Nice FL, Massie CE, Klampfl T and Green AR.
Elsevier. October 9, 2017, doi: 10.1016/j.exphem.2017.09.011
This publication presents a strategy of highly multiplexed genotyping of burst forming unit-erythroid (BFU-E) colonies based on NGS results to assess subclonal tumour structure. This allowed for the generation of complex clonal hierarchies and determination of order of mutation acquisition far more accurately than was possible from NGS data alone.
Camacho N, van Loo P, Edwards S, Kay JD, Matthews L, Haase K, Clark J, Dennis N, Thomas S, Kremeyer B, Zamora J, Butler AP, Gundem G, Merson S, Luxton H, Hawkins S, Ghori M, Marsden L, Lambert A, Karaszi K, Pelvender G, Massie CE, Kote-Jarai Z, Raine K, Jones D, Howat WJ, Hazell S, Livin N, Fisher C, Ogden C, Kumar P, Thompson A, Nicol D, Mayer E, Dudderidge T, Yu Y, Zhang H, Shah NC, Gnanapragasam VJ, CRUK-ICGC Prostate Group, Isaacs W, Visakorpi T, Hamdy F, Berney D, Verrill C, Warren AY, Wedge DC, Lynch AG, Foster CS, Lu YJ, Bova GS, Whitaker HC, McDermott U, Neal DE, Eeles R, Cooper CS and Brewer DS.
PLoS Med, September 25, 2017, doi: 10.137/journal.pgen.1007001
A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer. This study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively assess the role of the Knudson two hit genetic model in SCNA generation in prostate cancer.
Blundell JR, Schwartz K, Francois D, Fischer DS, Sherlock G and Levy SF.
bioRxiv. July 31, 2017, doi: 10.1101/170589
In this publication barcode lineage tracking, sequencing of adaptive clones, and mathematical modelling of mutational dynamics are combined to understand diversity changes during experimental evolution.
Lozano-Torres B, Galiana I, Rovira M, Garrido E, Chaib S, Bernardos A, Muñoz-Espín D, Serramo M, Martínez-Máñez R and Sancenón F.
Journal of the American Chemical Society. June 18, 2017, doi: 10.1021/jacs.7b04985
A naphthalimide-based two-photon probe (AHGa) for the detection of cell senescence is designed. The probe contains a naphthalimide core, an l-histidine methyl ester linker, and an acetylated galactose bonded to one of the aromatic nitrogen atoms of the l-histidine through a hydrolyzable N-glycosidic bond. Probe AHGa is transformed into AH in senescent cells resulting in an enhanced fluorescent emission intensity. In vivo detection of senescence is validated in mice bearing tumor xenografts treated with senescence-inducing chemotherapy.
Schlecht U, Liu Z, Blundell JR, St. Onge RP and Levy SF.
Nature Communications 8. May 25, 2017, doi: 10.1038/ncomms15586
Several large-scale efforts have systematically cataloged protein-protein interactions (PPIs) of a cell in a single environment. However, little is known about how the protein interactome changes across environmental perturbations. Current technologies only assay one PPI at a time, therefore a highly parallel protein-protein interaction sequencing (PPiSeq) platform is developed that uses a novel double barcoding system in conjuction with the dihydrofolate reductase protein-fragment complementation assay in Saccharomyces cerevisiae.
Tomasetti C, Li L and Vogelstein B.
Science. March 24, 2017. doi: 10.1126/science.aaf9011
Most textbooks attribute cancer-causing mutations to two major sources: inherited and environmental factors. A third source of mutations is unavoidable errors associated with DNA replication (R mutations). The study described in this paper suggests that R mutations are responsible for two-thirds of the mutations in human cancers. This new finding accentuates the importance of early detection and intervention to reduce deaths from the many cancer arising from unavoidable R mutations.
Wan JCM, Massie C, Garcia-Corbacho J, Mouliere F, Brenton JD, Caldas C, Pacey S, Baird R, Rosenfeld N.
Nat. Rev. Cancer February 2017 (online). doi:10.1038/nrc.2017.7
Improvements in genomic and molecular methods are expanding the range of potential applications for circulating tumour DNA (ctDNA), both in a research setting and as a ‘liquid biopsy’ for cancer management. This paper appraises potential approaches to ctDNA analysis and considers applications in personalised oncology and in cancer research.
Emmons KM and Colditz GA.
N Engl J Med 2017. March 9, 2017. doi: 10.1056/NEJMsb1609101
This paper describes how, in the US, application of existing knowledge about primary cancer prevention needs to improve to prevent unnecessary cancer deaths.
Freeman M, Offman J, Walter FM, Sasieni P, Smith SG.
BMJ Open 2017;7: e013901. February 7, 2017. doi:10.1136/bmjopen-2016-013901
This paper describes a study into the acceptability of the Cytosponge, a novel sampling device to detect Barrett’s oesophagus (BE), a precursor to oesophageal adenocarcinoma (EAC), among people with risk factors for this condition. These qualitative data suggest the Cytosponge was acceptable to the majority of participants with risk factors for BE.
Evangelou K, Lougiakis N, Rizou SV, Kotsinas A, Kletsas D, Muñoz-Espín D, Kastrinakis NG, Pouli N, Marakos P, Townsend P, Serrano M, Bartek J andGorgoulis VG.
Aging Cell. November 17, 2016, doi: 10.1111/acel.12545
Cellular senescence contributes to organismal development, aging, and diverse pathologies, yet available assays to detect senescent cells remain unsatisfactory. This publication proposes a new hybrid histo-/immunochemical method, easy to perform, reliable, and universally applicable to assess senescence in biomedicine, from cancer research to gerontology.
Venkataram S, Dunn B, Li Y, Agarwala A, Chang J, Ebel ER, Geiler-Samerotte K, Hérissant L, Blundell JR, Levy SF and Fisher DS.
CellPress volume 166, Issue 6. September 8 2016, doi: 10.1016/j.cell.2016.08.002
Adaptive evolution plays a large role in generating the phenotypic diversity observed in nature, yet current methods are impractical for characterizing the molecular basis and fitness effects of large numbers of individual adaptive mutations. In this publication, a DNA barcoding approach was used to generate the genotype-to-fitness map for adaptation-driving mutations from a Saccharomyces cerevisiae population experimentally evolved by serial transfer under limiting glucose.
Waterhouse DJ, Joseph J, Neves AA, di Pietro M, Brindle KM, Fitzgerald RC, Bohndiek SE.
J. Biomed. Opt. 21(8), 084001 (Aug 04, 2016). doi:10.1117/1.JBO.21.8.084001.
This paper describes the synthesis of near-infrared (NIR) fluorescent wheat germ agglutinin (WGA-IR800CW) and the construction of a clinically translatable bimodal NIR and white light endoscope to combat the lack of contrast in white light endoscopy when imaging patients with suspected Barrett’s oesophagus.
Castro MA, de Santiago I, Campbell TM, Vaughn C, Hickey TE, Ross E, Tilley WD, Markowetz F, Ponder BA, Meyer KB.
Nat Genet. 48(1):12-21 (2016).
The network approach used here provides a foundation for determining the regulatory circuits governing breast cancer as well as other disease settings, to identify targets for intervention.
Varghese S, Newton R, Ross-Innes CS, Lao-Sirieix P, Krishnadath KK, O’Donovan M, Novelli M, Wernisch L, Bergman J, Fitzgerald RC.
Gastroenterology 2015 Nov 149(6) 1511-18 Epub 2015.
This paper discovers and validates a 90 gene panel to accurately identify patients with low grade dysplasia in Barrett’s oesophagus who are at high risk of progression.
Gordon GSD, Joseph J, Bohndiek SE, Wilkinson TD.
J. Lightwave Technol, 2015, 33 (16): 3419-3425.
This study paves the way for the use of optical phase for lensless focusing in endoscopy.
Martincorena I, Roshan A, Gerstung M, Ellis P, Van Loo P, McLaren S, Wedge DC, Fullam A, Alexandrov LB, Tubio JM, Stebbings L, Menzies A, Widaa S, Stratton MR, Jones PH*, Campbell PJ*. (*co-corresponding authors).
Science 2015, 880-86. May 22, 2015. 348, doi: 10.1126/science.aaa6806
This paper describes how aged sun-exposed skin is a patchwork of thousands of evolving clones with over a quarter of cells carrying cancer-causing mutations while maintaining the physiological functions of the epidermis.
Walter FM, Rubin G, Bankhead C, Morris HC, Hall N, Mills K, Dobson C, Rintoul R, Hamilton W and Emery J.
Brit J Cancer. 2015 Mar 31;112 Suppl: S6-S13. doi: 10.1038/bjc.2015.30. PMID: 25734397.
This study found that haemoptysis is the strongest symptom predictor of lung cancer but occurs in only a fifth of patients, calling for programmes of early diagnosis to focus on multiple symptoms and their evolution.
Holguera I, Muñoz-Espín D and Salas M.
Nucleic Acids Research. February 26, 2015, doi: 10.1093/nar/gkv127
This publication describes the involvement of the TP N-terminal domain residues responsible for DNA binding in the different stages of viral DNA replication by assaying the in vitro activity of purified TP N-terminal mutant proteins.
Ross-Innes CS, Debiram-Beecham I, O'Donovan M, Walker E, Varghese S, Lao-Sirieix P, Lovat L, Griffin M, Ragunath K, Haidry R, Sami SS, Kaye P, Novelli M, Disep B, Ostler R, Aigret B, North BV, Bhandari P, Haycock A, Morris D, Attwood S, Dhar A, Rees C, Rutter MD, Sasieni PD, Fitzgerald RC.
BEST2 Study Group. PLoS Med 2015 Jan 29;12(1) eCollection 2015 Jan.
This paper describes the results of a case:control study using the Cytosponge in over 1,000 patients and shows that it is safe, acceptable and has a high degree of accuracy.
Weaver JMJ, Ross-Innes C, Shannon N, Lynch AG, Forshew T, Barbera M, Murtaza M, Ong C-AJ, Lao-Sirieix P, Dunning MJ, Smith L, Smith ML, Anderson CL, Carvalho B, O'Donovan M, Underwood TJ, May AP, Grehan N, Hardwick R, Davies J, Oloumi A, Aparicio S, Caldas C, Eldridge MD, Edwards PA, Rosenfeld N, Tavaré S and Fitzgerald RC.
OCCAMS Consortium. (2014) Nat Genet. 2014 Aug;46(8):837-43. doi: 10.1038/ng.3013. Epub 2014 Jun 22.
This paper demonstrates for the first time that somatic mutations occur early in pre-invasive disease and careful ordering of events is required in order to develop effective biomarker strategies for Early Detection.
Antoniou AC, Casadei S, Heikkinen T, Barrowdale D, Pylkäs K, Roberts J, Lee A, Subramanian D, De Leeneer K, Fostira F, Tomiak E, Neuhausen SL, Teo ZL, Khan S, Aittomäki K, Moilanen JS, Turnbull C, Seal S, Mannermaa A, Kallioniemi A, Lindeman GJ, Buys SS, Andrulis IL, Radice P, Tondini C, Manoukian S, Toland AE, Miron P, Weitzel JN, Domchek SM, Poppe B, Claes KB, Yannoukakos D, Concannon P, Bernstein JL, James PA, Easton DF, Goldgar DE, Hopper JL, Rahman N, Peterlongo P, Nevanlinna H, King MC, Couch FJ, Southey MC, Winqvist R, Foulkes WD and Tischkowitz M.
N Engl J Med. 2014, Aug 7 2014;371(6):497-506.
This study determined that loss-of-function mutations in PALB2 are an important cause of hereditary breast cancer, with respect to both frequency of mutations and risk associated with them.
Banks J, Hollinghurst S, Bigwood L, Peters TJ, Walter FM and Hamilton W.
Lancet Oncol. 2014;15(2):232-40. doi: 10.1016/S1470-2045(13)70588-6.
This paper investigated the barriers to presentation in primary care, symptom recognition and referral for specialist investigation in lung, pancreatic and colorectal cancers.
Pharoah PD, Tsai YY, Ramus SJ, Phelan CM, Goode EL, Lawrenson K, et al.
Nat Genet. 45, 362-70 (2013).
The result of this study was evidence for functional mechanisms underlying susceptibility and pathogenesis of ovarian cancer.