Latest publications from AEpiA members - 2024

Century-old chromatin architecture revealed in formalin-fixed vertebrates.

Hahn EE, Stiller J, Alexander MR, Grealy A, Taylor JM, Jackson N, Frere CH, Holleley CE. Nat Commun. 2024 Jul 29;15(1):6378. doi: 10.1038/s41467-024-50668-4. PMID: 39075073; PMCID: PMC11286846.

Exploring the Stability of Genomic Imprinting and X-Chromosome Inactivation in the Aged Brain

Mancino S, Seneviratne J, Mupo A, Krueger F, Oxley D, Eckersley-Maslin MA*, da Rocha ST*. Aging Biology; 2024 July 31; https://doi.org/10.59368/agingbio.20240030

Widespread genomic de novo DNA methylation occurs following CD8+ T cell activation and proliferation.

Seddon AR, Damiano OM, Hampton MB, Stevens AJ. Epigenetics. 2024 Dec;19(1):2367385. doi: 10.1080/15592294.2024.2367385. Epub 2024 Jun 20. PMID: 38899429; PMCID: PMC11195465.

Expansion of a versatile pathogen: Clostridioides difficile

Lucas T and Brown B. Hygiene and Environmental Health Advances 2024 Dec; vol 12, doi.org/10.1016/j.heha.2024.100108.

The CD8+ T cell tolerance checkpoint triggers a distinct differentiation state defined by protein translation defects.

Van Der Byl W, Nüssing S, Peters TJ, Ahn A, Li H, Ledergor G, David E, Koh AS, Wagle MV, Deguit CDT, de Menezes MN, Travers A, Sampurno S, Ramsbottom KM, Li R, Kallies A, Beavis PA, Jungmann R, Bastings MMC, Belz GT, Goel S, Trapani JA, Crabtree GR, Chang HY, Amit I, Goodnow CC, Luciani F, Parish IA. Immunity. 2024 Jun 11;57(6):1324-1344.e8. doi: 10.1016/j.immuni.2024.04.026. Epub 2024 May 21. PMID: 38776918.

Genome-wide analysis of early vascular tunic repair and regeneration for Botrylloides digenesis reveals striking similarities to human wound healing.

Clarke RM, Meier M, Wilson MJ. Dev Biol. 2024 May;509:28-42. doi: 10.1016/j.ydbio.2024.02.003. Epub 2024 Feb 10. PMID: 38342399.

Phosphoproteomic analysis of the adaption of epididymal epithelial cells to corticosterone challenge

Skerrett-Byrne DA, Stanger SJ, Trigg NA, Anderson AL, Sipilä P, Bernstein IR, Lord T, Schjenken JE, Murray HC, Verrills NM, Dun MD, Pang TY, Nixon B. Andrology. 2024 Jul;12(5):1038-1057. doi: 10.1111/andr.13636. Epub 2024 Apr 4. PMID: 38576152.

Targeting RNA modifications with pharmacological agents

Guan A, Wong JJ. New frontiers in cancer therapy. Cancer Med. 2024 Apr;13(7):e6989. doi: 10.1002/cam4.6989. PMID: 38545841; PMCID: PMC10974741.

Increasing histone acetylation improves sociability and restores learning and memory in KAT6B-haploinsufficient mice.

Bergamasco MI, Vanyai HK, Garnham AL, Geoghegan ND, Vogel AP, Eccles S, Rogers KL, Smyth GK, Blewitt ME, Hannan AJ, Thomas T, Voss AK. J Clin Invest. 2024 Apr 1;134(7):e167672. doi: 10.1172/JCI167672. PMID: 38557491; PMCID: PMC10977983.

Impact of Distinct Anti-Androgen Exposures on the Plasma Metabolome in Feminizing Gender-Affirming Hormone Therapy.

Shepherd R, Angus LM, Mansell T, Arman B, Kim BW, Lange K, Burgner D, Kerr JA, Pang K, Zajac JD, Saffery R, Cheung A, Novakovic B. J Clin Endocrinol Metab. 2024 Apr 13:dgae226. doi: 10.1210/clinem/dgae226. Epub ahead of print. PMID: 38609170.

The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer.

Achinger-Kawecka J, Stirzaker C, Portman N, Campbell E, Chia KM, Du Q, Laven-Law G, Nair SS, Yong A, Wilkinson A, Clifton S, Milioli HH, Alexandrou S, Caldon CE, Song J, Khoury A, Meyer B, Chen W, Pidsley R, Qu W, Gee JMW, Schmitt A, Wong ES, Hickey TE, Lim E, Clark SJ. Nat Struct Mol Biol. 2024 Mar;31(3):498-512. doi: 10.1038/s41594-023-01181-7. Epub 2024 Jan 5. PMID: 38182927; PMCID: PMC10948365.

Extensive DNA methylome rearrangement during early lamprey embryogenesis.

Angeloni A, Fissette S, Kaya D, Hammond JM, Gamaarachchi H, Deveson IW, Klose RJ, Li W, Zhang X, Bogdanovic O. Nat Commun. 2024 Mar 4;15(1):1977. doi: 10.1038/s41467-024-46085-2. PMID: 38438347; PMCID: PMC10912607.

Characterisation and reproducibility of the Human Methylation EPIC v2.0 BeadChip for DNA methylation profiling.

Peters TJ, Meyer B, Ryan L, Achinger-Kawecka J, Song J, Campbell EM, Qu W, Nair S, Loi-Luu P, Stricker P, Lim E, Stirzaker C, Clark SJ, Pidsley R. BMC Genomics. 2024 Mar 6;25(1):251. doi: 10.1186/s12864-024-10027-5. PMID: 38448820; PMCID: PMC10916044.

A low‑input high resolution sequential chromatin immunoprecipitation method captures genome‑wide dynamics of bivalent chromatin

Seneviratne J, Ho WHH, Glancy E, Eckersley-Maslin MA. Epigenetics & Chromatin. 2024 Feb 10;17:3 https://doi.org/10.1186/s13072-024-00527-9

CFTR is required for zinc-mediated antibacterial defense in human macrophages.

Das Gupta K, Curson JEB, Tarique AA, Kapetanovic R, Schembri MA, Fantino E, Sly PD, Sweet MJ. Proc Natl Acad Sci U S A. 2024 Feb 20;121(8):e2315190121. doi: 10.1073/pnas.2315190121. Epub 2024 Feb 16. PMID: 38363865; PMCID: PMC10895263.

Dietary fibre confers therapeutic effects in a preclinical model of Huntington's disease.

Gubert C, Kong G, Costello C, Adams CD, Masson BA, Qin W, Choo J, Narayana VK, Rogers G, Renoir T, Furness JB, Hannan AJ. Brain Behav Immun. 2024 Feb;116:404-418. doi: 10.1016/j.bbi.2023.12.023. Epub 2023 Dec 23. PMID: 38142919.

Bivalent chromatin: a developmental balancing act tipped in cancer.

Glancy E, Choy N, Eckersley-Maslin MA. Biochem Soc Trans. 2024 Feb 28;52(1):217-229. doi: 10.1042/BST20230426. PMID: 38385532; PMCID: PMC10903468.

Every repeat is unique: Exploring the genomic impact of human L1 retrotransposons at locus-specific resolution.

Workman S, Richardson SR. Cell Genom. 2024 Feb 14;4(2):100504. doi: 10.1016/j.xgen.2024.100504. PMID: 38359785; PMCID: PMC10879126.

Detailed DNA methylation characterisation of phyllodes tumours identifies a signature of malignancy and distinguishes phyllodes from metaplastic breast carcinoma.

Meyer B, Stirzaker C, Ramkomuth S, Harvey K, Chan B, Lee CS, Karim R, Deng N, Avery-Kiejda KA, Scott RJ, Lakhani S, Fox S, Robbins E, Shin JS, Beith J, Gill A, Sioson L, Chan C, Krishnaswamy M, Cooper C, Warrier S, Mak C, Rasko JE, Bailey CG, Swarbrick A, Clark SJ, O'Toole S, Pidsley R. J Pathol. 2024 Apr;262(4):480-494. doi: 10.1002/path.6250. Epub 2024 Feb 1. PMID: 38300122.

Novel insights on genetics and epigenetics as clinical targets for paediatric astrocytoma.

Johns DA, Williams RJ, Smith CM, Nadaminti PP, Samarasinghe RM. Clin Transl Med. 2024 Feb;14(2):e1560. doi: 10.1002/ctm2.1560. PMID: 38299304; PMCID: PMC10831580.

Reducing PHYTOENE SYNTHASE activity fine-tunes the abundance of a cis-carotene-derived signal that regulates the PIF3/HY5 module and plastid biogenesis.

Hou X, Alagoz Y, Welsch R, Mortimer MD, Pogson BJ, Cazzonelli CI. J Exp Bot. 2024 Feb 12;75(4):1187-1204. doi: 10.1093/jxb/erad443. PMID: 37948577.

PI3K/mTOR is a therapeutically targetable genetic dependency in diffuse intrinsic pontine glioma.

Duchatel RJ, Jackson ER, Parackal SG, Kiltschewskij D, Findlay IJ, Mannan A, Staudt DE, Thomas BC, Germon ZP, Laternser S, Kearney PS, Jamaluddin MFB, Douglas AM, Beitaki T, McEwen HP, Persson ML, Hocke EA, Jain V, Aksu M, Manning EE, Murray HC, Verrills NM, Sun CX, Daniel P, Vilain RE, Skerrett-Byrne DA, Nixon B, Hua S, de Bock CE, Colino-Sanguino Y, Valdes-Mora F, Tsoli M, Ziegler DS, Cairns MJ, Raabe EH, Vitanza NA, Hulleman E, Phoenix TN, Koschmann C, Alvaro F, Dayas CV, Tinkle CL, Wheeler H, Whittle JR, Eisenstat DD, Firestein R, Mueller S, Valvi S, Hansford JR, Ashley DM, Gregory SG, Kilburn LB, Nazarian J, Cain JE, Dun MD.J Clin Invest. 2024 Feb 6;134(6):e170329. doi: 10.1172/JCI170329. PMID: 38319732; PMCID: PMC10940093.

Molecular and Pathologic Characterization of YAP1-Expressing Small Cell Lung Cancer Cell Lines Leads to Reclassification as SMARCA4-Deficient Malignancies.

Ng J, Cai L, Girard L, Prall OWJ, Rajan N, Khoo C, Batrouney A, Byrne DJ, Boyd DK, Kersbergen AJ, Christie M, Minna JD, Burr ML, Sutherland KD. Clin Cancer Res. 2024 Jan 5:OF1-OF13. doi: 10.1158/1078-0432.CCR-23-2360. Epub ahead of print. PMID: 38180245.

Hot alkaline lysis gDNA extraction from formalin-fixed archival tissues.

Hahn EE, Alexander M, Stiller J, Grewe PM, Holleley CE. PLoS One. 2024 Jan 2;19(1):e0296491. doi: 10.1371/journal.pone.0296491. PMID: 38165968; PMCID: PMC10760679.

Amyloid beta 42 alters cardiac metabolism and impairs cardiac function in male mice with obesity.

Hall LG, Czeczor JK, Connor T, Botella J, De Jong KA, Renton MC, Genders AJ, Venardos K, Martin SD, Bond ST, Aston-Mourney K, Howlett KF, Campbell JA, Collier GR, Walder KR, McKenzie M, Ziemann M, McGee SL. Nat Commun. 2024 Jan 15;15(1):258. doi: 10.1038/s41467-023-44520-4. PMID: 38225272; PMCID: PMC10789867.

Paternal immune activation by Poly I:C modulates sperm noncoding RNA profiles and causes transgenerational changes in offspring behavior.

Kleeman EA, Reisinger SN, Adithya P, Houston B, Stathatos G, Garnham AL, McLaughlin S, O'Bryan MK, Gubert C, Hannan AJ. Brain Behav Immun. 2024 Jan;115:258-279. doi: 10.1016/j.bbi.2023.10.005. Epub 2023 Oct 10. PMID: 37820975.

Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on Bifidobacterium spp. in Australian Infants.

Parkin K, Palmer DJ, Verhasselt V, Amenyogbe N, Cooper MN, Christophersen CT, Prescott SL, Silva D, Martino D. Microorganisms. 2024 Jan 22;12(1):228. doi: 10.3390/microorganisms12010228. PMID: 38276213; PMCID: PMC10819277.

A modular dCas9-based recruitment platform for combinatorial epigenome editing.

Swain T, Pflueger C, Freytag S, Poppe D, Pflueger J, Nguyen TV, Li JK, Lister R. Nucleic Acids Res. 2024 Jan 11;52(1):474-491. doi: 10.1093/nar/gkad1108. PMID: 38000387; PMCID: PMC10783489.

Mary Lyon and the birth of X-inactivation research.

Blewitt ME. Nat Rev Genet. 2024 Jan;25(1):6. doi: 10.1038/s41576-023-00655-0. PMID: 37704716.

Publications from AEpiA members - 2023

Comprehensive evaluation of the implementation of episignatures for diagnosis of neurodevelopmental disorders (NDDs).

Giuili E, Grolaux R, Macedo CZNM, Desmyter L, Pichon B, Neuens S, Vilain C, Olsen C, Van Dooren S, Smits G, Defrance M. Hum Genet. 2023 Dec;142(12):1721-1735. doi: 10.1007/s00439-023-02609-2. Epub 2023 Oct 27. PMID: 37889307; PMCID: PMC10676303.

Imprinted gene alterations in the kidneys of growth restricted offspring may be mediated by a long non-coding RNA.

Doan TNA, Cowley JM, Phillips AL, Briffa JF, Leemaqz SY, Burton RA, Romano T, Wlodek ME, Bianco-Miotto T. Epigenetics. 2024 Dec;19(1):2294516. doi: 10.1080/15592294.2023.2294516. Epub 2023 Dec 21. PMID: 38126131; PMCID: PMC10761017.

Active maintenance of CD8+ T cell naivety through regulation of global genome architecture

Russ BE, Barugahare A, Dakle P, Tsyganov K, Quon S, Yu B, Li J, Lee JKC, Olshansky M, He Z, Harrison PF, See M, Nussing S, Morey AE, Udupa VA, Bennett TJ, Kallies A, Murre C, Collas P, Powell D, Goldrath AW, Turner SJ. Cell Rep. 2023 Oct 31;42(10):113301. doi: 10.1016/j.celrep.2023.113301. Epub 2023 Oct 19. PMID: 37858463.

The distribution of dietary choline intake and serum choline levels in Australian women during pregnancy and associated early life factors.

Staskova L, Marx W, Dawson SL, O'Hely M, Mansell T, Saffery R, Burgner D, Collier F, Novakovic B, Vuillermin P, Field CJ, Dewey D, Ponsonby AL; BIS Investigator Group. Eur J Nutr. 2023 Oct;62(7):2855-2872. doi: 10.1007/s00394-023-03186-w. Epub 2023 Jun 28. PMID: 37378694; PMCID: PMC10468947.

Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development.

Gerdes P, Chan D, Lundberg M, Sanchez-Luque FJ, Bodea GO, Ewing AD, Faulkner GJ, Richardson SR. Genome Res. 2023 Sep;33(9):1465-1481. doi: 10.1101/gr.278003.123. Epub 2023 Oct 5. PMID: 37798118; PMCID: PMC10620060.

Transient naive reprogramming corrects hiPS cells functionally and epigenetically.

Buckberry S, Liu X, Poppe D, Tan JP, Sun G, Chen J, Nguyen TV, de Mendoza A, Pflueger J, Frazer T, Vargas-Landín DB, Paynter JM, Smits N, Liu N, Ouyang JF, Rossello FJ, Chy HS, Rackham OJL, Laslett AL, Breen J, Faulkner GJ, Nefzger CM, Polo JM, Lister R. Nature. 2023 Aug 16. doi: 10.1038/s41586-023-06424-7. Epub ahead of print. PMID: 37587336.

Inhibition of METTL3 results in a cell-intrinsic interferon response that enhances anti-tumour immunity.

Guirguis AA, Ofir-Rosenfeld Y, Knezevic K, Blackaby W, Hardick D, Chan YC, Motazedian A, Gillespie A, Vassiliadis D, Lam EY, Tran K, Andrews B, Harbour ME, Vasiliauskaite L, Saunders CJ, Tsagkogeorga G, Azevedo A, Obacz J, Pilka ES, Carkill M, MacPherson L, Wainwright EN, Liddicoat B, Blyth BJ, Albertella MR, Rausch O, Dawson MA. Cancer Discov. 2023 Aug 7:CD-23-0007. doi: 10.1158/2159-8290.CD-23-0007. Epub ahead of print. PMID: 37548590.

Are we ready for cell-specific therapies in atherosclerosis?

Khan AW. Eur Heart J. 2023 Aug 22;44(32):3027-3030. doi: 10.1093/eurheartj/ehad147. PMID: 36928096; PMCID: PMC10443655.

Association between the timing of childhood adversity and epigenetic patterns across childhood and adolescence: findings from the Avon Longitudinal Study of Parents and Children (ALSPAC) prospective cohort.

Lussier AA, Zhu Y, Smith BJ, Cerutti J, Fisher J, Melton PE, Wood NM, Cohen-Woods S, Huang RC, Mitchell C, Schneper L, Notterman DA, Simpkin AJ, Smith ADAC, Suderman MJ, Walton E, Relton CL, Ressler KJ, Dunn EC. Lancet Child Adolesc Health. 2023 Aug;7(8):532-543. doi: 10.1016/S2352-4642(23)00127-X. Epub 2023 Jun 14. PMID: 37327798.

Readout of histone methylation by Trim24 locally restricts chromatin opening by p53

Isbel L, Iskar M, Durdu S, Weiss J, Grand RS, Hietter-Pfeiffer E, Kozicka Z, Michael AK, Burger L, Thomä NH, Schübeler D. Nat Struct Mol Biol. 2023 Jun 29. doi: 10.1038/s41594-023-01021-8. Epub ahead of print. PMID: 37386214.

Differential DNA methylation of steatosis and non-alcoholic fatty liver disease in adolescence.

Melton PE, Burton MA, Lillycrop KA, Godfrey KM, Rauschert S, Anderson D, Burdge GC, Mori TA, Beilin LJ, Ayonrinde OT, Craig JM, Olynyk JK, Holbrook JD, Pennell CE, Oddy WH, Moses EK, Adams LA, Huang RC. Hepatol Int. 2023 Jun;17(3):584-594. doi: 10.1007/s12072-022-10469-7. Epub 2023 Feb 3. PMID: 36737504; PMCID: PMC9897882.

Exercise is associated with younger methylome and transcriptome profiles in human skeletal muscle.

Voisin S, Seale K, Jacques M, Landen S, Harvey NR, Haupt LM, Griffiths LR, Ashton KJ, Coffey VG, Thompson JM, Doering TM, Lindholm ME, Walsh C, Davison G, Irwin R, McBride C, Hansson O, Asplund O, Heikkinen AE, Piirilä P, Pietiläinen KH, Ollikainen M, Blocquiaux S, Thomis M, Coletta DK, Sharples AP, Eynon N. Aging Cell. 2023 May 2:e13859. doi: 10.1111/acel.13859. Epub ahead of print. PMID: 37128843.

Decoding enhancer complexity with machine learning and high-throughput discovery.

Smith GD, Ching WH, Cornejo-Páramo P, Wong ES. Genome Biol. 2023 May 12;24(1):116. doi: 10.1186/s13059-023-02955-4. PMID: 37173718; PMCID: PMC10176946.

Overexpression of VIRMA confers vulnerability to breast cancers via the m6A-dependent regulation of unfolded protein response.

Lee Q, Song R, Phan DAV, Pinello N, Tieng J, Su A, Halstead JM, Wong ACH, van Geldermalsen M, Lee BS, Rong B, Cook KM, Larance M, Liu R, Lan F, Tiffen JC, Wong JJ. Cell Mol Life Sci. 2023 May 19;80(6):157. doi: 10.1007/s00018-023-04799-4. Erratum in: Cell Mol Life Sci. 2023 Jul 14;80(8):204. PMID: 37208522; PMCID: PMC10198946.

ONC201 in combination with paxalisib for the treatment of H3K27-altered diffuse midline glioma.

Jackson ER, Duchatel RJ, Staudt DE, Persson ML, Mannan A, Yadavilli S, Parackal S, Game S, Chong WC, Jayasekara WSN, Le Grand M, Kearney PS, Douglas AM, Findlay IJ, Germon ZP, McEwen HP, Beitaki TS, Patabendige A, Skerrett-Byrne DA, Nixon B, Smith ND, Day B, Manoharan N, Nagabushan S, Hansford JR, Govender D, McCowage GB, Firestein R, Howlett M, Endersby R, Gottardo NG, Alvaro F, Waszak SM, Larsen MR, Colino-Sanguino Y, Valdés-Mora F, Rakotomalala A, Meignan S, Pasquier E, Andre N, Hulleman E, Eisenstat DD, Vitanza NA, Nazarian J, Koschmann C, Mueller S, Cain JE, Dun MD. Cancer Res. 2023 May 5:CAN-23-0186. doi: 10.1158/0008-5472.CAN-23-0186. Epub ahead of print. PMID: 37145169.

Paternal early life stress exerts intergenerational effects on male C57Bl/6J offspring risk-taking behaviors and predator scent-induced c-Fos expression.

Thivisol UMCC, Ho P, Li B, Trompke M, Hoffmann LB, Hannan AJ, Pang TY. Neuronal Signal. 2023 Apr 28;7(2):NS20220097. doi: 10.1042/NS20220097. PMID: 37152245; PMCID: PMC10154287.

Emerging role of non-invasive and liquid biopsy biomarkers in pancreatic cancer.

Bararia A, Chakraborty P, Roy P, Chattopadhay BK, Das A, Chatterjee A, Sikdar N. World J Gastroenterol. 2023 Apr 21;29(15):2241-2260. doi: 10.3748/wjg.v29.i15.2241. PMID: 37124888; PMCID: PMC10134423.

KDM6A Mediated Regulation of Cranial Frontal Bone Suture Fusion in Mice is Sex-Dependent.

Pribadi C, Cakouros D, Camp E, Anderson PJ, Gronthos S. Stem Cells Dev. 2023 Apr 20. doi: 10.1089/scd.2023.0022. Epub ahead of print. PMID: 37078151.

Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data.

Moravec JC, Lanfear R, Spector DL, Diermeier SD, Gavryushkin A. J Comput Biol. 2023 Apr;30(4):518-537. doi: 10.1089/cmb.2022.0357. Epub 2022 Dec 6. PMID: 36475926; PMCID: PMC10125402.

Pathologically mislocalised TDP-43 in upper motor neurons causes a die-forward spread of ALS-like pathogenic changes throughout the mouse corticomotor system.

Reale LA, Dyer MS, Perry SE, Young KM, Dickson TC, Woodhouse A, Blizzard CA. Prog Neurobiol. 2023 Apr 1;226:102449. doi: 10.1016/j.pneurobio.2023.102449. Epub ahead of print. PMID: 37011806.

Epigenomic variability is associated with age-specific naïve CD4 T cell response to activation in infants and adolescents.

Imran S, Neeland MR, Martino DJ, Peng S, Koplin J, Dharmage SC, Tang ML, Sawyer S, Dang T, McWilliam V, Peters RL, Prescott S, Perrett KP, Novakovic B, Saffery R. Immunol Cell Biol. 2023 May;101(5):397-411. doi: 10.1111/imcb.12628. Epub 2023 Mar 1. PMID: 36760028.

Impact of Environmental and Epigenetic Changes on Mesenchymal Stem Cells during Aging.

Smith N, Shirazi S, Cakouros D, Gronthos S. Int J Mol Sci. 2023 Mar 30;24(7):6499. doi: 10.3390/ijms24076499. PMID: 37047469; PMCID: PMC10095074.

Histone H3-wild type diffuse midline gliomas with H3K27me3 loss are a distinct entity with exclusive EGFR or ACVR1 mutation and differential methylation of homeobox genes.

Ajuyah P, Mayoh C, Lau LMS, Barahona P, Wong M, Chambers H, Valdes-Mora F, Senapati A, Gifford AJ, D'Arcy C, Hansford JR, Manoharan N, Nicholls W, Williams MM, Wood PJ, Cowley MJ, Tyrrell V, Haber M, Ekert PG, Ziegler DS, Khuong-Quang DA. Sci Rep. 2023 Mar 7;13(1):3775. doi: 10.1038/s41598-023-30395-4. PMID: 36882456; PMCID: PMC9992705.

Reduced methylation correlates with diabetic nephropathy risk in type 1 diabetes.

Khurana I, Kaipananickal H, Maxwell S, Birkelund S, Syreeni A, Forsblom C, Okabe J, Ziemann M, Kaspi A, Rafehi H, Jørgensen A, Al-Hasani K, Thomas MC, Jiang G, Luk AO, Lee HM, Huang Y, Thewjitcharoen Y, Nakasatien S, Himathongkam T, Fogarty C, Njeim R, Eid A, Hansen TW, Tofte N, Ottesen EC, Ma RC, Chan JC, Cooper ME, Rossing P, Groop PH, El-Osta A. J Clin Invest. 2023 Feb 15;133(4):e160959. doi: 10.1172/JCI160959. PMID: 36633903; PMCID: PMC9927943.

Pitfalls and opportunities for applying latent variables in single-cell eQTL analyses.

Xue A, Yazar S, Neavin D, Powell JE. Genome Biol. 2023 Feb 23;24(1):33. doi: 10.1186/s13059-023-02873-5. PMID: 36823676; PMCID: PMC9948363.

Targeting Menin disrupts the KMT2A/B and polycomb balance to paradoxically activate bivalent genes.

Sparbier CE, Gillespie A, Gomez J, Kumari N, Motazedian A, Chan KL, Bell CC, Gilan O, Chan YC, Popp S, Gough DJ, Eckersley-Maslin MA, Dawson SJ, Lehner PJ, Sutherland KD, Ernst P, McGeehan GM, Lam EYN, Burr ML, Dawson MA. Nat Cell Biol. 2023 Feb;25(2):258-272. doi: 10.1038/s41556-022-01056-x. Epub 2023 Jan 12. PMID: 36635503; PMCID: PMC7614190.

Strategy for RNA-Seq Experimental Design and Data Analysis.

Gimenez G, Stockwell PA, Rodger EJ, Chatterjee A. Methods Mol Biol. 2023;2588:249-278. doi: 10.1007/978-1-0716-2780-8_16.PMID: 36418693

The Efficacy of Using Patient-Derived Organoids to Predict Treatment Response in Colorectal Cancer.

Su C, Olsen KA, Bond CE, Whitehall VLJ. Cancers (Basel). 2023 Jan 28;15(3):805. doi: 10.3390/cancers15030805. PMID: 36765763; PMCID: PMC9913532.

Size-Based Method for Enrichment of Circulating Tumor Cells from Blood of Colorectal Cancer Patients.

Vasantharajan SS, Barnett E, Gray ES, Rodger EJ, Eccles MR, Pattison S, Munro F, Chatterjee A. Methods Mol Biol. 2023;2588:231-248. doi: 10.1007/978-1-0716-2780-8_15.PMID: 36418692

HDAC7 is an immunometabolic switch triaging danger signals for engagement of antimicrobial versus inflammatory responses in macrophages.

Das Gupta K, Ramnath D, von Pein JB, Curson JEB, Wang Y, Abrol R, Kakkanat A, Moradi SV, Gunther KS, Murthy AMV, Stocks CJ, Kapetanovic R, Reid RC, Iyer A, Ilka ZC, Nauseef WM, Plan M, Luo L, Stow JL, Schroder K, Karunakaran D, Alexandrov K, Shakespear MR, Schembri MA, Fairlie DP, Sweet MJ. Proc Natl Acad Sci U S A. 2023 Jan 24;120(4):e2212813120. doi: 10.1073/pnas.2212813120. Epub 2023 Jan 17. PMID: 36649417; PMCID: PMC9942870.

Publications from AEpiA members - 2022

Single-Cell DNA Methylation Analysis in Cancer.

O'Neill H, Lee H, Gupta I, Rodger EJ, Chatterjee A. Cancers (Basel). 2022 Dec 14;14(24):6171. doi: 10.3390/cancers14246171. PMID: 36551655; PMCID: PMC9777108.

Immuno-epigenomic analysis identifies attenuated interferon responses in naïve CD4 T cells of adolescents with peanut and multi-food allergy.

Imran S, Neeland MR, Peng S, Vlahos A, Martino D, Dharmage SC, Tang MLK, Sawyer S, Dang TD, McWilliam V, Peters RL, Koplin JJ, Perrett KP, Novakovic B, Saffery R. Pediatr Allergy Immunol. 2022 Nov;33(11):e13890. doi: 10.1111/pai.13890. PMID: 36433861.

Mitochondrial succinate dehydrogenase function is essential for sperm motility and male fertility.

Woodhouse RM, Frolows N, Wang G, Hawdon A, Wong EHK, Dansereau LC, Su Y, Adair LD, New EJ, Philp AM, Tan WK, Philp A, Ashe A. iScience. 2022 Nov 14;25(12):105573. doi: 10.1016/j.isci.2022.105573. PMID: 36465130; PMCID: PMC9709242.

Comparative analysis of Illumina Mouse Methylation BeadChip and reduced-representation bisulfite sequencing for routine DNA methylation analysis.

Fennell LJ, Hartel G, McKeone DM, Bond CE, Kane A, Leggett BA, Patch AM, Whitehall VLJ. Cell Rep Methods. 2022 Nov 1;2(11):100323. doi: 10.1016/j.crmeth.2022.100323. PMID: 36452869; PMCID: PMC9701610.

Comprehensive methylome sequencing reveals prognostic epigenetic biomarkers for prostate cancer mortality.

Pidsley R, Lam D, Qu W, Peters TJ, Luu PL, Korbie D, Stirzaker C, Daly RJ, Stricker P, Kench JG, Horvath LG, Clark SJ. Clin Transl Med. 2022 Oct;12(10):e1030. doi: 10.1002/ctm2.1030. PMID: 36178085; PMCID: PMC9523674.

Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution.

Herring CA, Simmons RK, Freytag S, Poppe D, Moffet JJD, Pflueger J, Buckberry S, Vargas-Landin DB, Clément O, Echeverría EG, Sutton GJ, Alvarez-Franco A, Hou R, Pflueger C, McDonald K, Polo JM, Forrest ARR, Nowak AK, Voineagu I, Martelotto L, Lister R.Cell. 2022 Nov 10;185(23):4428-4447.e28. doi: 10.1016/j.cell.2022.09.039. Epub 2022 Oct 31.PMID: 36318921

LncRNA-Chromatin Pull-Down Using Biotin-Conjugated DNA Probes.

Sarkar D, Diermeier SD. Methods Mol Biol. 2022;2458:345-357. doi: 10.1007/978-1-0716-2140-0_19. PMID: 35103977.

Imprinting fidelity in mouse iPSCs depends on sex of donor cell and medium formulation.

Arez M, Eckersley-Maslin M, Klobučar T, von Gilsa Lopes J, Krueger F, Mupo A, Raposo AC, Oxley D, Mancino S, Gendrel AV, Bernardes de Jesus B, da Rocha ST. Nat Commun. 2022 Sep 16;13(1):5432. doi: 10.1038/s41467-022-33013-5. PMID: 36114205; PMCID: PMC9481624.

Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function.

Ravichandran M, Rafalski D, Davies CI, Ortega-Recalde O, Nan X, Glanfield CR, Kotter A, Misztal K, Wang AH, Wojciechowski M, Rażew M, Mayyas IM, Kardailsky O, Schwartz U, Zembrzycki K, Morison IM, Helm M, Weichenhan D, Jurkowska RZ, Krueger F, Plass C, Zacharias M, Bochtler M, Hore TA, Jurkowski TP. Sci Adv. 2022 Sep 9;8(36):eabm2427. doi: 10.1126/sciadv.abm2427. Epub 2022 Sep 7. PMID: 36070377; PMCID: PMC9451156.

Neonatal BCG vaccination is associated with a long-term DNA methylation signature in circulating monocytes.

Bannister S, Kim B, Domínguez-Andrés J, Kilic G, Ansell BRE, Neeland MR, Moorlag SJCFM, Matzaraki V, Vlahos A, Shepherd R, Germano S, Bahlo M, Messina NL, Saffery R, Netea MG, Curtis N, Novakovic B. Sci Adv. 2022 Aug 5;8(31):eabn4002. doi: 10.1126/sciadv.abn4002. Epub 2022 Aug 5. PMID: 35930640; PMCID: PMC9355358.

Assessment of a Size-Based Method for Enriching Circulating Tumour Cells in Colorectal Cancer.

Vasantharajan SS, Barnett E, Gray ES, McCall JL, Rodger EJ, Eccles MR, Munro F, Pattison S, Chatterjee A. Cancers (Basel). 2022 Jul 15;14(14):3446. doi: 10.3390/cancers14143446. PMID: 35884509; PMCID: PMC9319975.

Synthetic memory circuits for stable cell reprogramming in plants.

Lloyd JPB, Ly F, Gong P, Pflueger J, Swain T, Pflueger C, Fourie E, Khan MA, Kidd BN, Lister R. Nat Biotechnol. 2022 Dec;40(12):1862-1872. doi: 10.1038/s41587-022-01383-2. Epub 2022 Jul 4. PMID: 35788565.

Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability.

de Mendoza A, Nguyen TV, Ford E, Poppe D, Buckberry S, Pflueger J, Grimmer MR, Stolzenburg S, Bogdanovic O, Oshlack A, Farnham PJ, Blancafort P, Lister R. Genome Biol. 2022 Jul 26;23(1):163. doi: 10.1186/s13059-022-02728-5.PMID: 35883107

Genetic variation as a long-distance modulator of RAD21 expression in humans.

Schierding W, Horsfield JA, O'Sullivan J. Sci Rep. 2022 Jul 29;12(1):13035. doi: 10.1038/s41598-022-15081-1. PMID: 35906355; PMCID: PMC9338076.

Establishing gene regulatory networks from Parkinson's disease risk loci.

Farrow SL, Schierding W, Gokuladhas S, Golovina E, Fadason T, Cooper AA, O'Sullivan JM. Brain. 2022 Jul 29;145(7):2422-2435. doi: 10.1093/brain/awac022. PMID: 35094046; PMCID: PMC9373962.

Braf mutation induces rapid neoplastic transformation in the aged and aberrantly methylated intestinal epithelium.

Fennell L, Kane A, Liu C, McKeone D, Hartel G, Su C, Bond C, Bettington M, Leggett B, Whitehall V. Gut. 2022 Jun;71(6):1127-1140. doi: 10.1136/gutjnl-2020-322166. Epub 2021 Jul 6. PMID: 34230216; PMCID: PMC9120393.

Molecular Mechanisms of Neuroinflammation in ME/CFS and Long COVID to Sustain Disease and Promote Relapses.

Tate W, Walker M, Sweetman E, Helliwell A, Peppercorn K, Edgar C, Blair A, Chatterjee A. Front Neurol. 2022 May 25;13:877772. doi: 10.3389/fneur.2022.877772. PMID: 35693009; PMCID: PMC9174654.

Genome-wide DNA methylation of the liver reveals delayed effects of early-life exposure to 17-α-ethinylestradiol in the self-fertilizing mangrove rivulus.

Voisin AS, Suarez Ulloa V, Stockwell P, Chatterjee A, Silvestre F. Epigenetics. 2022 May;17(5):473-497. doi: 10.1080/15592294.2021.1921337. Epub 2021 May 5. PMID: 33892617; PMCID: PMC9067464.

The Promise of Single-cell Technology in Providing New Insights Into the Molecular Heterogeneity and Management of Acute Lymphoblastic Leukemia.

Pearson HCL, Hunt KV, Trahair TN, Lock RB, Lee HJ, de Bock CE. Hemasphere. 2022 May 26;6(6):e734. doi: 10.1097/HS9.0000000000000734. PMID: 35651714; PMCID: PMC9148686.

scTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs.

Hunt KV, Burnard SM, Roper EA, Bond DR, Dun MD, Verrills NM, Enjeti AK, Lee HJ. Sci Rep. 2022 Apr 6;12(1):5776. doi: 10.1038/s41598-022-09765-x. PMID: 35388081; PMCID: PMC8986802.

Combined Inhibition of G9a and EZH2 Suppresses Tumor Growth via Synergistic Induction of IL24-Mediated Apoptosis.

Casciello F, Kelly GM, Ramarao-Milne P, Kamal N, Stewart TA, Mukhopadhyay P, Kazakoff SH, Miranda M, Kim D, Davis FM, Hayward NK, Vertino PM, Waddell N, Gannon F, Lee JS. Cancer Res. 2022 Apr 1;82(7):1208-1221. doi: 10.1158/0008-5472.CAN-21-2218. PMID: 35149587.

Triiodothyronine (T3) Induces Limited Transcriptional and DNA Methylation Reprogramming in Human Monocytes.

Shepherd R, Kim B, Saffery R, Novakovic B. Biomedicines. 2022 Mar 4;10(3):608. doi: 10.3390/biomedicines10030608. PMID: 35327410; PMCID: PMC8945024.

Genome-wide DNA methylation of the liver reveals delayed effects of early-life exposure to 17-α-ethinylestradiol in the self-fertilizing mangrove rivulus.

Voisin AS, Suarez Ulloa V, Stockwell P, Chatterjee A, Silvestre F. Epigenetics. 2022 May;17(5):473-497. doi: 10.1080/15592294.2021.1921337. Epub 2021 May 5. PMID: 33892617; PMCID: PMC9067464.

The Promise of Single-cell Technology in Providing New Insights Into the Molecular Heterogeneity and Management of Acute Lymphoblastic Leukemia.

Pearson HCL, Hunt KV, Trahair TN, Lock RB, Lee HJ, de Bock CE. Hemasphere. 2022 May 26;6(6):e734. doi: 10.1097/HS9.0000000000000734. PMID: 35651714; PMCID: PMC9148686.

scTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs.

Hunt KV, Burnard SM, Roper EA, Bond DR, Dun MD, Verrills NM, Enjeti AK, Lee HJ. Sci Rep. 2022 Apr 6;12(1):5776. doi: 10.1038/s41598-022-09765-x. PMID: 35388081; PMCID: PMC8986802.

Combined Inhibition of G9a and EZH2 Suppresses Tumor Growth via Synergistic Induction of IL24-Mediated Apoptosis.

Casciello F, Kelly GM, Ramarao-Milne P, Kamal N, Stewart TA, Mukhopadhyay P, Kazakoff SH, Miranda M, Kim D, Davis FM, Hayward NK, Vertino PM, Waddell N, Gannon F, Lee JS. Cancer Res. 2022 Apr 1;82(7):1208-1221. doi: 10.1158/0008-5472.CAN-21-2218. PMID: 35149587.

Triiodothyronine (T3) Induces Limited Transcriptional and DNA Methylation Reprogramming in Human Monocytes.

Shepherd R, Kim B, Saffery R, Novakovic B. Biomedicines. 2022 Mar 4;10(3):608. doi: 10.3390/biomedicines10030608. PMID: 35327410; PMCID: PMC8945024.

Abundant small RNAs in the reproductive tissues and eggs of the honey bee, Apis mellifera.

Watson OT, Buchmann G, Young P, Lo K, Remnant EJ, Yagound B, Shambrook M, Hill AF, Oldroyd BP, Ashe A. BMC Genomics. 2022 Apr 4;23(1):257. doi: 10.1186/s12864-022-08478-9. PMID: 35379185; PMCID: PMC8978429.

Urgent need for consistent standards in functional enrichment analysis.

Wijesooriya K, Jadaan SA, Perera KL, Kaur T, Ziemann M. PLoS Comput Biol. 2022 Mar 9;18(3):e1009935. doi: 10.1371/journal.pcbi.1009935. PMID: 35263338; PMCID: PMC8936487.

Epigenetic basis and targeting of cancer metastasis.

Banerjee R, Smith J, Eccles MR, Weeks RJ, Chatterjee A. Trends Cancer. 2022 Mar;8(3):226-241. doi: 10.1016/j.trecan.2021.11.008. Epub 2021 Dec 22. PMID: 34952829.

Epigenetic Mechanisms Responsible for the Transgenerational Inheritance of Intrauterine Growth Restriction Phenotypes.

Doan TNA, Akison LK, Bianco-Miotto T. Front Endocrinol (Lausanne). 2022 Mar 31;13:838737. doi: 10.3389/fendo.2022.838737. PMID: 35432208; PMCID: PMC9008301.

BAF complex-mediated chromatin relaxation is required for establishment of X chromosome inactivation.

Keniry A, Jansz N, Gearing LJ, Wanigasuriya I, Chen J, Nefzger CM, Hickey PF, Gouil Q, Liu J, Breslin KA, Iminitoff M, Beck T, Tapia Del Fierro A, Whitehead L, Jarratt A, Kinkel SA, Taberlay PC, Willson T, Pakusch M, Ritchie ME, Hilton DJ, Polo JM, Blewitt ME. Nat Commun. 2022 Mar 29;13(1):1658. doi: 10.1038/s41467-022-29333-1. PMID: 35351876; PMCID: PMC8964718.

Gender-affirming hormone therapy induces specific DNA methylation changes in blood.

Shepherd R, Bretherton I, Pang K, Mansell T, Czajko A, Kim B, Vlahos A, Zajac JD, Saffery R, Cheung A, Novakovic B. Clin Epigenetics. 2022 Feb 17;14(1):24. doi: 10.1186/s13148-022-01236-4. PMID: 35177097; PMCID: PMC8851870.

Machine Learning Identifies Six Genetic Variants and Alterations in the Heart Atrial Appendage as Key Contributors to PD Risk Predictivity.

Ho D, Schierding W, Farrow SL, Cooper AA, Kempa-Liehr AW, O'Sullivan JM. Front Genet. 2022 Jan 3;12:785436. doi: 10.3389/fgene.2021.785436. PMID: 35047012; PMCID: PMC8762216.

Assigning function to SNPs: Considerations when interpreting genetic variation.

Fadason T, Farrow S, Gokuladhas S, Golovina E, Nyaga D, O'Sullivan JM, Schierding W. Semin Cell Dev Biol. 2022 Jan;121:135-142. doi: 10.1016/j.semcdb.2021.08.008. Epub 2021 Aug 24. PMID: 34446357.

Editing of DNA Methylation Patterns Using CRISPR-Based Tools.

Smith J, Banerjee R, Weeks RJ, Chatterjee A. Methods Mol Biol. 2022;2458:63-74. doi: 10.1007/978-1-0716-2140-0_4. PMID: 35103962.

Epigenome plasticity in plants.

Lloyd JPB, Lister R. Nat Rev Genet. 2022 Jan;23(1):55-68. doi: 10.1038/s41576-021-00407-y. Epub 2021 Sep 15. PMID: 34526697.

Generating Sequencing-Based DNA Methylation Maps from Low DNA Input Samples.

Al Momani S, Rodger EJ, Stockwell PA, Eccles MR, Chatterjee A. Methods Mol Biol. 2022;2458:3-21. doi: 10.1007/978-1-0716-2140-0_1. PMID: 35103959.

Publications from AEpiA members - 2021

Hairpin-bisulfite sequencing of cells exposed to decitabine documents the process of DNA demethylation.

Mayyas IM, Weeks RJ, Day RC, Magrath HE, O'Connor KM, Kardailsky O, Hore TA, Hampton MB, Morison IM. Epigenetics. 2021 Nov;16(11):1251-1259. doi: 10.1080/15592294.2020.1861169. Epub 2020 Dec 28. PMID: 33315501; PMCID: PMC8813075.

Maternal Dppa2 and Dppa4 are dispensable for zygotic genome activation but important for offspring survival.

Kubinyecz O, Santos F, Drage D, Reik W, Eckersley-Maslin MA. Development. 2021 Dec 15;148(24):dev200191. doi: 10.1242/dev.200191. Epub 2021 Dec 21. PMID: 34931676; PMCID: PMC8722389.

Epigenetic mechanisms involved in intrauterine growth restriction and aberrant kidney development and function.

Doan TNA, Briffa JF, Phillips AL, Leemaqz SY, Burton RA, Romano T, Wlodek ME, Bianco-Miotto T. J Dev Orig Health Dis. 2021 Dec;12(6):952-962. doi: 10.1017/S2040174420001257. Epub 2020 Dec 22. PMID: 33349286.

Curcumin Chemoprevention Reduces the Incidence of Braf Mutant Colorectal Cancer in a Preclinical Study.

Kane AM, Liu C, Akhter DT, McKeone DM, Bell CA, Thurecht KJ, Leggett BA, Whitehall VLJ. Dig Dis Sci. 2021 Dec;66(12):4326-4332. doi: 10.1007/s10620-020-06752-y. Epub 2021 Jan 2. PMID: 33387125.

DNA methylation profiling identifies epigenetic differences between early versus late stages of diabetic chronic kidney disease.

Lecamwasam A, Novakovic B, Meyer B, Ekinci EI, Dwyer KM, Saffery R. Nephrol Dial Transplant. 2021 Nov 9;36(11):2027-2038. doi: 10.1093/ndt/gfaa226. PMID: 33146725.

Locus-Specific DNA Methylation Editing in Melanoma Cell Lines Using a CRISPR-Based System.

Smith J, Banerjee R, Waly R, Urbano A, Gimenez G, Day R, Eccles MR, Weeks RJ, Chatterjee A. Cancers (Basel). 2021 Oct 29;13(21):5433. doi: 10.3390/cancers13215433. PMID: 34771597; PMCID: PMC8582460.

Identifying the lungs as a susceptible site for allele-specific regulatory changes associated with type 1 diabetes risk.

Ho D, Nyaga DM, Schierding W, Saffery R, Perry JK, Taylor JA, Vickers MH, Kempa-Liehr AW, O'Sullivan JM. Commun Biol. 2021 Sep 14;4(1):1072. doi: 10.1038/s42003-021-02594-0. PMID: 34521982; PMCID: PMC8440780.

Castration delays epigenetic aging and feminizes DNA methylation at androgen-regulated loci.

Sugrue VJ, Zoller JA, Narayan P, Lu AT, Ortega-Recalde OJ, Grant MJ, Bawden CS, Rudiger SR, Haghani A, Bond DM, Hore RR, Garratt M, Sears KE, Wang N, Yang XW, Snell RG, Hore TA, Horvath S. Elife. 2021 Jul 6;10:e64932. doi: 10.7554/eLife.64932. PMID: 34227937; PMCID: PMC8260231.

Estimating Global Methylation and Erasure Using Low-Coverage Whole-Genome Bisulfite Sequencing (WGBS ).

Ortega-Recalde O, Peat JR, Bond DM, Hore TA. Methods Mol Biol. 2021;2272:29-44. doi: 10.1007/978-1-0716-1294-1_3. Erratum in: Methods Mol Biol. 2021;2272:C1. PMID: 34009607.

Nutritional properties of selected superfood extracts and their potential health benefits.

Barsby JP, Cowley JM, Leemaqz SY, Grieger JA, McKeating DR, Perkins AV, Bastian SEP, Burton RA, Bianco-Miotto T. PeerJ. 2021 Nov 26;9:e12525. doi: 10.7717/peerj.12525. PMID: 34900436; PMCID: PMC8628624.

Mislocalisation of TDP-43 to the cytoplasm causes cortical hyperexcitability and reduced excitatory neurotransmission in the motor cortex.

Dyer MS, Reale LA, Lewis KE, Walker AK, Dickson TC, Woodhouse A, Blizzard CA. J Neurochem. 2021 May;157(4):1300-1315. doi: 10.1111/jnc.15214. Epub 2020 Nov 9. Erratum in: J Neurochem. 2021 Nov;159(4):789-790. PMID: 33064315.

The effect of zinc on human trophoblast proliferation and oxidative stress.

Jankovic-Karasoulos T, McAninch D, Dixon C, Leemaqz SY, François M, Leifert WR, McCullough D, Ricciardelli C, Roberts CT, Bianco-Miotto T. J Nutr Biochem. 2021 Apr;90:108574. doi: 10.1016/j.jnutbio.2020.108574. Epub 2020 Dec 31. PMID: 33388345.

Effect of Iodine and Selenium on Proliferation, Viability, and Oxidative Stress in HTR-8/SVneo Placental Cells.

Habibi N, Jankovic-Karasoulos T, Leemaqz SY, Francois M, Zhou SJ, Leifert WR, Perkins AV, Roberts CT, Bianco-Miotto T. Biol Trace Elem Res. 2021 Apr;199(4):1332-1344. doi: 10.1007/s12011-020-02277-7. Epub 2020 Jul 5. PMID: 32623623.

Mapping genomic and epigenomic evolution in cancer ecosystems.

Ushijima T, Clark SJ, Tan P. Science. 2021 Sep 24;373(6562):1474-1479. doi: 10.1126/science.abh1645. Epub 2021 Sep 23. PMID: 34554797.

Tumor dissociation of highly viable cell suspensions for single-cell omic analyses in mouse models of breast cancer.

Rodriguez de la Fuente L, Law AMK, Gallego-Ortega D, Valdes-Mora F. STAR Protoc. 2021 Sep 17;2(4):100841. doi: 10.1016/j.xpro.2021.100841. PMID: 34585168; PMCID: PMC8456108.

Low tolerance for transcriptional variation at cohesin genes is accompanied by functional links to disease-relevant pathways.

Schierding W, Horsfield JA, O'Sullivan JM. J Med Genet. 2021 Aug;58(8):534-542. doi: 10.1136/jmedgenet-2020-107095. Epub 2020 Sep 11. PMID: 32917770; PMCID: PMC8327319.

H2A.B is a cancer/testis factor involved in the activation of ribosome biogenesis in Hodgkin lymphoma.

Jiang X, Wen J, Paver E, Wu YH, Sun G, Bullman A, Dahlstrom JE, Tremethick DJ, Soboleva TA. EMBO Rep. 2021 Aug 4;22(8):e52462. doi: 10.15252/embr.202152462. Epub 2021 Jul 19. PMID: 34350706; PMCID: PMC8339673.

Gene name errors: Lessons not learned.

Abeysooriya M, Soria M, Kasu MS, Ziemann M. PLoS Comput Biol. 2021 Jul 30;17(7):e1008984. doi: 10.1371/journal.pcbi.1008984. PMID: 34329294; PMCID: PMC8357140.

A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program.

Alda-Catalinas C, Bredikhin D, Hernando-Herraez I, Santos F, Kubinyecz O, Eckersley-Maslin MA, Stegle O, Reik W. Cell Syst. 2020 Jul 22;11(1):25-41.e9. doi: 10.1016/j.cels.2020.06.004. Epub 2020 Jul 6. PMID: 32634384; PMCID: PMC7383230.

Genome instability and pressure on non-homologous end joining drives chemotherapy resistance via a DNA repair crisis switch in triple negative breast cancer.

Wiegmans AP, Ward A, Ivanova E, Duijf PHG, Adams MN, Najib IM, Van Oosterhout R, Sadowski MC, Kelly G, Morrical SW, O'Byrne K, Lee JS, Richard DJ. NAR Cancer. 2021 Jun 15;3(2):zcab022. doi: 10.1093/narcan/zcab022. PMID: 34316709; PMCID: PMC8210242.

Recent Advances in Oligonucleotide Therapeutics in Oncology.

Xiong H, Veedu RN, Diermeier SD. Int J Mol Sci. 2021 Mar 24;22(7):3295. doi: 10.3390/ijms22073295. PMID: 33804856; PMCID: PMC8036554.

Targeting histone acetylation dynamics and oncogenic transcription by catalytic P300/CBP inhibition.

Hogg SJ, Motorna O, Cluse LA, Johanson TM, Coughlan HD, Raviram R, Myers RM, Costacurta M, Todorovski I, Pijpers L, Bjelosevic S, Williams T, Huskins SN, Kearney CJ, Devlin JR, Fan Z, Jabbari JS, Martin BP, Fareh M, Kelly MJ, Dupéré-Richer D, Sandow JJ, Feran B, Knight D, Khong T, Spencer A, Harrison SJ, Gregory G, Wickramasinghe VO, Webb AI, Taberlay PC, Bromberg KD, Lai A, Papenfuss AT, Smyth GK, Allan RS, Licht JD, Landau DA, Abdel-Wahab O, Shortt J, Vervoort SJ, Johnstone RW. Mol Cell. 2021 May 20;81(10):2183-2200.e13. doi: 10.1016/j.molcel.2021.04.015. PMID: 34019788; PMCID: PMC8183601.

A Potential Role for Epigenetically Mediated Trained Immunity in Food Allergy.

Imran S, Neeland MR, Shepherd R, Messina N, Perrett KP, Netea MG, Curtis N, Saffery R, Novakovic B. iScience. 2020 Jun 26;23(6):101171. doi: 10.1016/j.isci.2020.101171. Epub 2020 May 17. PMID: 32480123; PMCID: PMC7262566.

Aspirin reduces the incidence of metastasis in a pre-clinical study of Braf mutant serrated colorectal neoplasia.

Kane AM, Liu C, Fennell LJ, McKeone DM, Bond CE, Pollock PM, Young G, Leggett BA, Whitehall VLJ. Br J Cancer. 2021 May;124(11):1820-1827. doi: 10.1038/s41416-021-01339-4. Epub 2021 Mar 29. PMID: 33782564; PMCID: PMC8144376.

G9a Inhibition Enhances Checkpoint Inhibitor Blockade Response in Melanoma.

Kelly GM, Al-Ejeh F, McCuaig R, Casciello F, Ahmad Kamal N, Ferguson B, Pritchard AL, Ali S, Silva IP, Wilmott JS, Long GV, Scolyer RA, Rao S, Hayward NK, Gannon F, Lee JS. Clin Cancer Res. 2021 May 1;27(9):2624-2635. doi: 10.1158/1078-0432.CCR-20-3463. Epub 2021 Feb 15. PMID: 33589432.

Comparison of Global DNA Methylation Patterns in Human Melanoma Tissues and Their Derivative Cell Lines.

Rodger EJ, Almomani SN, Ludgate JL, Stockwell PA, Baguley BC, Eccles MR, Chatterjee A. Cancers (Basel). 2021 Apr 28;13(9):2123. doi: 10.3390/cancers13092123. PMID: 33924927; PMCID: PMC8124222.

The Epigenetic landscape of Circulating tumour cells.

Vasantharajan SS, Eccles MR, Rodger EJ, Pattison S, McCall JL, Gray ES, Calapre L, Chatterjee A. Biochim Biophys Acta Rev Cancer. 2021 Apr;1875(2):188514. doi: 10.1016/j.bbcan.2021.188514. Epub 2021 Jan 23. PMID: 33497709.

Cytoplasmic Human TDP-43 Mislocalization Induces Widespread Dendritic Spine Loss in Mouse Upper Motor Neurons.

Dyer MS, Woodhouse A, Blizzard CA. Brain Sci. 2021 Jun 30;11(7):883. doi: 10.3390/brainsci11070883. PMID: 34209287; PMCID: PMC8301870.

How does epigenetics influence the course of evolution?

Ashe A, Colot V, Oldroyd BP. Philos Trans R Soc Lond B Biol Sci. 2021 Jun 7;376(1826):20200111. doi: 10.1098/rstb.2020.0111. Epub 2021 Apr 19. PMID: 33866814; PMCID: PMC8059608.

Small RNAs and chromatin in the multigenerational epigenetic landscape of Caenorhabditis elegans.

Frolows N, Ashe A. Philos Trans R Soc Lond B Biol Sci. 2021 Jun 7;376(1826):20200112. doi: 10.1098/rstb.2020.0112. Epub 2021 Apr 19. PMID: 33866817; PMCID: PMC8059974.

Effect of Selenium and Iodine on Oxidative Stress in the First Trimester Human Placenta Explants.

Habibi N, Labrinidis A, Leemaqz SY, Jankovic-Karasoulos T, McCullough D, Grieger JA, Gilbert S, Ricciardelli C, Zhou SJ, Perkins AV, Roberts CT, Bianco-Miotto T. Nutrients. 2021 Feb 28;13(3):800. doi: 10.3390/nu13030800. PMID: 33671070; PMCID: PMC7997475.

Pooled CRISPR-activation screening coupled with single-cell RNA-seq in mouse embryonic stem cells.

Alda-Catalinas C, Eckersley-Maslin MA, Reik W. STAR Protoc. 2021 Apr 9;2(2):100426. doi: 10.1016/j.xpro.2021.100426. PMID: 33899013; PMCID: PMC8055612.

Single-cell transcriptomics reveals involution mimicry during the specification of the basal breast cancer subtype.

Valdés-Mora F, Salomon R, Gloss BS, Law AMK, Venhuizen J, Castillo L, Murphy KJ, Magenau A, Papanicolaou M, Rodriguez de la Fuente L, Roden DL, Colino-Sanguino Y, Kikhtyak Z, Farbehi N, Conway JRW, Sikta N, Oakes SR, Cox TR, O'Donoghue SI, Timpson P, Ormandy CJ, Gallego-Ortega D. Cell Rep. 2021 Apr 13;35(2):108945. doi: 10.1016/j.celrep.2021.108945. PMID: 33852842.

The emergence of the brain non-CpG methylation system in vertebrates.

de Mendoza A, Poppe D, Buckberry S, Pflueger J, Albertin CB, Daish T, Bertrand S, de la Calle-Mustienes E, Gómez-Skarmeta JL, Nery JR, Ecker JR, Baer B, Ragsdale CW, Grützner F, Escriva H, Venkatesh B, Bogdanovic O, Lister R. Nat Ecol Evol. 2021 Mar;5(3):369-378. doi: 10.1038/s41559-020-01371-2. Epub 2021 Jan 18. PMID: 33462491; PMCID: PMC7116863.

G9a-mediated repression of CDH10 in hypoxia enhances breast tumour cell motility and associates with poor survival outcome.

Casciello F, Al-Ejeh F, Miranda M, Kelly G, Baxter E, Windloch K, Gannon F, Lee JS. Theranostics. 2020 Mar 15;10(10):4515-4529. doi: 10.7150/thno.41453. PMID: 32292512; PMCID: PMC7150496.

BRG1 knockdown inhibits proliferation through multiple cellular pathways in prostate cancer. Clin Epigenetics.

Giles KA, Gould CM, Achinger-Kawecka J, Page SG, Kafer GR, Rogers S, Luu PL, Cesare AJ, Clark SJ, Taberlay PC. 2021 Feb 17;13(1):37. doi: 10.1186/s13148-021-01023-7. PMID: 33596994; PMCID: PMC7888175.

Maternal folate, one-carbon metabolism and pregnancy outcomes.

Jankovic-Karasoulos T, Furness DL, Leemaqz SY, Dekker GA, Grzeskowiak LE, Grieger JA, Andraweera PH, McCullough D, McAninch D, McCowan LM, Bianco-Miotto T, Roberts CT. Matern Child Nutr. 2021 Jan;17(1):e13064. doi: 10.1111/mcn.13064. Epub 2020 Jul 28. PMID: 32720760; PMCID: PMC7729528.

Sexual Dimorphism in Innate Immunity: The Role of Sex Hormones and Epigenetics.

Shepherd R, Cheung AS, Pang K, Saffery R, Novakovic B. Front Immunol. 2021 Jan 21;11:604000. doi: 10.3389/fimmu.2020.604000. PMID: 33584674; PMCID: PMC7873844.

Circular RNAs: Potential Applications as Therapeutic Targets and Biomarkers in Breast Cancer.

Sarkar D, Diermeier SD. Noncoding RNA. 2021 Jan 5;7(1):2. doi: 10.3390/ncrna7010002. PMID: 33466455; PMCID: PMC7838774.

Genomic Targeting of TET Activity for Targeted Demethylation Using CRISPR/Cas9.

Nguyen TV, Lister R. Methods Mol Biol. 2021;2272:181-194. doi: 10.1007/978-1-0716-1294-1_10. PMID: 34009614.

The H2A.Z-nuclesome code in mammals: emerging functions.

Colino-Sanguino Y, Clark SJ, Valdes-Mora F. Trends Genet. 2022 Mar;38(3):273-289. doi: 10.1016/j.tig.2021.10.003. Epub 2021 Oct 24. Erratum in: Trends Genet. 2022 Feb 26;: PMID: 34702577.

Single-Cell RNA-Seq Reveals Heterogeneous lncRNA Expression in Xenografted Triple-Negative Breast Cancer Cells.

Pinkney HR, Black MA, Diermeier SD. Biology (Basel). 2021 Sep 30;10(10):987. doi: 10.3390/biology10100987. PMID: 34681087; PMCID: PMC8533545.

Publications from AEpiA members - 2020

The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis.

Pinkney HR, Wright BM, Diermeier SD. Noncoding RNA. 2020 Dec 16;6(4):49. doi: 10.3390/ncrna6040049. PMID: 33339309; PMCID: PMC7768357.

Keeping your options open: insights from Dppa2/4 into how epigenetic priming factors promote cell plasticity.

Eckersley-Maslin MA. Biochem Soc Trans. 2020 Dec 18;48(6):2891-2902. doi: 10.1042/BST20200873. PMID: 33336687; PMCID: PMC7752079.

Functional Screening Techniques to Identify Long Non-Coding RNAs as Therapeutic Targets in Cancer.

Lucere KM, O'Malley MMR, Diermeier SD. Cancers (Basel). 2020 Dec 9;12(12):3695. doi: 10.3390/cancers12123695. PMID: 33317042; PMCID: PMC7763270.

MaTAR25 lncRNA regulates the Tensin1 gene to impact breast cancer progression.

Chang KC, Diermeier SD, Yu AT, Brine LD, Russo S, Bhatia S, Alsudani H, Kostroff K, Bhuiya T, Brogi E, Pappin DJ, Bennett CF, Rigo F, Spector DL. Nat Commun. 2020 Dec 22;11(1):6438. doi: 10.1038/s41467-020-20207-y. PMID: 33353933; PMCID: PMC7755919.

Epigenetic Regulators of Mesenchymal Stem/Stromal Cell Lineage Determination.

Cakouros D, Gronthos S. Curr Osteoporos Rep. 2020 Oct;18(5):597-605. doi: 10.1007/s11914-020-00616-0. PMID: 32794139; PMCID: PMC7532954.

IMPLICON: an ultra-deep sequencing method to uncover DNA methylation at imprinted regions.

Klobučar T, Kreibich E, Krueger F, Arez M, Pólvora-Brandão D, von Meyenn F, da Rocha ST, Eckersley-Maslin M. Nucleic Acids Res. 2020 Sep 18;48(16):e92. doi: 10.1093/nar/gkaa567. PMID: 32621604; PMCID: PMC7498334.

The changing epigenetic landscape of Mesenchymal Stem/Stromal Cells during aging.

Cakouros D, Gronthos S. Bone. 2020 Aug;137:115440. doi: 10.1016/j.bone.2020.115440. Epub 2020 May 20. PMID: 32445894.

Common Variants Coregulate Expression of GBA and Modifier Genes to Delay Parkinson's Disease Onset.

Schierding W, Farrow S, Fadason T, Graham OEE, Pitcher TL, Qubisi S, Davidson AJ, Perry JK, Anderson TJ, Kennedy MA, Cooper A, O'Sullivan JM. Mov Disord. 2020 Aug;35(8):1346-1356. doi: 10.1002/mds.28144. Epub 2020 Jun 18. PMID: 32557794; PMCID: PMC7496525.

Determinants of placental leptin receptor gene expression and association with measures at birth.

Vlahos A, Mansell T, Burgner D, Collier F, Novakovic B, Saffery R; Barwon Infant Study Investigator Team. Placenta. 2020 Oct;100:89-95. doi: 10.1016/j.placenta.2020.08.010. Epub 2020 Aug 18. PMID: 32891006.

Epigenetic regulation of the ITGB4 gene in prostate cancer.

Wilkinson EJ, Woodworth AM, Parker M, Phillips JL, Malley RC, Dickinson JL, Holloway AF. Exp Cell Res. 2020 Jul 15;392(2):112055. doi: 10.1016/j.yexcr.2020.112055. Epub 2020 May 4. PMID: 32376286.

Epigenetic priming by Dppa2 and 4 in pluripotency facilitates multi-lineage commitment.

Eckersley-Maslin MA, Parry A, Blotenburg M, Krueger C, Ito Y, Franklin VNR, Narita M, D'Santos CS, Reik W. Nat Struct Mol Biol. 2020 Aug;27(8):696-705. doi: 10.1038/s41594-020-0443-3. Epub 2020 Jun 22. PMID: 32572255.

Unravelling the Epigenome of Myelodysplastic Syndrome: Diagnosis, Prognosis, and Response to Therapy.

Bond DR, Lee HJ, Enjeti AK. Cancers (Basel). 2020 Oct 26;12(11):3128. doi: 10.3390/cancers12113128. PMID: 33114584; PMCID: PMC7692163.

Sex matters: XIST and DDX3Y gene expression as a tool to determine fetal sex in human first trimester placenta.

Hoch D, Novakovic B, Cvitic S, Saffery R, Desoye G, Majali-Martinez A. Placenta. 2020 Aug;97:68-70. doi: 10.1016/j.placenta.2020.06.016. Epub 2020 Jun 26. PMID: 32792067.

Single-cell epigenomics in cancer: charting a course to clinical impact.

Bond DR, Uddipto K, Enjeti AK, Lee HJ. Epigenomics. 2020 Jul;12(13):1139-1151. doi: 10.2217/epi-2020-0046. Epub 2020 Aug 13. PMID: 32790506.

How do histone modifications contribute to transgenerational epigenetic inheritance in C. elegans?

Woodhouse RM, Ashe A. Biochem Soc Trans. 2020 Jun 30;48(3):1019-1034. doi: 10.1042/BST20190944. PMID: 32539084.

mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling data.

Kaspi A, Ziemann M. BMC Genomics. 2020 Jun 29;21(1):447. doi: 10.1186/s12864-020-06856-9. PMID: 32600408; PMCID: PMC7325150.

APC Mutation Marks an Aggressive Subtype of BRAF Mutant Colorectal Cancers.

Fennell LJ, Kane A, Liu C, McKeone D, Fernando W, Su C, Bond C, Jamieson S, Dumenil T, Patch AM, Kazakoff SH, Pearson JV, Waddell N, Leggett B, Whitehall VLJ. Cancers (Basel). 2020 May 6;12(5):1171. doi: 10.3390/cancers12051171. PMID: 32384699; PMCID: PMC7281581.

Promoter DNA Hypermethylation and Paradoxical Gene Activation.

Smith J, Sen S, Weeks RJ, Eccles MR, Chatterjee A. Trends Cancer. 2020 May;6(5):392-406. doi: 10.1016/j.trecan.2020.02.007. Epub 2020 Mar 4. PMID: 32348735.

Short Histone H2A Variants: Small in Stature but not in Function.

Jiang X, Soboleva TA, Tremethick DJ. Cells. 2020 Apr 2;9(4):867. doi: 10.3390/cells9040867. PMID: 32252453; PMCID: PMC7226823.

schex avoids overplotting for large single-cell RNA-sequencing datasets.

Freytag S, Lister R. Bioinformatics. 2020 Apr 1;36(7):2291-2292. doi: 10.1093/bioinformatics/btz907. PMID: 31794001.

Extensive Inter-Cyst DNA Methylation Variation in Autosomal Dominant Polycystic Kidney Disease Revealed by Genome Scale Sequencing.

Bowden SA, Stockwell PA, Rodger EJ, Parry MF, Eccles MR, Stayner C, Chatterjee A. Front Genet. 2020 Apr 15;11:348. doi: 10.3389/fgene.2020.00348. PMID: 32351541; PMCID: PMC7174623.

Alterations in signaling pathways that accompany spontaneous transition to malignancy in a mouse model of BRAF mutant microsatellite stable colorectal cancer.

Kane AM, Fennell LJ, Liu C, Borowsky J, McKeone DM, Bond CE, Kazakoff S, Patch AM, Koufariotis LT, Pearson J, Waddell N, Leggett BA, Whitehall VLJ. Neoplasia. 2020 Feb;22(2):120-128. doi: 10.1016/j.neo.2019.12.002. Epub 2020 Jan 11. PMID: 31935636; PMCID: PMC6961716.

Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer.

Achinger-Kawecka J, Valdes-Mora F, Luu PL, Giles KA, Caldon CE, Qu W, Nair S, Soto S, Locke WJ, Yeo-Teh NS, Gould CM, Du Q, Smith GC, Ramos IR, Fernandez KF, Hoon DS, Gee JMW, Stirzaker C, Clark SJ. Nat Commun. 2020 Jan 16;11(1):320. doi: 10.1038/s41467-019-14098-x. PMID: 31949157; PMCID: PMC6965612.

Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains.

Khoury A, Achinger-Kawecka J, Bert SA, Smith GC, French HJ, Luu PL, Peters TJ, Du Q, Parry AJ, Valdes-Mora F, Taberlay PC, Stirzaker C, Statham AL, Clark SJ. Nat Commun. 2020 Jan 7;11(1):54. doi: 10.1038/s41467-019-13753-7. PMID: 31911579; PMCID: PMC6946690.