Comparative whole genome analysis of face-derived Streptococcus infantis CX-4 unravels the functions related to skin barrier

BACKGROUND

The skin microbiome is essential in guarding against harmful pathogens and responding to environmental changes by generating substances useful in the cosmetic and pharmaceutical industries. Among these microorganisms, Streptococcus is a bacterial species identified in various isolation sources. In 2021, a strain of Streptococcus infantis, CX-4, was identified from facial skin and found to be linked to skin structure and elasticity. As the skin-derived strain differs from other S. infantis strains, which are usually of oral origin, it emphasizes the significance of bacterial variation by the environment.

OBJECTIVE

This study aims to explore the unique characteristics of the CX-4 compared to seven oral-derived Streptococcus strains based on the Whole-Genome Sequencing data, focusing on its potential role in skin health and its possible application in cosmetic strategies.

METHODS

The genome of the CX-4 strain was constructed using PacBio Sequencing, with the assembly performed using the SMRT protocol. Comparative whole-genome analysis was then performed with seven closely related strains, utilizing web-based tools like PATRIC, OrthoVenn3, and EggNOG-mapper, for various analyses, including protein association analysis using STRING.

RESULTS

Our analysis unveiled a substantial number of Clusters of Orthologous Groups in diverse functional categories in CX-4, among which sphingosine kinase (SphK) emerged as a unique product, exclusively present in the CX-4 strain. SphK is a critical enzyme in the sphingolipid metabolic pathway, generating sphingosine-1-phosphate. The study also brought potential associations with isoprene formation and retinoic acid synthesis, the latter being a metabolite of vitamin A, renowned for its crucial function in promoting skin cell growth, differentiation, and maintaining of skin barrier integrity. These findings collectively suggest the potential of the CX-4 strain in enhancing of skin barrier functionality.

CONCLUSION

Our research underscores the potential of the skin-derived S. infantis CX-4 strain by revealing unique bacterial compounds and their potential roles on human skin.

Dermatobacter hominis gen. nov., sp. nov., a new member of the family Iamiaceae, revealed the potential utilisation of skin-derived metabolites

A non-motile, novel actinobacterial strain, Kera-3T, which is a gram-positive, aerobic, rod-shaped bacterium, was isolated from human keratinocytes on 1/10 diluted R2A agar. Whole-cell hydrolysis of amino acids revealed the presence of meso-DAP, alanine, and glutamic acid. The predominant menaquinone was MK-9 (H8), whereas the primary fatty acids were C16:0 and C18:1 ω9c. The major phospholipids included diphosphatidylglycerol and aminophospholipids, along with an unidentified phosphoglycolipid and an aminophosphoglycolipid. The G+C content of the genomic DNA was 73.2%, based on the complete genome sequence. Phylogenetic analyses of the 16S rRNA gene sequence and phylogenomic analysis of 91 core genes showed that strain Kera-3T formed a new lineage in the family Iamiaceae, with the closest neighbour Rhabdothermincola sediminis SYSU G02662T having 91.19% 16S rRNA gene sequence identity. A comparative genomic study of the predicted general metabolism and carbohydrate-active enzymes supported the phylogenetic and phylogenomic data. Based on the analysis of physiological, biochemical, and genomic characteristics, strain Kera-3T can be distinguished from known genera in the family Iamiaceae and represents a novel genus and species. Therefore, the name Dermatobacter hominis gen. nov., sp. nov. was proposed, with the type strain Kera-3T (= KACC 22415T = LMG 32493T).

Growth Increase in the Herbaceous Plant Centella asiatica by the Plant Growth-Promoting Rhizobacteria Priestia megaterium HyangYak-01

Centella asiatica is a traditional herbaceous plant with numerous beneficial effects, widely known for its medicinal and cosmetic applications. Maximizing its growth can lead to beneficial effects, by focusing on the use of its active compounds. The use of plant growth-promoting rhizobacteria (PGPR) is known to be an alternative to chemical fertilizers. In this study, we used the PGPR Priestia megaterium HY-01 to increase the yield of C. asiatica. In vitro assays showed that HY-01 exhibited plant growth-promoting activities (IAA production, denitrification, phosphate solubilization, and urease activity). Genomic analyses also showed that the strain has plant growth-promoting-related genes that corroborate with the different PGP activities found in the assays. This strain was subsequently used in field experiments to test its effectiveness on the growth of C. asiatica. After four months of application, leaf and root samples were collected to measure the plant growth rate. Moreover, we checked the rhizosphere microbiome between the treated and non-treated plots. Our results suggest that treatment with Hyang-yak-01 not only improved the growth of C. asiatica (leaf length, leaf weight, leaf width, root length, root width, and chlorophyll content) but also influenced the rhizosphere microbiome. Biodiversity was higher in the treated group, and the bacterial composition was also different from the control group.

Genome-Wide Pathway Exploration of the Epidermidibacterium keratini EPI-7T

Functional cosmetics industries using skin microbiome screening and beneficial materials isolated from key microorganisms are receiving increasing attention. Since Epidermidibacterium keratini EPI-7T was first discovered in human skin, previous studies have confirmed that it can produce a new pyrimidine compound, 1,1′-biuracil, having anti-aging effects on human skin. Therefore, we conducted genomic analyses to judge the use value of E. keratini EPI-7T and provide up-to-date information. Whole-genome sequencing analysis of E. keratini EPI-7T was performed to generate new complete genome and annotation information. E. keratini EPI-7T genome was subjected to comparative genomic analysis with a group of closely-related strains and skin flora strains through bioinformatic analysis. Furthermore, based on annotation information, we explored metabolic pathways for valuable substances that can be used in functional cosmetics. In this study, the whole-genome sequencing (WGS) and annotation results of E. keratini EPI-7T were improved, and through comparative analysis, it was confirmed that the E. keratini EPI-7T has more metabolite-related genes than comparison strains. In addition, we annotated the vital genes for biosynthesis of 20 amino acids, orotic acid, riboflavin (B2) and chorismate. In particular, we were able to prospect that orotic acid could accumulate inside E. keratini EPI-7T under uracil-enriched conditions. Therefore, through a genomics approach, this study aims to provide genetic information for the hidden potential of E. keratini EPI-7T and the strain development and biotechnology utilization to be conducted in further studies.

OP0027 ASSOCIATION BETWEEN BASELINE CARDIOVASCULAR RISK AND INCIDENCE RATES OF MAJOR ADVERSE CARDIOVASCULAR EVENTS AND MALIGNANCIES IN PATIENTS WITH PSORIATIC ARTHRITIS AND PSORIASIS RECEIVING TOFACITINIB

Background

Common comorbidities of psoriatic arthritis (PsA) and psoriasis (PsO) are cardiovascular (CV) disease and metabolic syndrome (MetS).1,2 Risk of CV disease may be associated with increased risk of future malignancies.3 Tofacitinib is a JAK inhibitor for treatment of PsA and has been investigated for treatment of PsO.

Objectives

To examine baseline (BL) CV risk and its association with incidence rates (IRs) of major adverse CV events (MACE) and malignancies in tofacitinib-treated patients (pts) with PsA and PsO.

Methods

Analysis included data from 3 (Phase [P]3/long-term extension [LTE]) trials of pts with PsA and 7 (P2/3/LTE) trials of pts with PsO receiving ≥1 dose of tofacitinib (5 or 10 mg twice daily). IRs (pts with events/100 pt-yrs) for MACE and malignancies (excluding non-melanoma skin cancer) were stratified by: history of coronary artery disease (HxCAD [≥1 of myocardial infarction, coronary heart disease, coronary artery procedure or stable angina pectoris]); BL 10-yr atherosclerotic CV disease (ASCVD) risk (ASCVD-pooled cohort equations calculator [only in pts without HxCAD]); and BL MetS (≥3 of hypertension, raised triglycerides, reduced high-density lipoprotein cholesterol, high waist circumference or high fasting glucose levels).

Results

Of 783 and 3663 pts with PsA and PsO, total tofacitinib exposure was 2038 and 8950 pt-yrs, and median duration of exposure was 3.0 and 2.4 yrs, respectively. In pts with PsA and PsO, 5.0% and 2.5% had HxCAD, respectively; in those without HxCAD, >20% had intermediate/high BL 10-yr ASCVD risk (Figure 1). At BL, 40.9% and 32.7% of pts with PsA and PsO had MetS, respectively. IRs of MACE were greatest in pts with PsA and PsO who had HxCAD/high BL 10-yr ASCVD risk (Table 1). In the PsA cohort, 5/6 pts with MACE had BL MetS. IRs of malignancies in pts with PsA were greatest in those with intermediate/high BL 10-yr ASCVD risk; 8/9 pts with malignancies in these risk categories had BL MetS (Table 1). In the PsO cohort, IR of malignancies was notably greater in those with high vs low/intermediate BL 10-yr ASCVD risk (Table 1).

Table 1.

IRs of MACE and malignancies in pts with PsA and PsO receiving tofacitinib, stratified by HxCAD, BL 10-yr ASCVD risk and BL MetS

MACEMalignanciesPsAPsOPsAPsOn/N[n1]IR (95% CI)n/N[n1]IR (95% CI)n/N[n1]IR (95% CI)n/N[n1]IR (95% CI)HxCADYes1/39[0]0.97 (0.02, 5.38)3/93[0]1.49 (0.31, 4.36)0/39[0]0.00 (0.00, 3.52)0/93[0]0.00 (0.00, 1.83)No5/744[5]0.25 (0.08, 0.59)20/3570[10]0.22 (0.13, 0.34)15/744[10]0.75 (0.42, 1.24)60/3570[26]0.66 (0.51, 0.85)BL 10-yr ASCVD risk categoryHigh risk (≥20%)1/35[1]1.26 (0.03, 7.01)7/179[4]1.67 (0.67, 3.43)1/35[1]1.26 (0.03, 7.03)15/179[10]3.57 (2.00, 5.89)Intermediate risk(≥7.5–<20%)2/121[2]0.62 (0.07, 2.23)9/716[6]0.50 (0.23, 0.95)8/121[7]2.46 (1.06, 4.86)23/716[9]1.28 (0.81, 1.92)Borderline risk(≥5–<7.5%)1/91[1]0.42 (0.01, 2.32)2/400[0]0.19 (0.02, 0.67)2/91[1]0.83 (0.10, 3.01)5/400[1]0.47 (0.15, 1.09)Low risk (<5%)1/487[1]0.08 (0.00, 0.42)2/2241[0]0.03 (0.00, 0.13)4/487[1]0.30 (0.08, 0.77)17/2241[6]0.30 (0.17, 0.47)BL MetSYes5/3200.60 (0.20, 1.40)10/11970.34 (0.16, 0.63)10/3201.20 (0.58, 2.21)26/11970.89 (0.58, 1.31)No1/4630.08 (0.00, 0.44)13/24660.20 (0.11, 0.35)5/4630.40 (0.13, 0.92)34/24660.54 (0.37, 0.75)

Follow-up time calculated up to the day of the first event and subject to risk period of 28 days beyond the last dose of study drug.

CI, confidence interval; N, total pts; n, pts with MACE/malignancies; n1, pts with MACE/malignancies and BL MetS.

Conclusion

In tofacitinib-treated pts with PsA and PsO, raised CV risk and MetS at BL were potentially associated with higher IRs of MACE and malignancies. Our findings support assessing CV risk in pts with PsA and PsO and enhanced monitoring for malignancies in those with raised CV risk.

References

[1]Karmacharya et al. Ther Adv Musculoskel Dis 2021; 13: 1-15.

[2]Garshick et al. J Am Coll Cardiol 2021; 77: 1670-1680.

[3]Lau et al. JACC CardioOncol 2021; 3: 48-58.

Acknowledgements

Study sponsored by Pfizer Inc. Medical writing support was provided by Emma Mitchell, CMC Connect, and funded by Pfizer Inc.

Disclosure of Interests

Lars Erik Kristensen Speakers bureau: AbbVie, Amgen, Biogen, Bristol-Myers Squibb, Eli Lilly, Janssen, MSD, Novartis, Pfizer Inc and UCB, Grant/research support from: Biogen, Janssen, Novartis and UCB, Bruce Strober Speakers bureau: AbbVie, Amgen, Eli Lilly, Janssen and Ortho Dermatologics, Consultant of: AbbVie, Almirall, Amgen, Arcutis, Arena, Aristea, Boehringer Ingelheim, Bristol-Myers Squibb, Cara, Celgene, Dermavant, Dermira, Eli Lilly, GlaxoSmithKline, Janssen, Leo, Meiji Seika Pharma, Novartis, Ortho Dermatologics, Pfizer Inc, Regeneron, Sanofi-Genzyme, Sun Pharma and UCB, Denis Poddubnyy Speakers bureau: AbbVie, Bristol-Myers Squibb, Eli Lilly, MSD, Novartis, Pfizer Inc and UCB, Consultant of: AbbVie, BIOCAD, Gilead Sciences, GlaxoSmithKline, Eli Lilly, MSD, Novartis, Pfizer Inc, Samsung Bioepis and UCB, Grant/research support from: AbbVie, MSD, Novartis and Pfizer, Ying Ying Leung Consultant of: AbbVie, Eli Lilly, Janssen and Novartis, Hyejin Jo Consultant of: Pfizer Inc, Employee of: Syneos Health, Kenneth Kwok Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Ivana Vranic Shareholder of: Pfizer Inc, Employee of: Pfizer Ltd, Dona Fleishaker Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Lara Fallon Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Arne Yndestad Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Dafna D Gladman Consultant of: AbbVie, Amgen, Celgene, Eli Lilly, Galapagos, Gilead Sciences, Janssen, Novartis, Pfizer Inc and UCB.

Comparative analysis of human facial skin microbiome between topical sites compared to entire face

BACKGROUND

Skin is an essential outer barrier and supports the growth of commensal microorganisms that protects a host from the offense of foreign toxic organisms. With the rapid development of next-generation sequencing (NGS)-based applications, skin microbiome research for facial health care has reached industry growth, such as therapy and cosmetic product development. Despite the acceleration of skin microbiome research, experimental standardization protocol has not yet been established in the facial site and method of sampling.

OBJECTIVE

Thus, we aimed to investigate the differences in microbial composition at each facial site (cheek, mouth, forehead, and entire face) using comprehensive microbiome analysis.

METHODS

Twelve specimens from three men (four specimens per one person) were collected. The hypervariable regions (V3-V4) of the bacterial 16S rRNA gene were targeted for 16S amplicon library construction and classification of bacterial taxonomy. Skin microbial composition for all specimens was investigated, and the differences site-by-site in skin microbial composition were analyzed and evaluated by the various statistical tests.

RESULTS

We were able to validate the independent correlation between the skin microbiome composition and the facial sites. The cheek site showed the highest alpha-diversity in richness and evenness scores compared to the forehead and mouth. The cheek and mouth sites showed a positive correlation (R² value > 0.93) with the entire face, while the forehead sites were negatively correlated (R² value < 0.2). Given the relative abundance based on statistical correlation analysis, we estimated that the cheek site could be considered an optimal topical site to replace the entire face.

CONCLUSION

Our study suggests that skin microbiome profiling of four facial sites confirms that the cheek shows the most similar skin flora with the entire face. This study would be informative for preventing bias caused by sampling methods before researching and understanding skin cosmetics development or skin diseases.

AB0248 INFLUENZA ADVERSE EVENTS IN PATIENTS WITH RHEUMATOID ARTHRITIS IN THE TOFACITINIB CLINICAL PROGRAMME

Background:

Patients (pts) with rheumatoid arthritis (RA) have an increased susceptibility to seasonal influenza and its complications.1 In light of the COVID-19 pandemic, there is a need to better understand acute respiratory viral RNA infections, such as influenza, in pts with RA.

Objectives:

To present a comprehensive summary of data on influenza adverse events (AEs) occurring in the tofacitinib RA clinical programme.

Methods:

Influenza AEs were evaluated in pts with RA from 21 Phase (P)1–3b/4 trials and two open-label, long-term extension (LTE) studies from 2005–2019. These were analysed as two cohorts: P2–3b/4 cohort (pts who received tofacitinib 5 or 10 mg twice daily [BID] as monotherapy or with conventional synthetic [cs]DMARDs, adalimumab, methotrexate or placebo, in P2–3b/4 controlled studies) and Overall cohort (pts who received ≥1 tofacitinib dose, as monotherapy or with csDMARDs, in P1–3b/4 and LTE studies; data were summarised by average tofacitinib dose [average tofacitinib 5 or 10 mg BID based on average total daily dose of <15 or ≥15 mg, respectively]). Incidence rates (IRs; unique pts with events/100 pt-years of exposure; censored at day of first event or up to last dose +28 days) were evaluated for influenza AEs, influenza complication AEs, influenza-like illness (all composites of several MedDRA preferred/verbatim terms) and overall influenza AEs (composite of all preferred/verbatim terms included under influenza AEs, influenza complication AEs and influenza-like illness). In the Overall cohort, the incidence of serious non-influenza AEs within 28 days of the start of an overall influenza AE and time taken to resolution of overall influenza AEs by action taken were summarised descriptively.

Results:

In total, 7964 pts were included; 517 (6.5%) pts reported overall influenza AEs, three of which occurred outside the risk period. In the P2–3b/4 cohort (N=6690), IRs for influenza AEs, influenza-like illness and overall influenza AEs generally appeared similar across treatment arms (Figure 1a). In the Overall cohort, IRs for influenza AEs and influenza-like illness were similar between tofacitinib doses (Figure 1b), and IRs for overall influenza AEs were similar between tofacitinib doses and pt age groups (Figure 1c). No influenza complication AEs (eg pneumonia/encephalitis influenzal) were reported in either cohort. Among pts with overall influenza AEs, nine (1.7%) had serious overall influenza AEs (average tofacitinib 5 mg BID, n=6; average tofacitinib 10 mg BID, n=3). Of these pts, eight (1.5%) were hospitalised (average tofacitinib 5 mg BID, n=6; average tofacitinib 10 mg BID, n=2) and two (0.4%) died (average tofacitinib 5 mg BID, n=1; average tofacitinib 10 mg BID, n=1). Both deaths occurred in pts with H1N1 Influenza A. Twelve (2.3%) pts had a serious non-influenza AE within 28 days of the start of the overall influenza AE (average tofacitinib 5 mg BID, n=6; average tofacitinib 10 mg BID, n=6). The most common serious non-influenza AEs (one event each in average tofacitinib 5 and 10 mg BID groups) were acute respiratory distress syndrome and pneumonia. In most pts with overall influenza AEs, no change to tofacitinib treatment was made (70.2%, n=363) or treatment was stopped temporarily (28.2%, n=146) for a mean duration of 11.0 days. The mean number of days to resolution of overall influenza AEs was numerically similar, ranging from 10.4–11.8 days across tofacitinib doses, irrespective of these actions.

Conclusion:

This post hoc analysis of influenza AEs across the tofacitinib RA clinical programme, over 14–15 influenza seasons, showed generally similar rates between treatment groups, and between tofacitinib doses and pt age groups. Limitations include varying exposure across treatment arms in the P2–3b/4 cohort. Most influenza AEs were non-serious (98.3%), and were not associated with changes to tofacitinib treatment.

References:

[1]Blumentals et al. BMC Musculoskelet Disord 2012; 13: 158.

Acknowledgements:

Study sponsored by Pfizer Inc. Medical writing support was provided by Kirsten Woollcott, CMC Connect, and funded by Pfizer Inc.

Disclosure of Interests:

Kevin Winthrop Grant/research support from: AbbVie, Bristol-Myers Squibb, Eli Lilly, Galapagos, Gilead Sciences, Pfizer Inc, Roche, UCB, Arne Yndestad Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Dan Henrohn Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Hyejin Jo Consultant of: Pfizer Inc, Employee of: Syneos Health, Sara Marsal Shareholder of: IMIDomics, Consultant of: AbbVie, Celgene, Galapagos, Gilead Sciences, Pfizer Inc, Sandoz, Sanofi, Grant/research support from: AbbVie, Bristol-Myers Squibb, Celgene, Jansen-Cilag, MSD, Novartis, Pfizer Inc, Roche, Sandoz, Sanofi, UCB, María Galindo-Izquierdo Grant/research support from: AbbVie, Eli Lilly, GSK, Janssen-Cilag, Annette Diehl Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Andrea Shapiro Shareholder of: Pfizer Inc, Employee of: Pfizer Inc, Stanley B. Cohen Consultant of: AbbVie, Eli Lilly, Genentech, Gilead Sciences, Pfizer Inc, Grant/research support from: AbbVie, Eli Lilly, Genentech, Gilead Sciences, Pfizer Inc

Effect of a bioconverted product of Lotus corniculatus seed on the axillary microbiome and body odor

The skin microbiome, especially the axillary microbiome, consists of odor-causing bacteria that decompose odorless sweat into malodor compounds, which contributes to the formation of body odor. Plant-derived products are a cheap source of bioactive compounds that are common ingredients in cosmetics. Microbial bioconversion of natural products is an ecofriendly and economical method for production of new or improved biologically active compounds. Therefore, in this study, we tested the potential of a Lactobacillus acidophilus KNU-02-mediated bioconverted product (BLC) of Lotus corniculatus seed to reduce axillary malodor and its effect on the associated axillary microbiota. A chemical profile analysis revealed that benzoic acid was the most abundant chemical compound in BLC, which increased following bioconversion. Moreover, BLC treatment was found to reduce the intensity of axillary malodor. We tested the axillary microbiome of 18 study participants, divided equally into BLC and placebo groups, and revealed through 16S rRNA gene sequencing that Staphylococcus, Corynebacterium, and Anaerococcus were the dominant taxa, and some of these taxa were significantly associated with axillary malodor. After one week of BLC treatment, the abundance of Corynebacterium and Anaerococcus, which are associated with well-known odor-related genes that produce volatile fatty acids, had significantly reduced. Likewise, the identified odor-related genes decreased after the application of BLC. BLC treatment enhanced the richness and network density of the axillary microbial community. The placebo group, on the other hand, showed no difference in the microbial richness, odor associated taxa, and predicted functional genes after a week. The results demonstrated that BLC has the potential to reduce the axillary malodor and the associated odor-causing bacteria, which makes BLC a viable deodorant material in cosmetic products.

Extracellular ATP Induces Calcium Signaling in Odontoblasts

Odontoblasts form dentin at the outermost surface of tooth pulp. An increasing level of evidence in recent years, along with their locational advantage, implicates odontoblasts as a secondary role as sensory or immune cells. Extracellular adenosine triphosphate (ATP) is a well-characterized signaling molecule in the neuronal and immune systems, and its potential involvement in interodontoblast communications was recently demonstrated. In an effort to elaborate the ATP-mediated signaling pathway in odontoblasts, the current study performed single-cell reverse transcription polymerase chain reaction (RT-PCR) and immunofluorescent detection to investigate the expression of ATP receptors related to calcium signal in odontoblasts from incisal teeth of 8- to 10-wk-old rats, and demonstrated an in vitro response to ATP application via calcium imaging experiments. While whole tissue RT-PCR analysis detected P2Y₂, P2Y₄, and all 7 subtypes (P2X₁ to P2X₇) in tooth pulp, single-cell RT-PCR analysis of acutely isolated rat odontoblasts revealed P2Y₂, P2Y₄, P2X₂, P2X₄, P2X₆, and P2X₇ expression in only a subset (23% to 47%) of cells tested, with no evidence for P2X₁, P2X₃, and P2X₅ expression. An increase of intracellular Ca²⁺ concentration in response to 100μM ATP, which was repeated after pretreatment of thapsigargin or under the Ca²⁺-free condition, suggested function of both ionotropic and metabotropic ATP receptors in odontoblasts. The enhancement of ATP-induced calcium response by ivermectin and inhibition by 5-(3-bromophenyl)-1,3-dihydro-2H-benzofuro[3,2-e]-1,4-diazepin-2-one (5-BDBD) confirmed a functional P2X₄ subtype in odontoblasts. Positive calcium response to 2',3'-O-(benzoyl-4-benzoyl)-ATP (BzATP) and negative response to α,β-methylene ATP suggested P2X₂, P2X₄, and P2X₇ as functional subunits in rat odontoblasts. Single-cell RT-PCR analysis of the cells with confirmed calcium response and immunofluorescent detection further corroborated the expression of P2X₄ and P2X₇ in odontoblasts. Overall, this study demonstrated heterogeneous expression of calcium-related ATP receptor subtypes in subsets of individual odontoblasts, suggesting extracellular ATP as a potential signal mediator for odontoblastic functions.

Multi-threading the generation of Burrows-Wheeler Alignment

Along with recent progress in next-generation sequencing technology, it has become easier to process larger amounts of genome sequencing data at a lower cost. The most time-consuming step of next-generation sequencing data analysis involves the mapping of read data into a reference genome. Although the Burrows-Wheeler Alignment (BWA) tool is one of the most widely used open-source software tools for aligning read sequences, it still has a limitation in that it does not fully support a multi-thread mechanism during the alignment generation step. In this article, we propose a BWA-MT tool based on BWA that supports multi-thread mechanisms for processing alignment generation. To evaluate BWA-MT, we used an evaluation system equipped with 24 cores and 128 GB of memory. As workloads, we used the hg19 human genome reference sequence and sequences of various read sizes from the 1 to 40 M spots. In our evaluation, BWA-MT showed a maximum of 3.66-times better performance, and generated the same Sequence Alignment/Map result file as that of BWA. Although the ability to speed up the procedure might be dependent on computing resources, we confirmed that BWA-MT is a highly effective and fast alignment tool.

Inorganic phosphate induces mammalian growth plate chondrocyte apoptosis in a mitochondrial pathway involving nitric oxide and JNK MAP kinase

Chondrocytes in the hypertrophic zone of the growth plate undergo apoptosis during endochondral bone development via mechanisms that involve inorganic phosphate (Pi) and nitric oxide (NO). Recent evidence suggests that Pi-dependent NO production plays a role in apoptosis of cells in the resting zone as well. This study examined the mechanism by which Pi induces NO production and the signaling pathways by which NO mediates its effects on apoptosis in these cells. Pi decreased the number of viable cells based on MTT activity; the number of TUNEL-positive cells and the level of DNA fragmentation were increased, indicating an increase in apoptosis. Blocking NO production using the NO synthase (NOS) inhibitor L: -NAME or cells from eNOS(-/-) mice blocked Pi-induced chondrocyte apoptosis, indicating that NO production is necessary. NO donors NOC-18 and SNOG both induced chondrocyte apoptosis. SNOG also upregulated p53 expression, the Bax/Bcl-2 expression ratio, and cytochrome c release from mitochondria, as well as caspase-3 activity, indicating that NO induces apoptosis via a mitochondrial pathway. Inhibition of JNK, but not of p38 or ERK1/2, MAP kinase was able to block NO-induced apoptosis, indicating that JNK is necessary in this pathway. Pi elevates NO production via eNOS in resting zone chondrocytes, which leads to a mitochondrial apoptosis pathway dependent on JNK.

Molecular characterization of the human ABO blood group orthologus system in pigs

The selection and use of animals with blood group 0 in the process of transplanting pig organs or tissues into humans can positively contribute to the control of acute immune rejection due to differences in blood groups. Exon-specific PCRs for the porcine blood group A transferase gene against genomic DNA from either blood group A or 0 animals resulted in the amplification failure of the A0 blood group gene exon 8 from blood group 0 animals. To characterize the genetic abnormality in the genome of blood group 0 animals, we screened bacterial artificial chromosome (BAC) clones from a Korean native pig BAC library which had the blood group 0 allele, and carried out shotgun sequencing. The analysis showed that the 0 allele has a large deletion between exon 7 of the A0 blood group gene and the neighbouring SURF6. We also showed that the ABO blood group antigens in humans and the A0 blood group antigens in pigs are coded by mutations within the orthologous glycosyltransferase gene. In addition, we developed a multiplex genotyping method for the porcine A0 blood group gene.

Assessment of referral patterns for CT KUB in a tertiary setting

The purpose of this study was to assess the referral patterns and the use of unenhanced renal tract CT (CT KUB) for investigating patients presenting with clinically suspected renal colic. We retrospectively reviewed 500 consecutive CT KUB studies requested for suspected renal colic carried out at a single institution between December 2006 and July 2007. Follow-up radiology reports and discharge summaries on the hospital clinical Intranet were also reviewed. Studies were analysed for characteristics including patient demographics, referring clinical team, time of referral, final diagnosis and requirement for further imaging. The majority of requests were from Emergency (ED) or Urology Departments (49%, 245 out of 500, and 37%, 186 out of 500, respectively). The positive rate for urolithiasis was 67% (337 out of 500), the negative rate was 25% (123 out of 500), and 8% (40 out of 500) of patients had alternative significant findings. Female patients were more likely to have a negative study than male patients (35 versus 20%, P < 0.0001) and more likely to have alternative significant pathology (12 versus 6%, P < 0.0001). Patients referred by specialities other than Urology and ED were more likely to be female and have a negative or alternative finding (P < 0.0001). CT KUB is a widely used first method of investigation for patients with suspected renal colic with a high positive predictive value allowing rapid diagnosis and intervention. However, given the high rate of negative or alternative findings on CT KUB in young women, especially those referred by specialities other than ED or Urology, ultrasound should be considered as an alternative imaging method to minimise unnecessary radiation exposure.

The in vitro effects of dehydroepiandrosterone on human osteoarthritic chondrocytes

OBJECTIVE

To investigate the in vitro effects of dehydroepiandrosterone (DHEA) on human osteoarthritic chondrocytes.

DESIGN

Chondrocytes isolated from human osteoarthritic knee cartilage were three-dimensionally cultured in alginate beads, except for cell proliferation experiment. Cells were treated with DHEA in the presence or absence of IL-1beta. The effects on chondrocytes were analyzed using a 3-(4,5-dimethylthiazol-2yl)-5-(3-carboxymethoxy-phenyl)-2-(4-sulfophenyl)-2H-tetrazolium inner salt (MTS) assay (for chondrocyte proliferation), a dimethylmethylene blue (DMB) assay (for glycosaminoglycan (GAG) synthesis), and an indole assay (for DNA amount). Gene expressions of type I and II collagen, metalloproteinase-1 and -3 (MMP-1 and -3), and tissue inhibitor of metalloproteinase-1 (TIMP-1) as well as the IL-1beta-induced gene expressions of MMP-1 and -3 were analyzed by reverse transcription-polymerase chain reaction (RT-PCR). The protein synthesis of MMP-1 and -3 and TIMP-1 was determined by Western blotting.

RESULTS

The treatment of chondrocytes with DHEA did not affect chondrocyte proliferation or GAG synthesis up to 100 micro M of concentration. The gene expression of type II collagen increased in a dose-dependent manner, while that of type I decreased. DHEA suppressed the expression of MMP-1 significantly at concentrations exceeding 50 micro M. The gene expression of MMP-3 was also suppressed, but this was without statistical significance. The expression of TIMP-1 was significantly increased by DHEA at concentrations exceeding 10 micro M. The effects of DHEA on the gene expressions of MMP-1 and -3 were more prominent in the presence of IL-1beta, in which DHEA suppressed not only MMP-1, but also MMP-3 at the lower concentrations, 10 and 50 micro M, respectively. Western blotting results were in agreement with RT-PCR, which indicates that DHEA acts at the gene transcription level.

CONCLUSIONS

Our study demonstrates that DHEA has no toxic effect on chondrocytes up to 100 micro M of concentration and has an ability to modulate the imbalance between MMPs and TIMP-1 during OA at the transcription level, which suggest that it has a protective role against articular cartilage loss.

Endothelial NOS-dependent activation of c-Jun NH(2)- terminal kinase by oxidized low-density lipoprotein

Oxidized low-density lipoprotein (oxLDL) is known to activate a number of signal transduction pathways in endothelial cells. Among these are the c-Jun NH(2)-terminal kinase (JNK), also known as stress-activated protein kinase, and extracellular signal-regulated kinase (ERK). These mitogen-activated protein kinases (MAP kinase) determine cell survival in response to environmental stress. Interestingly, JNK signaling involves redox-sensitive mechanisms and is activated by reactive oxygen and nitrogen species derived from both NADPH oxidases, nitric oxide synthases (NOS), peroxides, and oxidized low-density lipoprotein (oxLDL). The role of endothelial NOS (eNOS) in the activation of JNK in response to oxLDL has not been examined. Herein, we show that on exposure of endothelial cells to oxLDL, both ERK and JNK are activated through independent signal transduction pathways. A key role of eNOS activation through a phosphatidylinositol-3-kinase-dependent mechanism leading to phosphorylation of eNOS is demonstrated for oxLDL-dependent activation of JNK. Moreover, we show that activation of ERK by oxLDL is critical in protection against the cytotoxicity of oxLDL.

Protein kinase B/Akt activates c-Jun NH(2)-terminal kinase by increasing NO production in response to shear stress

Laminar shear stress activates c-Jun NH(2)-terminal kinase (JNK) by the mechanisms involving both nitric oxide (NO) and phosphatidylinositide 3-kinase (PI3K). Because protein kinase B (Akt), a downstream effector of PI3K, has been shown to phosphorylate and activate endothelial NO synthase, we hypothesized that Akt regulates shear-dependent activation of JNK by stimulating NO production. Here, we examined the role of Akt in shear-dependent NO production and JNK activation by expressing a dominant negative Akt mutant (Akt(AA)) and a constitutively active mutant (Akt(Myr)) in bovine aortic endothelial cells (BAEC). As expected, pretreatment of BAEC with the PI3K inhibitor (wortmannin) prevented shear-dependent stimulation of Akt and NO production. Transient expression of Akt(AA) in BAEC by using a recombinant adenoviral construct inhibited the shear-dependent stimulation of NO production and JNK activation. However, transient expression of Akt(Myr) by using a recombinant adenoviral construct did not induce JNK activation. This is consistent with our previous finding that NO is required, but not sufficient on its own, to activate JNK in response to shear stress. These results and our previous findings strongly suggest that shear stress triggers activation of PI3K, Akt, and endothelial NO synthase, leading to production of NO, which (along with O(2-), which is also produced by shear) activates Ras-JNK pathway. The regulation of Akt, NO, and JNK by shear stress is likely to play a critical role in its antiatherogenic effects.

Development of virtual environment for treating acrophobia

Virtual Reality (VR) is a new technology that makes humans communicate with computer. It allows the user to see, hear, feel and interact in a three-dimensional virtual world created graphically. Virtual Reality Therapy (VRT), based on this sophisticated technology, has been recently used in the treatment of subjects diagnosed with acrophobia, a disorder that is characterized by marked anxiety upon exposure to heights, avoidance of heights, and a resulting interference in functioning. Conventional virtual reality system for the treatment of acrophobia has a limitation in scope that it is based on over-costly devices or somewhat unrealistic graphic scene. The goal of this study was to develop a inexpensive and more realistic virtual environment for the exposure therapy of acrophobia. We constructed two types virtual environment. One is constituted a bungee-jump tower in the middle of a city. It includes the open lift surrounded by props beside tower that allowed the patient to feel sense of heights. Another is composed of diving boards which have various heights. It provides a view of a lower diving board and people swimming in the pool to serve the patient stimuli upon exposure to heights.

Differential display analysis of gene expression altered by ras oncogene

The goal of the signal transduction pathways, such as those controlled by Ras, is in large part to ensure highly stringent regulation of the target genes in the nucleus, which are collectively responsible for the signal output, or phenotypes, of the cell. Understanding of the Ras effect ultimately requires the identification of these downstream target genes. Reverse genetic approaches would trace back the pathways by which they are regulated by Ras. While newer methods such as DNA microarray are emerging, differential display has allowed the identification of a greater number of differentially expressed genes than have been cloned by all the other methods combined, based on Medline search. Much of this success has been attributed to its simplicity (RT-PCR and DNA-sequencing gel) and versatility (compare more than two RNAs for both up- and downregulated genes). It has become obvious that finding the genes by either differential display or DNA microarray is only the first step toward the understanding of biological problems under investigation. It is hoped that finding the right genes through careful experimental designs, such as outlined here, will narrow down the number of relevant genes and increase the odds for solving the puzzles of nature, such as ras.

Fas-induced expression of chemokines in human glioma cells: involvement of extracellular signal-regulated kinase 1/2 and p38 mitogen-activated protein kinase

Fas transduces not only apoptotic signals through various pathways but also angiogenic and proinflammatory responses in vivo. Human glioma cells express Fas although sensitivity to Fas-mediated cell death is variable, suggesting that Fas may have functions other than apoptosis in these cells. In this study, we addressed alternative functions of Fas expressed on human gliomas by Fas ligation in three human glioma cell lines, CRT-MG, U373-MG, and U87-MG, and the in vivo expression of Fas and chemokines in human glioblastoma multiforme (GBM). Herein, we demonstrate that: (a) stimulation with agonistic anti-Fas monoclonal antibody CH-11 and human recombinant soluble Fas ligand induces expression of the CC chemokine MCP-1 and the CXC chemokine interleukin-8 by human glioma cell lines at the mRNA and protein levels in a dose- and time-dependent manner; (b) selective pharmacological inhibitors of MEK1 (U0126 and PD98059) and p38 mitogen-activated protein kinase (MAPK) (SB202190) suppress Fas-mediated chemokine expression in a dose-dependent manner; (c) Fas ligation on human glioma cells leads to activation of both extracellular signal-regulated kinases ERK1/ERK2 and p38 MAPK; and (d) GBM samples express higher levels of Fas compared with normal control brain, which correlates with increased interleukin 8 expression. These findings indicate that Fas ligation on human glioma cells leads to the selective induction of chemokine expression, which involves the ERK1/ERK2 and p38 MAPK signaling pathways. Therefore, the Fas-Fas ligand system in human brain tumors may be involved not only in apoptotic processes but also in the provocation of angiogenic and proinflammatory responses.

Mechanisms of cell signaling by nitric oxide and peroxynitrite: from mitochondria to MAP kinases

Many of the biological and pathological effects of nitric oxide (NO) are mediated through cell signaling pathways that are initiated by NO reacting with metalloproteins. More recently, it has been recognized that the reaction of NO with free radicals such as superoxide and the lipid peroxyl radical also has the potential to modulate redox signaling. Although it is clear that NO can exert both cytotoxic and cytoprotective actions, the focus of this overview are those reactions that could lead to protection of the cell against oxidative stress in the vasculature. This will include the induction of antioxidant defenses such as glutathione, activation of mitogen-activated protein kinases in response to blood flow, and modulation of mitochondrial function and its impact on apoptosis. Models are presented that show the increased synthesis of glutathione in response to shear stress and inhibition of cytochrome c release from mitochondria. It appears that in the vasculature NO-dependent signaling pathways are of three types: (i) those involving NO itself, leading to modulation of mitochondrial respiration and soluble guanylate cyclase; (ii) those that involve S-nitrosation, including inhibition of caspases; and (iii) autocrine signaling that involves the intracellular formation of peroxynitrite and the activation of the mitogen-activated protein kinases. Taken together, NO plays a major role in the modulation of redox cell signaling through a number of distinct pathways in a cellular setting.

Cell signaling by reactive nitrogen and oxygen species in atherosclerosis

The production of reactive oxygen and nitrogen species has been implicated in atherosclerosis principally as means of damaging low-density lipoprotein that in turn initiates the accumulation of cholesterol in macrophages. The diversity of novel oxidative modifications to lipids and proteins recently identified in atherosclerotic lesions has revealed surprising complexity in the mechanisms of oxidative damage and their potential role in atherosclerosis. Oxidative or nitrosative stress does not completely consume intracellular antioxidants leading to cell death as previously thought. Rather, oxidative and nitrosative stress have a more subtle impact on the atherogenic process by modulating intracellular signaling pathways in vascular tissues to affect inflammatory cell adhesion, migration, proliferation, and differentiation. Furthermore, cellular responses can affect the production of nitric oxide, which in turn can strongly influence the nature of oxidative modifications occurring in atherosclerosis. The dynamic interactions between endogenous low concentrations of oxidants or reactive nitrogen species with intracellular signaling pathways may have a general role in processes affecting wound healing to apoptosis, which can provide novel insights into the pathogenesis of atherosclerosis.

Caveolin-1 regulates shear stress-dependent activation of extracellular signal-regulated kinase

Fluid shear stress activates a member of the mitogen-activated protein (MAP) kinase family, extracellular signal-regulated kinase (ERK), by mechanisms dependent on cholesterol in the plasma membrane in bovine aortic endothelial cells (BAEC). Caveolae are microdomains of the plasma membrane that are enriched with cholesterol, caveolin, and signaling molecules. We hypothesized that caveolin-1 regulates shear activation of ERK. Because caveolin-1 is not exposed to the outside, cells were minimally permeabilized by Triton X-100 (0.01%) to deliver a neutralizing, polyclonal caveolin-1 antibody (pCav-1) inside the cells. pCav-1 then bound to caveolin-1 and inhibited shear activation of ERK but not c-Jun NH(2)-terminal kinase. Epitope mapping studies showed that pCav-1 binds to caveolin-1 at two regions (residues 1-21 and 61-101). When the recombinant proteins containing the epitopes fused to glutathione-S-transferase (GST-Cav(1-21) or GST-Cav(61-101)) were preincubated with pCav-1, only GST-Cav(61-101) reversed the inhibitory effect of the antibody on shear activation of ERK. Other antibodies, including m2234, which binds to caveolin-1 residues 1-21, had no effect on shear activation of ERK. Caveolin-1 residues 61-101 contain the scaffolding and oligomerization domains, suggesting that binding of pCav-1 to these regions likely disrupts the clustering of caveolin-1 or its interaction with signaling molecules involved in the shear-sensitive ERK pathway. We suggest that caveolae-like domains play a critical role in the mechanosensing and/or mechanosignal transduction of the ERK pathway.

NF-kappa B is required for H-ras oncogene induced abnormal cell proliferation and tumorigenesis

Oncogenic mutations in ras lead to constitutive activation of downstream signaling pathways that modulate the activities of transcription factors. In turn, these factors control the expression of a subset of genes responsible for neoplastic cell transformation. Recent studies suggest that transcription factor NF-kappa B contributes to cell transformation by inhibiting the cell death signal activated by oncogenic Ras. In this study, inhibition of NF-kappa B activity by forced expression of a super-repressor form of I kappa B alpha, the major inhibitor of NF-kappa B, markedly decreased the growth rate, saturation density and tumorigenicity of oncogenic H-Ras transformed rat embryo fibroblasts. Such clonally isolated cells overexpressing I kappa B alpha super-repressor not only were viable but also exhibited no sign of spontaneous apoptosis. Inhibition of NF-kappa B in these cells was functionally demonstrated by both the loss of cytokine induced DNA binding activity and a profoundly increased sensitivity to cell death in response to TNF-alpha treatment. In contrast, inhibition of NF-kappa B activity in non-transformed fibroblasts had minimal effect on growth, but rendered the cells resistant to a subsequent transformation by H-ras oncogene. Similar results were also obtained with rat intestinal epithelial cells harboring an inducible ras oncogene. Taken together, these findings suggest that NF-kappa B activity is essential for abnormal cell proliferation and tumorigenicity activated by the ras oncogene and highlight an alternative functional role for NF-kappa B in oncogenic Ras-mediated cell transformation that is distinct from its anti-apoptotic activity. Oncogene (2000) 19, 841 - 849.

Activation of mitogen-activated protein kinase pathways by cyclic GMP and cyclic GMP-dependent protein kinase in contractile vascular smooth muscle cells

Vascular smooth muscle cells (VSMC) exist in either a contractile or a synthetic phenotype in vitro and in vivo. The molecular mechanisms regulating phenotypic modulation are unknown. Previous studies have suggested that the serine/threonine protein kinase mediator of nitric oxide (NO) and cyclic GMP (cGMP) signaling, the cGMP-dependent protein kinase (PKG) promotes modulation to the contractile phenotype in cultured rat aortic smooth muscle cells (RASMC). Because of the potential importance of the mitogen-activated protein kinase (MAP kinase) pathways in VSMC proliferation and phenotypic modulation, the effects of PKG expression in PKG-deficient and PKG-expressing adult RASMC on MAP kinases were examined. In PKG-expressing adult RASMC, 8-para-chlorophenylthio-cGMP activated extracellular signal- regulated kinases (ERK1/2) and c-Jun N-terminal kinase (JNK). The major effect of PKG activation was increased activation by MAP kinase kinase (MEK). The cAMP analog, 8-Br-cAMP inhibited ERK1/2 activation in PKG-deficient and PKG-expressing RASMC but had no effect on JNK activity. The effects of PKG on ERK and JNK activity were additive with those of platelet-derived growth factor (PDGF), suggesting that PKG activates MEK through a pathway not used by PDGF. The stimulatory effects of cGMP on ERK and JNK activation were also observed in low-passaged, contractile RASMC still expressing endogenous PKG, suggesting that the effects of PKG expression were not artifacts of cell transfections. These results suggest that in contractile adult RASMC, NO-cGMP signaling increases MAP kinase activity. Increased activation of these MAP kinase pathways may be one mechanism by which cGMP and PKG activation mediate c-fos induction and increased proliferation of contractile adult RASMC.

Evidence for peroxynitrite as a signaling molecule in flow-dependent activation of c-Jun NH(2)-terminal kinase

The c-Jun NH(2)-terminal kinase (JNK), also known as stress-activated protein kinase, is a mitogen-activated protein kinase that determines cell survival in response to environmental stress. Activation of JNK involves redox-sensitive mechanisms and physiological stimuli such as shear stress, the dragging force generated by blood flow over the endothelium. Laminar shear stress has antiatherogenic properties and controls structure and function of endothelial cells by mechanisms including production of nitric oxide (NO) and superoxide (O(-)(2)). Here we show that both NO and O(-)(2) are required for activation of JNK by shear stress in endothelial cells. The present study also demonstrates that exposure of endothelial cells to shear stress increases tyrosine nitration, a marker of reactive nitrogen species formation. Furthermore, inhibitors or scavengers of NO, O(-)(2), or reactive nitrogen species prevented shear-dependent increase in tyrosine nitration and activation of JNK. Peroxynitrite alone, added to cells as a bolus or generated over 60 min by 3-morpholinosydnonimine, also activates JNK. These results suggest that reactive nitrogen species, in this case most likely peroxynitrite, act as signaling molecules in the mechanoactivation of JNK.