Bioactive lipid lysophosphatidic acid species are associated with disease progression in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive disease with significant mortality. Prognostic biomarkers to identify rapid progressors are urgently needed to improve patient management. Since the lysophosphatidic acid (LPA) pathway has been implicated in lung fibrosis in preclinical models and identified as a potential therapeutic target, we aimed to investigate if bioactive lipid LPA species could be prognostic biomarkers that predict IPF disease progression. LPAs and lipidomics were measured in baseline placebo plasma of a randomized IPF-controlled trial. The association of lipids with disease progression indices were assessed using statistical models. Compared to healthy, IPF patients had significantly higher levels of five LPAs (LPA16:0, 16:1, 18:1, 18:2, 20:4) and reduced levels of two triglycerides species (TAG48:4-FA12:0, -FA18:2) (false discovery rate < 0.05, fold change > 2). Patients with higher levels of LPAs had greater declines in diffusion capacity of carbon monoxide over 52 weeks (P < 0.01); additionally, LPA20:4-high (≥median) patients had earlier time to exacerbation compared to LPA20:4-low ( Collapse

Key Words

• DLCO
• Lysophosphatidic acid
• exacerbation
• idiopathic pulmonary fibrosis
• mortality

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MESH Headings

• Humans
• Idiopathic Pulmonary Fibrosis/metabolism
• Disease Progression
• Lysophospholipids
• Biomarkers

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Grants Collapse

Affiliation(s)

Margaret Neighbors OMNI Translational Medicine, Genentech Inc., South San Francisco, USA
Qingling Li Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, USA
Sha Joe Zhu PD Data Science, F Hoffmann-La Roche, Shanghai, China
Jia Liu PD Data Science, F Hoffmann-La Roche, Shanghai, China
Weng Ruh Wong Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, USA
Guiquan Jia Department of Biomarker Discovery OMNI, Genentech Inc., South San Francisco, USA
Wendy Sandoval Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, USA
Gaik W Tew I2O Technology and Translational Research, Genentech Inc., South San Francisco, USA.

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LOXL4, but not LOXL2, is the critical determinant of pathological collagen cross-linking and fibrosis in the lung

Idiopathic pulmonary fibrosis is a progressive fibrotic disease characterized by excessive deposition of (myo)fibroblast produced collagen fibrils in alveolar areas of the lung. Lysyl oxidases (LOXs) have been proposed to be the central enzymes that catalyze the cross-linking of collagen fibers. Here, we report that, while its expression is increased in fibrotic lungs, genetic ablation of LOXL2 only leads to a modest reduction of pathological collagen cross-linking but not fibrosis in the lung. On the other hand, loss of another LOX family member, LOXL4, markedly disrupts pathological collagen cross-linking and fibrosis in the lung. Furthermore, knockout of both Loxl2 and Loxl4 does not offer any additive antifibrotic effects when compared to Loxl4 deletion only, as LOXL4 deficiency decreases the expression of other LOX family members including Loxl2. On the basis of these results, we propose that LOXL4 is the main LOX activity underlying pathological collagen cross-linking and lung fibrosis.

Stress-induced vesicular assemblies of dual leucine zipper kinase are signaling hubs involved in kinase activation and neurodegeneration

Mitogen-activated protein kinases (MAPKs) drive key signaling cascades during neuronal survival and degeneration. The localization of kinases to specific subcellular compartments is a critical mechanism to locally control signaling activity and specificity upon stimulation. However, how MAPK signaling components tightly control their localization remains largely unknown. Here, we systematically analyzed the phosphorylation and membrane localization of all MAPKs expressed in dorsal root ganglia (DRG) neurons, under control and stress conditions. We found that MAP3K12/dual leucine zipper kinase (DLK) becomes phosphorylated and palmitoylated, and it is recruited to sphingomyelin-rich vesicles upon stress. Stress-induced DLK vesicle recruitment is essential for kinase activation; blocking DLK-membrane interaction inhibits downstream signaling, while DLK recruitment to ectopic subcellular structures is sufficient to induce kinase activation. We show that the localization of DLK to newly formed vesicles is essential for local signaling. Inhibition of membrane internalization blocks DLK activation and protects against neurodegeneration in DRG neurons. These data establish vesicular assemblies as dynamically regulated platforms for DLK signaling during neuronal stress responses.

NP Analyst: An Open Online Platform for Compound Activity Mapping

Few tools exist in natural products discovery to integrate biological screening and untargeted mass spectrometry data at the library scale. Previously, we reported Compound Activity Mapping as a strategy for predicting compound bioactivity profiles directly from primary screening results on extract libraries. We now present NP Analyst, an open online platform for Compound Activity Mapping that accepts bioassay data of almost any type, and is compatible with mass spectrometry data from major instrument manufacturers via the mzML format. In addition, NP Analyst will accept processed mass spectrometry data from the MZmine 2 and GNPS open-source platforms, making it a versatile tool for integration with existing discovery workflows. We demonstrate the utility of this new tool for both the dereplication of known compounds and the discovery of novel bioactive natural products using a challenging low-resolution antimicrobial bioassay data set. This new platform is available at www.npanalyst.org.

Sloth hair as a novel source of fungi with potent anti-parasitic, anti-cancer and anti-bacterial bioactivity

The extraordinary biological diversity of tropical forests harbors a rich chemical diversity with enormous potential as a source of novel bioactive compounds. Of particular interest are new environments for microbial discovery. Sloths – arboreal mammals commonly found in the lowland forests of Panama – carry a wide variety of micro- and macro-organisms on their coarse outer hair. Here we report for the first time the isolation of diverse and bioactive strains of fungi from sloth hair, and their taxonomic placement. Eighty-four isolates of fungi were obtained in culture from the surface of hair that was collected from living three-toed sloths (Bradypus variegatus, Bradypodidae) in Soberanía National Park, Republic of Panama. Phylogenetic analyses revealed a diverse group of Ascomycota belonging to 28 distinct operational taxonomic units (OTUs), several of which are divergent from previously known taxa. Seventy-four isolates were cultivated in liquid broth and crude extracts were tested for bioactivity in vitro. We found a broad range of activities against strains of the parasites that cause malaria (Plasmodium falciparum) and Chagas disease (Trypanosoma cruzi), and against the human breast cancer cell line MCF-7. Fifty fungal extracts were tested for antibacterial activity in a new antibiotic profile screen called BioMAP; of these, 20 were active against at least one bacterial strain, and one had an unusual pattern of bioactivity against Gram-negative bacteria that suggests a potentially new mode of action. Together our results reveal the importance of exploring novel environments for bioactive fungi, and demonstrate for the first time the taxonomic composition and bioactivity of fungi from sloth hair.

MS/MS-based networking and peptidogenomics guided genome mining revealed the stenothricin gene cluster in Streptomyces roseosporus

Most (75%) of the anti-infectives that save countless lives and enormously improve quality of life originate from microbes found in nature. Herein, we described a global visualization of the detectable molecules produced from a single microorganism, which we define as the 'molecular network' of that organism, followed by studies to characterize the cellular effects of antibacterial molecules. We demonstrate that Streptomyces roseosporus produces at least four non-ribosomal peptide synthetase-derived molecular families and their gene subnetworks (daptomycin, arylomycin, napsamycin and stenothricin) were identified with different modes of action. A number of previously unreported analogs involving truncation, glycosylation, hydrolysis and biosynthetic intermediates and/or shunt products were also captured and visualized by creation of a map through MS/MS networking. The diversity of antibacterial compounds produced by S. roseosporus highlights the importance of developing new approaches to characterize the molecular capacity of an organism in a more global manner. This allows one to more deeply interrogate the biosynthetic capacities of microorganisms with the goal to streamline the discovery pipeline for biotechnological applications in agriculture and medicine. This is a contribution to a special issue to honor Chris Walsh's amazing career.

Molecular networking as a dereplication strategy

A major goal in natural product discovery programs is to rapidly dereplicate known entities from complex biological extracts. We demonstrate here that molecular networking, an approach that organizes MS/MS data based on chemical similarity, is a powerful complement to traditional dereplication strategies. Successful dereplication with molecular networks requires MS/MS spectra of the natural product mixture along with MS/MS spectra of known standards, synthetic compounds, or well-characterized organisms, preferably organized into robust databases. This approach can accommodate different ionization platforms, enabling cross correlations of MS/MS data from ambient ionization, direct infusion, and LC-based methods. Molecular networking not only dereplicates known molecules from complex mixtures, it also captures related analogues, a challenge for many other dereplication strategies. To illustrate its utility as a dereplication tool, we apply mass spectrometry-based molecular networking to a diverse array of marine and terrestrial microbial samples, illustrating the dereplication of 58 molecules including analogues.

Development of quinoline-based disruptors of biofilm formation against Vibrio cholerae

Biofilm formation is a major cause of bacterial persistence in nosocomial infections, leading to extended treatment times and increased rates of morbidity and mortality. Despite this, there are currently no biofilm inhibitors approved for clinical use. The synthesis and biological evaluation of a library of amino alcohol quinolines as lead compounds for the disruption of biofilm formation in Vibrio cholerae is now reported. Application of selective metal-halogen exchange chemistry installed both stereocenters in one step, to afford a simpler scaffold than the initial lead molecule, with an EC50 < 10 μM.

Examining the fish microbiome: vertebrate-derived bacteria as an environmental niche for the discovery of unique marine natural products

Historically, marine invertebrates have been a prolific source of unique natural products, with a diverse array of biological activities. Recent studies of invertebrate-associated microbial communities are revealing microorganisms as the true producers of many of these compounds. Inspired by the human microbiome project, which has highlighted the human intestine as a unique microenvironment in terms of microbial diversity, we elected to examine the bacterial communities of fish intestines (which we have termed the fish microbiome) as a new source of microbial and biosynthetic diversity for natural products discovery. To test the hypothesis that the fish microbiome contains microorganisms with unique capacity for biosynthesizing natural products, we examined six species of fish through a combination of dissection and culture-dependent evaluation of intestinal microbial communities. Using isolation media designed to enrich for marine Actinobacteria, we have found three main clades that show taxonomic divergence from known strains, several of which are previously uncultured. Extracts from these strains exhibit a wide range of activities against both Gram-positive and Gram-negative human pathogens, as well as several fish pathogens. Exploration of one of these extracts has identified the novel bioactive lipid sebastenoic acid as an anti-microbial agent, with activity against Staphylococcus aureus, Bacillus subtilis, Enterococcus faecium, and Vibrio mimicus.

Acute paronychia heralding the exacerbation of pemphigus vulgaris

Acute paronychia, the suppurative inflammation involving the paronychium of the nails, is usually caused by bacterial or fungal infection and has been rarely reported as a presentation of pemphigus vulgaris (PV). We report a woman with PV who presented with suppurative paronychia of multiple fingernails and toenails, which preceded the exacerbation of other mucocutaneous lesions. A biopsy specimen of the paronychium revealed suprabasal vesicles due to acantholysis. Systemic corticosteroids and adjuvant immunosuppressants were effective in treating mucocutaneous lesions as well as nail disease. We conclude that in patients with PV, acute paronychia could be a manifestation of the disease per se, rather than an infectious process. Only the precise diagnosis with adequate immunosuppressive treatment can lead to good control of disease activity.

Association of pityriasis rosea with human herpesvirus-6 and human herpesvirus-7 in Taipei

BACKGROUND AND PURPOSE

Pityriasis rosea (PR) is a common papulosquamous skin disease with unknown etiology. The possible relationship of PR with human herpesvirus infection (HHV) has been extensively studied. This study used the polymerase chain reaction (PCR) to investigate the presence of human herpesvirus 6 and 7 (HHV-6 and HHV-7) in 41 PR patients from two hospitals in Northern Taiwan. The epidemiologic features of PR in patients were also studied.

METHODS

A total of 41 PR patients (11 males, 30 females) were enrolled in this study from April 1999 to March 2000. PCR of skin biopsy specimens from 24 PR patients was used to identify the existence of HHV-6 and HHV-7. Viral culture from PR biopsy specimens was also performed. Blood from these patients was sampled for Venereal Disease Research Laboratory tests. Skin biopsies from 20 age- and sex-matched controls with other skin diseases were also subjected to PCR study.

RESULTS

The ages of the 41 PR patients ranged from 8 to 62 years. An increased incidence (17/41) of PR episodes was observed during the spring. Both HHV-6 and HHV-7 DNA was below the limit of detection in all biopsy specimens from patients and healthy controls. Viral culture for HHV was negative in all patients.

CONCLUSION

The epidemiologic features of PR in this series are comparable to other studies except for an exaggerated female predominance (male:female ratio 1:2.7). Our data indicate a lack of association between HHV-6 and HHV-7 infection and PR.

Granulomatous variant of chronic pigmented purpuric dermatosis: report of two cases

Two patients presenting with chronic pigmented purpuric dermatosis (CPPD) on the dorsum of both feet were found to show granulomatous inflammation superimposed on the pathological changes of CPPD. Two similar cases have been reported from Japan. The unique clinicopathological features of this group of patients suggest that they have a rare granulomatous variant of CPPD.

Influence of cytokines on matrix metalloproteinases produced by fibroblasts cultured in monolayer and collagen gels

BACKGROUND

Extracellular matrix metalloproteinases (MMPs) are crucial factors involved in connective tissue remodeling that accompanies ultraviolet radiation-induced actinic damage. This study investigated whether the cytokines tumor necrosis factor (TNF)-alpha, interleukin (IL)-1 beta, and IL-10 modulate the expression of MMPs in cultured human newborn skin fibroblasts.

METHODS

Different concentrations of TNF-alpha, IL-1 beta, and IL-10 were added to human dermal fibroblasts grown in monolayers or embedded in three-dimensional (3D) collagen gels, a model closer to skin. Supernatant from the fibroblast cell culture was collected 24 hours later. The concentrations of MMP-1 and MMP-3 were assaysed by enzyme-linked immunosorbent assay (ELISA) while the concentrations of MMP-2 and MMP-9 were analysed by zymography.

RESULTS

Basal production of MMPs was significantly greater in fibroblasts grown in 3D gels than in cells grown as monolayers. TNF-alpha and IL-1 beta induced increases in the concentrations of MMP-1, MMP-3, and MMP-9, but not in MMP-2 or tissue inhibitor of matrix metalloproteinase (TIMP)-1 or -2. The inducibility of MMP secretion is more significant in 3D gels. IL-10 did not significantly modulate MMPs.

CONCLUSION

This study demonstrated that basal concentrations of MMPs are higher in fibroblasts cultured in 3D gels and their response to cytokines is different to that of cells grown as monolayers. Cytokines can increase the collagenolytic and gelatinolytic activity involved in extracellular matrix remodeling and hence contribute to photoaging.

Generalized granuloma annulare associated with granulomatous mycosis fungoides

We describe a 68-year-old man with plaque stage mycosis fungoides (MF) for 8 years. He developed tumorous lesions of granulomatous MF (GrMF) and generalized granuloma annulare (GA) after a previously indolent clinical course. Since then, the clinical course was aggressive with involvement of the bone marrow and lymph nodes, and leukemic change occurred. Systemic chemotherapy was given, but the patient died 9 months later due to neutropenic fever and septic shock. GA in malignant lymphoma has been reported most frequently in association with Hodgkin's disease. To the best of our knowledge, GA associated with GrMF has never been reported in the English language literature. The prognostic significance of the association of granulomatous inflammation and malignancy is reviewed.

Simultaneous occurrence of papulonecrotic tuberculide and erythema induratum and the identification of Mycobacterium tuberculosis DNA by polymerase chain reaction

The simultaneous occurrence of two tuberculides in one patient is rare. We report the case of a 32-year-old man presenting with both papulonecrotic tuberculide and erythema induratum. Mycobacterial DNA was identified from both skin lesions by polymerase chain reaction using formalin-fixed and paraffin-embedded tissues, suggesting that tuberculides are related to tuberculosis. New skin lesions developed after the patient discontinued his medication on his own initiative, 2 months after triple antituberculous therapy had been started. It is important to continue therapy for a prolonged period.