Nuclear phosphoinositide signaling promotes YAP/TAZ-TEAD transcriptional activity in breast cancer.

The Hippo pathway effectors Yes-associated protein 1 (YAP) and its homolog TAZ are transcriptional coactivators that control gene expression by binding to TEA domain (TEAD) family transcription factors. The YAP/TAZ-TEAD complex is a key regulator of cancer-specific transcriptional programs, which promote tumor progression in diverse types of cancer, including breast cancer. Despite intensive efforts, the YAP/TAZ-TEAD complex in cancer has remained largely undruggable due to an incomplete mechanistic understanding. Here, we report that nuclear phosphoinositides function as cofactors that mediate the binding of YAP/TAZ to TEADs. The enzymatic products of phosphoinositide kinases PIPKIα and IPMK, including phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and phosphatidylinositol 3,4,5-trisphosphate (P(I3,4,5)P3), bridge the binding of YAP/TAZ to TEAD. Inhibiting these kinases or the association of YAP/TAZ with PI(4,5)P2 and PI(3,4,5)P3 attenuates YAP/TAZ interaction with the TEADs, the expression of YAP/TAZ target genes, and breast cancer cell motility. Although we could not conclusively exclude the possibility that other enzymatic products of IPMK such as inositol phosphates play a role in the mechanism, our results point to a previously unrecognized role of nuclear phosphoinositide signaling in control of YAP/TAZ activity and implicate this pathway as a potential therapeutic target in YAP/TAZ-driven breast cancer.

Refining Classification of Cholangiocarcinoma Subtypes via Proteogenomic Integration Reveals New Therapeutic Prospects.

BACKGROUND & AIMS: Intrahepatic cholangiocarcinomas (iCCs) are characterized by their rarity, difficult diagnosis, and overall poor prognosis. The iCC molecular classification for developing precision medicine strategies was investigated. METHODS: Comprehensive genomic, transcriptomic, proteomic, and phosphoproteomic analyses were performed on treatment-naïve tumor samples from 102 patients with iCC who underwent surgical resection with curative intent. An organoid model was constructed for testing therapeutic potential. RESULTS: Three clinically supported subtypes (stem-like, poorly immunogenic, and metabolism) were identified. NCT-501 (aldehyde dehydrogenase 1 family member A1 [ALDH1A1] inhibitor) exhibited synergism with nanoparticle albumin-bound-paclitaxel in the organoid model for the stem-like subtype. The oncometabolite dysregulations were associated with different clinical outcomes in the stem-like and metabolism subtypes. The poorly immunogenic subtype harbors the non-T-cell tumor infiltration. Integrated multiomics analysis not only reproduced the 3 subtypes but also showed heterogeneity in iCC. CONCLUSIONS: This large-scale proteogenomic analysis provides information beyond that obtained with genomic analysis, allowing the functional impact of genomic alterations to be discerned. These findings may assist in the stratification of patients with iCC and in developing rational therapeutic strategies.

Fish and macroinvertebrate assemblages reveal extensive degradation of the world's rivers.

Rivers suffer from multiple stressors acting simultaneously on their biota, but the consequences are poorly quantified at the global scale. We evaluated the biological condition of rivers globally, including the largest proportion of countries from the Global South published to date. We gathered macroinvertebrate- and fish-based assessments from 72,275 and 37,676 sites, respectively, from 64 study regions across six continents and 45 nations. Because assessments were based on differing methods, different systems were consolidated into a 3-class system: Good, Impaired, or Severely Impaired, following common guidelines. The proportion of sites in each class by study area was calculated and each region was assigned a Köppen-Geiger climate type, Human Footprint score (addressing landscape alterations), Human Development Index (HDI) score (addressing social welfare), % rivers with good ambient water quality, % protected freshwater key biodiversity areas; and % of forest area net change rate. We found that 50% of macroinvertebrate sites and 42% of fish sites were in Good condition, whereas 21% and 29% were Severely Impaired, respectively. The poorest biological conditions occurred in Arid and Equatorial climates and the best conditions occurred in Snow climates. Severely Impaired conditions were associated (Pearson correlation coefficient) with higher HDI scores, poorer physico-chemical water quality, and lower proportions of protected freshwater areas. Good biological conditions were associated with good water quality and increased forested areas. It is essential to implement statutory bioassessment programs in Asian, African, and South American countries, and continue them in Oceania, Europe, and North America. There is a need to invest in assessments based on fish, as there is less information globally and fish were strong indicators of degradation. Our study highlights a need to increase the extent and number of protected river catchments, preserve and restore natural forested areas in the catchments, treat wastewater discharges, and improve river connectivity.

Alteration of gammaretroviral vector integration patterns by insertion of histone and leucine zipper into integrase.

Retroviral vectors show long-term gene expression in gene therapy through the integration of transgenes into the human cell genome. Murine leukemia virus (MLV), a well-studied gammaretrovirus, has been often used as a representative retroviral vector. However, frequent integrations of MLV-based vectors into transcriptional start sites (TSSs) could lead to the activation of oncogenes by enhancer effects of the genetic components within the vectors. Therefore, the MLV integration preference for TSSs limits its wider use in clinical applications. To reduce the integration preference of MLV-based vectors, we attempted to perturb the structure of the viral integrase that plays a key role in determining integration sites. For this goal, we inserted histones and leucine zippers, having DNA-binding property, into internal sites of MLV integrase. This integrase engineering yielded multiple mutant vectors that showed significantly different integration patterns compared with that of wild-type vector. Some mutant vectors did not prefer the key regulatory genomic domains of human cells, TSSs. Moreover, a couple of engineered vectors did not integrate into the genomic sites near the TSSs of oncogenes. Overall, this study suggests that structural perturbation of integrase is a simple way to develop safer MLV-based retroviral vectors for use in clinical applications.

Quantitative prediction of mixture toxicity of AgNO3 and ZnO nanoparticles on Daphnia magna.

Once metal-based engineered nanoparticles (NPs) are released into the aquatic environment, they are expected to interact with other existing co-contaminants. A knowledge gap exists as to how the interaction of NPs with other co-contaminants occurs. Here we selected ZnO NPs among various NPs, with Ag ion existing as a contaminant in the aquatic environment by Ag NPs widely used. A novel modeling strategy was demonstrated enabling quantitative and predictive evaluation of the aqueous mixture nanotoxicity. Individual and binary mixture toxicity tests of ZnO NPs and silver (as AgNO3) on Daphnia magna were conducted and compared to determine whether the presence of Ag ions affects the toxicity of ZnO NPs. Binary mixture toxicity was evaluated based on the concentration addition (CA) and independent action models. The CA dose-ratio dependent model was found to be the model of best fit for describing the pattern of mixture toxicity. The MIX I and MIX III suspensions (higher ratios of ZnO NPs to AgNO3) showed a synergism, whereas the MIX II suspension (lower ratio of ZnO NPs to AgNO3) showed an antagonism. The synergistic mixture toxicity at higher ratios of ZnO NPs to AgNO3 was caused by either the physiological or metabolic disturbance induced by the excessive ionic Zn or increased transport and accumulation in D. magna via the formation of complex of ionic Ag with ZnO NPs. Therefore, the toxicity level contributed via their aggregation and physicochemical properties and the dissolved ions played a crucial role in the mixture toxicities of the NPs.

Survival dynamics of stick insect and the impact of environmental factors on natural fungal infection during the rainy season.

Phasmatodea, commonly known as stick insects, are recognized as noteworthy pests globally, impacting agriculture and forest ecosystems. Among them, the outbreak of Ramulus mikado has emerged as a notable concern in East Asian forests. Recently, Metarhizium phasmatodeae has been identified as utilizing stick insects as hosts. We have observed evidence of this entomopathogenic fungus infecting stick insects. Given the increase in these occurrences during the rainy period, this study investigated the relationship between the survival of R. mikado and the M. phasmatodeae infection during the rainy seasons of 2022 and 2023. We collected stick insects in two representative forests of the Republic of Korea and examined insect survival, fungal infection, and various environmental factors. No infections were detected in specimens collected in June before the rainy season, but from July onwards, both the mortality of R. mikado and the fungal infection substantially increased. By the last sampling date of each year, 75% (2022), 71.4% (2023) of the specimens were infected, and over 90% of the total individuals succumbed as a result. Fungi isolated from deceased R. mikado were successfully identified as M. phasmatodeae using morphological and taxonomic approaches. Various statistical analyses, including principal component analysis and modeling, revealed a robust association between fungal infection and the survival of stick insects. The results highlight the correlation between mass deaths of stick insects and fungal infection, particularly during the summer rainy season. These findings offer valuable insights for forecasting R. mikado population in the upcoming year and developing effective pest control strategies.

Population genetic structure of a recent insect invasion: a gall midge, Asynapta groverae (Diptera: Cecidomyiidae) in South Korea since the first outbreak in 2008.

Outbreaks of Asynapta groverae, an invasive mycophagous gall midge, in South Korea have been repeatedly reported since the first occurrence in 2008. This species is a nuisance to residents owing to its mass emergence from newly built and furnished apartments. Here, the levels of genetic diversity, divergence, and structure of invasive A. groverae populations were investigated to understand their ability to survive in novel locations. Population genetic analyses were performed on seven invasive populations, including the first outbreak, sporadically emerged, and two laboratory-isolated (quarantined) populations, using the mitochondrial COI sequences and the ten novel microsatellite markers developed in this study. Non-indigenous A. groverae managed to maintain their populations for 12 years despite decreased genetic polymorphisms resulting from multiple incidences of founder effects by a small number of colonists. Additionally, the advantageous sustainability of A. groverae in the particle boards from which they emerge suggests that human-mediated dispersal is plausible, which may allow for the successful spread or invasion of A. groverae to new locations. This study is one of the few examples to demonstrate that an insect species successfully invaded new regions despite exhibiting decreased genetic diversity that was maintained for a decade. These findings indicate that the high genetic diversity of the initial founding population and asexual reproduction would contribute to the successful invasion of A. groverae in novel environments.

Diversity and DNA Barcode Analysis of Chironomids (Diptera: Chironomidae) from Large Rivers in South Korea.

Most large rivers in South Korea run through major cities, which often experience many environmental problems, including outbreaks of non-biting midges (Diptera: Chironomidae). However, chironomid species inhabiting large rivers have not been thoroughly investigated. We aimed to identify chironomid species collected from the four main large rivers in South Korea, construct a corresponding DNA barcode library, and examine the distribution and community structure of the identified riverine species. Adult chironomids were collected from nine sites along the rivers by using sweep nets and light traps during June and August 2015. Adults were morphologically identified, and COI nucleotide sequences were generated to verify the species identification and construct a DNA barcode library. The distribution and community structure of the identified species were also analyzed. A total of 124 COI sequences were established from 37 species belonging to 19 genera, and the resulting DNA barcode library effectively discriminated >90% of riverine Chironomidae in South Korea. Ten species, which are considered indicator species for large rivers, were collected from all four rivers. In addition, members of the subfamily Chironominae were collected more frequently than members of other subfamilies, with Tanytarsus tamagotoi being the most common and widespread chironomid species in South Korea. The DNA barcode library developed in this study will facilitate environmental studies of large rivers, such as biomonitoring chironomid larvae.

DNA Barcoding of Chironomid Larvae (Diptera: Chironomidae) from Large Rivers in South Korea to Facilitate Freshwater Biomonitoring and Public Health Surveillance.

Chironomid larvae are among the dominant benthic macroinvertebrates in all types of water systems in South Korea. They may pass through pipes in rivers (raw water) and occur in drinking water, thus creating public health issues. However, little is known about the larval stages of chironomids in large South Korean rivers. Therefore, we examined larval-adult associations in chironomids inhabiting major rivers used as water sources. The larvae were collected in 2015 and 2016 from nine locations along the four largest rivers in South Korea using a Ponar grab. Cytochrome oxidase subunit I (COI) sequences were generated from the larval specimens, and the species were identified by comparing these sequences to those in a newly constructed DNA barcode library of Chironomidae in South Korea. The samples from the four rivers yielded 61 mitochondrial COI sequences belonging to 18 species, including Hydrobaenus kondoi Saether, 1989, which was reported for the first time in the Korean Peninsula. Further, morphological identification of the larvae was conducted, and a pictorial taxonomic key to Chironomidae species in large rivers in South Korea was developed to facilitate freshwater biomonitoring research. Finally, an action flow chart was created for the rapid identification of chironomid larvae in infested drinking water or water purification facilities.

Protein-gene Expression Nexus: Comprehensive characterization of human cancer cell lines with proteogenomic analysis.

Researchers have gained new therapeutic insights using multi-omics platform approaches to study DNA, RNA, and proteins of comprehensively characterized human cancer cell lines. To improve our understanding of the molecular features associated with oncogenic modulation in cancer, we proposed a proteogenomic database for human cancer cell lines, called Protein-gene Expression Nexus (PEN). We have expanded the characterization of cancer cell lines to include genetic, mRNA, and protein data of 145 cancer cell lines from various public studies. PEN contains proteomic and phosphoproteomic data on 4,129,728 peptides, 13,862 proteins, 7,138 phosphorylation site-associated genomic variations, 117 studies, and 12 cancer. We analyzed functional characterizations along with the integrated datasets, such as cis/trans association for copy number alteration (CNA), single amino acid variation for coding genes, post-translation modification site variation for Single Amino Acid Variation, and novel peptide expression for noncoding regions and fusion genes. PEN provides a user-friendly interface for searching, browsing, and downloading data and also supports the visualization of genome-wide association between CNA and expression, novel peptide landscape, mRNA-protein abundance, and functional annotation. Together, this dataset and PEN data portal provide a resource to accelerate cancer research using model cancer cell lines. PEN is freely accessible at http://combio.snu.ac.kr/pen.

Topical application of autophagy-activating peptide improved skin barrier function and reduced acne symptoms in acne-prone skin.

BACKGROUND: Recent studies about the important roles of autophagy signaling in sebaceous lipogenesis and epidermal differentiation suggest potential benefits of autophagy activation in acne. AIMS: To investigate the effects of an autophagy activator on acne-prone skin. METHODS: Autophagy signaling in human immortalized SZ95 sebocytes, normal human epidermal keratinocytes, and 3D reconstituted skin was examined. Effects of an autophagy-activating peptide on sebaceous lipogenesis were measured by fluorescence microscopic analysis. The clinical efficacy in acne-prone skin was evaluated through an eight-week, double-blind, randomized, vehicle-controlled study. Changes in skin surface lipid compositions were further analyzed. RESULTS: In cultured sebocytes and keratinocytes, the investigated autophagy-activating peptide increased LC3-II expression, indicating a stimulation of autophagy signaling. Testosterone and linoleic acid treatment induced lipogenesis in cultured sebocytes and is further inhibited by the autophagy activator peptide treatment. Increased expression of differentiation marker proteins in cultured keratinocytes was also observed by autophagy-activating peptide. In clinical study, reduction of closed comedones and the amount of skin surface lipids as well as of trans-epidermal water loss (TEWL) were observed in acne-prone skin after autophagy-activating peptide application. In addition, reduction of squalene and increase in cholesterol were observed after an 8-week application. CONCLUSIONS: Topical application of an autophagy activator downregulated sebaceous lipogenesis and improved the skin barrier function. Considering the important roles of sebum and skin barrier function in acne pathogenesis, autophagy activation might represent a new therapeutic option in early forms of acne.

Prokaryotic Contig Annotation Pipeline Server: Web Application for a Prokaryotic Genome Annotation Pipeline Based on the Shiny App Package.

Genome annotation is a primary step in genomic research. To establish a light and portable prokaryotic genome annotation pipeline for use in individual laboratories, we developed a Shiny app package designated as "P-CAPS" (Prokaryotic Contig Annotation Pipeline Server). The package is composed of R and Python scripts that integrate publicly available annotation programs into a server application. P-CAPS is not only a browser-based interactive application but also a distributable Shiny app package that can be installed on any personal computer. The final annotation is provided in various standard formats and is summarized in an R markdown document. Annotation can be visualized and examined with a public genome browser. A benchmark test showed that the annotation quality and completeness of P-CAPS were reliable and compatible with those of currently available public pipelines.

Biological and genetic characteristics of Glyptotendipes tokunagai (Diptera: Chironomidae) on the basis of successive rearing of forty-two generations over seven years under laboratory conditions.

Members of the nonbiting midge family Chironomidae have been used worldwide as water-quality indicators or toxicity test organisms. The purpose of this study was to establish the chironomid Glyptotendipes tokunagai Sasa as a new test species by conducting successive rearing under laboratory conditions. We monitored biological and genetic aspects of >42 successive generations over 7 yr, and also compared the development of the 39th generation with the fourth generation under five constant temperatures of 15, 20, 25, 30, and 35°C. We observed that the number of eggs in an egg mass and the adult body sizes decreased rapidly in the early generations, and thereafter tended to stabilize from the fifth generation to the 42nd generation. In all generations, the mean hatching rate was >75%. Males were predominant in the early generations, but the sex ratio increased to 0.5 (ranged 0.24-0.61) in later generations. The genetic divergence of the reared generations, analyzed by using the mitochondrial cytochrome c oxidase subunit I gene, decreased from 0.0049 to 0.0004 as the generations progressed. In comparison with the fourth generation, the mortality and developmental time of the 39th generation were generally greater, and the adult body sizes were generally smaller. The estimated low developmental threshold temperatures of eggs, male larvae to male adults, and female larvae to female adults were 9.6, 11.3, and 9.7°C, respectively. The optimal rearing temperature was determined to be 25°C. This is the first record of domesticated rearing of a wild chironomid species under laboratory conditions for >7 yr.

Physiological disturbance of the Manila clam, Ruditapes philippinarum, by altered environmental conditions in a tidal flat on the west coast of Korea.

To examine the influence of habitat alteration by tideflat reclamation on the physiological ecology of Ruditapes philippinarum, seasonal variations in its condition, gross biochemical composition, and reproductive cycle were compared for a yearly cycle between a reclaimed flat (Gomsohang, GS) and a natural flat (Hajun, HJ) in Gomso Bay, Korea. Concentrations of chlorophyll a and seston (as well as its energy value as food available to the clam) were consistently higher at HJ than at GS. Condition, dry tissue weight, and energy reserves (proteins and carbohydrates) of the clams were much higher at HJ than at GS during spring-summer, when fast growth and gametogenic development occur. Furthermore, their spring gametogenic development and spawning were advanced at HJ compared with GS. Our results suggest that the Manila clam encounters nutritionally stressful environmental conditions in altered habitats after tideflat reclamation that lead to lowered nutrient accumulation and a changing reproductive cycle.

Life history and emergence pattern of Cloeon dipterum (Ephemeroptera: Baetidae) in Korea.

Cloeon dipterum (L.) (Ephemeroptera: Baetidae), the common wetland mayfly, emerges and oviposits every season, except winter, and has overlapping generations in the temperate region. We investigated the life history of C. dipterum associated with drought. Field experiments and sampling were conducted in a wetland (25 by 80 m) located in central Korea. Larvae were sampled weekly within two habitat types (a large, deep wetland and a small, shallow wetland) using a dredge sampler, and adults were sampled every 2 d with cube emergence traps, from July 2011 to September 2012 (except winter). C. dipterum had an extended emergence period from late April to early October with four peaks: early May, mid-June, July, and August/September. When the water depth was shallow because of drought, emergence was suppressed and delayed. The accumulated degree-days and body length of the overwintering cohort that emerged in spring 2012 were markedly larger and longer than those of other cohorts. Adults emerged intensively around sunset. C. dipterum has a multivoltine life cycle with four cohorts per year; its life history and population density can be changed by natural disturbances such as drought and fish predation.