Cells. 2023 Jan 21;12(3):388. doi: 10.3390/cells12030388.

ABSTRACT

Genes with similar expression patterns in a set of diverse samples may be considered coexpressed. Human Gene Coexpression Analysis 2.0 (HGCA2.0) is a webtool which studies the global coexpression landscape of human genes. The website is based on the hierarchical clustering of 55,431 Homo sapiens genes based on a large-scale coexpression analysis of 3500 GTEx bulk RNA-Seq samples of healthy individuals, which were selected as the best representative samples of each tissue type. HGCA2.0 presents subclades of coexpressed genes to a gene of interest, and performs various built-in gene term enrichment analyses on the coexpressed genes, including gene ontologies, biological pathways, protein families, and diseases, while also being unique in revealing enriched transcription factors driving coexpression. HGCA2.0 has been successful in identifying not only genes with ubiquitous expression patterns, but also tissue-specific genes. Benchmarking showed that HGCA2.0 belongs to the top performing coexpression webtools, as shown by STRING analysis. HGCA2.0 creates working hypotheses for the discovery of gene partners or common biological processes that can be experimentally validated. It offers a simple and intuitive website design and user interface, as well as an API endpoint.

PMID:36766730 | DOI:10.3390/cells12030388

Cells. 2023 Jan 17;12(3):344. doi: 10.3390/cells12030344.

ABSTRACT

Escherichia coli is one of the most common members of the intestinal microbiota. Many of its strains are associated with various inflammatory infections, including urinary or gut infections, especially when displaying antibiotic resistance or in patients with suppressed immune systems. According to recent reports, the biofilm-forming potential of E. coli is a crucial factor for its increased resistance against antibiotics. To overcome the limitations of using antibiotics against resistant E. coli strains, the world is turning once more towards bacteriophage therapy, which is becoming a promising candidate amongst the current personalized approaches to target different bacterial infections. Although matured and persistent biofilms pose a serious challenge to phage therapy, they can still become an effective alternative to antibiotic treatment. Here, we assess the efficiency of clinically isolated phages in phage therapy against representative clinical uropathogenic and invasive biofilm-forming E. coli strains. Our results demonstrate that irrespective of host specificity, bacteriophages producing clear plaques with a high burst size, and exhibiting depolymerizing activity, are good candidates against biofilm-producing E. coli pathogens as verified from our in vitro and in vivo experiments using Galleria mellonella where survival was significantly increased for phage-therapy-treated larvae.

PMID:36766686 | DOI:10.3390/cells12030344

Foods. 2023 Jan 28;12(3):571. doi: 10.3390/foods12030571.

ABSTRACT

Due to environmental and human factors, there is a growing amount of agri-food waste worldwide. The European Commission is incentivizing a zero-waste policy by 2025, pushing to find a "second life" for at least the avoidable ones. In this review, after summarizing the nutritional values of pork and the importance of its inclusion in human diet, a phylogenetic analysis was conducted to investigate potential differences in the structure and activity of HMGCR, which is a key enzyme in cholesterol metabolism. In addition, a bibliometric analysis combined with visual and meta-analytical studies on 1047 scientific articles was conducted to understand whether the inclusion of agro-food waste could affect the growth performance of pigs and reduce cholesterol levels in pork. Although some critical issues were highlighted, the overall data suggest a modern and positive interest in the reuse of agri-food waste as swine feed. However, although interesting and promising results have been reported in several experimental trials, further investigation is needed, since animal health and meat quality are often given marginal consideration.

PMID:36766100 | DOI:10.3390/foods12030571

Foods. 2023 Jan 27;12(3):558. doi: 10.3390/foods12030558.

ABSTRACT

As an easily spoiled source of valuable proteins and lipids, fish is preserved by fermentation in many cultures. Over time, diverse types of products have been produced from fish fermentation aside from whole fish, such as fermented fish paste and sauces. The consumption of fermented fish products has been shown to improve both physical and mental health due to the composition of the products. Fermented fish products can be dried prior to the fermentation process and include various additives to enhance the flavours and aid in fermentation. At the same time, the fermentation process and its conditions play a major role in determining the quality and safety of the product as the compositions change biochemically throughout fermentation. Additionally, the necessity of certain microorganisms and challenges in avoiding harmful microbes are reviewed to further optimise fermentation conditions in the future. Although several advanced technologies have emerged to produce better quality products and easier processes, the diversity of processes, ingredients, and products of fermented fish warrants further study, especially for the sake of the consumers' health and safety. In this review, the nutritional, microbial, and sensory characteristics of fermented fish are explored to better understand the health benefits along with the safety challenges introduced by fermented fish products. An exploratory approach of the published literature was conducted to achieve the purpose of this review using numerous books and online databases, including Google Scholar, Web of Science, Scopus, ScienceDirect, and PubMed Central, with the goal of obtaining, compiling, and reconstructing information on a variety of fundamental aspects of fish fermentation. This review explores significant information from all available library databases from 1950 to 2022. This review can assist food industries involved in fermented fish commercialization to efficiently ferment and produce better quality products by easing the fermentation process without risking the health and safety of consumers.

PMID:36766088 | DOI:10.3390/foods12030558

Cancers (Basel). 2023 Feb 1;15(3):936. doi: 10.3390/cancers15030936.

ABSTRACT

Pancreatic neuroendocrine neoplasms (panNENs) are a rare yet diverse type of neoplasia whose precise clinical-pathological classification is frequently challenging. Since incorrect classifications can affect treatment decisions, additional tools which support the diagnosis, such as machine learning (ML) techniques, are critically needed but generally unavailable due to the scarcity of suitable ML training data for rare panNENs. Here, we demonstrate that a multi-step ML framework predicts clinically relevant panNEN characteristics while being exclusively trained on widely available data of a healthy origin. The approach classifies panNENs by deconvolving their transcriptomes into cell type proportions based on shared gene expression profiles with healthy pancreatic cell types. The deconvolution results were found to provide a prognostic value with respect to the prediction of the overall patient survival time, neoplastic grading, and carcinoma versus tumor subclassification. The performance with which a proliferation rate agnostic deconvolution ML model could predict the clinical characteristics was found to be comparable to that of a comparative baseline model trained on the proliferation rate-informed MKI67 levels. The approach is novel in that it complements established proliferation rate-oriented classification schemes whose results can be reproduced and further refined by differentiating between identically graded subgroups. By including non-endocrine cell types, the deconvolution approach furthermore provides an in silico quantification of panNEN dedifferentiation, optimizing it for challenging clinical classification tasks in more aggressive panNEN subtypes.

PMID:36765893 | DOI:10.3390/cancers15030936

Cancers (Basel). 2023 Jan 28;15(3):815. doi: 10.3390/cancers15030815.

ABSTRACT

Cutaneous melanoma (CM) is the most aggressive type of skin cancer, and it is characterised by high mutational load and heterogeneity. In this study, we aimed to analyse the genomic and transcriptomic profile of primary melanomas from forty-six Formalin-Fixed, Paraffin-Embedded (FFPE) tissues from Greek patients. Molecular analysis for both germline and somatic variations was performed in genomic DNA from peripheral blood and melanoma samples, respectively, exploiting whole exome and targeted sequencing, and transcriptomic analysis. Detailed clinicopathological data were also included in our analyses and previously reported associations with specific mutations were recognised. Most analysed samples (43/46) were found to harbour at least one clinically actionable somatic variant. A subset of samples was profiled at the transcriptomic level, and it was shown that specific melanoma phenotypic states could be inferred from bulk RNA isolated from FFPE primary melanoma tissue. Integrative bioinformatics analyses, including variant prioritisation, differential gene expression analysis, and functional and gene set enrichment analysis by group and per sample, were conducted and molecular circuits that are implicated in melanoma cell programmes were highlighted. Integration of mutational and transcriptomic data in CM characterisation could shed light on genes and pathways that support the maintenance of phenotypic states encrypted into heterogeneous primary tumours.

PMID:36765773 | DOI:10.3390/cancers15030815

Cancers (Basel). 2023 Jan 25;15(3):737. doi: 10.3390/cancers15030737.

ABSTRACT

Receptor-interacting serine/threonine protein kinase 4 (RIPK4) and its kinase substrate the transcription factor interferon regulatory factor 6 (IRF6) play critical roles in the development and maintenance of the epidermis. In addition, ourselves and others have previously shown that RIPK4 is a NOTCH target gene that suppresses the development of cutaneous and head and neck squamous cell carcinomas (HNSCCs). In this study, we used autochthonous mouse models, where the expression of Pik3caH1047R oncogene predisposes the skin and oral cavity to tumor development, and show that not only loss of Ripk4, but also loss of its kinase substrate Irf6, triggers rapid SCC development. In vivo rescue experiments using Ripk4 or a kinase-dead Ripk4 mutant showed that the tumor suppressive function of Ripk4 is dependent on its kinase activity. To elucidate critical mediators of this tumor suppressive pathway, we performed transcriptional profiling of Ripk4-deficient epidermal cells followed by multiplexed in vivo CRISPR screening to identify genes with tumor suppressive capabilities. We show that Elovl4 is a critical Notch-Ripk4-Irf6 downstream target gene, and that Elovl4 loss itself triggers SCC development. Importantly, overexpression of Elovl4 suppressed tumor growth of Ripk4-deficient keratinocytes. Altogether, our work identifies a potent Notch1-Ripk4-Irf6-Elovl4 tumor suppressor axis.

PMID:36765696 | DOI:10.3390/cancers15030737

Commun Biol. 2023 Feb 10;6(1):165. doi: 10.1038/s42003-023-04540-8.

ABSTRACT

Pseudomonas aeruginosa is one of the leading causes of hospital-acquired infections. To decipher the metabolic mechanisms associated with virulence and antibiotic resistance, we have developed an updated genome-scale model (GEM) of P. aeruginosa. The model (iSD1509) is an extensively curated, three-compartment, and mass-and-charge balanced BiGG model containing 1509 genes, the largest gene content for any P. aeruginosa GEM to date. It is the most accurate with prediction accuracies as high as 92.4% (gene essentiality) and 93.5% (substrate utilization). In iSD1509, we newly added a recently discovered pathway for ubiquinone-9 biosynthesis which is required for anaerobic growth. We used a modified iSD1509 to demonstrate the role of virulence factor (phenazines) in the pathogen survival within biofilm/oxygen-limited condition. Further, the model can mechanistically explain the overproduction of a drug susceptibility biomarker in the P. aeruginosa mutants. Finally, we use iSD1509 to demonstrate the drug potentiation by metabolite supplementation, and elucidate the mechanisms behind the phenotype, which agree with experimental results.

PMID:36765199 | DOI:10.1038/s42003-023-04540-8

Sci Rep. 2023 Feb 10;13(1):2422. doi: 10.1038/s41598-023-29328-y.

NO ABSTRACT

PMID:36765160 | DOI:10.1038/s41598-023-29328-y

Nat Commun. 2023 Feb 10;14(1):749. doi: 10.1038/s41467-023-36344-z.

ABSTRACT

Despite insights gained by bulk DNA sequencing of cancer it remains challenging to resolve the admixture of normal and tumor cells, and/or of distinct tumor subclones; high-throughput single-cell DNA sequencing circumvents these and brings cancer genomic studies to higher resolution. However, its application has been limited to liquid tumors or a small batch of solid tumors, mainly because of the lack of a scalable workflow to process solid tumor samples. Here we optimize a highly automated nuclei extraction workflow that achieves fast and reliable targeted single-nucleus DNA library preparation of 38 samples from 16 pancreatic ductal adenocarcinoma patients, with an average library yield per sample of 2867 single nuclei. We demonstrate that this workflow not only performs well using low cellularity or low tumor purity samples but reveals genomic evolution patterns of pancreatic ductal adenocarcinoma as well.

PMID:36765116 | DOI:10.1038/s41467-023-36344-z

Nat Commun. 2023 Feb 10;14(1):757. doi: 10.1038/s41467-023-36548-3.

NO ABSTRACT

PMID:36765087 | DOI:10.1038/s41467-023-36548-3

Nat Commun. 2023 Feb 10;14(1):740. doi: 10.1038/s41467-023-35943-0.

ABSTRACT

In late 2020, the JCVI (the Joint Committee on Vaccination and Immunisation, which provides advice to the Department of Health and Social Care, England) made two important recommendations for the initial roll-out of the COVID-19 vaccine. The first was that vaccines should be targeted to older and vulnerable people, with the aim of maximally preventing disease rather than infection. The second was to increase the interval between first and second doses from 3 to 12 weeks. Here, we re-examine these recommendations through a mathematical model of SARS-CoV-2 infection in England. We show that targeting the most vulnerable had the biggest immediate impact (compared to targeting younger individuals who may be more responsible for transmission). The 12-week delay was also highly beneficial, estimated to have averted between 32-72 thousand hospital admissions and 4-9 thousand deaths over the first ten months of the campaign (December 2020-September 2021) depending on the assumed interaction between dose interval and efficacy.

PMID:36765050 | DOI:10.1038/s41467-023-35943-0

Methods Enzymol. 2023;681:169-188. doi: 10.1016/bs.mie.2022.08.013. Epub 2022 Sep 26.

ABSTRACT

Measurement of target engagement in cells is critical to understand the molecular pharmacology of drugs and chemical probes. Many targeted protein degraders engage the E3 ligase CRL4CRBN and induce proximity with target neosubstrates resulting in their polyubiquitination and subsequent proteasomal degradation. Here we describe the development of a sensitive and robust cellular NanoBRET-based assay that measures occupancy of the CRBN ligand binding site. The assay is based on a bioluminescence resonance energy transfer (BRET) between NanoLuc luciferase tagged CRBN and a BODIPY-lenalidomide tracer which can be competed out by CRBN ligands, including PROTACs and molecular glues. The assay is compatible with a 384-well plate setup, does not require transfections and can be performed in a single day with only 3-4h of laboratory time. The protocols can be used to design other NanoLuc fusion engagement assays based on BODIPY tracers.

PMID:36764756 | DOI:10.1016/bs.mie.2022.08.013

Sci Total Environ. 2023 Feb 8:162106. doi: 10.1016/j.scitotenv.2023.162106. Online ahead of print.

ABSTRACT

Anthropogenic disturbance on natural ecosystems is growing in frequency and magnitude affecting all ecosystems components. Understanding the response of different types of biocoenosis to human disturbance is urgently needed and it can be achieved by adopting a metacommunity framework. With the aid of advanced molecular techniques, we investigated sediment communities of Fungi, Bacteria and Archaea in four Italian show caves, aiming to disentangle the effects induced by tourism on their diversity and to highlight changes in the driving forces that shape their community composition. We modelled diversity measures against proxies of tourism pressure. With this approach we demonstrate that the cave tourism has a direct effect on the community of Bacteria and an indirect influence on Fungi and Archaea. By analysing the main driving forces influencing the community composition of the three microbial groups, we highlighted that stochastic factors override dispersal-related processes and environmental selection in show caves compared to undisturbed areas. Thanks to this approach, we provide new perspectives on the dynamics of microbial communities under human disturbance suggesting that a proper understanding of the underlying selective mechanisms requires a comprehensive and multi-taxonomic approach.

PMID:36764528 | DOI:10.1016/j.scitotenv.2023.162106

Heart Rhythm. 2023 Feb 8:S1547-5271(23)00130-3. doi: 10.1016/j.hrthm.2023.02.004. Online ahead of print.

ABSTRACT

BACKGROUND: The Worm Study, derived from a multi-generation pedigree segregating a single amino-acid deletion in SCN5A (c.4850_4852delTCT, p.(Phe1617del), rs749697698), is characterized by substantial phenotypic heterogeneity and overlap of sudden cardiac death, long-QT syndrome, cardiac conduction disease, Brugada syndrome and isorhythmic atrioventricular dissociation. Linkage analysis for a synthetic trait derived from these phenotypes identified a single peak (LOD=4.52) at the SCN5A/SCN10A/SCN11A locus on chromosome 3.

OBJECTIVE: This study explored the role of additional genetic variation in the chromosome 3 locus as a source of phenotypic heterogeneity in the Worm study population.

METHODS: Genotypes underlying the linkage peak (n=70) were characterized using microarrays. Haplotypes were determined using family-aware phasing and a population-specific reference panel. Variants with minor allele frequencies >0.10 were tested for association with cardiac conduction disease and isorhythmic dissociation using LAMP and logistic regression.

RESULTS: Only one haplotype carried the p.Phe1617del/rs749697698 deletion, suggesting relatively recent development (∼18 generations); this haplotype contained five other missense variants spanning SCN5A/SCN10A/SCN11A. Non-carrier haplotypes (n=74) ranged in frequency from 0.5-5%. Although no variants were associated with cardiac conduction disease, a homozygous missense variant in SCN10A was associated with isorhythmic dissociation after correction for multiple comparisons (OR[95% C.I.]=11.23[2.76,23.39], P=1.2x10-4). This variant (rs12632942) was previously associated with PR-interval duration.

CONCLUSIONS: Our data suggest that other variants, alongside a pathogenic mutation, are associated with phenotypic heterogeneity. Single-mutation screening may be insufficient to predict electrical heart disease in patients and family members. In the Worm study population, segregating a pathogenic SCN5A mutation, compound variation in the SCN5A/SCN10A/SCN11A locus determines arrhythmic outcome.

PMID:36764349 | DOI:10.1016/j.hrthm.2023.02.004

Forensic Sci Int Genet. 2023 Feb 1;64:102840. doi: 10.1016/j.fsigen.2023.102840. Online ahead of print.

ABSTRACT

We provide an internal validation study of a recently published precise DNA mixture algorithm based on Hamiltonian Monte Carlo sampling (Susik et al., 2022). We provide results for all 428 mixtures analysed by Riman et al. (2021) and compare the results with two state-of-the-art software products: STRmix™ v2.6 and Euroformix v3.4.0. The comparison shows that the Hamiltonian Monte Carlo method provides reliable values of likelihood ratios (LRs) close to the other methods. We further propose a novel large-scale precision benchmark and quantify the precision of the Hamiltonian Monte Carlo method, indicating its improvements over existing solutions. Finally, we analyse the influence of the factors discussed by Buckleton et al. (2022).

PMID:36764220 | DOI:10.1016/j.fsigen.2023.102840

Br J Dermatol. 2023 Feb 10;188(2):290-310. doi: 10.1093/bjd/ljac048.

NO ABSTRACT

PMID:36763877 | DOI:10.1093/bjd/ljac048

J Proteome Res. 2023 Feb 10. doi: 10.1021/acs.jproteome.2c00758. Online ahead of print.

ABSTRACT

Proteomics and metabolomics are essential in systems biology, and simultaneous proteo-metabolome liquid-liquid extraction (SPM-LLE) allows isolation of the metabolome and proteome from the same sample. Since the proteome is present as a pellet in SPM-LLE, it must be solubilized for quantitative proteomics. Solubilization and proteome extraction are critical factors in the information obtained at the proteome level. In this study, we investigated the performance of two surfactants (sodium deoxycholate (SDC), sodium dodecyl sulfate (SDS)) and urea in terms of proteome coverage and extraction efficiency of an interphase proteome pellet generated by methanol-chloroform based SPM-LLE. We also investigated how the performance differs when the proteome is extracted from the interphase pellet or by direct cell lysis. We quantified 12 lipids covering triglycerides and various phospholipid classes, and 25 polar metabolites covering central energy metabolism in chloroform and methanol extracts. Our study reveals that the proteome coverages between the two surfactants and urea for the SPM-LLE interphase pellet were similar, but the extraction efficiencies differed significantly. While SDS led to enrichment of basic proteins, which were mainly ribosomal and ribonuclear proteins, urea was the most efficient extraction agent for simultaneous proteo-metabolome analysis. The results of our study also show that the performance of surfactants for quantitative proteomics is better when the proteome is extracted through direct cell lysis rather than an interphase pellet. In contrast, the performance of urea for quantitative proteomics was significantly better when the proteome was extracted from an interphase pellet than by direct cell lysis. We demonstrated that urea is superior to surfactants for proteome extraction from SPM-LLE interphase pellets, with a particularly good performance for the extraction of proteins associated with metabolic pathways. Data are available via ProteomeXchange with identifier PXD027338.

PMID:36763818 | DOI:10.1021/acs.jproteome.2c00758

J Proteome Res. 2023 Feb 10. doi: 10.1021/acs.jproteome.2c00505. Online ahead of print.

ABSTRACT

Phosphorylation-dependent signal transduction plays an important role in regulating the functions and fate of skeletal muscle cells. Central players in the phospho-signaling network are the protein kinases AKT, S6K, and RSK as part of the PI3K-AKT-mTOR-S6K and RAF-MEK-ERK-RSK pathways. However, despite their functional importance, knowledge about their specific targets is incomplete because these kinases share the same basophilic substrate motif RxRxxp[ST]. To address this, we performed a multifaceted quantitative phosphoproteomics study of skeletal myotubes following kinase inhibition. Our data corroborate a cross talk between AKT and RAF, a negative feedback loop of RSK on ERK, and a putative connection between RSK and PI3K signaling. Altogether, we report a kinase target landscape containing 49 so far unknown target sites. AKT, S6K, and RSK phosphorylate numerous proteins involved in muscle development, integrity, and functions, and signaling converges on factors that are central for the skeletal muscle cytoskeleton. Whereas AKT controls insulin signaling and impinges on GTPase signaling, nuclear signaling is characteristic for RSK. Our data further support a role of RSK in glucose metabolism. Shared targets have functions in RNA maturation, stability, and translation, which suggests that these basophilic kinases establish an intricate signaling network to orchestrate and regulate processes involved in translation.

PMID:36763541 | DOI:10.1021/acs.jproteome.2c00505

Mol Biol Evol. 2023 Feb 10:msad030. doi: 10.1093/molbev/msad030. Online ahead of print.

ABSTRACT

Extreme environments, such as Antarctic habitats, present major challenges for many biological processes. Antarctic icefishes (Crynotothenioidea) represent a compelling system to investigate the molecular basis of adaptation to cold temperatures. Here we explore how the sub-zero habitats of Antarctic icefishes have impacted rhodopsin (RH1) function, the temperature-sensitive dim-light visual pigment found in rod photoreceptors. Using likelihood-models and ancestral reconstruction, we find that accelerated evolutionary rates in icefish RH1 underlie unique amino acid mutations absent from other deep-dwelling fishes, introduced before (S160A) and during (V259M) the onset of modern polar conditions. Functional assays reveal that these mutations red-shift rhodopsin spectral absorbance, consistent with spectral irradiance under sea-ice. These mutations also lower the activation energy associated with retinal release of the light-activated RH1, and accelerate its return to the dark-state, likely compensating for a cold-induced decrease in kinetic rates. These are adaptations in key properties of rhodopsin that mediate rod sensitivity and visual performance in the cold dark seas of the Antarctic.

PMID:36763103 | DOI:10.1093/molbev/msad030