Publications

Publications

2023


Oxygen-regulated post-translation modifications as master signalling pathway in cells

M Batie, T Fasanya, N S Kenneth, S Rocha

EMBO Rep. 2023 Dec 6;24(12):e57849. doi: 10.15252/embr.202357849.

PMID: 37877678


Enhancing radiotherapy outcomes in rectal cancer: A systematic review of targeting hypoxia-induced radioresistance

M Fok, R Hill, H Fowler, R Clifford, A Kler, J Uzzi-Daniel, S Rocha, G Grundy, J Parsons, D Vimalachandran

Clin Transl Radiat Oncol. 2023 Oct 28;44:100695. doi: 10.1016/j.ctro.2023.100695.

PMID: 37961749


Comprehensive analysis of the lysine succinylome in fish oil-treated prostate cancer cells

Y Jiang , C He , H Ye , Q Xu , X Chen , Y Chen , J Sun , S Rocha , M Wang

Life Sci Alliance. 2023 Sep 8;6(11):e202302131. doi: 10.26508/lsa.202302131.

PMID: 37684043


Targeting SOD1 via RNAi with PEGylated graphene oxide nanoparticles in platinum-resistant ovarian cancer

A Szénási, E Sivasudhan, H Du, P Zhang, J Huang, Z Zhang, S Rocha, M Wang

Cancer Gene Ther. 2023 Nov;30(11):1554-1568. doi: 10.1038/s41417-023-00659-2.

PMID: 37582934


The role of autophagy in hypoxia-induced radioresistance

R H Hill, M Fok, G Grundi, J L Parsons, S Rocha

Radiother Oncol. 2023 Dec;189:109951. doi: 10.1016/j.radonc.2023.109951.

PMID: 37838322


Fixed Cell Immunofluorescence for Quantification of Hypoxia-Induced Changes in Histone Methylation.

D Shakir, M Batie, S Rocha

Book chapter

Methods Mol Biol. 2023;2675:261-269. doi: 10.1007/978-1-0716-3247-5_19.

PMID: 37258769



Endotyping COPD: hypoxia-inducible factor-2 as a molecular “switch” between the vascular and airway phenotypes?

O Myronenko, V Foris, S Crnkovic, A Olschewski, S Rocha, MR Nicolls, H Olschewski

European Respiratory Review 32 (167) 2023 doi: 10.1183/16000617.0173-2022

PMID:36631133


Functional crosstalk between chromatin and hypoxia signalling

H Collier, A Albanese, CS Kwok, J Kou, S Rocha

Cellular Signalling, 110660 2023 doi.org/10.1016/j.cellsig.2023.110660

PMID:36990334



2021

Oxygen-dependent changes in binding partners and post-translational modifications regulate the abundance and activity of HIF-1α/2α

LA Daly, PJ Brownridge, M Batie, S Rocha, V Sée, CE Eyers

Science signaling 14 (692), eabf6685 2021 doi: 10.1126/scisignal.abf6685

PMID:34285132

PBRM1 cooperates with YTHDF2 to control HIF-1α protein translation

A Shmakova, M Frost, M Batie, NS Kenneth, S Rocha

Cells 10 (6), 1425 2021 2021 doi.org/10.3390/cells100614

PMID:34200988

Role of Hypoxia in the Control of the Cell Cycle

J Druker, JW Wilson, F Child, D Shakir, T Fasanya, S Rocha

International Journal of Molecular Sciences 22 (9), 4874 2021 doi.org/10.3390/ijms2209487

PMID:34062959


Von Hippel–Lindau (VHL) small-molecule inhibitor binding increases stability and intracellular levels of VHL protein

J Frost, S Rocha, A Ciulli

Journal of Biological Chemistry 297 (2) 2021 doi.org/10.1016/j.jbc.2021.100910

PMID:34174286


Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1

DJ Klionsky, AK Abdel-Aziz, S Abdelfatah, M Abdellatif, A Abdoli, S Abel, ...

Autophagy 17 (1), 1-382 2021 doi.org/10.1080/15548627.2020.1797280

PMID:33634751


Use of ChIP-qPCR to Study the Crosstalk Between HIF and NF-κB Signaling in Hypoxia and Normoxia

D Shakir, M Batie, S Rocha

NF-κB Transcription Factors: Methods and Protocols, 255-265. 2021 Book chapter

PMID:34236643



Roles of HIF and 2-Oxoglutarate-Dependent Dioxygenases in Controlling Gene Expression in Hypoxia.

J Frost, M Frost, M Batie, H Jiang, S Rocha

Cancers 2021, 13, 350. 2021 doi.org/10.3390/cancers13020350

PMID:33477877

Transcription| Regulation of gene transcription by hypoxia-inducible factor 1α

F Child, J Frost, D Shakir, JW Wilson, S Rocha

Elsevier 2021 book chapter

2020
Oxygen-sensing Mechanisms in Cells.
Wilson JJ, Shakir D, Batie M, Frost M, Rocha S.
FEBS J. 2020 May 23. doi: 10.1111/febs.15374.
PMID: 32446269

Gene Transcription and Chromatin Regulation in Hypoxia.
Batie M, Rocha S.
Biochem Soc Trans. 2020 May 5;BST20191106. doi: 10.1042/BST20191106.
PMID: 32369557

HIF-1β Positively Regulates NF-κB Activity via Direct Control of TRAF6 .
D'Ignazio L, Shakir D, Batie M, Muller HA, Rocha S.
Int J Mol Sci. 2020 Apr 24;21(8):3000. doi: 10.3390/ijms21083000.
PMID: 32344511

2019
JmjC histone demethylases act as chromatin oxygen sensors.
Batie M, Rocha S.
Mol Cell Oncol. 2019 May 7;6(4):1608501. doi: 10.1080/23723556.2019.1608501.

Hypoxia induces rapid changes to histone methylation and reprograms chromatin.
Batie M, Frost J, Frost M, Wilson JW, Schofield P, Rocha S.
Science. 2019 Mar 15;363(6432):1222-1226. doi: 10.1126/science.aau5870.

RNA-seq analysis of PHD and VHL inhibitors reveals differences and similarities to the hypoxia response.
Frost J, Ciulli A, Rocha S.
Wellcome Open Res. 2019 Jan 29;4:17. doi: 10.12688/wellcomeopenres.15044.1.
PMID: 30801039

2018

TNFSF14/LIGHT, a Non-Canonical NF-κB Stimulus, Induces the HIF Pathway.
D'Ignazio L, Batie M, Rocha S.
Cells. 2018 Aug 8;7(8). pii: E102. doi: 10.3390/cells7080102.
PMID: 30096845

SINHCAF/FAM60A and SIN3A specifically repress HIF-2α expression.
Biddlestone J, Batie M, Bandarra D, Munoz I, Rocha S.
Biochem J. 2018 Jun 29;475(12):2073-2090. doi: 10.1042/BCJ20170945.
PMID: 29784889

Hypoxia and Chromatin: A Focus on Transcriptional Repression Mechanisms.
Batie M, Del Peso L, Rocha S.
Biomedicines. 2018 Apr 22;6(2). pii: E47. doi: 10.3390/biomedicines6020047.
PMID: 29690561


2017

Homo-PROTACs: bivalent small-molecule dimerizers of the VHL E3 ubiquitin ligase to induce self-degradation.
Maniaci C, Hughes SJ, Testa A, Chen W, Lamont DJ, Rocha S, Alessi DR, Romeo R, Ciulli A.
Nat Commun. 2017 Oct 10;8(1):830. doi: 10.1038/s41467-017-00954-1.

Group-Based Optimization of Potent and Cell-Active Inhibitors of the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase: Structure-Activity Relationships Leading to the Chemical Probe (2S,4R)-1-((S)-2-(1-Cyanocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (VH298).
Soares P, Gadd MS, Frost J, Galdeano C, Ellis L, Epemolu O, Rocha S, Read KD, Ciulli A.
J Med Chem. 2018 Jan 25;61(2):599-618. doi: 10.1021/acs.jmedchem.7b00675. Epub 2017 Sep 18.
PMID:28853884

Hypoxia and Inflammation in Cancer, Focus on HIF and NF-κB.
D'Ignazio L, Batie M, Rocha S.
Biomedicines. 2017 May 9;5(2). pii: E21. doi: 10.3390/biomedicines5020021. Review.
PMID:28536364

KDM2 Family Members are Regulated by HIF-1 in Hypoxia.
Batie M, Druker J, D'Ignazio L, Rocha S.
Cells. 2017 Mar 17;6(1). pii: E8. doi: 10.3390/cells6010008.
PMID:28304334

 

2016

Potent and selective chemical probe of hypoxic signalling downstream of HIF-α hydroxylation via VHL inhibition.
Frost J, Galdeano C, Soares P, Gadd MS, Grzes KM, Ellis L, Epemolu O, Shimamura S, Bantscheff M, Grandi P, Read KD, Cantrell DA, Rocha S, Ciulli A.
Nat Commun. 2016 Nov 4;7:13312. doi: 10.1038/ncomms13312.

Pinto AT, Pinto ML, Velho S, Pinto MT, Cardoso AP, Figueira R, Monteiro A, Marques M, Seruca R, Barbosa MA, Mareel M, Oliveira MJ, Rocha S.
PLoS One. 2016 Aug 11;11(8):e0160891. doi: 10.1371/journal.pone.0160891. eCollection 2016.
PMID:27513864

Enhanced snoMEN Vectors Facilitate Establishment of GFP-HIF-1α Protein Replacement Human Cell Lines.
Ono M, Yamada K, Bensaddek D, Afzal V, Biddlestone J, Ortmann B, Mudie S, Boivin V, Scott MS, Rocha S, Lamond AI.
PLoS One. 2016 Apr 29;11(4):e0154759. doi: 10.1371/journal.pone.0154759. eCollection 2016.
PMID:27128805


The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors.
Wiechens N, Singh V, Gkikopoulos T, Schofield P, Rocha S, Owen-Hughes T.
PLoS Genet. 2016 Mar 28;12(3):e1005940. doi: 10.1371/journal.pgen.1005940. eCollection 2016 Mar. Erratum in: PLoS Genet. 2016 May;12(5):e1006086.
PMID:27019336

Hypoxia Induced NF-κB.
D'Ignazio L, Rocha S.
Cells. 2016 Mar 8;5(1). pii: E10. doi: 10.3390/cells5010010. Review.
PMID:27005664

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).
Klionsky DJ, Abdelmohsen K....
Autophagy. 2016;12(2):443. Selliez, Iban [corrected to Seiliez, Iban].
PMID:26799652

Ionizing radiation modulates human macrophages towards a pro-inflammatory phenotype preserving their pro-invasive and pro-angiogenic capacities.
Teresa Pinto A, Laranjeiro Pinto M, Patrícia Cardoso A, Monteiro C, Teixeira Pinto M, Filipe Maia A, Castro P, Figueira R, Monteiro A, Marques M, Mareel M, Dos Santos SG, Seruca R, Adolfo Barbosa M, Rocha S, José Oliveira M.
Sci Rep. 2016 Jan 6;6:18765. doi: 10.1038/srep18765.
PMID:26735768

CDK-dependent phosphorylation of PHD1 on serine 130 alters its substrate preference in cells.
Ortmann B, Bensaddek D, Carvalhal S, Moser SC, Mudie S, Griffis ER, Swedlow JR, Lamond AI, Rocha S.
J Cell Sci. 2016 Jan 1;129(1):191-205. doi: 10.1242/jcs.179911. Epub 2015 Dec 7.
PMID:26644182

NF-κB and HIF crosstalk in immune responses.
D'Ignazio L, Bandarra D, Rocha S.
FEBS J. 2016 Feb;283(3):413-24. doi: 10.1111/febs.13578. Epub 2015 Nov 24. Review.
PMID:26513405


2015

Cezanne regulates E2F1-dependent HIF2α expression.
Moniz S, Bandarra D, Biddlestone J, Campbell KJ, Komander D, Bremm A, Rocha S.
J Cell Sci. 2015 Aug 15;128(16):3082-93. doi: 10.1242/jcs.168864. Epub 2015 Jul 6.
PMID:26148512

HIF-1α restricts NF-κB-dependent gene expression to control innate immunity signals.
Bandarra D, Biddlestone J, Mudie S, Müller HA, Rocha S.
Dis Model Mech. 2015 Feb;8(2):169-81. doi: 10.1242/dmm.017285. Epub 2014 Dec 15.
PMID:25510503

Dose-dependent effects of allopurinol on human foreskin fibroblast cells and human umbilical vein endothelial cells under hypoxia.
Sun Y, George J, Rocha S.
PLoS One. 2015 Apr 1;10(4):e0123649. doi: 10.1371/journal.pone.0123649. eCollection 2015.
PMID:25830774

The role of hypoxia in inflammatory disease (review).
Biddlestone J, Bandarra D, Rocha S.
Int J Mol Med. 2015 Apr;35(4):859-69. doi: 10.3892/ijmm.2015.2079. Epub 2015 Jan 27. Review.
PMID:25625467

 

2014

PITX1, a specificity determinant in the HIF-1α-mediated transcriptional response to hypoxia.
Mudie S, Bandarra D, Batie M, Biddlestone J, Moniz S, Ortmann B, Shmakova A, Rocha S.
Cell Cycle. 2014;13(24):3878-91. doi: 10.4161/15384101.2014.972889.

Cezanne (OTUD7B) regulates HIF-1α homeostasis in a proteasome-independent manner.
Bremm A, Moniz S, Mader J, Rocha S, Komander D.
EMBO Rep. 2014 Dec;15(12):1268-77. doi: 10.15252/embr.201438850. Epub 2014 Oct 29.
PMID:25355043

Chromatin and oxygen sensing in the context of JmjC histone demethylases.
Shmakova A, Batie M, Druker J, Rocha S.
Biochem J. 2014 Sep 15;462(3):385-95. doi: 10.1042/BJ20140754. Review.
PMID:25145438

Hypoxia activates IKK-NF-κB and the immune response in Drosophila melanogaster.
Bandarra D, Biddlestone J, Mudie S, Muller HA, Rocha S.
Biosci Rep. 2014 Jul 29;34(4). pii: e00127. doi: 10.1042/BSR20140095.
PMID:24993778

Analysis of global RNA synthesis at the single cell level following hypoxia.
Biddlestone J, Druker J, Shmakova A, Ferguson G, Swedlow JR, Rocha S.
J Vis Exp. 2014 May 13;(87). doi: 10.3791/51420.
PMID:24895009

Grow₂: the HIF system, energy homeostasis and the cell cycle.
Moniz S, Biddlestone J, Rocha S.
Histol Histopathol. 2014 May;29(5):589-600. doi: 10.14670/HH-29.10.589. Epub 2014 Jan 10. Review.
PMID:24407868


2013

PHD1 links cell-cycle progression to oxygen sensing through hydroxylation of the centrosomal protein Cep192.
Moser SC, Bensaddek D, Ortmann B, Maure JF, Mudie S, Blow JJ, Lamond AI, Swedlow JR, Rocha S.
Dev Cell. 2013 Aug 26;26(4):381-92. doi: 10.1016/j.devcel.2013.06.014. Epub 2013 Aug 8.

FMN2 is a novel regulator of the cyclin-dependent kinase inhibitor p21.
Yamada K, Ono M, Bensaddek D, Lamond AI, Rocha S.
Cell Cycle. 2013 Aug 1;12(15):2348-54. doi: 10.4161/cc.25511. Epub 2013 Jul 1.
PMID:23839046

The P-body component USP52/PAN2 is a novel regulator of HIF1A mRNA stability.
Bett JS, Ibrahim AF, Garg AK, Kelly V, Pedrioli P, Rocha S, Hay RT.
Biochem J. 2013 Apr 15;451(2):185-94. doi: 10.1042/BJ20130026.
PMID:23398456

Identification and functional characterization of FMN2, a regulator of the cyclin-dependent kinase inhibitor p21.
Yamada K, Ono M, Perkins ND, Rocha S, Lamond AI.
Mol Cell. 2013 Mar 7;49(5):922-33. doi: 10.1016/j.molcel.2012.12.023. Epub 2013 Jan 31.
PMID:23375502

TfR1 interacts with the IKK complex and is involved in IKK-NF-κB signalling.
Kenneth NS, Mudie S, Naron S, Rocha S.
Biochem J. 2013 Jan 1;449(1):275-84. doi: 10.1042/BJ20120625.
PMID:23016877

2012

Family with sequence similarity 60A (FAM60A) protein is a cell cycle-fluctuating regulator of the SIN3-HDAC1 histone deacetylase complex.
Muñoz IM, MacArtney T, Sanchez-Pulido L, Ponting CP, Rocha S, Rouse J.
J Biol Chem. 2012 Sep 21;287(39):32346-53. Epub 2012 Aug 3.

Chromatin as an oxygen sensor and active player in the hypoxia response.
Melvin A, Rocha S.
Cell Signal. 2012 Jan;24(1):35-43. doi: 10.1016/j.cellsig.2011.08.019. Epub 2011 Sep 8. Review.
PMID:21924352


2011

The chromatin remodeler ISWI regulates the cellular response to hypoxia: role of FIH.
Melvin A, Mudie S, Rocha S.
Mol Biol Cell. 2011 Nov;22(21):4171-81. doi: 10.1091/mbc.E11-02-0163. Epub 2011 Sep 7.
PMID:21900490

The role of RelA (p65) threonine 505 phosphorylation in the regulation of cell growth, survival, and migration.
Msaki A, Sánchez AM, Koh LF, Barré B, Rocha S, Perkins ND, Johnson RF.
Mol Biol Cell. 2011 Sep;22(17):3032-40. doi: 10.1091/mbc.E11-04-0280. Epub 2011 Jul 7.
PMID:2173767

Antagonistic crosstalk between APC and HIF-1α.
Näthke I, Rocha S.
Cell Cycle. 2011 May 15;10(10):1545-7. Epub 2011 May 15.
PMID:21502812

HIF-1α depletion results in SP1-mediated cell cycle disruption and alters the cellular response to chemotherapeutic drugs.
Culver C, Melvin A, Mudie S, Rocha S.
Cell Cycle. 2011 Apr 15;10(8):1249-60. Epub 2011 Apr 15.
PMID:21412054

Further insights into the mechanism of hypoxia-induced NFκB. [corrected].
Melvin A, Mudie S, Rocha S.
Cell Cycle. 2011 Mar 15;10(6):879-82. Epub 2011 Mar 15. Erratum in: Cell Cycle. 2011 Jun 15;10(12):2041.
PMID:21325892

Evolutionary conserved regulation of HIF-1β by NF-κB.
van Uden P, Kenneth NS, Webster R, Müller HA, Mudie S, Rocha S.
PLoS Genet. 2011 Jan 27;7(1):e1001285. doi: 10.1371/journal.pgen.1001285.
PMID:21298084


2010

Adenomatous polyposis coli and hypoxia-inducible factor-1{alpha} have an antagonistic connection.
Newton IP, Kenneth NS, Appleton PL, Näthke I, Rocha S.
Mol Biol Cell. 2010 Nov 1;21(21):3630-8. doi: 10.1091/mbc.E10-04-0312. Epub 2010 Sep 15.

Mechanism of hypoxia-induced NF-kappaB.
Culver C, Sundqvist A, Mudie S, Melvin A, Xirodimas D, Rocha S.
Mol Cell Biol. 2010 Oct;30(20):4901-21. doi: 10.1128/MCB.00409-10. Epub 2010 Aug 9.
PMID:20696840

IKK and NF-kappaB-mediated regulation of Claspin impacts on ATR checkpoint function.
Kenneth NS, Mudie S, Rocha S.
EMBO J. 2010 Sep 1;29(17):2966-78. doi: 10.1038/emboj.2010.171. Epub 2010 Jul 23. Erratum in: EMBO J. 2012 May 30;31(11):2660-1.
PMID:20657549


2009

SWI/SNF regulates the cellular response to hypoxia.
Kenneth NS, Mudie S, van Uden P, Rocha S.
J Biol Chem. 2009 Feb 13;284(7):4123-31. doi: 10.1074/jbc.M808491200. Epub 2008 Dec 19.
PMID:19097995


2008

Regulation of gene expression by hypoxia.
Kenneth NS, Rocha S.
Biochem J. 2008 Aug 15;414(1):19-29. doi: 10.1042/BJ20081055. Review.
PMID:18651837

Regulation of hypoxia-inducible factor-1alpha by NF-kappaB.
van Uden P, Kenneth NS, Rocha S.
Biochem J. 2008 Jun 15;412(3):477-84. doi: 10.1042/BJ20080476.


2007

Gene regulation under low oxygen: holding your breath for transcription.
Rocha S.
Trends Biochem Sci. 2007 Aug;32(8):389-97. Epub 2007 Jul 10. Review.
PMID:17624786
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