Objective To investigate specific changes of T cell repertoire in convalescent patients infected by influenza A (H7N9) virus. Methods Peripheral blood samples from 8 convalescent patients infected by H7N9 virus and 10 healthy donors were collected. After extracting whole DNA from these samples, arm-PCR were performed and the products were submitted to Illumina HiSeq2000 platform to produce deep sequencing data of the nucleotide sequences of complementary determining region 3 of T cell receptor β chain (TRB). Differences were compared in TRB diversity and V-D-J gene usage and similarities of sequences between the patients and the healthy donors. Results Frequency of V-D-J gene usage was different between the H7N9 patient group and the healthy group, such as TRBV30, TRBV27, and TRBV18 (Student's t test, P < 05). Main component analysis showed V-J pairing pattern was significantly different between two groups, which may have potential in identifying patients from healthy people. A considerable number of shared CDR3s were found in patient-patient pairs and normal-normal pairs, while seldom were found in patient-normal pairs. The similarity between patients was also confirmed by overlap distance analysis. Indexes for assessing diversity of immune repertoires, Shannon-Weiner index and Simpson index, were both lower in the patients (Student's t test, P < 05), suggesting that the immune system of the patients had not recovered 6 months after H7N9 infection. Compared with the healthy donors, the number of hyper-expression clones increased in the patient group, and some of them showed similarity among patients. Conclusions TRB repertoires are less diverse in patients with increased hyper-expressed clones and identifiable V-J usage pattern, which is identifiable from normal population. These results suggest that there are H7N9-specific changes in TRB repertoires of H7N9 infected patients in convalescent phase, which have potential implication in diagnosis and therapeutic T cell development.
ObjectiveTo provide reference for further treatment by analyzing the relationship between mutant genes of breast cancer and histological classification and molecular typing of breast cancer.MethodsRetrospectively collectted the pathological specimens of 46 breast cancer patients who treated by the Dongguan Maternal and Child Health Hospital and the Dongguan Houjie Hospital between February 2016 and August 2017 without chemotherapy. Among the selected 46 breast cancer patients, we detected tumor tissue estrogen receptor (ER)/ pregnancy hormone receptor (PR)/human epidermal growth factor receptor-2 (HER-2) status by immunohistochemistry and classified the pathological tissue section. By using multiple PCR techniques, we detected 207 hot mutation regions of the 50 extended tumor-related genes on the semiconductor sequencing platform.ResultsThere were 8 cases of grade Ⅰ, 18 cases of grade Ⅱ, 20 cases of grade Ⅲ in 46 breast cancer patients according to histological grade. Of the 46 cases, there were 23 cases of Luminal B, 9 cases of Luminal A, 9 cases of HER-2 (+), 5 cases of type besal-like according to ER/PR/HER-2 expression status. Moreover, we found that there were 33 gene locus mutations of 8 genes, including AKT1, APC, BRAF, CDKN2A, KRAS, PTEN, PIK3CA, and TP53. Among of them, the mutation of PIK3CA gene took the most of 24 cases, followed by TP53 (18 cases), 2 cases of CDKN2A gene mutation, and 1 case in the remaining four types of genes respectively. we found that the gene mutations of breast cancer were not related to the histological classification and molecular type (P>0.05), the PIK3CA gene mutation was related to the histological classification of breast cancer, the lower the histological classification level, the higher PIK3CA gene mutation rate (P<0.05). TP53 gene mutation was not related to histological grading and molecular type (P>0.05).Conclusions The PIK3CA gene mutation rate in patients with histological grading Ⅰ level increased significantly. The combination of PIK3CA gene mutation and histological grading of breast cancer may become a molecular biological indicator to judge the degree of malignancy and prognosis of breast cancer.
ObjectiveTo detect the differentially expressed circular RNA (circRNA) in rotator cuff tendinopathy and analyze the potential molecular mechanism of these parental genes.MethodsTen supraspinatus tendons donated from patients who underwent tendon repair surgery between June 2018 and June 2019 were used for RNA-sequence. All rotator cuff tendinopathy and normal tendon samples were confirmed by MRI, histological staining, and observation by arthroscopy. All pathological tendons were matched with tendon samples for patients’ age, gender, body mass index, and Bonar score. The bioinformatic analysis was performed based on the differentially expressed circRNA and their parental genes, including gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and competing endogenous RNA (ceRNA) network construction.ResultsThere were 94 differentially expressed circRNAs, including 31 up-regulated and 63 down-regulated, detected between the rotator cuff tendinopathy and normal tendon samples with |log2 fold change (FC)| >2, P<0.05. GO analysis showed that the genes were mostly enriched in response to cyclic adenosine monophosphate (cAMP). KEGG pathway analysis showed that the most genes were enriched in extracellular matrix-receptor interaction, protein digestion and absorption, cell cycle, and nuclear factor κB signaling pathway. ceRNA networks showed the interactions among circRNAs, mRNAs, and miRNAs. And circRNA.8951-has-miR-6089-DNMT3B was the most sum max energy.ConclusionThis bioinformatic study reveals several potential therapeutic targets for rotator cuff tendinopathy, which paves the way to better treatment and prevention of this disorder.
ObjectiveTo summarize the research progress of the relationship between biliary flora and cholangiocarcinoma.MethodThe literatures on the relationship between biliary flora and cholangiocarcinoma were collected and reviewed.ResultsBiliary flora was closely related to the occurrence and development of biliary tract diseases. The inflammatory environment of the biliary tract was an important factor in the occurrence and development of cholangiocarcinoma. Microbes might induce chronic inflammation of the host tissue, leading to cell proliferation and genetic mutation, and ultimately leading to the occurrence of cholangiocarcinoma. Bacterial infection might play an important role in the pathogenesis of cholangiocarcinoma.ConclusionThe study of the role of biliary flora in the development of cholangiocarcinoma may open up a new direction for the prevention and treatment of cholangiocarcinoma.
ObjectiveTo explore the influence of enhanced recovery after surgery (ERAS) on intestinal flora in patients with colorectal cancer.MethodsBy convenient sampling method, 60 patients with colorectal cancer were selected from August 2018 to December 2019 in the Department of Gastrointestinal Surgery of West China Hospital of Sichuan University and randomly divided into ERAS group and traditional treatment group (traditional group). Among them, the perioperative clinical management was carried out according to the ERAS management and traditional treatment process in the the ERAS group and in the traditional group, respectively. The fresh fecal samples were collected within 24 h after admission and the first natural defecation after operation. The bacterial 16 Sr DNA V3–V4 region was sequenced by Illumina MiSeq sequencer, and the results were analyzed by bioinformatics.ResultsA total of 60 patients with colorectal cancer were included, 30 cases in the traditional group and 27 cases in the ERAS group (3 people temporarily withdrew from the study). There were no significant differences in the basic informations between the two groups (P>0.05). ① Before or after operation, there were no significant differences in Shannon index and Simpson index between the two groups. The difference between preoperative and postoperative comparison in the same group was also not statistically significant (P>0.05). ② Beta diversity analysis showed that there was no significant difference in community composition between the traditional group and the ERAS group before operation, and there was a clear boundary between the traditional group and the ERAS group after operation. ③ At the phylum level, compared with the preoperative abundance, the postoperative abundance Firmicutes decreased by 26.5% and 5.5% in the traditional and ERAS group, respectively; Bacteroidetes increased by 21.6% and 4.7% in the traditional and ERAS group, respectively; Proteobacteria increased by 7.2% and 2.2% in the traditional and ERAS group, respectively. At the genus level, compared with the preoperative abundance, the postoperative abundance of Bacteroides in the traditional group increased by 17.6% and in the ERAS group decreased by 1.6%; Bifidobacterium decreased by 1.8% and 1.3% in the traditional group and in the ERAS group, respectively.ConclusionsERAS does not affect species diversity of intestinal flora. Although ERAS has some damage to structure of intestinal flora, it is weaker than traditional process, so it is more conducive to reconstruction and restoration of intestinal microecological environment.
Objective To investigate the clinical manifestations, diagnosis, treatment and prognosis of psittacosis patients. Methods The clinical features, treatment and prognosis of severe pneumonia caused by Chlamydia psittaci were analyzed and relevant literatures were reviewed. Results An 83-year-old male with a history of type 2 diabetes mellitus was admitted to the hospital for "fever, cough for 5 days and dyspnea for 3 days". Chest CT showed a large mass of increased density in the right lung; CD4+ T lymphocytes had an absolute value of 23 cells/μL; Blood gas analysis showed type Ⅰ respiratory failure; Chlamydia psittaci was detected by metagenomic next-generation sequencing. The patient was diagnosed of severe pneumonia (Chlamydia psittaci), type 2 diabetes mellitus, suspected central nervous system infection. This patient was treated with doxycycline and macrolides antibiotics and discharged from hospital after complete recovery. Literature review showed that patients got infected from contacting sick bird, manifested with multiple system involvement. Respiratory symptoms were common, while central nervous system infection seemed to be rare. The diagnosis of psittacosis depended on serology, nucleic acid detection, pathogen isolation and culture. Metagenomic next-generation sequencing had superiority in the diagnosis of psittacosis. Tetracyclines were the preferable treatment, such as doxycycline or tetracycline, with a duration of at least 10 to 14 days. The prognosis of psittacosis was well, and most of the severe and even life-threatening cases were caused by unclear diagnosis and delayed treatment, and the overall mortality rate was about 1%. Conclusions Psittacosis is one kind of zoonoses. History of poultry exposure is helpful in diagnosis, and metagenomic next-generation sequencing has advantages in diagnosing psittacosis. Tetracyclines are preferred with adequate course of treatment. The overall prognosis is good.
Objective To analysis and explore the value of metagenomics next-generation sequencing (mNGS) and clinical characteristics of Chlamydia psittaci (C. psittaci) pneumonia. Methods Totally 5 patients who were diagnosed with C. psittaci pneumonia and were treated in the Department of Respiratory and Critical Care Medicine and the Department of Infectious Diseases of Huazhong University of Science and Technology Union Shenzhen Hospital from Febuary 2021 to March 2021 were enrolled in the study. The clinical data of the patients were analyzed, and the clinical characteristics of the disease and treatment experience were summarized. Results The main symptoms of the 5 patients were high fever and cough, 4 of them had a history of raising parrots. The white blood cell and the neutrophils were mostly normal or slightly increased, the C reactive protein and erythrocyte sedimentation rate were significantly increased. The chest CT showed exudation and consolidation of one or several lung lobes. The serious patients might develop respiratory failure, if they were not treated by effective antibiotics. The diagnosis was based on clinical manifestations, contact history and alveolar lavage fluid that were detected by mNGS technology of C. psittaci nucleic acid sequence. The accuracy of detecting pathogens in alveolar lavage fluid by mNGS was high. In addition, mNGS could also identify other bacteria or viruses. After the timely adjustment of treatment, the condition of the patients was improved relied on tetracycline drugs or quinolone drugs, which shortened the diagnosis time and course of C. psittaci pneumnonia and reduced the use of unnecessary antibacterial drugs. Conclusions mNGS is of great significance in diagnosing C. psittaci pneumonia. The timely use of appropriate antibacterial drugs can achieve favorable therapeutic effect.
Objective To summarize and explore the clinical features, diagnosis and treatment of severe pulmonary tuberculosis (TB). Methods One death case of pulmonary TB in The First Affiliated Hospital of Soochow University was analyzed, related publications of case reports and articles relevant on the analysis and study of pulmonary tuberculosis deaths from Pubmed between January 2012 and March 2022 were also reviewed. Results A 25-year-old female patient was admitted for "intermittent cough with sputum for more than 1 year, aggravated with chest tightness and shortness of breath for 5 days". She had no underlying disease. Pulmonary TB was diagnosed by TB bacterium smear and next-generation sequencing of bronchoalveolar lavage fluid. The patient was in shock compensation period and developed acute respiratory distress syndrome immediately after admission. Through active anti-tuberculosis, invasive mechanical ventilation, intra-aortic balloon counterpulsation and continuous renal replacement therapy, the disease continued to deteriorate and she died on the third day after admission. A total of 269 pulmonary TB deaths were retrieved. An analysis of 244 patients' past medical history showed that human immunodeficiency virus co-infection was the most common among young people and chronic diseases were the most common among the elderly. All 269 patients died of septic shock, respiratory failure and multiple organ dysfunction syndrome (MODS), among which hyponatremia was also a significant complication. The shortest time from admission to death was 7 days, while the longest average time was only 35 days. Conclusions Pulmonary TB could develop into septic shock and MODS with poor prognosis and high mortality. Health education on TB should be strengthened.
In recent years, pathogenic metagenomic next-generation sequencing (mNGS) technology has become more and more widely used in the field of clinical infection. Driven by clinical needs, mNGS technology is constantly being optimized and developed. From manual operation to automated process, from simple qualitative detection to quantitative monitoring, from infection identification to multi-dimensional diagnosis of “infection+tumor”, certain research results have been achieved. Of course, there are still some limitations in clinical application of this technology. For example, there are many mNGS detection related reagents in China, but a systematic and complete quality management control and evaluation system has not been established. Further research is needed. This article summarizes the development and application of pathogen metagenomic sequencing technology in recent years, as well as the standardization and normalized process of mNGS detection, in order to provide a reference for pathogen mNGS sequencing to better assist clinical infection diagnosis.