Keunsoo Kang

Flavobacterium eburneum sp. nov., isolated from reclaimed saline land soil

A novel Gram-stain-negative, motile by gliding, and aerobic bacterial strain, designated SA31T, was isolated from reclaimed saline land soil near a lake in Taean-gun, South Korea. Cells of the isolate formed ivory-coloured colonies. Growth occurred at 10-35 °C (optimum 25-30 °C), pH 6.0-9.0 (optimum pH 7.0-7.5), and 0-2.0 % (w/v) NaCl (optimum 0 %). Based on similarities of 16S rRNA gene sequences, strain SA31T was mostly affiliated with the genus Flavobacterium, exhibiting the highest sequence similarities with Flavobacterium palustre S44T (96.0 %), Flavobacterium glycines Gm-149T (95.9 %), Flavobacterium defluvii EMB117T (95.7 %) and Flavobacterium daejeonense GH1-10T (95.6 %). Phylogenetic analysis based on 16S rRNA gene sequences also indicated that strain SA31T was clustered with Flavobacterium daejeonense GH1-10T and Flavobacterium glycines Gm-149T. The predominant fatty acids (>7 % of total) of strain SA31T were iso-C15 : 0, summed feature 3 (C16 : 1ω7с and/or C16 : 1ω6с), iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids of the isolate comprised phosphatidylethanolamine, one unknown aminolipid, one unknown glycolipid, one unknown aminophospholipid and three unknown lipids. The major respiratory quinone was MK-6. The genomic DNA G+C content of strain SA31T was 33.5 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, strain SA31T represents a novel species the genus Flavobacterium, for which the name Flavobacterium eburneum sp. nov. is proposed. The type strain is SA31T (=KACC 18743T=JCM 31221T).

BANF1, PLOD3, SF3B4 as Early-stage Cancer Decision Markers and Drivers of Hepatocellular Carcinoma

An accurate tool enabling early diagnosis of hepatocellular carcinoma (HCC) is clinically important, since early detection of HCC markedly improves survival. We aimed to investigate the molecular markers underlying early progression of HCC that can be detected in precancerous lesions. We designed a gene selection strategy to identify potential driver genes by integrative analysis of transcriptome and clinicopathologic data of human multi-stage HCC tissues including precancerous lesions, lowand high-grade dysplastic nodules. The gene selection process was guided by detecting the selected molecules in both HCC and precancerous lesion. Using various computational approaches, we selected 10 gene elements as a candidate and, through immunohistochemical staining, showed that BANF1, PLOD3 and SF3B4 are HCC decision markers with superior capability to diagnose early-stage HCC in a large cohort of HCC patients, as compared to the currently popular trio of HCC diagnostic markers: glypican 3, glutamine synthetase, and heat-shock protein 70. Targeted inactivation of BANF1, PLOD3 and SF3B4 inhibits in vitro and in vivo liver tumorigenesis by selectively modulating EMT and cell cycle proteins. Treatment of nanoparticles containing siRNAs of the three genes suppressed liver tumor incidence as well as tumor growth rates in spontaneous mouse HCC model. We also demonstrated that SF3B4 overexpression triggers SF3b complex to splice tumor suppressor KLF4 transcript to non-functional skipped exon transcripts. This contributes to malignant transformation and growth of hepatocyte via transcriptional inactivation of p27 and simultaneously activation of Slug genes. Conclusion: The findings suggest novel molecular markers of BANF1, PLOD3 and SF3B4 indicating early-stage HCC in precancerous lesion, and also suggest drivers for understanding the development of hepatocarcinogenesis. Page 3 of 71 Hepatology Hepatology This article is protected by copyright. All rights reserved.An accurate tool enabling early diagnosis of hepatocellular carcinoma (HCC) is clinically important, given that early detection of HCC markedly improves survival. We aimed to investigate the molecular markers underlying early progression of HCC that can be detected in precancerous lesions. We designed a gene selection strategy to identify potential driver genes by integrative analysis of transcriptome and clinicopathological data of human multistage HCC tissues, including precancerous lesions, low‐ and high‐grade dysplastic nodules. The gene selection process was guided by detecting the selected molecules in both HCC and precancerous lesion. Using various computational approaches, we selected 10 gene elements as a candidate and, through immunohistochemical staining, showed that barrier to autointegration factor 1 (BANF1), procollagen‐lysine, 2‐oxoglutarate 5‐dioxygenase 3 (PLOD3), and splicing factor 3b subunit 4 (SF3B4) are HCC decision markers with superior capability to diagnose early‐stage HCC in a large cohort of HCC patients, as compared to the currently popular trio of HCC diagnostic markers: glypican 3, glutamine synthetase, and heat‐shock protein 70. Targeted inactivation of BANF1, PLOD3, and SF3B4 inhibits in vitro and in vivo liver tumorigenesis by selectively modulating epithelial‐mesenchymal transition and cell‐cycle proteins. Treatment of nanoparticles containing small‐interfering RNAs of the three genes suppressed liver tumor incidence as well as tumor growth rates in a spontaneous mouse HCC model. We also demonstrated that SF3B4 overexpression triggers SF3b complex to splice tumor suppressor KLF4 transcript to nonfunctional skipped exon transcripts. This contributes to malignant transformation and growth of hepatocyte through transcriptional inactivation of p27Kip1 and simultaneously activation of Slug genes. Conclusion: The findings suggest molecular markers of BANF1, PLOD3, and SF3B4 indicating early‐stage HCC in precancerous lesion, and also suggest drivers for understanding the development of hepatocarcinogenesis. (Hepatology 2018;67:1360‐1377).

Sediminibacterium aquarii sp. nov., isolated from sediment in a fishbowl.

A novel bacterial strain, designated AA5T, was isolated from sediment in a fishbowl. Cells were Gram-stain-negative, rod-shaped and strictly aerobic, showing gliding motility. Strain AA5T was able to grow at 15-37 °C, at pH 5.0-8.0 and in the absence of NaCl. 16S rRNA gene sequence analysis revealed that strain AA5T was most closely related to species in the genus Sediminibacterium, showing highest similarity to the type strain of S.ediminibacterium goheungense (96.6 %). Concordantly, a phylogenetic tree based on 16S rRNA gene sequences indicated that strain AA5T belongs to the genus Sediminibacterium. The DNA G+C content was 44.7 mol%. The major polar lipids were phosphatidylethanolamine, four unidentified aminolipids, two unknown aminophospholipids and four unidentified polar lipids. The only respiratory quinone of strain AA5T was menaquinone 7 (MK-7) and the major fatty acids (>5 % of the total) were iso-C15 : 0, iso-C15 : 1 G, iso-C16 : 0 3-OH, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. Based on data from this polyphasic study, strain AA5T represents a novel species, for which the name Sediminibacterium aquarii sp. nov. is proposed. The type strain is AA5T (=KACC 18509T=JCM 31013T).

RNA-seq data of invasive ductal carcinoma and adjacent normal tissues from a Korean patient with breast cancer

Invasive ductal carcinoma is the most common type of breast cancer. Here, we provide a whole transcriptome shotgun sequencing (called RNA-seq) dataset conducted with ten samples of invasive ductal carcinoma tissue and three samples of adjacent normal tissue from a single Korean breast cancer patient (luminal B subtype). Differentially expressed genes (DEGs) were identified with a false discovery rate (FDR)-adjusted p-value of 0.05. Gene ontology analysis identified several key pathways, including lymphocyte activation. A list of differentially expressed genes is provided. The raw data was uploaded to the sequence read archive (SRA) database and the BioProject ID is PRJNA432903.

Chthonobacter albigriseus gen. nov., sp. nov., isolated from grass-field soil

A novel aerobic, Gram-stain-negative and non-motile bacterial strain, designated ED7T, was isolated from grass-field soil in Cheonan, Korea. Strain ED7T utilized methanol and methylamine, but not formate, as carbon and energy sources. The strain was able to grow at 20-42 °C (optimum 30-35 °C), at pH 7.0-8.5 (optimum pH 7.5-8.0), and in the absence of NaCl. According to the similarities of the 16S rRNA gene sequences, strain ED7T was most closely related to the genera Labrenzia (≤93.3 % 16S rRNA gene sequence similarity), Pleomorphomonas (≤93.1 %) and Prosthecomicrobium (≤93.1 %). A phylogenetic analysis based on the 16S rRNA gene sequence of strain ED7T revealed that it was affiliated with the family Methylocystaceae, being most closely related to the genus Pleomorphomonas. In contrast to Pleomorphomonas koreensis and Pleomorphomonas oryzae, strain ED7T did not contain the nifH gene. The DNA G+C content of the genomic DNA of strain ED7T was 71.8 mol%. The predominant fatty acids of strain ED7T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 2 (C14 : 0 3-OH, and/or C16 : 1 iso I), 11-methyl C18 : 1ω7c and C16 : 0 3-OH. The major isoprenoid quinone was ubiquinone 10 (Q-10). The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unknown aminophospholipid. Based on phenotypic, chemotaxonomic and genotypic characteristic data, strain ED7T could be differentiated from other genera, suggesting that strain ED7T represents a novel species of a new genus in the family Methylocystaceae, for which the name Chthonobacter albigriseus gen. nov., sp. nov. is proposed. The type strain of the type species is ED7T (=JCM 30603T=KCTC 42450T).

RNA variant identification discrepancy among splice-aware alignment algorithms

Next-generation sequencing (NGS) techniques have been generating various molecular maps, including transcriptomes via RNA-seq. Although the primary purpose of RNA-seq is to quantify the expression level of known genes, RNA variants are also identifiable. However, care must be taken to account for RNA’s dynamic nature. In this study, we evaluated the following popular splice-aware alignment algorithms in the context of RNA variant-calling analysis: HISAT2, STAR, STAR (two-pass mode), Subread, and Subjunc. For this, we performed RNA-seq with ten pieces of invasive ductal carcinoma from breast tissue and three pieces of adjacent normal tissue from a single patient. These RNA-seq data were used to evaluate the performance of splice-aware aligners. Surprisingly, the number of common potential RNA editing sites (pRESs) identified by all alignment algorithms was less than 2% of the total. The main cause of this difference was the mapped reads on the splice junctions. In addition, the RNA quality significantly affected the outcome. Therefore, researchers must consider these experimental and bioinformatic features during RNA variant analysis. Further investigations of common pRESs discovered that BDH1, CCDC137, and TBC1D10A transcripts contained a single non-synonymous RNA variant that was unique to breast cancer tissue compared to adjacent normal tissue; thus, further clinical validation is required.

The transcription factor Foxp1 preserves integrity of an active Foxp3 locus in extrathymic Treg cells

Regulatory T (Treg) cells, which are broadly classified as thymically derived (tTreg) or extrathymically induced (iTreg), suppress immune responses and display stringent dependence to the transcription factor Foxp3. However precise understanding of molecular events that promote and preserve Foxp3 expression in Treg cells is still evolving. Here we show that Foxp1, a forkhead transcription factor and a sibling family member of Foxp3, is essential for sustaining optimal expression of Foxp3 specifically in iTreg cells. Deletion of Foxp1 renders iTreg cells to gradually lose Foxp3, resulting in dramatically reduced Nrp1−Helios− iTreg compartment as well as augmented intestinal inflammation in aged mice. Our finding underscores a mechanistic module in which evolutionarily related transcription factors establish a molecular program to ensure efficient immune homeostasis. Furthermore, it provides a novel target that can be potentially modulated to exclusively reinforce iTreg stability keeping their thymic counterpart unperturbed.Regulatory T (Treg) cells suppress immune cell activation to maintain immune homeostasis, and have their lineage enforced by the master transcription factor Foxp3. Here the authors show that Foxp3 expression is promoted and maintained by a related family member, Foxp1, specifically in peripherally induced Treg but not in Treg cells of thymic origin.

Flavobacterium parvum sp. nov., isolated from soil polluted by sewer water

A novel Gram-stain-negative, motile by means of gliding, and short rod-shaped bacterium, designated HS916T, was isolated from soil polluted by sewer water in Cheonan-si, South Korea. Growth occurred at 10–35°C (optimum 30°C), pH 6.0–8.0 (optimum pH 7.0), and 0–1% sodium chloride (NaCl, w/v). Based on similarities of 16S rRNA gene sequences, strain HS916T was closely related to members of the genus Flavobacterium, exhibiting the highest sequence similarities with Flavobacterium glycines Gm-149T (96.4%), followed by F. granuli Kw05T (96.3%), F. fluminis 3R17T (96.3%), F. aquicola TMd3a3T (96.2%), and F. nitratireducens N1T (96.2%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HS916T was placed in a monophyletic cluster with F. nitratireducens N1T and F. fluminis 3R17T. The predominant fatty acids (> 5% of the total) of strain HS916T were iso-C15:0, anteiso-C15:0, iso-C15:0 3-OH, C17:1ω6с, C16:0 3-OH, iso-C17:0 3-OH, and summed feature 3 (C16:1ω7с and/or C16:1ω6с). The major polar lipids of the strain comprised phosphatidylethanolamine, unidentified aminolipids, and five unidentified lipids. The predominant respiratory quinone and the major polyamine were menaquinone-6 (MK-6) and symhomospermidine, respectively. The DNA G + C content of strain HS916T was 34.9 mol%. Based on polyphasic analyses, strain HS916T represents a novel species belonging to the genus Flavobacterium, for which the name Flavobacterium parvum sp. nov. is proposed. The type strain is HS916T (= KACC 19448T = JCM 32368T).

Paludirhabdus telluriireducens gen. nov., sp. nov. and Paludirhabdus pumila sp. nov., isolated from soil of a mountain wetland and emended description of Gorillibacterium massiliense

Two strains of Gram-stain-positive, endospore-forming, motile by means of peritrichous flagella, aerobic or facultative anaerobic, and rod-shaped bacteria that were designated ON8T and ON6T were isolated from soil collected from a mountain wetland in Gwang-ju, Republic of Korea. The isolates were catalase-positive and oxidase-negative. Cells of ON8T and ON6T grew at 15-35 °C (optimal 30 °C) and 15-40 °C (optimal 30 °C), respectively. The major menaquinone was MK-7 and the major cellular fatty acids (>10 % of the total) were anteiso-C15 : 0, iso-C15 : 0, C14 : 0 and C16 : 0. The predominant polar lipids were diphosphatidylglycerol, aminophospholipid and phospholipid. Meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The DNA G+C contents of strains ON8T and ON6T were 50.6 and 53.5 mol%, respectively, and the 16S rRNA gene sequence analysis showed that the nearest phylogenetic neighbour of both strains was Gorillibacterium massiliense G5T (93.9 %), followed by the members of the genus Paenibacillus in the family Paenibacillaceae. The DNA-DNA hybridization relatedness value between ON8T and ON6T was 44.1 %, which indicated that they represented distinct species. Based on polyphasic characteristics, a novel genus is proposed with the name Paludirhabdus gen. nov., which consists of two species, Paludirhabdus telluriireducens sp. nov. (the type species; type strain ON8T=KACC 19267T=JCM 31958T) and Paludirhabdus pumila sp. nov. (type strain ON6T=KACC 19266T=JCM 31957T).

Uliginosibacterium sediminicola sp. nov., isolated from freshwater sediment

Strain M1-21T is a Gram-stain-negative, strictly aerobic and short-rod-shaped bacterium, motile by means of a single polar flagellum; it was isolated from freshwater sediment in Korea. It grew at 10-40 °C (optimum 25 °C), pH 6.0-8.0 (optimum pH 7.0) and with 0-0.75 % (w/v) NaCl (optimal growth occurred in the absence of NaCl) on R2A agar, and it accumulated poly-β-hydroxybutyrate granules inside the cells. According to 16S rRNA gene sequence analysis, strain M1-21T showed highest sequence similarity with Uliginosibacterium gangwonense (94.7 %) and Uliginosibacterium paludis (94.4 %). Phylogenetic analysis of the 16S rRNA gene sequences revealed that strain M1-21T belongs to the genus Uliginosibacterium. The DNA G+C content of strain M1-21T was 61.9 mol%. The predominant respiratory quinone was ubiquinone-8. The major fatty acids (>10 % of the total) were C16 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Strain M1-21T showed distinct phenotypic characteristics that differentiated it from species of the genus Uliginosibacterium. Based on these results, strain M1-21T represents a novel species of the genus Uliginosibacterium, for which the name Uliginosibacterium sediminicola sp. nov. is proposed. The type strain is M1-21T (=KACC 19271T=JCM 32000T).