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.

Polymyxin resistance caused by large-scale genomic inversion due to IS26 intramolecular translocation in Klebsiella pneumoniae

Polymyxin B and polymyxin E (colistin) are presently considered the last line of defense against human infections caused by multidrug-resistant Gram-negative organisms such as carbapenemase-producer Enterobacterales, Acinetobacter baumannii, and Klebsiella pneumoniae. Yet resistance to this last-line drugs is a major public health threat and is rapidly increasing. Polymyxin S2 (S2) is a polymyxin B analogue previously synthesized in our institute with obviously high antibacterial activity and lower toxicity than polymyxin B and colistin. To predict the possible resistant mechanism of S2 for wide clinical application, we experimentally induced bacterial resistant mutants and studied the preliminary resistance mechanisms. Mut-S, a resistant mutant of K. pneumoniae ATCC BAA-2146 (Kpn2146) induced by S2, was analyzed by whole genome sequencing, transcriptomics, mass spectrometry and complementation experiment. Surprisingly, large-scale genomic inversion (LSGI) of approximately 1.1 Mbp in the chromosome caused by IS26 mediated intramolecular transposition was found in Mut-S, which led to mgrB truncation, lipid A modification and hence S2 resistance. The resistance can be complemented by plasmid carrying intact mgrB. The same mechanism was also found in polymyxin B and colistin induced drug-resistant mutants of Kpn2146 (Mut-B and Mut-E, respectively). This is the first report of polymyxin resistance caused by IS26 intramolecular transposition mediated mgrB truncation in chromosome in K. pneumoniae. The findings broaden our scope of knowledge for polymyxin resistance and enriched our understanding of how bacteria can manage to survive in the presence of antibiotics.

Effect analysis of day surgery cost control based on propensity value matching / 中华医院管理杂志

Objective:To analyze the composition, the changes of expense structure and the influencing factors of hospitalization expenses, for reference in optimizing the cost control of day surgery.Methods:Collection of the first page data of patients with the top three diseases(varicose veins of lower limbs, chronic cholecystitis and varicocele)in the day surgery volume ranking in three tertiary general hospitals in a city in 2020. The confounding factors were eliminated through propensity matching. The structural change of hospitalization expenses was analyzed by structural change degree, and the influencing factors of hospitalization expenses were analyzed by grey correlation degree and multiple linear regression.Results:After 1∶1 propensity matching of the first page data of 752 patients with day surgery and non day surgery, 98 patients with lower extremity varicose veins, 356 patients with chronic cholecystitis and 38 patients with varicocele were finally included. Compared with non day hand, the total hospitalization cost of day surgical instruments decreased, and the cost structure changes of chronic cholecystitis, varicocele and varicose veins of lower limbs were 14.59%, 6.20% and 16.20% respectively. Among them, the general medical service fee, nursing fee and examination and laboratory fee showed a downward trend, and the fees of materials and drugs showed an upward trend. General medical service fee, nursing fee, examination and laboratory fee, clinical diagnosis fee, treatment fee, drug fee, material fee and other expenses presented a high correlation with the cost of day surgery(grey correlation>0.90). The payment method, wound healing type and discharge diagnosis can influence the cost of day surgery( P<0.05). Conclusions:Compared with non daytime surgery, the total hospitalization cost of day surgery has a certain cost control effect, but it can not reduce the cost of all projects. The main influencing factors are the internal composition of the cost, payment method and so on. The hospitals should focus on tapping the internal cost control potential of day surgery and further expanding the coverage of day surgery diseases.

In silico analysis of genomic variables associated to HPV16 integration sites / Análisis in silico de variables genómicas asociadas a sitios de integración de HPV16

Background: Despite current prophylactic interventions, a significant proportion of patients suffers a cancer-specific mortality, leading to a global awareness of the importance of identifying factors associated to the etiology of HPV-associated cancer. According to this, HPV-DNA integration into human genome is an important event in the pathogenesis. Purpose: To identify in silico, molecular regions of the genome where the HPV integration events occur Methods: We performed a bioinformatic study based on a systematic search in Medline through PubMed, Embase and Lilacs from inception to April 2019. We used the UCSC Genome Browser Home (https://genome.ucsc.edu) to evaluate the genetic environment. Results: HPV integration sites by anatomical location related to cervical cancer were 374 (61%). In addition, 325 (87%) of these integration sites had HPV-16, 21 (5%) had HPV-18 and 28 (7%) had another type of genotype. Oro-pharyngeal cavity was the second anatomic site with 162 (26%) integration sites. It is noteworthy that the HPV-16 was found integrated into 160 (99%) analyzed sites. Conclusion: Our results suggest that many of the integration sites reported in the scientific literature are HPV 16 from squamous cell carcinomas and 50% of HPV16 were integrated into transcriptional units that might affect the expression of gene target.

Antecedentes: A pesar de las intervenciones profilácticas actuales, una proporción significativa de pacientes muere debido al cáncer, lo que aumenta la conciencia global de la importancia de identificar los factores asociados a la etiología del cáncer asociado al VPH. Según esto, la integración del ADN-VPH en el genoma humano es un evento importante en la patogénesis. Propósito: Identificar in silico, las regiones moleculares del genoma donde ocurren los eventos de integración del VPH Métodos: Realizamos un estudio bioinformático basado en una búsqueda sistemática en Medline a través de PubMed, Embase y Lilacs desde el inicio hasta abril de 2019. Utilizamos el UCSC Genome Browser Home (https://genome.ucsc.edu) para evaluar el entorno genético. Resultados: Los sitios de integración del VPH relacionados con el cáncer de cuello uterino fueron 374 (61%). Además, 325 (87%) de estos sitios de integración tenían VPH-16, 21 (5%) tenían VPH-18 y 28 (7%) tenían otro tipo de genotipo. La cavidad orofaríngea fue el segundo sitio anatómico con 162 (26%) sitios de integración. Es de destacar que el VPH-16 se encontró integrado en 160 (99%) sitios analizados. Conclusión: Nuestros resultados sugieren que muchos de los sitios de integración reportados en la literatura científica que presentan al VPH-16 son carcinomas de células escamosas y que el 50% de estos VPH-16 se integraron en unidades transcripcionales que podrían afectar la expresión de algún gen objetivo.

Hospitalization Expense for Patients with Cerebral Infarction: Based on Degree of Structural Variation and Grey Correlation / 中国康复理论与实践

Objective:To analyze internal composition of hospitalization expense for patients with cerebral infarction. Methods:Data of hospitalization expenses from patients with cerebral infarction discharged from 2014 to 2018 were collected, and analyzed with grey correlation and degree of structural variation. Results:The costs for rehabilitation treatment, medicines and consumables mainly contributed to structural variation, accumulated to 74.63%. The costs for rehabilitation treatment (0.982), medicine (0.979), imaging (0.978) and laboratory tests (0.972) were the most relative to the average expense of hospitalization. Conclusion:It is preliminarily successful for cost control, and needs further impove to respond the contribution of professionals.

Analysis of unmapped regions associated with long deletions in Korean whole genome sequences based on short read data

While studies aimed at detecting and analyzing indels or single nucleotide polymorphisms within human genomic sequences have been actively conducted, studies on detecting long insertions/deletions are not easy to orchestrate. For the last 10 years, the availability of long read data of human genomes from PacBio or Nanopore platforms has increased, which makes it easier to detect long insertions/deletions. However, because long read data have a critical disadvantage due to their relatively high cost, many next generation sequencing data are produced mainly by short read sequencing machines. Here, we constructed programs to detect so-called unmapped regions (UMRs, where no reads are mapped on the reference genome), scanned 40 Korean genomes to select UMR long deletion candidates, and compared the candidates with the long deletion break points within the genomes available from the 1000 Genomes Project (1KGP). An average of about 36,000 UMRs were found in the 40 Korean genomes tested, 284 UMRs were common across the 40 genomes, and a total of 37,943 UMRs were found. Compared with the 74,045 break points provided by the 1KGP, 30,698 UMRs overlapped. As the number of compared samples increased from 1 to 40, the number of UMRs that overlapped with the break points also increased. This eventually reached a peak of 80.9% of the total UMRs found in this study. As the total number of overlapped UMRs could probably grow to encompass 74,045 break points with the inclusion of more Korean genomes, this approach could be practically useful for studies on long deletions utilizing short read data.

The gene polymorphism study of Mycobacterium tuberculosis in the drug-resistance surveillance and epidemi-ological survey field / 中国基层医药

Tuberculosis is a chronic infectious diseases caused by Mycobacterium tuberculosis(MTB).As the drug-resistance characteristics are different in patients with various genotypes,thus,the gene polymorphism study have critical clinical significance.Among the all kinds of techniques,some have been used to analyze polymorphism for a long time and new development in that respect has also been made recently.On the other hand,some techniques are e-merging but demonstrate promising application prospects.This study summarizes the gene polymorphism study of MTB which have been used or are emerging in recent years,and points out a few shortcomings briefly.Our object is to make a contribution to theoretical basis and knowledge accumulation in the drug-resistance and epidemiological survey field.

Mutations detection of circulating tumor DNA in patients with hepatocellular carcinoma and its clinical significance / 国际外科学杂志

Mutations detection of circulating tumor DNA can be divided into quantitative and qualitative classifications:the forumer mainly detects the total amount of circulating DNA (serum or plasma),whereas the latter mainly detects the specific genetic variations in serum or plasma DNA,such as gene mutations,methylations of tumor suppressor genes,and microsatellite alterations,etc.Both of them may reflect the tumor presence and disease severity.In this paper,mutations detection and its clinical significance of circulating tumor DNA in patients with hepatocellular carcinoma are reviewed.

Analysis on Structural Variation and Disability Index of Spinal-Pelvic in the High School Students with Low Back Pain / 대한스포츠의학회지

The purpose of this study was to evaluate the prevalence rate of low back pain (LBP) in the high school students and to analyze the differences and correlations with the spinal-pelvic structural variations and disability index with LBP. The subjects are 499 high school students (236 males, 263 females: mean age, 16.38 years). They were assessed for LBP with the numerical rating scale (NRS) and for disability with the Korean version Oswestry disability index (KODI). All subjects were to take the plain radiographic examination for spinal-pelvic structural variations including thoracic, lumbar, thoracolumbar Cobb's angle, lumbar lordotic curve, sacral slope, pelvic tilt and pelvic incidence. All subjects were divided into two groups by NRS scores (0, 1=no/minimum pain group [NMP group], 2-10=low back pain group [LBP group]). The prevalence rate of LBP of all subjects was 56.7% (n=283). NRS and total KODI scores were higher in the LBP group (3.38 cm/11.83%) than NMP group (0.07 cm/2.74%) (p0.05). NRS had significantly positive correlation with KODI (p0.05). In conclusion, this study showed high prevalence rate of LBP in the high school students, but did not show significant correlations with the spinal-pelvic structural variations and disability index.

Association between methylenetetrahydrofolate reductase gene C677T polymorphism and diabetic kidney disease in Chinese population: a meta-analysis / 中华老年医学杂志

Objective To evaluate the association between methylenetetrahydrofolate reductase gene (MTHFR) C677T polymorphism and diabetic kidney disease in Chinese population.Methods After searching the related literatures from PubMed,Medline,EMBASE databases and common Chinese journal literature databases,meta-analysis was performed to assess the association of MTHFR C677T polymorphism with diabetic kidney disease according to the principles of systematic review based on the recessive model and dominant model respectively.Fixed effect model (M-H) was used to pool odd ratio (OR) after heterogeneity test.The Begg and Egger analysis were conducted to evaluate the publication bias.Results 10 literatures including a total of 2018 cases were included in the metaanalysis.No significant heterogeneity was detected.Data were pooled by fixed effect model.The total OR was 2.41 (95％CI=1.85～3.13) and 2.33 (95％CI=1.82～2.98) in recessive and dominant models respectively.No obvious publication bias was observed by Begg and Egger analysis.Conclusions The T allele of C677T polymorphism in MTHFR gene is positively associated with diabetic kidney disease in Chinese population.

AnsNGS: An Annotation System to Sequence Variations of Next Generation Sequencing Data for Disease-Related Phenotypes / 대한의료정보학회지

OBJECTIVES: Next-generation sequencing (NGS) data in the identification of disease-causing genes provides a promising opportunity in the diagnosis of disease. Beyond the previous efforts for NGS data alignment, variant detection, and visualization, developing a comprehensive annotation system supported by multiple layers of disease phenotype-related databases is essential for deciphering the human genome. To satisfy the impending need to decipher the human genome, it is essential to develop a comprehensive annotation system supported by multiple layers of disease phenotype-related databases. METHODS: AnsNGS (Annotation system of sequence variations for next-generation sequencing data) is a tool for contextualizing variants related to diseases and examining their functional consequences. The AnsNGS integrates a variety of annotation databases to attain multiple levels of annotation. RESULTS: The AnsNGS assigns biological functions to variants, and provides gene (or disease)-centric queries for finding disease-causing variants. The AnsNGS also connects those genes harbouring variants and the corresponding expression probes for downstream analysis using expression microarrays. Here, we demonstrate its ability to identify disease-related variants in the human genome. CONCLUSIONS: The AnsNGS can give a key insight into which of these variants is already known to be involved in a disease-related phenotype or located in or near a known regulatory site. The AnsNGS is available free of charge to academic users and can be obtained from http://snubi.org/software/AnsNGS/.

Clinical Applications of Chromosomal Microarray Analysis

Chromosomal microarray analysis (CMA) enables the genome-wide detection of submicroscopic chromosomal imbalances with greater precision and accuracy. In most other countries, CMA is now a commonly used clinical diagnostic test, replacing conventional cytogenetics or targeted detection such as FISH or PCR-based methods. Recently, some consensus statements have proposed utilization of CMA as a first-line test in patients with multiple congenital anomalies not specific to a well-delineated genetic syndrome, developmental delay/intellectual disability, or autism spectrum disorders. CMA can be used as an adjunct to conventional cytogenetics to identify chromosomal abnormalities observed in G-banding analysis in constitutional or acquired cases, leading to a more accurate and comprehensive assessment of chromosomal aberrations. Although CMA has distinct advantages, there are several limitations, including its inability to detect balanced chromosomal rearrangements and low-level mosaicism, its interpretation of copy number variants of uncertain clinical significance, and significantly higher costs. For these reasons, CMA is not currently a replacement for conventional cytogenetics in prenatal diagnosis. In clinical applications of CMA, knowledge and experience based on genetics and cytogenetics are required for data analysis and interpretation, and appropriate follow-up with genetic counseling is recommended.

Structural variation in the brown alga Sargassum cymosum and its effects on associated amphipod assemblages

The presence of diverse biological substrates adds complexity to coastal landscapes and increases the number of ecological niches that can be used by the mobile epifauna. Studies on the influence of structural complexity have focused mainly on algal host species, but there is little information about the influence of intraspecific structural variation on the associated mobile epifauna. In this work, we examined whether intraspecific variation in the brown alga Sargassum cymosum influenced the structure of amphipod assemblages on two shores with different wave exposure. At least 15 fronds were randomly sampled at Fortaleza and Perequê-Mirim beaches, on the Atlantic coast of São Paulo state, southeastern Brazil, and 12 variables were measured for each alga. The amphipods were identified and counted. The greatest structural variation in S. cymosum occurred within shores, whereas the differences between shores were mainly related to algal size. These characteristics influenced amphipod assemblages differently on each shore, with the greatest effects being associated with variables related to morphological complexity, such as holdfast size, the number and size of branches, and the extent of cover by sessile colonial animals. These findings show that monospecific algal banks are not homogeneous, and that morphological differences and interactions with other biological substrates can influence the mobile epifaunal assemblages.

A presença de substratos biológicos aumenta a complexidade dos ambientes costeiros, proporcionando maior número de nichos ecológicos para a epifauna vágil. Estudos sobre os efeitos da complexidade estrutural das algas têm enfocado principalmente as espécies presentes entre os seus ramos, porém há poucos dados sobre a influência da variação estrutural intra-específica sobre essa fauna. Neste trabalho, foi analisada a influência da variação da alga parda Sargassum cymosum sobre a estrutura da assembléia de anfípodes entre duas praias com diferentes graus de exposição às ondas, e em cada uma delas, no SE do Brasil. Pelo menos 15 frondes foram individualmente coletadas aleatoriamente nos costões das praias de Fortaleza e Perequê-Mirim, e diversas variáveis (12) foram medidas para cada fronde de alga. Os anfípodes foram identificados e contados. As maiores variações nas características de S. cymosum foram obtidas em cada praia, enquanto que diferenças entre as praias foram principalmente relacionadas ao tamanho das algas. Estas características influenciaram as assembléias de anfípodes de maneira diferente em cada praia, sendo que os maiores efeitos foram atribuídos a variáveis relacionadas com a morfologia das algas como o tamanho do apressório, o número e tamanho dos ramos e a cobertura por organismos coloniais sésseis. Portanto, bancos monoespecíficos de algas não são homogêneos e tanto as diferenças morfológicas como as interações com outros substratos biológicos podem influenciar as assembléias da epifauna vágil.