Machine learning models-based on integration of next-generation sequencing testing and tumor cell sizes improve subtype classification of mature B-cell neoplasms.

Background: Next-generation sequencing (NGS) panels for mature B-cell neoplasms (MBNs) are widely applied clinically but have yet to be routinely used in a manner that is suitable for subtype differential diagnosis. This study retrospectively investigated newly diagnosed cases of MBNs from our laboratory to investigate mutation landscapes in Chinese patients with MBNs and to combine mutational information and machine learning (ML) into clinical applications for MBNs, especially for subtype classification. Methods: Samples from the Catalogue Of Somatic Mutations In Cancer (COSMIC) database were collected for ML model construction and cases from our laboratory were used for ML model validation. Five repeats of 10-fold cross-validation Random Forest algorithm was used for ML model construction. Mutation detection was performed by NGS and tumor cell size was confirmed by cell morphology and/or flow cytometry in our laboratory. Results: Totally 849 newly diagnosed MBN cases from our laboratory were retrospectively identified and included in mutational landscape analyses. Patterns of gene mutations in a variety of MBN subtypes were found, important to investigate tumorigenesis in MBNs. A long list of novel mutations was revealed, valuable to both functional studies and clinical applications. By combining gene mutation information revealed by NGS and ML, we established ML models that provide valuable information for MBN subtype classification. In total, 8895 cases of 8 subtypes of MBNs in the COSMIC database were collected and utilized for ML model construction, and the models were validated on the 849 MBN cases from our laboratory. A series of ML models was constructed in this study, and the most efficient model, with an accuracy of 0.87, was based on integration of NGS testing and tumor cell sizes. Conclusions: The ML models were of great significance in the differential diagnosis of all cases and different MBN subtypes. Additionally, using NGS results to assist in subtype classification of MBNs by method of ML has positive clinical potential.

MYD88-Mutated Chronic Lymphocytic Leukaemia/Small Lymphocytic Lymphoma as a Distinctive Molecular Subgroup Is Associated with Atypical Immunophenotypes in Chinese Patients.

Chronic lymphocytic leukaemia/small lymphocytic lymphoma (CLL/SLL) is a heterogeneous disease in Western and Chinese populations, and it is still not well characterized in Chinese patients. Based on a large cohort of newly diagnosed CLL/SLL patients from China, we investigated immunophenotypes, genetic abnormalities, and their correlations. Eighty-four percent of the CLL/SLL patients showed typical immunophenotypes with scores of 4 or 5 points in the Royal Marsden Hospital (RMH) scoring system (classic group), and the remaining 16% of patients were atypical with scores lower than 4 points (atypical group). Trisomy 12 and variants of TP53, NOTCH1, SF3B1, ATM, and MYD88 were the most recurrent genetic aberrations. Additionally, unsupervised genomic analysis based on molecular genetics revealed distinctive characteristics of MYD88 variants in CLL/SLL. By overlapping different correlation grouping analysis from genetics to immunophenotypes, the results showed MYD88 variants to be highly related to atypical CLL/SLL immunophenotypes. Furthermore, compared with mantle cell lymphoma (MCL), the genetic landscape showed potential value in clinical differential diagnosis of atypical CLL/SLL and MCL patients. These results reveal immunophenotypic and genetic features, and may provide insights into the tumorigenesis and clinical management of Chinese CLL/SLL patients.

Prevalence and diversity of Trichomonas gallinae in meat pigeons (Columba livia) in Guangdong Province, People's Republic of China.

Pigeon farming for meat has developed into an important economic industry in most countries, especially in China. Trichomoniasis, caused by the protozoan parasite Trichomonas gallinae, is a worldwide disease in pigeons. However, studies of the prevalence and distribution of T. gallinae lineages in domestic pigeons in southern China are limited. In this study, a total of 636 pigeon throat swabs samples from four regions in Guangdong Province were screened for T. gallinae by in vitro culture assays and microscopy. The results revealed an overall prevalence of T. gallinae infection in southern China of 26.6% (169/636). There were significant differences in the infection rate of T. gallinae between the four regions (χ2 = 117.948, df = 4, P = 0.000), with up to 44.6% in the Pearl River Delta region. The infection rate of young pigeons was as high as 70.8%. The rDNA sequences (18S rRNA/ITS1-5.8S rRNA-ITS2) of 153 positive samples were amplified and sequenced. Results identified 58.2% (89/153) overall as ITS-A (18S-VI) (also known as ITS-OBT-Tg-1) and 41.8% (64/153) as ITS-B (18S-IV) (also known as ITS-OBT-Tg-2). Thus, ITS-A (18S-VI) was the dominant T. gallinae genotype in southern China, especially in young pigeon (97.0%, 32/33). In conclusion, a high prevalence of T. gallinae infection in domestic pigeons was identified in southern China, particularly in the Pearl River Delta region. The ITS-A (18S-VI) was the dominant genotype highly pathogenic, which may weaken the immune system of pigeons, and cause a negative impact on the development of the pigeon industry in China.

Virome of Rhipicephalus ticks by metagenomic analysis in Guangdong, southern China.

Tick-borne viruses (TBVs) have increasingly caused a global public health concern. This study collected Rhipicephalus ticks in Guangdong, southern China to identify RNA viruses. Meta-transcriptome analysis revealed the virome in Rhipicephalus ticks, resulting in the discovery of 10 viruses, including Lihan tick virus, Brown dog tick phlebovirus 1 and 2 in the family Phenuiviridae, Mivirus and Wuhan tick virus 2 in the family Chuviridae, Wuhan tick virus 1 in the family Rhabdoviridae, bovine hepacivirus in the family Flaviviridae, Guangdong tick quaranjavirus (GTQV) in the family Orthomyxoviridae, Guangdong tick orbivirus (GTOV) in the family Reoviridae, and Guangdong tick Manly virus (GTMV) of an unclassified family. Phylogenetic analysis showed that most of these TBVs were genetically related to the strains in countries outside China, and GTQV, GTOV, and GTMV may represent novel viral species. These findings provided evidence of the long-distance spread of these TBVs in Guangdong, southern China, suggesting the necessity and importance of TBV surveillance.

Efficient and reusable photocatalytic river water disinfection by addictive graphitic carbon nitride/magnesium oxide nano-onions with particular "nano-magnifying glass effect".

Photocatalytic disinfection is a promising way to combat bacterial pollution in the water environment. Inefficient use of visible light and undirected diffusion of reactive oxygen species (ROS) reduce photocatalytic disinfection efficiency. Herein, inspired by the concentrating effect of convex lens, photocatalysts with particular "nano-magnifying glass effect" (TCNMgNOs) were designed by embedding magnesium oxide with "converge effect" into the tailored hierarchical triple-shell porous g-C3N4 with "one light multi-purpose effect" to boost the visible-light utilization. Meanwhile, the ATPase hydrolysis homeostasis of bacteria was destroyed by TCNMgNOs to achieve the targeted movement of ROS. The results confirmed that the photocatalytic sterilization efficiency of TCNMgNOs was amplified by 30 times over g-C3N4, which was achieved by focusing visible light, multiple reflecting visible light and light transmission within the porous thin shells as well as the "addictive sterilization mechanism". The sterilization efficiency still maintains 98.8 % (15 min) after 6 rounds recycling and reusing in practical river water disinfection. A novel pathway for fighting against microbial contaminants in natural water was explored.

Enhanced functional properties of chitosan films incorporated with curcumin-loaded hollow graphitic carbon nitride nanoparticles for bananas preservation.

The exploration of novel functional packaging films is of great scientific and technological interest. Herein, a novel chitosan/hollow g-C3N4/curcumin (CS-HCNS-Cur) biocomposite films was successful fabricated with integrated functions of slow release, antimicrobial activity and food freshness preservation. CS-HCNS-Cur films take the advantages of the excellent thermal stability and slow-release ability of HCNS to curcumin. Among the characterizations including scanning electron microscopy, transmission electron microscope, atomic force microscopy, fourier transform infrared spectroscopy, mechanical properties and the rheological properties measurements confirmed the successful fabrication of CS-HCNS-Cur films. The averaged water contact angle and water vapor permeability of this film were 105.83° and 105.03 × 10-5 g·mm (m2·h·kPa)-1, respectively. This film showed pH-responsive and slow-release ability. Moreover, this film can effectively store bananas for 10 days. Therefore, CS-HCNS-Cur films have promising potential for applications in functional food packaging.

Identification of a novel COL10A1: c.1952 G>T variant in a family with Schmid metaphyseal chondrodysplasia and development of a noninvasive prenatal testing method.

BACKGROUND: The collagen alpha-1(X) chain gene (COL10A1) is a known causative gene for Schmid metaphyseal chondrodysplasia (SMCD). This study clinically examined a Chinese family (n = 42) for SMCD and inheritance pattern. Fifteen individuals were diagnosed with SMCD based on characteristic skeletal phenotypes with autosomal dominant inheritance mode. METHODS: Four clinically diagnosed patients and three healthy relatives were selected for subsequent genetic tests. Trio-whole exome sequencing (Trio-WES) followed by Sanger sequencing and familial co-segregation analysis were performed to identify SMCD-associated variants. RESULTS: COL10A1 (NM_000493.4):c.1952 G>T(p.Trp651Leu) variant was detected only in the four patients and not in the three healthy relatives. The variant was evaluated as "likely pathogenic" according to the American College of Medical Genetics and Genomics variation classification guidelines with evidence of PM2, PM5, PP1, and PP3. To test the presence of the target variant in proband's fetal offspring, we developed a noninvasive prenatal testing method by extracting cell-free fetal DNA in maternal plasma followed by high-depth sequencing. The variant was also detected in the fetus and later confirmed by amniocentesis. CONCLUSION: We identified a new disease-causing variant in COL10A1. Cell-free fetal DNA in maternal peripheral blood can be used as the rapid and noninvasive prenatal diagnostic method to detect the pathogenic/or likely pathogenic variant.

Subarachnoid transplantation of human umbilical cord mesenchymal stem cell in rodent model with subacute incomplete spinal cord injury: Preclinical safety and efficacy study.

Functional multipotency renders human umbilical cord mesenchymal stem cell (hUC-MSC) a promising candidate for the treatment of spinal cord injury (SCI). However, its safety and efficacy have not been fully understood for clinical translation. In this study, we performed cellular, kinematic, physiological, and anatomical analyses, either in vitro or in vivo, to comprehensively evaluate the safety and efficacy associated with subarachnoid transplantation of hUC-MSCs in rats with subacute incomplete SCI. Concerning safety, hUC-MSCs were shown to have normal morphology, excellent viability, steady proliferation, typical biomarkers, stable karyotype in vitro, and no tumorigenicity both in vitro and in vivo. Following subarachnoid transplantation of hUC-MSCs in the subject rodents, the biodistribution of hUC-MSCs was restricted to the spinal cord, and no toxicity to immune system or organ function was observed. Body weight, organ weight, and the ratio of the latter upon the former between stem cell-transplanted rats and placebo-injected rats revealed no statistical differences. Regarding efficacy, hUC-MSCs could differentiate into osteoblasts, chondrocytes, adipocytes and neural progenitor cells in vitro. While in vivo studies revealed that subarachnoid transplantation of stem cells resulted in significant improvement in locomotion, earlier automatic micturition recovery and reduced lesion size, which correlated with increased regeneration of tracking fiber and reduced parenchymal inflammation. In vivo luminescence imaging showed that a few of the transplanted luciferase-labeled hUC-MSCs tended to migrate towards the lesion epicenter. Shortened latency and enhanced amplitude were also observed in both motor and sensory evoked potentials, indicating improved signal conduction in the damaged site. Immunofluorescent staining confirmed that a few of the administrated hUC-MSCs integrated into the spinal cord parenchyma and differentiated into astrocytes and oligodendrocytes, but not neurons. Moreover, decreased astrogliosis, increased remyelination, and neuron regeneration could be observed. To the best of our knowledge, this preclinical study provides detailed safety and efficacy evidence regarding intrathecal transplantation of hUC-MSCs in treating SCI for the first time and thus, supports its initiation in the following clinical trial.

The i5k Workspace@NAL--enabling genomic data access, visualization and curation of arthropod genomes.

The 5000 arthropod genomes initiative (i5k) has tasked itself with coordinating the sequencing of 5000 insect or related arthropod genomes. The resulting influx of data, mostly from small research groups or communities with little bioinformatics experience, will require visualization, dissemination and curation, preferably from a centralized platform. The National Agricultural Library (NAL) has implemented the i5k Workspace@NAL (http://i5k.nal.usda.gov/) to help meet the i5k initiative's genome hosting needs. Any i5k member is encouraged to contact the i5k Workspace with their genome project details. Once submitted, new content will be accessible via organism pages, genome browsers and BLAST search engines, which are implemented via the open-source Tripal framework, a web interface for the underlying Chado database schema. We also implement the Web Apollo software for groups that choose to curate gene models. New content will add to the existing body of 35 arthropod species, which include species relevant for many aspects of arthropod genomic research, including agriculture, invasion biology, systematics, ecology and evolution, and developmental research.

[Application of methylation-specific multiplex ligation-dependent probe amplification for the study of DNA methylation in placenta tissues].

OBJECTIVE: To study the feasibility of using methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) for the detection of DNA methylation in placenta tissue. METHODS: For blood cells from 13 non-pregnant women and 9 euploid placenta, the ratios of DNA methylation were evaluated for 4 genes including CGI149, CGI113, HLCS and ACTB with MS-MLPA and bisulfite sequencing, respectively. RESULTS: The methylation ratio of the ACTB gene was 0-0.1 for the blood cells when the digestion control was completely digested. The cutoff value for the methylation ratio of MS-MLPA has been determined as 0.1. For the 9 placenta samples, results of MS-MLPA and bisulfite sequencing were concordant for all of the four genes. CONCLUSION: MS-MLPA is an effective alternative to bisulfite sequencing for the assessment of methylation ratios in placental tissues.

Placental methylation markers in normal and trisomy 21 tissues.

OBJECTIVE: The objective of this study is to combine multiplex ligation-dependent probe amplification (MLPA) and bisulfite sequencing to determine DNA methylation markers for noninvasive prenatal diagnosis of Down syndrome. METHODS: DNA methylation ratios (MR) of four fragments (CGI149, CGI045, HLCS-1, and HLCS-2) on chromosome 21 were evaluated in blood cells from 13 nonpregnant women, 15 euploidies, and 11 Down Syndrome (DS) placentae. Ratios were measured by bisulfite sequencing and methylation-specific (MS)-MLPA. RESULTS: The MS-MLPA and bisulfite sequencing results were concordant. CGI149, CGI045, and HLCS-2 were unmethylated in all nonpregnant blood cells. CGI149, CGI045, HLCS-1, and HLCS-2 were methylated in most of the euploid (13, 11, 15, and 15, respectively) and DS placentae (10, 11, 11, and 11, respectively). The median placental DNA MR in CGI149 was 0.4578 (interquartile range, 0.3568-0.5169) and 0.5918 (interquartile range, 0.5618-0.6659) in euploid and DS placentae, respectively (p = 0.001). Using placental MR at 0.5390 as a threshold, we detected DS at 90.9% sensitivity and 93.3% specificity. CONCLUSION: The MS-MLPA is an effective alternative to bisulfite sequencing in assessing placental MR. CGI149 is a potential marker for the noninvasive diagnosis of Down syndrome.

An improved facile method for extraction and determination of steroidal saponins in Tribulus terrestris by focused microwave-assisted extraction coupled with GC-MS.

An improved fast method for extraction of steroidal saponins in Tribulus terrestris based on the use of focus microwave-assisted extraction (FMAE) is proposed. Under optimized conditions, four steroidal saponins were extracted from Tribulus terrestris and identified by GC-MS, which are Tigogenin (TG), Gitogenin (GG), Hecogenin (HG) and Neohecogenin (NG). One of the most important steroidal saponins, namely TG was quantified finally. The recovery of TG was in the range of 86.7-91.9% with RSD<5.2%. The convention heating reflux extraction was also conducted in order to validate the reliability of this new FMAE method. The yield of total steroidal saponins was 90.3% in a one-step FMAE, while the yield of 65.0% was achieved during heating reflux extraction, and the extraction time was reduced from 3 h to 5 min by using less solvent. The method was successfully applied to analyze the steroidal saponins of Tribulus terrestris from different areas of occurrence. The difference in chromatographic characteristics of steroidal saponins was proved to be related to the different areas of occurrence. The results showed that FMAE-GC-MS is a simple, rapid, solvent-saving method for the extraction and determination of steroidal saponins in Tribulus terrestris.

SCA8 mRNA expression suggests an antisense regulation of KLHL1 and correlates to SCA8 pathology.

An increasing number of inherited neurodegenerative diseases are known to be caused by the expansion of unstable trinucleotide repeat tracts. Spinocerebellar ataxia type 8 (SCA8) has been identified as being partly caused by a CTG expansion in an untranslated, endogenous antisense RNA that overlaps the Kelch-like 1 (KLHL1) gene. Clinically, SCA8 patients show similar features to those with the other SCAs, including limb and truncal ataxia, ataxic dysarthria and horizontal nystagmus, all of which are signs of dysfunction of the cerebellar system. However, allele sizes within the SCA8 proposed pathogenic range have been reported in patients with ataxia of unknown etiology, in individuals from pedigrees with other SCA or Friedreich's ataxia, and in patients with Alzheimer's disease, schizophrenia or parkinsonism. These observations suggest that mutation of the SCA8 locus might affect neurons other than the cerebellum. Antisense transcripts are known to regulate complementary sense transcripts and are involved in several biologic functions, such as development, adaptive response, and viral infection. In order to test whether SCA8 affects the KLHL1 expression by antisense RNA in brain cells, we examined the expression pattern of KLHL1 and SCA8 in human tissues and in mouse brain regions. SCA8 expression was colocalized with KLHL1 transcript in many brain regions whose functions are correlated to the clinical symptoms of SCA8 patients. These findings lead to the hypothesis of a possible relevance that SCA8 transcript downregulates KLHL1 expression through an antisense mechanism, which then leads to SCA8 neuropathogenesis.