Publications by authors named "Kyudong Han"

115 Publications

High-accuracy quantitative principle of a new compact digital PCR equipment: Lab On An Array.

Genomics Inform 2021 Sep 30;19(3):e34. Epub 2021 Sep 30.

Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea.

Digital PCR (dPCR) is the third-generation PCR that enables real-time absolute quantification without reference materials. Recently, global diagnosis companies have developed new dPCR equipment. In line with the development, the Lab On An Array (LOAA) dPCR analyzer (Optolane) was launched last year. The LOAA dPCR is a semiconductor chip-based separation PCR type equipment. The LOAA dPCR includes Micro Electro Mechanical System that can be injected by partitioning the target gene into 56 to 20,000 wells. The amount of target gene per wells is digitized to 0 or 1 as the number of well gradually increases to 20,000 wells because its principle follows Poisson distribution, which allows the LOAA dPCR to perform precise absolute quantification. LOAA determined region of interest first prior to dPCR operation. To exclude invalid wells for the quantification, the LOAA dPCR has applied various filtering methods using brightness, slope, baseline, and noise filters. As the coronavirus disease 2019 has now spread around the world, needs for diagnostic equipment of point of care testing (POCT) are increasing. The LOAA dPCR is expected to be suitable for POCT diagnosis due to its compact size and high accuracy. Here, we describe the quantitative principle of the LOAA dPCR and suggest that it can be applied to various fields.
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http://dx.doi.org/10.5808/gi.21035DOI Listing
September 2021

Diagnostic evaluation of qRT-PCR-based kit and dPCR-based kit for COVID-19.

Genes Genomics 2021 11 15;43(11):1277-1288. Epub 2021 Sep 15.

Department of Bio-Convergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea.

Background: Coronavirus disease of 2019 (COVID-19) is well known as a fatal disease, first discovered at Wuhan in China, ranging from mild to death, such as shortness of breath and fever. Early diagnosis of COVID-19 is a crucial point in preventing global prevalence.

Objective: We aimed to evaluate the diagnostic competency and efficiency with the Allplex™ 2019-nCoV Assay kit and the Dr. PCR 20 K COVID-19 Detection kit, designed based on the qRT-PCR and dPCR technologies, respectively.

Methods: A total of 30 negative and 20 COVID-19 positive specimens were assigned to the diagnostic test by using different COVID-19 diagnosis kits. Diagnostic accuracy was measured by statistical testing with sensitivity, specificity, and co-efficiency calculations.

Results: Comparing both diagnostic kits, we confirmed that the diagnostic results of 30 negative and 20 positive cases were the same pre-diagnostic results. The diagnostic statistics test results were perfectly matched with value (1). Cohen's Kappa coefficient was demonstrated that the given kits in two different ways were "almost perfect" with value (1). In evaluating the detection capability, the dilutional linearity experiments substantiate that the Dr. PCR 20 K COVID-19 Detection kit could detect SARS-CoV-2 viral load at a concentration ten times lower than that of the Allplex™ 2019-nCoV Assay kit.

Conclusions: In this study, we propose that the dPCR diagnosis using LOAA dPCR could be a powerful method for COVID-19 point-of-care tests requiring immediate diagnosis in a limited time and space through the advantages of relatively low sample concentration and small equipment size compared to conventional qRT-PCR.
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http://dx.doi.org/10.1007/s13258-021-01162-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8441239PMC
November 2021

A comprehensive analysis of gorilla-specific LINE-1 retrotransposons.

Genes Genomics 2021 Oct 18;43(10):1133-1141. Epub 2021 Aug 18.

Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea.

Background: Long interspersed element-1 (LINE-1 or L1) is the most abundant retrotransposons in the primate genome. They have approximately 520,000 copies and make up ~ 17% of the primate genome. Full-length L1s can mobilize to a new genomic location using their enzymatic machinery. Gorilla is the second closest species to humans after the chimpanzee, and human-gorilla split 7-12 million years ago. The gorilla genome provides an opportunity to explore primate origins and evolution.

Objective: L1s have contributed to genome diversity and variations during primate evolution. This study aimed to identify gorilla-specific L1s using a more recent version of the gorilla reference genome (Mar. 2016 GSMRT3/gorGor5).

Methods: We collected gorilla-specific L1 candidates through computational analysis and manual inspection. L1Xplorer was used to identify whether full-length gorilla-specific L1s were intact. In addition, to determine the level of sequence conservation between intact fulllength gorilla-specific L1s, two ORFs of intact L1s were aligned with the L1PA2 consensus sequence.

Results: 2002 gorilla-specific L1 candidates were identified through computational analysis. Among them, we manually inspected 1,883 gorilla-specific L1s, among which most of them belong to the L1PA2 subfamily and 12 were intact L1s that could influence genomic variations in the gorilla genome. Interestingly, the 12 intact full-length gorilla-specific L1s have 14 highly conserved nonsynonymous mutations, including 6 mutations and 8 mutations in ORF1 and ORF2, respectively. In comparison to the intact full-length chimpanzee-specific L1s and human-specific hot-L1s, two of these in ORF1 (L256F and E293G) were shown as gorilla-specific nonsynonymous mutations.

Conclusion: The gorilla-specific L1s may have had significantly affected the gorilla genome to compose a genome different form that of other primates during primate evolution.
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http://dx.doi.org/10.1007/s13258-021-01146-4DOI Listing
October 2021

Comparative Analysis for Genetic Characterization in Korean Native Jeju Horse.

Animals (Basel) 2021 Jun 28;11(7). Epub 2021 Jun 28.

Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea.

The Jeju horse is a native Korean species that has been breeding on Jeju Island since the 13th century. Their shape has a distinct appearance from the representative species, Thoroughbred. Here, we performed a comparison of the Jeju horse and Thoroughbred horse for the identification of genome-wide structure variation by using the next-generation sequencing (NGS) technique. We generated an average of 95.59 Gb of the DNA sequence, resulting in an average of 33.74 X sequence coverage from five Jeju horses. In addition, reads obtained from WGRS data almost covered the horse reference genome (mapped reads 98.4%). Based on our results, we identified 1,244,064 single nucleotide polymorphisms (SNPs), 113,498 genomic insertions, and 114,751 deletions through bioinformatics analysis. Interestingly, the results of the WGRS comparison indicated that the eqCD1a6 gene contains signatures of positive natural selection in Jeju horses. The eqCD1a6 gene is known to be involved in immunity. The eqCD1a6 gene of Jeju horses commonly contained 296 variants (275 SNPs and 21 INDELs) that were compared with its counterpart of two Thoroughbred horses. In addition, we used LOAA, digital PCR, to confirm the possibility of developing a molecular marker for species identification using variant sites. As a result, it was possible to confirm the result of the molecular marker with high accuracy. Nevertheless, eqCD1a6 was shown to be functionally intact. Taken together, we have found significant genomic variation in these two different horse species.
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http://dx.doi.org/10.3390/ani11071924DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8300358PMC
June 2021

Influence of yeast hydrolysate supplement on growth performance, nutrient digestibility, microflora, gas emission, blood profile, and meat quality in broilers.

J Anim Sci Technol 2021 May 31;63(3):563-574. Epub 2021 May 31.

Department of Animal Resource and Science, Dankook University, Cheonan 31116, Korea.

A total of 1512 Ross 308 broilers (one - day - old) were assigned (random blocks) to 1of 3 dietary treatments with 28 replicates of 18 chicks/cage. The dietary treatments were Corn-soybean-meal based basal diet supplemented with 0%, 0.1%, and 0.2% of commercial yeast hydrolysate (YH []). The graded level of YH supplementation has linearly increased broilers body weight gain on d 21, 35, and overall ( = 0.044, 0.029, and 0.036, respectively) experimental period. In addition, the increased level of YH supplementation has linearly reduced feed conversation ratio of broilers on d 21, 35, and overall trial period ( = 0.041, 0.052, and 0.032, respectively). However, the feed intake and mortality of broilers were not affected by the graded level of YH supplementation. Though nutrient digestibility of dry matter ( = 0.012) and nitrogen ( = 0.021) was linearly increased in broilers fed YH supplementation, at the end of the trial it fails to affect the total track digestible energy. Dietary inclusion of YH supplementation showed a beneficial effect on the microbial population as linearly improved ( = 0.011) and reduced counts ( = 0.042). An increasing level of YH supplementation has tended to decrease NH ( = 0.069) and linearly decrease HS ( = 0.027) of noxious gas emission in broilers. Moreover, dietary YH supplements trend to increase the glucose ( = 0.066) and reduced cholesterol ( = 0.069) level. At the end of the test, YH supplementation elicited a linear reduction in drip loss on days 5 and 7, respectively ( = 0.045, and 0.021). Furthermore, dietary inclusion of YH supplementation had linearly increased villus height ( = 0.051) but fails to affect crypt depth. Therefore, in terms of positive effects on the broiler's overall performance, we suggest that dietary supplements containing graded YH levels in the broilers diet could serve as a potential alternative for growth promoters.
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http://dx.doi.org/10.5187/jast.2021.e61DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8203994PMC
May 2021

Investigation of high correlation with carcass traits of SNPs of the PLCB1, C/EBPα, and TDRKH genes and the combinations of SNPs using the MDR method in the Hanwoo.

Genes Genomics 2021 Aug 15;43(8):961-973. Epub 2021 Jun 15.

Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan-si, 31116, Republic of Korea.

Background: Recently, many researchers focus on the best way to produce high-quality meat, as the trend in food consumption today is to focus on quality. In general, consumers' preferences in beef differ depending on taste and meatiness. Therefore, researchers are interested in how the marbling score affects the flavors of meat or the various factors that make up the meatiness to captivate the consumers' tastes.

Objective: This study identifies single nucleotide polymorphisms (SNPs) or gene combinations that affect the carcass traits of Korean cattle (Hanwoo) by using the multifactor dimensionality reduction (MDR) method.

Methods: We collected the candidate SNPs to identify SNPs related to marbling scores from whole-exome sequencing and bovine SNP genotyping data. Using 96 Hanwoo samples, we performed PCR amplification to investigate the polymorphism status. In addition, we investigated genetic relationships between carcass traits and SNPs using 612 Hanwoo samples. Furthermore, each candidate SNP genotype and the combinations of SNP genotypes were verified to improve the accuracy of genetic relationships using MDR method.

Results: Twenty-four candidate SNPs associated with carcass trait and marbling scores were identified from SNP genotyping and whole-exome sequencing. Among them, three SNP markers (c.459 T > C of the PLCB1 gene, c.271 A > C of the C/EBPα gene, and g.17257 A > G of the TDRKH gene) were showed statistically significant differences between intramuscular fat and genotypes. Especially, two candidate SNPs, including c.459 T > C located in the PLCB1 gene and c.271 A > C located in the C/EBPα gene, could be highly associated with the intramuscular fat of Hanwoo quality grade. In addition, the combination of SNP genotypes is showed higher significant differences with carcass weight, backfat thickness, and longissimus dorsi muscle area.

Conclusion: Three SNP genotypes and the combination of SNP genotypes in the PLCB1, C/EBPα, and TDRKH genes may be useful genetic markers for improving beef quality.
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http://dx.doi.org/10.1007/s13258-021-01122-yDOI Listing
August 2021

Human Endogenous Retrovirus (HERV)-K Gene Knockout Affects Tumorigenic Characteristics of Gene in DLD-1 Colorectal Cancer Cells.

Int J Mol Sci 2021 Apr 11;22(8). Epub 2021 Apr 11.

Department of Parasitology and Genetics, Kosin University College of Medicine, Busan 49267, Korea.

Human endogenous retroviruses (HERVs) are suggested to be involved in the development of certain diseases, especially cancers. To elucidate the function of HERV-K Env protein in cancers, an HERV-K gene knockout (KO) in DLD-1 colorectal cancer cell lines was generated using the CRISPR-Cas9 system. Transcriptome analysis of HERV-K KO cells using next-generation sequencing (NGS) was performed to identify the key genes associated with the function of HERV-K Env protein. The proliferation of HERV-K KO cells was significantly reduced in in vitro culture as well as in in vivo nude mouse model. Tumorigenic characteristics, including migration, invasion, and tumor colonization, were also significantly reduced in HERV-K KO cells. Whereas, they were enhanced in HERV-K over-expressing DLD-1 cells. The expression of nuclear protein-1 (NUPR1), an ER-stress response factor that plays an important role in cell proliferation, migration, and reactive oxygen species (ROS) generation in cancer cells, significantly reduced in HERV-K KO cells. ROS levels and ROS-related gene expression was also significantly reduced in HERV-K KO cells. Cells transfected with NUPR1 siRNA (small interfering RNA) exhibited the same phenotype as HERV-K KO cells. These results suggest that the HERV-K gene affects tumorigenic characteristics, including cell proliferation, migration, and tumor colonization through NUPR1 related pathway.
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http://dx.doi.org/10.3390/ijms22083941DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8070087PMC
April 2021

A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome.

Exp Mol Med 2021 Apr 8;53(4):615-630. Epub 2021 Apr 8.

Department of Biological Sciences, Pusan National University, Busan, 46283, Republic of Korea.

Advances in next-generation sequencing (NGS) technology have made personal genome sequencing possible, and indeed, many individual human genomes have now been sequenced. Comparisons of these individual genomes have revealed substantial genomic differences between human populations as well as between individuals from closely related ethnic groups. Transposable elements (TEs) are known to be one of the major sources of these variations and act through various mechanisms, including de novo insertion, insertion-mediated deletion, and TE-TE recombination-mediated deletion. In this study, we carried out de novo whole-genome sequencing of one Korean individual (KPGP9) via multiple insert-size libraries. The de novo whole-genome assembly resulted in 31,305 scaffolds with a scaffold N50 size of 13.23 Mb. Furthermore, through computational data analysis and experimental verification, we revealed that 182 TE-associated structural variation (TASV) insertions and 89 TASV deletions contributed 64,232 bp in sequence gain and 82,772 bp in sequence loss, respectively, in the KPGP9 genome relative to the hg19 reference genome. We also verified structural differences associated with TASVs by comparative analysis with TASVs in recent genomes (AK1 and TCGA genomes) and reported their details. Here, we constructed a new Korean de novo whole-genome assembly and provide the first study, to our knowledge, focused on the identification of TASVs in an individual Korean genome. Our findings again highlight the role of TEs as a major driver of structural variations in human individual genomes.
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http://dx.doi.org/10.1038/s12276-021-00586-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8102501PMC
April 2021

L1 retrotransposons exploit RNA mA modification as an evolutionary driving force.

Nat Commun 2021 02 9;12(1):880. Epub 2021 Feb 9.

Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea.

L1 retrotransposons can pose a threat to genome integrity. The host has evolved to restrict L1 replication. However, mechanisms underlying L1 propagation out of the host surveillance remains unclear. Here, we propose an evolutionary survival strategy of L1, which exploits RNA mA modification. We discover that mA 'writer' METTL3 facilitates L1 retrotransposition, whereas mA 'eraser' ALKBH5 suppresses it. The essential mA cluster that is located on L1 5' UTR serves as a docking site for eukaryotic initiation factor 3 (eIF3), enhances translational efficiency and promotes the formation of L1 ribonucleoprotein. Furthermore, through the comparative analysis of human- and primate-specific L1 lineages, we find that the most functional mA motif-containing L1s have been positively selected and became a distinctive feature of evolutionarily young L1s. Thus, our findings demonstrate that L1 retrotransposons hijack the RNA mA modification system for their successful replication.
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http://dx.doi.org/10.1038/s41467-021-21197-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7873242PMC
February 2021

Role of Transposable Elements in Gene Regulation in the Human Genome.

Life (Basel) 2021 Feb 4;11(2). Epub 2021 Feb 4.

Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada.

Transposable elements (TEs), also known as mobile elements (MEs), are interspersed repeats that constitute a major fraction of the genomes of higher organisms. As one of their important functional impacts on gene function and genome evolution, TEs participate in regulating the expression of genes nearby and even far away at transcriptional and post-transcriptional levels. There are two known principal ways by which TEs regulate the expression of genes. First, TEs provide cis-regulatory sequences in the genome with their intrinsic regulatory properties for their own expression, making them potential factors for regulating the expression of the host genes. TE-derived cis-regulatory sites are found in promoter and enhancer elements, providing binding sites for a wide range of trans-acting factors. Second, TEs encode for regulatory RNAs with their sequences showed to be present in a substantial fraction of miRNAs and long non-coding RNAs (lncRNAs), indicating the TE origin of these RNAs. Furthermore, TEs sequences were found to be critical for regulatory functions of these RNAs, including binding to the target mRNA. TEs thus provide crucial regulatory roles by being part of cis-regulatory and regulatory RNA sequences. Moreover, both TE-derived cis-regulatory sequences and TE-derived regulatory RNAs have been implicated in providing evolutionary novelty to gene regulation. These TE-derived regulatory mechanisms also tend to function in a tissue-specific fashion. In this review, we aim to comprehensively cover the studies regarding these two aspects of TE-mediated gene regulation, mainly focusing on the mechanisms, contribution of different types of TEs, differential roles among tissue types, and lineage-specificity, based on data mostly in humans.
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http://dx.doi.org/10.3390/life11020118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7913837PMC
February 2021

The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology.

Sci Rep 2021 01 18;11(1):1727. Epub 2021 Jan 18.

Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.

Characterizing the microbial communities inhabiting specimens is one of the primary objectives of microbiome studies. A short-read sequencing platform for reading partial regions of the 16S rRNA gene is most commonly used by reducing the cost burden of next-generation sequencing (NGS), but misclassification at the species level due to its length being too short to consider sequence similarity remains a challenge. Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S). We compared a 16S full-length-based synthetic long-read (sFL16S) and V3-V4 short-read (V3V4) methods using 24 human GUT microbiota samples. Our comparison analyses of sFL16S and V3V4 sequencing data showed that they were highly similar at all classification resolutions except the species level. At the species level, we confirmed that sFL16S showed better resolutions than V3V4 in analyses of alpha-diversity, relative abundance frequency and identification accuracy. Furthermore, we demonstrated that sFL16S could overcome the microbial misidentification caused by different sequence similarity in each 16S variable region through comparison the identification accuracy of Bifidobacterium, Bacteroides, and Alistipes strains classified from both methods. Therefore, this study suggests that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.
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http://dx.doi.org/10.1038/s41598-020-80826-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7814050PMC
January 2021

The nature of triple-negative breast cancer classification and antitumoral strategies.

Genomics Inform 2020 Dec 22;18(4):e35. Epub 2020 Dec 22.

Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea.

Identifying the patterns of gene expression in breast cancers is essential to understanding their pathophysiology and developing anticancer drugs. Breast cancer is a heterogeneous disease with different subtypes determined by distinct biological features. Luminal breast cancer is characterized by a relatively high expression of estrogen receptor (ER) and progesterone receptor (PR) genes, which are expressed in breast luminal cells. In ~25% of invasive breast cancers, human epidermal growth factor receptor 2 (HER2) is overexpressed; these cancers are categorized as the HER2 type. Triple-negative breast cancer (TNBC), in which the cancer cells do not express ER/PR or HER2, shows highly aggressive clinical outcomes. TNBC can be further classified into specific subtypes according to genomic mutations and cancer immunogenicity. Herein, we discuss the brief history of TNBC classification and its implications for promising treatments.
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http://dx.doi.org/10.5808/GI.2020.18.4.e35DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7808875PMC
December 2020

Alpha 1 Antitrypsin-Deficient Macrophages Have Impaired Efferocytosis of Apoptotic Neutrophils.

Front Immunol 2020 20;11:574410. Epub 2020 Nov 20.

Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida, Gainesville, FL, United States.

Alpha 1 antitrypsin deficiency (AATD) is an autosomal co-dominant disorder characterized by a low level of circulating AAT, which significantly reduces protection for the lower airways against proteolytic burden caused by neutrophils. Neutrophils, which are terminally differentiated innate immune cells and play a critical role to clear pathogens, accumulate excessively in the lung of AATD individuals. The neutrophil burden in AATD individuals increases the risk for early-onset destructive lung diseases by producing neutrophil products such as reactive oxygen radicals and various proteases. The level of AAT in AATD individuals is not sufficient to inhibit the activity of neutrophil chemotactic factors such as CXCL-8 and LTB4, which could lead to alveolar neutrophil accumulation in AATD individuals. However, as neutrophils have a short lifespan, and apoptotic neutrophils are rapidly cleared by alveolar macrophages that outnumber the apoptotic neutrophils in the pulmonary alveolus, the increased chemotaxis activity does not fully explain the persistent neutrophil accumulation and the resulting chronic inflammation in AATD individuals. Here, we propose that the ability of alveolar macrophages to clear apoptotic neutrophils is impaired in AATD individuals and it could be the main driver to cause neutrophil accumulation in their lung. This study demonstrates that Z-AAT variant significantly increases the expression of pro-inflammatory cytokines including CXCL-8, CXCL1, LTB4, and TNFα in LPS-treated macrophages. These cytokines play a central role in neutrophil recruitment to the lung and in clearance of apoptotic neutrophils by macrophages. Our result shows that LPS treatment significantly reduces the efferocytosis ability of macrophages with the Z-AAT allele by inducing TNFα expression. We incubated monocyte-derived macrophages (MDMs) with apoptotic neutrophils and found that after 3 h of co-incubation, the expression level of CXCL-8 is reduced in M-MDMs but increased in Z-MDMs. This result shows that the expression of inflammatory cytokines could be increased by impaired efferocytosis. It indicates that the efferocytosis ability of macrophages plays an important role in regulating cytokine expression and resolving inflammation. Findings from this study would help us better understand the multifaceted effect of AAT on regulating neutrophil balance in the lung and the underlying mechanisms.
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http://dx.doi.org/10.3389/fimmu.2020.574410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7714766PMC
June 2021

A High Quality Asian Genome Assembly Identifies Features of Common Missing Regions.

Genes (Basel) 2020 11 13;11(11). Epub 2020 Nov 13.

Bioinformatics Institute, Macrogen Inc., Seoul 08511, Korea.

The current human reference genome (GRCh38), with its superior quality, has contributed significantly to genome analysis. However, GRCh38 may still underrepresent the ethnic genome, specifically for Asians, though exactly what we are missing is still elusive. Here, we juxtaposed GRCh38 with a high-contiguity genome assembly of one Korean (AK1) to show that a part of AK1 genome is missing in GRCh38 and that the missing regions harbored ~1390 putative coding elements. Furthermore, we found that multiple populations shared some certain parts in the missing genome when we analyzed the "unmapped" (to GRCh38) reads of fourteen individuals (five East-Asians, four Europeans, and five Africans), amounting to ~5.3 Mb (~0.2% of AK1) of the total genomic regions. The recovered AK1 regions from the "unmapped reads", which were the estimated missing regions that did not exist in GRCh38, harbored candidate coding elements. We verified that most of the common (shared by ≥7 individuals) missing regions exist in human and chimpanzee DNA. Moreover, we further identified the occurrence mechanism and ethnic heterogeneity as well as the presence of the common missing regions. This study illuminates a potential advantage of using a pangenome reference and brings up the need for further investigations on the various features of regions globally missed in GRCh38.
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http://dx.doi.org/10.3390/genes11111350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7697454PMC
November 2020

Molecular subtypes of triple-negative breast cancer: understanding of subtype categories and clinical implication.

Genes Genomics 2020 12 3;42(12):1381-1387. Epub 2020 Nov 3.

Department of Pathology, School of Medicine, Chungnam National University, 266 Munwha-Ro, Jung-Gu, Daejeon, 35015, Republic of Korea.

Background: Triple-negative breast cancer (TNBC) is a heterogeneous entity that encompasses several subtypes with distinct molecular characteristics. The patients with TNBCs show unpredictable response to the chemotherapy, and further there is the lack of effective agents. Thus, many studies have been underway to discover targeted therapy suitable for patients with specific genetic alterations in each molecular subtypes. TNBCs are classified as four major molecular subtypes according to the gene expression patterns. These are luminal androgen receptor (LAR), mesenchymal-like, immunomodulatory (IM), and basal-like types.

Conclusion: Here, we discuss the unique molecular features of each subtype as well as promising targets for anti-cancer therapy.
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http://dx.doi.org/10.1007/s13258-020-01014-7DOI Listing
December 2020

Clinical usefulness of anti-muscarinic type 3 receptor autoantibodies in patients with primary Sjögren's syndrome.

Clin Exp Rheumatol 2021 Jul-Aug;39(4):795-803. Epub 2020 Oct 6.

Division of Oral Medicine, Department of Oral and Maxillofacial Diagnostic Sciences, and Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, USA.

Objectives: To elucidate the clinical values of anti-M3R in Sjögren's syndrome (SS) in the largest cohort for an anti-M3R study.

Methods: The plasma of 361 subjects (156 primary SS [pSS], 62 non-SS-sicca [SICCA], 40 systemic lupus erythematosus [SLE], 50 rheumatoid arthritis [RA], and 53 healthy controls [HC]) was screened using our modified On-Cell-Western assay. Saliva from pSS (n=37) compared to SICCA (n=26) was also analysed. The sensitivity and specificity of anti-M3R and its association with comprehensive clinical and laboratory features were determined.

Results: Plasma-anti-M3R was higher in pSS compared to other groups, differentiating pSS with good-to-excellent diagnostic power with a specificity of 85% and a sensitivity between 75% and 98%. pSS plasma-anti-M3R was positively correlated with ocular staining scores, anti-Ro/SSA, IgG, β2-microglobulin, ESR, and ESSDAI. It was negatively correlated with WBC, C4, and salivary scintigraphic indices. Saliva-anti-M3R was 3.59 times higher in pSS than in SICCA. Interestingly, the agreement between the 2002 American European Consensus Group criteria and the criteria substituted with plasma-anti-M3R for the lip biopsy reached 92%, with a significant kappa of 0.824.

Conclusions: Anti-M3R enhances sensitivity and specificity for SS diagnosis, correlating with ocular dryness and glandular hypofunction, and the haematological/biological domains of the ESSDAI. Our findings also highlight the clinical significance of anti-M3R in SS diagnosis, especially where clinical assessments, such as lip biopsy, sialometry, or ocular evaluation, by multi-disciplinary specialists are limited.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8021605PMC
July 2021

AbaR is a LuxR type regulator essential for motility and the formation of biofilm and pellicle in Acinetobacter baumannii.

Genes Genomics 2020 11 6;42(11):1339-1346. Epub 2020 Oct 6.

Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea.

Background: Acinetobacter baumannii is a major opportunistic pathogen causing nosocomial infections. Acinetobacter baumannii possesses a quorum sensing system consisting of abaI, encoding an autoinducer synthase, and abaR, encoding a putative LuxR type regulator. AbaI is required for motility and biofilm formation in A. baumannii. However, the functions of AbaR on the expression of abaI, motility, and the formation of biofilm and pellicle have not yet been explored.

Objective: The aim of this study was to investigate the effects of abaR mutation on the expression of abaI, motility, and the formation of biofilm and pellicle.

Methods: Functions of AbaR were assessed by the construction of an isogenic mutant and by evaluating the effects of abaR mutation on the expression of abaI, motility, and the formation of biofilm and pellicle.

Results: The abaR mutant revealed a significant decrease in the expression of abaI. The disruption of abaR resulted in substantial defects in motility and the formation of biofilm and pellicle. Introduction of abaR in trans complemented the defects.

Conclusions: AbaR of A. baumannii is required for the expression of abaI and plays important roles in motility and the formation of biofilm and pellicle. AbaR may be considered to be a target of anti-biofilm agents.
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http://dx.doi.org/10.1007/s13258-020-01005-8DOI Listing
November 2020

A single-tube sample preparation method based on a dual-electrostatic interaction strategy for molecular diagnosis of gram-negative bacteria.

Mikrochim Acta 2020 09 10;187(10):558. Epub 2020 Sep 10.

Department of Convergence System Engineering, Department of Biomedical Engineering, and Department of Technology Education, Chungnam National University, Daejeon, 34134, Republic of Korea.

A single-tube method based on a dual-electrostatic interaction (EI) strategy for bacteria capture and DNA extraction was designed to enable the highly sensitive detection of nucleic acids. Specially designed magnetic nanoparticles were developed to meet the opposing requirements of a single-tube method, which exist between the strong EI required for efficient bacteria capture and the weak EI required for DNA extraction with minimal DNA adsorption. A dual-EI strategy for the single-tube (DESIGN) method was thus developed to integrate bacteria enrichment, bacteria cell lysis, and DNA recovery in a single tube, thereby minimizing precious sample loss and reducing handling time. Subsequently, we evaluated the performance with a variety of concentrations from 5 to 100 colony-forming units (CFU)/10 mL human urine and milk samples. The DESIGN method achieved the simple and sensitive detection of Salmonella enterica serovar Typhimurium in 10 mL of human urine and milk samples up to 5 CFU by quantitative PCR. Furthermore, the DESIGN method detected Brucella ovis and Escherichia coli from 10 mL of human urine with a detection limit up to 5 CFU/10 mL. Graphical abstract.
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http://dx.doi.org/10.1007/s00604-020-04536-9DOI Listing
September 2020

A comprehensive analysis of chimpanzee (Pan Troglodytes)-specific AluYb8 element.

Genes Genomics 2020 10 29;42(10):1207-1213. Epub 2020 Aug 29.

Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.

Background: Alu elements are most abundant retrotransposons with > 1.2 million copies in the primate genome. AluYb8 subfamily was diverged from AluY lineage, and has accumulated eight diagnostic mutations and 7-bp duplication during primate evolution. A total of 1851 AluYb copies are present in the human genome, and most of them are human-specific. On the other hand, only a few AluYb8 copies were identified in the chimpanzee genome by previous studies on AluYb8. The significantly different number of species-specific AluYb8 elements between human and chimpanzee might result from the incompletion of chimpanzee reference genome sequences at the time of the previous study.

Objective: AluYb8 elements could generate genomic structural variations in the chimpanzee genome. This study aimed to identify and characterize chimpanzee-specific AluYb elements using the most updated chimpanzee reference genome sequences (Jan. 2018, panTro6).

Methods: To identify chimpanzee-specific AluYb8, we carried out genomic comparison with non-chimpanzee primate genome using the UCSC table browser. In addition, chimpanzee-specific AluYb8 candidates were manually inspected and experimentally verified using PCR and Sanger sequencing.

Results: Among a total of 231 chimpanzee-specific AluYb8 candidates, 11 of the candidates are chimpanzee-specific AluYb8, and 29 elements are shared between the chimpanzee and non-chimpanzee primate genomes. Through the sequence analysis of AluYb8 and other Alu subfamilies, we were able to observe various diagnostic mutations and variable length duplications in 7-bp duplication region of AluYb8 element. In addition, we further validated two of the chimpanzee-specific AluYb8 elements (CS8 and CS20) that were not previously discovered by display PCR and Sanger sequencing. Interestingly, we identified a AluYb8 insertion-mediated deletion (CS8 locus) in the chimpanzee genome.

Conclusion: Our study found that AluYb8 elements are much more abundant in the human genome than chimpanzee genome, and that it could be due to the absence of hyperactive "master" AluYb8 elements in the chimpanzee genome.
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http://dx.doi.org/10.1007/s13258-020-00989-7DOI Listing
October 2020

Performance comparison of fecal preservative and stock solutions for gut microbiome storage at room temperature.

J Microbiol 2020 Aug 25;58(8):703-710. Epub 2020 Jun 25.

Theragen Bio Co., Ltd., Suwon, Gyeonggi-do, 16229, Republic of Korea.

The gut microbiome, which is symbiotic within the human body, assists in human digestion. It plays significant roles in identifying intestinal disease as well as in maintaining a healthy body with functional immune and metabolic activities. To confirm the consistency of fecal intestinal microbial research, it is necessary to study the changes in intestinal microbial flora according to the fecal collection solution and storage period. We collected fecal samples from three healthy Korean adults. To examine the efficacy of fecal collection solution, we used NBgene-Gut, OMNIgene-Gut, 70% ethanol (Ethanol-70%), and RNAlater. The samples were stored for up to two months at room temperature using three different methods, and we observed changes in microbial communities over time. We analyzed clusters of changes in the microbial flora by observing fecal stock solutions and metagenome sequencing performed over time. In particular, we confirmed the profiling of alpha and beta diversity and microbial classification according to the differences in intestinal environment among individuals. We also confirmed that the microbial profile remained stable for two months and that the microbial profile did not change significantly over time. In addition, our results suggest the possibility of verifying microbial profiling even for long-term storage of a single sample. In conclusion, collecting fecal samples using a stock solution rather than freezing feces seems to be relatively reproducible and stable for GUT metagenome analysis. Therefore, stock solution tubes in intestinal microbial research can be used without problems.
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http://dx.doi.org/10.1007/s12275-020-0092-6DOI Listing
August 2020

Differential expressions of L1-chimeric transcripts in normal and matched-cancer tissues.

Anal Biochem 2020 07 8;600:113769. Epub 2020 May 8.

Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea; NGS Clinical Laboratory, Dankook University Hospital, Cheonan, 31116, Republic of Korea; Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea. Electronic address:

L1s are a cis-regulatory elements and contain bidirectional internal promoters within the 5' untranslated region (UTR). L1s provide bidirectional promoters that generate alternative transcripts and affect differential expressions in the human genome. In particular, L1 antisense promoters (L1ASPs) could produce aberrant transcripts in cancer tissues compared to normal tissues. In this study, we identified the L1-chimeric transcripts derived from L1ASPs and analyzed relative expression of L1-chimeric transcripts between normal and matched-cancer tissues. First, we collected 425 L1-chimeric transcripts by referring to previous studies. Through the manual inspection, we identified 144 L1-chimeric transcripts derived from 44 L1 antisense promoters, suggesting that the antisense promoter acted as an alternative promoter. We analyzed relative gene expression levels of 16 L1-chimeric transcripts between matched cancer-normal tissue pair (lung, liver, gastric, kidney, thyroid, breast, ovary, uterus, and prostate) using real-time quantitative PCR (RT-qPCR) and investigated putative transcription factor binding motifs to determine activity of L1ASPs. Taken together, we propose that L1ASPs could contribute to the differential gene expression between normal and cancer tissues.
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http://dx.doi.org/10.1016/j.ab.2020.113769DOI Listing
July 2020

Enhanced Inner-Ear Organoid Formation from Mouse Embryonic Stem Cells by Photobiomodulation.

Mol Ther Methods Clin Dev 2020 Jun 13;17:556-567. Epub 2020 Mar 13.

Beckman Laser Institute Korea, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea.

Photobiomodulation (PBM) stimulates different types of stem cells to migrate, proliferate, and differentiate and . However, little is known about the effects of PBM on the differentiation of embryonic stem cells (ESCs) toward the otic lineage. Only a few reports have documented the differentiation of ESCs into inner-ear hair cells (HCs) due to the complexity of HCs compared with other target cell types. In this study, we determined the optimal condition to differentiate the ESCs into the otic organoid using different culture techniques and PBM parameters. The efficiency of organoid formation within the embryoid body (EB) was dependent on the cell density of the hanging drop. PBM, using 630 nm wavelength light-emitting diodes (LEDs), further improved the differentiation of inner-ear hair cell-like cells coupled with reactive oxygen species (ROS) overexpression. Transcriptome analysis showed the factors that are responsible for the effect of PBM in the formation of otic organoids, notably, the downregulation of neural development-associated genes and the hairy and enhancer of split 5 () gene, which inhibits the differentiation of prosensory cells to hair cells. These data enrich the current differentiation protocols for generating inner-ear hair cells.
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http://dx.doi.org/10.1016/j.omtm.2020.03.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118273PMC
June 2020

Quantitative evaluation of the molecular marker using droplet digital PCR.

Genomics Inform 2020 Mar 31;18(1):e4. Epub 2020 Mar 31.

Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116, Korea.

Transposable elements (TEs) constitute approximately half of Bovine genome. They can be a powerful species-specific marker without regression mutations by the structure variation (SV) at the time of genomic evolution. In a previous study, we identified the Hanwoo-specific SV that was generated by a TE-association deletion event using traditional PCR method and Sanger sequencing validation. It could be used as a molecular marker to distinguish different cattle breeds (i.e., Hanwoo vs. Holstein). However, PCR is defective with various final copy quantifications from every sample. Thus, we applied to the droplet digital PCR (ddPCR) platform for accurate quantitative detection of the Hanwoo-specific SV. Although samples have low allele frequency variation within Hanwoo population, ddPCR could perform high sensitive detection with absolute quantification. We aimed to use ddPCR for more accurate quantification than PCR. We suggest that the ddPCR platform is applicable for the quantitative evaluation of molecular markers.
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http://dx.doi.org/10.5808/GI.2020.18.1.e4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120350PMC
March 2020

Application of NanoString technologies in angioimmunoblastic T cell lymphoma.

Genes Genomics 2020 04 7;42(4):485-494. Epub 2020 Mar 7.

Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.

Background: Angioimmunoblastic T-cell lymphoma (AITL) is an aggressive disease. Most cancer diagnoses are determined by anatomical histology. Therefore, many samples are stored in FFPE blocks for H&E staining. However, RNAs extracted from the FFPE block have a high level of fragmentation, making it difficult to perform accurate DEG analysis using RNA sequencing.

Objective: To overcome fragmented RNA's drawback in NGS application, we applied the NanoString nCounter technique of hybridization method that can be used for DEG analysis without PCR amplification.

Methods: We characterized the gene expression profiling of AITLs though transcriptome analysis based on the nCounter PanCancer IO 360™ Panel and NanoString platform. To perform the analysis of differential expression gene (DEG) profiles in AITLs, we compared the NanoString data from eight AITL patients with a healthy control donor.

Results: Ninety-one genes were up-regulated and six genes were down-regulated in AITLs compared to control. The Gene Ontology (GO) analysis of 97-DEGs revealed that they were closely related to cytokine, MAPK cascade, leukocyte differentiation, and immune response, suggesting that this affect the immune system. In addition, KEGG analysis revealed that AITL DEGs were found to be highly involved in cytokine-cytokine receptor interaction and PI3K-Akt signaling pathway.

Conclusion: We believe that comprehensive multiplex studies, along with NanoString analysis, may be helpful to understand the molecular mechanisms of AITL, including mutations, gene expression, and protein expression studies.
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http://dx.doi.org/10.1007/s13258-020-00919-7DOI Listing
April 2020

Genetic risk of extranodal natural killer T-cell lymphoma: a genome-wide association study in multiple populations.

Lancet Oncol 2020 02 23;21(2):306-316. Epub 2019 Dec 23.

Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, School of Public Health, Nanjing Medical University, Nanjing, China.

Background: Extranodal natural killer T-cell lymphoma (NKTCL; nasal type) is an aggressive malignancy with a particularly high prevalence in Asian and Latin American populations. Epstein-Barr virus infection has a role in the pathogenesis of NKTCL, and HLA-DPB1 variants are risk factors for the disease. We aimed to identify additional novel genetic variants affecting risk of NKTCL.

Methods: We did a genome-wide association study of NKTCL in multiple populations from east Asia. We recruited a discovery cohort of 700 cases with NKTCL and 7752 controls without NKTCL of Han Chinese ancestry from 19 centres in southern, central, and northern regions of China, and four independent replication samples including 717 cases and 12 650 controls. Three of these independent samples (451 cases and 5301 controls) were from eight centres in the same regions of southern, central, and northern China, and the fourth (266 cases and 7349 controls) was from 11 centres in Hong Kong, Taiwan, Singapore, and South Korea. All cases had primary NKTCL that was confirmed histopathologically, and matching with controls was based on geographical region and self-reported ancestry. Logistic regression analysis was done independently by geographical regions, followed by fixed-effect meta-analyses, to identify susceptibility loci. Bioinformatic approaches, including expression quantitative trait loci, binding motif and transcriptome analyses, and biological experiments were done to fine-map and explore the functional relevance of genome-wide association loci to the development of NKTCL.

Findings: Genetic data were gathered between Jan 1, 2008, and Jan 23, 2019. Meta-analysis of all samples (a total of 1417 cases and 20 402 controls) identified two novel loci significantly associated with NKTCL: IL18RAP on 2q12.1 (rs13015714; p=2·83 × 10; odds ratio 1·39 [95% CI 1·28-1·50]) and HLA-DRB1 on 6p21.3 (rs9271588; 9·35 × 10 1·53 [1·41-1·65]). Fine-mapping and experimental analyses showed that rs1420106 at the promoter of IL18RAP was highly correlated with rs13015714, and the rs1420106-A risk variant had an upregulatory effect on IL18RAP expression. Cell growth assays in two NKTCL cell lines (YT and SNK-6 cells) showed that knockdown of IL18RAP inhibited cell proliferation by cell cycle arrest in NKTCL cells. Haplotype association analysis showed that haplotype 47F-67I was associated with reduced risk of NKTCL, whereas 47Y-67L was associated with increased risk of NKTCL. These two positions are component parts of the peptide-binding pocket 7 (P7) of the HLA-DR heterodimer, suggesting that these alterations might account for the association at HLA-DRB1, independent of the previously reported HLA-DPB1 variants.

Interpretation: Our findings provide new insights into the development of NKTCL by showing the importance of inflammation and immune regulation through the IL18-IL18RAP axis and antigen presentation involving HLA-DRB1, which might help to identify potential therapeutic targets. Taken in combination with additional genetic and other risk factors, our results could potentially be used to stratify people at high risk of NKTCL for targeted prevention.

Funding: Guangdong Innovative and Entrepreneurial Research Team Program, National Natural Science Foundation of China, National Program for Support of Top-Notch Young Professionals, Chang Jiang Scholars Program, Singapore Ministry of Health's National Medical Research Council, Tanoto Foundation, National Research Foundation Singapore, Chang Gung Memorial Hospital, Recruitment Program for Young Professionals of China, First Affiliated Hospital and Army Medical University, US National Institutes of Health, and US National Cancer Institute.
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http://dx.doi.org/10.1016/S1470-2045(19)30799-5DOI Listing
February 2020

Transposable element-mediated structural variation analysis in dog breeds using whole-genome sequencing.

Mamm Genome 2019 10 15;30(9-10):289-300. Epub 2019 Aug 15.

Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.

Naturally occurring diseases in dogs provide an important animal model for studying human disease including cancer, heart disease, and autoimmune disorders. Transposable elements (TEs) make up ~ 31% of the dog (Canis lupus familiaris) genome and are one of main drivers to cause genomic variations and alter gene expression patterns of the host genes, which could result in genetic diseases. To detect structural variations (SVs), we conducted whole-genome sequencing of three different breeds, including Maltese, Poodle, and Yorkshire Terrier. Genomic SVs were detected and visualized using BreakDancer program. We identified a total of 2328 deletion SV events in the three breeds compared with the dog reference genome of Boxer. The majority of the genetic variants were found to be TE insertion polymorphism (1229) and the others were TE-mediated deletion (489), non-TE-mediated deletion (542), simple repeat-mediated deletion (32), and other indel (36). Among the TE insertion polymorphism, 286 elements were full-length LINE-1s (L1s). In addition, the 49 SV candidates located in the genic regions were experimentally verified and their polymorphic rates within each breed were examined using PCR assay. Polymorphism analysis of the genomic variants revealed that some of the variants exist polymorphic in the three dog breeds, suggesting that their SV events recently occurred in the dog genome. The findings suggest that TEs have contributed to the genomic variations among the three dog breeds of Maltese, Poodle, and Yorkshire Terrier. In addition, the polymorphic events between the dog breeds indicate that TEs were recently retrotransposed in the dog genome.
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http://dx.doi.org/10.1007/s00335-019-09812-5DOI Listing
October 2019

Comparison of library construction kits for mRNA sequencing in the Illumina platform.

Genes Genomics 2019 10 26;41(10):1233-1240. Epub 2019 Jul 26.

Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.

Background: The emergence of next-generation sequencing (NGS) technologies has made a tremendous contribution to the deciphering and significance of transcriptome analysis in biological fields. Since the advent of NGS technology in 2007, Illumina, Inc. has provided one of the most widely used sequencing platforms for NGS analysis.

Objective: Although reagents and protocols provided by Illumina are adequately performed in transcriptome sequencing, recently, alternative reagents and protocols which are relatively cost effective are accessible. However, the kits derived from various manufacturers have advantages and disadvantages when researchers carry out the transcriptome library construction.

Methods: We compared them using a variety of protocols to produce Illumina-compatible libraries based on transcriptome. Three different mRNA sequencing kits were selected for this study: TruSeq RNA Sample Preparation V2 (Illumina, Inc., USA), Universal Plus mRNA-Seq (NuGEN, Ltd., UK), and NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ltd., USA). We compared them focusing on cost, experimental time, and data output.

Results: The quality and quantity of sequencing data obtained through the NGS technique were strongly influenced by the type of the sequencing library kits. It suggests that for transcriptome studies, researchers should select a suitable library construction kit according to the goal and resources of experiments.

Conclusion: The present work will help researchers to choose the right sequencing library construction kit for transcriptome analyses.
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http://dx.doi.org/10.1007/s13258-019-00853-3DOI Listing
October 2019

Complete genome sequence and phylogenetic analysis of nosocomial pathogen Acinetobacter nosocomialis strain NCTC 8102.

Genes Genomics 2019 09 8;41(9):1063-1075. Epub 2019 Jun 8.

Department of Microbiology and Medical Science, Chungnam National University School of Medicine, 266 Munwha-ro, Jung-gu, Daejeon, 35015, South Korea.

Background: Acinetobacter has emerged recently as one of the most challenging nosocomial pathogens because of its increased rate of antimicrobial resistance. The genetic complexity and genome diversity, as well as the lack of adequate knowledge on the pathogenic determinants of Acinetobacter strains often hinder with pathogenesis studies for the development of better therapeutics to tackle this nosocomial pathogen.

Objectives: In this study, we comparatively analyzed the whole genome sequence of a virulent Acinetobacternosocomialis strain NCTC 8102.

Methods: The genomic DNA of A. nosocomialis NCTC 8102 was isolated and sequenced using PacBio RS II platform. The sequenced genome was functionally annotated and gene prediction was carried out using the program, Glimmer 3. The phylogenetic analysis of the genome was performed using Mega 6 program and the comparative genome analysis was carried out by BLAST (Basic Local Alignment Search Tool).

Results: The complete genome analysis depicted that the genome consists of a circular chromosome with an average G + C content of 38.7%. The genome comprises 3700 protein-coding genes, 96 RNA genes (18 rRNA, 74 tRNA and 4 ncRNA genes), and 91 pseudogenes. In addition, 6 prophage regions comprising 2 intact, 1 incomplete and 3 questionable ones and 18 genomic islands were identified in the genome, suggesting the possible occurrence of horizontal gene transfer in this strain. Comparative genome analysis of A. nosocomialis NCTC 8102 genome with the already sequenced A. nosocomialis strain SSA3 showed an average nucleotide identity of 99.0%. In addition, the number of prophages and genomic islands were higher in the A. nosocomialis NCTC 8102 genome compared to that of the strain SSA3. 14 of the genomic islands were unique to A. nosocomialis NCTC 8102 compared to strain SSA3 and they harbored genes which are involved in virulence, multidrug resistance, biofilm formation and bacterial pathogenesis.

Conclusion: We sequenced the whole genome of A. nosocomialis strain NCTC 8102 followed by comparatively genome analysis. The study provides valuable information on the genetic features of A. nosocomialis strain and the data from this study would assist in further studies for the development of control measures for this nosocomial pathogen.
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http://dx.doi.org/10.1007/s13258-019-00834-6DOI Listing
September 2019

A comprehensive analysis of the Baboon-specific full-length LINE-1 retrotransposons.

Genes Genomics 2019 07 18;41(7):831-837. Epub 2019 Mar 18.

Department of Nanobiomedical Science, BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.

Background: Long interspersed elements-1 (LINE-1s or L1s) and Alu elements are most successful retrotransposons that have generated genetic diversity and genomic fluidity in the primate genome. They account for ~ 27.7% of the primate genome. Interestingly, a previous study has shown that the retrotransposition rate of Alu elements is nine times higher in baboons than in humans.

Objective: The expansion of Alu copies could be dependent on the activity of L1-encoded proteins. Thus, we aimed to investigate full-length baboon-specific L1s and characterize structurally and functionally intact baboon-specific L1s (ORF1p/ORF2p and ORF2p only) that could induce trans-mobilization of Alu elements in the baboon genome.

Results: A total of 673 baboon-specific L1 candidates (> 4 kb) were identified through the comparative genomic analysis. Applying the baboon-specific correction value obtained from the experimental validation, it demonstrated that approximately 446 baboon-specific L1s (> 4 kb) were present in the baboon reference genome (papAnu2). In addition, we observed phylogenetic relationship of the baboon-specific L1s through the neighbor-joining method and they diverged from the L1PA6 consensus sequence. Finally, we identified 36 full-length baboon-specific L1s that were intact both ORF1p and ORF2p.

Conclusion: The number of baboon-specific full-length L1s is fewer than the number of human-specific full-length L1s. Therefore, there is possibility that the "L1 master gene" or "L1 source gene" is more abundant in the baboon genome, or that in trans retrotransposition activity of baboon-specific L1s is relatively stronger than in the other genomes.
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http://dx.doi.org/10.1007/s13258-019-00794-xDOI Listing
July 2019
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