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Article ; Online: The N6-methyladenosine demethylase ALKBH5 regulates the hypoxic HBV transcriptome.

Tsukuda, Senko / Harris, James M / Magri, Andrea / Balfe, Peter / Siddiqui, Aleem / Wing, Peter A C / McKeating, Jane A

2024 Volume 20, Issue 1, Page(s) e1011917

Abstract: Chronic hepatitis B is a global health problem and current treatments only suppress hepatitis B virus (HBV) infection, highlighting the need for new curative treatments. Oxygen levels influence HBV replication and we previously reported that hypoxia ... ...

Abstract	Chronic hepatitis B is a global health problem and current treatments only suppress hepatitis B virus (HBV) infection, highlighting the need for new curative treatments. Oxygen levels influence HBV replication and we previously reported that hypoxia inducible factors (HIFs) activate the basal core promoter (BCP). Here we show that the hypoxic-dependent increase in BCP-derived transcripts is dependent on N6-methyladenosine (m6A) modifications in the 5' stem loop that regulate RNA half-life. Application of a probe-enriched long-read sequencing method to accurately map the HBV transcriptome showed an increased abundance of pre-genomic RNA under hypoxic conditions. Mapping the transcription start sites of BCP-RNAs identified a role for hypoxia to regulate pre-genomic RNA splicing that is dependent on m6A modification. Bioinformatic analysis of published single cell RNA-seq of murine liver showed an increased expression of the RNA demethylase ALKBH5 in the peri-central low oxygen region. In vitro studies with a human hepatocyte derived HepG2-NTCP cell line showed increased ALKBH5 gene expression under hypoxic conditions and a concomitant reduction in m6A-modified HBV BCP-RNA and host RNAs. Silencing the demethylase reduced the level of BCP-RNAs and host gene (CA9, NDRG1, VEGFA, BNIP3, FUT11, GAP and P4HA1) transcripts and this was mediated via reduced HIFα expression. In summary, our study highlights a previously unrecognized role for ALKBH5 in orchestrating viral and cellular transcriptional responses to low oxygen.
MeSH term(s)	Animals ; Humans ; Mice ; AlkB Homolog 5, RNA Demethylase/genetics ; AlkB Homolog 5, RNA Demethylase/metabolism ; Fucosyltransferases/genetics ; Hepatitis B/genetics ; Hepatitis B virus/metabolism ; Hypoxia ; Oxygen ; RNA ; Transcriptome
Chemical Substances	AlkB Homolog 5, RNA Demethylase (EC 1.14.11.-) ; ALKBH5 protein, human (EC 1.14.11.-) ; Fucosyltransferases (EC 2.4.1.-) ; FUT11 protein, human (EC 2.4.1.-) ; Oxygen (S88TT14065) ; RNA (63231-63-0) ; ALKBH5 protein, mouse (EC 1.14.11.-)
Language	English
Publishing date	2024-01-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1011917
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Article ; Online: Oxygen-dependent histone lysine demethylase 4 restricts hepatitis B virus replication.

Harris, James M / Magri, Andrea / Faria, Ana Rita / Tsukuda, Senko / Balfe, Peter / Wing, Peter A C / McKeating, Jane A

The Journal of biological chemistry

2024 Volume 300, Issue 3, Page(s) 105724

Abstract: Mammalian cells have evolved strategies to regulate gene expression when oxygen is limited. Hypoxia-inducible factors (HIF) are the major transcriptional regulators of host gene expression. We previously reported that HIFs bind and activate hepatitis B ... ...

Abstract	Mammalian cells have evolved strategies to regulate gene expression when oxygen is limited. Hypoxia-inducible factors (HIF) are the major transcriptional regulators of host gene expression. We previously reported that HIFs bind and activate hepatitis B virus (HBV) DNA transcription under low oxygen conditions; however, the global cellular response to low oxygen is mediated by a family of oxygenases that work in concert with HIFs. Recent studies have identified a role for chromatin modifiers in sensing cellular oxygen and orchestrating transcriptional responses, but their role in the HBV life cycle is as yet undefined. We demonstrated that histone lysine demethylase 4 (KDM4) can restrict HBV, and pharmacological or oxygen-mediated inhibition of the demethylase increases viral RNAs derived from both episomal and integrated copies of the viral genome. Sequencing studies demonstrated that KDM4 is a major regulator of the hepatic transcriptome, which defines hepatocellular permissivity to HBV infection. We propose a model where HBV exploits cellular oxygen sensors to replicate and persist in the liver. Understanding oxygen-dependent pathways that regulate HBV infection will facilitate the development of physiologically relevant cell-based models that support efficient HBV replication.
MeSH term(s)	Humans ; DNA, Viral/genetics ; Genome, Viral/genetics ; Hepatitis B/enzymology ; Hepatitis B/metabolism ; Hepatitis B/virology ; Hepatitis B virus/genetics ; Hepatitis B virus/growth & development ; Hepatitis B virus/metabolism ; Jumonji Domain-Containing Histone Demethylases/metabolism ; Liver/enzymology ; Liver/metabolism ; Liver/virology ; Oxygen/metabolism ; Plasmids/genetics ; Transcriptome ; Virus Replication/genetics
Chemical Substances	DNA, Viral ; Jumonji Domain-Containing Histone Demethylases (EC 1.14.11.-) ; Oxygen (S88TT14065)
Language	English
Publishing date	2024-02-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2024.105724
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Article: The N6-methyladenosine demethylase ALKBH5 regulates the hypoxic HBV transcriptome.

Tsukuda, Senko / Harris, James M / Magri, Andrea / Balfe, Peter / Wing, Peter Ac / Siddiqui, Aleem / McKeating, Jane A

bioRxiv : the preprint server for biology

2023

Abstract	Chronic hepatitis B is a global health problem and current treatments only suppress hepatitis B virus (HBV) infection, highlighting the need for new curative treatments. Oxygen levels influence HBV replication and we previously reported that hypoxia inducible factors (HIFs) activate the basal core promoter to transcribe pre-genomic RNA. Application of a probe-enriched long-read sequencing method to map the HBV transcriptome showed an increased abundance of all viral RNAs under low oxygen or hypoxic conditions. Importantly, the hypoxic-associated increase in HBV transcripts was dependent on N6-methyladenosine (m
Language	English
Publishing date	2023-11-01
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.10.31.564956
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Article ; Online: Oxygen Sensing and Viral Replication: Implications for Tropism and Pathogenesis.

Liu, Peter Jianrui / Balfe, Peter / McKeating, Jane A / Schilling, Mirjam

Viruses

2020 Volume 12, Issue 11

Abstract: The ability to detect and respond to varying oxygen tension is an essential prerequisite to life. Several mechanisms regulate the cellular response to oxygen including the prolyl hydroxylase domain (PHD)/factor inhibiting HIF (FIH)-hypoxia inducible ... ...

Abstract	The ability to detect and respond to varying oxygen tension is an essential prerequisite to life. Several mechanisms regulate the cellular response to oxygen including the prolyl hydroxylase domain (PHD)/factor inhibiting HIF (FIH)-hypoxia inducible factor (HIF) pathway, cysteamine (2-aminoethanethiol) dioxygenase (ADO) system, and the lysine-specific demethylases (KDM) 5A and KDM6A. Using a systems-based approach we discuss the literature on oxygen sensing pathways in the context of virus replication in different tissues that experience variable oxygen tension. Current information supports a model where the PHD-HIF pathway enhances the replication of viruses infecting tissues under low oxygen, however, the reverse is true for viruses with a selective tropism for higher oxygen environments. Differences in oxygen tension and associated HIF signaling may play an important role in viral tropism and pathogenesis. Thus, pharmaceutical agents that modulate HIF activity could provide novel treatment options for viral infections and associated pathological conditions.
MeSH term(s)	Animals ; Humans ; Hypoxia ; Hypoxia-Inducible Factor 1/metabolism ; Mice ; Oxygen/metabolism ; Repressor Proteins/metabolism ; Signal Transduction ; Viral Tropism ; Virus Replication ; Viruses/classification ; Viruses/metabolism ; Viruses/pathogenicity
Chemical Substances	Hypoxia-Inducible Factor 1 ; Repressor Proteins ; Oxygen (S88TT14065)
Language	English
Publishing date	2020-10-25
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v12111213
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Article ; Online: Time-of-Day Variation in SARS-CoV-2 RNA Levels during the Second Wave of COVID-19.

Zhuang, Xiaodong / Wang, Wei / Borrmann, Helene / Balfe, Peter / Matthews, Philippa C / Eyre, David W / Klerman, Elizabeth B / McKeating, Jane A

Viruses

2022 Volume 14, Issue 8

Abstract: Circadian rhythms influence and coordinate an organism's response to its environment and to invading pathogens. We studied the diurnal variation in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in nasal/throat swabs collected in late ... ...

Abstract	Circadian rhythms influence and coordinate an organism's response to its environment and to invading pathogens. We studied the diurnal variation in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in nasal/throat swabs collected in late 2020 to spring 2021 in a population immunologically naïve to SARS-CoV-2 and prior to widespread vaccination. SARS-CoV-2 diagnostic PCR data from 1698 participants showed a significantly higher viral load in samples obtained in the afternoon, in males, and in hospitalised patients when linear mixed modelling was applied. This study illustrates the importance of recording sample collection times when measuring viral replication parameters in clinical and research studies.
MeSH term(s)	COVID-19/diagnosis ; COVID-19 Testing ; Humans ; Male ; RNA, Viral/analysis ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; Specimen Handling
Chemical Substances	RNA, Viral
Language	English
Publishing date	2022-08-05
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14081728
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Article ; Online: TNF superfamily members promote hepatitis C virus entry via an NF-κB and myosin light chain kinase dependent pathway.

Fletcher, N F / Clark, A R / Balfe, P / McKeating, J A

The Journal of general virology

2017 Volume 98, Issue 3, Page(s) 405–412

Abstract: Preventing virally induced liver disease begins with an understanding of the host factors that define susceptibility to infection. Hepatitis C virus (HCV) is a global health issue, with an estimated 170 million infected individuals at risk of developing ... ...

Abstract	Preventing virally induced liver disease begins with an understanding of the host factors that define susceptibility to infection. Hepatitis C virus (HCV) is a global health issue, with an estimated 170 million infected individuals at risk of developing liver disease including fibrosis and hepatocellular carcinoma. The liver is the major reservoir supporting HCV replication and this hepatocellular tropism is defined by HCV engagement of cellular entry receptors. Hepatocytes are polarized in vivo and this barrier function limits HCV entry. We previously reported that activated macrophages promote HCV entry into polarized hepatocytes via a TNF-α-dependent process; however, the underlying mechanism was not defined. In this study, we show that several TNF superfamily members, including TNF-α, TNF-β, TWEAK and LIGHT, promote HCV entry via NF-κB-mediated activation of myosin light chain kinase (MLCK) and disruption of tight junctions. These observations support a model where HCV hijacks an inflammatory immune response to stimulate infection and uncovers a role for NF-κB-MLCK signalling in maintaining hepatocellular tight junctions.
MeSH term(s)	Carcinoma, Hepatocellular/virology ; Enzyme Activation ; Hepacivirus/physiology ; Hepatitis C/metabolism ; Hepatitis C/virology ; Hepatocytes/virology ; Humans ; Liver/metabolism ; Liver/virology ; Liver Cirrhosis/virology ; Liver Neoplasms/virology ; Myosin-Light-Chain Kinase/metabolism ; NF-kappa B/metabolism ; Signal Transduction ; Tight Junctions/metabolism ; Tight Junctions/virology ; Transcription Factor RelA/metabolism ; Tumor Necrosis Factors/metabolism ; Virus Internalization
Chemical Substances	NF-kappa B ; RELA protein, human ; Transcription Factor RelA ; Tumor Necrosis Factors ; Myosin-Light-Chain Kinase (EC 2.7.11.18)
Language	English
Publishing date	2017-04-01
Publishing country	England
Document type	Journal Article
ZDB-ID	219316-4
ISSN	1465-2099 ; 0022-1317
ISSN (online)	1465-2099
ISSN	0022-1317
DOI	10.1099/jgv.0.000689
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Article: A rare cause of acute abdomen--plasmodium falciparum leading to splenic infarction and haemorrhage.

Balfe, P / Reynolds, J V

Irish medical journal

2008 Volume 101, Issue 5, Page(s) 150–151

MeSH term(s)	Abdomen, Acute/etiology ; Adult ; Animals ; Gastrointestinal Hemorrhage/etiology ; Humans ; Malaria/complications ; Male ; Plasmodium falciparum/isolation & purification ; Risk Factors ; Splenic Infarction/etiology
Language	English
Publishing date	2008-05
Publishing country	Ireland
Document type	Case Reports ; Journal Article
ZDB-ID	193134-9
ISSN	0332-3102 ; 0021-129X
ISSN	0332-3102 ; 0021-129X
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Article ; Online: Molecular components of the circadian clock regulate HIV-1 replication.

Borrmann, Helene / Ulkar, Görkem / Kliszczak, Anna E / Ismed, Dini / Schilling, Mirjam / Magri, Andrea / Harris, James M / Balfe, Peter / Vasudevan, Sridhar / Borrow, Persephone / Zhuang, Xiaodong / McKeating, Jane A

iScience

2023 Volume 26, Issue 7, Page(s) 107007

Abstract: Human immunodeficiency virus 1 (HIV-1) causes major health burdens worldwide and still lacks curative therapies and vaccines. Circadian rhythms are endogenous daily oscillations that coordinate an organism's response to its environment and invading ... ...

Abstract	Human immunodeficiency virus 1 (HIV-1) causes major health burdens worldwide and still lacks curative therapies and vaccines. Circadian rhythms are endogenous daily oscillations that coordinate an organism's response to its environment and invading pathogens. Peripheral viral loads of HIV-1 infected patients show diurnal variation; however, the underlying mechanisms remain unknown. Here, we demonstrate a role for the cell-intrinsic clock to regulate rhythmic HIV-1 replication in circadian-synchronized systems. Silencing the circadian activator
Language	English
Publishing date	2023-05-29
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.107007
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Article ; Online: An enrichment protocol and analysis pipeline for long read sequencing of the hepatitis B virus transcriptome.

Ng, Esther / Dobrica, Mihaela-Olivia / Harris, James M / Wu, Yanxia / Tsukuda, Senko / Wing, Peter A C / Piazza, Paolo / Balfe, Peter / Matthews, Philippa C / Ansari, M Azim / McKeating, Jane A

The Journal of general virology

2023 Volume 104, Issue 5

Abstract: Hepatitis B virus (HBV) is one of the smallest human DNA viruses and its 3.2 Kb genome encodes multiple overlapping open reading frames, making its viral transcriptome challenging to dissect. Previous studies have combined quantitative PCR and Next ... ...

Abstract	Hepatitis B virus (HBV) is one of the smallest human DNA viruses and its 3.2 Kb genome encodes multiple overlapping open reading frames, making its viral transcriptome challenging to dissect. Previous studies have combined quantitative PCR and Next Generation Sequencing to identify viral transcripts and splice junctions, however the fragmentation and selective amplification used in short read sequencing precludes the resolution of full length RNAs. Our study coupled an oligonucleotide enrichment protocol with state-of-the-art long read sequencing (PacBio) to identify the repertoire of HBV RNAs. This methodology provides sequencing libraries where up to 25 % of reads are of viral origin and enable the identification of canonical (unspliced), non-canonical (spliced) and chimeric viral-human transcripts. Sequencing RNA isolated from
MeSH term(s)	Humans ; Transcriptome ; Hepatitis B virus/genetics ; High-Throughput Nucleotide Sequencing ; RNA, Viral/genetics
Chemical Substances	RNA, Viral
Language	English
Publishing date	2023-05-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	219316-4
ISSN	1465-2099 ; 0022-1317
ISSN (online)	1465-2099
ISSN	0022-1317
DOI	10.1099/jgv.0.001856
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Article ; Online: Effective communication enhances the patients' endoscopy experience.

Toomey, D P / Hackett-Brennan, M / Corrigan, G / Singh, C / Nessim, G / Balfe, P

Irish journal of medical science

2016 Volume 185, Issue 1, Page(s) 203–214

Abstract: Background: Undergoing an endoscopy is a stressful experience for patients.: Aims: To audit the endoscopy pathway to improve patient satisfaction.: Methods: A prospective survey of endoscopy patients to identify system improvements that were then ... ...

Abstract	Background: Undergoing an endoscopy is a stressful experience for patients. Aims: To audit the endoscopy pathway to improve patient satisfaction. Methods: A prospective survey of endoscopy patients to identify system improvements that were then implemented. Results: The survey was performed before (N = 71) and after (N = 60) process improvements identified by the initial survey. Information provision and staff communication skills were identified for optimisation. Patient anxiety at home was significantly reduced (median 2 vs. 1, p < 0.01). Education of endoscopy staff significantly improved the quality of information provided before and after the procedure with regard to sedation (median 4 vs. 5, p < 0.01), discomfort (median 4 vs. 5, p < 0.01), complications (28 vs. 82 %, p < 0.01), findings (89 vs. 100 %, p < 0.01) and follow-up (73 vs. 90 %, p = 0.015). Gloucester Comfort Scores during endoscopy improved (median 1 vs. 0, p < 0.01) without increasing sedation levels. Patient feelings of invasion/trauma significantly decreased. Overall 95 % of patients were satisfied. Conclusion: Structured information leaflets and improved staff communication skills reduce anxiety and enhance patients' experiences. They are now standard operating procedures.
MeSH term(s)	Adult ; Aged ; Anxiety/prevention & control ; Anxiety/psychology ; Colonoscopy/psychology ; Colonoscopy/statistics & numerical data ; Endoscopy, Gastrointestinal/psychology ; Endoscopy, Gastrointestinal/statistics & numerical data ; Female ; Health Education/statistics & numerical data ; Humans ; Male ; Middle Aged ; Pain Measurement ; Patient Satisfaction ; Prospective Studies
Language	English
Publishing date	2016-02
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	390895-1
ISSN	1863-4362 ; 0021-1265
ISSN (online)	1863-4362
ISSN	0021-1265
DOI	10.1007/s11845-015-1270-0
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