Application and consideration of metagenomic next-generation sequencing technology in the diagnosis of insect-borne diseases / 中华检验医学杂志

Insect-borne diseases are serious life-threatening infectious diseases. Rapid and accurate etiological diagnosis are the premise of timely and effective clinical treatments, reducing mortality and sequelae. Laboratory diagnoses of insect-borne diseases mainly focus on targeted serological detection and polymerase chain reaction, which is difficult to detect rare insect borne pathogens. At present, the metagenomic next-generation sequencing (mNGS) technology has moved from scientific research into clinical application. The detection of nucleic acid sequences of all organisms in infected samples by mNGS exhibited significant advantages in the diagnosis and traceability of rare pathogens. But at the same time, mNGS is also suffered with challenges such as background microbial interference, false results caused by database restrictions, pathogen resistance and host immune status information that are urgently needed for clinical treatments. This article systematically summarized applications of mNGS in the diagnosis of insect-borne pathogens and the challenges and difficulties it faces. With the continuous optimization of mNGS in the detection, it will bring new development and innovation to the etiology diagnosis of clinical infectious diseases.

Clinical characteristics of the host DNA-removed metagenomic next-generation sequencing technology for detecting SARS-CoV-2, revealing host local immune signaling and assisting genomic epidemiology.

Background: Metagenomic next-generation sequencing (mNGS) technology has been central in detecting infectious diseases and helping to simultaneously reveal the complex interplay between invaders and their hosts immune response characteristics. However, it needs to be rigorously assessed for clinical utility. The present study is the first to evaluate the clinical characteristics of the host DNA-removed mNGS technology for detecting SARS-CoV-2, revealing host local immune signaling and assisting genomic epidemiology. Methods: 46 swab specimens collected from COVID-19 patients were assayed by two approved commercial RT-qPCR kits and mNGS. The evolutionary tree of SARS-CoV-2 was plotted using FigTree directly from one sample. The workflow of removing the host and retaining the host was compared to investigate the influence of host DNA removal on the performances of mNGS. Functional enrichment analysis of DEGs and xCell score were used to explore the characteristics of host local immune signaling. Results: The detection rate of mNGS achieved 92.9% (26/28) for 28 samples with a Ct value ≤ 35 and 81.1% (30/37) for all 46 samples. The genome coverage of SARS-CoV-2 could reach up to 98.9% when the Ct value is about 20 in swab samples. Removing the host could enhance the sensitivity of mNGS for detecting SARS-CoV-2 from the swab sample but does not affect the species abundance of microbes RNA. Improving the sequencing depth did not show a positive effect on improving the detection sensitivity of SARS-CoV-2. Cell type enrichment scores found multiple immune cell types were differentially expressed between patients with high and low viral load. Conclusions: The host DNA-removed mNGS has great potential utility and superior performance on comprehensive identification of SARS-CoV-2 and rapid traceability, revealing the microbiome's transcriptional profiles and host immune responses.

Drug response biomarkers of Pien Tze Huang treatment for hepatic fibrosis induced by carbon tetrachloride.

OBJECTIVE: To explore biomarkers of Pien Tze Huang that ameliorated the symptoms of hepatic fibrosis. METHODS: Two groups of carbon tetrachloride-induced hepatic fibrosis (HF) mice model were constructed in our study: one group received PZH treatment and another group received no treatment. We performed this study to investigate the role of PZH in the regulation process of hepatic fibrosis. RESULTS: We identified 31 down-regulated and 39 up-regulated miRNAs using small RNA-seq analysis. Combining RNA-Seq data analysis, our study revealed 7 significant target genes (Sp4, Slc2a6, Tln2, Hmga2, Ank3, Pax9, Fgf9). The results of real-time quantitative polymerase chain reaction analysis suggested that the expression level of 6 genes (Sp4, Tln2, Hmga2, Ank3, Pax9, Fgf9) were down-regulated compared to control group. On the other hand, the expression level of Slc2a6 appeared to be up-regulated. The protein mass spectrometry showed that PZH group had lower protein expression of Tln2 compared to control group. CONCLUSION: We identified 7 genes that were significantly related to PZH response in HF mice using multiple conjoint analysis methods. These genes could participate in underlying regulation mechanism of hepatic fibrosis during PZH treatment.

A FKBP5 mutation is associated with Paget's disease of bone and enhances osteoclastogenesis

Paget's disease of bone (PDB) is a common metabolic bone disease that is characterized by aberrant focal bone remodeling, which is caused by excessive osteoclastic bone resorption followed by disorganized osteoblastic bone formation. Genetic factors are a critical determinant of PDB pathogenesis, and several susceptibility genes and loci have been reported, including SQSTM1, TNFSF11A, TNFRSF11B, VCP, OPTN, CSF1 and DCSTAMP. Herein, we report a case of Chinese familial PDB without mutations in known genes and identify a novel c.163G>C (p.Val55Leu) mutation in FKBP5 (encodes FK506-binding protein 51, FKBP51) associated with PDB using whole-exome sequencing. Mutant FKBP51 enhanced the Akt phosphorylation and kinase activity in cells. A study of osteoclast function using FKBP51V55L KI transgenic mice proved that osteoclast precursors from FKBP51V55L mice were hyperresponsive to RANKL, and osteoclasts derived from FKBP51V55L mice displayed more intensive bone resorbing activity than did FKBP51WT controls. The osteoclast-specific molecules tartrate-resistant acid phosphatase, osteoclast-associated receptor and transcription factor NFATC1 were increased in bone marrow-derived monocyte/macrophage cells (BMMs) from FKBP51V55L mice during osteoclast differentiation. However, c-fos expression showed no significant difference in the wild-type and mutant groups. Akt phosphorylation in FKBP51V55L BMMs was elevated in response to RANKL. In contrast, IκB degradation, ERK phosphorylation and LC3II expression showed no difference in wild-type and mutant BMMs. Micro-CT analysis revealed an intensive trabecular bone resorption pattern in FKBP51V55L mice, and suspicious osteolytic bone lesions were noted in three-dimensional reconstruction of distal femurs from mutant mice. These results demonstrate that the mutant FKBP51V55L promotes osteoclastogenesis and function, which could subsequently participate in PDB development.