High-performance deep learning pipeline predicts individuals in mixtures of DNA using sequencing data.

In this study, we proposed a deep learning (DL) model for classifying individuals from mixtures of DNA samples using 27 short tandem repeats and 94 single nucleotide polymorphisms obtained through massively parallel sequencing protocol. The model was trained/tested/validated with sequenced data from 6 individuals and then evaluated using mixtures from forensic DNA samples. The model successfully identified both the major and the minor contributors with 100% accuracy for 90 DNA mixtures, that were manually prepared by mixing sequence reads of 3 individuals at different ratios. Furthermore, the model identified 100% of the major contributors and 50-80% of the minor contributors in 20 two-sample external-mixed-samples at ratios of 1:39 and 1:9, respectively. To further demonstrate the versatility and applicability of the pipeline, we tested it on whole exome sequence data to classify subtypes of 20 breast cancer patients and achieved an area under curve of 0.85. Overall, we present, for the first time, a complete pipeline, including sequencing data processing steps and DL steps, that is applicable across different NGS platforms. We also introduced a sliding window approach, to overcome the sequence length variation problem of sequencing data, and demonstrate that it improves the model performance dramatically.

Prevalence of Tumor Genomic Alterations in Homologous Recombination Repair Genes Among Taiwanese Breast Cancers.

PURPOSE: Deleterious germline BRCA1/2 mutations are among the most highly pathogenic variants in hereditary breast and ovarian cancer syndrome. Recently, genes implicated in homologous recombination repair (HRR) pathways have been investigated extensively. Defective HRR genes may indicate potential clinical benefits from PARP (poly ADP ribose polymerase) inhibitors beyond BRCA1/2 mutations. METHODS: We evaluated the prevalence of BRCA1/2 mutations as well as alterations in HRR genes with targeted sequencing. A total of 648 consecutive breast cancer samples were assayed, and HRR genes were evaluated for prevalence in breast cancer tissues. RESULTS: Among 648 breast cancers, there were 17 truncating and 2 missense mutations in BRCA1 and 45 truncating and 1 missense mutation in BRCA2, impacting 3% and 5% of the study population (collectively altered in 6%) with cooccurrence of BRCA1/2 in 7 breast cancers. On the other hand, HRR genes were altered in 122 (19%) breast cancers, while TBB (Talazoparib Beyond BRCA) trial-interrogated genes (excluding BRCA1/2) were mutated in 107 (17%) patients. Beyond BRCA1/2, the most prevalent HRR mutant genes came from ARID1A (7%), PALB2 (7%), and PTEN (6%). Collectively, 164 (25%) of the 648 Taiwanese breast cancer samples harbored at least one mutation among HRR genes. CONCLUSIONS: The prevalence of BRCA1/2 mutations was far below one tenth, while the prevalence of HRR mutations was much higher and approached one-fourth among Taiwanese breast cancers. Further opportunities to take advantage of defective HRR genes for breast cancer treatment should be sought for the realization of precision medicine.

Comprehensive Analysis of Prognostic and Genetic Signatures for General Transcription Factor III (GTF3) in Clinical Colorectal Cancer Patients Using Bioinformatics Approaches.

Colorectal cancer (CRC) has the fourth-highest incidence of all cancer types, and its incidence has steadily increased in the last decade. The general transcription factor III (GTF3) family, comprising GTF3A, GTF3B, GTF3C1, and GTFC2, were stated to be linked with the expansion of different types of cancers; however, their messenger (m)RNA expressions and prognostic values in colorectal cancer need to be further investigated. To study the transcriptomic expression levels of GTF3 gene members in colorectal cancer in both cancerous tissues and cell lines, we first performed high-throughput screening using the Oncomine, GEPIA, and CCLE databases. We then applied the Prognoscan database to query correlations of their mRNA expressions with the disease-specific survival (DSS), overall survival (OS), and disease-free survival (DFS) status of the colorectal cancer patient. Furthermore, proteomics expressions of GTF3 family members in clinical colorectal cancer specimens were also examined using the Human Protein Atlas. Finally, genomic alterations of GTF3 family gene expressions in colorectal cancer and their signal transduction pathways were studied using cBioPortal, ClueGO, CluePedia, and MetaCore platform. Our findings revealed that GTF3 family members' expressions were significantly correlated with the cell cycle, oxidative stress, WNT/ß-catenin signaling, Rho GTPases, and G-protein-coupled receptors (GPCRs). Clinically, high GTF3A and GTF3B expressions were significantly correlated with poor prognoses in colorectal cancer patients. Collectively, our study declares that GTF3A was overexpressed in cancer tissues and cell lines, particularly colorectal cancer, and it could possibly step in as a potential prognostic biomarker.

Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection induces dysregulation of immunity: in silico gene expression analysis.

Highly pathogenic coronaviruses (CoVs) induce acute respiratory distress syndrome, and the severe acute respiratory syndrome coronavirus (SARS-CoV)-2 has caused a pandemic since late 2019. The diversity of clinical manifestations after SARS-CoV-2 infection results in great challenges to diagnose CoV disease 2019 (COVID-19). There is a growing body of published research on this topic; however, effective medications are still undergoing a long process of being assessed. In the search for potential genetic targets for this infection, we applied a holistic bioinformatics approach to study alterations of gene signatures between SARS-CoV-2-infected cells and mock-infected controls. Two different kinds of lung epithelial cells, A549 with angiotensin-converting enzyme 2 (ACE2) overexpression and normal human bronchial epithelial (NHBE) cells, were infected with SARS-CoV-2. We performed bioinformatics analyses of RNA-sequencing in this study. Through a Venn diagram, Database for Annotation, Visualization and Integrated Discovery, Gene Ontology, Ingenuity Pathway Analysis, and Gene Set Enrichment Analysis, the pathways and networks were constructed from commonly upregulated genes in SARS-CoV-2-infected lung epithelial cells. Genes associated with immune-related pathways, responses of host cells after intracellular infection, steroid hormone biosynthesis, receptor signaling, and the complement system were enriched. Dysregulation of the immune system and malfunction of interferon contribute to a failure to kill SARS-CoV-2 and exacerbate respiratory distress in severely ill patients. Current findings from this study provide a comprehensive investigation of SARS-CoV-2 infection using high-throughput technology.

Upregulation of peroxisome proliferator-activated receptor-α and the lipid metabolism pathway promotes carcinogenesis of ampullary cancer.

Ampullary cancer is a rare periampullary cancer currently with no targeted therapeutic agent. It is important to develop a deeper understanding of the carcinogenesis of ampullary cancer. We attempted to explore the characteristics of ampullary cancer in our dataset and a public database, followed by a search for potential drugs. We used a bioinformatics pipeline to analyze complementary (c)DNA microarray data of ampullary cancer and surrounding normal duodenal tissues from five patients. A public database from the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO) was applied for external validation. Bioinformatics tools used included the Gene Set Enrichment Analysis (GSEA), Database for Annotation, Visualization and Integrated Discovery (DAVID), MetaCore, Kyoto Encyclopedia of Genes and Genomes (KEGG), Hallmark, BioCarta, Reactome, and Connectivity Map (CMap). In total, 9097 genes were upregulated in the five ampullary cancer samples compared to normal duodenal tissues. From the MetaCore analysis, genes of peroxisome proliferator-activated receptor alpha (PPARA) and retinoid X receptor (RXR)-regulated lipid metabolism were overexpressed in ampullary cancer tissues. Further a GSEA of the KEGG, Hallmark, Reactome, and Gene Ontology databases revealed that PPARA and lipid metabolism-related genes were enriched in our specimens of ampullary cancer and in the NCBI GSE39409 database. Expressions of PPARA messenger (m)RNA and the PPAR-α protein were higher in clinical samples and cell lines of ampullary cancer. US Food and Drug Administration (FDA)-approved drugs, including alvespimycin, trichostatin A (a histone deacetylase inhibitor), and cytochalasin B, may have novel therapeutic effects in ampullary cancer patients as predicted by the CMap analysis. Trichostatin A was the most potent agent for ampullary cancer with a half maximal inhibitory concentration of < 0.3 µM. According to our results, upregulation of PPARA and lipid metabolism-related genes are potential pathways in the carcinogenesis and development of ampullary cancer. Results from the CMap analysis suggested potential drugs for patients with ampullary cancer.

Gene signatures and prognostic analyses of the Tob/BTG pituitary tumor-transforming gene (PTTG) family in clinical breast cancer patients.

Breast cancer is the most common cancer type in females, and exploring the mechanisms of disease progression is playing a crucial role in the development of potential therapeutics. Pituitary tumor-transforming gene (PTTG) family members are well documented to be involved in cell-cycle regulation and mitosis, and contribute to cancer development by their involvement in cellular transformation in several tumor types. The critical roles of PTTG family members as crucial transcription factors in diverse types of cancers are recognized, but how they regulate breast cancer development still remains mostly unknown. Meanwhile, a holistic genetic analysis exploring whether PTTG family members regulate breast cancer progression via the cell cycle as well as the energy metabolism-related network is lacking. To comprehensively understand the messenger RNA expression profiles of PTTG proteins in breast cancer, we herein conducted a high-throughput screening approach by integrating information from various databases such as Oncomine, Kaplan-Meier Plotter, Metacore, ClueGo, and CluePedia. These useful databases and tools provide expression profiles and functional analyses. The present findings revealed that PTTG1 and PTTG3 are two important genes with high expressions in breast cancer relative to normal breast cells, implying their unique roles in breast cancer progression. Results of our coexpression analysis demonstrated that PTTG family genes were positively correlated with thiamine triphosphate (TTP), deoxycytidine triphosphate (dCTP) metabolic, glycolysis, gluconeogenesis, and cell-cycle related pathways. Meanwhile, through Cytoscape analyzed indicated that in addition to the metastasis markers AURKA, AURKB, and NDC80, many of the kinesin superfamily (KIF) members including KIFC1, KIF2C, KIF4A, KIF14, KIF20A, KIF23, were also correlated with PTTG family transcript expression. Finally, we revealed that high levels of PTTG1 and PTTG3 transcription predicted poor survival, which provided useful insights into prospective research of cancer associated with the PTTG family. Therefore, these members of the PTTG family would serve as distinct and essential prognostic biomarkers in breast cancer.

PODXL2 maintains cellular stemness and promotes breast cancer development through the Rac1/Akt pathway.

The cluster of differentiation 34 (CD34) family, which includes CD34, podocalyxin-like protein 1 (PODXL), and PODXL2, are type-I transmembrane sialomucins and markers of hematopoietic stem cells (HSCs) and vascular-associated tissues. CD34 family proteins are expressed by endothelial cells and hematopoietic precursors. PODXL is well known to be associated with invadopodia formation and to promote the epithelial-mesenchymal transition, tumor migration and invasion. PODXL expression was correlated with poor survival of cancer patients. However, the role of PODXL2 in cancer has been less fully explored. To reveal the novel role of PODXL2 in breast cancer, the present study evaluated PODXL2 levels in relation to clinical outcomes of cancer patients by performing a bioinformatics analysis using the Oncomine database, Kaplan-Meier plots, and the CCLE database. Empirical validation of bioinformatics predictions was conducted utilizing the short hairpin (sh)-RNA silencing method for PODXL2 in the BT474 invasive ductal breast carcinoma cell line. The bioinformatics analysis revealed that PODXL2 overexpression was correlated with poor survival of breast cancer patients, suggesting an oncogenic role of PODXL2 in breast carcinoma. In a validation experiment, knockdown of PODXL2 in BT474 cells slightly influenced cell proliferation, suppressed migration, and inhibited expressions of downstream molecules, including Ras-related C3 botulinum toxin substrate 1 (Rac1), phosphorylated (p)-Akt (S473), and p-paxillin (Y31) proteins. In addition, knockdown of PODXL2 reduced expression levels of cancer stem cell (CSC) markers, including Oct-4 and Nanog, and the breast CSC marker aldehyde dehydrogenase 1 (ALDH1). Collectively, our present study demonstrated that PODXL2 plays a crucial role in cancer development and could serve as a potential prognostic biomarker in breast cancer patients.

Arsenic induces cardiac rhythm dysfunction and acylcarnitines metabolism perturbation in rats.

BACKGROUND: Arsenic has been shown to cause various diseases (such as blackfoot disease, cardiovascular diseases, bladder cancer and skin cancer) in many areas of the world. However, the effects of arsenic on cardiac rhythm functions still lack investigation. METHODS: In this study, different concentrations of arsenic were orally applied to Sprague Dawley rats in order to examine the relationship between arsenic and cardiovascular rhythm (i.e. long QT) via electrocardiography measurement. In addition, QT correction formulas were used to correct the QT interval. Linear regression analysis was used to examine the correlation between the QT interval and cardiac cycle length, corrected QT and heart rate. A metabolomic approach was applied to study carnitine-derived metabolites under arsenic exposure by using an ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF MS) system. RESULTS: The present findings showed that exposure to arsenic causes QT and corrected (QTc) prolongation and heart rate declines. However, the linear correlation analysis showed that there is no significant correlation between cardiac cycle length and the QT interval in both the uncorrected QT and corrected QT. The expression of acylcarnitine metabolites can be used to discriminate the control and arsenic-treated groups. CONCLUSIONS: This study provides information concerning the effect of arsenic at different concentrations on cardiac rhythm (such as QT, QTc, and heart rate) but not on cardiac cycle length. The metabolism of acylcarnitine metabolites can be a potential pathway for arsenic-induced cardiac rhythm dysfunction in rats.

Utilizing multimodal approach to identify candidate pathways and biomarkers and predicting frailty syndrome in individuals from UK Biobank.

Frailty, a prevalent clinical syndrome in aging adults, is characterized by poor health outcomes, represented via a standardized frailty-phenotype (FP), and Frailty Index (FI). While the relevance of the syndrome is gaining awareness, much remains unclear about its underlying biology. Further elucidation of the genetic determinants and possible underlying mechanisms may help improve patients' outcomes allowing healthy aging.Genotype, clinical and demographic data of subjects (aged 60-73 years) from UK Biobank were utilized. FP was defined on Fried's criteria. FI was calculated using electronic-health-records. Genome-wide-association-studies (GWAS) were conducted and polygenic-risk-scores (PRS) were calculated for both FP and FI. Functional analysis provided interpretations of underlying biology. Finally, machine-learning (ML) models were trained using clinical, demographic and PRS towards identifying frail from non-frail individuals.Thirty-one loci were significantly associated with FI accounting for 12% heritability. Seventeen of those were known associations for body-mass-index, coronary diseases, cholesterol-levels, and longevity, while the rest were novel. Significant genes CDKN2B and APOE, previously implicated in aging, were reported to be enriched in lipoprotein-particle-remodeling. Linkage-disequilibrium-regression identified specific regulation in limbic-system, associated with long-term memory and cognitive-function. XGboost was established as the best performing ML model with area-under-curve as 85%, sensitivity and specificity as 0.75 and 0.8, respectively.This study provides novel insights into increased vulnerability and risk stratification of frailty syndrome via a multi-modal approach. The findings suggest frailty as a highly polygenic-trait, enriched in cholesterol-remodeling and metabolism and to be genetically associated with cognitive abilities. ML models utilizing FP and FI + PRS were established that identified frailty-syndrome patients with high accuracy.

Deep Learning Empowers Endoscopic Detection and Polyps Classification: A Multiple-Hospital Study.

The present study aimed to develop an AI-based system for the detection and classification of polyps using colonoscopy images. A total of about 256,220 colonoscopy images from 5000 colorectal cancer patients were collected and processed. We used the CNN model for polyp detection and the EfficientNet-b0 model for polyp classification. Data were partitioned into training, validation and testing sets, with a 70%, 15% and 15% ratio, respectively. After the model was trained/validated/tested, to evaluate its performance rigorously, we conducted a further external validation using both prospective (n = 150) and retrospective (n = 385) approaches for data collection from 3 hospitals. The deep learning model performance with the testing set reached a state-of-the-art sensitivity and specificity of 0.9709 (95% CI: 0.9646-0.9757) and 0.9701 (95% CI: 0.9663-0.9749), respectively, for polyp detection. The polyp classification model attained an AUC of 0.9989 (95% CI: 0.9954-1.00). The external validation from 3 hospital results achieved 0.9516 (95% CI: 0.9295-0.9670) with the lesion-based sensitivity and a frame-based specificity of 0.9720 (95% CI: 0.9713-0.9726) for polyp detection. The model achieved an AUC of 0.9521 (95% CI: 0.9308-0.9734) for polyp classification. The high-performance, deep-learning-based system could be used in clinical practice to facilitate rapid, efficient and reliable decisions by physicians and endoscopists.

Prediction of Breast Cancer Recurrence Using a Deep Convolutional Neural Network Without Region-of-Interest Labeling.

PURPOSE: The present study aimed to assign a risk score for breast cancer recurrence based on pathological whole slide images (WSIs) using a deep learning model. METHODS: A total of 233 WSIs from 138 breast cancer patients were assigned either a low-risk or a high-risk score based on a 70-gene signature. These images were processed into patches of 512x512 pixels by the PyHIST tool and underwent color normalization using the Macenko method. Afterward, out of focus and pixelated patches were removed using the Laplacian algorithm. Finally, the remaining patches (n=294,562) were split into 3 parts for model training (50%), validation (7%) and testing (43%). We used 6 pretrained models for transfer learning and evaluated their performance using accuracy, precision, recall, F1 score, confusion matrix, and AUC. Additionally, to demonstrate the robustness of the final model and its generalization capacity, the testing set was used for model evaluation. Finally, the GRAD-CAM algorithm was used for model visualization. RESULTS: Six models, namely VGG16, ResNet50, ResNet101, Inception_ResNet, EfficientB5, and Xception, achieved high performance in the validation set with an overall accuracy of 0.84, 0.85, 0.83, 0.84, 0.87, and 0.91, respectively. We selected Xception for assessment of the testing set, and this model achieved an overall accuracy of 0.87 with a patch-wise approach and 0.90 and 1.00 with a patient-wise approach for high-risk and low-risk groups, respectively. CONCLUSIONS: Our study demonstrated the feasibility and high performance of artificial intelligence models trained without region-of-interest labeling for predicting cancer recurrence based on a 70-gene signature risk score.

Predicting Breast Cancer Gene Expression Signature by Applying Deep Convolutional Neural Networks From Unannotated Pathological Images.

We proposed a highly versatile two-step transfer learning pipeline for predicting the gene signature defining the intrinsic breast cancer subtypes using unannotated pathological images. Deciphering breast cancer molecular subtypes by deep learning approaches could provide a convenient and efficient method for the diagnosis of breast cancer patients. It could reduce costs associated with transcriptional profiling and subtyping discrepancy between IHC assays and mRNA expression. Four pretrained models such as VGG16, ResNet50, ResNet101, and Xception were trained with our in-house pathological images from breast cancer patient with recurrent status in the first transfer learning step and TCGA-BRCA dataset for the second transfer learning step. Furthermore, we also trained ResNet101 model with weight from ImageNet for comparison to the aforementioned models. The two-step deep learning models showed promising classification results of the four breast cancer intrinsic subtypes with accuracy ranging from 0.68 (ResNet50) to 0.78 (ResNet101) in both validation and testing sets. Additionally, the overall accuracy of slide-wise prediction showed even higher average accuracy of 0.913 with ResNet101 model. The micro- and macro-average area under the curve (AUC) for these models ranged from 0.88 (ResNet50) to 0.94 (ResNet101), whereas ResNet101_imgnet weighted with ImageNet archived an AUC of 0.92. We also show the deep learning model prediction performance is significantly improved relatively to the common Genefu tool for breast cancer classification. Our study demonstrated the capability of deep learning models to classify breast cancer intrinsic subtypes without the region of interest annotation, which will facilitate the clinical applicability of the proposed models.

Prognoses and genomic analyses of proteasome 26S subunit, ATPase (PSMC) family genes in clinical breast cancer.

Breast cancer is a complex disease, and several processes are involved in its development. Therefore, potential therapeutic targets need to be discovered for these patients. Proteasome 26S subunit, ATPase gene (PSMC) family members are well reported to be involved in protein degradation. However, their roles in breast cancer are still unknown and need to be comprehensively researched. Leveraging publicly available databases, such as cBioPortal and Oncomine, for high-throughput transcriptomic profiling to provide evidence-based targets for breast cancer is a rapid and robust approach. By integrating the aforementioned databases with the Kaplan-Meier plotter database, we investigated potential roles of six PSMC family members in breast cancer at the messenger RNA level and their correlations with patient survival. The present findings showed significantly higher expression profiles of PSMC2, PSMC3, PSMC4, PSMC5, and PSMC6 in breast cancer compared to normal breast tissues. Besides, positive correlations were also revealed between PSMC family genes and ubiquinone metabolism, cell cycle, and cytoskeletal remodeling. Meanwhile, we discovered that high levels of PSMC1, PSMC3, PSMC4, PSMC5, and PSMC6 transcripts were positively correlated with poor survival, which likely shows their importance in breast cancer development. Collectively, PSMC family members have the potential to be novel and essential prognostic biomarkers for breast cancer development.

Molecular subtyping of breast cancer intrinsic taxonomy with oligonucleotide microarray and NanoString nCounter.

Breast cancer intrinsic subtypes have been identified based on the transcription of a predefined gene expression (GE) profiles and algorithm (prediction analysis of microarray 50 gene set, PAM50). The present study compared molecular subtyping with oligonucleotide microarray and NanoString nCounter assay. A total of 109 Taiwanese breast cancers (24 with adjacent normal breast tissues) were assayed with Affymetrix Human Genome U133 plus 2.0 microarrays and 144 were assayed with the NanoString nCounter while 64 patients were assayed for both platforms. Subtyping with the nearest centroid (single sample prediction (SSP)) was performed, and 16 out of 24 (67%) matched normal breasts were categorized as the normal breast-like subtype. For 64 breast cancers assayed for both platforms, 41 (65%, one unclassified by microarray) were predicted with an identical subtype, resulting in a fair κ statistic of 0.60. Taking nCounter subtyping as the gold standard, prediction accuracy was 43% (3/7), 81% (13/16), 25% (5/20), and 100% (20/20) for basal-like, human epidermal growth factor receptor II (HER2)-enriched, luminal A and luminal B subtypes predicted from microarray GE profiles. Microarray identified more luminal B cases from luminal A subtype predicted by nCounter. It is not uncommon to use microarray for breast cancer molecular subtyping for research. Our study showed that fundamental discrepancy existed between distinct GE assays, and cross-platform equivalence should be carefully appraised when molecular subtyping was conducted with oligonucleotide microarray.

Potential Therapeutic and Prognostic Values of LSM Family Genes in Breast Cancer.

In recent decades, breast cancer (BRCA) has become one of the most common diseases worldwide. Understanding crucial genes and their signaling pathways remain an enormous challenge in evaluating the prognosis and possible therapeutics. The "Like-Smith" (LSM) family is known as protein-coding genes, and its member play pivotal roles in the progression of several malignancies, although their roles in BRCA are less clear. To discover biological processes associated with LSM family genes in BRCA development, high-throughput techniques were applied to clarify expression levels of LSMs in The Cancer Genome Atlas (TCGA)-BRCA dataset, which was integrated with the cBioPortal database. Furthermore, we investigated prognostic values of LSM family genes in BCRA patients using the Kaplan-Meier database. Among genes of this family, LSM4 expression levels were highly associated with poor prognostic outcomes with a hazard ratio of 1.35 (95% confidence interval 1.21-1.51, p for trend = 3.4 × 10-7). MetaCore and GlueGo analyses were also conducted to examine transcript expression signatures of LSM family members and their coexpressed genes, together with their associated signaling pathways, such as "Cell cycle role of APC in cell cycle regulation" and "Immune response IL-15 signaling via MAPK and PI3K cascade" in BRCA. Results showed that LSM family members, specifically LSM4, were significantly correlated with oncogenesis in BRCA patients. In summary, our results suggested that LSM4 could be a prospective prognosticator of BRCA.

Gene signatures and potential therapeutic targets of Middle East respiratory syndrome coronavirus (MERS-CoV)-infected human lung adenocarcinoma epithelial cells.

BACKGROUND: Pathogenic coronaviruses include Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), and SARS-CoV-2. These viruses have induced outbreaks worldwide, and there are currently no effective medications against them. Therefore, there is an urgent need to develop potential drugs against coronaviruses. METHODS: High-throughput technology is widely used to explore differences in messenger (m)RNA and micro (mi)RNA expression profiles, especially to investigate protein-protein interactions and search for new therapeutic compounds. We integrated miRNA and mRNA expression profiles in MERS-CoV-infected cells and compared them to mock-infected controls from public databases. RESULTS: Through the bioinformatics analysis, there were 251 upregulated genes and eight highly differentiated miRNAs that overlapped in the two datasets. External validation verified that these genes had high expression in MERS-CoV-infected cells, including RC3H1, NF-κB, CD69, TNFAIP3, LEAP-2, DUSP10, CREB5, CXCL2, etc. We revealed that immune, olfactory or sensory system-related, and signal-transduction networks were discovered from upregulated mRNAs in MERS-CoV-infected cells. In total, 115 genes were predicted to be related to miRNAs, with the intersection of upregulated mRNAs and miRNA-targeting prediction genes such as TCF4, NR3C1, and POU2F2. Through the Connectivity Map (CMap) platform, we suggested potential compounds to use against MERS-CoV infection, including diethylcarbamazine, harpagoside, bumetanide, enalapril, and valproic acid. CONCLUSIONS: The present study illustrates the crucial roles of miRNA-mRNA interacting networks in MERS-CoV-infected cells. The genes we identified are potential targets for treating MERS-CoV infection; however, these could possibly be extended to other coronavirus infections.

Identification of Dipeptidyl Peptidase (DPP) Family Genes in Clinical Breast Cancer Patients via an Integrated Bioinformatics Approach.

Breast cancer is a heterogeneous disease involving complex interactions of biological processes; thus, it is important to develop therapeutic biomarkers for treatment. Members of the dipeptidyl peptidase (DPP) family are metalloproteases that specifically cleave dipeptides. This family comprises seven members, including DPP3, DPP4, DPP6, DPP7, DPP8, DPP9, and DPP10; however, information on the involvement of DPPs in breast cancer is lacking in the literature. As such, we aimed to study their roles in this cancerous disease using publicly available databases such as cBioportal, Oncomine, and Kaplan-Meier Plotter. These databases comprise comprehensive high-throughput transcriptomic profiles of breast cancer across multiple datasets. Furthermore, together with investigating the messenger RNA expression levels of these genes, we also aimed to correlate these expression levels with breast cancer patient survival. The results showed that DPP3 and DPP9 had significantly high expression profiles in breast cancer tissues relative to normal breast tissues. High expression levels of DPP3 and DPP4 were associated with poor survival of breast cancer patients, whereas high expression levels of DPP6, DPP7, DPP8, and DPP9 were associated with good prognoses. Additionally, positive correlations were also revealed of DPP family genes with the cell cycle, transforming growth factor (TGF)-beta, kappa-type opioid receptor, and immune response signaling, such as interleukin (IL)-4, IL6, IL-17, tumor necrosis factor (TNF), and interferon (IFN)-alpha/beta. Collectively, DPP family members, especially DPP3, may serve as essential prognostic biomarkers in breast cancer.

Analysis of LAGEs Family Gene Signature and Prognostic Relevance in Breast Cancer.

Breast cancer (BRCA) is one of the most complex diseases and involves several biological processes. Members of the L-antigen (LAGE) family participate in the development of various cancers, but their expressions and prognostic values in breast cancer remain to be clarified. High-throughput methods for exploring disease progression mechanisms might play a pivotal role in the improvement of novel therapeutics. Therefore, gene expression profiles and clinical data of LAGE family members were acquired from the cBioportal database, followed by verification using the Oncomine and The Cancer Genome Atlas (TCGA) databases. In addition, the Kaplan-Meier method was applied to explore correlations between expressions of LAGE family members and prognoses of breast cancer patients. MetaCore, GlueGo, and GluePedia were used to comprehensively study the transcript expression signatures of LAGEs and their co-expressed genes together with LAGE-related signal transduction pathways in BRCA. The result indicated that higher LAGE3 messenger (m)RNA expressions were observed in BRCA tissues than in normal tissues, and they were also associated with the stage of BRCA patients. Kaplan-Meier plots showed that overexpression of LAGE1, LAGE2A, LAGE2B, and LAGE3 were highly correlated to poor survival in most types of breast cancer. Significant associations of LAGE family genes were correlated with the cell cycle, focal adhesion, and extracellular matrix (ECM) receptor interactions as indicated by functional enrichment analyses. Collectively, LAGE family members' gene expression levels were related to adverse clinicopathological factors and prognoses of BRCA patients; therefore, LAGEs have the potential to serve as prognosticators of BRCA patients.

Novel signaling pathways regulate SARS-CoV and SARS-CoV-2 infectious disease.

ABSTRACT: Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 induces severe infection, and it is responsible for a worldwide disease outbreak starting in late 2019. Currently, there are no effective medications against coronavirus. In the present study, we utilized a holistic bioinformatics approach to study gene signatures of SARS-CoV- and SARS-CoV-2-infected Calu-3 lung adenocarcinoma cells. Through the Gene Ontology platform, we determined that several cytokine genes were up-regulated after SARS-CoV-2 infection, including TNF, IL6, CSF2, IFNL1, IL-17C, CXCL10, and CXCL11. Differentially regulated pathways were detected by the Kyoto Encyclopedia of Genes and Genomes, gene ontology, and Hallmark platform, including chemokines, cytokines, cytokine receptors, cytokine metabolism, inflammation, immune responses, and cellular responses to the virus. A Venn diagram was utilized to illustrate common overlapping genes from SARS-CoV- and SARS-CoV-2-infected datasets. An Ingenuity pathway analysis discovered an enrichment of tumor necrosis factor- (TNF-) and interleukin (IL)-17-related signaling in a gene set enrichment analysis. Downstream networks were predicted by the Database for Annotation, Visualization, and Integrated Discovery platform also revealed that TNF and TNF receptor 2 signaling elicited leukocyte recruitment, activation, and survival of host cells after coronavirus infection. Our discovery provides essential evidence for transcript regulation and downstream signaling of SARS-CoV and SARS-CoV-2 infection.