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Cell subpopulations in the blood and joint fluid of patients with gout are poorly understood. Single-cell RNA sequencing and bioinformatic tools were used to identify cell subsets and their gene signatures in blood and synovial fluid (SF) cells, determine their relationships, characterize the diversity, and evaluate interactions among specific cell types. We identified 34 subpopulations (5 types of B cells, 16 types of T and natural killer cells, 9 types of monocytes, and 4 other cell types) in the blood of five healthy subjects and seven patients with acute gouty, and the SF of three patients with acute gout. We found that naïve CD4 T cells and classical monocytes cell populations were enriched in patients with gout, whereas plasmacytoid dendritic cells and intermediate monocytes were more abundant in healthy subjects. SF was enriched in Th1/Th17 cells, effector memory CD8 T cells, mucosal-associated invariant T cells, and macrophages. Subclusters of these cell subpopulations showed different compositions between healthy subjects and those with acute gout, according to blood and SF samples. At the cellular level, the inflammation score of a subpopulation or subcluster was highest in SF, following by the blood of acute gout patients and healthy person, whereas energy score showed the opposite trend. We also detected specific cell–cell interactions for interleukin-1, tumor necrosis factor-α, and transforming growth factor-β1 expression in the cells of patients with acute gout. Our study reveals cellular and molecular insights on inflammatory responses to hyperuricemia or uric crystal and may provide therapeutic guidance to improve treatments for gout. [ABSTRACT FROM AUTHOR]

Spinal muscular atrophy (SMA) is an autosomal recessive disease characterized by the degeneration of motor neurons in the spinal cord, leading to muscular atrophy. SMA is caused by deletions or mutations in the survival motor neuron gene ( SMN1 ) on chromosome 5q13. A second copy of the SMN gene ( SMN2 ) also exists on chromosome 5, and both genes can produce functional protein. However, due to alternative splicing of the exon 7, the majority of SMN protein produced by SMN2 is truncated and unable to compensate for the loss of SMN1 . Increasing full-length SMN protein production by promoting the exon 7 inclusion in SMN2 mRNA or increasing SMN2 gene transcription could be a therapeutic approach for SMA. In this study, we screened for the compounds that enhance SMN2 exon 7 inclusion by using SMN2 minigene-luciferase reporter system. We found that securinine can increase luciferase activity, indicating that securinine promoted SMN2 exon 7 inclusion. In addition, securinine increased full-length SMN2 mRNA and SMN protein expression in SMA patient-derived lymphoid cell lines. To investigate the mechanism of securinine effect on SMN2 splicing, we compared the protein levels of relevant splicing factors between securinine-treated and untreated cells. We found that securinine downregulated hnRNP A1 and Sam68 and upregulated Tra2-β1 expression. However, securinine, unlike HDAC inhibitors, did not enhance tra2-β1 gene transcription, indicating a post-transcriptional mechanism for Tra2-β1 upregulation. Furthermore, we treated SMA-like mice with securinine by i.p. injection and found that securinine treatment increased SMN2 exon 7 inclusion and SMN protein expression in the brain and spinal cord. According to our results, securinine might have the potential to become a therapeutic drug for SMA disease. [ABSTRACT FROM AUTHOR]

Spinal muscular atrophy (SMA) is an inherited neuromuscular disease caused by deletion or mutation of SMN1 gene. All SMA patients carry a nearly identical SMN2 gene, which produces low level of SMN protein due to mRNA exon 7 exclusion. Previously, we found that the testis of SMA mice (smn−/− SMN2) expresses high level of SMN2 full-length mRNA, indicating a testis-specific mechanism for SMN2 exon 7 inclusion. To elucidate the underlying mechanism, we established primary cultures of testis cells from SMA mice and analyzed them for SMN2 exon 7 splicing. We found that primary testis cells after a 2-hour culture still expressed high level of SMN2 full-length mRNA, but the level decreased after longer cultures. We then compared the protein levels of relevant splicing factors, and found that the level of Tra2-β1 also decreased during testis cell culture, correlated with SMN2 full-length mRNA downregulation. In addition, the testis of SMA mice expressed the highest level of Tra2-β1 among the many tissues examined. Furthermore, overexpression of Tra2-β1, but not ASF/SF2, increased SMN2 minigene exon 7 inclusion in primary testis cells and spinal cord neurons, whereas knockdown of Tra2-β1 decreased SMN2 exon 7 inclusion in primary testis cells of SMA mice. Therefore, our results indicate that high expression level of Tra2-β1 is responsible for increased SMN2 exon 7 inclusion in the testis of SMA mice. This study also suggests that the expression level of Tra2-β1 may be a modifying factor of SMA disease and a potential target for SMA treatment. [ABSTRACT FROM AUTHOR]

Abstract: High-resolution melting (HRM) analysis is a feasible and powerful method for mutation scanning of sequence variants. Denatured doubled-stranded DNA can be detected in fluorescence changes by increasing the melting temperature and wild-type and heterozygous samples can be easily differentiated in the melting plots. HRM analysis represents the next generation of mutation-scanning technology and offers considerable time and cost savings compared to other screening methods. HRM analysis is a closed-tube method, indicating that polymerase chain reaction amplification and subsequent analysis are sequentially performed in the well, making HRM analysis more convenient than other scanning methodologies. Taken together, HRM analysis can be used for high-throughput mutation screening for research, as well as for molecular diagnostic and clinical purposes. This review summarizes the effectiveness of HRM analysis in the diagnosis of autosomal recessive, dominant, and X-linked genetic disorders. Notably, we will also discuss the limitations of HRM analysis and how to overcome them. [Copyright &y& Elsevier]

Abstract: Thy1/CD90 is an important marker of many types of stem cells. It functions as a tumor suppressor in ovarian cancer and in nasopharyngeal carcinoma. In this study, the expression status of Thy1 in clinical hepatocellular carcinoma (HCC) tissue samples was investigated. Relationships of Thy1 expression with clinical parameters and patient survival rate were analyzed. The quantities of Thy1 mRNA were statistically higher in tumor tissues than those in the adjacent non-tumor tissues (p <0.001). Immunohistochemical data confirmed that Thy1 protein was increased in 73% of HCC samples. Thy1 expression was not influenced by chronic alcohol exposure or cirrhosis. Overexpression in Thy1 was correlated with age (p =0.006), hepatitis B virus (HBV) infection (p =0.044), and histological grade (p =0.014). Patients with the highest level of Thy1 expression showed the poorest prognosis (p =0.040). In conclusion, overexpression of Thy1 may not suppress the development of HCC. Thy1 could provide a clinical prognostic marker for HCC. [Copyright &y& Elsevier]

Patients with β-thalassemia (thal) major are subject to peroxidative tissue injury by iron over-load. Glutathione S-transferases work as antioxidants, and their activity is determined genetically. In this study, we used multiplex polymerase chain reaction (m-PCR) to analyze polymorphisms of two endogenous antioxidant agents, glutathione S-transferase M1 (GSTM1) and glutathione S-transferase T1 (GSTT1), and to determine their roles in 41 patients with β-thaI major. Our results showed that the GSTM1 and GSTT1 null genotypes were not associated with any incidence of endocrine dysfunction (including diabetes mellitus, hypogonadism, hypothyroidism, and growth hormone deficiency), liver function, or impaired left ventricular ejection fraction (LVEF). The GSTM1 null genotype, but not the GSTT1 null genotype, was associated with a decreased signal intensity ratio on cardiac magnetic resonance imaging (MRI). Our results suggest that genetic variations of the GSTM1 enzyme are associated with cardiac iron deposition in patients with β-thal major. [ABSTRACT FROM AUTHOR]

Abstract: The NPHS2 gene is expressed in podocytes and encodes the integral membrane protein called podocin, which is believed to play an important role in the renal function of glomerular filtration. Mutations in this gene can cause serious renal function disorders. In this study, we used data-mining techniques and bioinformatic tools to search for the mouse ortholog of the NPHS2-related gene. It might be valuable for future studies of renal diseases. We employed repeated cycles of searching, comparison, and assembling to extend the assembled EST sequences. The discovered gene sequence mslp2, an ortholog of the human SLP2 gene, was found to have a total length of 1253bp with the amino acid coding region located in 32–1093nt. It was further verified using the RT-PCR and RACE techniques to ensure its biological accuracy and then registered with the GenBank. When ClustalW was used for comparing the mslp2 and human SLP2 genes for similarities, the similarities were as high as 88% for nucleotide and 92% for amino acid sequences. In conclusion, we propose a method for rapid identification of the mouse ortholog gene from the human genome. [Copyright &y& Elsevier]

Studies a Taiwanese family in which the mother was a carrier of beta-thalassemia with an alpha chain variant and the father was a carrier of a beta chain variant. Correlations between clinical manifestations and genotypes; Analysis of key issues of interest; Theoretical significance to scientific studies on hemoglobin.

Examines an unstable hemoglobin in a Taiwanese patient. Substitution of the leucine for a proline residue at position 32 of the beta-globin gene; Findings of hemograms; Mutation of codon 32 for beta-globin gene.

Abstract The origins of the Taiwan aborigines have not been fully resolved. Anthropological and linguistic studies have indicated that their ancestry is mainly Austronesian or Malayopolynesian. Some polymorphisms and mutations in the secretor type α (1,2)-fucosyltransferase (FUT2) gene are found in Taiwan aborigines. In this study, we analyzed the frequency of eight mutations and one polymorphism of the FUT2 gene in Taiwan aborigines and other ethnic groups in order to explore the origins of these groups. The results showed that the C302T, G428A, and fusion gene mutations were specific for Thai, Caucasians, and Japanese, respec-tively. The A385T mutation was specific for Asians includ-ing Taiwan aborigines. The genetic frequencies of C571T were much higher in Taiwan aborigines (1.96% to 20.4%), Filipinos (13.2%), and Indonesians (3.30%) as compared with Thai (0.57%), Chinese (0.65% to 1.12%), Japanese (0%), and Caucasians (0%). The frequencies of the G849A mutation were also higher in Taiwan aborigines (0.38% to 21.57%), Filipinos (6.80%), and Indonesians (1.48%) than in Thai (0.94%), Chinese (0-0.37%), Japanese (0%), or Caucasians (0%). Deletion of a 3-bp region (nt 688 to nt 690) was found only in Filipinos (0.85%), Indonesians (0.74%), and three tribes (0.42% to 2.70%) of Taiwan ab-origines, but not in other populations. The C628T mutation... [ABSTRACT FROM AUTHOR]

The survival motor neuron gene is present in humans in a telomeric copy, SMN1, and several centromeric copies, SMN2. Homozygous mutation of SMN1 is associated with proximal spinal muscular atrophy (SMA), a severe motor neuron disease characterized by early childhood onset of progressive muscle weakness. To understand the functional role of SMN1 in SMA, we produced mouse lines deficient for mouse Smn and transgenic mouse lines that expressed human SMN2. Smn-/- mice died during the peri-implantation stage. In contrast, transgenic mice harbouring SMN2 in the Smn-/- background showed pathological changes in the spinal cord and skeletal muscles similar to those of SMA patients. The severity of the pathological changes in these mice correlated with the amount of SMN protein that contained the region encoded by exon 7. Our results demonstrate that SMN2 can partially compensate for lack of SMN1. The variable phenotypes of Smn-/-SMN2 mice reflect those seen in SMA patients, providing a mouse model for this disease. [ABSTRACT FROM AUTHOR]

Targeting the activities of endoplasmic reticulum (ER)–mitochondrial-dependent metabolic reprogramming is considered one of the most promising strategies for cancer treatment. Here, we present biochemical subcellular fractionation, coimmunoprecipitation, gene manipulation, and pharmacologic evidence that induction of mitochondria-localized phospho (p)-cyclin dependent kinase 1 (CDK1) (Thr 161)–cyclin B1 complexes by apigenin in nasopharyngeal carcinoma (NPC) cells impairs the ER–mitochondrial bioenergetics and redox regulation of calcium (Ca++) homeostasis through suppressing the B cell lymphoma 2 (BCL-2)/BCL-2/B-cell lymphoma-extra large (BCL-xL)-modulated anti-apoptotic and metabolic functions. Using a specific inducer, inhibitor, or short hairpin RNA for acid sphingomyelinase (ASM) demonstrated that enhanced lipid raft-associated ASM activity confers alteration of the lipid composition of lipid raft membranes, which leads to perturbation of protein trafficking, and induces formation of p110α free p85α–unphosphorylated phosphatase and tensin homolog deleted from chromosome 10 complexes in the lipid raft membranes, causing disruption of phosphatidylinositol 3-kinase (PI3K)−protein kinase B (Akt)−GTP-ras-related C3 botulinum toxin substrate 1 (Rac1)-mediated signaling, thus triggering the p-CDK1 (Thr 161))–cyclin B1-mediated BCL-2 (Thr 69/Ser 87)/BCL-xL (Ser 62) phosphorylation and accompanying impairment of ER–mitochondria-regulated bioenergetic, redox, and Ca++ homeostasis. Inhibition of apigenin-induced reactive oxygen species (ROS) generation by a ROS scavenger N-acetyl-L-cysteine blocked the lipid raft membrane localization and activation of ASM and formation of ceramide-enriched lipid raft membranes, returned PI3K−Akt−GTP-Rac1-modulated CDK1–cyclin B1 activity, and subsequently restored the BCL-2/BCL-xL-regulated ER–mitochondrial bioenergetic activity. Thus, this study reveals a novel molecular mechanism of the pro-apoptotic activity of ASM controlled by oxidative stress to modulate the ER–mitochondrial bioenergetic metabolism, as well as suggests the disruption of CDK1–cyclin B1-mediated BCL-2/BCL-xL oncogenic activity by triggering oxidative stress−ASM-induced PI3K−Akt−GTP-Rac1 inactivation as a therapeutic approach for NPC. [ABSTRACT FROM AUTHOR]

Examines the hemoglobin variant in a Chinese family. Replacement of glutamic acid by a glutamine residue at position 30 of alpha-globin; Amplification of alpha1- and alpha2-globin genes; Findings of the hemogram.

Reports on the discovery of hemoglobin (Hb) variant Hb Manitoba in a Taiwanese family as of November 2001. Substitution of the amino acid serine for an arginine residue; Identification of two different coding sequences of Hb Manitoba; Techniques used to detect mutations.

Background: Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal carcinoma and patients at advanced stage showed poor survival rate. Despite microRNAs (miRNAs) are used as potential biomarkers in many cancers, miRNA biomarkers for predicting the tumor stage of ccRCC are still limitedly identified. Therefore, we proposed a new integrated machine learning (ML) strategy to identify a novel miRNA signature related to tumor stage and prognosis of ccRCC patients using miRNA expression profiles. A multivariate Cox regression model with three hybrid penalties including Least absolute shrinkage and selection operator (Lasso), Adaptive lasso and Elastic net algorithms was used to screen relevant prognostic related miRNAs. The best subset regression (BSR) model was used to identify optimal prognostic model. Five ML algorithms were used to develop stage classification models. The biological significance of the miRNA signature was analyzed by utilizing DIANA-mirPath. Results: A four-miRNA signature associated with survival was identified and the expression of this signature was strongly correlated with high risk patients. The high risk patients had unfavorable overall survival compared with the low risk group (HR = 4.523, P-value = 2.86e−08). Univariate and multivariate analyses confirmed independent and translational value of this predictive model. A combined ML algorithm identified six miRNA signatures for cancer staging prediction. After using the data balancing algorithm SMOTE, the Support Vector Machine (SVM) algorithm achieved the best classification performance (accuracy = 0.923, sensitivity = 0.927, specificity = 0.919, MCC = 0.843) when compared with other classifiers. Furthermore, enrichment analysis indicated that the identified miRNA signature involved in cancer-associated pathways. Conclusions: A novel miRNA classification model using the identified prognostic and tumor stage associated miRNA signature will be useful for risk and stage stratification for clinical practice, and the identified miRNA signature can provide promising insight to understand the progression mechanism of ccRCC. [ABSTRACT FROM AUTHOR]

Aim: The objective of this study was to explore the association between mitochondrial DNA (mtDNA) haplogroups and physical performances in Han older adults. Methods: This study was an 8‐year follow‐up prospective cohort study. A total of 104 Han older adults completed the measurements of the 6‐min walk test, grip strength and mitochondrial DNA sequencing. The mtDNA haplogroups were classified by using HaploGrep2 software. We used the mixed model to analyze the longitudinal effect of mtDNA haplogroups on physical performance tests among three waves of data. Results: The mean age at wave 3 among men and women were 78.3 and 77.2 years, respectively. The overall proportions of mtDNA haplogroups in this study population was 26.9% F, 21.2% M, 15.4% R, 14.4% D, 8.7% B and others. After adjusted for age, sex, ethnicity, body mass index and exercise, the interaction of mtDNA haplogroup M and waves significantly affected the 6‐min walk distance. Notably, the adjusted mean of the 6‐min walk distance among the group of mtDNA haplogroup M was significantly lower than other haplogroups at wave 3. The adjusted mean of grip strength among the group of mtDNA haplogroup R was significantly higher than other haplogroups at wave 3. Conclusions: This finding suggests that mtDNA haplogroups might have effects on the 6‐min walk test and grip strength in Han older adults, although studies of the physical performance of older adults with larger sample sizes are necessary to further substantiate these findings. Geriatr Gerontol Int 2021; 21: 166–171. [ABSTRACT FROM AUTHOR]

Liver cancer is caused by complex interactions among genetic factors, viral infection, alcohol abuse, and metabolic diseases. We conducted a genome-wide association study and polygenic risk score (PRS) model in Taiwan, employing a nonspecific etiology approach, to identify genetic risk factors for hepatocellular carcinoma (HCC). Our analysis of 2836 HCC cases and 134,549 controls revealed 13 novel associated loci such as the FAM66C gene, noncoding genes, liver-fibrosis-related genes, metabolism-related genes, and HCC-related pathway genes. We incorporated the results from the UK Biobank and Japanese database into our study for meta-analysis to validate our findings. We also identified specific subtypes of the major histocompatibility complex that influence both viral infection and HCC progression. Using this data, we developed a PRS to predict HCC risk in the general population, patients with HCC, and HCC-affected families. The PRS demonstrated higher risk scores in families with multiple HCCs and other cancer cases. This study presents a novel approach to HCC risk analysis, identifies seven new genes associated with HCC development, and introduces a reproducible PRS model for risk assessment. [ABSTRACT FROM AUTHOR]

• aHUS patients had poor T-cell responses compared to healthy controls. • COVID 19 vaccines effectively shield aHUS patients from severe COVID-19. • A double booster dose for the third vaccine is essential for optimal efficacy. • Anti-complement therapy did not influence vaccination effectiveness. Atypical hemolytic uremic syndrome is a rare, life-threatening disorder which can be triggered by COVID 19 infection and COVID 19 vaccination then induce multiple organ failure. Our study is the first to evaluate immune responses to COVID-19 vaccination and safety in a cohort of patients in a local single-center study in Taiwan.. Results indicate that vaccines effectively shield aHUS patients from severe COVID-19 complications without significant safety concerns. A double booster dose for the third vaccine is essential for optimal efficacy. Anti-complement therapy did not influence vaccination effectiveness. Transplant aHUS patients had the lowest immune response titers, indicating a need for additional vaccine doses. Compared to healthcare workers, aHUS patients had poor T-cell responses. We noted a superior trend with mixed-type COVID-19 vaccinations in aHUS patients, while fixed-type mRNA demonstrated better results in healthcare workers. Our findings endorse COVID-19 vaccination as a potent strategy to safeguard aHUS patients from severe complications, emphasizing the importance of vigilant monitoring pre- and post-vaccination. [ABSTRACT FROM AUTHOR]

Simple Summary: Human endogenous retrovirus (HERV) plays important roles in the development of cancer, and most studies use data from The Cancer Genome Atlas to analyze the whole HERV alterations in cancer cells. For HCCs, most studies have focused on LINE-1 and specific HERVs to explore their importance. In this study, we used our total RNA sequencing data from 254 Taiwanese HCCs and many bioinformatic tools to analyze HERV alterations, and then explored the correlations between HERV activation and pathways and certain gene panels. Unique pathways for a higher expression of survival-related HERVs including immunity and infection, lipid and atherosclerosis, MAPK and NF-kB signaling, and cytokine-cytokine receptor interaction pathways were activated; the mRNA surveillance pathway, nucleocytoplasmic transport, ribosome biogenesis, and transcriptional misregulation in cancer pathways were suppressed. We found that many overexpressed HERV-related nearby genes were correlated with high HERV activation and poor survival. The implementation of comprehensive and integrated approaches to assess HERV expression and their association with specific pathways is poised to offer novel companion diagnostics and therapeutic strategies for HCC. Background: Human endogenous retroviruses (HERVs) play an important role in the development of cancer and many diseases. Here, we comprehensively explored the impact of HERVs on hepatocellular carcinomas (HCCs). Methods: We employed Telescope to identify HERVs and quantify their expression in the total RNA sequencing data obtained from 254 HCC samples, comprising 254 tumor tissues and 34 matched normal tissues. Results: In total, 3357 locus-specific activations of HERVs were differentially expressed, and 180 were correlated with patient survival. Using these 180 HERVs for classification, we found four subgroups with survival correlation. Higher expression levels of the 180 HERVs were correlated with poorer survival, while age, AFP, some mutations, and copy and structural variants differed among subgroups. The differential expression of host genes in high expression of these 180 HERVs primarily involved the activation of pathways related to immunity and infection, lipid and atherosclerosis, MAPK and NF-kB signaling, and cytokine–cytokine receptor interactions. Conversely, there was a suppression of pathways associated with RNA processing, including nucleocytoplasmic transport, surveillance and ribosome biogenesis, and transcriptional misregulation in cancer pathways. Almost all genes involved in HERV activation restriction, KRAB zinc finger proteins, RNA nucleocytoplasmic transport, stemness, HLA and antigen processing and presentation, and immune checkpoints were overexpressed in cancerous tissues, and many over-expressed HERV-related nearby genes were correlated with high HERV activation and poor survival. Twenty-three immune and stromal cells showed higher expression in non-cancerous than cancerous tissues, and seven were correlated with HERV activation. Small-molecule modulation of alternative splicing (AS) altered the expression of survival-related HERVs and their activation-related genes, as well as nearby genes. Conclusion: Comprehensive and integrated approaches for evaluating HERV expression and their correlation with specific pathways have the potential to provide new companion diagnostics and therapeutic strategies for HCC. [ABSTRACT FROM AUTHOR]

Atypical hemolytic uremic syndrome (aHUS) is a rare, life-threatening thrombotic microangiopathy. Definitive biomarkers for disease diagnosis and activity remain elusive, making the exploration of molecular markers paramount. We conducted single-cell sequencing on peripheral blood mononuclear cells from 13 aHUS patients, 3 unaffected family members of aHUS patients, and 4 healthy controls. We identified 32 distinct subpopulations encompassing 5 B-cell types, 16 T- and natural killer (NK) cell types, 7 monocyte types, and 4 other cell types. Notably, we observed a significant increase in intermediate monocytes in unstable aHUS patients. Subclustering analysis revealed seven elevated expression genes, including NEAT1, MT-ATP6, MT-CYB, VIM, ACTG1, RPL13, and KLRB1, in unstable aHUS patients, and four heightened expression genes, including RPS27, RPS4X, RPL23, and GZMH genes, in stable aHUS patients. Additionally, an increase in the expression of mitochondria-related genes suggested a potential influence of cell metabolism on the clinical progression of the disease. Pseudotime trajectory analysis revealed a unique immune cell differentiation pattern, while cell—cell interaction profiling highlighted distinctive signaling pathways among patients, family members, and controls. This single-cell sequencing study is the first to confirm immune cell dysregulation in aHUS pathogenesis, offering valuable insights into molecular mechanisms and potential new diagnostic and disease activity markers. [ABSTRACT FROM AUTHOR]

Lung cancer remains a major health problem despite the considerable research into prevention and treatment methods. Through a deeper understanding of tumors, patient‐specific ex vivo spheroid models with high specificity can be used to accurately investigate the cause, metastasis, and treatment strategies for lung cancer. Biofabricate lung tumors are presented, consisting of patient‐derived tumor spheroids, endothelial cells, and lung decellularized extracellular matrix, which maintain a radial oxygen gradient, as well as biophysicochemical behaviors of the native tumors for precision medicine. It is also demonstrated that the developed lung‐cancer spheroid model reproduces patient responses to chemotherapeutics and targeted therapy in a co‐clinical trial, with 85% accuracy, 86.7% sensitivity, and 80% specificity. RNA sequencing analysis validates that the gene expression in the spheroids replicates that in the patient's primary tumor. This model can be used as an ex vivo predictive model for personalized cancer therapy and to improve the quality of clinical care. [ABSTRACT FROM AUTHOR]

Background: Previous studies on the association of enterobiasis and chronic inflammatory diseases have revealed contradictory results. The interaction of Enterobius vermicularis infection in particular with gut microbiota and induced immune responses has never been thoroughly examined. Methodology/Findings: In order to answer the question of whether exposure to pinworm and mebendazole can shift the intestinal microbial composition and immune responses, we recruited 109 (30 pinworm-negative, 79 pinworm-infected) first and fourth grade primary school children in Taichung, Taiwan, for a gut microbiome study and an intestinal cytokine and SIgA analysis. In the pinworm-infected individuals, fecal samples were collected again at 2 weeks after administration of 100 mg mebendazole. Gut microbiota diversity increased after Enterobius infection, and it peaked after administration of mebendazole. At the phylum level, pinworm infection and mebendazole deworming were associated with a decreased relative abundance of Fusobacteria and an increased proportion of Actinobacteria. At the genus level, the relative abundance of the probiotic Bifidobacterium increased after enterobiasis and mebendazole treatment. The intestinal SIgA level was found to be lower in the pinworm-infected group, and was elevated in half of the mebendazole-treated group. A higher proportion of pre-treatment Salmonella spp. was associated with a non-increase in SIgA after mebendazole deworming treatment. Conclusions/Significance: Childhood exposure to pinworm plus mebendazole is associated with increased bacterial diversity, an increased abundance of Actinobacteria including the probiotic Bifidobacterium, and a decreased proportion of Fusobacteria. The gut SIgA level was lower in the pinworm-infected group, and was increased in half of the individuals after mebendazole deworming treatment. [ABSTRACT FROM AUTHOR]

Objectives To identify genetic variants and polygenic risk score (PRS) relating to female gout and asymptomatic hyperuricaemia (AH) in a genome-wide association study (GWAS). Methods Gout, AH and normouricemia controls were included from Taiwan biobank and China Medical University Hospital. All participants were divided into discovery and replication cohorts for GWAS. PRS was estimated according to whether the variant exhibited a protective effect on the phenotypes or not. Each cohort was separated into two groups by the age of 50 years old. Results A total of 59 472 females were enrolled, and gout and AH occupied 1.60% and 19.59%, respectively. Six variants located in genes SLC2A9 , C5orf22 , CNTNAP2 and GLRX5 were significantly predictors of female gout in those aged ≥50. For those aged <50 years old, only the variant rs147750368 (SPANXN1) on chromosome X was found. Most variants located in genes SLC2A9 , ZNF518B , PKD2 and ABCG2 were found to be significantly related to AH in both age groups. The PRS could explain ∼0.59% to 0.89% of variance of gout in variants with protective effects, which showed 6.2 times of mean PRS in the risk variants, but only 1.2 times in the AH phenotype. Moreover, the PRS also revealed a dose-response trend between AH rates and quartile scores. Conclusion The variants in gene SLC2A9 are the major genetic factors for females associated with gout in those aged ≥50. PRS can provide a more robust prediction of the gout/AH under a homogeneous selection of variants that show effects on the traits. [ABSTRACT FROM AUTHOR]

Background: Cancer is a major cause of death, and its early identification and intervention have potential for clinical actionability and benefits for human health. The studies using whole‐genome sequencing (WGS) and large samples analysis of cancer‐related genes have been rarely done. Methods: We performed WGS to explore germline mutations in coding and non‐coding areas of cancer‐related genes and non‐coding driver genes and regulatory areas. Structural variants (SVs) was also analyzed. We used several tools and a subgrouping method to analyze the variants in 1491 healthy participants. Moreover, 275 cancer‐related genes sequencing was carried out in 125 cancer patients. Results: The incidence of familial cancer in the Taiwanese general population is 8.79% (131/1491). Cancer carrier rate of cancer‐related genes is about 7.04% (105/1491) for pathogenic/likely pathogenic variants (P/LP) on ClinVar database only, and 28.24% (421/1491) for P/LP and loss of function variants. The carrier frequencies of cancer‐related genes P/LP on ClinVar database were as follows: 8.40% (11/131), 7.11% (28/394), and 6.83% (66/966) in FC, 1MC, and nMC, respectively. The SVs and non‐coding driver gene variants are uncommon. There are 1.54% (23/1491) of actionable cancer genes in American College of Medical Genetics and Genomics (ACMG), and the germline mutation rate of 275 cancer‐related genes is 7.2% (9/125) in cancer patients including 4.0% (5/125) of actionable cancer genes in ACMG. After analyzing the frequencies of P/LP variants on GJB2 and SLC25A13 genes, we suggest that these two genes may not be cancer‐related genes and need be re‐evaluated. Conclusions: WGS analysis can completely detect germline mutations in cancer carriers. This study use subgrouping approach for samples provides a strategy to study whether a gene or variant is a cancer‐related gene or variant in the future studies. [ABSTRACT FROM AUTHOR]

Adolescent idiopathic scoliosis (AIS) is a three-dimensional spinal curvature deformity that appears in the adolescent period. In this study, we performed whole-exome sequencing on 11 unrelated Taiwanese patients with a Cobb's angle greater than 40 degrees. Our results identified more than 200 potential pathogenic rare variants, however, most of which were carried only by one individual. By in silico pathogenicity annotation studies, we found that TTN, CLCN1, and SOX8 were the most important genes, as multiple pathogenic variants were within these genes. Furthermore, biological functional annotation indicated critical roles of these AIS candidate genes in the skeletal muscle. Importantly, a pathogenic variant on SOX8 was shared by over 35% of the patients. These results highlighted TTN, CLCN1, and SOX8 as the most likely susceptibility genes for severe AIS. [ABSTRACT FROM AUTHOR]

Simple Summary: The characters of Taiwanese hepatocellular carcinoma (HCC) are different from other parts of the world. We characterized the molecular features of HCC using a newly developed classification system based on the expression of the Wnt–Hippo signaling pathway-related genes. We analyzed the data in terms of prognostic value, transcriptome features, immune infiltration, and clinical characteristics, and compared the resulting subclasses with previously published classifications. A new molecular classification method based on a 272 gene panel of Wnt–Hippo pathways that may provide a new target for the treatment. In Taiwan, a combination of hepatitis B and C infection, economic boom-related food and alcohol overconsumption, and Chinese medicine prescriptions has led to a high rate of hepatocellular carcinoma (HCC). However, the causative factors and underlying tumor biology for this unique HCC environment have not been identified. Wnt and Hippo signaling pathways play an important regulatory role in HCC development, and their functions are generally considered as positive and negative regulators of cell proliferation, respectively. In this study, we characterized the molecular features of HCC using a newly developed classification system based on the expression of the Wnt–Hippo signaling pathway-related genes. RNA sequencing (RNA-Seq) was performed on liver tumor tissues from 100 patients with liver cancer. RNA-Seq data for 272 previously characterized Wnt–Hippo signaling pathway-related genes were used for hierarchical clustering. We analyzed the data in terms of prognostic value, transcriptome features, immune infiltration, and clinical characteristics, and compared the resulting subclasses with previously published classifications. Four subclasses of HCC (HCCW1–4) were identified. Subclass HCCW1 displayed the highest PCDHB4 expression. Subclass HCCW2 displayed lower Edmondson–Steiner grades (I and II) and CTNNB1 mutation frequencies. Subclass HCCW3 was associated with a good prognosis, the highest PCDHGB7 expression, high CD8+ naïve T cells abundance, and relatively low TP53 mutation rates. Subclass HCCW4 was associated with a poor prognosis, the highest PCDHB2 and PCDHB6 expression, a relatively high abundance of Th1 cells, NKT and class-switched memory B cells, relatively low enrichment of cDC, iDC, and CD4+ memory T cells, and high Edmondson–Steiner grades (III and IV). We also identified Wnt–Hippo signaling pathway-related genes that may influence immune cell infiltration. We developed a panel of 272 Wnt–Hippo signaling pathway-related genes to classify HCC into four groups based on Taiwanese HCC and The Cancer Genome Atlas Liver Hepatocellular Carcinoma datasets. This novel molecular classification system may aid the treatment of HCC. [ABSTRACT FROM AUTHOR]

Background: This study was to determine the prevalence and clinical significance of clonal hematopoiesis (CH)-related variants, and somatic and germline mutations in cancer patients and healthy individuals. Methods: We performed next-generation sequencing of 275 cancer-related genes be-tween plasma and white blood cells in 92 cancer patients and 47 controls without cancer. Blood samples were recruited from May 2017 to July 2021, and blood cancer patients were excluded. For all statistical analysis in this study, p < 0.05 was considered statistically significant. Results: Overall, 38.04% of patients and 46.81% of controls harbored at least one CH-related mutation in plasma cell-free DNA. Based on our results, older cancer patients exhibited a CH phenomenon more frequently than younger patients (p = 0.0024). A total of 39 somatic pathogenic (P)/likely pathogenic (LP) mutations were identified in 17 genes in 21 of 92 patients. We found that the presence of P/LP variants in cancer-related gene predicted shorter overall survival (OS) (p = 0.001). Multivariate analysis adjusted for CH-related mutations, germline mutations, and tumor stage, also indicated that somatic mutations correlated significantly with OS (p = 0.022). Moreover, the frequency of a germline P/LP variant was that of seven of 92 individuals in the cancer group and one of 42 individuals in the control group. Conclusions: We characterized the CH-related variants, and somatic and germline mutations in cancer patients and healthy individuals, and the results have important clinical significance. [ABSTRACT FROM AUTHOR]

Background: This study was to determine the prevalence and clinical significance of clonal hematopoiesis (CH)-related variants, and somatic and germline mutations in cancer patients and healthy individuals.Methods: We performed next-generation sequencing of 275 cancer-related genes be-tween plasma and white blood cells in 92 cancer patients and 47 controls without cancer. Blood samples were recruited from May 2017 to July 2021, and blood cancer patients were excluded. For all statistical analysis in this study, p < 0.05 was considered statistically significant.Results: Overall, 38.04% of patients and 46.81% of controls harbored at least one CH-related mutation in plasma cell-free DNA. Based on our results, older cancer patients exhibited a CH phenomenon more frequently than younger patients (p = 0.0024). A total of 39 somatic pathogenic (P)/likely pathogenic (LP) mutations were identified in 17 genes in 21 of 92 patients. We found that the presence of P/LP variants in cancer-related gene predicted shorter overall survival (OS) (p = 0.001). Multivariate analysis adjusted for CH-related mutations, germline mutations, and tumor stage, also indicated that somatic mutations correlated significantly with OS (p = 0.022). Moreover, the frequency of a germline P/LP variant was that of seven of 92 individuals in the cancer group and one of 42 individuals in the control group.Conclusions: We characterized the CH-related variants, and somatic and germline mutations in cancer patients and healthy individuals, and the results have important clinical significance. [ABSTRACT FROM AUTHOR]

Head and neck cancer has poor overall survival. Patients with head and neck cancer more frequently develop second primary tumors than do patients with other cancers, leading to a poor prognosis. In this study, we used next-generation sequencing to analyze and compare mutations between first tumors and second tumors in oral cancer. We retrieved tumor tissues collected from 13 patients who were diagnosed twice as having cancer. We used driver gene and trunk mutations to distinguish between recurrent cancer and primary cancer in oral cancer. We observed unique driver gene mutations in three patients with an initial clinical diagnosis of recurrent cancer; hence, we believe that the corresponding patients had primary cancer. Four patients with an initial clinical diagnosis of primary cancer were found to actually have recurrent cancer according to our results. Genetic testing can be used to enhance the accuracy of clinical diagnosis. [ABSTRACT FROM AUTHOR]

Abstract: Background: Recent studies have demonstrated the importance of long non-coding RNAs (lncRNAs) in chromatin remodeling, and in transcriptional and post-transcriptional regulation. However, only a few specific lncRNAs are well understood, whereas others are completely uncharacterized. To address this, there is a need for user-friendly platform to studying the putative regulatory functions of human lncRNAs. Description: lncRNAMap is an integrated and comprehensive database relating to exploration of the putative regulatory functions of human lncRNAs with two mechanisms of regulation, by encoding siRNAs and by acting as miRNA decoys. To investigate lncRNAs producing siRNAs that regulate protein-coding genes, lncRNAMap integrated small RNAs (sRNAs) that were supported by publicly available deep sequencing data from various sRNA libraries and constructed lncRNA-derived siRNA–target interactions. In addition, lncRNAMap demonstrated that lncRNAs can act as targets for miRNAs that would otherwise regulate protein-coding genes. Previously studies indicated that intergenic lncRNAs (lincRNAs) either positive or negative regulated neighboring genes, therefore, lncRNAMap surveyed neighboring genes within a 1Mb distance from the genomic location of specific lncRNAs and provided the expression profiles of lncRNA and its neighboring genes. The gene expression profiles may supply the relationship between lncRNA and its neighboring genes. Conclusions: lncRNAMap is a powerful user-friendly platform for the investigation of putative regulatory functions of human lncRNAs with producing siRNAs and acting as miRNA decoy. lncRNAMap is freely available on the web at http://lncRNAMap.mbc.nctu.edu.tw/. [Copyright &y& Elsevier]

Abstract: Background: Childhood acute lymphoblastic leukemia (ALL), a heterogeneous disease that includes multiple subtypes is defined by cell lineage and chromosome anomalies. Previous genome-wide association studies have reported several ARID5B and IKZF1 single nucleotide polymorphisms (SNPs) associated with the incidence of ALL. High-resolution melting (HRM) analysis is a rapid and convenient technique to detect SNPs; we thereby detected SNPs in ARID5B and IKZF1 genes. Methods: We enrolled 79 pediatric ALL patients and 80 healthy controls. Polymorphic variants of IKZF1 (rs6964823, rs4132601, and rs6944602) and ARID5B (rs7073837, rs10740055, and rs7089424) were detected by HRM, and SNPs were analyzed for association with childhood ALL. Results: The distribution of genotype rs7073837 in ARID5B significantly differed between ALL and controls (P =0.046), while those of IKZF1 (rs6964823, rs4132601, and rs6944602) and ARID5B (rs10740055 and rs7089424) did not. We analyzed the association for SNPs with B lineage ALL to find rs7073837 in ARID5B, conferring a higher risk for B lineage ALL (odds ratio, OR=1.70, 95% confidence interval, CI=1.01–2.87, P =0.049). Conclusion: HRM is a practical method to detect SNPs in ARID5B and IKZF1 genes. We found that rs7073837 in ARID5B correlated with a risk for childhood B lineage ALL. [Copyright &y& Elsevier]

Apoptosis is a key mechanism for enhanced cellular radiosensitivity in radiation therapy. Studies suggest that Akt signaling may play a role in apoptosis and radioresistance. This study evaluates the possible modulating role of amiloride, an antihypertensive agent with a modulating effect to alternative splicing for regulating apoptosis, in the antiproliferative effects induced by ionizing radiation (IR) in glioblastoma multiforme (GBM) 8401 cells. Analysis of cell viability showed that amiloride treatment significantly inhibited cell proliferation in irradiated GBM8401 cells ( p<0.05) in a time-dependent manner, especially in cells treated with amiloride with IR post-treatment. In comparison with GBM8401 cells treated with amiloride alone, with GBM8401 cells treated with IR alone, and with human embryonic lung fibroblast control cells (HEL 299), GBM8401 cells treated with IR combined with amiloride showed increased overexpression of phosphorylated Akt, regardless of whether IR treatment was performed before or after amiloride administration. The alternative splicing pattern of apoptotic protease-activating factor-1 ( APAF1) in cells treated with amiloride alone, IR alone, and combined amiloride-IR treatments showed more consistent cell proliferation compared to that in other apoptosis-related genes such as baculoviral IAP repeat containing 5 ( BIRC5), Bcl-X, and homeodomain interacting protein kinase-3 ( HIPK3). In GBM8401 cells treated with amiloride with IR post-treatment, the ratio of prosurvival (-XL,-LC) to proapoptotic (-LN,-S) splice variants of APAF1 was lower than that seen in cells treated with amiloride with IR pretreatment, suggesting that proapoptotic splice variants of APAF1 ( APAF1-LN,-S) were higher in the glioblastoma cells treated with amiloride with IR post-treatment, as compared to glioblastoma cells and fibroblast control cells that had received other treatments. Together, these results suggest that amiloride modulates cell radiosensitivity involving the Akt phosphorylation and the alternative splicing of APAF1, especially for the cells treated with amiloride with IR post-treatment. Therefore, amiloride may improve the effectiveness of radiation therapy for GBMs. Treatment of irradiated GBM tumors with amiloride inhibited cell proliferation in a time-dependent manner. Drug treatment alone showed increased expression of pAkt. [ABSTRACT FROM AUTHOR]

Abstract: Background: Multiple acyl-CoA dehydrogenase deficiency (MADD) or gluaric aciduria type II is an autosomal recessive disease caused by defects in mitochondrial electron transfer system and metabolism of fatty acid. Recently, ETFDH mutations were reported to be major causes of riboflavin-responsive MADD. The present study is aimed at screening ETFDH mutations. Methods: High resolution melting (HRM) analysis was performed to screen ETFDH mutations. Genomic DNA was extracted from peripheral blood samples of the 9 patients with MADD and normal controls. Total 13 exons of ETFDH were screened by HRM analysis. The results were subsequently confirmed by direct DNA sequencing. Results: This diagnostic strategy proved to be feasible in detecting 3 known (c.250G>A, c380T>A, c.524G>T) and 1 novel (c.1831G>A) ETFDH mutations. Each mutation could be readily and accurately identified in the difference plot curves. We estimated the carrier frequency of the hotspot mutation, c.250G>A, in the Taiwanese population to be 1:125 (0.8%). Conclusions: HRM analysis can be successfully applied to screen ETFDH mutations. Since riboflavin-responsive MADD is often treatable, especially with mutations in ETFDH, identifying ETFDH mutations is crucial for these patients. [Copyright &y& Elsevier]

Abstract: Background: Janus kinase 2 (JAK2) is a tyrosine kinase involved in the cytokine signaling of several growth factors such as erythropoietin and thrombopoietin in normal and neoplastic cells. The G to T exchange at nucleotide 1849 in exon 14 of the JAK2 gene leads to a substitution of valine with phenylalanine at the amino acid position 617 (V617F) of the JAK2 protein. Currently, the occurrence of the JAK2 V617F mutation is well recognized in chronic myeloproliferative disorders (MPDs). Methods: We identified JAK2 V617F missense mutation in patients with MPD by high resolution melting (HRM) analysis. HRM analysis is a new gene scan tool that quickly performs the PCR and identifies sequences alterations without requiring post-PCR treatment. This study included 7 PV patients (41.1%), 6 ET patients (35.3%), and 4 myelofibrosis patients (23.5%). Additionally, our methodology was compared with amplification refractory mutation system (ARMS) assay. Results: Up to 5% of the JAK2 V617F mutation was successfully detected in patients with MPD using HRM analysis. Eleven out of 17 patients (64.7%) were positive for the presence of JAK2 V617F mutation. The prevalence of mutation in the different subtypes of MPDs was 85.7% in PV (6 of 7 patients), 66.7% in ET (4 of 6) and 5.9% in myelofibrosis (1 of 4). The results proved 100% comparable to those obtained by ARMS assay. Conclusions: The HRM analysis is a rapid and effective technique for the detection of JAK2 V617F missense mutation. [Copyright &y& Elsevier]

Abstract: Point mutations of the K-ras gene located in codons 12 and 13 cause poor responses to the anti-epidermal growth factor receptor (anti-EGFR) therapy of colorectal cancer (CRC) patients. Besides, mutations of K-ras gene have also been proven to play an important role in human tumor progression. We established a simple and effective capillary electrophoresis (CE) method for simultaneous point mutation detection in codons 12 and 13 of K-ras gene. We combined one universal fluorescence-based nonhuman-sequence primer and two fragment-oriented primers in one tube, and performed this two-in-one polymerase chain reaction (PCR). PCR fragments included wild type and seven point mutations at codons 12 and 13 of K-ras gene. The amplicons were analyzed by single-strand conformation polymorphism (SSCP)-CE method. The CE analysis was performed by using a 1× Tris–borate–EDTA (TBE) buffer containing 1.5% (w/v) hydroxyethylcellulose (HEC) (MW 250 000) under reverse polarity with 15°C and 30°C. Ninety colorectal cancer patients were blindly genotyped using this developed method. The results showed good agreement with those of DNA sequencing method. The SSCP-CE was feasible for mutation screening of K-ras gene in populations. [Copyright &y& Elsevier]

Abstract: Background: Spinal muscular atrophy (SMA) is a degenerative motor neuron disease caused by homozygous mutations of the survival motor neuron 1 (SMN1) gene. Effective treatment for SMA is unavailable at present. The aim of this study was to investigate the effect of hydroxyurea (HU) in SMA cells and patients. Materials and methods: Fifteen SMA lymphoid and three fibroblast cell lines, 2 from SMA patients and 1 control, were treated with HU at different concentrations, and 33 patients (types II, III) randomized into three groups on different HU dosage, 20, 30, 40 mg/kg/day, were treated for 8 weeks and followed up for another drug-free 8 weeks. The effect of HU on SMN2 gene expression and clinical manifestations was evaluated. Results: After treatment, in vitro, full-length mRNA level and gems number increased significantly, and hnRNP A1 protein decreased. In vivo, there were slight increases in muscle strength scores at 4 weeks and full-length SMN mRNA at 8 weeks in 30 mg/kg/day subgroup. Conclusions: Treating with HU enhanced SMN2 gene expression in SMA cells and showed slight trend towards improvement in some clinical outcome measures in SMA patients which suggests HU may be safe to use in SMA patients but larger randomized, placebo-controlled, double-blind trials are needed to further investigate its efficacy. [Copyright &y& Elsevier]

Background/purpose. 5-Fluorouracil (5-FU) remains the most frequently used chemotherapy agent in various human cancers. Over 80% of the 5-FU administered is metabolized by dihydropyrimidine dehydrogenase (DPD) in the liver. However, mutations in the DPD gene have been found to be associated with low DPD activity causing severe complications. The aim of this study was to determine the frequency of 11 known mutations in Taiwanese subjects and the relationship between mutation and DPD level. Methods. Samples from a total of 300 subjects were investigated in this study. The PCR-RFLP method was used to identify 11 mutations of the DPYD gene, including 62G>A, 74A>G, 85T>C (DPYD*9A), 812delT, 1003G>T, 1156G>T, 1627A>G (DPYD*5), 1714C>G, 1897delC (DPYD*3), 2194G>A (DPYD*6), and IVS14+1G>A (DPYD*2A). DPD protein levels were determined using a DPD ELISA kit. Results. Four mutations, including 74A>G, 85T>C (DPYD*9A), 1627A>G (DPYD*5), and 2194G>A (DPYD*6), were found in our 300 samples. The following mutations were not detected: 62G>A, 812delT, 1003G>T, 1156G>T, 1714C>G, 1897delC (DPYD*3), and IVS14+1G>A (DPYD*2A). The phenotype analysis by DPD protein level indicated that the 1627A>G (DPYD*5) mutation was not associated with the DPD protein level and might be a polymorphism in the DPD gene. The DPD level was also not correlated with gender. Conclusion. No significant correlations between these 11 mutations and DPD protein level were found indicating that examination of these mutations is insufficient to provide a high-value prediction of the 5-FU pharmacogenetic syndrome in Taiwanese. Genotype and phenotype analysis indicated the 1627A>G (DPYD*5) mutation to be a polymorphism. [ABSTRACT FROM AUTHOR]

Studies a Taiwanese family in which the father carried an alpha chain variant and the mother was a carrier of alpha-thalassemia-1 with assorted genotypes in their offspring. Hematological and genetic analyses of blood samples; Correlations between the clinical manifestations and genotypes.

The deposition of amyloid beta-peptide (Aβ) plays a crucial role in the pathogenesis of Alzheimer’s disease (AD). Beta-site APP cleaving enzyme (BACE) is the rate-limiting enzyme in the Aβ formation. BACE mutations/polymorphisms may be associated with AD. We searched the BACE coding region mutations/polymorphisms of cDNA in 25 AD patients and 100 healthy controls by single-strand conformational polymorphism. A polymorphism at BACE coding region was identified and confirmed to be 786C/G polymorphism by nucleotide sequencing. Based on these findings, we investigated the association of this polymorphism with the occurrence of AD by PCR-RFLP. A total of 98 AD patients along with 138 controls were recruited in the present study. The allele frequencies of the 786C/G polymorphism were 0.622 for C and 0.378 for G in AD. In controls, the C and G allele frequencies were 0.691 and 0.309, respectively. No significant association of this polymorphism with the occurrence of AD can be established. Larger sample size may be necessary to identify other potential mutations/polymorphisms among BACE gene. [Copyright &y& Elsevier]

Recently, a tumour susceptibility gene, TSG101, has been identified at chromosome 11p15. A large intragenic deletion of this gene has been demonstrated in primary breast tumours. To evaluate the role of the TSG101 gene in leukaemia, bone marrow and/or peripheral blood from 68 acute myeloid leukaemia patients, five haemopoietic cell lines (HL60, U937, Raji, KG-1, K562) and 30 normal controls were analysed by reverse transcription of the TSG101 mRNA, followed by PCR amplification and sequencing of the products. The results showed aberrant TSG101 transcripts in 24/68 (35%) acute myeloid leukaemia (AML) patients, all of the cell lines (100%) and 3/30 (10%) normal controls. Our study indicated that the abnormal transcripts may have resulted from aberrant RNA splicing as evidenced by these aberrant transcripts. Also, normal full-length transcripts were present in all specimens examined. The aberrant transcript occurred more frequently in the AML and cell lines. However, because aberrant transcripts of TSG101 were also found in the normal controls, the role of TSG101 as a tumour suppressor gene should be evaluated carefully. [ABSTRACT FROM AUTHOR]

Background: Precision therapy for lung cancer requires comprehensive genomic analyses. Specific effects of targeted therapies have been reported in Asia populations, including Taiwanese, but genomic studies have rarely been performed in these populations.Method: We enrolled 72 patients with non-small cell lung cancer, of whom 61 had adenocarcinoma, 10 had squamous cell carcinoma, and 1 had combined adenocarcinoma and squamous cell carcinoma. Whole-exome or targeted gene sequencing was performed. To identify trunk mutations, we performed whole-exome sequencing in two tumor regions in four patients.Results: Nineteen known driver mutations in EGFR, PIK3CA, KRAS, CTNNB1, and MET were identified in 34 of the 72 tumors evaluated (47.22%). A comparison with the Cancer Genome Atlas dataset showed that EGFR was mutated at a much higher frequency in our cohort than in Caucasians, whereas KRAS and TP53 mutations were found in only 5.56% and 25% of our Taiwanese patients, respectively. We also identified new mutations in ARID1A, ARID2, CDK12, CHEK2, GNAS, H3F3A, KDM6A, KMT2C, NOTCH1, RB1, RBM10, RUNX1, SETD2, SF3B1, SMARCA4, THRAP3, TP53, and ZMYM2. Moreover, all ClinVar pathogenic variants were trunk mutations present in two regions of a tumor. RNA sequencing revealed that the trunk or branch genes were expressed at similar levels among different tumor regions.Conclusions: We identified novel variants potentially associated with lung cancer tumorigenesis. The specific mutation pattern in Taiwanese patients with non-small cell lung cancer may influence targeted therapies. [ABSTRACT FROM AUTHOR]

Background: Gastrointestinal (GI) cancer including colorectal cancer, gastric cancer, pancreatic cancer, etc., are among the most frequent malignancies diagnosed annually and represent a major public health problem worldwide.Methods: This paper reports an aided curation pipeline to identify potential influential genes for gastrointestinal cancer. The curation pipeline integrates biomedical literature to identify named entities by Bi-LSTM-CNN-CRF methods. The entities and their associations can be used to construct a graph, and from which we can compute the sets of co-occurring genes that are the most influential based on an influence maximization algorithm.Results: The sets of co-occurring genes that are the most influential that we discover include RARA - CRBP1, CASP3 - BCL2, BCL2 - CASP3 - CRBP1, RARA - CASP3 - CRBP1, FOXJ1 - RASSF3 - ESR1, FOXJ1 - RASSF1A - ESR1, FOXJ1 - RASSF1A - TNFAIP8 - ESR1. With TCGA and functional and pathway enrichment analysis, we prove the proposed approach works well in the context of gastrointestinal cancer.Conclusions: Our pipeline that uses text mining to identify objects and relationships to construct a graph and uses graph-based influence maximization to discover the most influential co-occurring genes presents a viable direction to assist knowledge discovery for clinical applications. [ABSTRACT FROM AUTHOR]

• G6PD-deficient patients have a shorter RBC lifespan, HbA1c is underestimated. • DM patients with G6PD deficiency had significantly higher FG/HbA1c ratios. • The AUC value indicated excellent reliability for predicting the FG/HbA1c ratio. Patients with glucose-6-phosphate dehydrogenase (G6PD) deficiency or thalassemia have a shorter red blood cell lifespan; therefore, HbA1c is underestimated in these patients. To address these issues, we sought an early indicator for G6PD deficiency or thalassemia in DM patients. A total of 4908 patients with DM and 1848 subjects without DM were included in this study. Fasting glucose (FG) levels, HbA1c levels, hemogram profiles and G6PD activities were measured. Genotypic analyses of G6PD deficiency and thalassemia were performed. DM patients with G6PD deficiency had significantly higher FG/HbA1c ratios than did those without G6PD deficiency (26.54 vs. 18.36; p < 0.0001). We divided the FG level into four categories: ≤150, 151–250, 251–350, and ≥351 mg/dL. Among all groups, only patients with DM and G6PD deficiency had higher FG/HbA1c ratios than those of patients with DM alone or DM with thalassemia. To evaluate the reliability of the FG/HbA1c ratio, receiver operating characteristic analyses were performed. The areas under the curve for detecting FG ≤ 150, 151–250, 251–350, and ≥351 mg/dL with G6PD deficiency based on the FG/HbA1c ratio were 0.839 (p < 0.001), 0.888 (p < 0.001), 0.891 (p < 0.001), and 0.640 (p = 0.3954), respectively. G6PD deficiency was confirmed by genetic analysis. We found common mutations that influenced G6PD activity and HbA1c levels. The FG/HbA1c ratio is a good indicator of DM with G6PD deficiency. If this ratio is determined to be high in a clinical setting, then the clinician must consider whether the patient has a G6PD deficiency, and HbA1c reference values must be adjusted to avoid misdiagnosis and incorrect treatment decisions. [ABSTRACT FROM AUTHOR]

Background: Congenital dyserythropoiesis anemia type Ia (OMIM:224120), is a rare hereditary anemia. The diagnosis is difficult to make and usually delayed in part due to its rarity and nonspecific clinical manifestations. Methods: Whole exome sequencing was applied for the genetic diagnosis of a 12‐year‐old boy who has suffered from hemolytic anemia since birth and who requires regular transfusions. Sanger sequencing of the variants detected in whole exome sequencing was performed in the patient and his parents. Results: Compound heterozygous mutations of CDAN1 gene, including one previously reported and one novel mutation, which is a splicing change, were detected in the whole exome sequencing and confirmed by Sanger sequencing. The autosomal recessive inheritance was confirmed by pedigree analysis. Conclusion: To our knowledge, this is the first case report of congenital dyserythropoiesis anemia type Ia with genetic diagnosis to be located in Taiwan. Because of the rarity of CDA Ia and the overlapping of the clinical manifestations with other hereditary anemias, the next‐generation sequencing approach is effective for conclusive diagnosis of CDA Ia. [ABSTRACT FROM AUTHOR]

Williams-Beuren Syndrome (WBS; OMIM #194050) is a rare neurodevelopmental disorder that results from a deletion at 7q11.23 spanning 25-27 genes. We performed chromosomal microarray analysis (CMA) in 9 Taiwanese patients with WBS to confirm the diagnosis. These samples had already been examined by FISH and diagnosed as WBS. Pathogenic copy number variations (CNVs) were identified in all patients, including 24 genes (spanning from FKBP6 to GTF2I) with typical 7q11.23 microdeletion. A deletion in TRIM50 was common in Taiwanese patients with WBS (8/9). Furthermore, 1 patient had 2 additional gene deletions in NCF1 and GTF2IRD2. We also found 4 patients with duplications of 4p16.1, 16p13.11, 10q26.3, and 21q22.3. All 9 WBS patients exhibited distinctive facial dysmorphisms, including a wide mouth, thick prominent lips, short nose with anteverted nares, and periorbital puffiness. However, cardiac defects were not frequent in our patients (3/9). In conclusion, we detected CNVs associated with WBS in a Taiwanese population using CMA. Although CMA is expensive and labor-intensive, it is useful for identifying typical/atypical CNVs, delineating distal break points, and detecting other CNVs. [ABSTRACT FROM AUTHOR]

Next‐generation sequencing (NGS) technology is currently used to establish mutational profiles in many heterogeneous diseases. The aim of this study was to evaluate the mutational spectrum in Taiwanese patients with colorectal cancer (CRC) to help clinicians identify the best treatment method. Whole‐exome sequencing was conducted in 32 surgical tumor tissues from patients with CRC. DNA libraries were generated using the Illumina TruSeq DNA Exome, and sequencing was performed on the Illumina NextSeq 500 system. Variants were annotated and compared to those obtained from publicly available databases. The analysis revealed frequent mutations in APC (59.38%), TP53 (50%), RAS (28.13%), FBXW7 (18.75%), RAF (9.38%), PIK3CA (9.38%), SMAD4 (9.38%), and SOX9 (9.38%). A mutation in TCF7L2 was also detected, but at lower frequencies. Two or more mutations were found in 22 (68.75%) samples. The mutation rates for the WNT, P53, RTK‐RAS, TGF‐β, and PI3K pathways were 78.13%, 56.25%, 40.63%, 18.75%, and 15.63%, respectively. RTK‐RAS pathway mutations were correlated with tumor size (P = 0.028). We also discovered 23 novel mutations in NRAS, PIK3CA, SOX9, APC, SMAD4, MSH3, MSH4, PMS1 PMS2, AXIN2, ERBB2, PIK3R1, TGFBR2, and ATM that were not reported in the COSMIC, The Cancer Genome Atlas, and dbSNP databases. In summary, we report the mutational landscape of CRC in a Taiwanese population. NGS is a cost‐effective and time‐saving method, and we believe that NGS will help clinicians to treat CRC patients in the near future. [ABSTRACT FROM AUTHOR]

Purpose: To understand the association between genetic mutations and radiomics of 2-deoxy-2-[18F]fluoro-D-glucose ([18F]FDG) positron emission tomography (PET)/x-ray computed tomography (CT) in patients with colorectal cancer (CRC).Procedures: This study included 74 CRC patients who had undergone preoperative [18F]FDG PET/CT. A total of 65 PET/CT-related features including intensity, volume-based, histogram, and textural features were calculated. High-resolution melting methods were used for genetic mutation analysis.Results: Genetic mutants were found in 21 KRAS tumors (28 %), 31 TP53 tumors (42 %), and 17 APC tumors (23 %). Tumors with a mutated KRAS had an increased value at the 25th percentile of maximal standardized uptake value (SUVmax) within their metabolic tumor volume (MTV) (P < .0001; odds ratio [OR] 1.99; 95 % confidence interval [CI] 1.37-2.90) and their contrast from the gray-level cooccurrence matrix (P = .005; OR 1.52; 95 % CI 1.14-2.04). A mutated TP53 was associated with an increased value of short-run low gray-level emphasis derived from the gray-level run length matrix (P = .001; OR 243006.0; 95 % CI 59.2-996,872,313). APC mutants exhibited lower low gray-level zone emphasis derived from the gray-level zone length matrix (P = .006; OR < .0001; 95 % CI 0.000-0.22).Conclusion: PET/CT-derived radiomics can provide supplemental information to determine KRAS, TP53, and APC genetic alterations in CRC. [ABSTRACT FROM AUTHOR]

Abstract Purpose: Congenital hemolytic anemia caused by red blood cell (RBC) membrane defects is a heterogeneous group of disorders. The present study aimed to search the causative gene mutations in patients with RBC membrane disorders in Taiwan. Materials and Methods: Next-generation sequencing approach using whole-exome sequencing (WES) was performed. Sanger sequencing was performed for confirmation of variants detected in WES in patients and their family members. Results: Five causative variants, including two ANK1 , two SPTA and one SPTB variants, were detected in four patients. All these variants, except one SPTA1 variant c.83G > A (p.R28H), are novel variants. Their pedigree analysis showed one de novo SPTA1 mutation c.83G > A (p.R28H) combined with αLELY, one de novo ANK1 mutation c.1034C > A (p.A345E), one autosomal dominant combined SPTA1 c.4604A > C (p.Q1535P) and SPTB c.6203 T > C (p.L2068P) mutations and one autosomal dominant ANK1 c.4462C > T (p.R1488X) mutation. Conclusions: Our data demonstrated that WES is an efficient tool for determining genetic etiologies of RBC membrane disorders and can facilitate accurate diagnosis and genetic counseling. Additional studies should be conducted on larger cohorts to investigate the distribution of gene mutations in patients with RBC membrane disorders in Taiwan. Highlights • RBC membrane disorders are highly heterogeneous in genetic background. • Genetic diagnosis of RBC membrane disorders is laborious using traditional sequencing. • Next-generation sequencing is effective in searching for causative variants. [ABSTRACT FROM AUTHOR]

Purpose: Analysis of circulating tumor DNA (ctDNA) offers an unbiased and noninvasive way to assess the genetic profiles of tumors. This study aimed to analyze mutations in ctDNA and their correlation with tissue mutations in patients with a variety of cancers.Methods: We included 21 cancer patients treated with surgical resection for whom we collected paired tissue and plasma samples. Next-generation sequencing (NGS) of all exons was performed in a targeted human comprehensive cancer panel consisting of 275 genes.Results: Six patients had at least one mutation that was concordant between tissue and ctDNA sequencing. Among all mutations (n = 35) detected by tissue and blood sequencing, 20% (n = 7) were concordant at the gene level. Tissue and ctDNA sequencing identified driver mutations in 66.67% and 47.62% of the tested samples, respectively. Tissue and ctDNA NGS detected actionable alterations in 57.14% and 33.33% of patients, respectively. When somatic alterations identified by each test were combined, the total proportion of patients with actionable mutations increased to 71.43%. Moreover, variants of unknown significance that were judged likely pathogenic had a higher percentage in ctDNA exclusively. Across six representative genes (PIK3CA, CTNNB1, AKT1, KRAS, TP53, and MET), the sensitivity and specificity of detection using mutations in tissue sample as a reference were 25 and 96.74%, respectively.Conclusions: This study indicates that tissue NGS and ctDNA NGS are complementary rather than exclusive approaches; these data support the idea that ctDNA is a promising tool to interrogate cancer genetics. [ABSTRACT FROM AUTHOR]

This model demonstrates the excellent prediction results (accuracy: 85%; sensitivity: 86.7% and specificity: 80%) for applying in patient-specific precision therapies. Highly Mimetic Ex Vivo Lung-Cancer Spheroid-Based Physiological Model for Clinical Precision Therapeutics (Adv. Sci. 16/2023) B Biofabricate Lung Tumors b In article number 2206603 by Mien-Chie Hung, Der-Yang Cho, Yi-Wen Chen, and co-workers, a facile route to construct sophisticated ex vivo lung tumors models consisting of patientderived tumor spheroids, vasculature barrier, and bovine lung ECMs, which maintained a radial oxygen gradient, as well as biophysical and biochemical behaviors of the native tumors is established. [Extracted from the article]