bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving Genomic Prediction of Crossbred and Purebred Dairy Cattle
Authors: Khansefid Majid , Goddard Michael E. , Haile-Mariam Mekonnen , Konstantinov Kon V. , Schrooten Chris , de Jong Gerben , Jewell Erica G. , O’Connor Erin , Pryce Jennie E. , Daetwyler Hans D. , MacLeod Iona M.
Published: December 2020

This study assessed the accuracy and bias of genomic prediction (GP) in purebred Holstein (H) and Jersey (J) as well as crossbred (H and J) validation cows using different reference sets and prediction strategies. The reference sets were made up of different combinations of 36,695 H and J purebreds and crossbreds. Additionally, the effect of using different sets of marker genotypes on GP was studied (conventional panel: 50k, custom panel enriched with, or close to, causal mutations: XT_50k, and conventional high-density with a limited custom set: pruned HDnGBS). We also compared the use of genomic best linear unbiased prediction (GBLUP) and Bayesian (emBayesR) models, and the traits tested were milk, fat, and protein yields. On average, by including crossbred cows in the reference population, the prediction accuracies increased by 0.01–0.08 and were less biased (regression coefficient closer to 1 by 0.02–0.16), and the benefit was greater for crossbreds compared to purebreds. The accuracy of prediction increased by 0.02 using XT_50k compared to 50k genotypes without affecting the bias. Although using pruned HDnGBS instead of 50k also increased the prediction accuracy by about 0.02, it increased the bias for purebred predictions in emBayesR models. Generally, emBayesR outperformed GBLUP for prediction accuracy when using 50k or pruned HDnGBS genotypes, but the benefits diminished with XT_50k genotypes. Crossbred predictions derived from a joint pure H and J reference were similar in accuracy to crossbred predictions derived from the two separate purebred reference sets and combined proportional to breed composition. However, the latter approach was less biased by 0.13. Most interestingly, using an equalized breed reference instead of an H-dominated reference, on average, reduced the bias of prediction by 0.16–0.19 and increased the accuracy by 0.04 for crossbred and J cows, with a little change in the H accuracy. In conclusion, we observed improved genomic predictions for both crossbreds and purebreds by equalizing breed contributions in a mixed breed reference that included crossbred cows. Furthermore, we demonstrate, that compared to the conventional 50k or high-density panels, our customized set of 50k sequence markers improved or matched the prediction accuracy and reduced bias with both GBLUP and Bayesian models.
Integrated Analysis of lncRNA-Mediated ceRNA Network Reveals a Prognostic Signature for Hepatocellular Carcinoma
Authors: Sun Jian-Rong , Kong Chen-Fan , Xiao Kun-Min , Yang Jia-Lu , Qu Xiang-Ke , Sun Jing-Hui
Published: December 2020

Hepatocellular carcinoma (HCC) is one of the most common types of malignancy and is associated with high mortality. Prior research suggests that long non-coding RNAs (lncRNAs) play a crucial role in the development of HCC. Therefore, it is necessary to identify lncRNA-associated therapeutic biomarkers to improve the accuracy of HCC prognosis. Transcriptomic data of HCC obtained from The Cancer Genome Atlas (TCGA) database were used in the present study. Differentially expressed RNAs (DERNAs), including 74 lncRNAs, 16 miRNAs, and 35 mRNAs, were identified using bioinformatics analysis. The DERNAs were subsequently used to reconstruct a competing endogenous RNA (ceRNA) network. A lncRNA signature was revealed using Cox regression analysis, including LINC00200, MIR137HG, LINC00462, AP002478.1, and HTR2A-AS1. Kaplan-Meier plot demonstrated that the lncRNA signature is highly accurate in discriminating high- and low-risk patients (P < 0.05). The area under curve (AUC) value exceeded 0.7 in both training and validation cohort, suggesting a high prognostic potential of the signature. Furthermore, multivariate Cox regression analysis indicated that both the TNM stage and the lncRNA signature could serve as independent prognostic factors for HCC (P < 0.05). Then, a nomogram comprising the TNM stage and the lncRNA signature was determined to raise the accuracy in predicting the survival of HCC patients. In the present study, we have introduced a ceRNA network that could contribute to provide a new insight into the identification of potential regulation mechanisms for the development of HCC. The five-lncRNA signature could serve as a reliable biosignature for HCC prognosis, while the nomogram possesses strong potential in clinical applications.
MiR-144-3p Targets FoxO1 to Reduce Its Regulation of Adiponectin and Promote Adipogenesis
Authors: Lin Weimin , Tang Yonghang , Zhao Yuelei , Zhao Jindi , Zhang Lifan , Wei Wei , Chen Jie
Published: December 2020

MicroRNAs (miRNAs), as a series of important short-chain non-coding RNAs, play an important post-transcriptional role in many biological activities, including adipogenesis. miR-144 is significantly upregulated in type II diabetes (T2D), and is considered to be an important biomarker for T2D. However, although the occurrence of T2D is inextricably linked to adipogenesis, whether miR-144 directly regulates adipogenesis remains to be further explored. In this paper, we demonstrate that miR-144 has a higher expression level in a porcine high backfat group, and it has a significant positive effect on promoting the differentiation of pre-adipocytes. FoxO1 is a target gene of miR-144, and inhibits the differentiation of pre-adipocytes. On the other hand, we demonstrate that FoxO1 can bind to the AdipoQ gene promoter, then regulate the AdipoQ expression by binding to the FoxO1 binding site in the AdipoQ promoter -1,499 to -1,489 bp and -1,238 to -1,228 bp regions, especially the -1,499 to -1,489 bp region. Meanwhile, miR-144 and FoxO1 co-expressional research has also shown that both factors regulate adipogenesis. To sum up, our research indicates that miR-144 targets FoxO1, thus reducing its expression and inhibiting its promotional effect on adiponectin, thereby alleviating the inhibitory effect of adiponectin on adipogenesis.
TRPV4 Plays a Role in Matrix Stiffness-Induced Macrophage Polarization
Authors: Dutta Bidisha , Goswami Rishov , Rahaman Shaik O.
Published: December 2020

Phenotypic polarization of macrophages is deemed essential in innate immunity and various pathophysiological conditions. We have now determined key aspects of the molecular mechanism by which mechanical cues regulate macrophage polarization. We show that Transient Receptor Potential Vanilloid 4 (TRPV4), a mechanosensitive ion channel, mediates substrate stiffness-induced macrophage polarization. Using atomic force microscopy, we showed that genetic ablation of TRPV4 function abrogated fibrosis-induced matrix stiffness generation in skin tissues. We have determined that stiffer skin tissue promotes the M1 macrophage subtype in a TRPV4-dependent manner; soft tissue does not. These findings were further validated by ourin vitroresults which showed that stiff matrix (50 kPa) alone increased expression of macrophage M1 markers in a TRPV4-dependent manner, and this response was further augmented by the addition of soluble factors; neither of which occurred with soft matrix (1 kPa). A direct requirement for TRPV4 in M1 macrophage polarization spectrum in response to increased stiffness was evident from results of gain-of-function assays, where reintroduction of TRPV4 significantly upregulated the expression of M1 markers in TRPV4 KO macrophages. Together, these data provide new insights regarding the role of TRPV4 in matrix stiffness-induced macrophage polarization spectrum that may be explored in tissue engineering and regenerative medicine and targeted therapeutics.
Case Report: A Spinal Ischemic Lesion in a 24-Year-Old Patient With Fabry Disease
Authors: Krämer Julia , Glaser Felix , Hasselblatt Martin , Brand Eva , Pogoda Christian , Lenders Malte , Wiendl Heinz , Meuth Sven G. , Duning Thomas
Published: December 2020

Background

While cerebral lesions are common in Fabry disease (FD), spinal lesions have not been described, and their presence was suggested to be indicative of multiple sclerosis. Here, we present a FD patient with histopathological confirmed spinal ischemic stroke.

Case presentation

A patient with genetically and biochemically diagnosed FD and characteristic manifestations (acroparesthesia, angiokeratomas, hypohidrosis, microalbuminuria, myocardial hypertrophy) presented with paraplegia, loss of all sensory modalities below Th9, and loss of bowel and bladder function. While cranial MRI was inconspicuous, spinal MRI showed a T2 hyperintense, non-contrast-enhancing lesion of the thoracic spinal cord. Lumbar puncture revealed mild pleocytosis, increased total protein and lactate levels, decreased glucose ratio, and negative oligoclonal bands. Rheumatic, neoplastic, and infectious disorders were excluded. The patient received intravenous and intrathecal methylprednisolone, plasmapheresis, intravenous immunoglobulins, and cyclophosphamide without clinical improvement. A biopsy of the thoracic lesion was performed. A histopathological examination revealed necrotic tissue consistent with spinal cord ischemia. Diagnostic work-up for stroke etiology clarification was not conspicuous. Two years onward, the patient suffered from a pontine infarction and a transient ischemic attack.

Conclusion

The current case highlights the possible occurrence of spinal ischemic lesions in FD. Thus, the diagnosis of FD should not be prematurely discarded in the presence of spinal lesions.
Resolving the Paradox of Colon Cancer Through the Integration of Genetics, Immunology, and the Microbiota
Authors: Fidelle Marine , Yonekura Satoru , Picard Marion , Cogdill Alexandria , Hollebecque Antoine , Roberti Maria Paula , Zitvogel Laurence
Published: December 2020

While colorectal cancers (CRC) are paradigmatic tumors invaded by effector memory lymphocytes, the mechanisms accounting for the relative resistance of MSI negative CRC to immunogenic cell death mediated by oxaliplatin and immune checkpoint inhibitors has remained an open conundrum. Here, we propose the viewpoint where its microenvironmental contexture could be explained -at least in part- by macroenvironmental cues constituted by the complex interplay between the epithelial barrier, its microbial ecosystem, and the local immune system. Taken together this dynamic ménage-à-trois offers novel coordinated actors of the humoral and cellular immune responses actionable to restore sensitivity to immune checkpoint inhibition. Solving this paradox involves breaking tolerance to crypt stem cells by inducing the immunogenic apoptosis of ileal cells in the context of an ileal microbiome shifted towards immunogenic bacteria using cytotoxicants. This manoeuver results in the elicitation of a productive Tfh and B cell dialogue in mesenteric lymph nodes culminating in tumor-specific memory CD8+ T cell responses sparing the normal epithelium.
From Chickens to Humans: The Importance of Peptide Repertoires for MHC Class I Alleles
Authors: Kaufman Jim
Published: December 2020

In humans, killer immunoglobulin-like receptors (KIRs), expressed on natural killer (NK) and thymus-derived (T) cells, and their ligands, primarily the classical class I molecules of the major histocompatibility complex (MHC) expressed on nearly all cells, are both polymorphic. The variation of this receptor-ligand interaction, based on which alleles have been inherited, is known to play crucial roles in resistance to infectious disease, autoimmunity, and reproduction in humans. However, not all the variation in response is inherited, since KIR binding can be affected by a portion of the peptide bound to the class I molecules, with the particular peptide presented affecting the NK response. The extent to which the large multigene family of chicken immunoglobulin-like receptors (ChIRs) is involved in functions similar to KIRs is suspected but not proven. However, much is understood about the two MHC-I molecules encoded in the chicken MHC. The BF2 molecule is expressed at a high level and is thought to be the predominant ligand of cytotoxic T lymphocytes (CTLs), while the BF1 molecule is expressed at a much lower level if at all and is thought to be primarily a ligand for NK cells. Recently, a hierarchy of BF2 alleles with a suite of correlated properties has been defined, from those expressed at a high level on the cell surface but with a narrow range of bound peptides to those expressed at a lower level on the cell surface but with a very wide repertoire of bound peptides. Interestingly, there is a similar hierarchy for human class I alleles, although the hierarchy is not as wide. It is a question whether KIRs and ChIRs recognize class I molecules with bound peptide in a similar way, and whether fastidious to promiscuous hierarchy of class I molecules affect both T and NK cell function. Such effects might be different from those predicted by the similarities of peptide-binding based on peptide motifs, as enshrined in the idea of supertypes. Since the size of peptide repertoire can be very different for alleles with similar peptide motifs from the same supertype, the relative importance of these two properties may be testable.
Extracellular Reef Metabolites Across the Protected Jardines de la Reina, Cuba Reef System
Authors: Weber Laura , Armenteros Maickel , Kido Soule Melissa , Longnecker Krista , Kujawinski Elizabeth B. , Apprill Amy
Published: December 2020

Coral reef ecosystems are incredibly diverse marine biomes that rely on nutrient cycling by microorganisms to sustain high productivity in generally oligotrophic regions of the ocean. Understanding the composition of extracellular reef metabolites in seawater, the small organic molecules that serve as the currency for microorganisms, may provide insight into benthic-pelagic coupling as well as the complexity of nutrient cycling in coral reef ecosystems. Jardines de la Reina (JR), Cuba is an ideal environment to examine extracellular metabolites across protected and high-quality reefs. Here, we used liquid chromatography mass spectrometry (LC-MS) to quantify specific known metabolites of interest (targeted metabolomics approach) and to survey trends in metabolite feature composition (untargeted metabolomics approach) from surface and reef depth (6 – 14 m) seawater overlying nine forereef sites in JR. We found that untargeted metabolite feature composition was surprisingly similar between reef depth and surface seawater, corresponding with other biogeochemical and physicochemical measurements and suggesting that environmental conditions were largely homogenous across forereefs within JR. Additionally, we quantified 32 of 53 detected metabolites using the targeted approach, including amino acids, nucleosides, vitamins, and other metabolic intermediates. Two of the quantified metabolites, riboflavin and xanthosine, displayed interesting trends by depth. Riboflavin concentrations were higher in reef depth compared to surface seawater, suggesting that riboflavin may be produced by reef organisms at depth and degraded in the surface through photochemical oxidation. Xanthosine concentrations were significantly higher in surface reef seawater. 5′-methylthioadenosine (MTA) concentrations increased significantly within the central region of the archipelago, displaying biogeographic patterns that warrant further investigation. Here we lay the groundwork for future investigations of variations in metabolite composition across reefs, sources and sinks of reef metabolites, and changes in metabolites over environmental, temporal, and reef health gradients.
Inorganic Phosphate Solubilization by Rhizosphere Bacterium Paenibacillus sonchi: Gene Expression and Physiological Functions
Authors: Brito Luciana F. , López Marina Gil , Straube Lucas , Passaglia Luciane M. P. , Wendisch Volker F.
Published: December 2020

Due to the importance of phosphorus (P) in agriculture, crop inoculation with phosphate-solubilizing bacteria is a relevant subject of study. Paenibacillus sonchi genomovar Riograndensis SBR5 is a promising candidate for crop inoculation, as it can fix nitrogen and excrete ammonium at a remarkably high rate. However, its trait of phosphate solubilization (PS) has not yet been studied in detail. Here, differential gene expression and functional analyses were performed to characterize PS in this bacterium. SBR5 was cultivated with two distinct P sources: NaH2PO4 as soluble phosphate source (SPi) and hydroxyapatite as insoluble phosphate source (IPi). Total RNA of SBR5 cultivated in those two conditions was isolated and sequenced, and bacterial growth and product formation were monitored. In the IPi medium, the expression of 68 genes was upregulated, whereas 100 genes were downregulated. Among those, genes involved in carbon metabolism, including those coding for subunits of 2-oxoglutarate dehydrogenase, were identified. Quantitation of organic acids showed that the production of tricarboxylic acid cycle-derived organic acids was reduced in IPi condition, whereas acetate and gluconate were overproduced. Increased concentrations of proline, trehalose, and glycine betaine revealed active osmoprotection during growth in IPi. The cultivation with hydroxyapatite also caused the reduction in the motility of SBR5 cells as a response to Pi depletion at the beginning of its growth. SBR5 was able to solubilize hydroxyapatite, which suggests that this organism is a promising phosphate-solubilizing bacterium. Our findings are the initial step in the elucidation of the PS process in P. sonchi SBR5 and will be a valuable groundwork for further studies of this organism as a plant growth-promoting rhizobacterium.
Impacts of Citric Acid and Malic Acid on Fermentation Quality and Bacterial Community of Cassava Foliage Silage
Authors: Li Mao , Zhang Lidong , Zhang Qing , Zi Xuejuan , Lv Renlong , Tang Jun , Zhou Hanlin
Published: December 2020

The microbiota and fermentation quality of cassava foliage (CF) ensiled in the absence of additive (CK), or the presence of citric acid (CA), malic acid (MA), and their combination with aLactobacillus plantarumstrain (CAL and MAL)were investigated. These additives reduced (P< 0.05) the pH, butyric acid, and ammonia-N contents but increased (P< 0.05) the lactic acid content, and CAL and MAL showed similar remarkable effects.Paenibacillus(mean, 27.81%) andBacillus(mean, 16.04%) were the predominant strains in CF silage. The addition of CA or MAL increased the abundance ofPaenibacillus(25.81–52.28% and 47.97%, respectively), and the addition of MA increased the abundance ofBacillus(15.76–32.48%) compared with the CK group. Moreover, CAL and MAL increased the abundances of the potentially desirable bacteriaCellulosimicrobium(CAL 0–12.73%),Hyphomicrobium(0–7.90% and 8.94%), andOceanobacillus(0–8.37% and 3.08%) compared with the CK group. These findings suggested that CA and MA could enhance the silage quality of CF, and their combinations withLactobacillus plantarumwere more effective.
Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for the Diagnosis of External Ventricular and Lumbar Drainage-Associated Ventriculitis and Meningitis
Authors: Qian Lingye , Shi Yijun , Li Fangqiang , Wang Yufei , Ma Miao , Zhang Yanfang , Shao Yang W. , Zheng Guanghui , Zhang Guojun
Published: December 2020

Metagenomic next-generation sequencing (mNGS) has become a widely used technology that can accurately detect individual pathogens. This prospective study was performed between February 2019 and September 2019 in one of the largest clinical neurosurgery centers in China. The study aimed to evaluate the performance of mNGS on cerebrospinal fluid (CSF) from neurosurgical patients for the diagnosis of external ventricular and lumbar drainage (EVD/LD)-associated ventriculitis and meningitis (VM). We collected CSF specimens from neurosurgical patients with EVD/LD for more than 24 h to perform conventional microbiological studies and mNGS analyses in a pairwise manner. We also investigated the usefulness of mNGS of CSF for the diagnosis of EVD/LD-associated VM. In total, 102 patients were enrolled in this study and divided into three groups, including confirmed VM (cVM) (39), suspected VM (sVM) (49), and non-VM (nVM) (14) groups. Of all the patients, mNGS detected 21 Gram-positive bacteria, 20 Gram-negative bacteria, and five fungi. The three primary bacteria detected were Staphylococcus epidermidis (9), Acinetobacter baumannii (5), and Staphylococcus aureus (3). The mNGS-positive coincidence rate of confirmed EVD/LD-associated VM was 61.54% (24/39), and the negative coincidence rate of the nVM group was 100% (14/14). Of 15 VM pathogens not identified by mNGS in the cVM group, eight were negative with mNGS and seven were inconsistent with the conventional microbiological identification results. In addition, mNGS identified pathogens in 22 cases that were negative using conventional methods; of them, 10 patients received a favorable clinical treatment; thus, showing the benefit of mNGS-guided therapy.
Creation of a Low-Alcohol-Production Yeast by a Mutated SPT15 Transcription Regulator Triggers Transcriptional and Metabolic Changes During Wine Fermentation
Authors: Du Qing , Liu Yanlin , Song Yuyang , Qin Yi
Published: December 2020

There is significant interest in the wine industry to develop methods to reduce the ethanol content of wine. Here the global transcription machinery engineering (gTME) technology was used to engineer a yeast strain with decreased ethanol yield, based on the mutation of theSPT15gene. We created a strain ofSaccharomyces cerevisiae(YS59-409), which possessed ethanol yield reduced by 34.9%; this was accompanied by the increase in CO2, biomass, and glycerol formation. Five mutation sites were identified in the mutatedSPT15gene of YS59-409. RNA-Seq and metabolome analysis of YS59-409 were conducted compared with control strain, suggesting that ribosome biogenesis, nucleotide metabolism, glycolysis flux, Crabtree effect, NAD+/NADH homeostasis and energy metabolism might be regulated by the mutagenesis ofSPT15gene. Furthermore, two genes related to energy metabolism,RGI1andRGI2, were found to be associated with the weakened ethanol production capacity, although the precise mechanisms involved need to be further elucidated. This study highlighted the importance of applying gTME technology when attempting to reduce ethanol production by yeast, possibly reprogramming yeast’s metabolism at the global level.
The Structure, Function, and Mechanisms of Action of Enterovirus Non-structural Protein 2C
Authors: Wang Shao-Hua , Wang Kuan , Zhao Ke , Hua Shu-Cheng , Du Juan
Published: December 2020

Enteroviruses are a group of RNA viruses belonging to the familyPicornaviridae. They include human enterovirus groups A, B, C, and D as well as non-human enteroviruses. Enterovirus infections can lead to hand, foot, and mouth disease and herpangina, whose clinical manifestations are often mild, although some strains can result in severe neurological complications such as encephalitis, myocarditis, meningitis, and poliomyelitis. To date, research on enterovirus non-structural proteins has mainly focused on the 2A and 3C proteases and 3D polymerase. However, another non-structural protein, 2C, is the most highly conserved protein, and plays a vital role in the enterovirus life cycle. There are relatively few studies on this protein. Previous studies have demonstrated that enterovirus 2C is involved in virus uncoating, host cell membrane rearrangements, RNA replication, encapsidation, morphogenesis, ATPase, helicase, and chaperoning activities. Despite ongoing research, little is known about the pathogenesis of enterovirus 2C proteins in viral replication or in the host innate immune system. In this review, we discuss and summarize the current understanding of the structure, function, and mechanism of the enterovirus 2C proteins, focusing on the key mutations and motifs involved in viral infection, replication, and immune regulation. We also focus on recent progress in research into the role of 2C proteins in regulating the pattern recognition receptors and type I interferon signaling pathway to facilitate viral replication. Given these functions and mechanisms, the potential application of the 2C proteins as a target for anti-viral drug development is also discussed. Future studies will focus on the determination of more crystal structures of enterovirus 2C proteins, which might provide more potential targets for anti-viral drug development against enterovirus infections.
Comprehensive Analysis of Clinically Significant Hepatitis B Virus Mutations in Relation to Genotype, Subgenotype and Geographic Region
Authors: Araujo Natalia M. , Teles Sheila A. , Spitz Natália
Published: December 2020

Hepatitis B virus (HBV) is a highly variable DNA virus due to its unique life cycle, which involves an error-prone reverse transcriptase. The high substitution rate drives the evolution of HBV by generating genetic variants upon which selection operates. HBV mutants with clinical implications have been documented worldwide, indicating the potential for spreading and developing their own epidemiology. However, the prevalence of such mutants among the different HBV genotypes and subgenotypes has not been systematically analyzed. In the current study, we performed large-scale analysis of 6,479 full-length HBV genome sequences from genotypes A-H, with the aim of gaining comprehensive insights into the relationships of relevant mutations associated with immune escape, antiviral resistance and hepatocellular carcinoma (HCC) development with HBV (sub)genotypes and geographic regions. Immune escape mutations were detected in 10.7% of the sequences, the most common being I/T126S (1.8%), G145R (1.2%), M133T (1.2%), and Q129R (1.0%). HBV genotype B showed the highest rate of escape mutations (14.7%) while genotype H had no mutations (P< 0.001). HCC-associated mutations were detected in 33.7% of the sequences, with significantly higher frequency of C1653T, T1753V and A1762T/G1764A in genotype G than C (P< 0.001). The overall frequencies of lamivudine-, telbivudine-, adefovir-, and entecavir-resistant mutants were 7.3, 7.2, 0.5, and 0.2%, respectively, while only 0.05% showed reduced susceptibility to tenofovir. In particular, the highest frequency of lamivudine-resistant mutations was observed in genotype G and the lowest frequency in genotype E (32.5 and 0.3%;P< 0.001). The prevalence of HBV mutants was also biased by geographic location, with North America identified as one of the regions with the highest rates of immune escape, antiviral resistance, and HCC-associated mutants. The collective findings were discussed in light of natural selection and the known characteristics of HBV (sub)genotypes. Our data provide relevant information on the prevalence of clinically relevant HBV mutations, which may contribute to further improvement of diagnostic procedures, immunization programs, therapeutic protocols, and disease prognosis.
Metabolomic Biomarkers of Multiple Sclerosis: A Systematic Review
Authors: Porter Lachlan , Shoushtarizadeh Alireza , Jelinek George A. , Brown Chelsea R. , Lim Chai K. , de Livera Alysha M. , Jacobs Kelly R. , Weiland Tracey J.
Published: December 2020

Background

Magnetic resonance imaging (MRI), cerebrospinal fluid (CSF) analysis, and the McDonald’s clinical criteria are currently utilized tools in diagnosing multiple sclerosis. However, a more conclusive, consistent, and efficient way of diagnosing multiple sclerosis (MS) is yet to be discovered. A potential biomarker, discovered using advances in high-throughput sequencing such as nuclear magnetic resonance (NMR) spectroscopy and other “Omics”-based techniques, may make diagnosis and prognosis more reliable resulting in a more personalized and targeted treatment regime and improved outcomes. The aim of this review was to systematically search the literature for potential biomarkers from any bodily fluid that could consistently and accurately diagnose MS and/or indicate disease progression.

Methods

A systematic literature review of EMBASE, PubMed (MEDLINE), The Cochrane Library, and CINAHL databases produced over a thousand potential studies. Inclusion criteria stated studies with potential biomarker outcomes for people with MS were to be included in the review. Studies were limited to those with human participants who had a clinically defined diagnosis of MS and published in English, with no limit placed on date of publication or the type of bodily fluid sampled.

Results

A total of 1,805 studies were recorded from the literature search. A total of 1,760 studies were removed based on their abstract, with a further 18 removed after considering the full text. A total of 30 studies were considered relevant and had their data retrieved and analyzed. Due to the heterogeneity of focus and results from the refined studies, a narrative synthesis was favored.

Conclusion

Several promising candidate biomarkers suitable for clinical application in MS have been studied. It is recommended follow-up studies with larger sample sizes be completed on several potential biomarkers.
Identification of Immune-Related Genes MSR1 and TLR7 in Relation to Macrophage and Type-2 T-Helper Cells in Osteosarcoma Tumor Micro-Environments as Anti-metastasis Signatures
Authors: Chen Zhiyu , Huang Huanhuan , Wang Yang , Zhan Fangbiao , Quan Zhengxue
Published: December 2020

Metastasis of osteosarcoma (OS) is an essential factor affecting the prognosis and survival of patients. The tumor microenvironment, including tumor immune-infiltrating cells (TIIC), is closely related to tumor progression. The purpose of this study was to investigate the differences between metastatic and non-metastatic immune-infiltrating cells in OS and to identify key immune-related genes. The differences in immune infiltration in OS metastasis were calculated based on the ssGSEA algorithm of 28 immuno-infiltrating cells. Weighted gene co-expression network analysis (WGCNA) and intersection analysis were used to screen immune-related modules and hubgenes. Univariate/multivariate/Lasso Cox regressions were used for models construction and signatures screening. The receiver operating characteristic (ROC) and Kaplan–Meier (K–M) curves were constructed to observe the metastases of different groups. Both internal and external data were verified. We found that macrophages and Type-2 T-helper cells were significantly decreased in patients with OS metastases. The high-risk groups obtained from multivariate/Lasso Cox models constructed with 11 immune-related hubgenes almost all underwent distant metastases within 5 years. Interestingly and importantly, two genes, MSR1 and TLR7, appeared in various models and various hubgenes, which play an anti-metastasis role and may prolong overall survival in OS. Our study may help elucidate the impact of TIIC on OS metastasis outcomes and to identify biomarkers and therapeutic targets.
Hierarchical Graph Representation of Pharmacophore Models
Authors: Arthur Garon , Oliver Wieder , Klaus Bareis , Thomas Seidel , Gökhan Ibis , Sharon Bryant , Isabelle Theret , Pierre Ducrot , Thierry Langer
Published: December 2020

For the investigation of protein-ligand interaction patterns, the current accessibility of a wide variety of sampling methods allows quick access to large-scale data. The main example is the intensive use of molecular dynamics simulations applied to crystallographic structures which provide dynamic information on the binding interactions in protein-ligand complexes. Chemical feature interaction based pharmacophore models extracted from these simulations, were recently used with consensus scoring approaches to identify potentially active molecules. While this approach is rapid and can be fully automated for virtual screening, additional relevant information from such simulations is still opaque and so far the full potential has not been entirely exploited. To address these aspects, we developed the hierarchical graph representation of pharmacophore models (HGPM). This single graph representation enables an intuitive observation of numerous pharmacophore models from long MD trajectories and further emphasizes their relationship and feature hierarchy. The resulting interactive depiction provides an easy-to-apprehend tool for the selection of sets of pharmacophores as well as visual support for analysis of pharmacophore feature composition and virtual screening results. Furthermore, the representation can be adapted to include information involving interactions between the same protein and multiple different ligands. Herein, we describe the generation, visualization and use of HGPMs generated from MD simulations of two x-ray crystallographic derived structures of the human glucokinase protein in complex with allosteric activators. The results demonstrate that a large number of pharmacophores and their relationships can be visualized in an interactive, efficient manner, unique binding modes identified and a combination of models derived from long MD simulations can be strategically prioritized for VS campaigns.
Identification of the Prognostic Value of Tumor Microenvironment-Related Genes in Esophageal Squamous Cell Carcinoma
Authors: Zhang Donglei , Qian Changlin , Wei Huabing , Qian Xiaozhe
Published: December 2020

Background: Esophageal squamous cell carcinoma (ESCC) is the most prevalent histological type of esophageal cancer, but there is a lack of definite prognostic markers for this cancer.

Methods: We used the ESTIMATE algorithm to access the tumor microenvironment (TME) of ESCC cases deposited in the TCGA database, and identified TME-related prognostic genes using Cox regression analysis. A least absolute shrinkage and selector operation or LASSO algorithm was used to identify key prognostic genes. Risk scores were calculated, and a clinical predictive model was constructed to evaluate the prognostic value of TME-related genes.

Results: We found that high immune and stromal scores were significantly associated with poor overall survival (p < 0.05). We identified a total of 1,151 TME-related differently expression genes, among which 67 were prognosis-related genes. Through the LASSO method, 13 key prognostic genes were selected, namely, ADAMTS16, LOC51089, CH25H, CORO2B, DLGAP1, GYS2, HAL, MXRA8, NPTX1, OTX1, RET, SLC24A2, and SPI1, and a 13-gene risk score was constructed. A higher score was indicative of a poorer prognosis than a lower risk score (hazard ratio = 8.21, 95% confidence interval: 2.56–26.31; P < 0.001). The risk score was significantly correlated with immune/stromal scores and various types of infiltrating immune cells, including CD8 cells, regulatory T cells, and resting macrophages.

Conclusion: We characterized the tumor microenvironment in ESCC, and identified the key prognosis genes. The risk score based on the expression profiles of these genes is proposed as an indicator of TME status and is instrumental in predicting patient prognosis.
Distinctive Metabolomics Patterns Associated With Insulin Resistance and Type 2 Diabetes Mellitus
Authors: Gu Xinyun , Al Dubayee Mohammed , Alshahrani Awad , Masood Afshan , Benabdelkamel Hicham , Zahra Mahmoud , Li Liang , Abdel Rahman Anas M. , Aljada Ahmad
Published: December 2020

Obesity is associated with an increased risk of insulin resistance (IR) and type 2 diabetes mellitus (T2DM) which is a multi-factorial disease associated with a dysregulated metabolism and can be prevented in pre-diabetic individuals with impaired glucose tolerance. A metabolomic approach emphasizing metabolic pathways is critical to our understanding of this heterogeneous disease. This study aimed to characterize the serum metabolomic fingerprint and multi-metabolite signatures associated with IR and T2DM. Here, we have used untargeted high-performance chemical isotope labeling (CIL) liquid chromatography-mass spectrometry (LC-MS) to identify candidate biomarkers of IR and T2DM in sera from 30 adults of normal weight, 26 obese adults, and 16 adults newly diagnosed with T2DM. Among the 3633 peak pairs detected, 62% were either identified or matched. A group of 78 metabolites were up-regulated and 111 metabolites were down-regulated comparing obese to lean group while 459 metabolites were up-regulated and 166 metabolites were down-regulated comparing T2DM to obese groups. Several metabolites were identified as IR potential biomarkers, including amino acids (Asn, Gln, and His), methionine (Met) sulfoxide, 2-methyl-3-hydroxy-5-formylpyridine-4-carboxylate, serotonin,L-2-amino-3-oxobutanoic acid, and 4,6-dihydroxyquinoline. T2DM was associated with dysregulation of 42 metabolites, including amino acids, amino acids metabolites, and dipeptides. In conclusion, these pilot data have identified IR and T2DM metabolomics panels as potential novel biomarkers of IR and identified metabolites associated with T2DM, with possible diagnostic and therapeutic applications. Further studies to confirm these associations in prospective cohorts are warranted.
Can Tumor Location on Pre-treatment MRI Predict Likelihood of Pseudo-Progression vs. Tumor Recurrence in Glioblastoma?—A Feasibility Study
Authors: Ismail Marwa , Hill Virginia , Statsevych Volodymyr , Mason Evan , Correa Ramon , Prasanna Prateek , Singh Gagandeep , Bera Kaustav , Thawani Rajat , Ahluwalia Manmeet , Madabhushi Anant , Tiwari Pallavi
Published: December 2020

A significant challenge in Glioblastoma (GBM) management is identifying pseudo-progression (PsP), a benign radiation-induced effect, from tumor recurrence, on routine imaging following conventional treatment. Previous studies have linked tumor lobar presence and laterality to GBM outcomes, suggesting that disease etiology and progression in GBM may be impacted by tumor location. Hence, in this feasibility study, we seek to investigate the following question: Can tumor location on treatment-naïve MRI provide early cues regarding likelihood of a patient developing pseudo-progression vs. tumor recurrence? In this study, 74 pre-treatment Glioblastoma MRI scans with PsP (33) and tumor recurrence (41) were analyzed. First, enhancing lesion on Gd-T1w MRI and peri-lesional hyperintensities on T2w/FLAIR were segmented by experts and then registered to a brain atlas. Using patients from the two phenotypes, we construct two atlases by quantifying frequency of occurrence of enhancing lesion and peri-lesion hyperintensities, by averaging voxel intensities across the population. Analysis of differential involvement was then performed to compute voxel-wise significant differences (p-value < 0.05) across the atlases. Statistically significant clusters were finally mapped to a structural atlas to provide anatomic localization of their location. Our results demonstrate that patients with tumor recurrence showed prominence of their initial tumor in the parietal lobe, while patients with PsP showed a multi-focal distribution of the initial tumor in the frontal and temporal lobes, insula, and putamen. These preliminary results suggest that lateralization of pre-treatment lesions toward certain anatomical areas of the brain may allow to provide early cues regarding assessing likelihood of occurrence of pseudo-progression from tumor recurrence on MRI scans.
Acylated Ghrelin as a Multi-Targeted Therapy for Alzheimer's and Parkinson's Disease
Authors: Reich Niklas , Hölscher Christian
Published: December 2020

Much thought has been given to the impact of Amyloid Beta, Tau and Alpha-Synuclein in the development of Alzheimer's disease (AD) and Parkinson's disease (PD), yet the clinical failures of the recent decades indicate that there are further pathological mechanisms at work. Indeed, besides amyloids, AD and PD are characterized by the culminative interplay of oxidative stress, mitochondrial dysfunction and hyperfission, defective autophagy and mitophagy, systemic inflammation, BBB and vascular damage, demyelination, cerebral insulin resistance, the loss of dopamine production in PD, impaired neurogenesis and, of course, widespread axonal, synaptic and neuronal degeneration that leads to cognitive and motor impediments. Interestingly, the acylated form of the hormone ghrelin has shown the potential to ameliorate the latter pathologic changes, although some studies indicate a few complications that need to be considered in the long-term administration of the hormone. As such, this review will illustrate the wide-ranging neuroprotective properties of acylated ghrelin and critically evaluate the hormone's therapeutic benefits for the treatment of AD and PD.
Strategies for Targeting Gene Therapy in Cancer Cells With Tumor-Specific Promoters
Authors: Montaño-Samaniego Mariela , Bravo-Estupiñan Diana M. , Méndez-Guerrero Oscar , Alarcón-Hernández Ernesto , Ibáñez-Hernández Miguel
Published: December 2020

Cancer is the second cause of death worldwide, surpassed only by cardiovascular diseases, due to the lack of early diagnosis, and high relapse rate after conventional therapies. Chemotherapy inhibits the rapid growth of cancer cells, but it also affects normal cells with fast proliferation rate. Therefore, it is imperative to develop other safe and more effective treatment strategies, such as gene therapy, in order to significantly improve the survival rate and life expectancy of patients with cancer. The aim of gene therapy is to transfect a therapeutic gene into the host cells to express itself and cause a beneficial biological effect. However, the efficacy of the proposed strategies has been insufficient for delivering the full potential of gene therapy in the clinic. The type of delivery vehicle (viral or non viral) chosen depends on the desired specificity of the gene therapy. The first gene therapy trials were performed with therapeutic genes driven by viral promoters such as the CMV promoter, which induces non-specific toxicity in normal cells and tissues, in addition to cancer cells. The use of tumor-specific promoters over-expressed in the tumor, induces specific expression of therapeutic genes in a given tumor, increasing their localized activity. Several cancer- and/or tumor-specific promoters systems have been developed to target cancer cells. This review aims to provide up-to-date information concerning targeting gene therapy with cancer- and/or tumor-specific promoters including cancer suppressor genes, suicide genes, anti-tumor angiogenesis, gene silencing, and gene-editing technology, as well as the type of delivery vehicle employed. Gene therapy can be used to complement traditional therapies to provide more effective treatments.
Barriers and Considerations for Diagnosing Rare Diseases in Indigenous Populations
Authors: D'Angelo Carla S. , Hermes Azure , McMaster Christopher R. , Prichep Elissa , Richer Étienne , van der Westhuizen Francois H. , Repetto Gabriela M. , Mengchun Gong , Malherbe Helen , Reichardt Juergen K. V. , Arbour Laura , Hudson Maui , du Plessis Kelly , Haendel Melissa , Wilcox Phillip , Lynch Sally Ann , Rind Shamir , Easteal Simon , Estivill Xavier , Thomas Yarlalu , Baynam Gareth
Published: December 2020

Advances in omics and specifically genomic technologies are increasingly transforming rare disease diagnosis. However, the benefits of these advances are disproportionately experienced within and between populations, with Indigenous populations frequently experiencing diagnostic and therapeutic inequities. The International Rare Disease Research Consortium (IRDiRC) multi-stakeholder partnership has been advancing toward the vision of all people living with a rare disease receiving an accurate diagnosis, care, and available therapy within 1 year of coming to medical attention. In order to further progress toward this vision, IRDiRC has created a taskforce to explore the access barriers to diagnosis of rare genetic diseases faced by Indigenous peoples, with a view of developing recommendations to overcome them. Herein, we provide an overview of the state of play of current barriers and considerations identified by the taskforce, to further stimulate awareness of these issues and the passage toward solutions. We focus on analyzing barriers to accessing genetic services, participating in genomic research, and other aspects such as concerns about data sharing, the handling of biospecimens, and the importance of capacity building.
Kostmann Syndrome With Neurological Abnormalities: A Case Report and Literature Review
Authors: Lyu Baiyu , Lyu Wei , Zhang Xiaoying
Published: December 2020

Background:Severe congenital neutropenia (SCN), also known as Kostmann syndrome, is a rare heterogeneous group of diseases characterized by arrested neutrophil maturation in the bone marrow.

Case Presentation:We report a case of Kostmann syndrome and review previously reported SCN cases with neurological abnormalities. A 10-year-old boy had a history of recurrent, once a month, infection starting at 6 months of age. He had neutropenia for more than 9 years, as well as intellectual disability. He was homozygous for the exon 3 c.430dupG mutation of the HAX1 gene NM-006118. After treatment of antibiotics and G-CSF, his symtoms were relieved and was 3 months free of infection. The search revealed 29 articles related to Kostmann syndrome caused by HAX1 gene mutation; they were screened, and the main clinical features of 13 cases of Kostmann syndrome with neurological abnormalities were summarized and analyzed.

Conclusions:Kostmann syndrome has three main characteristics: severe neutropenia (<0.2 × 109/L), maturation arrest of granulopoiesis at the promyelocyte stage, and death due to infections. HAX1 gene mutations affecting both isoforms A and B are associated with additional neurological symptoms. G-CSF can improve and maintain neutrophil counts, and improve prognosis and quality of life. At present, hematopoietic stem cell transplantation is the only cure.
Investigating Pregnancy and Its Complications Using Circulating Cell-Free RNA in Women's Blood During Gestation
Authors: Moufarrej Mira N. , Wong Ronald J. , Shaw Gary M. , Stevenson David K. , Quake Stephen R.
Published: December 2020

In recent years, there have been major advances in the application of non-invasive techniques to predict pregnancy-related complications, for example by measuring cell-free RNA (cfRNA) in maternal blood. In contrast to cell-free DNA (cfDNA), which is already in clinical use to diagnose fetal aneuploidy, circulating RNA levels can correspond with tissue-specific gene expression and provide a snapshot of prenatal health across gestation. Here, we review the physiologic origins of cfRNA and its novel applications and corresponding challenges to monitor fetal and maternal health and predict pregnancy-related complications.