Proteogenomic Characterization Reveals Estrogen Signaling as a Target for Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations.

Never-smoker lung adenocarcinoma (NSLA) is prevalent in Asian populations, particularly in women. EGFR mutations and anaplastic lymphoma kinase (ALK) fusions are major genetic alterations observed in NSLA, and NSLA with these alterations have been well studied and can be treated with targeted therapies. To provide insights into the molecular profile of NSLA without EGFR and ALK alterations (NENA), we selected 141 NSLA tissues and performed proteogenomic characterization, including whole genome sequencing (WGS), transcriptomic, methylation EPIC array, total proteomic, and phosphoproteomic analyses. Forty patients with NSLA harboring EGFR and ALK alterations and seven patients with NENA with microsatellite instability were excluded. Genome analysis revealed that TP53 (25%), KRAS (22%), and SETD2 (11%) mutations and ROS1 fusions (14%) were the most frequent genetic alterations in NENA patients. Proteogenomic impact analysis revealed that STK11 and ERBB2 somatic mutations had broad effects on cancer-associated genes in NENA. DNA copy number alteration analysis identified 22 prognostic proteins that influenced transcriptomic and proteomic changes. Gene set enrichment analysis revealed estrogen signaling as the key pathway activated in NENA. Increased estrogen signaling was associated with proteogenomic alterations, such as copy number deletions in chromosomes 14 and 21, STK11 mutation, and DNA hypomethylation of LLGL2 and ST14. Finally, saracatinib, an Src inhibitor, was identified as a potential drug for targeting activated estrogen signaling in NENA and was experimentally validated in vitro. Collectively, this study enhanced our understanding of NENA NSLA by elucidating the proteogenomic landscape and proposed saracatinib as a potential treatment for this patient population that lacks effective targeted therapies. SIGNIFICANCE: The proteogenomic landscape in never-smoker lung cancer without known driver mutations reveals prognostic proteins and enhanced estrogen signaling that can be targeted as a potential therapeutic strategy to improve patient outcomes.

Complete chloroplast genome sequence of the liverwort, Porella grandiloba Lindb. (Porellaceae).

Porella grandiloba Lindb. is a liverwort species of Porellaceae, primarily distributed in East Asia. Here, we determined the complete chloroplast (cp) genome sequence of P. grandiloba. The complete cp genome was 121,433 bp in length with a typical quadripartite structure consisting of a large single-copy region (83,039 bp), a small single-copy region (19,586 bp), and two copies of inverted repeat regions (9,404 bp, each). Genome annotation predicted 131 genes, including 84 protein-coding, 36 tRNA, and eight rRNA genes. The maximum likelihood tree indicated that P. grandiloba was sister to P. perrottetiana, which species formed a clade with Radula japonica (Radulaceae).

The Liverwort and Hornwort Flora of Jeju Island, Republic of Korea: A Volcanic Island with a Unique Mixture of Subtropical, Temperate, Boreal, and Arctomontane Taxa.

Jeju Island, due to its position at the southern tip of the Korean Peninsula in Northeast Asia, is a on the unique enclave of the many southern elements in the area and features a mixture of subtropical, temperate, boreal, and arctomontane taxa. Among the arctomontane species recorded in this study was Anthelia juratzkana; among the temperate species was Dactyloradula brunnea, and subtropical species were Cavicularia densa, Pallavicinia subciliata, Wiesnerella denudata, and Megaceros flagellaris. A valuable species as first recorded for the Jeju Island is Cryptocoleopsis imbricata. The distribution patterns of these species suggest that the flora of Jeju Island is a meeting place between boreal and subtropical floras. We recorded 222 taxa belonging to 45 families, 80 genera, 209 species, 9 subspecies, and 4 varieties. Among these, 86 species are reported as new to the flora of Jeju Island. A checklist based on a study of 1697 specimens is also provided.

Ultrasonography of intrascrotal torsed appendages: size and interval between symptom onset and the ultrasonographic examination according to echogenicity.

PURPOSE: This study investigated the size of torsed appendages and the interval between symptom onset and the ultrasonographic examination according to the echogenicity of the torsed appendages. METHODS: This was a retrospective analysis of 54 cases in 46 patients with torsion of the testicular appendages between December 2008 and July 2021. Eight patients received follow-up ultrasonography 7-48 days after initial ultrasonography. The echogenicity of torsed appendages was classified into three groups: hypoechoic, hyperechoic, or isoechoic. RESULTS: The 54 torsed appendages were hypoechoic (n=40), hyperechoic (n=9), or isoechoic (n=5). The size of the torsed appendages ranged from 4 to 14 mm (8.0±3.1 mm) in hypoechoic torsed appendages and from 2.6 to 5.0 mm (3.7±0.9 mm) in hyperechoic torsed appendages. The interval between symptom onset and the ultrasonographic examination ranged from 0 to 17 days (4.2±4.4 days) in hypoechoic torsed appendages and from 8 to 48 days (29.8±16.0 days) in hyperechoic torsed appendages. The hyperechoic torsed appendages were smaller and had longer intervals between symptom onset and the ultrasonographic examination than the hypoechoic torsed appendages (P<0.05). Three hypoechoic torsed appendages and a single isoechoic torsed appendage on initial ultrasonography became hyperechoic on follow-up ultrasonography. CONCLUSION: The size of the torsed appendages and the interval between symptom onset and the ultrasonographic examination varied according to the echogenicity of the torsed appendages. The hyperechoic torsed appendages were smaller and had longer intervals until the examination than the hypoechoic torsed appendages.

The complete chloroplast genome of Porella gracillima Mitt. (Porellaceae) and phylogenetic relationships to other bryophytes.

Porella gracillima Mitt. (Jungermanniidae, Porellaceae), a bryophyte is widespread in temperate Asia and North America. In Korea, P. gracillima is mainly observed in shaded and dried rocks or tree trunks on mountains. Here, we determined the complete chloroplast (cp) genome sequence of P. gracillima to provide useful genetic information in the phylogenetic relationship, phylogeographic history, and conservation of the species. The complete cp genome of P. gracillima was assembled using NGS Illumina HiSeqX platform. The cp genome was 121,867 bp in length (GC contents, 33.7%) and showed a typical quadripartite structure, consisting of a large single copy (LSC) of 83,406 bp, a small single copy (SSC) of 19,692 bp, and two inverted repeats (IRs) of 9,385 bp. Phylogenetic analysis shows that Porellaceae was a sister group of Radulaceae, which agrees with the findings of the previous phylogenetic studies. Our cp genome data of P. gracillima may contribute to a better understanding of the evolution of the Porella in Porellaceae and will help to infer its molecular identification, thereby providing a guideline for conservation.

Downregulation of SETD5 Suppresses the Tumorigenicity of Hepatocellular Carcinoma Cells.

Hepatocellular carcinoma (HCC) is an aggressive and incurable cancer. Although understanding of the molecular pathogenesis of HCC has greatly advanced, therapeutic options for the disease remain limited. In this study, we demonstrated that SETD5 expression is positively associated with poor prognosis of HCC and that SETD5 depletion decreased HCC cell proliferation and invasion while inducing cell death. Transcriptome analysis revealed that SETD5 loss downregulated the interferon-mediated inflammatory response in HCC cells. In addition, SETD5 depletion downregulated the expression of a critical glycolysis gene, PKM (pyruvate kinase M1/2), and decreased glycolysis activity in HCC cells. Finally, SETD5 knockdown inhibited tumor growth in xenograft mouse models. These results collectively suggest that SETD5 is involved in the tumorigenic features of HCC cells and that targeting SETD5 may suppress HCC progression.

Transcriptomic Analysis of Papillary Thyroid Cancer: A Focus on Immune-Subtyping, Oncogenic Fusion, and Recurrence.

OBJECTIVES: Thyroid cancer is the most common endocrine tumor, with rapidly increasing incidence worldwide. However, its transcriptomic characteristics associated with immunological signatures, driver fusions, and recurrence markers remain unclear. We aimed to investigate the transcriptomic characteristics of advanced papillary thyroid cancer. METHODS: This study included 282 papillary thyroid cancer tumor samples and 155 normal samples from Chungnam National University Hospital and Seoul National University Hospital. Transcriptomic quantification was determined by high-throughput RNA sequencing. We investigated the associations of clinical parameters and molecular signatures using RNA sequencing. We validated predictive biomarkers using the Cancer Genome Atlas database. RESULTS: Through a comparison of differentially expressed genes, gene sets, and pathways in papillary thyroid cancer compared to normal tumor-adjacent tissue, we found increased immune signaling associated with cytokines or T cells and decreased thyroid hormone synthetic pathways. In addition, patients with recurrence presented increased CD8+ T-cell and Th1-cell signatures. Interestingly, we found differentially overexpressed genes related to immune-escape signaling such as CTLA4, IDO1, LAG3, and PDCD1 in advanced papillary thyroid cancer with a low thyroid differentiation score. Fusion analysis showed that the PI3K and mitogen-activated protein kinase (MAPK) signaling pathways were regulated differently according to the RET fusion partner genes (CCDC6 or NCOA4). Finally, we identified HOXD9 as a novel molecular biomarker that predicts the recurrence of thyroid cancer in addition to known risk factors (tumor size, lymph node metastasis, and extrathyroidal extension). CONCLUSION: We identified a high association with immune-escape signaling in the immune-hot group with aggressive clinical characteristics among Korean thyroid cancer patients. Moreover, RET fusion differentially regulated PI3K and MAPK signaling depending on the partner gene of RET, and HOXD9 was found to be a recurrence marker for advanced papillary thyroid cancer.

Laryngopharyngeal reflux in chronic rhinosinusitis patients and the role of endoscopic sinus surgery.

OBJECTIVES: Latest literature proposes laryngopharyngeal reflux (LPR) as the underlying contributory factor for chronic inflammation in both upper and lower airways. In this study, we investigated LPR symptoms and signs of CRS patients and the various factors on their LPR symptoms and signs. We also evaluated the effect of the LPR symptoms and signs of CRS patients after endoscopic sinus surgery (ESS). METHODS: We performed a retrospective analysis from 91 patients who underwent primary ESS. They were assessed for LPR symptoms with Reflux Symptom Index (RSI) and Reflux Finding Scores (RFS) before ESS. Sino-Nasal Outcome Test (SNOT)-22, Lund-Mackay (LM) scoring system, and Lund-Kennedy (LK) scoring system were evaluated for CRS severity. They had to fulfill SNOT-22, RSI, and RFS at 6 months after surgery. RESULTS: Nasal polyps, smoking, asthma, allergy, LM scores and LK scores didn't have significant correlations with preoperative RSI and RFS (P > .05 for all). RSI had significant correlations with SNOT-22 preoperatively and postoperatively (P < .05 for all). RFS had a significant correlation with postoperative SNOT-22 (P = 0.034). RSI and RFS decreased significantly more after ESS (P < 0.001 for both). Smoking had a significant effect on the postoperative RFS (P = 0.003). Non-smoker showed significantly lower scores of postoperative RFS (P = .0.003). CONCLUSION: Our study suggests that subjective CRS symptoms were related with subjective LPR symptoms and ESS was effective in reducing signs and symptoms of LPR in CRS patients. Especially, smoking was associated with less improvement of laryngoscopic findings after ESS.

Revision of Gymnomitriaceae (Marchantiophyta) in the Korean Peninsula.

This paper provides a revision of Gymnomitrion and Marsupella in the Korean Peninsula based on a study of the collections housed in the herbaria of Jeonbuk National University (JNU) and the Botanical Garden-Institute in Vladivostok (VBGI). In total, 12 species were recorded (six in Gymnomitrion and seven in Marsupella), including four taxa whose identity was not confirmed with the available materials and suspected to be recorded wrongly. Each confirmed species is annotated by morphological descriptions based on available Korean material, data on ecology, distribution, specimens examined as well as illustrations.

Integrating continental mainland and islands in temperate East Asia: liverworts and hornworts of the Korean Peninsula.

The liverwort and hornwort flora of the Korean Peninsula possesses some unique traits arising from the geographic position of the Peninsula, where the mainland flora meets insular flora. This flora is still not exhaustively studied, due not only to political reasons, but also because much less attention has been paid than to adjacent lands by hepaticologists. A checklist presented is based on a study of ca. 15,500 specimens collected by the authors and a review of relevant literature. This study provides the checklist of liverworts and hornworts known from Korea and the geographical distribution of each species within the peninsula. The liverworts and hornworts in Korean flora include 346 taxa (326 species, 16 subspecies and four varieties) in 112 genera and 50 families. Since 2007, 75 taxa of liverworts and four taxa of hornworts are reported as new to the Korean Peninsula, with a number of the new records arising following application of new taxonomic concepts that have become apparent over the last few decades. While compiling the checklist, 42 species, previously reported to Korea, are excluded from the Korean liverwort flora.

Comparison between MGI and Illumina sequencing platforms for whole genome sequencing.

BACKGROUND: Illumina next generation sequencing (NGS) systems are the major sequencing platform in worldwide next-generation sequencing market. On the other hand, MGI Tech launched a series of new NGS equipment that promises to deliver high-quality sequencing data faster and at lower prices than Illumina's sequencing instruments. OBJECTIVE: In this study, we compared the performance of the two platform's major sequencing instruments-Illumina's NovaSeq 6000 and MGI's MGISEQ-2000 and DNBSEQ-T7-to test whether the MGISEQ-2000 and DNBSEQ-T7 sequencing instruments are also suitable for whole genome sequencing. METHODS: We sequenced two pairs of normal and tumor tissues from Korean lung cancer patients using the three platforms. Then, we called single nucleotide variants (SNVs) and insertion and deletion (indels) for somatic and germline variants to compare the performance among the three platforms. RESULTS: In quality control analysis, all of the three platforms showed high-quality scores and deep coverages. Comparison among the three platforms revealed that MGISEQ-2000 is most concordant with NovaSeq 6000 for germline SNVs and indels, and DNBSEQ-T7 is most concordant with NovaSeq 6000 for somatic SNVs and indels. CONCLUSIONS: These results suggest that the performances of the MGISEQ-2000 and DNBSEQ-T7 platforms are comparable to that of the Illumina NovaSeq 6000 platform and support the potential applicability of the MGISEQ-2000 and DNBSEQ-T7 platforms in actual genome analysis fields.

Ethacrynic acid inhibits STAT3 activity through the modulation of SHP2 and PTP1B tyrosine phosphatases in DU145 prostate carcinoma cells.

To identify signal transducer and activator of transcription factor 3 (STAT3) inhibitors, we generated STAT3-dependent gene expression signature by analyzing gene expression profiles of DU145 cancer cells treated with STAT3 inhibitor, piperlongumine and 2-hydroxycinnamaldehyde. Then we explored gene expression signature-based strategies using a connectivity map database and identified several STAT3 inhibitors, including ethacrynic acid (EA). EA is currently used as a diuretic drug. EA inhibited STAT3 activation in DU145 prostate cancer cells and consequently decreased the levels of STAT3 target genes such as cyclin A and MCL-1. Furthermore, EA treatment inhibited tumor growth in mice xenografted with DU145 cells and decreased p-STAT3 expression in tumor tissues. Knockdown of Src homology region 2 domain-containing phosphatase-2 (SHP2) or Protein tyrosine phosphatase 1B (PTP1B) gene expression by siRNA suppressed the ability of EA to inhibit STAT3 activation. When EA was combined with an activator of SHP2 or PTP1B, p-STAT3 expression was synergistically decreased; when EA was combined with an inhibitor of SHP2 or PTP1B, p-STAT3 expression was rescued. By using an affinity pulldown assay with biotinyl-EA, EA was shown to associate with SHP2 and PTP1B in vitro. Additionally, the drug affinity responsive target stability (DARTS) assay confirmed the direct binding of EA to SHP2 and PTP1B. SHP2 is activated by EA through active phosphorylation at Y580 and direct binding to SHP2. Collectively, our results suggest that EA inhibits STAT3 activity through the modulation of phosphatases such as SHP2 and PTP1B and may be a potential anticancer drug to target STAT3 in cancer progression.

BaSDAS: a web-based pooled CRISPR-Cas9 knockout screening data analysis system.

We developed the BaSDAS (Barcode-Seq Data Analysis System), a GUI-based pooled knockout screening data analysis system, to facilitate the analysis of pooled knockout screen data easily and effectively by researchers with limited bioinformatics skills. The BaSDAS supports the analysis of various pooled screening libraries, including yeast, human, and mouse libraries, and provides many useful statistical and visualization functions with a user-friendly web interface for convenience. We expect that BaSDAS will be a useful tool for the analysis of genome-wide screening data and will support the development of novel drugs based on functional genomics information.

Pimozide suppresses cancer cell migration and tumor metastasis through binding to ARPC2, a subunit of the Arp2/3 complex.

ARPC2 is a subunit of the Arp2/3 complex, which is essential for lamellipodia, invadopodia and filopodia, and ARPC2 has been identified as a migrastatic target molecule. To identify ARPC2 inhibitors, we generated an ARPC2 knockout DLD-1 human colon cancer cell line using the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system and explored gene signature-based strategies, such as a connectivity map (CMap) using the gene expression profiling data of ARPC2 knockout and knockdown cells. From the CMap-based drug discovery strategy, we identified pimozide (a clinically used antipsychotic drug) as a migrastatic drug and ARPC2 inhibitor. Pimozide inhibited the migration and invasion of various cancer cells. Through drug affinity responsive target stability (DARTS) analysis and cellular thermal shift assay (CETSA), it was confirmed that pimozide directly binds to ARPC2. Pimozide increased the lag phase of Arp2/3 complex-dependent actin polymerization and inhibited the vinculin-mediated recruitment of ARPC2 to focal adhesions in cancer cells. To validate the likely binding of pimozide to ARPC2, mutant cells, including ARPC2F225A , ARPC2F247A and ARPC2Y250F cells, were prepared using ARPC2 knockout cells prepared by gene-editing technology. Pimozide strongly inhibited the migration of mutant cells because the mutated ARPC2 likely has a larger binding pocket than the wild-type ARPC2. Therefore, pimozide is a potential ARPC2 inhibitor, and ARPC2 is a new molecular target. Taken together, the results of the present study provide new insights into the molecular mechanism and target that are responsible for the antitumor and antimetastatic activity of pimozide.

GENT2: an updated gene expression database for normal and tumor tissues.

BACKGROUND: Gene Expression database of Normal and Tumor tissues 2 (GENT2) is an updated version of GENT, which has provided a user-friendly search platform for gene expression patterns across different normal and tumor tissues compiled from public gene expression data sets. RESULTS: We refactored GENT2 with recent technologies such as Apache Lucene indexing for fast search and Google Web Toolkit (GWT) framework for a user-friendly web interface. Now, GENT2 contains more than 68,000 samples and has several new useful functions. First, GENT2 now provides gene expression across 72 different tissues compared to 57 in GENT. Second, with increasing importance of tumor subtypes, GENT2 provides an option to study the differential expression and its prognostic significance based on tumor subtypes. Third, whenever available, GENT2 provides prognostic information of a gene of interest. Fourth, GENT2 provides a meta-analysis of survival information to provide users more reliable prognostic value of a gene of interest. CONCLUSIONS: In conclusion, with these significant improvements, GENT2 will continue to be a useful tool to a wide range of researchers. GENT2 is freely available at http://gent2.appex.kr .

Lactate Activates the E2F Pathway to Promote Cell Motility by Up-Regulating Microtubule Modulating Genes.

Excess lactate production due to enhanced aerobic glycolysis is characteristic of malignant cancers, which is also intimately associated with poor cancer prognoses. Although tumor-associated lactate contributes to all major steps in carcinogenesis, its action mechanism remains obscure. To understand the molecular mechanism of the lactate-induced tumor metastatic process, we identified an array of lactate-responsive genes via transcriptome analysis of a metformin-induced hyper-glycolytic liver cancer model. Gene set enrichment analysis suggested E2F-RB pathway as the dominant regulator of the lactate-induced gene expression. We experimentally verified that lactate indeed activates E2F-mediated transcription by promoting E2F1 protein accumulation through a posttranscriptional mechanism. Literature-based analysis of target pathways potentially modulated by 136 top-ranked genes indicated that genes functioning in cell-cell or cell-matrix communications dominate the lactate-induced gene expression. Especially, those regulating microtubule functions, including a group of kinesin family members, were significantly up-regulated in lactate- and E2F1-dependent manners. Depletion of E2F1 or kinesins (KIF2C, KIF18B, KIF20A) led to deformation of microtubule structures, impairing cell motility as much as the deficit in lactate production. These results indicate that E2F pathway activation by tumor-associated lactate and subsequent transcriptional activation of microtubule functions play crucial roles in tumor metastasis, providing mechanistic clues to cell motility-directed anti-cancer strategies.

Comparison of Clinical Presentation and Surgical Outcomes Between Recurrent Acute Rhinosinusitis and Chronic Rhinosinusitis.

INTRODUCTION: The authors assessed clinical presentations and anatomic variants among patients with recurrent acute rhinosinusitis (RARS), chronic rhinosinusitis (CRS) without nasal polyps (CRSsNP), and CRS with nasal polyps (CRSwNP). Additionally, differences in the postoperative improvement of each category were evaluated. METHODS: The authors performed an analysis of 304 patients who underwent endoscopic sinus surgery. They were divided into groups with RARS, CRSsNP, and CRSwNP. Patients had to complete the Sino-Nasal Outcome Test (SNOT-20) on surgery 1 day before and 6 months after surgery. Patient demographics and comorbidities were reviewed. We reviewed all patients' computed tomographic findings to analyze anatomic variants. RESULTS: No significant differences were found among the average preoperative SNOT-20 scores of the 3 groups. Patients with RARS were significantly more likely to show agger nasi cells, Haller cells, and septal deviation on computed tomography. Those with CRSwNP had significantly smaller mean infundibular widths. All groups showed significantly improved SNOT-20 scores postoperatively. CONCLUSION: The different anatomic variants found among patients with RARS, CRSsNP, and CRSwNP can facilitate surgical prognostic evaluation.

A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages.

Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. 'dada2' performs trimming of the high-throughput sequencing data. 'QuasR' and 'mosaics' perform quality control and mapping of the input reads to the reference genome and peak calling, respectively. Finally, 'ChIPseeker' performs annotation and visualization of the called peaks. This workflow runs well independently of operating systems (e.g., Windows, Mac, or Linux) and processes the input fastq files into various results in one run. R code is available at github: https://github.com/ddhb/Workflow_of_Chipseq.git.

Comparisons of Subthreshold Versus Full Posttraumatic Stress Disorder Distinguished by Subjective Functional Impairment Among Train Drivers: A Population-Based Nationwide Study in South Korea.

OBJECTIVE: Subthreshold posttraumatic stress disorder (SPTSD), a condition that meets the full symptomatic criteria of posttraumatic stress disorder (PTSD) without subjective functional impairment, has yet to be fully investigated. In this study, we aimed to determine the prevalence and characteristics of SPTSD. METHODS: The web-based survey including psychiatric diagnosis and experience of human error was conducted in actively working train drivers in South Korea. RESULTS: Of the 4,634 subjects, 103 (2.23%) were categorized as full PTSD and 322 (6.96%) were categorized as having SPTSD. Individuals with full PTSD showed higher impulsivity and anxiety compared to those with SPTSD and those without PTSD, while those with SPTSD had more frequent clinically meaningful depression, posttraumatic stress, and alcohol and nicotine dependence and significant human error. CONCLUSION: Despite not qualifying as a subjective functional disability, SPTSD still had significant psychiatric symptoms. More clinical attentions need to be given to the diagnosis and treatment of SPTSD.