Quantitative proteome comparison of human hearts with those of model organisms

Delineating human cardiac pathologies and their basic molecular mechanisms relies on research conducted in model organisms. Yet translating findings from preclinical models to humans present a significant challenge, in part due to differences in cardiac protein expression between humans and model organisms. Proteins immediately determine cellular function, yet their large-scale investigation in hearts has lagged behind those of genes and transcripts. Here, we set out to bridge this knowledge gap: By analyzing protein profiles in humans and commonly used model organisms across cardiac chambers, we determine their commonalities and regional differences. We analyzed cardiac tissue from each chamber of human, pig, horse, rat, mouse, and zebrafish in biological replicates. Using mass spectrometry–based proteomics workflows, we measured and evaluated the abundance of approximately 7,000 proteins in each species. The resulting knowledgebase of cardiac protein signatures is accessible through an online database: atlas.cardiacproteomics.com. Our combined analysis allows for quantitative evaluation of protein abundances across cardiac chambers, as well as comparisons of cardiac protein profiles across model organisms. Up to a quarter of proteins with differential abundances between atria and ventricles showed opposite chamber-specific enrichment between species; these included numerous proteins implicated in cardiac disease. The generated proteomics resource facilitates translational prospects of cardiac studies from model organisms to humans by comparisons of disease-linked protein networks across species.

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Long-Term Subculture Affects Rooting Competence via Changes in the Hormones and Protein Profiles in Cedrela Fissilis Vell. (Meliaceae) Shoots

10.21203/rs.3.rs-689426/v1 ◽

2021 ◽

Author(s):

Tadeu dos Reis Oliveira ◽

Damián Balfagón ◽

Kariane Rodrigues Sousa ◽

Victor Paulo Mesquita Aragão ◽

Leandro Francisco de Oliveira ◽

...

Keyword(s):

Large Scale ◽

Molecular Mechanisms ◽

Monodehydroascorbate Reductase ◽

Protein Profiles ◽

Ex Vitro ◽

Plantlet Production ◽

Auxin Binding Protein ◽

Indole 3 Acetic Acid

Abstract Long-term subculture plays an essential role in the large-scale multiplication and production of somatic plantlets. We investigated the effects of long-term subculture on in vitro shoot development and ex vitro rooting associated with changes in the hormones and protein profiles in C. fissilis. The number of subcultures of shoots induced a decrease in the ex vitro rooting response. The reduction in adventitious root (AR) formation was associated with decreases in the contents of indole-3-acetic acid (IAA), abscisic acid (ABA), 12-oxo phytodienoic acid (OPDA), putrescine (Put), and spermine and increases in jasmonic acid (JA), jasmonoyl-isoleucine, trans-cinnamic acid, and salicylic acid contents in shoots at the fourth subculture compared to the first. The ornithine decarboxylase enzyme preferentially functions in the Put biosynthesis pathway and was related to the highest AR formation in shoots at the first subculture. Down-accumulation of the auxin-binding protein ABP19a in shoots from the fourth subculture compared to the first subculture was related to a decrease in both IAA contents and AR formation. In addition, down-accumulation of glucose-6-phosphate isomerase, glutamine synthetase leaf isozyme chloroplastic, 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase, L-ascorbate peroxidase, cytosolic, monodehydroascorbate reductase, and 2-Cys peroxiredoxin BAS1-like, chloroplastic and up-accumulation of caffeoyl-CoA O-methyltransferase 1 and isoforms of peroxidase 4 proteins in shoots from the fourth relative to the first subculture were associated with a reduction in AR formation. These results showed that the understanding of hormonal and molecular mechanisms related to the potential of AR formation in shoots under successive subcultures is relevant to improving large-scale plantlet production in C. fissilis.

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EGCG binds intrinsically disordered N-terminal domain of p53 and disrupts p53-MDM2 interaction

Nature Communications ◽

10.1038/s41467-021-21258-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Jing Zhao ◽

Alan Blayney ◽

Xiaorong Liu ◽

Lauren Gandy ◽

Weihua Jin ◽

...

Keyword(s):

Large Scale ◽

Molecular Mechanisms ◽

Epigallocatechin Gallate ◽

Cancer Drug ◽

Dynamic Interactions ◽

Cancer Drug Discovery ◽

Intrinsically Disordered ◽

Terminal Domain ◽

Cancerous Cells

AbstractEpigallocatechin gallate (EGCG) from green tea can induce apoptosis in cancerous cells, but the underlying molecular mechanisms remain poorly understood. Using SPR and NMR, here we report a direct, μM interaction between EGCG and the tumor suppressor p53 (KD = 1.6 ± 1.4 μM), with the disordered N-terminal domain (NTD) identified as the major binding site (KD = 4 ± 2 μM). Large scale atomistic simulations (>100 μs), SAXS and AUC demonstrate that EGCG-NTD interaction is dynamic and EGCG causes the emergence of a subpopulation of compact bound conformations. The EGCG-p53 interaction disrupts p53 interaction with its regulatory E3 ligase MDM2 and inhibits ubiquitination of p53 by MDM2 in an in vitro ubiquitination assay, likely stabilizing p53 for anti-tumor activity. Our work provides insights into the mechanisms for EGCG’s anticancer activity and identifies p53 NTD as a target for cancer drug discovery through dynamic interactions with small molecules.

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mtDNAcombine: tools to combine sequences from multiple studies

BMC Bioinformatics ◽

10.1186/s12859-021-04048-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Eleanor F. Miller ◽

Andrea Manica

Keyword(s):

Sequence Data ◽

Data Extraction ◽

Bayesian Skyline Plot ◽

Model Organisms ◽

Data Sets ◽

Data Handling ◽

Online Database ◽

Genetic Studies ◽

Wide Range ◽

Existing Data

Abstract Background Today an unprecedented amount of genetic sequence data is stored in publicly available repositories. For decades now, mitochondrial DNA (mtDNA) has been the workhorse of genetic studies, and as a result, there is a large volume of mtDNA data available in these repositories for a wide range of species. Indeed, whilst whole genome sequencing is an exciting prospect for the future, for most non-model organisms’ classical markers such as mtDNA remain widely used. By compiling existing data from multiple original studies, it is possible to build powerful new datasets capable of exploring many questions in ecology, evolution and conservation biology. One key question that these data can help inform is what happened in a species’ demographic past. However, compiling data in this manner is not trivial, there are many complexities associated with data extraction, data quality and data handling. Results Here we present the mtDNAcombine package, a collection of tools developed to manage some of the major decisions associated with handling multi-study sequence data with a particular focus on preparing sequence data for Bayesian skyline plot demographic reconstructions. Conclusions There is now more genetic information available than ever before and large meta-data sets offer great opportunities to explore new and exciting avenues of research. However, compiling multi-study datasets still remains a technically challenging prospect. The mtDNAcombine package provides a pipeline to streamline the process of downloading, curating, and analysing sequence data, guiding the process of compiling data sets from the online database GenBank.

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Comprehensive Analysis of Cardiac Xeno-Graft Unveils Rejection Mechanisms

International Journal of Molecular Sciences ◽

10.3390/ijms22020751 ◽

2021 ◽

Vol 22 (2) ◽

pp. 751

Author(s):

Min Young Park ◽

Bala Murali Krishna Vasamsetti ◽

Wan Seop Kim ◽

Hee Jung Kang ◽

Do-Young Kim ◽

...

Keyword(s):

Graft Rejection ◽

Molecular Mechanisms ◽

Cardiac Fibrosis ◽

Cardiac Tissue ◽

Inflammatory Responses ◽

Blood Parameters ◽

Quantitative Real Time Pcr ◽

Porcine Heart ◽

End Stage Heart Failure ◽

End Stage

Porcine heart xenotransplantation is a potential treatment for patients with end-stage heart failure. To understand molecular mechanisms of graft rejection after heart transplantation, we transplanted a 31-day-old alpha-1,3-galactosyltransferase knockout (GTKO) porcine heart to a five-year-old cynomolgus monkey. Histological and transcriptome analyses were conducted on xenografted cardiac tissue at rejection (nine days after transplantation). The recipient monkey’s blood parameters were analyzed on days −7, −3, 1, 4, and 7. Validation was conducted by quantitative real-time PCR (qPCR) with selected genes. A non-transplanted GTKO porcine heart from an age-matched litter was used as a control. The recipient monkey showed systemic inflammatory responses, and the rejected cardiac graft indicated myocardial infarction and cardiac fibrosis. The transplanted heart exhibited a total of 3748 differentially expressed genes compared to the non-transplanted heart transcriptome, with 2443 upregulated and 1305 downregulated genes. Key biological pathways involved at the terminal stage of graft rejection were cardiomyopathies, extracellular interactions, and ion channel activities. The results of qPCR evaluation were in agreement with the transcriptome data. Transcriptome analysis of porcine cardiac tissue at graft rejection reveals dysregulation of the key molecules and signaling pathways, which play relevant roles on structural and functional integrities of the heart.

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Endurance Training Regulates Expression of Some Angiogenesis-Related Genes in Cardiac Tissue of Experimentally Induced Diabetic Rats

Biomolecules ◽

10.3390/biom11040498 ◽

2021 ◽

Vol 11 (4) ◽

pp. 498

Author(s):

Mojdeh Khajehlandi ◽

Lotfali Bolboli ◽

Marefat Siahkuhian ◽

Mohammad Rami ◽

Mohammadreza Tabandeh ◽

...

Keyword(s):

Gene Expression ◽

Endurance Training ◽

Molecular Mechanisms ◽

Cardiac Tissue ◽

Critical Role ◽

Diabetic Rats ◽

Moderate Intensity ◽

Pcr Analysis ◽

Cardiac Tissues ◽

The Impact

Exercise can ameliorate cardiovascular dysfunctions in the diabetes condition, but its precise molecular mechanisms have not been entirely understood. The aim of the present study was to determine the impact of endurance training on expression of angiogenesis-related genes in cardiac tissue of diabetic rats. Thirty adults male Wistar rats were randomly divided into three groups (N = 10) including diabetic training (DT), sedentary diabetes (SD), and sedentary healthy (SH), in which diabetes was induced by a single dose of streptozotocin (50 mg/kg). Endurance training (ET) with moderate-intensity was performed on a motorized treadmill for six weeks. Training duration and treadmill speed were increased during five weeks, but they were kept constant at the final week, and slope was zero at all stages. Real-time polymerase chain reaction (RT-PCR) analysis was used to measure the expression of myocyte enhancer factor-2C (MEF2C), histone deacetylase-4 (HDAC4) and Calmodulin-dependent protein kinase II (CaMKII) in cardiac tissues of the rats. Our results demonstrated that six weeks of ET increased gene expression of MEF2C significantly (p < 0.05), and caused a significant reduction in HDAC4 and CaMKII gene expression in the DT rats compared to the SD rats (p < 0.05). We concluded that moderate-intensity ET could play a critical role in ameliorating cardiovascular dysfunction in a diabetes condition by regulating the expression of some angiogenesis-related genes in cardiac tissues.

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Integrative cBioPortal Analysis Revealed Molecular Mechanisms That Regulate EGFR-PI3K-AKT-mTOR Pathway in Diffuse Gliomas of the Brain

Cancers ◽

10.3390/cancers13133247 ◽

2021 ◽

Vol 13 (13) ◽

pp. 3247

Author(s):

Petar Brlek ◽

Anja Kafka ◽

Anja Bukovac ◽

Nives Pećina-Šlaus

Keyword(s):

Large Scale ◽

Molecular Mechanisms ◽

In Silico Analysis ◽

Total Sample ◽

Mtor Signaling ◽

Biological Behavior ◽

Mrna Transcription ◽

Diffuse Gliomas ◽

New Treatment ◽

Using Data

Diffuse gliomas are a heterogeneous group of tumors with aggressive biological behavior and a lack of effective treatment methods. Despite new molecular findings, the differences between pathohistological types still require better understanding. In this in silico analysis, we investigated AKT1, AKT2, AKT3, CHUK, GSK3β, EGFR, PTEN, and PIK3AP1 as participants of EGFR-PI3K-AKT-mTOR signaling using data from the publicly available cBioPortal platform. Integrative large-scale analyses investigated changes in copy number aberrations (CNA), methylation, mRNA transcription and protein expression within 751 samples of diffuse astrocytomas, anaplastic astrocytomas and glioblastomas. The study showed a significant percentage of CNA in PTEN (76%), PIK3AP1 and CHUK (75% each), EGFR (74%), AKT2 (39%), AKT1 (32%), AKT3 (19%) and GSK3β (18%) in the total sample. Comprehensive statistical analyses show how genomics and epigenomics affect the expression of examined genes differently across various pathohistological types and grades, suggesting that genes AKT3, CHUK and PTEN behave like tumor suppressors, while AKT1, AKT2, EGFR, and PIK3AP1 show oncogenic behavior and are involved in enhanced activity of the EGFR-PI3K-AKT-mTOR signaling pathway. Our findings contribute to the knowledge of the molecular differences between pathohistological types and ultimately offer the possibility of new treatment targets and personalized therapies in patients with diffuse gliomas.

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Antihyperglycaemic therapies and cancer risk

Diabetes and Vascular Disease Research ◽

10.1177/1479164114549553 ◽

2014 ◽

Vol 11 (6) ◽

pp. 371-389 ◽

Cited By ~ 17

Author(s):

Stefan Z Lutz ◽

Harald Staiger ◽

Andreas Fritsche ◽

Hans-Ulrich Häring

Keyword(s):

Cancer Risk ◽

Large Scale ◽

Tumour Growth ◽

Molecular Mechanisms ◽

Growth Promotion ◽

Protective Effects ◽

Antidiabetic Drug ◽

Safety Issues ◽

Drug Classes ◽

Few Data

Aims: This review is aimed at highlighting the potential mitogenic/tumour growth–promoting or antimitogenic/tumour growth–inhibiting effects of the main antihyperglycaemic drug classes. Methods: We review and discuss the most current studies evaluating the association between antidiabetic medications used in clinical practice and malignancies as described so far. Results: Metformin seems to be the only antidiabetic drug to exert protective effects both on monotherapy and also when combined with other oral antidiabetic drugs or insulins in several site-specific cancers. In contrast, several other drug classes may increase cancer risk. Some reason for concern remains regarding sulphonylureas and also the incretin-based therapies regarding pancreas and thyroid cancers and the sodium glucose cotransporter-2 inhibitors as well as pioglitazone regarding bladder cancer. The majority of meta-analyses suggest that there is no evidence for a causal relationship between insulin glargine and elevated cancer risk, although the studies have been controversially discussed. For α-glucosidase inhibitors and glinides, neutral or only few data upon cancer risk exist. Conclusion: Although the molecular mechanisms are not fully understood, a potential risk of mitogenicity and tumour growth promotion cannot be excluded in case of several antidiabetic drug classes. However, more large-scale, randomized, well-designed clinical studies with especially long follow-up time periods are needed to get reliable answers to these safety issues.

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Sex differences in white adipose tissue expansion: emerging molecular mechanisms

Clinical Science ◽

10.1042/cs20210086 ◽

2021 ◽

Vol 135 (24) ◽

pp. 2691-2708

Author(s):

Simon T. Bond ◽

Anna C. Calkin ◽

Brian G. Drew

Keyword(s):

Sex Differences ◽

Sexual Dimorphism ◽

Gene Networks ◽

Large Scale ◽

Molecular Mechanisms ◽

Association Studies ◽

Tissue Expansion ◽

Economic Systems ◽

Genomic Association ◽

Males And Females

Abstract The escalating prevalence of individuals becoming overweight and obese is a rapidly rising global health problem, placing an enormous burden on health and economic systems worldwide. Whilst obesity has well described lifestyle drivers, there is also a significant and poorly understood component that is regulated by genetics. Furthermore, there is clear evidence for sexual dimorphism in obesity, where overall risk, degree, subtype and potential complications arising from obesity all differ between males and females. The molecular mechanisms that dictate these sex differences remain mostly uncharacterised. Many studies have demonstrated that this dimorphism is unable to be solely explained by changes in hormones and their nuclear receptors alone, and instead manifests from coordinated and highly regulated gene networks, both during development and throughout life. As we acquire more knowledge in this area from approaches such as large-scale genomic association studies, the more we appreciate the true complexity and heterogeneity of obesity. Nevertheless, over the past two decades, researchers have made enormous progress in this field, and some consistent and robust mechanisms continue to be established. In this review, we will discuss some of the proposed mechanisms underlying sexual dimorphism in obesity, and discuss some of the key regulators that influence this phenomenon.

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MIC-Drop: A platform for large-scale in vivo CRISPR screens

Science ◽

10.1126/science.abi8870 ◽

2021 ◽

pp. eabi8870

Author(s):

Saba Parvez ◽

Chelsea Herdman ◽

Manu Beerens ◽

Korak Chakraborti ◽

Zachary P. Harmer ◽

...

Keyword(s):

Large Scale ◽

Cultured Cells ◽

Cardiac Development ◽

Droplet Microfluidics ◽

Model Organisms ◽

Genetic Screens ◽

Large Numbers ◽

And Function ◽

Genome Scale

CRISPR-Cas9 can be scaled up for large-scale screens in cultured cells, but CRISPR screens in animals have been challenging because generating, validating, and keeping track of large numbers of mutant animals is prohibitive. Here, we report Multiplexed Intermixed CRISPR Droplets (MIC-Drop), a platform combining droplet microfluidics, single-needle en masse CRISPR ribonucleoprotein injections, and DNA barcoding to enable large-scale functional genetic screens in zebrafish. The platform can efficiently identify genes responsible for morphological or behavioral phenotypes. In one application, we show MIC-Drop can identify small molecule targets. Furthermore, in a MIC-Drop screen of 188 poorly characterized genes, we discover several genes important for cardiac development and function. With the potential to scale to thousands of genes, MIC-Drop enables genome-scale reverse-genetic screens in model organisms.

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The daunting polygenicity of mental illness: making a new map

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2017.0031 ◽

2018 ◽

Vol 373 (1742) ◽

pp. 20170031 ◽

Cited By ~ 18

Author(s):

Steven E. Hyman

Keyword(s):

Mental Health ◽

Large Scale ◽

Computational Models ◽

Model Organisms ◽

Human Biology ◽

Genetic Studies ◽

Computational Tools ◽

Experimental Systems ◽

Terra Incognita ◽

Phenotypic Complexity

An epochal opportunity to elucidate the pathogenic mechanisms of psychiatric disorders has emerged from advances in genomic technology, new computational tools and the growth of international consortia committed to data sharing. The resulting large-scale, unbiased genetic studies have begun to yield new biological insights and with them the hope that a half century of stasis in psychiatric therapeutics will come to an end. Yet a sobering picture is coming into view; it reveals daunting genetic and phenotypic complexity portending enormous challenges for neurobiology. Successful exploitation of results from genetics will require eschewal of long-successful reductionist approaches to investigation of gene function, a commitment to supplanting much research now conducted in model organisms with human biology, and development of new experimental systems and computational models to analyse polygenic causal influences. In short, psychiatric neuroscience must develop a new scientific map to guide investigation through a polygenic terra incognita . This article is part of a discussion meeting issue ‘Of mice and mental health: facilitating dialogue between basic and clinical neuroscientists’.

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