Papers January 2025

• Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics.
  • Biggs GS, Cawood EE, Vuorinen A, McCarthy WJ, Wilders H, Riziotis IG, van der Zouwen AJ, Pettinger J, Nightingale L, Chen P, Powell AJ, House D, Boulton SJ, Skehel JM, Rittinger K, Bush JT
  • Nature Communications
  • doi: 10.1038/s41467-024-55057-5
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• Prospective validation of ORACLE, a clonal expression biomarker associated with survival of patients with lung adenocarcinoma.
  • Biswas D, Liu Y-H, Herrero J, Wu Y, Moore DA, Karasaki T, Grigoriadis K, Lu W-T, Veeriah S, Naceur-Lombardelli C, Magno N, Ward S, Frankell AM, Hill MS, Colliver E, de Carné Trécesson S, East P, Malhi A, Snell DM, O'Neill O, Leonce D, Mattsson J, Lindberg A, Micke P, Moldvay J, Megyesfalvi Z, Dome B, Fillinger J, Nicod J, Downward J, Szallasi Z, TRACERx Consortium, Hackshaw A, Jamal-Hanjani M, Kanu N, Birkbak NJ, Swanton C
  • Nature Cancer
  • doi: 10.1038/s43018-024-00883-1
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• Ultrasensitive ctDNA detection for preoperative disease stratification in early-stage lung adenocarcinoma.
  • Black JRM, Bartha G, Abbott CW, Boyle SM, Karasaki T, Li B, Chen R, Harris J, Veeriah S, Colopi M, Al Bakir M, Liu WK, Lyle J, Navarro FCP, Northcott J, Pyke RM, Hill MS, Thol K, Huebner A, Bailey C, Colliver EC, Martínez-Ruiz C, Grigoriadis K, Pawlik P, Moore DA, Marinelli D, Shutkever OG, Murphy C, Sivakumar M, TRACERx consortium, Shaw JA, Hackshaw A, McGranahan N, Jamal-Hanjani M, Frankell AM, Chen RO, Swanton C
  • Nature Medicine
  • doi: 10.1038/s41591-024-03216-y
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• Initiation and maintenance of the pluripotent epiblast in pre-implantation human development is independent of NODAL signaling.
  • Brumm AS, McCarthy A, Gerri C, Fallesen T, Woods L, McMahon R, Papathanasiou A, Elder K, Snell P, Christie L, Garcia P, Shaikly V, Taranissi M, Serhal P, Odia RA, Vasilic M, Osnato A, Rugg-Gunn PJ, Vallier L, Hill CS, Niakan KK
  • Developmental Cell
  • doi: 10.1016/j.devcel.2024.10.020
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• RNA therapy for oncogenic NRAS-driven naevi induces apoptosis.
  • Bryant D, Barberan-Martin S, Maeshima R, Torres IDV, Rabii M, Baird W, Sauvadet A, Demetriou C, Jones P, Knöpfel N, Michailidis F, Riachi M, Bennett DC, Zecchin D, Pittman A, Polubothu S, Hart S, Kinsler VA
  • Journal of Investigative Dermatology
  • doi: 10.1016/j.jid.2024.04.031
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• Unidirectional MCM translocation away from ORC drives origin licensing.
  • Butryn A, Greiwe JF, Costa A
  • Nature Communications
  • doi: 10.1038/s41467-025-56143-y
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• TRACERx analysis identifies a role for FAT1 in regulating chromosomal instability and whole-genome doubling via Hippo signalling.
  • Lu W-T, Zalmas L-P, Bailey C, Black JRM, Martinez-Ruiz C, Pich O, Gimeno-Valiente F, Usaite I, Magness A, Thol K, Webber TA, Jiang M, Saunders RE, Liu Y-H, Biswas D, Ige EO, Aerne B, Grönroos E, Venkatesan S, Stavrou G, Karasaki T, Al Bakir M, Renshaw M, Xu H, Schneider-Luftman D, Sharma N, Tovini L, TRACERx Consortium, Jamal-Hanjani M, McClelland SE, Litchfield K, Birkbak NJ, Howell M, Tapon N, Fugger K, McGranahan N, Bartek J, Kanu N, Swanton C
  • Nature Cell Biology
  • doi: 10.1038/s41556-024-01558-w
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• Characterizing the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER
  • Lucas O, Ward S, Zaidi R, Bunkum A, Frankell AM, Moore DA, Hill MS, Liu WK, Marinelli D, Lim EL, Hessey S, Naceur-Lombardelli C, Rowan A, Purewal-Mann SK, Zhai H, Dietzen M, Ding B, Royle G, Aparicio S, TRACERx Consortium, PEACE Consortium, Mcgranahan N, Jamal-Hanjani M, Kanu N, Swanton C, Zaccaria S
  • Nature Genetics
  • doi: 10.1038/s41588-024-01989-z
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• Emergence of SARS-CoV-2 subgenomic RNAs that enhance viral fitness and immune evasion.
  • Mears HV, Young GR, Sanderson T, Harvey R, Barrett-Rodger J, Penn R, Cowton V, Furnon W, De Lorenzo G, Crawford M, Snell DM, Fowler AS, Chakrabarti AM, Hussain S, Gilbride C, Emmott E, Finsterbusch K, Luptak J, Peacock TP, Nicod J, Patel AH, Palmarini M, Wall E, Williams B, Gandhi S, Swanton C, Bauer DLV
  • PLoS Biology
  • doi: 10.1371/journal.pbio.3002982
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• Optimizing approaches for targeted integration of transgenic cassettes by integrase mediated cassette exchange in mouse and human stem cells.
  • Rath P, Kramer P, Biggs D, Preece C, Hortin N, Diaz R, Perez-Alcantara M, Li X, Bolard A, Beer N, McCarthy M, Davies B
  • Stem Cells
  • doi: 10.1093/stmcls/sxae092
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• Timely TGFβ signalling inhibition induces notochord.
  • Rito T, Libby ARG, Demuth M, Domart M-C, Cornwall-Scoones J, Briscoe J
  • Nature
  • doi: 10.1038/s41586-024-08332-w
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• Real-time estimation of immunological responses against emerging SARS-CoV-2 variants in the UK: a mathematical modelling study.
  • Russell TW, Townsley H, Hellewell J, Gahir J, Shawe-Taylor M, Greenwood D, Hodgson D, Hobbs A, Dowgier G, Penn R, Sanderson T, Stevenson-Leggett P, Bazire J, Harvey R, Fowler AS, Miah M, Smith C, Miranda M, Bawumia P, Mears HV, Adams L, Hatipoglu E, O'Reilly N, Warchal S, Ambrose K, Strange A, Kelly G, Kjaer S, Papineni P, Corrah T, Gilson R, Libri V, Kassiotis G, Gamblin S, Lewis NS, Williams B, Swanton C, Gandhi S, Beale R, Wu MY, Bauer DLV, Carr EJ, Wall EC, Kucharski AJ
  • The Lancet Infectious Diseases
  • doi: 10.1016/S1473-3099(24)00484-5
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• North Pontic crossroads: Mobility in Ukraine from the Bronze Age to the early modern period.
  • Saag L, Utevska O, Zadnikov S, Shramko I, Gorbenko K, Bandrivskyi M, Pavliv D, Bruyako I, Grechko D, Okatenko V, Toshev G, Andrukh S, Radziyevska V, Buynov Y, Kotenko V, Smyrnov O, Petrauskas O, Magomedov B, Didenko S, Heiko A, Reida R, Sapiehin S, Aksonov V, Laptiev O, Terskyi S, Skorokhod V, Zhyhola V, Sytyi Y, Järve M, Scheib CL, Anastasiadou K, Kelly M, Williams M, Silva M, Barrington C, Gilardet A, Macleod R, Skoglund P, Thomas MG
  • Science Advances
  • doi: 10.1126/sciadv.adr0695
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• High-resolution genomic history of early medieval Europe.
  • Speidel L, Silva M, Booth T, Raffield B, Anastasiadou K, Barrington C, Götherström A, Heather P, Skoglund P
  • Nature
  • doi: 10.1038/s41586-024-08275-2
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• Systematic identification of Y-chromosome gene functions in mouse spermatogenesis.
  • Subrini J, Varsally W, Balaguer Balsells I, Bensberg M, Sioutas G, Ojarikre O, Maciulyte V, Gylemo B, Crawley K, Courtis K, de Rooij DG, Turner JMA
  • Science
  • doi: 10.1126/science.ads6495
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• APP antisense oligonucleotides are effective in rescuing mitochondrial phenotypes in human iPSC-derived trisomy 21 astrocytes.
  • Thirumalai S, Livesey FJ, Patani R, Hung C
  • Alzheimer's and Dementia
  • doi: 10.1002/alz.14560
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• Quantifying spectral information about source separation in multisource odour plumes.
  • Tootoonian S, True AC, Stark E, Crimaldi JP, Schaefer AT
  • PLoS ONE
  • doi: 10.1371/journal.pone.0297754
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• Enantioselective OTUD7B fragment discovery through chemoproteomics screening and high-throughput optimisation.
  • Vuorinen A, Kennedy CR, McPhie KA, McCarthy W, Pettinger J, Skehel JM, House D, Bush JT, Rittinger K
  • Communications Chemistry
  • doi: 10.1038/s42004-025-01410-8
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• Distinct virologic trajectories in chronic hepatitis B identify heterogeneity in response to nucleos(t)ide analogue therapy
  • Wang T, Campbell C, Stockdale AJ, Todd S, McIntyre K, Frankland A, Jaworski J, Glampson B, Papadimitriou D, Mercuri L, Mayer E, Jones CR, Salih H, Roadknight G, Little S, Noble T, Várnai KA, Davis C, Heinson AI, George M, Borca F, English L, Romão L, Ramlakhan D, NIHR HIC Viral Hepatitis and Liver Disease Consortium, Woods K, Davies J, Nastouli E, Khakoo SI, Gelson W, Cooke GS, Barnes E, Matthews PC
  • JHEP Reports
  • doi: 10.1016/j.jhepr.2024.101229
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• Advancing the chemotherapy of tuberculous meningitis: a consensus view.
  • Wasserman S, Donovan J, Kestelyn E, Watson JA, Aarnoutse RE, Barnacle JR, Boulware DR, Chow FC, Cresswell FV, Davis AG, Dooley KE, Figaji AA, Gibb DM, Huynh J, Imran D, Marais S, Meya DB, Misra UK, Modi M, Raberahona M, Ganiem AR, Rohlwink UK, Ruslami R, Seddon JA, Skolimowska KH, Solomons RS, Stek CJ, Thuong NTT, van Crevel R, Whitaker C, Thwaites GE, Wilkinson RJ
  • The Lancet Infectious Diseases
  • doi: 10.1016/S1473-3099(24)00512-7
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Preprints January 2025

• Transcriptomic analysis of repeat expansion-ataxias uncovers distinct non-neuronal cell type-specific signatures of disease across the human brain
  • Chen Z, Hicks A, Brenton J, Grant-Peters M, Reynolds RH, Gustavsson EK, Rocca C, Rocamora-Perez G, Garza R, Garcia-Ruiz S, Dominik N, Anderson C, Curless T, Montgomery K, Macpherson H, Nethisinghe S, Gavriouchkina D, Blunskyte-Hendley M, Fairbrother-Browne A, Lee J, Luo H, Efthymiou S, Murphy D, Hinton F, Botia J, Cortese A, Wood N, Giunti P, Hardy J, Jakobsson J, Gandhi S, Tucci A, McLean C, Jaunmuktane Z, Houlden H, Ryten M
  • doi: 10.1101/2025.01.03.631007

• Evolutionary trajectories of immune escape across cancers
  • Chen W, Baker T, Zhang Z, Ogilvie HA, Van Loo P, Gu SS
  • doi: 10.1101/2025.01.17.632799

• Arp2/3-mediated bidirectional actin assembly by SPIN90 dimers in metazoans
  • Liu T, Cao L, Mladenov M, Romet-Lemonne G, Way M, Moores CA
  • doi: 10.1101/2025.01.31.635869