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International Journal of Molecular... May 2024A common result of infection is an abnormal immune response, which may be detrimental to the host. To control the infection, the immune system might undergo regulation,...
A common result of infection is an abnormal immune response, which may be detrimental to the host. To control the infection, the immune system might undergo regulation, therefore producing an excess of either pro-inflammatory or anti-inflammatory pathways that can lead to widespread inflammation, tissue damage, and organ failure. A dysregulated immune response can manifest as changes in differentiated immune cell populations and concentrations of circulating biomarkers. To propose an early diagnostic system that enables differentiation and identifies the severity of immune-dysregulated syndromes, we built an artificial intelligence tool that uses input data from single-cell RNA sequencing. In our results, single-cell transcriptomics successfully distinguished between mild and severe sepsis and COVID-19 infections. Moreover, by interpreting the decision patterns of our classification system, we identified that different immune cells upregulating or downregulating the expression of the genes , , , , , and can accurately differentiate between different degrees of infection. Our research has identified genes of significance that effectively distinguish between infections, offering promising prospects as diagnostic markers and providing potential targets for therapeutic intervention.
Topics: Humans; COVID-19; Machine Learning; RNA-Seq; Biomarkers; SARS-CoV-2; Single-Cell Analysis; Sepsis; Transcriptome; Gene Expression Profiling; Sequence Analysis, RNA; Single-Cell Gene Expression Analysis
PubMed: 38892107
DOI: 10.3390/ijms25115920 -
International Journal of Molecular... May 2024The Epstein-Barr virus (EBV) is frequently found in endomyocardial biopsies (EMBs) from patients with heart failure, but the detection of EBV-specific DNA has not been...
The Epstein-Barr virus (EBV) is frequently found in endomyocardial biopsies (EMBs) from patients with heart failure, but the detection of EBV-specific DNA has not been associated with progressive hemodynamic deterioration. In this paper, we investigate the use of targeted next-generation sequencing (NGS) to detect EBV transcripts and their correlation with myocardial inflammation in EBV-positive patients with heart failure with reduced ejection fraction (HFrEF). Forty-four HFrEF patients with positive EBV DNA detection and varying degrees of myocardial inflammation were selected. EBV-specific transcripts from EMBs were enriched using a custom hybridization capture-based workflow and, subsequently, sequenced by NGS. The short-read sequencing revealed the presence of EBV-specific transcripts in 17 patients, of which 11 had only latent EBV genes and 6 presented with lytic transcription. The immunohistochemical staining for CD3 T lymphocytes showed a significant increase in the degree of myocardial inflammation in the presence of EBV lytic transcripts, suggesting a possible influence on the clinical course. These results imply the important role of EBV lytic transcripts in the pathogenesis of inflammatory heart disease and emphasize the applicability of targeted NGS in EMB diagnostics as a basis for specific treatment.
Topics: Humans; Herpesvirus 4, Human; Heart Failure; Male; Female; Epstein-Barr Virus Infections; Middle Aged; Myocarditis; Aged; High-Throughput Nucleotide Sequencing; Myocardium; DNA, Viral; Adult; Biopsy
PubMed: 38892033
DOI: 10.3390/ijms25115845 -
International Journal of Molecular... May 2024Negeviruses are insect-specific enveloped RNA viruses that exhibit a wide geographic distribution. A novel nege-like virus, tentatively named nege-like virus (AGNLV,...
Negeviruses are insect-specific enveloped RNA viruses that exhibit a wide geographic distribution. A novel nege-like virus, tentatively named nege-like virus (AGNLV, GenBank: OR880429.1), was isolated from aphids () in Lijiang City, Yunnan, China. AGNLV has a genome sequence of 9258 nt (excluding the polyA tail) encoding three open reading frames (ORFs). ORF1 (7149 nt) encodes a viral methyltransferase, a viral RNA helicase, and an RNA-dependent RNA polymerase. ORF2 (1422 nt) encodes a DiSB-ORF2_chro domain and ORF3 encodes an SP24 domain. The genome sequence of AGNLV shares the highest nucleotide identity of 60.0% and 59.5% with Wuhan house centipede virus 1 (WHCV1) and Astegopteryx formosana nege-like virus (AFNLV), respectively. Phylogenetic analysis based on the RNA-dependent RNA polymerase shows that AGNLV is clustered with other negeviruses and nege-like viruses discovered in aphids, forming a distinct "unclassified clade". Interestingly, AGNLV only encodes three ORFs, whereas AFNLV and WHCV1 have four ORFs. Structure and transmembrane domain predictions show the presence of eight alpha helices and five transmembrane helices in the AGNLV ORF3. Translational enhancement of the AGNLV 5' UTR was similar to that of the 5' UTR of plant viruses. Our findings provide evidence of the diversity and structure of nege-like viruses and are the first record of such a virus from a member of the genus .
Topics: Animals; Aphids; Genome, Viral; Phylogeny; Open Reading Frames; China; RNA Viruses; RNA-Dependent RNA Polymerase; Viral Proteins; Insect Viruses; RNA, Viral
PubMed: 38891989
DOI: 10.3390/ijms25115802 -
International Journal of Molecular... May 2024Information generated via next-generation sequencing (NGS) technologies is often termed multi-omics data [...].
Information generated via next-generation sequencing (NGS) technologies is often termed multi-omics data [...].
Topics: Precision Medicine; Humans; Medical Oncology; High-Throughput Nucleotide Sequencing; Neoplasms; Data Science; Genomics
PubMed: 38891982
DOI: 10.3390/ijms25115797 -
International Journal of Molecular... May 2024The tyrosine kinase domain of the FMS-Like tyrosine kinase 3 (-TKD) is recurrently mutated in acute myeloid leukemia (AML). Common molecular techniques used in its...
The tyrosine kinase domain of the FMS-Like tyrosine kinase 3 (-TKD) is recurrently mutated in acute myeloid leukemia (AML). Common molecular techniques used in its detection include PCR and capillary electrophoresis, Sanger sequencing and next-generation sequencing with recognized sensitivity limitations. This study aims to validate the use of droplet digital PCR (ddPCR) in the detection of measurable residual disease (MRD) involving the common -TKD mutations (D835Y, D835H, D835V, D835E). Twenty-two diagnostic samples, six donor controls, and a commercial D835Y positive control were tested using a commercial Bio-rad ddPCR assay. All known variants were identified, and no false positives were detected in the wild-type control (100% specificity and sensitivity). The assays achieved a limit of detection suitable for MRD testing at 0.01% variant allelic fraction. Serial samples from seven intensively-treated patients with -TKD variants at diagnosis were tested. Five patients demonstrated clearance of -TKD clones, but two patients had -TKD persistence in the context of primary refractory disease. In conclusion, ddPCR is suitable for the detection and quantification of -TKD mutations in the MRD setting; however, the clinical significance and optimal management of MRD positivity require further exploration.
Topics: Humans; fms-Like Tyrosine Kinase 3; Neoplasm, Residual; Leukemia, Myeloid, Acute; Polymerase Chain Reaction; Mutation; Female; Male; Middle Aged; Aged; Adult; High-Throughput Nucleotide Sequencing
PubMed: 38891959
DOI: 10.3390/ijms25115771 -
International Journal of Molecular... May 2024Retinitis pigmentosa (RP) is an inherited retinal dystrophy caused by the loss of photoreceptors and retinal pigment epithelial atrophy, leading to severe visual...
Retinitis pigmentosa (RP) is an inherited retinal dystrophy caused by the loss of photoreceptors and retinal pigment epithelial atrophy, leading to severe visual impairment or blindness. RP can be classified as nonsyndromic or syndromic with complex clinical phenotypes. Three unrelated Polish probands affected with retinitis pigmentosa coexisting with cerebellar ataxia were recruited for this study. Clinical heterogeneity and delayed appearance of typical disease symptoms significantly prolonged the patients' diagnostic process. Therefore, many clinical and genetic tests have been performed in the past. Here, we provide detailed clinical and genetic analysis results of the patients. Whole-exome sequencing (WES) and targeted NGS analysis allow the identification of four novel and two previously reported variants in the following genes: , , and The use of next-generation sequencing (NGS) methods finally allowed for confirmation of the clinical diagnosis. Ultra-rare diseases such as PHARC, PCARP, and Oliver-McFarlane syndromes were diagnosed in patients, respectively. Our findings confirmed the importance of the application of next-generation sequencing methods, especially in ultra-rare genetic disorders with overlapping features.
Topics: Humans; Retinitis Pigmentosa; Male; Female; Exome Sequencing; Pedigree; High-Throughput Nucleotide Sequencing; Adult; Cerebellar Ataxia; Membrane Transport Proteins; Monoacylglycerol Lipases; Mutation; Ataxia; Phenotype; Acyltransferases; Cataract; Phospholipases; Polyneuropathies
PubMed: 38891946
DOI: 10.3390/ijms25115759 -
International Journal of Molecular... May 2024Developmental and epileptic encephalopathy-9 (DEE9) is characterized by seizure onset in infancy, mild to severe intellectual impairment, and psychiatric features and is...
Developmental and epileptic encephalopathy-9 (DEE9) is characterized by seizure onset in infancy, mild to severe intellectual impairment, and psychiatric features and is caused by a mutation in the gene on chromosome Xq22. The rare, unusual X-linked type of disorder affects heterozygous females and mosaic males; transmitting males are unaffected. In our study, 165 patients with epilepsy were tested by Next Generation Sequencing (NGS)-based panel and exome sequencing using Illumina technology. screening identified three point mutations, one indel, and one 29 bp-long deletion in five unrelated female probands. Two novel mutations, c.1152_1180del (p.Gln385Serfs*6) and c.830_831delinsAA (p.Phe277*), were identified and found to be de novo pathogenic. Moreover, among the three inherited mutations, two originated from asymptomatic mothers and one from an affected father. The c.1682C>T and c.1711G>T mutations were present in the DNA samples of asymptomatic mothers. After targeted parental testing, X chromosome inactivation tests and Sanger sequencing were carried out for mosaicism examination on maternal saliva samples in the two asymptomatic mutation carrier subjects. Tissue mosaicism and X-inactivation tests were negative. Our results support the opportunity for reduced penetrance in DEE9 and contribute to expanding the genotype-phenotype spectrum of -related epilepsy.
Topics: Humans; Protocadherins; Female; Cadherins; Epilepsy; High-Throughput Nucleotide Sequencing; Mutation; Pedigree; Male; Child, Preschool; Child; Infant; Age of Onset
PubMed: 38891919
DOI: 10.3390/ijms25115732 -
Cells May 2024The identification of anticancer therapies using next-generation sequencing (NGS) is necessary for the treatment of cholangiocarcinoma. NGS can be easily performed when...
The identification of anticancer therapies using next-generation sequencing (NGS) is necessary for the treatment of cholangiocarcinoma. NGS can be easily performed when cell blocks (CB) are obtained from bile stored overnight. We compared NGS results of paired CB and surgically resected specimens (SRS) from the same cholangiocarcinoma cases. Of the prospectively collected 64 bile CBs from 2018 to 2023, NGS was performed for three cases of cholangiocarcinoma that could be compared with the SRS results. The median numbers of DNA and RNA reads were 95,077,806 [CB] vs. 93,161,788 [SRS] and 22,101,328 [CB] vs. 24,806,180 [SRS], respectively. We evaluated 588 genes and found that almost all genetic alterations were attributed to single-nucleotide variants, insertions/deletions, and multi-nucleotide variants. The coverage rate of variants in SRS by those found in CB was 97.9-99.2%, and the coverage rate of SRS genes by CB genes was 99.6-99.7%. The NGS results of CB fully covered the variants and genetic alterations observed in paired SRS samples. As bile CB is easy to prepare in general hospitals, our results suggest the potential use of bile CB as a novel method for NGS-based evaluation of cholangiocarcinoma.
Topics: Cholangiocarcinoma; Humans; High-Throughput Nucleotide Sequencing; Bile; Male; Middle Aged; Female; Bile Duct Neoplasms; Aged; Mutation
PubMed: 38891057
DOI: 10.3390/cells13110925 -
Scientific Reports Jun 2024The composition of cell-type is a key indicator of health. Advancements in bulk gene expression data curation, single cell RNA-sequencing technologies, and computational...
The composition of cell-type is a key indicator of health. Advancements in bulk gene expression data curation, single cell RNA-sequencing technologies, and computational deconvolution approaches offer a new perspective to learn about the composition of different cell types in a quick and affordable way. In this study, we developed a quantile regression and deep learning-based method called Neural Network Immune Contexture Estimator (NNICE) to estimate the cell type abundance and its uncertainty by automatically deconvolving bulk RNA-seq data. The proposed NNICE model was able to successfully recover ground-truth cell type fraction values given unseen bulk mixture gene expression profiles from the same dataset it was trained on. Compared with baseline methods, NNICE achieved better performance on deconvolve both pseudo-bulk gene expressions (Pearson correlation R = 0.9) and real bulk gene expression data (Pearson correlation R = 0.9) across all cell types. In conclusion, NNICE combines statistic inference with deep learning to provide accurate and interpretable cell type deconvolution from bulk gene expression.
Topics: Neural Networks, Computer; Deep Learning; Humans; Algorithms; Gene Expression Profiling; Single-Cell Analysis; Computational Biology; RNA-Seq; Sequence Analysis, RNA; Transcriptome
PubMed: 38890415
DOI: 10.1038/s41598-024-65053-w -
Scientific Reports Jun 2024Canine liposarcoma is an uncommon tumor that shares morphological similarities with its human counterpart. In dogs, the genetic features of this tumor are unknown and,...
Canine liposarcoma is an uncommon tumor that shares morphological similarities with its human counterpart. In dogs, the genetic features of this tumor are unknown and, based on immunohistochemical studies, amplification of the gene MDM2 and the mutation of TP53 are suspected. In this study 51 cases of primary liposarcomas were immunohistochemically stained for MDM2 and p53 and subjected to fluorescent in situ hybridization and next-generation sequencing to detect MDM2 amplification and TP53 mutations, respectively. MDM2 and p53 were expressed in 21 and 6 cases, respectively. MDM2 amplification and TP53 mutations were identified in 10 and 15 cases, respectively. Statistical analysis revealed an association of the myxoid subtype and the mitotic count with p53 expression and TP53 mutation. No association was found between MDM2 amplification and MDM2 expression or tumor subtype. These results suggest that despite morphological similarities, canine liposarcoma differs from its human counterpart, for which MDM2 amplification is diagnostic for well differentiated and de-differentiated variants, and TP53 mutations are more common in pleomorphic liposarcoma rather than the myxoid one as occur in our cases. Furthermore, canine myxoid liposarcoma likely represents a distinct disease rather than a mere morphological variant.
Topics: Proto-Oncogene Proteins c-mdm2; Dogs; Animals; Liposarcoma; Tumor Suppressor Protein p53; Dog Diseases; Mutation; Female; Male; In Situ Hybridization, Fluorescence; High-Throughput Nucleotide Sequencing; Gene Amplification; Immunohistochemistry
PubMed: 38890407
DOI: 10.1038/s41598-024-64963-z