Overview of Yersinia bacteriophage genomics / 中华地方病学杂志

Yersinia bacteriophage is a virus that hosts Yersinia bacteria, which not only affects the survival and evolution of the host bacteria, but also plays an important role in biomass cycling and energy flow. As of November 2022, the National Center for Biotechnology Information (NCBI) in the United States has uploaded the complete genome sequences of 119 Yersinia bacteriophages. The genome size and genetic content of different Yersinia bacteriophages vary, and the similarity between the genomes is relatively low. This article reviews the basic genomic characteristics and gene functions of Yersinia bacteriophages, and studies the differences between the genomes of different species of Yersinia bacteriophages, in order to provide reference for understanding the functional differences and genetic evolution of Yersinia bacteriophage.

Multiomics research on stroke and its potential significance / 中华检验医学杂志

Stroke is an acute cerebrovascular disease, and a group of diseases that cause brain tissue damage due to sudden rupture of brain blood vessels or blockage of blood vessels, mainly including ischemic stroke and hemorrhagic stroke. In recent years, although some progresses have been achieved, there are still few biomarkers that can be used for effective warning and monitoring for people at high risk of stroke. Omics research is an important research strategy for discovering differential genes, molecules, and epigenetic markers in the process of disease occurrence and development. A systematic summary of progress made in recent years, in stroke genomics, transcriptomics, proteomics, and metabolomics in recent years, as well as their potential applications in stroke warning, diagnosis, and monitoring, was systematically discussed in the presence review, in order to provide reference for future research on stroke biomarkers.

Advances in the multi-omics research on nonalcoholic fatty liver disease / 临床肝胆病杂志

The prevalence rate of nonalcoholic fatty liver disease （NAFLD） reaches up to 30% around the world， and the disease has a serious impact on human health and constitutes a public health burden. Due to difficulties in the diagnosis and monitoring of NAFLD， it is important to identify potential drug targets and biomarkers， and multi-omics techniques hold great promise in the search for early diagnostic markers， therapeutic targets， and outcome and prognostic assessment of NAFLD. This article reviews the research advances in multi-omics techniques in the field of NAFLD in recent years， in order to provide a richer theoretical basis and new strategies for the prevention and treatment of NAFLD.

Baitouweng Tang Inhibits Growth of Esophageal Cancer Cells Through BUB1/STAT3 Signaling Pathway / 中国实验方剂学杂志

ObjectiveTo investigate the mechanism of Baitouweng Tang in inhibiting the growth of esophageal cancer （EC） cells by regulating budding uninhibited by benzimidazoles 1 （BUB1）/signal transducer and activator of transcription 3 （STAT3） signaling pathway. MethodGene chip technology was used to explore the differential gene expression between esophageal cancer tissues and normal tissues and identified differentially expressed genes. The differentially expressed genes were analyzed by bioinformatics methods. EC cells were treated with 25， 50， 100， 200， 400， 800 mg·L-1 Baitouweng Tang. EC cell viability was detected by Thiazolyl Blue （MTT） colorimetry. Cell cycle and apoptosis were measured by flow cytometry. The expression of BUB1 was measured by real time quantitative polymerase chain reaction （Real-time PCR）. The protein levels of BUB1， STAT3， phosphorylated （p）-STAT3， Cyclin B1 （CCNB1）， cyclin-dependent kinase 1 （CDK1）， B-cell lymphoma-2 （Bcl-2）， cysteinyl aspartate-specific proteinase（Caspase）-3， and Caspase-9 were measured by Western blot. The migration and invasion abilities of the cells were measured by wound-healing and Transwell invasion assays. ResultDifferentially expressed genes were primarily involved in biological processes， signaling pathways， and network construction related to cell mitosis， with BUB1 identified as a key core gene. Compared with the control group， Baitouweng Tang inhibited BUB1 expression （P<0.05，P<0.01）. In vitro experiments showed that compared with the control group， Baitouweng Tang could significantly inhibit the growth （P<0.05，P<0.01）， migration and invasion （P<0.05，P<0.01） of EC cells， induce apoptosis （P<0.05，P<0.01）， and cause G2/M phase increase （P<0.01）. After treatment with Baitouweng Tang， compared with the results in the control group， the expression of Caspase-3， and Caspase-9 in EC cells increased significantly （P<0.05，P<0.01）， while the expression of Bcl-2， BUB1， CCNB1， and CDK1 decreased significantly （P<0.05，P<0.01）. Moreover， the STAT3 signaling pathway was also found to play an important role in this process. ConclusionBaitouweng Tang may inhibit the growth of EC cells by downregulating BUB1 and mediating the STAT3 signaling pathway.

Considerations for Familial Chylomicronemia Diagnosis in the Era of Next-Generation Sequencing: A Latin American Perspective

Abstract Familial chylomicronemia syndrome (FCS) is an autosomal recessive disorder, characterized by alterations in the catabolism of chylomicrons and by increased levels of plasma triglycerides. It has been shown that about 60-90% of FCS patients have biallelic mutations in the LPL gene and the remaining patients have mutations in genes encoding proteins closely related to LPL function. The objective of this manuscript is to illustrate the different clinical scenarios of FCS presentation, and to guide practitioners on the usefulness of genetic tests in each of them. To this end, several published papers about recommendations for the diagnosis of FCS are discussed briefly, in addition to the presentation of several hypothetical cases, highlighting different clinical presentations and possible associated genetic findings. These cases illustrate the multiplicity of potential aspects of family history, clinical manifestations, biochemical parameters, and patterns of genetic variants found in genomic analyses of FCS.

Os subtipos moleculares de câncer versus o arsenal da indústria. qual deles determina o tratamento do câncer gástrico? / The molecular cancer subtypes versus the industry arsenal. which one drives gastric cancer treatment?

ABSTRACT Molecular medicine opened new horizons in understanding disease mechanisms and discovering target interventions. The wider availability of DNA and RNA sequencing, immunohistochemical analysis, proteomics, and other molecular tests changed how physicians manage diseases. The gastric cancer molecular classification proposed by The Cancer Genome Atlas Program divides gastric adenocarcinomas into four subtypes. However, the available targets and/or immunotherapies approved for clinical use seem to be dissociated from these molecular subtypes. Until a more reliable interpretation of the stupendous amount of data provided by the molecular classifications is presented, the clinical guidelines will rely on available actionable targets and approved therapies to guide clinicians in conducting cancer management in the era of molecular therapies.

RESUMO A medicina molecular abriu novos horizontes na compreensão dos mecanismos das doenças e na descoberta de intervenções alvo. A maior disponibilidade de sequenciação de DNA e RNA, análise imuno-histoquímica, proteômica e outros testes moleculares mudou a forma como os médicos conduzem as doenças. A classificação molecular do câncer gástrico proposta pelo Atlas do Genoma do Câncer divide os adenocarcinomas gástricos em quatro subtipos. No entanto, os alvos disponíveis e/ou imunoterapias aprovadas para uso clínico parecem estar dissociados desses subtipos moleculares. Até que seja apresentada uma interpretação mais confiável da estupenda quantidade de dados fornecidos pelas classificações moleculares, as diretrizes clínicas irão se basear nos alvos acionáveis disponíveis e nas terapias aprovadas para orientar os médicos na condução da gestão do câncer na era das terapias moleculares.

Holoprosencefalia alobar. reporte de caso

Desde el advenimiento de la ecografía obstétrica y estudios invasivos además genéticos fetales han ayudado en la detección antenatal de anormalidades congénitas siendo uno de los objetivos básicos de la vigilancia fetal anteparto. La combinación de ambas técnicas ofrece, hoy en día un abordaje completo en términos de diagnóstico prenatal. Se cree que muchos trastornos del desarrollo surgen de factores de riesgos genéticos y ambientales. Uno de estos es la holoprosencefalia, sirve como modelo para comprender diversas formas de etiología multifactorial. El análisis genómico, la epidemiología y estudios mecánicos de modelos animales han revelado que factores de riesgo interactúan para producir resultados de desarrollo adversos. La holoprosencefalia es consecuencia de factores genéticos y/o ambientales que interrumpen la especificación de la línea media del prosencéfalo en formación. Estas alteraciones dan lugar a una amplia gama de consecuencias fenotípicas para el cerebro y la cara del nuevo ser humano en formación. Son comunes en 1 de 250 fetos humanos, pero el 97% no sobrevive al nacimiento. La patogenia molecular precisa de la holoprosencefalia sigue siendo desconocida. Aquí, describimos nuestra comprensión de los principales factores impulsores que conducen a patologías de holoproscencefalia y elaboramos nuestro enfoque de genómica integrada multifactorial. Las tecnologías genómicas proporcionan una visión sin precedentes de la variación asociada a la enfermedad. A continuación, se describe un caso de diagnóstico prenatal de trisomía 13 y holoprosencefalia. En éste, se logró establecer un diagnóstico antenatal anatómico y genético preciso.

Since the advent of obstetric ultrasound and invasive studies, fetal genetics have helped in the antenatal detection of congenital abnormalities, being one of the basic objectives of antepartum fetal surveillance. The combination of both techniques currently offers a complete approach in terms of prenatal diagnosis. Many developmental disorders are thought to arise from genetic and environmental risk factors. One of these is holoprosencephaly, which serves as a model for understanding various forms of multifactorial etiology. Genomic analysis, epidemiology, and mechanistic studies of animal models have revealed that risk factors interact to produce adverse developmental outcomes. Holoprosencephaly results from genetic and/or environmental factors that disrupt the specification of the midline of the forming forebrain. These alterations result in a wide range of phenotypic consequences for the brain and face of the newly developing human being. They are common in 1 in 250 human fetuses, but 97% do not survive birth. The precise molecular pathogenesis of holoprosencephaly remains unknown. Here, we describe our understanding of the main drivers leading to holoproscencephaly pathologies and elaborate on our multifactorial integrated genomics approach. Genomic technologies provide unprecedented insight into disease-associated variation. A case of prenatal diagnosis of trisomy 13 and holoprosencephaly is described below. In this study, it was possible to establish an accurate anatomical and genetic antenatal diagnosis.

Errores innatos del metabolismo. avances en el diagnostico y terapeutica / Inborn errors of metabolism. Advances in diagnosis and therapeutic

Resumen Las novedades en el campo de los errores innatos del metabolismo (EIM) son espectaculares. Se han descrito nuevos EIM, se conoce mejor sus bases fisiopatológicas y las implicaciones para el organismo. Con la llegada de las nuevas técnicas de metabolómica, lípidomica y genómica se han multiplicado los avances en el diag nóstico y permiten explorar nuevas opciones terapéu ticas. Se ha establecido una nueva clasificación de los EIM en base a los más de 1.450 EIM identificados. Está irrumpiendo una nueva especialidad, que es la medici na metabólica. El cribado neonatal se estáempezando a universalizar y nos permite hoy en día, con tándem masas, el diagnóstico de más de 20 enfermedades me tabólicas del período neonatal que tienen opciones de tratamiento. Se están creando unidades de EIM para adultos para seguir niños con EIM que sobreviven a la enfermedad y con cada vez mejor calidad de vida y se diagnostican EIM que debutan en la adolescencia o laedad adulta. Aparecen las terapias personalizadas y las guías de práctica clínica para muchos EIM. Finalmente están emergiendo cada vez nuevas opciones terapéuticas que permiten una mayor supervivencia y mejor calidad de vida. La terapia génica convencional ya se está aplicando en algunos EIM.Sin embargo, las estrategias de edición de genes con terapias de ARN pueden permitir corregir la mutación genética mini mizando los problemas asociados con la terapia génica de compensación convencional.

Abstract The advances in the field of inborn errors of metabo lism (IEM) are spectacular. New IEM have been described, their pathophysiological bases and implications for the organism are better known. With the advent of new metabolomics, lipidomics and genomics techniques, advances in diagnosis have multiplied and allow new therapeutic options to be explored. A new IEM classi fication has been established based on the more than 1.450 IEM identified. A new specialty is emerging, which is metabolic medicine. Neonatal screening is becom ing universal and allows us today, with tandem mass, to diagnose more than 20 metabolic diseases of the neonatal period, with treatment options. IEM units for adults are being created to follow-up children with IEM who survive the disease and with an increasingly better quality of life, and some IEM that start in adolescence or adulthood are diagnosed. Personalized therapies and clinical practice guidelines appear for any IEM. Finally, new therapeutic options are emerging day to day that allow a longer survival and better quality of life. Con ventional gene therapy is already being applied in some IEM. However, gene editing strategies with RNA thera pies may allow the correction of the genetic mutation, minimizing the problems associated with conventional compensation gene therapy.

Herramientas de la medicina genómica para la práctica clínica: el ejemplo de la psiquiatría / Tools of genomic medicine for clinical practice: The example of psychiatry

La mayoría de los trastornos psiquiátricos tienen una heredabilidad de moderada a alta, con diferentes arquitecturas genéticas. Aunque la investigación genética en psiquiatría ha tenido un avance progresivo, sus hallazgos, interpretación e impacto en la psiquiatría clínica resultan desconocidos para la mayoría de los profesionales de salud mental. En este artículo se abordan conceptos clave sobre genética para el entendimiento de algunas entidades clínicas, con énfasis en la nomenclatura genética y los tipos de mutaciones. Particularmente, se plantea el rol de la herencia en los inicios de la investigación genética en psiquiatría, los diseños de estudio más utilizados y sus principales objetivos. Por otro lado, se revisan algunas bases de datos genéticas y genómicas que pueden ser de utilidad para la práctica clínica. Entre ellas destacan , ClinVar, Ensembl y . Finalmente, se plantea una viñeta clínica en donde es posible aplicar algunas de las herramientas de la medicina genómica. Debido a que la evidencia en genética psiquiátrica se basa en estudios realizados en poblaciones con origen ancestral europeo o norteamericano, es de suma relevancia desarrollar estudios locales para incrementar el conocimiento y la aplicación de la medicina genómica sobre poblaciones subrepresentadas.

Most psychiatric disorders are moderate to highly heritable, often with different genetic architectures. Although genetic research in psychiatry has progressed, its findings, interpretation, and impact on clinical psychiatry are unknown to most mental healthcare professionals. This article addresses key genetic concepts to understand some clinical entities, emphasizing genetic terminology and types of mutations. Particularly, we describe the role of heritability in the early days of psychiatry genetic research, the most used study designs, and their main objectives. On the other hand, we review some genetic and genomic databases useful for clinical practice. These include Online Mendelian Inheritance in Man, ClinVar, Ensembl, and The Single Nucleotide Polymorphism Database. Finally, a clinical vignette is presented in which we can apply genomic medicine tools. Since the evidence in psychiatric genetics is based on studies carried out in European or North American ancestral populations, we must develop local studies to increase the knowledge and application of genomic medicine on underrepresented populations.

Implementación asistencial de estudios genómicos aplicados al diagnóstico molecular / Implementation of genomic studies applied to molecular diagnostics

El Hospital Garrahan ha sido pionero en el diagnóstico molecular de patologías pediátricas en Argentina. Los avances tecnológicos de las últimas décadas en el área de la biología molecular, sentaron las bases para la optimización y ampliación del diagnóstico molecular a partir de la secuenciación masiva en paralelo de múltiples genes. El presente trabajo describe el proceso de implementación de los estudios de secuenciación de nueva generación y el desarrollo de la Unidad de Genómica en un hospital público pediátrico de alta complejidad, así como su impacto en las capacidades diagnósticas de enfermedades poco frecuentes de origen genético. La creación del Grupo Interdisciplinario de Estudios Genómicos constituyó la vía institucional para la toma de decisiones que implican la implementación de nuevos estudios genómicos y el establecimiento de prioridades diagnósticas, extendiendo la disponibilidad del diagnóstico molecular a más disciplinas. La Unidad de Genómica trabaja en diseñar las estrategias que permitan la mayor optimización de los recursos con los que cuenta el hospital, teniendo en cuenta el equipamiento disponible, las prioridades establecidas y la frecuencia de las distintas patologías. Se demuestra el salto significativo operado en nuestras capacidades diagnósticas, tanto en la variedad de enfermedades como en el número de genes analizados, habiendo estudiado a la fecha alrededor de 2.000 pacientes, muchos de los cuales ven de este modo finalizada su odisea diagnóstica. Los estudios de NGS se han convertido en una herramienta de la práctica diaria para la atención de un número importante de pacientes de nuestro hospital. Continuaremos trabajando para ampliar su aplicación a la mayor cantidad de patologías, a través de los mecanismos institucionales ya existentes (AU)

The Garrahan Hospital has been a pioneer in the molecular diagnosis of pediatric diseases in Argentina. The technological advances of the last decades in the area of molecular biology have laid the foundations for the optimization and expansion of molecular diagnostics through massive parallel sequencing of multiple genes. This study describes the process of implementation of next-generation sequencing studies and the development of the Genomics Unit in a public pediatric tertiary hospital, and its impact on the capacity to diagnose rare diseases of genetic origin. The creation of the Interdisciplinary Group of Genomic Studies constituted the institutional pathway for decision-making involving the implementation of new genomic studies and the establishment of diagnostic priorities, extending the availability of molecular diagnostics to additional disciplines. The Genomics Unit is working to design strategies that allow for optimization of the resources available to the hospital, taking into account the equipment available, the priorities established, and the frequency of the different diseases. It demonstrates the significant leap in our diagnostic capabilities, both in the variety of diseases and in the number of genes analyzed. To date, around 2,000 patients have been studies, many of whom have thus completed their diagnostic odyssey. NGS studies have become a tool in daily practice for the care of a significant number of patients in our hospital. We will continue working to expand its application to as many diseases as possible, through the existing institutional mechanisms (AU)

Review on Applicability of Bioinformatics in Current Research and Database Management

A generation of new science has evolved with the development of bioinformatics and computational biology, which have molecular biology as an integrated part. In the past decade, technological advances have promoted a prominent development in expertise and knowledge in the molecular basis of phenotypes. In Bioinformatics, biological data is evaluated by computational science and processed in a more statistical and meaningful way. It includes the collection classification storage and evaluation of biochemical and organic statistics using computers in particular as implemented in molecular genetics and genomics. Computational Biology and Bioinformatics are emerging branches of science and include the use of techniques and concepts from informatics statistics, mathematics, chemistry, biochemistry, physics and linguistics. Therefore, bioinformatics and computational biology have sought to triumph over many challenges of which a few are listed in this overview. This evaluation intends to provide insight into numerous bioinformatics databases and their uses in the analysis of biological records exploring approaches emerging methodologies strategies tools that can provide scientific meaning to the information generated.

Concordancia entre la prueba de puntuación de recurrencia de 21 genes y modelos clínico-patológicos predictivos en pacientes con cáncer de mama temprano en un centro oncológico en Colombia / Concordance between 21-gene recurrence score assay and clinicopathological predictive models in early-breast cancer patients cared for at a cancer center in Colombia

Resumen Introducción: La prueba genómica de recurrencia de 21 genes (PGR21) permite determinar la utilidad de la quimioterapia adyuvante en pacientes con cáncer de mama temprano luminal (CMTL). Se han desarrollado modelos predictivos adicionales, como las ecuaciones de Magee (EM), el modelo Predict (MP) y la puntuación del nomograma de la Universidad de Tennessee (NT). Objetivo: Evaluar la concordancia entre PGR21, EM, MP y NT. Métodos: Se incluyeron pacientes con CMTL unifocal y con resultados de PGR21, EM, MP y NT. Se efectuó subanálisis de mujeres mayores de 50 años. La concordancia se evaluó mediante índice kappa de Cohen (IK). Resultados: Se incluyeron 122 mujeres. La concordancia entre PGR21 y EM (IK = 0.35) y MP (IK = 0.24) fue aceptable (p < 0.001); entre PGR21 y NT fue inferior (IK = 0.16, p = 0.04). Se incluyeron 80 pacientes mayores de 50 años con datos suficientes para calcular los tres modelos. Se encontró concordancia entre la clasificación de bajo riesgo mediante PGR21 y los tres modelos combinados en 36/37 pacientes (valor predictivo negativo de 97.3 %). Conclusión: Se puede omitir la PGR21 en las mujeres mayores de 50 años con CMTL que se clasifica de bajo riesgo en los tres modelos predictivos.

Abstract Introduction: The genomic-based 21-gene recurrence score assay (21-GRSA) allows to determine the usefulness of adjuvant chemotherapy in patients with luminal-type early breast cancer (LTEBC). Additional predictive models have also been developed, such as Magee equations (ME), the Predict model (PM), and the Tennessee nomogram score (TNS). Objective: To evaluate the concordance between 21-GRSA, ME, PM and TNS. Methods: Patients with unifocal LTEBC and 21-GRSA, ME, PM and TNS results were included. A subgroup analysis of women older than 50 years was carried out. Concordance between the models and 21-GRSA was evaluated using Cohen's kappa index (KI). Results: One-hundred and twenty-two women were included. Concordance between 21-GRSA and ME (KI = 0.35) and PM (KI = 0.24) was fair (p < 0.001). Concordance between 21-GRSA and TNS was inferior (KI = 0.16, p = 0.04). Eighty patients older than 50 years with sufficient data to calculate all three predictive models were included. Concordance was found between the low-risk classification on 21-GRSA and all three combined models in 36/37 patients (negative predictive value of 97.3%). Conclusion: 21-GRSA can be omitted in women older than 50 years with LTEBC classified with low risk scores on all three predictive models.

Dried blood spots: a robust tool for malaria surveillance in countries targeting elimination

With the advancements in analytical and molecular techniques, Dried Blood Spots (DBS) are re-emerging as attractive and cost-effective alternatives for global health surveillance. The use of DBS has been well-characterized in the neonatal screening of metabolic diseases, therapeutic screening as well as in epidemiological studies for biomonitoring. Malaria is one such infectious disease where DBS use can expedite molecular surveillance for assessing drug resistance and for refining drug usage policies. In India, malaria cases have reduced significantly over the past decade but to achieve malaria elimination by 2030, country-wide DBS-based screening should be conducted to identify the presence of molecular markers of artemisinin resistance and to study parasite reservoirs in asymptomatic populations. DBS has wide applications in genomics, proteomics, and metabolomic studies concerning both host and pathogen factors. Hence, it is a comprehensive tool for malaria surveillance that can capture both host and parasite information. In this review, we elucidate the current and prospective role of DBS in malaria surveillance and its applications in studies ranging from genetic epidemiology, parasite and vector surveillance, drug development and polymorphisms to ultimately how they can pave the roadmap for countries aiming malaria elimination

Analysis of potential diagnostic genes for eosinophilic chronic rhinosinusitis with nasal polyps based on GEO datasets / 中国耳鼻咽喉头颈外科

OBJECTIVE To utilize RNA sequencing(RNA-seq)data from the GEO database to identify genes with potential diagnostic value for eosinophilic chronic rhinosinusitis with nasal polyps(ECRSwNP).METHODS Three datasets were obtained,and samples were divided into ECRSwNP and nonECRSwNP groups based on the expression levels of CST1 and CLC.A diagnostic model for ECRSwNP was established using R software and algorithms,and its accuracy was assessed.RESULTS The samples were grouped as follows:GSE136825(ECRSwNP 7,nonECRSwNP 19),GSE72713(ECRSwNP 3,nonECRSwNP 3),and GSE179265(ECRSwNP 11,nonECRSwNP 2).The diagnostic performance of the upregulated gene model(ADH1C,CCL26,HRH1,NOS2)and the downregulated gene model(LCN2,MUC5B,PLAT,TMEM45A,XDH)constructed based on the support vector machine(SVM)algorithm for ECRSwNP was excellent.CONCLUSION The diagnostic genes identified by the SVM model may serve as biological markers for the non-invasive diagnosis of ECRSwNP and potentially play a crucial role in the pathogenesis of ECRSwNP.

Analysis on the application of omics and its combination technique in toxicity study of Chinese materia medica / 国际中医中药杂志

Various omics and their combined techniques have certain applications in the study of the mechanism of toxicity of Chinese materia medica, the screening of toxic biomarkers, and the prediction of the toxicity of Chinese materia medica. It has been found that the current application scope of exploring the toxicity of Chinese materia medica based on omics technology still needs to be expanded. In terms of organ damage caused by Chinese materia medica, omics technology is mostly used to study hepatotoxicity. In terms of the attenuation mechanism of TCM, proteomics and metabolomics have more advantages, and the two have potential prospects in exploring the processing or compatibility of TCM to reduce toxicity and increase efficiency. The combination of omics technology with network pharmacology, bioinformatics and other technologies is more conducive to providing references for the in-depth study of the toxicity of Chinese materia medica.

Diagnostic value of metagenomic next-generation sequencing in tuberculous meningitis / 中华传染病杂志

Objective:To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) in tuberculous meningitis (TBM).Methods:From August 1, 2020 to August 31, 2022, 99 patients with suspected TBM admitted to the Tuberculosis Diagnosis and Treatment Center, Hangzhou Chest Hospital, Zhejiang University School of Medicine were enrolled. The cerebrospinal fluid (CSF) was tested for mNGS, GeneXpert Mycobacterium tuberculosis/rifampin (GeneXpert MTB/RIF) and mycobacterium culture. The sensitivity, specificity, positive predictive value, negative predictive value, agreement rate, Kappa value of the diagnostic efficacy of the three test methods were compared.The receiver-operating characteristic (ROC) curve of the diagnostic efficacy of mNGS was drawn. Chi-square test and rank sum test were used for statistical analysis. Results:Among the 99 suspected patients with TBM, 67 were diagnosed with TBM and 32 were non-TBM. Based on the results of 67 cases clinically diagnosed with TBM, the sensitivity, specificity, positive predictive value, negative predictive value, agreement rate and Kappa value of mNGS for the diagnosis of TBM were 82.1%, 100.0%, 100.0%, 72.7%, 87.9% and 0.748, respectively. The sensitivity of mNGS was higher than that of GeneXpert MTB/RIF (50.7%) and mycobacterium culture (28.4%). The differences were statistically significant ( χ2=12.61 and 32.42, respectively, both P<0.01). The detection time of mNGS was 1.0 (1.0, 2.0) day, which was shorter than 42.0 (42.0, 42.0) days of mycobacterium culture with statistical significance ( Z=10.80, P<0.001). ROC curve analysis showed that mNGS had the best diagnostic efficacy when the number of Mycobacterium tuberculosis sequences in CSF was one. Conclusions:The sensitivity and specificity of mNGS in the diagnosis of TBM are high, and the detection time is shorter, which could be used in the early diagnosis of TBM.

Research progress in multi-omics biomarkers involved in post-traumatic stress disorder / 中华创伤杂志

Post-traumatic stress disorder (PTSD) is a psychiatric illness induced by exposure to severe stress-induced traumatic events. Repeated traumatic re-experience, avoidance, negative cognition and emotional changes seriously reduce the quality of life of PTSD patients. Currently, it is urgent to further clarify the etiology and molecular mechanism of PTSD in order to guide the diagnosis and treatment of PTSD. Considering the underlying pathophysiology is not entirely known, to identify the pertinent biomarkers of PTSD is critical in researching its incidence and progression. In contrast with the single-omics researches, multi-omics studies may methodically expand on biomolecular interactions from a range of angles, creating a new potential to comprehend the development of complicated human illnesses. Therefore, the authors review the research progress in PTSD biomarkers from aspects of genomics, transcriptomics and proteomics, hoping to provide a reference for future research and treatment of PTSD.

Osteosarcoma with bone metastasis or pulmonary metastasis show distinct genomic manifestations / 中华骨科杂志

Objective:To investigate the genomic manifestation and pathogenesis of osteosarcoma with different relapse pattens, which were respectively initially presented with bone metastasis or pulmonary metastasis.Methods:From May 1, 2021 to October 1, 2021, 38 fresh tumor specimens and some paraffin-embedded specimens of high-grade osteosarcoma were collected in Peking University People's Hospital, including 29 males and 9 females, aged 19.6±2.2 years (range, 6-61 years). Among the 38 cases, 12 cases had initial bone metastasis (group A) and 26 cases had initial lung metastasis (group B), of which 15 cases (40%, 15/38) had paired specimens of primary and metastatic lesions. Based on Illumina NovaSeq 6000, we analyzed whole-exome sequencing (WES) as well as transcriptome for osteosarcoma with paired samples in different relapse patterns. During all their treatment courses, we also collected their paired samples to reveal these tumors' evolution. We sought to redefine disease subclassifications for osteosarcoma based on genetic alterations and correlate these genetic profiles with clinical treatment courses to elucidate potential evolving cladograms.Results:We found that osteosarcoma in group A mainly carried single-nucleotide variations (83%, 10/12), displaying higher tumor mutation burden [4.9 (2.8, 12.0) & 2.4 (1.4, 4.5), P=0.010] and neoantigen load [743.0 (316.5, 1,034.5) & 128.5 (49.0, 200.5), P=0.003], while those in group B mainly exhibit structural variants (58%, 15/26). The mutation spectrum showed that there was a significant difference in age-related gene imprinting 1 between the bone metastasis group and the lung metastasis group ( P=0.005). Samples were randomly selected from group A (3 patients) to investigate immunologic landscape by multiplex immunohistochemistry, from which we noticed tertiary lymphatic structure from one patient from group A. High conservation of reported genetic sequencing over time was found in their evolving cladograms. Conclusion:Osteosarcoma with mainly single-nucleotide variations other than structural variants might exhibit biological behavior predisposing toward bone metastases with older in age as well as better immunogenicity in tumor microenvironment.

Precision medicine in Parkinson′s disease: current status and future prospects / 中华神经科杂志

Parkinson′s disease is a common neurodegenerative disease with high clinical heterogeneity. With the development of precision medicine, numerous researches have been conducted on the pathological mechanism, clinical classification, diagnosis and treatment of Parkinson′s disease through multi-omics, bioformatics and molecular imaging. This article will elaborate the current practice and future research directions of precision medicine in the diagnosis and treatment of Parkinson′s disease.

Identification and characterization of one Spiroplasma species isolated from blood culture of a rare case of sepsis / 中华微生物学和免疫学杂志

Objective:To identify and characterize one Spiroplasma strain (designated as DGKH1) isolated from the blood of a patient with sepsis. Methods:The traditional bacterial culture, staining, morphological observation, physiological and biochemical identification, 16S rRNA gene sequencing, phylogenetic analysis, genome sequencing, and the genome-related index analysis were performed to accurately determine the taxonomic status of the strain DGKH1. Antibiotic susceptibility testing was performed using a specific kit for culturing and testing Ureaplasma urealyticum/ Metamycoplasma hominis. Results:The strain DGKH1 could weakly grow on Columbia blood agar, chocolate agar, and Haemophilus chocolate 2 agar. However, it did not grow in liquid culture medium containing tetracycline (4 μg/ml), doxycycline (1 μg/ml), minocycline (1 μg/ml), josamycin (2 μg/ml), roxithromycin (1 μg/ml), clarithromycin (1 μg/ml), or telithromycin (1 μg/ml). DGKH1 resembling Metamycoplasma hominis formed "fried egg-like colonies" on Mycoplasma solid culture medium. DGKH1 could not be stained by Gram staining. When observed under transmission electron microscopy (TEM) using phosphate buffer as the matrix, the bacteria were spiral-shaped. Results of 16S rRNA gene sequence alignment showed that DGKH1 was highly similar (99.85%) to Spiroplasma eriocheiris CCTCC M 207170 T. However, the urea decomposition test was positive, which was different from all of the known Spiroplasma species. The phylogenetic analysis based on whole genome showed that DGKH1 was clustered in a small branch along with Spiroplasma eriocheiris CCTCC M 207170 T. However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 94.14% and 56.00%, respectively, both below the threshold for prokaryotic species identification. Conclusions:DGKH1 represented a potential new species of genus Spiroplasma, closely related to Spiroplasma eriocheiris. Some microbiological characteristics of DGKH1 were similar to Mycoplasmas. However, the natural host and epidemiological data of DGKH1 need to be further studied.