DNA Link (South Korea)

A Gram-stain-negative, aerobic, non-spore-forming, non-motile, coccus-shaped, and red-pigmented bacterial strain designated as CJ14T was isolated from lettuce cultivation soil in Yong-In, South Korea. Strain CJ14T grew optimally on Luria-Bertani agar at 37℃ and pH 7.0 in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CJ14T belonged to the genus Rhodoligotrophos in the family Rhodoligotrophaceae and was closely related to Rhodoligotrophos defluvii lm1T (98.4% similarity). The genome size of strain CJ14T was 4.8Mbp consisting of a single contig, and the DNA G + C content of strain CJ14T was 61.8%. The genomic comparison of strain CJ14T to R. defluvii lm1T showed an average nucleotide identity value of 77.9%, and the digital DNA-DNA hybridization value was 22.4%. Genomic analyses revealed that strain CJ14T possessed a gene cluster for ochrobactin biosynthesis, highly homologous to the siderophore gene cluster from Nitratireductor thuwali Nit1536T. Strain CJ14T contained ubiquinone (Q-10) as the predominant respiratory quinone. The major cellular fatty acids of strain CJ14T were C16:0, C19:0 cyclo ω8c and summed feature 8. The polar lipid profile was composed of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, one unidentified aminolipid, one unidentified glycolipid and five unidentified lipids. Based on polyphasic taxonomy study, strain CJ14T could be classified as a novel species of the genus Rhodoligotrophos, for which the name Rhodoligotrophos ferricapiens sp. nov. is proposed. The type strain is CJ14T (= KACC 23063T = JCM 36057T).

Patients with severe eosinophilic asthma often require systemic medication, including corticosteroids and anti-type 2 (T2) cytokine biologics, to control the disease. While anti-IL5 and anti-IL4Rα antibodies suppress the effects of IL-4, IL-5 and IL-13, the molecular pathways modified by these biologics that are associated with clinical improvement remain unclear. Therefore, we aimed to describe the effects of T2-targeting biologics on the gene expression of blood immune cells. We conducted single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) from eight patients with severe eosinophilic asthma treated with mepolizumab, reslizumab, or dupilumab. PBMCs were obtained before the initiation of biologics and at 1- and 6-month timepoints after the initiation of treatment to elucidate treatment-induced changes. During treatment, the proportions of T cells/natural killer (NK) cells, myeloid cells, and B cells did not change. However, the composition of classical monocytes (CMs) changed: IL1B+ CMs were reduced, and S100A+ CMs were increased. The subsets of T cells also changed, and significant downregulation of the NF-κB pathway was observed. The genes related to the NF-κB pathway were suppressed across T/NK, myeloid, and B cells. The transcriptional landscape did not significantly change after the first month of treatment, but marked changes occurred at six-month intervals. In conclusion, regardless of the type of biologics used, suppression of T2-mediated pathways ultimately reduces the expression of genes related to NF-κB signaling in circulating immune cells. Further studies are warranted to identify potential biomarkers related to treatment response and long-term outcomes.Clinical trial registration number: NCT05164939

BackgroundRelatives share more genomic regions than unrelated individuals, with closer relatives sharing more regions. This concept, paired with the increased availability of high-throughput single nucleotide polymorphism (SNP) genotyping technologies, has made it feasible to measure the shared chromosomal regions between individuals to assess their level of relation to each other. However, such techniques have remained in the conceptual rather than practical stages in terms of applying measures or indices. Recently, we developed an index called “genetic distance-based index of chromosomal sharing (GD-ICS)” utilizing large-scale SNP data from Korean family samples and demonstrated its potential for practical applications in kinship determination. In the current study, we present validation results from various real cases demonstrating the utility of this method in resolving complex familial relationships where information obtained from traditional short tandem repeats (STRs) or lineage markers is inconclusive.MethodsWe obtained large-scale SNP data through microarray analysis from Korean individuals involving 13 kinship cases and calculated GD-ICS values using the method described in our previous study. Based on the GD-ICS reference constructed for Korean families, each disputed kinship was evaluated and validated using a combination of traditional STRs and lineage markers.ResultsThe cases comprised those A) that were found to be inconclusive using the traditional approach, B) for which it was difficult to apply traditional testing methods, and C) that were more conclusively resolved using the GD-ICS method. This method has overcome the limitations faced by traditional STRs in kinship testing, particularly in a paternity case with STR mutational events and in confirming distant kinship where the individual of interest is unavailable for testing. It has also been demonstrated to be effective in identifying various relationships without specific presumptions and in confirming a lack of genetic relatedness between individuals.ConclusionThis method has been proven effective in identifying familial relationships across diverse complex and practical scenarios. It is not only useful when traditional testing methods fail to provide conclusive results, but it also enhances the resolution of challenging kinship cases, which suggests its applicability in various types of practical casework.

Abstract Patient-derived xenograft(PDX) models of primary lung cancer have been reported. However, varying engraftment rates and their underlying mechanisms for specific subtypes of lung cancer (adenocarcinoma, squamous cell carcinoma, and large cell neuroendocrine carcinoma) have not been studied. The authors prepared subcutaneous tumors grown in NSG™ mice with primary tumors of lung cancer patients to develop lung cancer PDX models. Pathological features of the subcutaneous tumors were compared with those of the patients. One hundred seventeen lung cancer PDX models retaining the original pathologic features were obtained from 642 primary lung cancer patients. Nineteen PDX tumors and the corresponding patient tumors, representing three subtypes of cell lung cancer, were selected and analyzed with in-depth genomic and transcriptomic profiling. Results showed the PDX tumors retained most of the somatic and oncogenic mutations with limited levels of additional xenograft-specific mutations. Significant downregulation of the genes involved in hypoxia-associated angiogenesis was found compared with the corresponding human tumors. This downregulation was associated with murine fibroblasts in the PDX tumor microenvironment, which might be an important factor in low engraftment rates in primary lung cancer PDX models.

Abstract Circulating tumor DNA has few applications for detecting early-stage lung cancers. Bronchial washing (BW) is minimally invasive, and BW fluids can contain tumor DNA. Thus, analysis of BW fluids could be used for precision medicine. Forty-eight paired specimens (primary tumor tissue, normal tissue, BW supernatant, and BW precipitate) from twelve patients with early-stage non-small cell lung cancer were analyzed using ultradeep next-generation sequencing with a custom panel containing 113 genes. In primary tumors, 130 missense mutations/indels (5–16 per patient) and 20 driver mutations (0–3) were found; 105 (80.8%) and 97 (74.6%) of these missense mutations/indels were identified in BW supernatants and precipitates, respectively, and 19 (95.0%) of the driver mutations in both BW supernatants and precipitates. Concordance between EGFR mutations in primary tumors, BW supernatants, and BW precipitates was 100%. The median allele frequencies (AFs) for missense mutations/indels in primary tumors, BW supernatants, and BW precipitates were 13.0%, 0.3%, and 0.1%, respectively. The AFs of missense mutations/indels in BW supernatants correlated with those in primary tumors and in BW precipitates (P<0.001). In conclusion, this study provides evidence that the BW fluids, especially supernatants, can be an alternative to overcome the limitation that clinical utility of ctDNA is often not reliable in early-stage NSCLC. Citation Format: Jeong Seon Ryu, Myoung Kyu Lee, Seung Jae Lee. Feasibility of bronchial washing fluid-based approach to early-stage lung cancer diagnosis [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B10.

Abstract Non-small cell lung cancer is the most prevalent type of lung cancer, and one of its subtype, squamous cell carcinoma (SCC) has the genomic complexity and high overall mutation due to the chemical carcinogens so that limited therapeutic options are available in comparison with adenocarcinoma. We constructed the patient-derived xenograft models of Korean primary lung cancer and then focused on the SCC PDX models for this particular ethnic subgroup. PDX models were established using the tissues of patients who underwent surgery as primary lung cancer at Samsung Medical Center during the period between October, 2014 and September, 2017. Briefly, tumor tissues from patients were subcutaneously engrafted and passaged two more times in NOD-scid-IL2Rγnull mouse. Models were selected whose tumor tissues showed the histopathology and genomics similar to the patient tumor tissues. Statistics of established PDX models are summarized in the Table. Successful engraftmentSuccess rate (%)Primary lung cancer (n=532)19937.41Histology--Non-small cell lung cancer (n=524)19437.02- Adenocarcinoma (n=355)8925.07- Squamous cell carcinoma (n=135)8361.48- Other NSCLC (n=34)2264.71Small cell carcinoma (n=8)562.5Type of resection--Curative lung resection (n=458)17437.99Biopsy (n=74)2533.78Pathologic staging of ADC (n=355)--I (n=162)4024.69II (n=58)1525.86III (n=68)1927.94IV (n=67)1522.39 In order to help facilitate the target drug development of SCC, we concentrated on the construction of comprehensive database of fourteen SCC PDX models integrating the information from whole exome sequencing, whole transcriptome sequencing and clinical profiles. We detected mutations commonly reported in SCC genes including EGFR, BRAF, CUL3, DDR2, TP53, MYD88, PIK3CA, PTEN, MED12, SMAD4, AKT1, CTNNB1, IDH1, HRAS, KRAS, NRAS, SMARCA4, GNAS, CDKN2A, APC, CDKN2A and RRAS2. Specifically potential therapeutic targets such as EFGR, BRAF, CUL3, DDR2, TP53 and KRAS which are currently under several clinical trials were found in our SCC PDX models, and intriguingly one model had five mutations in CUL3, KRAS, TP53, and EGFR simultaneously. We expect these SCC PDX models could be valuable resource for target drug development and interpretation of their therapeutic responses in the pre- or co-clinical trials. Detailed information on pathology and genomic information on all PDX models will be available at DNA Link PDX webpage. Citation Format: Tae Ho Kim, Hyunjin Heo, Soo Jung Lee, Seungje Lee, Eunjoo Hwang, Jinseon Lee, Heekyoung Lee, Kevin Koo, Hanna Lee, Seungjae Lee, Hwanseok Rhee, Jong Eun Lee, Jhingook Kim. Establishment and molecular profiling of patient-derived xenograft models of Korean patients with primary lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1036.

Woojong Jang, Nam-Hoon Kim, Junki Lee, Nomar Espinosa Waminal, Sang-Choon Lee, Murukarthick Jayakodi, Hong-Il Choi, Jee Young Park, Jong-Eun Lee, and Tae-Jin Yang. Plant Breeding and Biotechnology 2017;5:25-35. https://doi.org/10.9787/PBB.2017.5.1.25