Second-generation Sequencing Research Articles

A case of squamous cell carcinoma of the lung misdiagnosed as tuberculosis. Is HPV infected by oral sex the causative agent?

BackgroundThe integration of high-risk human papilloma virus (HPV) DNA into the human genome has been implicated in cervical carcinogenesis and head and neck squamous cell cancer. However, its role in lung squamous cell carcinoma is not well understood. In addition, tuberculosis (TB) and lung cancer(LC) share similar clinical symptoms and imaging features, increasing the risk of misdiagnosis.Case PresentationThe patient presented with a 16-month history of hemoptysis, chest pain, and occasional fatigue, without fever, chills, or history of mechanical damage or autoimmune diseases. Examination revealed normal vital signs and laboratory parameters, except for a positive interferon-gamma release assay indicating tuberculosis infection. Bronchoscopic examinations identified congestion and edema of the tracheal wall, along with a tiny lesion in the right wall of the trachea. She had been misdiagnosed with tuberculosis. However, the diagnosis of squamous cell carcinoma was eventually confirmed by endoscopic biopsy. The patient’s macrogenomic second-generation sequencing (mNGS) of the bronchoscopic biopsy specimen was positive for HPV-16.The patient’s sex partner tested positive for HPV-16 in penile scrapings, indicating HPV transmission through oral sex.ConclusionsThis case highlights the potential for HPV infection acquired through oral sex to lead to lung squamous cell carcinoma. It emphasizes the importance of considering HPV-associated malignancies in patients with respiratory symptoms who engage in oral sexual behaviors.

Comprehensive sequencing of the genome and transcriptome of the Xishuangbanna game fowl

The Xishuangbanna game fowl, a local Chinese chicken breed renowned for its athleticism, is facing extinction. Despite its significance, research on its genome assembly and resequencing remains sparse, limiting our understanding of its genetic structure and function. In this study, we assembled a chromosome-level genome using second-generation sequencing and high-throughput chromosome conformation capture (Hi-C), along with transcriptome sequencing. We also resequenced 62 individuals. The resulting assembly yielded a 1.09 gigabase (Gb) high-quality genome, 994.34 Gb of resequencing data, and 141.38 Gb of transcriptome data from 15 tissues. This comprehensive dataset provides valuable insights into the artificial selection processes shaping the breed and offers a solid foundation for further genetic and population studies.

Sequence comparison of the mitochondrial genomes of five caridean shrimps of the infraorder Caridea: phylogenetic implications and divergence time estimation

BackgroundThe Caridea, affiliated with Malacostraca, Decapoda, and Pleocyemata, constitute one of the most significant shrimp groups. They are widely distributed across diverse aquatic habitats worldwide, enriching their evolutionary history. In recent years, considerable attention has been focused on the classification and systematic evolution of Caridea, yet controversies still exist regarding the phylogenetic relationships among families.MethodsHere, the complete mitochondrial genome (mitogenome) sequences of five caridean species, namely Heterocarpus sibogae, Procletes levicarina, Macrobrachium sp., Latreutes anoplonyx, and Atya gabonensis, were determined using second-generation high-throughput sequencing technology. The basic structural characteristics, nucleotide composition, amino acid content, and codon usage bias of their mitogenomes were analyzed. Selection pressure values of protein-coding genes (PCGs) in species within the families Pandalidae, Palaemonidae, and Atyidae were also computed. Phylogenetic trees based on the nucleotide and amino acid sequences of 13 PCGs from 103 caridean species were constructed, and divergence times for various families within Caridea were estimated.ResultsThe mitogenome of these five caridean species vary in length from 15,782 to 16,420 base pairs, encoding a total of 37 or 38 genes, including 13 PCGs, 2 rRNA genes, and 22 or 23 tRNA genes. Specifically, L. anoplonyx encodes an additional tRNA gene, bringing its total gene count to 38. The base composition of the mitogenomes of these five species exhibited a higher proportion of adenine-thymine (AT) bases. Six start codons and four stop codons were identified across the five species. Analysis of amino acid content and codon usage revealed variations among the five species. Analysis of selective pressure in Pandalidae, Palaemonidae, and Atyidae showed that the Ka/Ks values of PCGs in all three families were less than 1, indicating that purifying selection is influencing on their evolution. Phylogenetic analysis revealed that each family within Caridea is monophyletic. The results of gene rearrangement and phylogenetic analysis demonstrated correlations between these two aspects. Divergence time estimation, supported by fossil records, indicated that the divergence of Caridea species occurred in the Triassic period of the Mesozoic era, with subsequent differentiation into two major lineages during the Jurassic period.ConclusionsThis study explored the fundamental characteristics and phylogenetic relationships of mitogenomes within the infraorder Caridea, providing valuable insights into their classification, interspecific evolutionary patterns, and the evolutionary status of various Caridea families. The findings provide essential references for identifying shrimp species and detecting significant gene rearrangements within the Caridea infraorder.

Comparative Genomics of Eight Complete Chloroplast Genomes of Phyllostachys Species

(1) Background: The genus Phyllostachys belongs to the subfamily Bambusoideae within the family Gramineae. Bamboos of this genus are distinguished by their remarkable genetic traits, including exceptional resistance to both cold and drought conditions. These species possess considerable economic, ecological, and aesthetic value, finding extensive use in forestry and landscape design across China. (2) Methods: This study employed Illumina’s second-generation sequencing technology to sequence the chloroplast genomes of eight Phyllostachys species, followed by their assembly and annotation. (3) Results: The chloroplast genomes of the genus exhibit a characteristic tetrad structure with an average sequence length of 139,699 bp and an average GC content of 38.9%. A total of 130 genes have been annotated across eight bamboo species, comprising 75 protein-coding genes, 28 tRNA genes, and four rRNA genes. Global alignment and nucleotide polymorphism analyses indicate that the chloroplast genome of Phyllostachys is highly conserved overall. The boundaries of the four chloroplast regions are relatively conserved and exhibit minimal differences. Among these regions, three coding region genes—atpH, trnQ-UUG, and petB—and five non-coding regions—rpl32-trnL-UAG, rpl14-rpl16, rpl22-rps19, rps12-clpP, and trnR-UCU-trnM-CAU—exhibit high polymorphism and can be used as potential hotspot areas for subsequent research. A total of 266 simple sequence repeat (SSR) loci were identified by SSR analysis in the chloroplast genomes of eight bamboo species; the largest number of mononucleotide repeats was 154, predominantly consisting of A/T. Codon bias in the chloroplast genomes of the eight bamboo species indicates a preference for codons ending with A and U. Additionally, the UUA codon, which encodes leucine (Leu), is positioned between codons encoding phenylalanine (Phe), lysine (Lys), leucine (Leu), serine (Ser), and tyrosine (Tyr), indicating certain differences among these species. (4) Conclusions: This study aims to offer novel insights into the population genetics, phylogenetic relationships, and evolutionary patterns of Phyllostachys.

CDT1 is a Potential Therapeutic Target for the Progression of NAFLD to HCC and the Exacerbation of Cancer

Aims: This study aimed to identify potential therapeutic targets in the progression from non-alcoholic fatty liver disease (NAFLD) to hepatocellular carcinoma (HCC), with a focus on genes that could influence disease development and progression. Background: Hepatocellular carcinoma, significantly driven by non-alcoholic fatty liver disease, represents a major global health challenge due to late-stage diagnosis and limited treatment options. This study utilizes bioinformatics to analyze data from GEO and TCGA, aiming to uncover molecular biomarkers that bridge NAFLD to HCC. Through identifying critical genes and pathways, our research seeks to advance early detection and develop targeted therapies, potentially improving prognosis and personalizing treatment for NAFLD-HCC patients. Objective: Identify key genes that differ between NAFLD and HCC; Analyze these genes to understand their roles in disease progression; Validate the functions of these genes in NAFLD to HCC transition. Methods: Initially, we identified a set of genes differentially expressed in both NAFLD and HCC using second-generation sequencing data from the GEO and TCGA databases. We then employed a Cox proportional hazards model and a Lasso regression model, applying machine learning techniques to the large sample data from TCGA. This approach was used to screen for key disease-related genes, and an external dataset was utilized for model validation. Additionally, pseudo-temporal sequencing analysis of single-cell sequencing data was performed to further examine the variations in these genes in NAFLD and HCC. Results: The machine learning analysis identified IGSF3, CENPW, CDT1, and CDC6 as key genes. Furthermore, constructing a machine learning model for CDT1 revealed it to be the most critical gene, with model validation yielding an ROC value greater than 0.80. The single-cell sequencing data analysis confirmed significant variations in the four predicted key genes between the NAFLD and HCC groups. Conclusion: Our study underscores the pivotal role of CDT1 in the progression from NAFLD to HCC. This finding opens new avenues for early diagnosis and targeted therapy of HCC, highlighting CDT1 as a potential therapeutic target.

An innovative CRISPR/Cas9 mouse model of human isolated microtia indicates the potential contribution of CNVs near HMX1 gene

BackgroundMicrotia is a prevalent congenital malformation, the precise etiology and pathogenesis of which remain elusive. Mutations in the non-coding region of the HMX1 gene have been implicated in isolated cases of microtia, emerging as a significant focus of contemporary research. Several pathogenic copy number variations (CNVs) proximal to the HMX1 gene have been documented in wild animal populations, whereas only a single large segmental duplication in this region has been identified in humans. However, the absence of a gene-edited animal model has impeded the investigation of the unclear gene function associated with HMX1 mutations in human isolated microtia. In this study, we sought to precisely identify the pathogenic mutation by analyzing three pedigrees alongside population controls. Subsequently, our objective was to develop a CRISPR/Cas9 gene-edited mouse model to elucidate the functional implications of the identified mutation. MethodsGenomic DNA was collected from 32 affected individuals across three pedigrees, as well as from 2,000 control subjects. Comprehensive genomic analyses, including genome-wide linkage analysis, targeted capture, second-generation sequencing, and copy number analysis, were conducted to identify potential mutations associated with congenital auricle malformation. CRISPR/Cas9 gene-edited murine models were generated in response to the identified mutation. The auricular phenotypes of these gene-edited mice were systematically monitored. Small-animal Micro-CT scanning was employed to identify potential craniofacial or skeletal abnormalities. Furthermore, the expression of the HMX1 gene in the PA2 region of mouse embryos was quantified using RT-qPCR. ResultsA co-segregated 600 base pair duplication located on chromosome 4 (chr4:8701900-8702500, hg19) was identified in affected individuals across three pedigrees, but was absent in healthy controls. Two types of CRISPR/Cas9 gene-edited mice were subsequently generated. The knock-in (KI) mouse model was engineered by inserting one copy of the duplicated sequence directly adjacent to the mutated site, whereas the knockout (KO) mouse model was created by excising the mutation sequence. The phenotypes of different group of CRISPR/Cas9 gene-edited mice demonstrated distinct auricular deformities. Furthermore, an increase in the copy number of the mutated sequence was associated with elevated expression levels of HMX1 in the gene-edited mouse model. ConclusionsIn this study, we further narrowed down and identified a 600 base pair copy number variation (CNV) located at chr4:8701900-8702500 (hg19), which is implicated in human bilateral, isolated microtia. Utilizing CRISPR/Cas9 technology, we developed novel mouse models harboring the identified mutation. These models serve as a robust platform for the comprehensive investigation of the underlying mechanisms of the disease.

A transcriptomic analysis of incisional hernia based on high-throughput sequencing technology.

Incisional hernia is a common postoperative complication; however, few transcriptomic studies have been conducted on it. In this study, we used second-generation high-throughput sequencing to explore the pathogenesis and potential therapeutic targets of incisional hernias. Superficial fasciae were collected from 15 patients without hernia and 21 patients with an incisional hernia. High-throughput sequencing of the fascia was performed to generate an expression matrix. We analyzed the matrix to identify differentially expressed genes (DEGs) and performed gene ontology and enrichment analyses of these DEGs. Additionally, an external dataset was utilized to identify key DEGs. We identified 1,823 DEGs closely associated with extracellular matrix (ECM) imbalance, bacterial inflammatory response, and fibrillar collagen trimerization. TNNT3, CMAY5, ATP1B4, ASB5, CILP, SIX4, FBN1 and FNDC5 were identified as key DEGs at the intersection of the two expression matrices. Moreover, non-alcoholic fatty liver disease-related, TNF, and IL-17 signaling pathways were identified as key enrichment pathways. We identified eight key DEGs and three pathways associated with incisional hernias. Our findings offer new insights into the pathogenesis of incisional hernias and highlight potential targets for their prevention and treatment.

Varicella-Zoster Virus Encephalitis with Hyponatremia in an Immunocompetent Elderly Patient: A Case Report

As a common cause of viral encephalitis, varicella-zoster virus (VZV) may invade the central nervous system of immunosuppressed patients during reactivation. Herein, we report a rare case of an immunocompetent patient with VZV encephalitis who developed severe hyponatremia and was considered to have a suspected primary infection. The patient was diagnosed with the support of second-generation sequencing and had persistent hyponatremia after being cured. Although rare, this case suggests that VZV encephalitis may occur in unexpected patients and present with unusual clinical manifestations, requiring advanced detection methods and clinical expertise for resolution.

Comprehensive analysis of the mRNA and miRNA transcriptome implicated in the immune response of Procambarus clarkii to Spiroplasma eriocheiris

In recent years, the red swamp crayfish (Procambarus clarkii, P. clarkii) farming industry has suffered huge economic losses due to the pathogenic bacterium Spiroplasma eriocheiris (S. eriocheiris). To elucidate the immune response mechanism and identify hub immune genes as well as their associated microRNAs that regulate the host response of P. clarkii against S. eriocheiris infection, we conducted a comprehensive analysis on P. clarkii hemocyte mRNA and microRNA (miRNA) transcriptomes at different infection stages using third- and second-generation sequencing technologies. In full-length transcriptome functional annotation, 8155 unigenes were annotated, and 1168 potential new transcripts were predicted. In the mRNA transcriptome, a total of 3168 differentially expressed genes were identified at different infection stages, including 1492 upregulated and 1676 downregulated genes (duplicate genes excluded). Transcriptome analysis revealed 880 differentially expressed genes involved in multiple pathways and processes such as endocytosis, autophagy, lysosome, mTOR signaling, phagosome, and the Fanconi anemia pathway. Mfuzz analysis was employed to integrate and cluster the differential expression trends of genes across the three infection stages. In the miRNA transcriptome, 234 miRNAs and 966 predicted target genes were identified, with 86 differentially expressed miRNAs identified across the three time periods. A significant difference (P < 0.05) was observed for miRNAs including pcl-miR-146-3p, pcl-miR-74-3p, pcl-miR-225-5p, and pcl-miR-68-5p. These miRNAs are involved in multiple immune and autophagy-related pathways and have regulatory effects on immune genes including Vps26, lqf, and ERK-A. Based on the differentially expressed immune-related genes, we constructed a protein-protein interaction (PPI) network, which revealed the interactions among hub genes including Rac1, Akt1, Rho1, and Egfr. We also constructed a miRNA-gene interaction network in immune and autophagy-related processes, highlighting the potential regulatory effects of miRNAs including pcl-miR-183-5p, pcl-miR-146-3p, pcl-miR-176-5p, and pcl-miR-225-5p on proteins including LST8, SNAP29, Rab-7A, and ERK-A. To conclude, this study has identified hub immune genes and corresponding regulatory miRNAs in P. clarkii hemocytes in response to S. eriocheiris infection and explored the roles of these genes in selected pathways and processes. These findings are expected to provide further insights into the molecular mechanisms that confer resistance to S. eriocheiris infection in P. clarkii.

Primed and ready: nanopore metabarcoding can now recover highly accurate consensus barcodes that are generally indel-free

BackgroundDNA metabarcoding applies high-throughput sequencing approaches to generate numerous DNA barcodes from mixed sample pools for mass species identification and community characterisation. To date, however, most metabarcoding studies employ second-generation sequencing platforms like Illumina, which are limited by short read lengths and longer turnaround times. While third-generation platforms such as the MinION (Oxford Nanopore Technologies) can sequence longer reads and even in real-time, application of these platforms for metabarcoding has remained limited possibly due to the relatively high read error rates as well as the paucity of specialised software for processing such reads.ResultsWe show that this is no longer the case by performing nanopore-based, cytochrome c oxidase subunit I (COI) metabarcoding on 34 zooplankton bulk samples, and benchmarking the results against conventional Illumina MiSeq sequencing. Nanopore R10.3 sequencing chemistry and super accurate (SUP) basecalling model reduced raw read error rates to ~ 4%, and consensus calling with amplicon_sorter (without further error correction) generated metabarcodes that were ≤ 1% erroneous. Although Illumina recovered a higher number of molecular operational taxonomic units (MOTUs) than nanopore sequencing (589 vs. 471), we found no significant differences in the zooplankton communities inferred between the sequencing platforms. Importantly, 406 of 444 (91.4%) shared MOTUs between Illumina and nanopore were also found to be free of indel errors, and 85% of the zooplankton richness could be recovered after just 12–15 h of sequencing.ConclusionOur results demonstrate that nanopore sequencing can generate metabarcodes with Illumina-like accuracy, and we are the first study to show that nanopore metabarcodes are almost always indel-free. We also show that nanopore metabarcoding is viable for characterising species-rich communities rapidly, and that the same ecological conclusions can be obtained regardless of the sequencing platform used. Collectively, our study inspires confidence in nanopore sequencing and paves the way for greater utilisation of nanopore technology in various metabarcoding applications.

Mitochondrial genome study of Camellia oleifera revealed the tandem conserved gene cluster of nad5-nads in evolution.

Camellia oleifera is a kind of high-quality oil supply species. Its seeds contain rich unsaturated fatty acids and antioxidant active ingredients, which is a kind of high-quality edible oil. In this study, we used bioinformatics methods to decipher a hexaploid Camellia oil tree's mitochondrial (mt) genome based on second-generation sequencing data. A 709,596 bp circular map of C. oleifera mt genome was found for the first time. And 74 genes were annotated in the whole genome. Mt genomes of C. oleifera and three Theaceae species had regions with high similarity, including gene composition and gene sequence. At the same time, five conserved gene pairs were found in 20 species. In all of the mt genomes, most of nad genes existed in tandem pairs. In addition, the species classification result, which, according to the gene differences in tandem with nad5 genes, was consistent with the phylogenetic tree. These initial results provide a valuable basis for the further researches of Camellia oleifera and a reference for the systematic evolution of plant mt genomes.

The Characterization of the Mitochondrial Genome of Fulgoraria rupestris and Phylogenetic Considerations within the Neogastropoda.

Fulgoraria rupestris is a predatory marine gastropod belonging to Neogastropoda and possessing considerable taxonomic significance. However, research on this species remains limited. We acquired the complete mitochondrial genome of F. rupestris through second-generation sequencing and conducted an analysis of its genome structural features. The mitochondrial genome of F. rupestris spans a total length of 16,223 bp and encompasses 37 genes (13 protein-coding genes (PCGs), 22 transfer RNAs, and 2 ribosomal RNAs). Notably, most tRNAs exhibit the typical cloverleaf structure, but there is an absence of the Dihydrouridine (DHU) arm in the trnS1 and trnS2 genes. The A + T content is 68.67%, indicating a pronounced AT bias. Additionally, we conducted a selection pressure analysis on the mitochondrial genomes of four species within Volutidae, revealing that all PCGs are subjected to purifying selection. In comparison to other species within Neogastropoda, F. rupestris shares an identical gene arrangement. Additionally, based on mitochondrial genome sequences of the 13 PCGs from 50 species within Neogastropoda, we constructed a phylogenetic tree. The phylogenetic tree indicates F. rupestris forms a clade with species within the family Volutidae (Cymbium olla, Neptuneopsis gilchristi, and Melo melo). This study serves as a valuable reference for future research on F. rupestris, offering insights for the upcoming phylogenetic and taxonomic classification within Neogastropoda. Furthermore, the findings provide valuable information for the development of genetic resources in this context.

Application of the second-generation sequencing technology of metagenomics in the detection of pathogens in respiratory patients

ObjectiveTo explore the application value of the second-generation metagenomic next-generation sequencing (mNGS) in the detection of pathogens in patients with pulmonary infection. MethodsWe conducted a retrospective analysis of 65 pulmonary infection cases treated at our institution and the Fifth People's Hospital of Shanghai between January 2021 and May 2023. All subjects were subjected to mNGS, targeted next-generation sequencing (tNGS), and conventional microbiological culture. A comparative analysis was performed to evaluate the diversity and quantity of pathogens identified by these methodologies and to appraise their respective diagnostic capabilities in pulmonary infection diagnostics. ResultsThe mNGS successfully identified etiological agents in 60 of the 65 cases, compared to tNGS, which yielded positive results in 42 cases, and conventional laboratory cultures, which detected pathogens in 24 cases. At the bacterial genus level, mNGS discerned 9 genera, 11 species, and 92 isolates of pathogenic bacteria, whereas tNGS identified 8 genera, 8 species, and 71 isolates. Conventional methods were less sensitive, detecting only 6 genera, 7 species, and 33 isolates. In terms of fungal detection, mNGS identified 4 fungal species, tNGS detected 4 isolates of the Candida genus, and conventional methods identified 2 isolates of the same genus. Viral detection at the species level revealed 10 species and 46 isolates by mNGS, whereas tNGS detected only 3 species and 7 isolates. The area under the receiver operating characteristic curve (AUC) with 95% confidence intervals for diagnosing pulmonary infections was 0.818 (0.671 to 0.966) for mNGS, 0.668 (0.475 to 0.860) for tNGS, and 0.721 (0.545 to 0.897) for conventional culture.The mNGS demonstrates superior diagnostic efficacy and pathogen detection breadth in critically ill patients with respiratory infections, offering a significant advantage by reducing the time to diagnosis. The enhanced sensitivity and comprehensive pathogen profiling of mNGS underscore its potential as a leading diagnostic tool in clinical microbiology.

Characteristic Analysis of Adult Acute Myeloid Leukemia Patients with PTPN11 Gene Mutation

To investigate the incidence of PTPN11 gene mutation and its associated gene mutations in adult patients with acute myeloid leukemia (AML), and analyze its clinical characteristics. Second-generation sequencing and Sanger sequencing were used to detect 51 gene mutations, and multiplex-PCR was used to detect 41 fusion genes from 451 newly diagnosed adult AML patients admitted to Affiliated Hospital of Jiangnan University, Changzhou Second People's Hospital, Wuxi People's Hospital and Wuxi Second People's Hospital from January 2017 to July 2022. Among 451 primary adult AML patients, the PTPN11 gene mutation was detected in 34 cases, and the mutation rate was 7.5%. In the 34 patients, 37 PTPN11 alterations were found, which were exclusively missense mutations affecting residues located within the N-SH2 (31 cases) and PTP (6 cases) domains and clustered overwhelmingly in exon 3. The platelet count of PTPN11 mutation patients was 76.5(23.5, 119.0)×109/L, which was significantly higher than 41.0(22.0, 82.5)×109/L of wild-type patients (P < 0.05). While, there were no significant differences in sex, age, peripheral white blood cell count, hemoglobin, and bone marrow blast between PTPN11 mutation and wild-type patients (P >0.05). In FAB subtypes, PTPN11 mutations were mainly distributed in M5, followed by M2 and M4, less frequently in M3 and M6. There was no significant difference in the distribution of FAB subtypes between PTPN11 mutation and wild-type patients (P >0.05). A total of 118 AML patients were detected positive fusion gene, among which patients with PTPN11 mutations had a higher incidence of positive MLL-AF6 than wild-type ones (P < 0.01). 97.1% of 34 patients with PTPN11 mutations were accompanied by other mutations, in descending order, they were respectively NPM1 (38.2%), NRAS (32.4%), FLT3-ITD (32.4%), DNMT3A (32.4%) and KRAS (23.5%), etc . PTPN11 mutation has a certain incidence in AML patients and is clustered overwhelmingly in exon 3. ALL of them are exclusively missense mutations, and most often present in conjunction with NPM1 mutations. FAB typing of PTPN11 mutation is mostly manifested as M5 subtype, which is associated with higher platelet counts.

Anti-inflammatory and DNA Repair Effects of Astragaloside IV on PC12 Cells Damaged by Lipopolysaccharide.

This study aimed to establish a neural cell injury model in vitro by stimulating PC12 cells with lipopolysaccharide (LPS) and to examine the effects of astragaloside IV on key targets using high-throughput sequence technology and bioinformatics analyses. PC12 cells in the logarithmic growth phase were treated with LPS at final concentrations of 0.25, 0.5, 0.75, 1, and 1.25 mg/mL for 24 h. Cell morphology was evaluated, and cell survival rates were calculated. A neurocyte inflammatory model was established with LPS treatment, which reached a 50% cell survival rate. PC12 cells were treated with 0.01, 0.1, 1, 10, or 100 µmol/L astragaloside IV for 24 h. The concentration of astragaloside IV that did not affect the cell survival rate was selected as the treatment group for subsequent experiments. NOS activity was detected by colorimetry; the expression levels of ERCC2, XRCC4, XRCC2, TNF-α, IL-1β, TLR4, NOS and COX-2 mRNA and protein were detected by RT-qPCR and Western blotting. The differentially expressed genes (DEGs) between the groups were screened using a second-generation sequence (fold change>2, P<0.05) with the following KEGG enrichment analysis, RT-qPCR and Western blotting were used to detect the mRNA and protein expression of DEGs related to the IL-17 pathway in different groups of PC12 cells. The viability of PC12 cells was not altered by treatment with 0.01, 0.1, or 1 µmol/L astragaloside IV for 24 h (P>0.05). However, after treatment with 0.5, 0.75, 1, or 1.25 mg/mL LPS for 24 h, the viability steadily decreased (P<0.01). The mRNA and protein expression levels of ERCC2, XRCC4, XRCC2, TNF-α, IL-1β, TLR4, NOS, and COX-2 were significantly increased after PC12 cells were treated with 1 mg/mL LPS for 24 h (P<0.01); however, these changes were reversed when PC12 cells were pretreated with 0.01, 0.1, or 1 µmol/L astragaloside IV in PC12 cells and then treated with 1 mg/mL LPS for 24 h (P<0.05). Second-generation sequencing revealed that 1026 genes were upregulated, while 1287 genes were downregulated. The DEGs were associated with autophagy, TNF-α, interleukin-17, MAPK, P53, Toll-like receptor, and NOD-like receptor signaling pathways. Furthermore, PC12 cells treated with a 1 mg/mL LPS for 24 h exhibited increased mRNA and protein expression of CCL2, CCL11, CCL7, MMP3, and MMP10, which are associated with the IL-17 pathway. RT-qPCR and Western blotting analyses confirmed that the DEGs listed above corresponded to the sequence assay results. LPS can damage PC12 cells and cause inflammatory reactions in nerve cells and DNA damage. astragaloside IV plays an anti-inflammatory and DNA damage protective role and inhibits the IL-17 signaling pathway to exert a neuroprotective effect in vitro.

Chinese guidelines for integrated diagnosis and treatment of intestinal microecology technologies in tumor application (2024 Edition).

Intestinal microecology (IM) is the largest and most important microecological system of the human body. Furthermore, it is the key factor for activating and maintaining the physiological functions of the intestine. Numerous studies have investigated the effects of the gut microbiota on the different tissues and organs of the human body as well as their association with various diseases, and the findings are gradually being translated into clinical practice. The gut microbiota affects the occurrence, progression, treatment response, and toxic side effects of tumors. The deepening of research related to IM and tumors has opened a new chapter in IM research driven by methods and technologies such as second-generation sequencing and bioinformatics. The IM maintains the function of the host immune system and plays a pivotal role in tumor-control drug therapy. Increasing evidence has proven that the efficacy of tumor-control drugs largely depends on the IM balance, and strategies based on the IM technology show promising application prospects in the diagnosis and treatment of tumor. The Tumor and Microecology Professional Committee of the Chinese Anti-cancer Association gathered relevant experts to discuss and propose the "Chinese guidelines for integrated diagnosis and treatment of IM technologies in tumor application (2024 Edition)," which was established based on the research progress of the application of the IM technology in tumor to provide a basis for the standardization of the diagnosis and treatment of the IM technology in the tumor.

Ethnicity-based analysis of supragingival plaque composition and dental health behaviours in healthy subjects without caries

ObjectiveThe primary objective of this study was to scrutinise the disparities in the diversity, structure, and function of the oral microbiome among caries-free children from the Zhuang and Han ethnic groups with a focus on the influence of ethnically distinct oral health behaviours on the composition of the oral microbiota. MethodsA questionnaire survey was conducted to assess oral health behaviours and dental plaque samples were collected from 96 Zhuang and Han children aged 4–5 years living in Guangxi, southern China for high-throughput sequencing. PCR amplification was performed for sequencing of the V4 region of the 16S rDNA gene, and second-generation sequencing was performed using the Illumina MiSeq platform to compare and analyse the diversity, structure and function of the microbiota. ResultsSingle-factor analysis revealed significant differences between the Zhuang and Han ethnic groups regarding juice consumption, the frequency of consuming sugar-sweetened food or beverages before bedtime, the age that individuals started toothbrushing, the frequency of toothbrushing and the frequency of parental assistance with toothbrushing (p < 0.001). The dominant phyla were Proteobacteria, Firmicutes, etc., and the dominant genera included Streptococcus and Neisseria. The dental plaques of the caries-free Zhuang and Han ethnic groups had similar core microbiomes, with no significant differences in the diversity and structure of the microbiota and no significant differences in the abundance of the dominant genera. In addition, no significant difference in metabolic function was observed between the Zhuang and Han ethnic groups. ConclusionThe core oral microbiota was consistent in caries-free Zhuang and Han children. Despite differences in dietary habits and oral hygiene behaviours between the Zhuang and Han ethnic groups, with a high frequency of sugary food intake but better oral health behaviours in the Zhuang group, there were no significant differences in the diversity, structure and function of the oral microbiota of caries-free children in the Zhuang and Han ethnic groups.

Clinical Characteristics and Prognostic Relevance of Co-Mutated Genes in Acute Myeloid Leukemia Patients with FLT3 Mutations

To investigate the clinical characteristics and influence of co-mutated gene on acute myeloid leukemia patients (AML) with FMS-like tyrosine kinase-3 (FLT3) mutations. A total of 273 FLT3+ AML patients were enrolled, and the co-mutation gene data of the patients were collected to further analyze the prognosis of the patients. FLT3 and other common mutations were quantified by PCR amplification products direct sequencing and second-generation sequencing (NGS). When patients were divided into FLT3- ITD +, FLT3- TKD +, FLT3- ITD ++TKD + and FLT3- ITD -+TKD - group according to the type of FLT3 mutations, it was found that the frequencies of TET2, GATA2, NRAS and ASXL1 mutation were significantly different among the 4 groups (all P < 0.05). When patients were divided into allelic ratio (AR) ≥0.5 and <0.5 group, it was found that the frequencies of FLT3- ITD +, FLT3 -ITD - +TKD -, NPM1, NRAS and C-kit were significantly different between the two groups (all P < 0.05). When patients were divided into normal and abnormal karyotype group, it was found that the frequencies of FLT3- ITD +, FLT3- TKD +, NPM1, GATA2 and C-kit were significantly different between the two groups (all P < 0.05). The median overall survival (OS) of AML patients with FLT3 -TKD + (including FLT3- ITD ++TKD +) was longer than that of patients with FLT3- ITD + alone (P < 0.05). The OS and relapse-free survival (RFS) of AML patients with FLT3++TET2+ were both shorter than those of patients with FLT3++TET2- (both P < 0.05). The mutation frequencies of co-mutated genes are correlated with subtypes of FLT3, karyotype and AR. AML patients with FLT3 -TKD + have longer OS than patients with FLT3- ITD + alone, and patients with co-mutation of TET2 have shorter median OS and RFS.

Application of Second-Generation Sequencing Technology in Lower Respiratory Tract Infection.

Lower respiratory tract infection (LRTI) has long been an important threat to people's life and health, so the rapid diagnosis of LRTI is of great significance in clinical treatment. In recent years, the development of the sequencing technology provides a new direction for the rapid diagnosis of LRTI. In this review, the advantages and disadvantages of second-generation sequencing techniques represented by metagenomics next-generation sequencing (mNGS) and droplet digital polymerase chain reaction (ddPCR) in LRTI were reviewed. Furthermore, it offers insights into the future trajectory of this technology, highlighting its potential to revolutionise the field of respiratory infection diagnostics. This review summarises developments in mechanistic research of second-generation sequencing technology their relationship with clinical practice, providing insights for future research. Authors conducted a search on PubMed and Web of Science using the professional terms 'Lower respiratory tract infection' and 'droplet digital polymerase chain reaction' and 'metagenomics next generation sequencing'. The obtained literature was then roughly categorised based on their research content. Similar studies were grouped into the same sections, and further searches were conducted based on the keywords of each section. Different studies discussed the application of second-generation sequencing technology in LRTI from different angles, including the detection of pathogens of LRTI by mNGS and ddPCR, the prediction ability of drug-resistant bacteria, and comparison with traditional methods. We try to analyse the advantages and disadvantages of the second-generation sequencing technology by combing the research results of mNGS and ddPCR. In addition, the development direction of the second-generation sequencing technology is prospected.

Clinical Characteristics and Prognosis of Myelodysplastic Syndromes Patients with RUNX1 Gene Mutation

To investigate the clinical characteristics and survival analysis of myelodysplastic syndromes (MDS) with RUNX1 gene mutation. Clinical data of 177 newly diagnosed MDS patients admitted to the Department of Hematology, the Second Affiliated Hospital of Air Force Military Medical University from October 1, 2015 to October 31, 2022 were retrospectively analyzed. Gene mutation detection was performed by second-generation sequencing technology, and clinical characteristics and prognosis of patients with RUNX1 gene mutation were analyzed. A total of 30 cases (16.95%) of RUNX1 gene mutations were detected, including 15 missense mutations (50.0%), 9 frameshift deletion mutations (30.0%), 4 splice site mutations (13.3%), 1 insertion mutation (3.3%), and 1 nonsense mutation (3.3%). Patients with RUNX1 mutations had a median age of 68.5 years at diagnosis (range: 62.25-78.50 years old). There were no significantly differences between RUNX1 mutations and wild type patients in age distribution, gender, peripheral blood white blood cell count, hemoglobin level, bone marrow and peripheral blood blasts ratio, IPSS-R cytogenetics, IPSS-R stage, etc. (P >0.05). However, there were statistically significant differences in platelet count and whether complicated karyotype. Compared with patients without RUNX1 gene mutation, patients with RUNX1 gene mutation had lower platelet count (P =0.018), and were less likely to have complicatedkaryotype at initial diagnosis (P =0.01). Cox proportional hazards model analysis showed that when other covariates remained unchanged, the higher the platelet count, the better the survival of patients (HR=0.995, 95%CI : 0.990-0.999, P =0.036); In the IPSS-M prognostic stratification, keeping other covariates unchanged, the risk of progression or death of myelodysplastic syndrome was significantly lower in the medium to high-risk and low-risk groups compared with the high-risk group (HR=0.149, 95%CI : 0.031-0.721, P =0.018; HR=0.026, 95%CI : 0.003-0.234, P =0.001). Survival analysis showed that MDS patients with RUNX1 gene mutation had worse overall survival time (P < 0.001). Patients with RUNX1 mutation had worse OS than non-mutation patients in the early WHO group. RUNX1 mutation and IPSS-M risk stratification mean OS and mean LFS were worse in low-risk patients than in non-mutated patients. RUNX1 gene mutation is an adverse prognostic factor in MDS patients, especially in the IPSS-M prognosis stratification group of low-risk, medium-low risk, medium-high risk and WHO classification of early patients.