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Article ; Online: Exciting new tools for studying TREM2 in dementia.

Menzies, Georgina E / Torvell, Megan

Structure (London, England : 1993)

2021 Volume 29, Issue 11, Page(s) 1215–1216

Abstract: TREM2 has long been implicated as an Alzheimer's disease (AD) risk gene. In this issue of Structure, Szykowska et al. (2021) generate antibody single-chain variable fragments (scFvs) to the immunoglobulin(Ig)-like domain of human TREM2. They present two ... ...

Abstract	TREM2 has long been implicated as an Alzheimer's disease (AD) risk gene. In this issue of Structure, Szykowska et al. (2021) generate antibody single-chain variable fragments (scFvs) to the immunoglobulin(Ig)-like domain of human TREM2. They present two co-crystalized structures and characterize the functional impact of these scFvs on TREM2.
MeSH term(s)	Alzheimer Disease ; Humans ; Membrane Glycoproteins ; Receptors, Immunologic
Chemical Substances	Membrane Glycoproteins ; Receptors, Immunologic ; TREM2 protein, human
Language	English
Publishing date	2021-11-29
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2021.10.009
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Article ; Online: Carcinogen-induced DNA structural distortion differences in the RAS gene isoforms; the importance of local sequence.

Menzies, Georgina E / Prior, Ian A / Brancale, Andrea / Reed, Simon H / Lewis, Paul D

BMC chemistry

2021 Volume 15, Issue 1, Page(s) 51

Abstract: Background: Local sequence context is known to have an impact on the mutational pattern seen in cancer. The RAS genes and a smoking carcinogen, Benzo[a]pyrene diol epoxide (BPDE), have been utilised to explore these context effects. BPDE is known to ... ...

Abstract	Background: Local sequence context is known to have an impact on the mutational pattern seen in cancer. The RAS genes and a smoking carcinogen, Benzo[a]pyrene diol epoxide (BPDE), have been utilised to explore these context effects. BPDE is known to form an adduct at the guanines in a number of RAS gene sites, KRAS codons 12, 13 and 14, NRAS codon 12, and HRAS codons 12 and 14. Results: Molecular modelling techniques, along with multivariate analysis, have been utilised to determine the sequence influenced differences between BPDE-adducted RAS gene sequences as well as the local distortion caused by the adducts. Conclusions: We conclude that G:C > T:A mutations at KRAS codon 12 in the tumours of lung cancer patients (who smoke), proposed to be predominantly caused by BPDE, are due to the effect of the interaction methyl group at the C5 position of the thymine base in the KRAS sequence with the BPDE carcinogen investigated causing increased distortion. We further suggest methylated cytosine would have a similar effect, showing the importance of methylation in cancer development.
Language	English
Publishing date	2021-09-14
Publishing country	Switzerland
Document type	Journal Article
ISSN	2661-801X
ISSN (online)	2661-801X
DOI	10.1186/s13065-021-00777-8
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Article ; Online: Characterizing the original anti-C5 function-blocking antibody, BB5.1, for species specificity, mode of action and interactions with C5.

Zelek, Wioleta M / Menzies, Georgina E / Brancale, Andrea / Stockinger, Brigitta / Morgan, Bryan Paul

Immunology

2020 Volume 161, Issue 2, Page(s) 103–113

Abstract: The implication of complement in multiple diseases over the last 20 years has fuelled interest in developing anti-complement drugs. To date, the focus has been on C5; blocking cleavage of C5 prevents formation of two pro-inflammatory activities, C5a ... ...

Abstract	The implication of complement in multiple diseases over the last 20 years has fuelled interest in developing anti-complement drugs. To date, the focus has been on C5; blocking cleavage of C5 prevents formation of two pro-inflammatory activities, C5a anaphylatoxin and membrane attack complex. The concept of C5 blockade to inhibit inflammation dates back 30 years to the description of BB5.1, an anti-C5 blocking monoclonal antibody raised in C5-deficient mice. This antibody proved an invaluable tool to demonstrate complement involvement in mouse disease models and catalysed enthusiasm for anti-complement drug development, culminating in the anti-human C5 monoclonal antibody eculizumab, the most successful anti-complement drug to date, already in clinical use for several rare diseases. Despite its key role in providing proof-of-concept for C5 blockade, the mechanism of BB5.1 inhibition remains poorly understood. Here, we characterized BB5.1 cross-species inhibition, C5 binding affinity and chain specificity. BB5.1 efficiently inhibited C5 in mouse serum but not in human or other rodent sera; it prevented C5 cleavage and C5a generation. BB5.1 bound the C5 α-chain with high affinity and slow off-rate. BB5.1 complementarity-determining regions were obtained and docking algorithms were used to predict the likely binding interface on mouse C5.
MeSH term(s)	Animals ; Antibodies, Monoclonal/genetics ; Antibodies, Monoclonal/metabolism ; Antibodies, Monoclonal, Humanized/genetics ; Antibodies, Monoclonal, Humanized/therapeutic use ; Complement C5/genetics ; Complement C5/metabolism ; Computer Simulation ; Cross Reactions ; Guinea Pigs ; Humans ; Hybridomas ; Inflammation/therapy ; Mice ; Mice, Knockout ; Molecular Docking Simulation ; Protein Binding ; Proteolysis ; Rabbits ; Species Specificity
Chemical Substances	Antibodies, Monoclonal ; Antibodies, Monoclonal, Humanized ; Complement C5 ; eculizumab (A3ULP0F556)
Language	English
Publishing date	2020-07-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80124-0
ISSN	1365-2567 ; 0019-2805 ; 0953-4954
ISSN (online)	1365-2567
ISSN	0019-2805 ; 0953-4954
DOI	10.1111/imm.13228
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Article ; Online: Glycosylation increases active site rigidity leading to improved enzyme stability and turnover.

Ramakrishnan, Krithika / Johnson, Rachel L / Winter, Samuel D / Worthy, Harley L / Thomas, Christopher / Humer, Diana C / Spadiut, Oliver / Hindson, Sarah H / Wells, Stephen / Barratt, Andrew H / Menzies, Georgina E / Pudney, Christopher R / Jones, D Dafydd

The FEBS journal

2023 Volume 290, Issue 15, Page(s) 3812–3827

Abstract: Glycosylation is the most prevalent protein post-translational modification, with a quarter of glycosylated proteins having enzymatic properties. Yet, the full impact of glycosylation on the protein structure-function relationship, especially in enzymes, ...

Abstract	Glycosylation is the most prevalent protein post-translational modification, with a quarter of glycosylated proteins having enzymatic properties. Yet, the full impact of glycosylation on the protein structure-function relationship, especially in enzymes, is still limited. Here, we show that glycosylation rigidifies the important commercial enzyme horseradish peroxidase (HRP), which in turn increases its turnover and stability. Circular dichroism spectroscopy revealed that glycosylation increased holo-HRP's thermal stability and promoted significant helical structure in the absence of haem (apo-HRP). Glycosylation also resulted in a 10-fold increase in enzymatic turnover towards o-phenylenediamine dihydrochloride when compared to its nonglycosylated form. Utilising a naturally occurring site-specific probe of active site flexibility (Trp117) in combination with red-edge excitation shift fluorescence spectroscopy, we found that glycosylation significantly rigidified the enzyme. In silico simulations confirmed that glycosylation largely decreased protein backbone flexibility, especially in regions close to the active site and the substrate access channel. Thus, our data show that glycosylation does not just have a passive effect on HRP stability but can exert long-range effects that mediate the 'native' enzyme's activity and stability through changes in inherent dynamics.
MeSH term(s)	Enzyme Stability ; Glycosylation ; Catalytic Domain ; Protein Processing, Post-Translational ; Spectrometry, Fluorescence
Language	English
Publishing date	2023-04-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16783
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Article ; Online: Glycosylation increases active site rigidity leading to improved enzyme stability and turnover

Ramakrishnan, Krithika / Johnson, Rachel L. / Winter, Samuel D. / Worthy, Harley L. / Thomas, Christopher / Humer, Diana C. / Spadiut, Oliver / Hindson, Sarah H. / Wells, Stephen / Barratt, Andrew H. / Menzies, Georgina E. / Pudney, Christopher R. / Jones, D. Dafydd

The FEBS Journal. 2023 Aug., v. 290, no. 15 p.3812-3827

2023

Abstract: Glycosylation is the most prevalent protein post‐translational modification, with a quarter of glycosylated proteins having enzymatic properties. Yet, the full impact of glycosylation on the protein structure–function relationship, especially in enzymes, ...

Abstract	Glycosylation is the most prevalent protein post‐translational modification, with a quarter of glycosylated proteins having enzymatic properties. Yet, the full impact of glycosylation on the protein structure–function relationship, especially in enzymes, is still limited. Here, we show that glycosylation rigidifies the important commercial enzyme horseradish peroxidase (HRP), which in turn increases its turnover and stability. Circular dichroism spectroscopy revealed that glycosylation increased holo‐HRP's thermal stability and promoted significant helical structure in the absence of haem (apo‐HRP). Glycosylation also resulted in a 10‐fold increase in enzymatic turnover towards o‐phenylenediamine dihydrochloride when compared to its nonglycosylated form. Utilising a naturally occurring site‐specific probe of active site flexibility (Trp117) in combination with red‐edge excitation shift fluorescence spectroscopy, we found that glycosylation significantly rigidified the enzyme. In silico simulations confirmed that glycosylation largely decreased protein backbone flexibility, especially in regions close to the active site and the substrate access channel. Thus, our data show that glycosylation does not just have a passive effect on HRP stability but can exert long‐range effects that mediate the ‘native’ enzyme's activity and stability through changes in inherent dynamics.
Keywords	active sites ; circular dichroism spectroscopy ; computer simulation ; enzyme stability ; fluorescence emission spectroscopy ; glycosylation ; peroxidase ; structure-activity relationships ; thermal stability
Language	English
Dates of publication	2023-08
Size	p. 3812-3827.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16783
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Article ; Online: Base damage, local sequence context and TP53 mutation hotspots: a molecular dynamics study of benzo[a]pyrene induced DNA distortion and mutability.

Menzies, Georgina E / Reed, Simon H / Brancale, Andrea / Lewis, Paul D

Nucleic acids research

2015 Volume 43, Issue 19, Page(s) 9133–9146

Abstract: The mutational pattern for the TP53 tumour suppressor gene in lung tumours differs to other cancer types by having a higher frequency of G:C>T:A transversions. The aetiology of this differing mutation pattern is still unknown. Benzo[a]pyrene,diol epoxide ...

Abstract	The mutational pattern for the TP53 tumour suppressor gene in lung tumours differs to other cancer types by having a higher frequency of G:C>T:A transversions. The aetiology of this differing mutation pattern is still unknown. Benzo[a]pyrene,diol epoxide (BPDE) is a potent cigarette smoke carcinogen that forms guanine adducts at TP53 CpG mutation hotspot sites including codons 157, 158, 245, 248 and 273. We performed molecular modelling of BPDE-adducted TP53 duplex sequences to determine the degree of local distortion caused by adducts which could influence the ability of nucleotide excision repair. We show that BPDE adducted codon 157 has greater structural distortion than other TP53 G:C>T:A hotspot sites and that sequence context more distal to adjacent bases must influence local distortion. Using TP53 trinucleotide mutation signatures for lung cancer in smokers and non-smokers we further show that codons 157 and 273 have the highest mutation probability in smokers. Combining this information with adduct structural data we predict that G:C>T:A mutations at codon 157 in lung tumours of smokers are predominantly caused by BPDE. Our results provide insight into how different DNA sequence contexts show variability in DNA distortion at mutagen adduct sites that could compromise DNA repair at well characterized cancer related mutation hotspots.
MeSH term(s)	7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide/chemistry ; Base Sequence ; Benzo(a)pyrene/chemistry ; Carcinogens/chemistry ; Codon ; DNA/chemistry ; DNA Adducts/chemistry ; DNA Damage ; Genes, p53 ; Humans ; Hydrogen Bonding ; Lung Neoplasms/genetics ; Molecular Dynamics Simulation ; Mutation ; Smoking
Chemical Substances	Carcinogens ; Codon ; DNA Adducts ; benzo(a)pyrene-DNA adduct ; Benzo(a)pyrene (3417WMA06D) ; 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide (55097-80-8) ; DNA (9007-49-2)
Language	English
Publishing date	2015-09-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkv910
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Article ; Online: PIP2 depletion and altered endocytosis caused by expression of Alzheimer's disease-protective variant PLCγ2 R522.

Maguire, Emily / Menzies, Georgina E / Phillips, Thomas / Sasner, Michael / Williams, Harriet M / Czubala, Magdalena A / Evans, Neil / Cope, Emma L / Sims, Rebecca / Howell, Gareth R / Lloyd-Evans, Emyr / Williams, Julie / Allen, Nicholas D / Taylor, Philip R

The EMBO journal

2021 Volume 40, Issue 17, Page(s) e105603

Abstract: Variants identified in genome-wide association studies have implicated immune pathways in the development of Alzheimer's disease (AD). Here, we investigated the mechanistic basis for protection from AD associated with PLCγ2 R522, a rare coding variant of ...

Abstract	Variants identified in genome-wide association studies have implicated immune pathways in the development of Alzheimer's disease (AD). Here, we investigated the mechanistic basis for protection from AD associated with PLCγ2 R522, a rare coding variant of the PLCG2 gene. We studied the variant's role in macrophages and microglia of newly generated PLCG2-R522-expressing human induced pluripotent cell lines (hiPSC) and knockin mice, which exhibit normal endogenous PLCG2 expression. In all models, cells expressing the R522 mutation show a consistent non-redundant hyperfunctionality in the context of normal expression of other PLC isoforms. This manifests as enhanced release of cellular calcium ion stores in response to physiologically relevant stimuli like Fc-receptor ligation or exposure to Aβ oligomers. Expression of the PLCγ2-R522 variant resulted in increased stimulus-dependent PIP
MeSH term(s)	Alzheimer Disease/genetics ; Amyloid beta-Peptides/metabolism ; Animals ; Cell Line ; Cells, Cultured ; Endocytosis ; Humans ; Macrophages/metabolism ; Mice ; Mice, Inbred C57BL ; Mutation, Missense ; Neuroglia/metabolism ; Phosphatidylinositol 4,5-Diphosphate/metabolism ; Protein Kinase C/genetics ; Protein Kinase C/metabolism
Chemical Substances	Amyloid beta-Peptides ; Phosphatidylinositol 4,5-Diphosphate ; protein kinase C gamma (EC 2.7.1.-) ; Protein Kinase C (EC 2.7.11.13)
Language	English
Publishing date	2021-07-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	586044-1
ISSN	1460-2075 ; 0261-4189
ISSN (online)	1460-2075
ISSN	0261-4189
DOI	10.15252/embj.2020105603
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Article ; Online: Topical, immunomodulatory epoxy-tiglianes induce biofilm disruption and healing in acute and chronic skin wounds.

Science translational medicine

2022 Volume 14, Issue 662, Page(s) eabn3758

Abstract: The management of antibiotic-resistant, bacterial biofilm infections in chronic skin wounds is an increasing clinical challenge. Despite advances in diagnosis, many patients do not derive benefit from current anti-infective/antibiotic therapies. Here, we ...

Abstract	The management of antibiotic-resistant, bacterial biofilm infections in chronic skin wounds is an increasing clinical challenge. Despite advances in diagnosis, many patients do not derive benefit from current anti-infective/antibiotic therapies. Here, we report a novel class of naturally occurring and semisynthetic epoxy-tiglianes, derived from the Queensland blushwood tree (
MeSH term(s)	Animals ; Anti-Bacterial Agents/pharmacology ; Biofilms ; Cattle ; Humans ; Keratinocytes ; Mice ; Phorbols ; Wound Healing
Chemical Substances	Anti-Bacterial Agents ; Phorbols
Language	English
Publishing date	2022-09-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2518854-9
ISSN	1946-6242 ; 1946-6234
ISSN (online)	1946-6242
ISSN	1946-6234
DOI	10.1126/scitranslmed.abn3758
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Article ; Online: Polygenic risk for schizophrenia and subcortical brain anatomy in the UK Biobank cohort.

Grama, Steluta / Willcocks, Isabella / Hubert, John J / Pardiñas, Antonio F / Legge, Sophie E / Bracher-Smith, Matthew / Menzies, Georgina E / Hall, Lynsey S / Pocklington, Andrew J / Anney, Richard J L / Bray, Nicholas J / Escott-Price, Valentina / Caseras, Xavier

Translational psychiatry

2020 Volume 10, Issue 1, Page(s) 309

Abstract: Research has shown differences in subcortical brain volumes between participants with schizophrenia and healthy controls. However, none of these differences have been found to associate with schizophrenia polygenic risk. Here, in a large sample (n = 14, ... ...

Abstract	Research has shown differences in subcortical brain volumes between participants with schizophrenia and healthy controls. However, none of these differences have been found to associate with schizophrenia polygenic risk. Here, in a large sample (n = 14,701) of unaffected participants from the UK Biobank, we test whether schizophrenia polygenic risk scores (PRS) limited to specific gene-sets predict subcortical brain volumes. We compare associations with schizophrenia PRS at the whole genome level ('genomic', including all SNPs associated with the disorder at a p-value threshold < 0.05) with 'genic' PRS (based on SNPs in the vicinity of known genes), 'intergenic' PRS (based on the remaining SNPs), and genic PRS limited to SNPs within 7 gene-sets previously found to be enriched for genetic association with schizophrenia ('abnormal behaviour,' 'abnormal long-term potentiation,' 'abnormal nervous system electrophysiology,' 'FMRP targets,' '5HT2C channels,' 'CaV2 channels' and 'loss-of-function intolerant genes'). We observe a negative association between the 'abnormal behaviour' gene-set PRS and volume of the right thalamus that survived correction for multiple testing (ß = -0.031, p
MeSH term(s)	Biological Specimen Banks ; Brain/diagnostic imaging ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; Multifactorial Inheritance ; Schizophrenia/genetics ; United Kingdom
Language	English
Publishing date	2020-09-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2609311-X
ISSN	2158-3188 ; 2158-3188
ISSN (online)	2158-3188
ISSN	2158-3188
DOI	10.1038/s41398-020-00940-0
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Article ; Online: MutAIT: an online genetic toxicology data portal and analysis tools.

Avancini, Daniele / Menzies, Georgina E / Morgan, Claire / Wills, John / Johnson, George E / White, Paul A / Lewis, Paul D

Mutagenesis

2016 Volume 31, Issue 3, Page(s) 323–328

Abstract: Assessment of genetic toxicity and/or carcinogenic activity is an essential element of chemical screening programs employed to protect human health. Dose-response and gene mutation data are frequently analysed by industry, academia and governmental ... ...

Abstract	Assessment of genetic toxicity and/or carcinogenic activity is an essential element of chemical screening programs employed to protect human health. Dose-response and gene mutation data are frequently analysed by industry, academia and governmental agencies for regulatory evaluations and decision making. Over the years, a number of efforts at different institutions have led to the creation and curation of databases to house genetic toxicology data, largely, with the aim of providing public access to facilitate research and regulatory assessments. This article provides a brief introduction to a new genetic toxicology portal called Mutation Analysis Informatics Tools (MutAIT) (www.mutait.org) that provides easy access to two of the largest genetic toxicology databases, the Mammalian Gene Mutation Database (MGMD) and TransgenicDB. TransgenicDB is a comprehensive collection of transgenic rodent mutation data initially compiled and collated by Health Canada. The updated MGMD contains approximately 50 000 individual mutation spectral records from the published literature. The portal not only gives access to an enormous quantity of genetic toxicology data, but also provides statistical tools for dose-response analysis and calculation of benchmark dose. Two important R packages for dose-response analysis are provided as web-distributed applications with user-friendly graphical interfaces. The 'drsmooth' package performs dose-response shape analysis and determines various points of departure (PoD) metrics and the 'PROAST' package provides algorithms for dose-response modelling. The MutAIT statistical tools, which are currently being enhanced, provide users with an efficient and comprehensive platform to conduct quantitative dose-response analyses and determine PoD values that can then be used to calculate human exposure limits or margins of exposure.
Language	English
Publishing date	2016-05
Publishing country	England
Document type	Journal Article
ZDB-ID	632903-2
ISSN	1464-3804 ; 0267-8357
ISSN (online)	1464-3804
ISSN	0267-8357
DOI	10.1093/mutage/gev050
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