural network prognostic model to predict survival and identify tumor subtypes in HNSCC patients. This novel assessment system is useful for prediction, providing ideas for clinical treatment.

Multimorbidity measures associated with cognitive function among community-dwelling older Chinese adults.

INTRODUCTION: Older adults with multimorbidity are at high risk of cognitive impairment development. There is a lack of research on the associations between different multimorbidity measures and cognitive function among older Chinese adults living in the community. METHODS: We used the Chinese Longitudinal Healthy Longevity Survey from 2002 to 2018 and included data on dementia-free participants aged ≥65 years. Multimorbidity measures included condition counts, multimorbidity patterns, and trajectories. The association of multimorbidity measures with cognitive function was examined by generalized estimating equation and linear and logistic regression models. RESULTS: Among 14,093 participants at baseline, 43.2% had multimorbidity. Multimorbidity patterns were grouped into cancer-inflammatory, cardiometabolic, and sensory patterns. Multimorbidity trajectories were classified as "onset-condition," "newly developing," and "severe condition." The Mini-Mental State Examination scores were significantly lower for participants with more chronic conditions, with cancer-inflammatory/cardiometabolic/sensory patterns, and with developing multimorbidity trajectories. DISCUSSION: Condition counts, sensory pattern, cardiometabolic pattern, cancer-inflammatory pattern, and multimorbidity developmental trajectories were prospectively associated with cognitive function. HIGHLIGHTS: Elderly individuals with a higher number of chronic conditions were associated with lower MMSE scores in the Chinese Longitudinal Healthy Longevity Survey data. MMSE scores were significantly lower for participants with specific multimorbidity patterns. Individuals with developing trajectories of multimorbidity were associated with lower MMSE scores and a higher risk of mild cognitive impairment.

Co-expression module analysis reveals high expression homogeneity for both coding and non-coding genes in sepsis.

Sepsis is a life-threatening condition characterized by a harmful host response to infection with organ dysfunction. Annually about 20 million people are dead owing to sepsis and its mortality rates is as high as 20%. However, no studies have been carried out to investigate sepsis from the system biology point of view, as previous research predominantly focused on individual genes without considering their interactions and associations. Here, we conducted a comprehensive exploration of genome-wide expression alterations in both mRNAs and long non-coding RNAs (lncRNAs) in sepsis, using six microarray datasets. Co-expression networks were conducted to identify mRNA and lncRNA modules, respectively. Comparing these sepsis modules with normal modules, we observed a homogeneous expression pattern within the mRNA/lncRNA members, with the majority of them displaying consistent expression direction. Moreover, we identified consistent modules across diverse datasets, consisting of 20 common mRNA members and two lncRNAs, namely CHRM3-AS2 and PRKCQ-AS1, which are potential regulators of sepsis. Our results reveal that the up-regulated common mRNAs are mainly involved in the processes of neutrophil mediated immunity, while the down-regulated mRNAs and lncRNAs are significantly overrepresented in T-cell mediated immunity functions. This study sheds light on the co-expression patterns of mRNAs and lncRNAs in sepsis, providing a novel perspective and insight into the sepsis transcriptome, which may facilitate the exploration of candidate therapeutic targets and molecular biomarkers for sepsis.

A network-based algorithm for the identification of moonlighting noncoding RNAs and its application in sepsis.

Moonlighting proteins provide more options for cells to execute multiple functions without increasing the genome and transcriptome complexity. Although there have long been calls for computational methods for the prediction of moonlighting proteins, no method has been designed for determining moonlighting long noncoding ribonucleicacidz (RNAs) (mlncRNAs). Previously, we developed an algorithm MoonFinder for the identification of mlncRNAs at the genome level based on the functional annotation and interactome data of lncRNAs and proteins. Here, we update MoonFinder to MoonFinder v2.0 by providing an extensive framework for the detection of protein modules and the establishment of RNA-module associations in human. A novel measure, moonlighting coefficient, was also proposed to assess the confidence of an ncRNA acting in a moonlighting manner. Moreover, we explored the expression characteristics of mlncRNAs in sepsis, in which we found that mlncRNAs tend to be upregulated and differentially expressed. Interestingly, the mlncRNAs are mutually exclusive in terms of coexpression when compared to the other lncRNAs. Overall, MoonFinder v2.0 is dedicated to the prediction of human mlncRNAs and thus bears great promise to serve as a valuable R package for worldwide research communities (https://cran.r-project.org/web/packages/MoonFinder/index.html). Also, our analyses provide the first attempt to characterize mlncRNA expression and coexpression properties in adult sepsis patients, which will facilitate the understanding of the interaction and expression patterns of mlncRNAs.

meGPS: a multi-omics signature for hepatocellular carcinoma detection integrating methylome and transcriptome data.

MOTIVATION: Hepatocellular carcinoma (HCC) is a primary malignancy with a poor prognosis. Recently, multi-omics molecular-level measurement enables HCC diagnosis and prognosis prediction, which is crucial for early intervention of personalized therapy to diminish mortality. Here, we introduce a novel strategy utilizing DNA methylation and RNA expression data to achieve a multi-omics gene pair signature (GPS) for HCC discrimination. RESULTS: The immune genes with negative correlations between expression and promoter methylation are enriched in the highly connected cancer-related pathway network, which are considered as the candidates for HCC detection. After that, we separately construct a methylation GPS (mGPS) and an expression GPS (eGPS), and then assemble them as a meGPS with five gene pairs, in which the significant methylation and expression changes occur between HCC tumor and non-tumor groups. Reliable performance has been validated by independent tissue (age, gender and etiology) and blood datasets. This study proposes a procedure for multi-omics GPS identification and develops a novel HCC signature using both methylome and transcriptome data, suggesting potential molecular targets for the detection and therapy of HCC. AVAILABILITY AND IMPLEMENTATION: Models are available at https://github.com/bioinformaticStudy/meGPS.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

5-Methylcytosine-related lncRNAs: predicting prognosis and identifying hot and cold tumor subtypes in head and neck squamous cell carcinoma.

BACKGROUND: 5-Methylcytosine (m5C) methylation is recognized as an mRNA modification that participates in biological progression by regulating related lncRNAs. In this research, we explored the relationship between m5C-related lncRNAs (mrlncRNAs) and head and neck squamous cell carcinoma (HNSCC) to establish a predictive model. METHODS: RNA sequencing and related information were obtained from the TCGA database, and patients were divided into two sets to establish and verify the risk model while identifying prognostic mrlncRNAs. Areas under the ROC curves were assessed to evaluate the predictive effectiveness, and a predictive nomogram was constructed for further prediction. Subsequently, the tumor mutation burden (TMB), stemness, functional enrichment analysis, tumor microenvironment, and immunotherapeutic and chemotherapeutic responses were also assessed based on this novel risk model. Moreover, patients were regrouped into subtypes according to the expression of model mrlncRNAs. RESULTS: Assessed by the predictive risk model, patients were distinguished into the low-MLRS and high-MLRS groups, showing satisfactory predictive effects with AUCs of 0.673, 0.712, and 0.681 for the ROCs, respectively. Patients in the low-MLRS groups exhibited better survival status, lower mutated frequency, and lower stemness but were more sensitive to immunotherapeutic response, whereas the high-MLRS group appeared to have higher sensitivity to chemotherapy. Subsequently, patients were regrouped into two clusters: cluster 1 displayed immunosuppressive status, but cluster 2 behaved as a hot tumor with a better immunotherapeutic response. CONCLUSIONS: Referring to the above results, we established a m5C-related lncRNA model to evaluate the prognosis, TME, TMB, and clinical treatments for HNSCC patients. This novel assessment system is able to precisely predict the patients' prognosis and identify hot and cold tumor subtypes clearly for HNSCC patients, providing ideas for clinical treatment.

Systematic prediction of autophagy-related proteins using Arabidopsis thaliana interactome data.

Autophagy is a self-degradative process that is crucial for maintaining cellular homeostasis by removing damaged cytoplasmic components and recycling nutrients. Such an evolutionary conserved proteolysis process is regulated by the autophagy-related (Atg) proteins. The incomplete understanding of plant autophagy proteome and the importance of a proteome-wide understanding of the autophagy pathway prompted us to predict Atg proteins and regulators in Arabidopsis. Here, we developed a systems-level algorithm to identify autophagy-related modules (ARMs) based on protein subcellular localization, protein-protein interactions, and known Atg proteins. This generates a detailed landscape of the autophagic modules in Arabidopsis. We found that the newly identified genes in each ARM tend to be upregulated and coexpressed during the senescence stage of Arabidopsis. We also demonstrated that the Golgi apparatus ARM, ARM13, functions in the autophagy process by module clustering and functional analysis. To verify the in silico analysis, the Atg candidates in ARM13 that are functionally similar to the core Atg proteins were selected for experimental validation. Interestingly, two of the previously uncharacterized proteins identified from the ARM analysis, AGD1 and Sec14, exhibited bona fide association with the autophagy protein complex in plant cells, which provides evidence for a cross-talk between intracellular pathways and autophagy. Thus, the computational framework has facilitated the identification and characterization of plant-specific autophagy-related proteins and novel autophagy proteins/regulators in higher eukaryotes.

RST1 Is a FREE1 Suppressor That Negatively Regulates Vacuolar Trafficking in Arabidopsis.

FYVE domain protein required for endosomal sorting1 (FREE1), a plant-specific endosomal sorting complex required for transport-I component, is essential for the biogenesis of multivesicular bodies (MVBs), vacuolar degradation of membrane protein, cargo vacuolar sorting, autophagic degradation, and vacuole biogenesis in Arabidopsis (Arabidopsis thaliana). Here, we report the characterization of RESURRECTION1 (RST1) as a suppressor of free1 that, when mutated as a null mutant, restores the normal MVB and vacuole formation of a FREE1-RNAi knockdown line and consequently allows survival. RST1 encodes an evolutionarily conserved multicellular organism-specific protein, which contains two Domain of Unknown Function 3730 domains, showing no similarity to known proteins, and predominantly localizes in the cytosol. The depletion of FREE1 causes substantial accumulation of RST1, and transgenic Arabidopsis plants overexpressing RST1 display retarded seedling growth with dilated MVBs, and inhibition of endocytosed FM4-64 dye to the tonoplast, suggesting that RST1 has a negative role in vacuolar transport. Consistently, enhanced endocytic degradation of membrane vacuolar cargoes occurs in the rst1 mutant. Further transcriptomic comparison of rst1 with free1 revealed a negative association between gene expression profiles, demonstrating that FREE1 and RST1 have antagonistic functions. Thus, RST1 is a negative regulator controlling membrane protein homeostasis and FREE1-mediated functions in plants.

Identification of cuproptosis-related subtypes and characterization of the tumor microenvironment landscape in head and neck squamous cell carcinoma.

BACKGROUND: Cuproptosis is considered a novel copper-dependent cell death model. In this study, we established a novel scoring system based on 10 cuproptosis-related genes (CRGs) to predict the prognosis and immune landscape of head and neck squamous cell carcinoma (HNSCC). METHODS: The RNA-seq data of HNSCC patients were downloaded from the GEO and TCGA databases and were merged into a novel HNSCC cohort. Multiomics landscape analyses were conducted, including tumor mutation burden (TMB), copy number variations and the interaction network of CRGs. Patients were then divided into different cuproptosis subtypes based on the expression of 10 CRGs and subsequently regrouped into novel gene clusters referring to differentially expressed genes. A cuproptosis score (CS) system was established using principal component analysis. The CIBERSORT, ssGSEA and ESTIMATE algorithms were used to assess the tumor immune microenvironment. Moreover, the immunotherapeutic and chemotherapeutic responses were assessed. RESULTS: Patients were divided into three cuproptosis subtypes and subsequently regrouped into three gene clusters, reflecting different immune infiltration. Assessed by the CS system, those with higher CSs exhibited worse prognosis and higher TMB frequency. Nevertheless, the immune-related analysis revealed patients in the low-CS group appeared immunosuppressive and easily suffered from immune escape. High CSs possibly show high expression of immune checkpoint genes and enhance chemotherapy sensitivity to cisplatin, docetaxel, and gemcitabine. CONCLUSION: We established a novel scoring system to predict the prognosis and immune landscape of HNSCC patients. This signature exhibits satisfactory predictive effects and the potential to guide comprehensive treatment for patients.