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Article ; Online: A novel soluble di-iron monooxygenase from the soil bacterium Solimonas soli.

Yang, Sui Nin Nicholas / Haritos, Victoria / Kertesz, Michael A / Coleman, Nicholas V

2024 Volume 26, Issue 2, Page(s) e16567

Abstract: Soluble di-iron monooxygenase (SDIMO) enzymes enable insertion of oxygen into diverse substrates and play significant roles in biogeochemistry, bioremediation and biocatalysis. An unusual SDIMO was detected in an earlier study in the genome of the soil ... ...

Abstract	Soluble di-iron monooxygenase (SDIMO) enzymes enable insertion of oxygen into diverse substrates and play significant roles in biogeochemistry, bioremediation and biocatalysis. An unusual SDIMO was detected in an earlier study in the genome of the soil organism Solimonas soli, but was not characterized. Here, we show that the S. soli SDIMO is part of a new clade, which we define as 'Group 7'; these share a conserved gene organization with alkene monooxygenases but have only low amino acid identity. The S. soli genes (named zmoABCD) could be functionally expressed in Pseudomonas putida KT2440 but not in Escherichia coli TOP10. The recombinants made epoxides from C
MeSH term(s)	Mixed Function Oxygenases/genetics ; Mixed Function Oxygenases/metabolism ; Alkenes/metabolism ; Gammaproteobacteria/metabolism ; Vinyl Chloride ; Biodegradation, Environmental ; Pseudomonas putida/genetics ; Pseudomonas putida/metabolism
Chemical Substances	Mixed Function Oxygenases (EC 1.-) ; Alkenes ; Vinyl Chloride (WD06X94M2D)
Language	English
Publishing date	2024-01-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.16567
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Article ; Online: Serum tumour markers for testicular cancer recurrence.

Murray, Matthew J / Scarpini, Cinzia G / Coleman, Nicholas

Nature reviews. Urology

2023 Volume 20, Issue 8, Page(s) 459–460

MeSH term(s)	Male ; Humans ; Testicular Neoplasms ; Biomarkers, Tumor ; Neoplasms, Germ Cell and Embryonal/diagnosis ; Neoplasm Recurrence, Local/diagnosis
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2023-05-30
Publishing country	England
Document type	Journal Article ; Comment
ZDB-ID	2493737-X
ISSN	1759-4820 ; 1759-4812
ISSN (online)	1759-4820
ISSN	1759-4812
DOI	10.1038/s41585-023-00782-7
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Article: Association behavior between sand tiger sharks and round scad is driven by mesopredators.

Coleman, Nicholas C / Burge, Erin J

PeerJ

2021 Volume 9, Page(s) e11164

Abstract: In marine systems, behaviorally-mediated indirect interactions between prey, mesopredators, and higher trophic-level, large predators are less commonly investigated than other ecologic interactions, likely because of inherent difficulties associated with ...

Abstract	In marine systems, behaviorally-mediated indirect interactions between prey, mesopredators, and higher trophic-level, large predators are less commonly investigated than other ecologic interactions, likely because of inherent difficulties associated with making observations. Underwater videos (
Language	English
Publishing date	2021-04-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.11164
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Article ; Online: Virus and Host Events in Squamous Carcinogenesis.

Coleman, Nicholas

The Keio journal of medicine

2016 Volume 65, Issue 4, Page(s) 78

Abstract: Our group investigates early and late stages in the development of squamous cell carcinomas (SCCs), in order to identify new approaches to diagnosis and therapy. The principal themes are:1. Transcriptional deregulation of high-risk human papillomavirus ( ... ...

Abstract	Our group investigates early and late stages in the development of squamous cell carcinomas (SCCs), in order to identify new approaches to diagnosis and therapy. The principal themes are:1. Transcriptional deregulation of high-risk human papillomavirus (HRHPV)We study mechanisms of HRHPV transcriptional deregulation and competitive cell selection during SCC progression, focussing on the causes and effects of integration of HPV16 into the host genome. We showed that HPV16 integration does not necessarily lead to a competitive growth advantage or increased levels of virus oncogenes. Selection of individual cells is determined through multiple layers of epigenetic regulation of the integrated virus genome. We are currently studying whether the epigenetic landscape of integrated HPV16 reflects that of the host genome at the integration site and/or sites of long-range chromatin interactions of the virus DNA. This work may ultimately identify targets for epigenetic therapies in SCCs containing integrated HRHPV.2. The oncostatin-M receptor (OSMR) in metastasisThe cell-surface oncostatin-M receptor (OSMR) has emerged as an exciting therapeutic target in SCCs. Both copy number gain and over-expression of OSMR have a strong adverse prognostic effect in SCCs. Carcinoma cells that over-expressed OSMR were more sensitive to the major ligand OSM, which induced multiple pro-malignant effects, including epithelial-mesenchymal transition, increased metastasis and the ability to induce pro-malignant changes in cells from the tumour microenvironment (TME). We are now studying the effectiveness of OSM:OSMR blockade on the growth and metastasis of SCC cells in vivo, as well as effects on the TME in immunocompetent hosts.(Presented at the 1923th Meeting, August 10, 2016).
MeSH term(s)	Carcinogenesis/genetics ; Carcinogenesis/metabolism ; Carcinogenesis/pathology ; Carcinoma, Squamous Cell/genetics ; Carcinoma, Squamous Cell/metabolism ; Carcinoma, Squamous Cell/pathology ; Carcinoma, Squamous Cell/virology ; Epigenesis, Genetic ; Epithelial-Mesenchymal Transition/genetics ; Female ; Gene Expression Regulation, Neoplastic ; Host-Pathogen Interactions ; Human papillomavirus 16/pathogenicity ; Human papillomavirus 16/physiology ; Humans ; Oncostatin M/genetics ; Oncostatin M/metabolism ; Oncostatin M Receptor beta Subunit/genetics ; Oncostatin M Receptor beta Subunit/metabolism ; Signal Transduction ; Uterine Cervical Neoplasms/genetics ; Uterine Cervical Neoplasms/metabolism ; Uterine Cervical Neoplasms/pathology ; Uterine Cervical Neoplasms/virology
Chemical Substances	OSMR protein, human ; Oncostatin M Receptor beta Subunit ; Oncostatin M (106956-32-5)
Language	English
Publishing date	2016-12-26
Publishing country	Japan
Document type	Journal Article
ZDB-ID	390981-5
ISSN	1880-1293 ; 0022-9717
ISSN (online)	1880-1293
ISSN	0022-9717
DOI	10.2302/kjm.65-004-ABST
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Ua VI Zs.412: Show issues

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Article: Synthetic Biology Approaches to Hydrocarbon Biosensors: A Review.

Moratti, Claudia F / Scott, Colin / Coleman, Nicholas V

Frontiers in bioengineering and biotechnology

2022 Volume 9, Page(s) 804234

Abstract: Monooxygenases are a class of enzymes that facilitate the bacterial degradation of alkanes and alkenes. The regulatory components associated with monooxygenases are nature's own hydrocarbon sensors, and once functionally characterised, these components ... ...

Abstract	Monooxygenases are a class of enzymes that facilitate the bacterial degradation of alkanes and alkenes. The regulatory components associated with monooxygenases are nature's own hydrocarbon sensors, and once functionally characterised, these components can be used to create rapid, inexpensive and sensitive biosensors for use in applications such as bioremediation and metabolic engineering. Many bacterial monooxygenases have been identified, yet the regulation of only a few of these have been investigated in detail. A wealth of genetic and functional diversity of regulatory enzymes and promoter elements still remains unexplored and unexploited, both in published genome sequences and in yet-to-be-cultured bacteria. In this review we examine in detail the current state of research on monooxygenase gene regulation, and on the development of transcription-factor-based microbial biosensors for detection of alkanes and alkenes. A new framework for the systematic characterisation of the underlying genetic components and for further development of biosensors is presented, and we identify focus areas that should be targeted to enable progression of more biosensor candidates to commercialisation and deployment in industry and in the environment.
Language	English
Publishing date	2022-01-10
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2719493-0
ISSN	2296-4185
ISSN	2296-4185
DOI	10.3389/fbioe.2021.804234
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Article ; Online: The clinical utility of dysregulated microRNA expression in paediatric solid tumours.

Chadda, Karan R / Blakey, Ellen E / Coleman, Nicholas / Murray, Matthew J

European journal of cancer (Oxford, England : 1990)

2022 Volume 176, Page(s) 133–154

Abstract: MicroRNAs (miRNAs) are short, non-protein-coding genes that regulate the expression of numerous protein-coding genes. Their expression is dysregulated in cancer, where they may function as oncogenes or tumour suppressor genes. As miRNAs are highly ... ...

Abstract	MicroRNAs (miRNAs) are short, non-protein-coding genes that regulate the expression of numerous protein-coding genes. Their expression is dysregulated in cancer, where they may function as oncogenes or tumour suppressor genes. As miRNAs are highly resistant to degradation, they are ideal biomarker candidates to improve the diagnosis and clinical management of cancer, including prognostication. Furthermore, miRNAs dysregulated in malignancy represent potential therapeutic targets. The use of miRNAs for these purposes is a particularly attractive option to explore for paediatric malignancies, where the mutational burden is typically low, in contrast to cancers affecting adult patients. As childhood cancers are rare, it has taken time to accumulate the necessary body of evidence showing the potential for miRNAs to improve clinical management across this group of tumours. Here, we review the current literature regarding the potential clinical utility of miRNAs in paediatric solid tumours, which is now both timely and justified. Exploring such avenues is warranted to improve the management and outcomes of children affected by cancer.
MeSH term(s)	Humans ; Child ; Gene Expression Regulation, Neoplastic ; Neoplasms/therapy ; Oncogenes ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism
Chemical Substances	MicroRNAs ; Biomarkers, Tumor
Language	English
Publishing date	2022-10-07
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	82061-1
ISSN	1879-0852 ; 0277-5379 ; 0959-8049 ; 0964-1947
ISSN (online)	1879-0852
ISSN	0277-5379 ; 0959-8049 ; 0964-1947
DOI	10.1016/j.ejca.2022.09.010
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Zs.A 456: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 583: Show issues

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Article ; Online: Circulating microRNA profiles in Wilms tumour (WT): A systematic review and meta-analysis of diagnostic test accuracy.

Benlhachemi, Sara / Abouqal, Redouane / Coleman, Nicholas / Murray, Matthew Jonathan / Khattab, Mohammed / El Fahime, Elmostafa

Non-coding RNA research

2023 Volume 8, Issue 3, Page(s) 413–425

Abstract: Background: Wilms tumour (WT) is caused by aberrant embryonic kidney development and associated with dysregulated expression of short, non-protein-coding RNAs termed microRNAs (miRNAs). At present, there is no reliable circulating biomarker of WT, and ... ...

Abstract	Background: Wilms tumour (WT) is caused by aberrant embryonic kidney development and associated with dysregulated expression of short, non-protein-coding RNAs termed microRNAs (miRNAs). At present, there is no reliable circulating biomarker of WT, and this remains an urgent unmet clinical need. Such biomarkers may assist diagnosis, subtyping/prognostication, and disease-monitoring. Here, we established the list of dysregulated circulating miRNAs in WT from the existing published literature. Methods: Regardless of publication date, PubMed, Scopus, Web-of-Science, and Wiley online library databases were searched for English/French studies on WT circulating miRNAs. The PRISMA-compliant search was registered in PROSPERO. The QUADAS tool measured retained article quality. The meta-analysis assessed the sensitivity and specificity of miRNAs for WT diagnosis. Results: Qualitative analysis included 280 samples (172 WT patients; 108 healthy controls) from five of 450 published articles. The study uncovered 301 dysregulated miRNAs (144 up-regulated, 143 down-regulated, 14 conflicting). The pooled sensitivity, specificity, and AUC of the 49 significantly dysregulated microRNAs from two studies was 0.67 [0.62; 0.73], 0.95 [0.92; 0.96] and 0.77 [0.73; 0.81] respectively, indicating a stronger diagnostic potential for WT. Conclusions: Circulating miRNAs show promise for WT diagnosis and prognosis. More research is needed to confirm these findings and determine associations with tumour stage/subtype. Prospero registration number: CRD42022301597.
Language	English
Publishing date	2023-05-26
Publishing country	Netherlands
Document type	Journal Article
ISSN	2468-0540
ISSN (online)	2468-0540
DOI	10.1016/j.ncrna.2023.05.007
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Article ; Online: MicroRNA Dysregulation in Malignant Germ Cell Tumors: More Than a Biomarker?

Murray, Matthew J / Coleman, Nicholas

Journal of clinical oncology : official journal of the American Society of Clinical Oncology

2019 Volume 37, Issue 16, Page(s) 1432–1435

MeSH term(s)	Biomarkers ; Humans ; Male ; MicroRNAs ; Neoplasms, Germ Cell and Embryonal ; Testicular Neoplasms
Chemical Substances	Biomarkers ; MicroRNAs
Language	English
Publishing date	2019-04-22
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	604914-x
ISSN	1527-7755 ; 0732-183X
ISSN (online)	1527-7755
ISSN	0732-183X
DOI	10.1200/JCO.19.00578
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Zs.A 1847: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 650: Show issues

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Article ; Online: Can circulating microRNAs solve clinical dilemmas in testicular germ cell malignancy?

Murray, Matthew J / Coleman, Nicholas

Nature reviews. Urology

2019 Volume 16, Issue 9, Page(s) 505–506

MeSH term(s)	Circulating MicroRNA/blood ; Humans ; Male ; Neoplasms, Germ Cell and Embryonal/blood ; Neoplasms, Germ Cell and Embryonal/diagnosis ; Testicular Neoplasms/blood ; Testicular Neoplasms/diagnosis
Chemical Substances	Circulating MicroRNA
Language	English
Publishing date	2019-07-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2493737-X
ISSN	1759-4820 ; 1759-4812
ISSN (online)	1759-4820
ISSN	1759-4812
DOI	10.1038/s41585-019-0214-2
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Article ; Online: Human papillomavirus genome integration in squamous carcinogenesis: what have next-generation sequencing studies taught us?

Groves, Ian J / Coleman, Nicholas

The Journal of pathology

2018 Volume 245, Issue 1, Page(s) 9–18

Abstract: Human papillomavirus (HPV) infection is associated with ∼5% of all human cancers, including a range of squamous cell carcinomas. Persistent infection by high-risk HPVs (HRHPVs) is associated with the integration of virus genomes (which are usually stably ...

Abstract	Human papillomavirus (HPV) infection is associated with ∼5% of all human cancers, including a range of squamous cell carcinomas. Persistent infection by high-risk HPVs (HRHPVs) is associated with the integration of virus genomes (which are usually stably maintained as extrachromosomal episomes) into host chromosomes. Although HRHPV integration rates differ across human sites of infection, this process appears to be an important event in HPV-associated neoplastic progression, leading to deregulation of virus oncogene expression, host gene expression modulation, and further genomic instability. However, the mechanisms by which HRHPV integration occur and by which the subsequent gene expression changes take place are incompletely understood. The advent of next-generation sequencing (NGS) of both RNA and DNA has allowed powerful interrogation of the association of HRHPVs with human disease, including precise determination of the sites of integration and the genomic rearrangements at integration loci. In turn, these data have indicated that integration occurs through two main mechanisms: looping integration and direct insertion. Improved understanding of integration sites is allowing further investigation of the factors that provide a competitive advantage to some integrants during disease progression. Furthermore, advanced approaches to the generation of genome-wide samples have given novel insights into the three-dimensional interactions within the nucleus, which could act as another layer of epigenetic control of both virus and host transcription. It is hoped that further advances in NGS techniques and analysis will not only allow the examination of further unanswered questions regarding HPV infection, but also direct new approaches to treating HPV-associated human disease. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
MeSH term(s)	Carcinoma, Squamous Cell/virology ; Cell Transformation, Neoplastic ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; Papillomaviridae/genetics ; Papillomavirus Infections/genetics ; Papillomavirus Infections/virology ; Virus Integration/genetics
Language	English
Publishing date	2018-03-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	3119-7
ISSN	1096-9896 ; 0022-3417
ISSN (online)	1096-9896
ISSN	0022-3417
DOI	10.1002/path.5058
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