Protein Catabolic Pathways Research Articles

Efficacy and mechanism study of cordycepin against brain metastases of small cell lung cancer based on zebrafish

BackgroundSmall cell lung cancer (SCLC) is an aggressive tumor with high brain metastasis (BM) potential. There has been no significant progress in the treatment of SCLC for more than 30 years. Cordycepin has shown the therapeutic potential for cancer by modulating multiple cellular signaling pathways. However, the effect and mechanism of cordycepin on anti-SCLC BM remain unknown. PurposeIn this study, we focused on the anti-SCLC BM effect of cordycepin in the zebrafish model and its potential mechanism. Study design and methodsA SCLC xenograft model based on zebrafish embryos and in vitro cell migration assay were established. Cordycepin was administrated by soaking and microinjection in the zebrafish model. RNA-seq assay was performed to analyze transcriptomes of different groups. Geno Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were performed to reveal the underlying mechanism. Real-time qPCR was used to verify the effects of cordycepin on the key genes. ResultsCordycepin showed lower cytotoxicity in vitro compared with cisplatin, anlotinib and etoposide, but showed comparable anti-proliferation and anti-BM effects in zebrafish SCLC xenograft model. Cordycepin showed significant anti-SCLC BM effects when administrated by both soaking and microinjection. RNA-seq demonstrated that cordycepin was involved in vitamin D metabolism, lipid transport, and proteolysis in cellular protein catabolic process pathways in SCLC BM microenvironment in zebrafish, and was involved in regulating the expressions of key genes such as cyp24a1, apoa1a, ctsl. The anti-BM effect of cordycepin in SCLC was mediated by reversing the expression of these genes. ConclusionOur work is the first to describe the mechanism of cordycepin against SCLC BM from the perspective of regulating the brain microenvironment, providing new evidence for the anti-tumor effect of cordycepin.

Quantitative Sequencing Analysis of the Striatal Transcriptome in a Mouse Model of Alzheimer Disease.

The purpose of this study was to analyze the transcriptomic changes in the striatum of amyloid precursor protein/presenilin 1 (APP/PS1) transgenic mice and uncover its association with the methyl-CpG binding protein 2 (MeCP2) mediated-changes in striatal epigenetic signature during Alzheimer disease (AD) pathological progression. To observe transcriptomic alterations in the striatum before the onset of cognitive impairment in APP/PS1 mice, quantitative 3'mRNA sequencing was performed with RNA extracted from the striatum of 6-month-old and 12-month-old wildtype and APP/PS1 mice. In addition, chromatin immunoprecipitation sequencing was conducted with the DNA from wildtype and APP/PS1 mice of the same age as aforementioned. For transcriptomic analysis, comparison terms were constructed based on aging and transgene expression-normal-aging (12-month-old wildtype/6-month-old wildtype), early-AD (6-month-old APP/PS1/6-month-old wildtype), and late-AD (12-month-old APP/PS1/6-month-old wildtype). To compare the changes in biological pathways and networks, we analyzed gene lists from each comparison term via bioinformatics tools including DAVID (Database for Annotation, Visualization, and Integrated Discovery), STRING (Search Tool for the Retrieval of Interacting Genes/Proteins), and SynGO (Synaptic Gene Ontologies). Furthermore, to assume the effect MeCP2 in AD pathological conditions may have on the transcriptome regulation, analysis of the common genes from Quant-Seq and MeCP2-ChIP-Seq was performed. Enriched pathways including immune system and inflammatory response were confirmed in normal- aging and lateAD, respectively. In particular, enriched pathways of gene expression regulation, transcriptional regulation, and protein catabolic pathways were found to be significantly altered in early-AD. MeCP2-bound genes that were significantly altered in the transcriptome were suggested to be target genes that have a role in the striatum of the early-stage AD model. This study confirmed that the alteration of the striatal transcriptomic profile in APP/PS1 mice was involved with several biological pathways. Additionally, comparative analysis of the transcriptomic changes and the MeCP2 bound regions found that a group of differentially expressed genes may be regulated under the epigenetic control of MeCP2.

Gardeniae Fructus Extract Alleviates Dexamethasone-Induced Muscle Atrophy in Mice.

Muscle atrophy (MA) is a case in which protein degeneration occurs excessively due to an imbalance between protein synthesis and breakdown, and is characterized by decreased muscle mass and weakened muscle strength. Despite mounting concern about MA, the number of patients with MA is increasing every year. The aim of the present study was to assess the impact of Gardeniae Fructus (GF) hot water extract on dexamethasone (DEX)-induced MA in mice. C57BL/6N mice were grouped (n = 8) as follows: Normal mice (Normal), MA mice were treated with distilled water (Control), MA mice were treated with GF 100 mg/kg (GF100), MA mice were treated with GF 200 mg/kg (GF200). For 10 days, DEX (25 mg/kg body weight, i.p.) injection was used to induce MA, and GF was administered. GF treatment restored the muscle weight decreased due to MA, and in particular, the weights of EDL+TA and Sol were significantly increased in the GF200 group. Also, it was confirmed that the swimming time was improved in the GF200 group. In addition, the expression of NADPH oxidase related to oxidative stress was significantly reduced, and protective (insulin-like growth factor I/phosphoinositide 3-kinase/protein kinase B pathway) and catabolic (AMP-activated kinase [AMPK]/sirtuin 1 [SIRT1]/proliferator-activated receptor-gamma coactivator-1α (PGC-1α)-forkhead box O (FOXO) pathway) pathways were significantly modulated. These results demonstrate that GF regulates muscle protein synthesis and catabolic pathways, and in particular, it is judged to improve MA by regulating the proteolytic AMPK/SIRT1/PGC-1α-FOXO pathway.

Intraperitoneal and intracranial experimental cysticercosis present different metabolic preferences after treatment with isolated or combined albendazole and nitazoxanide

Cysticercosis is a zoonotic public health issue especially severe when the parasite is in the central nervous system although it may be found all over the human organism. Taenia crassiceps cysticerci inoculated in mice is the experimental model used to study cysticercosis. The most used cysticercosis treatment is with albendazole (ABZ). Nitazoxanide (NTZ) has been experimentally tested against this parasite. Metabolic analysis has been used to determine drugs impact on the parasite. The aim of this study was to determine the in vivo metabolic impact of the ABZ-NTZ combination in T. crassiceps cysticerci inoculated in mice peritoneal and intracranial cavities. Mice were experimentally inoculated with T. crassiceps cysticerci in the intraperitoneal cavity or in the intracranial one. Thirty days after the infection they were treated with NaCl 0.9% (control group), 50 mg/kg of ABZ, 50 mg/kg of NTZ or 50 mg/kg of NTZ and ABZ (ABZ/NTZ combination). 24 h after treatment the animals were euthanized and the cysticerci analyzed through high performance chromatography and spectrophotometry in order to detect the glycolytic, mitochondrial and protein catabolism pathways. The intracranial parasites used more intensely the homolactic fermentation while the intraperitoneal ones presented a greater use of the mitochondrial pathways and protein catabolism. Regarding the glycolytic pathways, it was possible to observe a significant impact induced by the drugs used, both isolated or in combination. It was possible to detect an increase in the fumarate reductase pathway after the drugs exposure and no impact in the protein's catabolism. Therefore, the cysticerci showed different uses of metabolic pathways regarding the site of inoculation due to the availability of nutrients inherent of each environment. This study showed the parasite metabolic resilience and capability of use of different biochemical pathways in order to ensure survival in spite of a hostile environment.

Deubiquitinating enzymes (DUBs): decipher underlying basis of neurodegenerative diseases.

Neurodegenerative diseases (NDs) are characterized by the aggregation of neurotoxic proteins in the central nervous system. Aberrant protein accumulation in NDs is largely caused by the dysfunction of the two principal protein catabolism pathways, the ubiquitin-proteasome system (UPS), and the autophagy-lysosomal pathway (ALP). The two protein quality control pathways are bridged by ubiquitination, a post-translational modification that can induce protein degradation via both the UPS and the ALP. Perturbed ubiquitination leads to the formation of toxic aggregates and inclusion bodies that are deleterious to neurons. Ubiquitination is promoted by a cascade of ubiquitinating enzymes and counter-regulated by deubiquitinating enzymes (DUBs). As fine-tuning regulators of ubiquitination and protein degradation, DUBs modulate the stability of ND-associated pathogenic proteins including amyloid β protein, Tau, and α-synuclein. Besides, DUBs also influence ND-associated mitophagy, protein secretion, and neuroinflammation. Given the various and critical functions of DUBs in NDs, DUBs may become potential therapeutic targets for NDs.

Weighted gene co-expression network analysis and drug-gene interaction bioinformatics uncover key genes associated with various presentations of malaria infection in African children and major drug candidates.

Malaria is a fatal parasitic disease with unelucidated pathogenetic mechanism. Herein, we aimed to uncover genes associated with different clinical aspects of malaria based on the GSE1124 dataset that is publicly accessible by using WGCNA. We obtained 16 co-expression modules and their correlations with clinical features. Using the MCODE tool, we identified THEM4, STYX, VPS36, LCOR, KIAA1143, EEA1, RAPGEF6, LOC439994, ZBTB33, PTPN22, ESCO1, and KLF3 as hub genes positively associated with Plasmodium falciparum infection (ASPF). These hub genes were involved in the biological processes of endosomal transport, regulation of natural killer cell proliferation, and KEGG pathways of endocytosis and fatty acid elongation. For the purple module negatively correlated with ASPF, we identified 19 hub genes that were involved in the biological processes of positive regulation of cellular protein catabolic process and KEGG pathways of other glycan degradation. For the salmon module positively correlated with severe malaria anemia (SMA), we identified 17 hub genes that were among those driving the biological processes of positive regulation of erythrocyte differentiation. For the brown module positively correlated with cerebral malaria (CM), we identified eight hub genes and these genes participated in phagolysosome assembly and positive regulation of exosomal secretion, and animal mitophagy pathway. For the tan module negatively correlated with CM, we identified four hub genes that were involved in CD8-positive, alpha-beta T cell differentiation and notching signaling pathway. These findings may provide new insights into the pathogenesis of malaria and help define new diagnostic and therapeutic approaches for malaria patients.

Comparative proteomic analysis of Rhizopus oryzae hyphae displaying filamentous and pellet morphology.

Industrial strains of Rhizopus oryzae is known for its strong ability to produce L-( +)-lactic acid, ethanol, and fumaric acid at high yields. To better understand the underlying mechanism behind the physiology of R. oryzae, we conducted the proteome changes between two different morphologies using two-dimensional polyacrylamide gel electrophoresis and mass spectrometry. R. oryzae exhibited pellet morphology and filamentous morphology when the initial pH of the culture medium was 3.0 and 5.0, respectively. The concentration of lactic acid reached 63.5g L-1 in the samples containing the pellet morphology, compared to 41.5g L-1 produced by filamentous R. oryzae. Proteomic analysis indicated that expression levels of 128 proteins changed significantly. Of these, 17 protein spots were successfully identified by mass spectrometry and were deemed to be mainly involved in carbohydrate metabolism, genetic information processing, chitin metabolism, protein catabolism, protein folding, and antioxidative pathway. L-lactate dehydrogenase (RO3G_06188), enolase (RO3G_05466) and 2, 3-bisphosphoglycerate-independent phosphoglycerate mutase (RO3G_02462) were found to be upregulated, while isocitrate dehydrogenase (RO3G_13820) was downregulated in the samples with pellet morphology compared to the filamentous hyphae. These results suggested that more carbon flow was directed towards lactic acid biosynthesis in R. oryzae hyphae with pellet morphology.

Intermittent leucine pulses during continuous feeding alters novel components involved in skeletal muscle growth of neonatal pigs.

When neonatal pigs continuously fed formula are supplemented with leucine pulses, muscle protein synthesis and body weight gain are enhanced. To identify the responsible mechanisms, we combined plasma metabolomic analysis with transcriptome expression of the transcriptome and protein catabolic pathways in skeletal muscle. Piglets (n = 23, 7-day-old) were fed continuously a milk replacement formula via orogastric tube for 21days with an additional parenteral infusion (800μmolkg-1h-1) of either leucine (LEU) or alanine (CON) for 1h every 4h. Plasma metabolites were measured by liquid chromatography-mass spectrometry. Gene and protein expression analyses of longissimus dorsi muscle were performed by RNA-seq and Western blot, respectively. Compared with CON, LEU pigs had increased plasma levels of leucine-derived metabolites, including 4-methyl-2-oxopentanoate, beta-hydroxyisovalerate, β-hydroxyisovalerylcarnitine, and 3-methylglutaconate (P ≤ 0.05). Leucine pulses downregulated transcripts enriched in the Kyoto Encyclopedia of Genes and Genomes terms "spliceosome," "GAP junction," "endocytosis," "ECM-receptor interaction," and "DNA replication". Significant correlations were identified between metabolites derived from leucine catabolism and muscle genes involved in protein degradation, transcription and translation, and muscle maintenance and development (P ≤ 0.05). Further, leucine pulses decreased protein expression of autophagic markers and serine/threonine kinase 4, involved in muscle atrophy (P ≤ 0.01). In conclusion, results from our studies support the notion that leucine pulses during continuous enteral feeding enhance muscle mass gain in neonatal pigs by increasing protein synthetic activity and downregulating protein catabolic pathways through concerted responses in the transcriptome and metabolome.

Burn injury and restoration of muscle function.

Burn injury in children results in a systemic inflammatory reaction as well as a stress response. Consequences of these non-specific adaptive responses include resorptive bone loss and muscle catabolism. These adverse events can result in a post-burn fracture rate of approximately 15% and long-term muscle weakness that prolongs recovery. A randomized controlled trial of a single dose of the bisphosphonate pamidronate within the first ten days of burn injury resulted in the prevention of resorptive bone loss and continuous bone accrual. Examining the muscle protein kinetics in pediatric burn patients enrolled in that randomized controlled trial revealed that those who had been given the single dose bisphosphonate experienced preservation of muscle mass and strength. An in vitro study of mouse myoblasts incubated with serum from patients who participated in the randomized controlled study demonstrated that mouse myoblasts exposed to serum from patients given the single dose bisphosphonate exhibited greater myotube diameter than those from burned children given placebo. Moreover, the serum from bisphosphonate treated patients stimulated the protein anabolic pathways and suppressed protein catabolic pathways in these cells. Inasmuch as incubation of the myotubes with an antibody to transforming growth factor beta (TGFβ) rescued myotube size in the cultures with serum from patients who received the placebo to the same magnitude as cultures with serum from patients treated with single dose bisphosphonate, we postulate that post-burn bone resorption liberates muscle catabolic factors which cause muscle wasting. Future uses of bisphosphonates could include studies designed to prevent short-term acute bone resorption in conditions that may result in muscle wasting as well as in short-term interventions in chronic inflammatory conditions which may flare and cause acute bone and muscle loss.

Growth and Extended Survival of Escherichia coli O157:H7 in Soil Organic Matter.

Enterohaemorrhagic Escherichia coli, such as serotype O157:H7, are a leading cause of food-associated outbreaks. While the primary reservoir is associated with cattle, plant foods have been associated as sources of human infection. E. coli is able to grow in the tissue of food plants such as spinach. While fecal contamination is the primary suspect, soil has been underestimated as a potential reservoir. Persistence of bacterial populations in open systems is the product of growth, death, predation, and competition. Here we report that E. coli O157:H7 can grow using the soluble compounds in soil, and characterize the effect of soil growth on the stationary phase proteome. E. coli 933D (stxII−) was cultured in Soil Extracted Soluble Organic Matter (SESOM) and the culturable count determined for 24d. The proteomes of exponential and stationary phase populations were characterized by 2D gel electrophoresis and protein spots were identified by MALDI-TOF mass spectrometry. While LB controls displayed a death phase, SESOM grown population remained culturable for 24d, indicating an altered physiological state with superior longevity. This was not due to decreased cell density on entry to stationary phase as 24 h SESOM populations concentrated 10-fold retained their longevity. Principal component analysis showed that stationary phase proteomes from SESOM and LB were different. Differences included proteins involved in stress response, motility, membrane and wall composition, nutrient uptake, translation and protein turnover, and anabolic and catabolic pathways, indicating an altered physiological state of soil-grown cells entering stationary phase. The results suggest that E. coli may be a soil commensal that, in absence of predation and competition, maintains stable populations in soil.

Defective Protein Catabolism in Atherosclerotic Vascular Inflammation.

Vascular inflammation in atheroprone vessels propagates throughout the arterial tree in dyslipidemic patients, thereby accelerating atherosclerotic progression. To elucidate the mechanism of vascular inflammation, most previous studies have focused on inflammation-related signals that are sent in response to vasoactive stimuli. However, it is also important to understand how normal blood vessels become defective and start degenerating. Growing evidence suggests that major protein catabolism pathways, including the ubiquitin-proteasome, autophagy, and calpain systems, are disturbed in atheroprone vessels and contribute to the pathogenesis of atherosclerosis. Indeed, dysregulation of ubiquitin–proteasome pathways results in the accumulation of defective proteins in blood vessels, leading to vascular endothelial dysfunction and apoptosis in affected cells. Impaired autophagy-lysosomal degradation affects smooth muscle cell transformation and proliferation, as well as endothelial integrity and phagocytic clearance of cellular corpses. Dysregulation of the calpain system confers proatherogenic properties to endothelial cells, smooth muscle cells, and macrophages. In this review article, we will discuss the current information available on defective protein catabolism in atheroprone vessels and its potential interrelation with inflammation-related signals.

Saturated or unsaturated fat supplemented maternal diets influence omental adipose tissue proteome of suckling goat-kids

The aim of the present study was to investigate how maternal diet can influence the adipose tissue of goat kids. Omental adipose tissue proteomes of goat-kids from mothers fed with diet enriched with stearic acid (ST-kids), fish oil (FO-kids) and standard diets (CTRL) were determined by quantitative iTRAQ 2D-LC-MS/MS analysis. Twenty proteins were found to be differentially expressed in suckling kids' omental adipose tissue. Stearic acid induces changes in a higher number of proteins when compared to fish oil. Eleven proteins, namely AARS, ECl1, PMSC2, CP, HSPA8, GPD1, RPL7, OGDH, RPL24, FGA and RPL5 were decreased in ST-kids only. Four proteins, namely DLST, EEF1G, BCAP31 and RALA were decreased in FO-kids only, and one, NUCKS1, was increased. Four proteins, namely PMSC1, PPIB, TUB5×2 and EIF5A1, were be less abundant in both ST- and FO- kids. Most of the protein whose abundance was decreased in ST kids (10 out of 15) are involved in protein metabolism and catabolism pathways. Qualitative gene expression analysis confirmed that all the proteins identified by mass spectrometry, with the exception of FGA, were produced by adipose tissue. Quantitative gene expression analysis demonstrated that two proteins, namely CP, a minor acute phase protein, and ECl1, involved in fatty acid beta oxidation, were downregulated at mRNA level as well. ECl1 gene expression was downregulated in ST-kids AT as compared to Ctrl-kids and CP was downregulated in both ST- and FO-kids. The present results demonstrate that it is possible to influence adipose goat-kid proteome by modifying the maternal diet.

Low-Intensity Pulsed Ultrasound Promotes Exercise-Induced Muscle Hypertrophy

The purpose of this study was to investigate whether low-intensity pulsed ultrasound (LIPUS) promotes exercise-induced muscle hypertrophy. Twenty-four adult Sprague-Dawley (SD) rats were randomly assigned to three groups (n = 8 per group): normal control group (NC), treadmill exercise group (TE) and treadmill exercise + LIPUS group (TE + LIPUS). The TE + LIPUS group received a LIPUS treatment (1 MHz, 30 mW/cm2) at the gastrocnemius for 20 min/d after treadmill exercise. The TE group was sham-treated. Eight weeks of treadmill training successfully established the exercise-induced muscle hypertrophy model. Muscle strength, muscle mass and muscle fiber cross-sectional area were significantly increased in the TE + LIPUS group compared with the TE group. Moreover, LIPUS treatment significantly upregulated the expression of Akt, mTOR, p-Akt and p-mTOR and significantly downregulated the expression of MSTN, ActRIIB, FoxO1 and its phosphorylation. The results indicated that LIPUS promotes exercise-induced muscle hypertrophy by facilitating protein synthesis and inhibiting the protein catabolism pathway.

Anaerobic Metabolism in T4 Acanthamoeba Genotype.

Members of the genus Acanthamoeba are of the most common protozoa that has been isolated from a variety of environment and affect immunocompromised individuals, causing granulomatous amoebic encephalitis and skin lesions. Acanthamoeba, in immunocompetent patients, may cause a keratitis related to corneal microtrauma. These free-living amoebas easily adapt to the host environment and wield metabolic pathways such as the energetic and respiratory ones in order to maintain viability for long periods. The energetic metabolism of cysts and trophozoites remains mostly unknown. There are a few reports on the energetic metabolism of these organisms as they are mitochondriate eukaryotes and some studies under aerobic conditions showing that Acanthamoeba hydrolyzes glucose into pyruvate via glycolysis. The aim of this study was to detect the energetic metabolic pathways with emphasis on anaerobic metabolism in trophozoites of three isolates of Acanthamoeba sp belonging to the T4 genotype. Two samples were collected in the environment and one was a clinical sample. The evaluation of these microorganisms proceeded as follows: rupture of trophozoites (7.5 × 103 parasites/ml) and biochemical analysis with high performance liquid chromatography and spectrophotometry. The anaerobic glycolysis was identified through the detection of glucose, pyruvate, and lactate. The protein catabolism was identified through the detection of fumarate, urea, and creatinine. The fatty acid oxidation was identified through the detection of acetate, beta-hydroxybutyrate, and propionate. The detected substances are the result of the consumption of energy reserves such as glycogen and lipids. The anaerobic glycolysis and protein catabolism pathways were observed in all three isolates: one clinical and two environmental. This study represents the first report of energetic pathways used by trophozoites from different isolates of the T4 genotype Acanthamoeba.

Autophagy is required for PTEN-loss driven prostate cancer

Protein catabolic pathways are of critical importance to cellular physiology. The breakdown of proteins and organelles serves not only as a form of protein and organelle quality control, but also to generate amino acids and free fatty acids for reuse by the cell. Macroautophagy (hereafter referred to as autophagy) is a major pathway of protein degradation in eukaryotic cells that has been preserved through evolution. There has been much interest in the role of autophagy and cancer because mutations in autophagy genes have been observed in human cancers, autophagic activity is altered in cancer cells, and suppression of autophagy could be utilized as a cancer therapy (1,2). A recent report by the DiPaola group (3) demonstrated for the first time that autophagy is essential for the development of prostate cancer driven by PTEN -loss in a mouse model.

Intermittent Leucine Pulses during Continuous Feeding Alters Novel Components Involved in Skeletal Muscle Growth of Neonatal Pigs

Extra‐uterine growth restriction in low‐birth‐weight (LBW) infants is associated with the development of chronic metabolic derangements, and emphasizes the need for improved nutritional protocols to optimize growth. Supplementation with intermittent pulses of leucine in continuously fed neonatal pigs enhanced skeletal muscle protein synthesis through the upregulation of mammalian target of rapamycin signaling. Piglets (n = 23, 7‐d‐old) were continuously fed a milk formula via orogastric tube for 21 d, with an additional parenteral infusion of either leucine (800 μmol·kg−1·h−1, LEU) or alanine (CON) for 1 h every 4 h. To identify novel genes by which LEU may promote neonatal muscle growth, we performed RNA‐Seq analysis of longissimus dorsi muscle from 4 pigs per group, followed by gene ontology (GO) analysis of differentially expressed genes (DEG). In addition, protein abundance/activation of DEG products involved in both muscle protein anabolic or catabolic pathways was assessed by immunoblots. RNA‐Seq was performed on a HiSeq2000 sequencer analyzer. Reads were analyzed using CLCBio Genomics workbench software, assembled against the porcine reference genome, and normalized by a threshold of ‘reads per kilo base per million mapped reads’ (RPKM) ≥ 0.2. A total of 465 genes were differentially expressed between LEU and CON groups (RPKM P < 0.05). GO analyses showed developmental processes, cell junction assembly, regulation of cellular process and organ development as the terms most significantly enriched among the 465 genes. Applying more stringent parameters (RPKM P < 0.01 + >2 fold change), 18 differential expressed genes were identified between CON and LEU pigs, of which tumor necrosis factor receptor‐associated factor 6 (TRAF6) and mammalian Ste20‐like kinase 1 (MST1), both negative regulators of muscle growth, were decreased by > 2‐fold (P < 0.01) in LEU compared to CON. Western blot analysis also showed a downregulation of MST1 and TRAF6 abundance in LEU animals (P < 0.01) compared to CON. Together, these findings suggest that intermittent leucine pulses in continuously fed neonate pigs lead to downregulation in the gene and protein expression of signaling components that limit muscle growth.Support or Funding InformationNIH AR444474, NIHHD072891, USDA NIFA 2013‐67015‐20438, and USDA/ARS 6250‐51000‐055

COPD subtypes identified by network-based clustering of blood gene expression

One of the most common smoking-related diseases, chronic obstructive pulmonary disease (COPD), results from a dysregulated, multi-tissue inflammatory response to cigarette smoke. We hypothesized that systemic inflammatory signals in genome-wide blood gene expression can identify clinically important COPD-related disease subtypes, and we leveraged pre-existing gene interaction networks to guide unsupervised clustering of blood microarray expression data. Using network-informed non-negative matrix factorization, we analyzed genome-wide blood gene expression from 229 former smokers in the ECLIPSE Study, and we identified novel, clinically relevant molecular subtypes of COPD. These network-informed clusters were more stable and more strongly associated with measures of lung structure and function than clusters derived from a network-naïve approach, and they were associated with subtype-specific enrichment for inflammatory and protein catabolic pathways. These clusters were successfully reproduced in an independent sample of 135 smokers from the COPDGene Study.

Energy metabolism of hyperthyroid gilthead sea bream Sparus aurata L.

Thyroid hormones, in particular 3,5,3′-triiodothyronine or T3, are involved in multiple physiological processes in mammals such as protein, fat and carbohydrate metabolism. However, the metabolic actions of T3 in fish are still not fully elucidated. We therefore tested the effects of T3 on Sparus aurata energy metabolism and osmoregulatory system, a hyperthyroid-induced model that was chosen. Fish were implanted with coconut oil depots (containing 0, 2.5, 5.0 and 10.0μgT3/g body weight) and sampled at day 3 and 6 post-implantation. Plasma levels of free T3 as well as glucose, lactate and triglyceride values increased with increasing doses of T3 at days 3 and 6 post-implantation. Changes in plasma and organ metabolite levels (glucose, glycogen, triglycerides, lactate and total α amino acid) and enzyme activities related to carbohydrate, lactate, amino acid and lipid pathways were detected in organs involved in metabolism (liver) and osmoregulation (gills and kidney). Our data implicate that the liver uses amino acids as an energy source in response to the T3 treatment, increasing protein catabolism and gluconeogenic pathways. The gills, the most important extruder of ammonia, are fuelled not only by amino acids, but also by lactate. The kidney differs significantly in its substrate preference from the gills, as it obtained metabolic energy from lactate but also from lipid oxidation processes. We conclude that in S. aurata lipid catabolism and protein turnover are increased as a consequence of experimentally induced hyperthyroidism, with secondary osmoregulatory effects.

Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores

Mammals host gut microbiomes of immense physiological consequence, but the determinants of diversity in these communities remain poorly understood. Diet appears to be the dominant factor, but host phylogeny also seems to be an important, if unpredictable, correlate. Here we show that baleen whales, which prey on animals (fish and crustaceans), harbor unique gut microbiomes with surprising parallels in functional capacity and higher level taxonomy to those of terrestrial herbivores. These similarities likely reflect a shared role for fermentative metabolisms despite a shift in primary carbon sources from plant-derived to animal-derived polysaccharides, such as chitin. In contrast, protein catabolism and essential amino acid synthesis pathways in baleen whale microbiomes more closely resemble those of terrestrial carnivores. Our results demonstrate that functional attributes of the microbiome can vary independently even given an animal-derived diet, illustrating how diet and evolutionary history combine to shape microbial diversity in the mammalian gut.

Metabolomic Evaluation of Neutrophilic Airway Inflammation in Cystic Fibrosis

Metabolomic evaluation of cystic fibrosis (CF) airway secretions could identify metabolites and metabolic pathways involved in neutrophilic airway inflammation that could serve as biomarkers and therapeutic targets. Mass spectrometry (MS)-based metabolomics was performed on a discovery set of BAL fluid samples from 25 children with CF, and targeted MS methods were used to identify and quantify metabolites related to neutrophilic inflammation. A biomarker panel of these metabolites was then compared with neutrophil counts and clinical markers in independent validation sets of lavage from children with CF and adults with COPD compared with control subjects. Of the 7,791 individual peaks detected by positive-mode MS metabolomics discovery profiling, 338 were associated with neutrophilic inflammation. Targeted MS determined that many of these peaks were generated by metabolites from pathways related to the metabolism of purines, polyamines, proteins, and nicotinamide. Analysis of the independent validation sets verified that, in subjects with CF or COPD, several metabolites, particularly those from purine metabolism and protein catabolism pathways, were strongly correlated with neutrophil counts and were related to clinical markers, including airway infection and lung function. MS metabolomics identified multiple metabolic pathways associated with neutrophilic airway inflammation. These findings provide insight into disease pathophysiology and can serve as the basis for developing disease biomarkers and therapeutic interventions for airways diseases.