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Article: Parenclitic and Synolytic Networks Revisited.

Nazarenko, Tatiana / Whitwell, Harry J / Blyuss, Oleg / Zaikin, Alexey

2021 Volume 12, Page(s) 733783

Abstract: Parenclitic networks provide a powerful and relatively new way to coerce multidimensional data into a graph form, enabling the application of graph theory to evaluate features. Different algorithms have been published for constructing parenclitic ... ...

Abstract	Parenclitic networks provide a powerful and relatively new way to coerce multidimensional data into a graph form, enabling the application of graph theory to evaluate features. Different algorithms have been published for constructing parenclitic networks, leading to the question-which algorithm should be chosen? Initially, it was suggested to calculate the weight of an edge between two nodes of the network as a deviation from a linear regression, calculated for a dependence of one of these features on the other. This method works well, but not when features do not have a linear relationship. To overcome this, it was suggested to calculate edge weights as the distance from the area of most probable values by using a kernel density estimation. In these two approaches only one class (typically controls or healthy population) is used to construct a model. To take account of a second class, we have introduced synolytic networks, using a boundary between two classes on the feature-feature plane to estimate the weight of the edge between these features. Common to all these approaches is that topological indices can be used to evaluate the structure represented by the graphs. To compare these network approaches alongside more traditional machine-learning algorithms, we performed a substantial analysis using both synthetic data with
Language	English
Publishing date	2021-10-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2021.733783
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Article ; Online: HiLight-PTM: an online application to aid matching peptide pairs with isotopically labelled PTMs.

Whitwell, Harry J / DiMaggio, Peter

Bioinformatics (Oxford, England)

2019 Volume 36, Issue 3, Page(s) 938–939

Abstract: Motivation: Database searching of isotopically labelled PTMs can be problematic and we frequently find that only one, or neither in a heavy/light pair are assigned. In such cases, having a pair of MS/MS spectra that differ due to an isotopic label can ... ...

Abstract	Motivation: Database searching of isotopically labelled PTMs can be problematic and we frequently find that only one, or neither in a heavy/light pair are assigned. In such cases, having a pair of MS/MS spectra that differ due to an isotopic label can assist in identifying the relevant m/z values that support the correct peptide annotation or can be used for de novo sequencing. Results: We have developed an online application that identifies matching peaks and peaks differing by the appropriate mass shift (difference between heavy and light PTM) between two MS/MS spectra. Furthermore, the application predicts, from the exact-match peaks, the mass of their complementary ions and highlights these as high confidence matches between the two spectra. The result is a tool to visually compare two spectra, and downloadable peaks lists that can be used to support de novo sequencing. Availability and implementation: HiLight-PTM is released using shinyapps.io by RStudio, and can be accessed from any internet browser at https://harrywhitwell.shinyapps.io/hilight-ptm/. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Peptides ; Software ; Tandem Mass Spectrometry
Chemical Substances	Peptides
Language	English
Publishing date	2019-08-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btz654
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Article ; Online: Characterization of emergent toxigenic M1

Li, Ho Kwong / Zhi, Xiangyun / Vieira, Ana / Whitwell, Harry J / Schricker, Amelia / Jauneikaite, Elita / Li, Hanqi / Yosef, Ahmed / Andrew, Ivan / Game, Laurence / Turner, Claire E / Lamagni, Theresa / Coelho, Juliana / Sriskandan, Shiranee

Microbial genomics

2023 Volume 9, Issue 4

Abstract: Streptococcus ... ...

Abstract	Streptococcus pyogenes
MeSH term(s)	Streptococcus pyogenes/genetics ; Phylogeny ; Proteomics ; Antigens, Bacterial/genetics ; England
Chemical Substances	Antigens, Bacterial
Language	English
Publishing date	2023-04-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2835258-0
ISSN	2057-5858 ; 2057-5858
ISSN (online)	2057-5858
ISSN	2057-5858
DOI	10.1099/mgen.0.000994
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Article ; Online: Non-Histone Protein Methylation: Biological Significance and Bioengineering Potential.

Di Blasi, Roberto / Blyuss, Oleg / Timms, John F / Conole, Daniel / Ceroni, Francesca / Whitwell, Harry J

ACS chemical biology

2021 Volume 16, Issue 2, Page(s) 238–250

Abstract: Protein methylation is a key post-translational modification whose effects on gene expression have been intensively studied over the last two decades. Recently, renewed interest in non-histone protein methylation has gained momentum for its role in ... ...

Abstract	Protein methylation is a key post-translational modification whose effects on gene expression have been intensively studied over the last two decades. Recently, renewed interest in non-histone protein methylation has gained momentum for its role in regulating important cellular processes and the activity of many proteins, including transcription factors, enzymes, and structural complexes. The extensive and dynamic role that protein methylation plays within the cell also highlights its potential for bioengineering applications. Indeed, while synthetic histone protein methylation has been extensively used to engineer gene expression, engineering of non-histone protein methylation has not been fully explored yet. Here, we report the latest findings, highlighting how non-histone protein methylation is fundamental for certain cellular functions and is implicated in disease, and review recent efforts in the engineering of protein methylation.
MeSH term(s)	Alzheimer Disease/physiopathology ; Animals ; Bioengineering ; Cell Cycle/physiology ; Humans ; Methylation ; Mitochondria/metabolism ; Neoplasms/physiopathology ; Protein Processing, Post-Translational ; Proteins/metabolism
Chemical Substances	Proteins
Language	English
Publishing date	2021-01-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.0c00771
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Article ; Online: Impact of modular mitochondrial epistatic interactions on the evolution of human subpopulations.

Shinde, Pramod / Whitwell, Harry J / Verma, Rahul Kumar / Ivanchenko, Mikhail / Zaikin, Alexey / Jalan, Sarika

Mitochondrion

2021 Volume 58, Page(s) 111–122

Abstract: Investigation of human mitochondrial (mt) genome variation has been shown to provide insights to the human history and natural selection. By analyzing 24,167 human mt-genome samples, collected for five continents, we have developed a co-mutation network ... ...

Abstract	Investigation of human mitochondrial (mt) genome variation has been shown to provide insights to the human history and natural selection. By analyzing 24,167 human mt-genome samples, collected for five continents, we have developed a co-mutation network model to investigate characteristic human evolutionary patterns. The analysis highlighted richer co-mutating regions of the mt-genome, suggesting the presence of epistasis. Specifically, a large portion of COX genes was found to co-mutate in Asian and American populations, whereas, in African, European, and Oceanic populations, there was greater co-mutation bias in hypervariable regions. Interestingly, this study demonstrated hierarchical modularity as a crucial agent for these co-mutation networks. More profoundly, our ancestry-based co-mutation module analyses showed that mutations cluster preferentially in known mitochondrial haplogroups. Contemporary human mt-genome nucleotides most closely resembled the ancestral state, and very few of them were found to be ancestral-variants. Overall, these results demonstrated that subpopulation-based biases may favor mitochondrial gene specific epistasis.
MeSH term(s)	Epistasis, Genetic ; Evolution, Molecular ; Genes, Mitochondrial ; Humans ; Mutation ; Population Groups/genetics
Language	English
Publishing date	2021-02-20
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2056923-3
ISSN	1872-8278 ; 1567-7249
ISSN (online)	1872-8278
ISSN	1567-7249
DOI	10.1016/j.mito.2021.02.004
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Article ; Online: Commentary on "The road to reliable peptide assays is paved with good guidelines".

Kowalka, Anna M / Alexiadou, Kleopatra / Cuenco, Joyceline / Clarke, Rosemary E / Camuzeaux, Stephane / Minnion, James / Williams, Emma L / Bech, Paul / Purkayastha, Sanjay / Ahmed, Ahmed R / Takats, Zoltan / Khoo, Bernard / Whitwell, Harry J / Romero, Maria G / Bloom, Stephen R / Lewis, Matthew R / Tan, Tricia M-M

Clinical endocrinology

2023 Volume 98, Issue 6, Page(s) 763–765

MeSH term(s)	Humans ; Peptides ; Obesity
Chemical Substances	Peptides
Language	English
Publishing date	2023-03-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	121745-8
ISSN	1365-2265 ; 0300-0664
ISSN (online)	1365-2265
ISSN	0300-0664
DOI	10.1111/cen.14894
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Article ; Online: Generation of novel trimeric fragments of human SP-A and SP-D after recombinant soluble expression in E. coli.

Watson, Alastair / Sørensen, Grith L / Holmskov, Uffe / Whitwell, Harry J / Madsen, Jens / Clark, Howard

Immunobiology

2020 Volume 225, Issue 4, Page(s) 151953

Abstract: Surfactant treatment for neonatal respiratory distress syndrome has dramatically improved survival of preterm infants. However, this has resulted in a markedly increased incidence of sequelae such as neonatal chronic inflammatory lung disease. The ... ...

Abstract	Surfactant treatment for neonatal respiratory distress syndrome has dramatically improved survival of preterm infants. However, this has resulted in a markedly increased incidence of sequelae such as neonatal chronic inflammatory lung disease. The current surfactant preparations in clinical use lack the natural lung defence proteins surfactant proteins (SP)-A and D. These are known to have anti-inflammatory and anti-infective properties essential for maintaining healthy non-inflamed lungs. Supplementation of currently available animal derived surfactant therapeutics with these anti-inflammatory proteins in the first few days of life could prevent the development of inflammatory lung disease in premature babies. However, current systems for production of recombinant versions of SP-A and SP-D require a complex solubilisation and refolding protocol limiting expression at scale for drug development. Using a novel solubility tag, we describe the expression and purification of recombinant fragments of human (rfh) SP-A and SP-D using Escherichia coli without the need for refolding. We obtained a mean (± SD) of 23.3 (± 5.4) mg and 86 mg (± 3.5) per litre yield of rfhSP-A and rfhSP-D, respectively. rfhSP-D was trimeric and 68% bound to a ManNAc-affinity column, giving a final yield of 57.5 mg/litre of highly pure protein, substantially higher than the 3.3 mg/litre obtained through the standard refolding protocol. Further optimisation of this novel lab based method could potentially make rfhSP-A and rfhSP-D production more commercially feasible to enable development of novel therapeutics for the treatment of lung infection and inflammation.
MeSH term(s)	Cloning, Molecular ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression ; Humans ; Models, Molecular ; Protein Conformation ; Protein Multimerization ; Receptors, Cell Surface/chemistry ; Receptors, Cell Surface/genetics ; Receptors, Cell Surface/isolation & purification ; Receptors, Cell Surface/metabolism ; Receptors, Immunologic/chemistry ; Receptors, Immunologic/genetics ; Receptors, Immunologic/isolation & purification ; Receptors, Immunologic/metabolism ; Recombinant Proteins ; Structure-Activity Relationship
Chemical Substances	Receptors, Cell Surface ; Receptors, Immunologic ; Recombinant Proteins ; glycoprotein 340 ; surfactant protein A receptor
Language	English
Publishing date	2020-05-27
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	563292-4
ISSN	1878-3279 ; 0171-2985
ISSN (online)	1878-3279
ISSN	0171-2985
DOI	10.1016/j.imbio.2020.151953
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Article ; Online: Serum biomarker-based early detection of pancreatic ductal adenocarcinomas with ensemble learning.

Nené, Nuno R / Ney, Alexander / Nazarenko, Tatiana / Blyuss, Oleg / Johnston, Harvey E / Whitwell, Harry J / Sedlak, Eva / Gentry-Maharaj, Aleksandra / Apostolidou, Sophia / Costello, Eithne / Greenhalf, William / Jacobs, Ian / Menon, Usha / Hsuan, Justin / Pereira, Stephen P / Zaikin, Alexey / Timms, John F

Communications medicine

2023 Volume 3, Issue 1, Page(s) 10

Abstract: Background: Earlier detection of pancreatic ductal adenocarcinoma (PDAC) is key to improving patient outcomes, as it is mostly detected at advanced stages which are associated with poor survival. Developing non-invasive blood tests for early detection ... ...

Abstract	Background: Earlier detection of pancreatic ductal adenocarcinoma (PDAC) is key to improving patient outcomes, as it is mostly detected at advanced stages which are associated with poor survival. Developing non-invasive blood tests for early detection would be an important breakthrough. Methods: The primary objective of the work presented here is to use a dataset that is prospectively collected, to quantify a set of cancer-associated proteins and construct multi-marker models with the capacity to predict PDAC years before diagnosis. The data used is part of a nested case-control study within the UK Collaborative Trial of Ovarian Cancer Screening and is comprised of 218 samples, collected from a total of 143 post-menopausal women who were diagnosed with pancreatic cancer within 70 months after sample collection, and 249 matched non-cancer controls. We develop a stacked ensemble modelling technique to achieve robustness in predictions and, therefore, improve performance in newly collected datasets. Results: Here we show that with ensemble learning we can predict PDAC status with an AUC of 0.91 (95% CI 0.75-1.0), sensitivity of 92% (95% CI 0.54-1.0) at 90% specificity, up to 1 year prior to diagnosis, and at an AUC of 0.85 (95% CI 0.74-0.93) up to 2 years prior to diagnosis (sensitivity of 61%, 95% CI 0.17-0.83, at 90% specificity). Conclusions: The ensemble modelling strategy explored here outperforms considerably biomarker combinations cited in the literature. Further developments in the selection of classifiers balancing performance and heterogeneity should further enhance the predictive capacity of the method.
Language	English
Publishing date	2023-01-20
Publishing country	England
Document type	Journal Article
ISSN	2730-664X
ISSN (online)	2730-664X
DOI	10.1038/s43856-023-00237-5
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Article ; Online: Intracellular Chloride Channels Regulate Endothelial Metabolic Reprogramming in Pulmonary Arterial Hypertension.

Alzaydi, Mai M / Abdul-Salam, Vahitha B / Whitwell, Harry J / Russomanno, Giusy / Glynos, Angelos / Capece, Daria / Szabadkai, Gyorgy / Wilkins, Martin R / Wojciak-Stothard, Beata

American journal of respiratory cell and molecular biology

2022 Volume 68, Issue 1, Page(s) 103–115

Abstract: Mitochondrial fission and a metabolic switch from oxidative phosphorylation to glycolysis are key features of vascular pathology in pulmonary arterial hypertension (PAH) and are associated with exuberant endothelial proliferation and apoptosis. The ... ...

Abstract	Mitochondrial fission and a metabolic switch from oxidative phosphorylation to glycolysis are key features of vascular pathology in pulmonary arterial hypertension (PAH) and are associated with exuberant endothelial proliferation and apoptosis. The underlying mechanisms are poorly understood. We describe the contribution of two intracellular chloride channel proteins, CLIC1 and CLIC4, both highly expressed in PAH and cancer, to mitochondrial dysfunction and energy metabolism in PAH endothelium. Pathological overexpression of CLIC proteins induces mitochondrial fragmentation, inhibits mitochondrial cristae formation, and induces metabolic shift toward glycolysis in human pulmonary artery endothelial cells, consistent with changes observed in patient-derived cells. Interactions of CLIC proteins with structural components of the inner mitochondrial membrane offer mechanistic insights. Endothelial CLIC4 excision and mitofusin 2 supplementation have protective effects in human PAH cells and preclinical PAH. This study is the first to demonstrate the key role of endothelial intracellular chloride channels in the regulation of mitochondrial structure, biogenesis, and metabolic reprogramming in expression of the PAH phenotype.
MeSH term(s)	Humans ; Pulmonary Arterial Hypertension/metabolism ; Hypertension, Pulmonary/pathology ; Endothelial Cells/metabolism ; Familial Primary Pulmonary Hypertension/metabolism ; Pulmonary Artery/pathology ; Endothelium/metabolism ; Chloride Channels/genetics ; Chloride Channels/metabolism
Chemical Substances	Chloride Channels ; CLIC4 protein, human ; CLIC1 protein, human
Language	English
Publishing date	2022-10-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1025960-0
ISSN	1535-4989 ; 1044-1549
ISSN (online)	1535-4989
ISSN	1044-1549
DOI	10.1165/rcmb.2022-0111OC
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Article ; Online: Parenclitic networks for predicting ovarian cancer.

Whitwell, Harry J / Blyuss, Oleg / Menon, Usha / Timms, John F / Zaikin, Alexey

Oncotarget

2018 Volume 9, Issue 32, Page(s) 22717–22726

Abstract: Prediction and diagnosis of complex disease may not always be possible with a small number of biomarkers. Modern 'omics' technologies make it possible to cheaply and quantitatively assay hundreds of molecules generating large amounts of data from ... ...

Abstract	Prediction and diagnosis of complex disease may not always be possible with a small number of biomarkers. Modern 'omics' technologies make it possible to cheaply and quantitatively assay hundreds of molecules generating large amounts of data from individual samples. In this study, we describe a parenclitic network-based approach to disease classification using a synthetic data set modelled on data from the United Kingdom Collaborative Trial of Ovarian Cancer Screening (UKCTOCS) and serological assay data from a nested set of samples from the same study. This approach allows us to integrate quantitative proteomic and categorical metadata into a single network, and then use network topologies to construct logistic regression models for disease classification. In this study of ovarian cancer, comprising of 30 controls and cases with samples taken <14 months to diagnosis (
Language	English
Publishing date	2018-04-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2560162-3
ISSN	1949-2553 ; 1949-2553
ISSN (online)	1949-2553
ISSN	1949-2553
DOI	10.18632/oncotarget.25216
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