IFOM Publications Francesca Buffa
  1. Home
  2. Research
  3. Publications
  4. Publications Francesca Buffa

Selected Publications Francesca Buffa

Selected peer-reviewed papers

  • Barberis A, Buffa FM. Sigscores: summary scores for molecular signatures in R. Bioinfomatics Advances, 2025 (In Print) Di Giovannantonio M, Hartley F, Elshenawy B, Barberis A, Hudson D, Shafique HS, Allott VES, Harris DA, Lord SR, Haider S, Harris AL, Harris BHL - Buffa FM (co-last, co-corresponding). Defining hypoxia in cancer: A landmark evaluation of hypoxia gene expression signatures. Cell Genomics 2025 Feb 12;5(2):100764. doi: 10.1016/j.xgen.2025.100764. Epub 2025 Jan 31. PMID: 39892389; PMCID: PMC11872601.
  • Taylor A, Macaulay VM, Miossec MJ, Maurya AK, Buffa FM. GeneFEAST?: the pivotal, gene-centric step in functional enrichment analysis interpretation. Bioinformatics. 2025 Mar 4;41(3):btaf100. doi: 10.1093/bioinformatics/btaf100. PMID: 40037522; PMCID: PMC11919446.
  • Harris BHL, Di Giovannantonio M, Zhang P, Harris DA, Lord SR, Allen NE, Maughan TS, Bryant RJ, Harris AL, Bond GL, Buffa FM (corresponding). New role of fat-free mass in cancer risk linked with genetic predisposition. Sci Rep. 2024 Mar 27;14(1):7270. doi: 10.1038/s41598-024-54291-7. PMID: 38538606; PMCID: PMC10973462.
  • Jayathilake PG, Victori P, Pavillet CE, Lee CH, Voukantsis D, Miar A, Arora A, Harris AL, Morten KJ, Buffa FM (corresponding). Metabolic symbiosis between oxygenated and hypoxic tumour cells: An agent-based modelling study. PLoS? Comput Biol. 2024 Mar 15;20(3):e1011944. doi: 10.1371/journal.pcbi.1011944. PMID: 38489376; PMCID: PMC10971686.
  • Domingo E, Rathee S, Blake A, Samuel L, Murray G, Sebag-Montefiore D, Gollins S, West N, Begum R, Richman S, Quirke P, Redmond K, Chatzipli A, Barberis A, Hassanieh S, Mahmood U, Youdell M, McDermott? U, Koelzer V, Leedham S, Tomlinson I, Dunne P; S:CORT consortium; Maughan TS - Buffa FM (joint-last and co-corresponding). Identification and validation of a machine learning model of complete response to radiation in rectal cancer reveals immune infiltrate and TGFβ as key predictors. EBioMedicine? 2024 doi:10.1016/j.ebiom.2024.105228. PMID: 39013324
  • Barberis A, Aerts HJWL, Buffa FM (Corresponding). Robustness and reproducibility for AI learning in biomedical sciences: RENOIR. Sci Rep. 2024 Jan 22;14(1):1933. doi:10.1038/s41598-024-51381-4. PMID: 38253545.
  • Triantafyllidis CP, Barberis A, Hartley F, Cuervo AM, Gjerga E, Charlton P, van Bijsterveldt L, Rodriguez JS, Buffa FM (corresponding). A machine learning and directed network optimization approach to uncover TP53 regulatory patterns. iScience. 2023 Oct 26;26(12):108291. doi: 10.1016/j.isci.2023.108291. PMID:38047081; PMCID: PMC10692668.
  • Di Giovannantonio M, Harris BH, Zhang P, Kitchen-Smith I, Xiong L, Sahgal N, Stracquadanio G, Wallace M, Blagden S, Lord S, Harris D, Harris AHL, Bond GL - Buffa FM (co-last and co-corresponding). Heritable genetic variants in key cancer genes link cancer risk with anthropometric traits. J Med Genet.: jmedgenet-2019-106799 (2020)
  • Dhawan A, Barberis A, Cheng WC, Domingo E, West C, Maughan T, Scott JG, Harris AL, Buffa FM (corresponding). Guidelines for using sigQC for systematic evaluation of gene signatures. Nature Protocols 14(5):1377-1400. doi: 10.1038/s41596-019-0136-8 (2019)
  • Voukantsis D, Kahn K, Hadley M, Wilson R, Buffa FM (corresponding). Modeling genotypes in their microenvironment to predict single- and multi-cellular behaviour. Gigascience. 8(3). pii: giz010. doi: 10.1093/gigascience/giz010. PMID: 30715320 (2019)
  • Lord SR, Cheng W, Liu D, Gaude E, Haider S, Metcalf T, Patel N, Teoh EJ, Gleeson F, Bradley K, Wigfield S, Zois C, McGowan? D, Ah-See M, Thompson A, Sharma A, Bidaut L, Pollak M, Roy P, Karpe F, James T, English R, Adams R, Campo L, Ayers L, Snell C, Roxanis I, Frezza C, Fenwick J, Buffa FM - Harris AL (joint last). Integrated Pharmacodynamic Analysis Identifies Metabolic Adaption Pathways to Metformin in Breast Cancer. Cell Metabolism 28(5)679-688 (2018)
  • Dhawan A, Scott J, Harris AL, Buffa FM (corresponding). Pan-cancer characterisation of microRNA across cancer hallmarks reveals microRNA mediated downregulation of tumour suppressors. Nature Communications, 9 (1), 5228 (2018) Haider S, McIntyre? A, van Stiphout RG, Winchester LM, Wigfield S, Harris AL, Buffa FM (corresponding). Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia. Genome Biology 17(1)140 (2016)
  • Mehta S, Hughes NP, Li S, Jubb A, Adams R, Lord S, Koumakis L, van Stiphout R, Padhani A, Makris A, Harris AL -Buffa FM (joint last and co-corresponding). Radiogenomics Monitoring in Breast Cancer Identifies Metabolism and Immune Checkpoints as Early Actionable Mechanisms of Resistance to Anti-angiogenic Treatment. EBioMedicine?. (2016) 10109-16.
  • Masiero M, Costa Simões F, Dong Han H, Snell C, Peterkin T, Bridges E, Mangala L, Yen-Yao Wu S, Pradeep S, Li D, Han C, Dalton H, Lopez-Berestein G, Tuynman J, Mortensen N, Li J, Patient R, Sood AK, Banham A, Harris A, Buffa FM (corresponding). A core human primary tumor angiogenesis signature identifies the endothelial orphan receptor ELTD1 as a key regulator of angiogenesis. Cancer Cell 24229-41 (2013) *This paper was featured in the Highlights of the American Association of Cancer Research, Cancer Res 73; 5299 (2013)
  • Buffa FM (corresponding), Camps C, Winchester L, Snell CE, Gee HE, Sheldon H, Taylor M, Harris AL, Ragoussis J. microRNA-associated progression pathways and potential therapeutic targets identified by integrated mRNA and microRNA expression profiling in breast cancer. Cancer Res. 715635-45 (2011) *This paper was featured in Key Paper Evaluation. Expert Rev Anticancer Ther 2012 Mar;12(3)323-30.
  • Korpal M, Ell BJ, Buffa FM, Ibrahim T, Blanco MA, Celià-Terrassa T, Mercatali L, Khan Z, Goodarzi H, Hua Y, Wei Y, Hu G, Garcia BA, Ragoussis J, Amadori D, Harris A, Kang Y. Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization. Nature Med 171101-8 (2011)
  • Moskwa P, Buffa FM, Pan Y, Panchakshari R, Gottipati P, Muschel R, Beech J, Kulshrestha R, Abdelmohsen K, Weinstock D, Gorospe M, Harris A, Helleday T, Chowdhury D. miR-182-mediated downregulation of BRCA1 impacts DNA repair and sensitivity to PARP inhibitors. Mol Cell 41210-20 (2011)
  • Buffa FM (corresponding), Harris AL, West CM, Miller CJ. Large-meta analysis of multiple cancers reveals a common, compact and highly prognostic hypoxia metagene. Br J Cancer 102428-35 (2010) Chalmers AJ, Bentzen SM, Buffa FM (corresponding). A general framework for quantifying the effects of DNA repair inhibitors on radiation sensitivity as a function of dose. Theor Biol Med Model. 19;4:25 (2007)
  • Generali D - Buffa FM (joint first), Berruti A, Brizzi MP, Campo L, Bonardi S, Bersiga A, Allevi G, Milani M, Aguggini S, Papotti M, Dogliotti L, Bottini A, Harris AL, Fox SB. Phosphorylated ERa, HIF-1a and MAPK signalling, as predictors of primary endocrine treatment response and resistance in breast cancer patients. J Clin Oncol 27227-234 (2009)
  • Buffa FM (corresponding), Bentzen SM, Daley FM, Dische S, Saunders MI, Richman PI, Wilson GD. Molecular marker profiles predict loco-regional control of head and neck squamous cell carcinoma in a randomized trial of continuous hyperfractionated accelerated radiotherapy. Clin Cancer Res 10 3745-3754 (2004) *This paper was featured in the Press Release of the American Association of Cancer Research (Nov. 2003)

Other peer-reviewed papers (since 2011)

  • A. Fabbricatore, F. M. Buffa and A. Tangherloni, "Knowledge-Enriched Cell-Type Annotation in Single-Cell Transcriptomics via LLM Embeddings," 2025 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), Tainan, Taiwan, 2025, pp. 1-8, doi: 10.1109/CIBCB66090.2025.11177124
  • Carter RD, Purnama U, Castro-Guarda M, Montes-Aparicio CN, Chandran A, Mbasu R, Ruby M, Daly C, Brisk K, Christian HC, Miller JJJJ, Buffa FM, Heather LC, Carr CA. Systems Biology and Functional Assessments of Human iPSC-Cardiomyocyte Models of Insulin Resistance Capture Key Hallmarks of Diabetic Cardiomyopathy. Diabetes. 2025 Nov 1;74(11):1929-1945. doi: 10.2337/db25-0204. PMID: 40956683; PMCID: PMC12585165.
  • Ward JC, Morgan M, Wood J, Woolley C, de Menezes AAN, Finch A, Sherwood K, Huang Q, Henry CS, Fernández-Tajes J, Soriano I, Thorn S, Legge I, McCullagh? J, Kerr D, Kerr R, Hejmadi RK, Arends MJ; S:CORT Consortium; Domingo E, Maughan T, Bardella C, Tomlinson I. Analysis of IDH1 and IDH2 mutations as causes of the hypermethylator phenotype in colorectal cancer. J Pathol. 2025 Sep;267(1):40-55. doi: 10.1002/path.6446. Epub 2025 Jun 22. PMID: 40545636; PMCID: PMC12337813.
  • Schoenpflug LA, Chatzipli A, Sirinukunwattana K, Richman S, Blake A, Robineau J, Mertz KD, Verrill C, Leedham SJ, Hardy C, Whalley C, Redmond K, Dunne P, Walker S, Beggs AD, McDermott? U, Murray GI, Samuel LM, Seymour M, Tomlinson I, Quirke P; S:CORT consortium; Rittscher J, Maughan T, Domingo E, Koelzer VH. Tumour purity assessment with deep learning in colorectal cancer and impact on molecular analysis. J Pathol. 2025 Feb;265(2):184-197. doi: 10.1002/path.6376. PMID: 39710952; PMCID: PMC11717495.
  • Mahmood U, Blake A, Rathee S, Samuel L, Murray G, Sebag-Montefiore D, Gollins S, West NP, Begum R, Bach SP, Richman SD, Quirke P, Redmond KL, Salto-Tellez M, Koelzer VH, Leedham SJ, Tomlinson I, Dunne PD, Buffa FM; S:CORT consortium; Maughan TS, Domingo E. Stratification to Neoadjuvant Radiotherapy in Rectal Cancer by Regimen and Transcriptional Signatures. Cancer Res Commun. 2024 Jul 1;4(7):1765-1776. doi: 10.1158/2767-9764.CRC-23-0502. PMID: 39023969; PMCID: PMC11257085.
  • Charlton PV, O'Reilly D, Philippou Y, Rao SR, Lamb ADG, Mills IG, Higgins GS, Hamdy FC, Verrill C, Buffa FM, Bryant RJ (co-corresponding). Molecular analysis of archival diagnostic prostate cancer biopsies identifies genomic similarities in cases with progression post-radiotherapy, and those with de novo metastatic disease. Prostate. 2024 Jul;84(10):977-990. doi: 10.1002/pros.24715. Epub 2024 Apr 23. PMID: 38654435; PMCID: PMC11253896.
  • Tan KL, Haider S, Zois CE, Hu J, Turley H, Leek R, Buffa F, Acuto O, Harris AL, Pezzella F. Low cytoplasmic NUB1 protein exerts hypoxic cell death with poorer prognosis in oestrogen receptor negative breast cancer patients. Transl Oncol. 2024 Nov;49:102106. doi: 10.1016/j.tranon.2024.102106. Epub 2024 Aug 24.PMID: 39182365; PMCID: PMC11387679.
  • Yang H, Fouad S, Smith P, Bae EY, Ji Y, Lan X, Van Ess A, Buffa FM, Fischer R, Vendrell I, Kessler BM, D'Angiolella V. Cyclin F-EXO1 axis controls cell cycle-dependent execution of double-strand break repair. Sci Adv. 2024 Aug 9;10(32):eado0636. doi: 10.1126/sciadv.ado0636. Epub 2024 Aug 9. PMID: 39121215; PMCID: PMC11313846.
  • Domingo E, Rathee S, Blake A, Samuel L, Murray G, Sebag-Montefiore D, Gollins S, West N, Begum R, Richman S, Quirke P, Redmond K, Chatzipli A, Barberis A, Hassanieh S, Mahmood U, Youdell M, McDermott? U, Koelzer V, Leedham S, Tomlinson I, Dunne P; S:CORT consortium; Buffa FM, Maughan TS. Identification and validation of a machine learning model of complete response to radiation in rectal cancer reveals immune infiltrate and TGFβ as key predictors. EBioMedicine?. 2024 Aug;106:105228. doi: 10.1016/j.ebiom.2024.105228. Epub 2024 Jul 16. PMID: 39013324; PMCID: PMC11663784.
  • Charlton PV, O'Reilly D, Philippou Y, Rao SR, Lamb ADG, Mills IG, Higgins GS, Hamdy FC, Verrill C, Buffa FM, Bryant RJ (co-last, co-corresponding). Molecular analysis of archival diagnostic prostate cancer biopsies identifies genomic similarities in cases with progression post-radiotherapy, and those with de novo metastatic disease. Prostate. 2024 Jul;84(10):977-990. doi: 10.1002/pros.24715. Epub 2024 Apr 23. PMID: 38654435; PMCID: PMC11253896.
  • Rao S, Verrill C, Cerundolo L, Alham NK, Kaya Z, O'Hanlon M, Hayes A, Lambert A, James M, Tullis IDC, Niederer J, Lovell S, Omer A, Lopez F, Leslie T, Buffa F, Bryant RJ, Lamb AD, Vojnovic B, Wedge DC, Mills IG, Woodcock DJ, Tomlinson I, Hamdy FC. Intra-prostatic tumour evolution, steps in metastatic spread and histogenomic associations revealed by integration of multi-region whole-genome sequencing with histopathological features. Genome Med. 2024 Feb 19;16(1):35. doi: 10.1186/s13073-024-01302-x. PMID: 38374116; PMCID: PMC10877771.
  • Rodriguez-Berriguete G, Puliyadi R, Machado N, Barberis A, Prevo R, McLaughlin? M, Buffa FM, Harrington KJ, Higgins GS. Antitumour effect of the mitochondrial complex III inhibitor Atovaquone in combination with anti-PD-L1 therapy in mouse cancer models. Cell Death Dis. 2024 Jan 11;15(1):32. doi:10.1038/s41419-023-06405-8. PMID: 38212297; PMCID: PMC10784292.
  • Mehanna H, Rapozo D, von Zeidler SV, Harrington KJ, Winter SC, Hartley A, Nankivell P, Schache AG, Sloan P, Odell EW, Thavaraj S, Hunter KD, Shah KA, Thomas GJ, Long A, Amel-Kashipaz R, Brown RM, Conn B, Hall GL, Matthews P, Weir J, Yeo Y, Pring M, West CML, McCaul? J, Golusinski P, Sitch A, Spruce R, Batis N, Bryant JL, Brooks JM, Jones TM, Buffa F, Haider S, Robinson M. Developing and Validating a Multivariable Prognostic-Predictive Classifier for Treatment Escalation of Oropharyngeal Squamous Cell Carcinoma: The PREDICTR-OPC Study. Clin Cancer Res. 2024 Jan 17;30(2):356-367. doi: 10.1158/1078-0432.CCR-23-1013. PMID: 37870417; PMCID: PMC10792360.
  • Tangherloni A, Riva SG, Myers B, Buffa FM, Cazzaniga P. MAGNETO: Cell type marker panel generator from single-cell transcriptomic data. J Biomed Inform. doi: 10.1016/j.jbi.2023.104510. Online ahead of print (2023)
  • Javaid H, Barberis A, Chervova O, Nassiri I, Voloshin V, Sato Y, Ogawa S, Fairfax B, Buffa F, Humphrey TC. A role for SETD2 loss in tumorigenesis through DNA methylation dysregulation. BMC Cancer. 2023 Aug 1;23(1):721. doi: 10.1186/s12885-023-11162-0. PMID: 37528416; PMCID: PMC10394884.
  • Pai CC, Durley SC, Cheng WC, Chiang NY, Peters J, Kasparek T, Blaikley E, Wee BY, Walker C, Kearsey SE, Buffa F, Murray JM, Humphrey TC. Homologous recombination suppresses transgenerational DNA end resection and chromosomal instability in fission yeast. Nucleic Acids Res. 2023 Apr 24;51(7):3205-3222. doi: 10.1093/nar/gkad160. PMID: 36951111; PMCID: PMC10123110.
  • Coupe N, Guo L, Bridges E, Campo L, Espinosa O, Colling R, Marshall A, Nandakumar A, van Stiphout R, Buffa FM, Corrie PG, Middleton MR, Macaulay VM. WNT5A-ROR2 axis mediates VEGF dependence of BRAF mutant melanoma. Cell Oncol (Dordr). doi: 10.1007/s13402-022-00757-7 (2023)
  • Zois CE, Hendriks AM, Haider S, Pires E, Bridges E, Kalamida D, Voukantsis D, Lagerholm BC, Fehrmann RSN, den Dunnen WFA, Tarasov AI, Baba O, Morris J, Buffa FM, McCullagh? JSO, Jalving M, Harris AL. Liver glycogen phosphorylase is upregulated in glioblastoma and provides a metabolic vulnerability to high dose radiation. Cell Death Dis. 2022 Jun 28;13(6):573. doi: 10.1038/s41419-022-05005-2.
  • Ralli GP, Carter RD, McGowan? DR, Cheng WC, Liu D, Teoh EJ, Patel N, Gleeson F, Harris AL, Lord SR, Buffa FM (co-last), Fenwick JD. Radiogenomic analysis of primary breast cancer reveals [18F]-fluorodeoxglucose dynamic flux-constants are positively associated with immune pathways and outperform static uptake measures in associating with glucose metabolism. Breast Cancer Res. 2022 May 17;24(1):34. doi: 10.1186/s13058-022-01529-9.
  • Chen Z, Ioris RM, Richardson S, Van Ess AN, Vendrell I, Kessler BM, Buffa FM, Busino L, Clifford SC, Bullock AN, D'Angiolella V. Disease-associated KBTBD4 mutations in medulloblastoma elicit neomorphic ubiquitylation activity to promote CoREST? degradation. Cell Death Differ. 29(10):1955-1969. doi: 10.1038/s41418-022-00983-4 (2022)
  • Sheldon H, Zhang W, Bridges E, Ang KH, Lin S, Masiero M, Li D, Handford PA, Whiteman P, Fischer R, Buffa F, Vatish M, Banham AH, Harris AL. ELTD1 is present in extracellular vesicles derived from endothelial cells as a cleaved extracellular domain which induces in vivo angiogenesis. J Extracell Biol. 2022 Aug 2;1(8):e52. doi: 10.1002/jex2.52. PMID: 38939053; PMCID: PMC11080856.
  • Chauhan JS, Hölzel M, Lambert JP, Goding CR - Buffa FM (co-last and co-corresponding). The MITF regulatory network in melanoma. Pigment Cell Melanoma Res. 35(5):517-533. doi: 10.1111/pcmr.13053 (2022)
  • Kaeppler JR, Chen J, Buono M, Vermeer J, Kannan P, Cheng WC, Voukantsis D, Thompson JM, Hill MA, Allen D, Gomes A, Kersemans V, Kinchesh P, Smart S, Buffa F, Nerlov C, Muschel RJ, Markelc B. Endothelial cell death after ionizing radiation does not impair vascular structure in mouse tumor models. EMBO Rep. 2022 Sep 5;23(9):e53221. doi: 10.15252/embr.202153221. Epub 2022 Jul 18. PMID: 35848459; PMCID: PMC9442312.
  • Sheldon H, Bridges E, Silva I, Masiero M, Favara DM, Wang D, Leek R, Snell C, Roxanis I, Kreuzer M, Gileadi U, Buffa FM, Banham A, Harris AL. ADGRL4/ELTD1 Expression in Breast Cancer Cells Induces Vascular Normalization and Immune Suppression. Mol Cancer Res. 19(11):1957-1969. doi: 10.1158/1541-7786.MCR-21-0171 (2022)
  • Bader SB, Ma TS, Simpson CJ, Liang J, Maezono SEB, Olcina MM, Buffa FM, Hammond EM. Replication catastrophe induced by cyclic hypoxia leads to increased APOBEC3B activity. Nucleic Acids Res. 2021 Jul 21;49(13):7492-7506. doi: 10.1093/nar/gkab551.
  • Ramachandran S, Ma TS, Griffin J, Ng N, Foskolou IP, Hwang MS, Victori P, Cheng WC, Buffa FM, Leszczynska KB, El-Khamisy SF, Gromak N, Hammond EM. Nat Commun. Hypoxia-induced SETX links replication stress with the unfolded protein response. 12(1):3686. doi: 10.1038/s41467-021-24066-z (2021)
  • Skwarski M, McGowan? DR, Belcher E, Di Chiara F, Stavroulias D, McCole? MG, Derham J, Chu KY, Teoh E, Chauhan J, O'Reilly D, Harris BHL, Macklin PS, Bull JA, Green M, Rodriguez-Berriguete G, Prevo R, Folkes LK, Campo L, Ferencz P, Croal P, Flight H, Qi C, Holmes J, O'Connor JPB, Gleeson F, McKenna? WG, Harris AL, Bulte D, Buffa FM, Macpherson RE, Higgins GS. Mitochondrial Inhibitor Atovaquone Increases Tumor Oxygenation and Inhibits Hypoxic Gene Expression in Patients with Non-Small Cell Lung Cancer. Clin Cancer Res:clincanres.4128.2020 (2021)
  • Goedegebuure RSA, Kleibeuker EA, Buffa FM, Castricum KCM, Haider S, Schulkens IA, Ten Kroode L, van den Berg J, Jacobs MAJM, van Berkel AM, van Grieken NCT, Derks S, Slotman BJ, Verheul HMW, Harris AL, Thijssen VL. J Interferon- and STING-independent induction of type I interferon stimulated genes during fractionated irradiation.Exp Clin Cancer Res. 2021 May 8;40(1):161. doi: 10.1186/s13046-021-01962-2.
  • Walsh CA, Akrap N, Garre E, Magnusson Y, Harrison H, Andersson D, Jonasson E, Rafnsdottir S, Choudhry H, Buffa F, Ragoussis J, Ståhlberg A, Harris A, Landberg G. The mevalonate precursor enzyme HMGCS1 is a novel marker and key mediator of cancer stem cell enrichment in luminal and basal models of breast cancer. PLoS? One. 2020 Jul 21;15(7):e0236187. doi: 10.1371/journal.pone.0236187. eCollection 2020. PMID: 32692762
  • Kawashima M, Bensaad K, Zois CE, Barberis A, Bridges E, Wigfield S, Lagerholm C, Dmitriev RI, Tokiwa M, Toi M, Papkovsky DB, Buffa FM, Harris AL. Disruption of hypoxia-inducible fatty acid binding protein 7 induces beige fat-like differentiation and thermogenesis in breast cancer cells. Cancer Metab. 2020 Jul 6;8:13. doi: 10.1186/s40170-020-00219-4. eCollection 2020.
  • Dhawan A, Scott J, Sundaresan P, Veness M, Porceddu S, Hau E, Harris AL, Buffa FM, Gee HE. Role of gene signatures combined with pathology in classification of oropharynx head and neck cancer. Sci Rep. 2020 Jun 23;10(1):10226. doi: 10.1038/s41598-020-66983-x.
  • Morotti M, Bridges E, Valli A, Choudhry H, Sheldon H, Wigfield S, Gray N, Zois CE, Grimm F, Jones D, Teoh EJ, Cheng WC, Lord S, Anastasiou D, Haider S, McIntyre? A, Goberdhan DCI, Buffa FM, Harris AL. Hypoxia-induced switch in SNAT2/SLC38A2 regulation generates endocrine resistance in breast cancer. Proc Natl Acad Sci U S A. 116(25):12452-12461 (2019)
  • Dhawan A, Harris AL, Buffa FM, Scott JG. Endogenous miRNA sponges mediate the generation of oscillatory dynamics for a non-coding RNA network. J Theor Biol. 481:54-60. doi: 10.1016/j.jtbi.2018.10.055 (2019)
  • Lord SR, Collins JM, Cheng WC, Haider S, Wigfield S, Gaude E, Fielding BA, Pinnick KE, Harjes U, Segaran A, Jha P, Hoefler G, Pollak MN, Thompson AM, Roy PG, English R, Adams RF, Frezza C, Buffa FM, Karpe F, Harris AL. Transcriptomic analysis of human primary breast cancer identifies fatty acid oxidation as a target for metformin. Br J Cancer. 2020 Jan;122(2):258-265. doi: 10.1038/s41416-019-0665-5. Epub 2019 Dec 10.
  • Burdova K, Yang H, Faedda R, Hume S, Chauhan J, Ebner D, Kessler BM, Vendrell I, Drewry DH, Wells CI, Hatch SB, Dianov GL, Buffa FM, D'Angiolella V. E2F1 proteolysis via SCF-cyclin F underlies synthetic lethality between cyclin F loss and Chk1 inhibition. EMBO J. 2019 Oct 15;38(20):e101443. doi: 10.15252/embj.2018101443. Epub 2019 Aug 19. PMID: 31424118
  • Louphrasitthiphol P, Ledaki I, Chauhan J, Falletta P, Siddaway R, Buffa FM, Mole DR, Soga T, Goding CR. MITF controls the TCA cycle to modulate the melanoma hypoxia response. Pigment Cell Melanoma Res. 2019 Nov;32(6):792-808. doi: 10.1111/pcmr.12802. Epub 2019 Jul 8. PMID: 31207090
  • Morotti M, Bridges E, Valli A, Choudhry H, Sheldon H, Wigfield S, Gray N, Zois CE, Grimm F, Jones D, Teoh EJ, Cheng WC, Lord S, Anastasiou D, Haider S, McIntyre? A, Goberdhan DCI, Buffa F, Harris AL. Hypoxia-induced switch in SNAT2/SLC38A2 regulation generates endocrine resistance in breast cancer. Proc Natl Acad Sci U S A. 2019 Jun 18;116(25):12452-12461. doi: 10.1073/pnas.1818521116. Epub 2019 May 31. PMID: 31152137
  • Carter R, Cheraghchi-Bashi A, Westhorpe A, Yu S, Shanneik Y, Seraia E, Ouaret D, Inoue Y, Koch C, Wilding J, Ebner D, Ryan AJ, Buffa FM, Sharma RA. Identification of anticancer drugs to radiosensitise BRAF-wild-type and mutant colorectal cancer. Cancer Biol Med. 2019 May;16(2):234-246. doi: 10.20892/j.issn.2095-3941.2018.0284. PMID: 31516745
  • Valli A, Morotti M, Zois CE, Albers PK, Soga T, Feldinger K, Fischer R, Frejno M, McIntyre? A, Bridges E, Haider S, Buffa FM, Baban D, Rodriguez M, Yanes O, Whittington HJ, Lake HA, Zervou S, Lygate CA, Kessler BM, Harris AL. Adaptation to HIF1α Deletion in Hypoxic Cancer Cells by Upregulation of GLUT14 and Creatine Metabolism. Mol Cancer Res. 17(7):1531-1544. doi: 10.1158/1541-7786.MCR-18-0315 (2019)
  • Lord SR, Collins JM, Cheng WC, Haider S, Wigfield S, Gaude E, Fielding BA, Pinnick KE, Harjes U, Segaran A, Jha P, Hoefler G, Pollak MN, Thompson AM, Roy PG, English R, Adams RF, Frezza C, Buffa FM, Karpe F, Harris AL. Transcriptomic analysis of human primary breast cancer identifies fatty acid oxidation as a target for metformin. Br J Cancer. doi: 10.1038/s41416-019-0665-5 [EPub head of print] (2019)
  • Carter R, Cheraghchi-Bashi A, Westhorpe A, Yu S, Shanneik Y, Seraia E, Ouaret D, Inoue Y, Koch C, Wilding J, Ebner D, Ryan AJ, Buffa FM, Sharma RA. Identification of anticancer drugs to radiosensitise BRAF-wild-type and mutant colorectal cancer. Cancer Biol Med. 16(2):234-246 (2019)
  • Burdova K, Yang H, Faedda R, Hume S, Chauhan J, Ebner D, Kessler BM, Vendrell I, Drewry DH, Wells CI, Hatch SB, Dianov GL, Buffa FM, D'Angiolella V. E2F1 proteolysis via SCF-cyclin F underlies synthetic lethality between cyclin F loss and Chk1 inhibition. EMBO J. 38(20):e101443. doi:10.15252/embj.2018101443 (2019)
  • Louphrasitthiphol P, Ledaki I, Chauhan J, Falletta P, Siddaway R, Buffa FM, Mole DR, Soga T, Goding CR. MITF controls the TCA cycle to modulate the melanoma hypoxia response. Pigment Cell Melanoma Res. 32(6):792-808. doi: 10.1111/pcmr.12802 (2019)
  • Cross W, Kovac M, Mustonen V, Temko D, Davis H, Baker AM, Biswas S, Arnold R, Chegwidden L, Gatenbee C, Anderson A, Koelzer V, Martinez P, Jiang X, Domingo E, Woodcock DJ, Feng Y, Kovacova M, Maughan T; SCORT Consortium, Jansen M, Rodriguez-Justo M, Ashraf S, Guy R, Cunningham C, East JE, Wedge DC, Wang LM, Palles C, Heinimann K, Sottoriva A, Leedham SJ, Graham TA, Tomlinson IPM. The evolutionary landscape of colorectal tumorigenesis. Nat Ecol Evol. 2(10)1661-1672 (2018)
  • Rodriguez-Berriguete G, Granata G, Puliyadi R, Tiwana G, Prevo R, Wilson RS, Yu S, Buffa F, Humphrey TC, McKenna? WG, Higgins GS. Nucleoporin 54 contributes to homologous recombination repair and post-replicative DNA integrity. Nucleic Acids Res. 46(15)7731-7746 (2018)
  • MacGregor? TP, Carter R, Gillies RS, Findlay JM, Kartsonaki C, Castro-Giner F, Sahgal N, Wang LM, Chetty R, Maynard ND, Cazier JB, Buffa F, McHugh? PJ, Tomlinson I, Middleton MR, Sharma RA. Translational study identifies XPF and MUS81 as predictive biomarkers for oxaliplatin-based peri-operative chemotherapy in patients with esophageal adenocarcinoma. Sci Rep. 8(1)7265 (2018)
  • Yang L, Roberts D, Takhar M, Erho N, Bibby BAS, Thiruthaneeswaran N, Bhandari V, Cheng WC, Haider S, McCorry? AMB, McArt? D, Jain S, Alshalalfa M, Ross A, Schaffer E, Den RB, Jeffrey Karnes R, Klein E, Hoskin PJ, Freedland SJ, Lamb AD, Neal DE, Buffa FM, Bristow RG, Boutros PC, Davicioni E, Choudhury A, West CML. Development and Validation of a 28-gene Hypoxia-related Prognostic Signature for Localized Prostate Cancer. EBioMedicine?. 31182-189 (2018)
  • Robbe P, Popitsch N, Knight SJL, Antoniou P, Becq J, He M, Kanapin A, Samsonova A, Vavoulis DV, Ross MT, Kingsbury Z, Cabes M, Ramos SDC, Page S, Dreau H, Ridout K, Jones LJ, Tuff-Lacey A, Henderson S, Mason J, Buffa FM, Verrill C, Maldonado-Perez D, Roxanis I, Collantes E, Browning L, Dhar S, Damato S, Davies S, Caulfield M, Bentley DR, Taylor JC, Turnbull C, Schuh A; 100,000 Genomes Project. Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens pilot study for the 100,000 Genomes Project. Genet Med. 20(10)1196-1205 (2018)
  • Papaspyropoulos A, Bradley L, Thapa A, Leung CY, Toskas K, Koennig D, Pefani DE, Raso C, Grou C, Hamilton G, Vlahov N, Grawenda A, Haider S, Chauhan J, Buti L, Kanapin A, Lu X, Buffa F, Dianov G, von Kriegsheim A, Matallanas D, Samsonova A, Zernicka-Goetz M, O'Neill E. RASSF1A uncouples Wnt from Hippo signalling and promotes YAP mediated differentiation via p73. Nat Commun. 9(1)424 (2018)
  • Pajic M, Froio D, Daly S, Doculara L, Millar E, Graham PH, Drury A, Steinmann A, de Bock CE, Boulghourjian A, Zaratzian A, Carroll S, Toohey J, O'Toole SA, Harris AL, Buffa FM, Gee HE, Hollway GE,
  • Molloy TJ. miR-139-5p Modulates Radiotherapy Resistance in Breast Cancer by Repressing Multiple Gene Networks of DNA Repair and ROS Defense. Cancer Res. 78(2)501-515 (2018)
  • Aleksic T, Verrill C, Bryant RJ, Han C, Worrall AR, Brureau L, Larré S, Higgins GS, Fazal F, Sabbagh A, Haider S, Buffa FM, Cole D, Macaulay VM. IGF-1R associates with adverse outcomes after radical radiotherapy for prostate cancer. Br J Cancer. 117(11)1600-1606 (2017)
  • Meier JC, Tallant C, Fedorov O, Witwicka H, Hwang SY, van Stiphout RG, Lambert JP, Rogers C, Yapp C, Gerstenberger BS, Fedele V, Savitsky P, Heidenreich D, Daniels DL, Owen DR, Fish PV, Igoe NM, Bayle ED, Haendler B, Oppermann UCT, Buffa F, Brennan PE, Müller S, Gingras AC, Odgren PR, Birnbaum MJ, Knapp S. Selective Targeting of Bromodomains of the Bromodomain-PHD Fingers Family Impairs Osteoclast Differentiation. ACS Chem Biol. 12(10)2619-2630 (2017)
  • D'Costa Z, Jones K, Azad A, van Stiphout R, Lim SY, Gomes AL, Kinchesh P, Smart SC, Gillies McKenna? W, Buffa FM, Sansom OJ, Muschel RJ, O'Neill E, Fokas E. Gemcitabine-Induced TIMP1 Attenuates Therapy Response and Promotes Tumor Growth and Liver Metastasis in Pancreatic Cancer. Cancer Res. 77(21)5952-5962 (2017)
  • Pirovano G, Ashton TM, Herbert KJ, Bryant RJ, Verrill CL, Cerundolo L, Buffa FM, Prevo R, Harrap I, Ryan AJ, Macaulay V, McKenna? WG, Higgins GS. TOPK modulates tumour-specific radiosensitivity and correlates with recurrence after prostate radiotherapy. Br J Cancer. 117(4)503-512 (2017)
  • Abu-Jamous B, Buffa FM, Harris AL, Nandi AK. In vitro downregulated hypoxia transcriptome is associated with poor prognosis in breast cancer. Mol Cancer. 16(1)105 (2017)
  • Alonso-Calvo R, Paraiso-Medina S, Perez-Rey D, Alonso-Oset E, van Stiphout R, Yu S, Taylor M, Buffa F, Fernandez-Lozano C, Pazos A, Maojo V. A semantic interoperability approach to support integration of gene expression and clinical data in breast cancer. Comput Biol Med. 87179-186. (2017)
  • Prevo R, Tiwana GS, Maughan TS, Buffa FM, McKenna? WG, Higgins GS. Depletion of Signal Recognition Particle 72kDa increases radiosensitivity. Cancer Biol Ther. 18(6)425-432 (2017) Oon CE, Bridges E, Sheldon H, Sainson R, Jubb A, Turley H, Leek R, Buffa F, Harris A, Li J. Role of Delta-like 4 in Jagged1-induced tumour angiogenesis and tumour growth Oncotarget 840115-40131 (2017)
  • Yang L, Taylor J, Eustace A, Irlam J, Denley H, Hoskin PJ, Alsner J, Buffa FM, Harris AL, Choudhury A, West CM. A Gene Signature for Selecting Benefit from Hypoxia Modification of Radiotherapy for High Risk Bladder Cancer Patients. Clin Cancer Res. 23(16)4761-4768 (2017)
  • Falletta P, Sanchez-Del-Campo L, Chauhan J, Effern M, Kenyon A, Kershaw CJ, Siddaway R, Lisle R, Freter R, Daniels MJ, Lu X, Tüting T, Middleton M, Buffa FM, Willis AE, Pavitt G, Ronai ZA, Sauka-Spengler T, Hölzel M, Goding CR. Translation reprogramming is an evolutionarily conserved driver of phenotypic plasticity and therapeutic resistance in melanoma. Genes Dev. 31(1)18-33 (2017)
  • Lord SR, Patel N, Liu D, Fenwick J, Gleeson F, Buffa F, Harris AL. Neoadjuvant Window Studies of Metformin and Biomarker Development for Drugs Targeting Cancer Metabolism. J Natl Cancer Inst Monogr. 5181-6. (2016)
  • Ashton TM, Fokas E, Kunz-Schughart LA, Folkes LK, Anbalagan S, Huether M, Kelly CJ, Pirovano G, Buffa FM, Hammond EM, Stratford M, Muschel RJ, Higgins GS, McKenna? WG. The anti-malarial atovaquone increases radiosensitivity by alleviating tumour hypoxia. Nat Commun. 712308. (2016)
  • Timosenko E, Ghadbane H, Silk JD, Shepherd D, Gileadi U, Howson LJ, Laynes R, Zhao Q, Strausberg RL, Olsen LR, Taylor S, Buffa FM, Boyd R, Cerundolo V. Nutritional Stress Induced by Tryptophan-Degrading Enzymes Results in ATF4-Dependent Reprogramming of the Amino Acid Transporter Profile in Tumor Cells. Cancer Res. 76(21)6193-6204. (2016)
  • Gascoyne D, Lyne L, Spearman H, Buffa F, Soilleux E, Banham A. VDR expression in plasmablastic lymphoma and myeloma confers susceptibility to vitamin D. Endocrinology 158(3)503-515 (2016)
  • Michl J, Zimmer J, Buffa FM, McDermott? U, Tarsounas M. FANCD2 limits replication stress and genome instability in cells lacking BRCA2. Nat Struct Mol Biol. 23(8)755-7. (2016)
  • Findlay JM, Castro-Giner F, Makino S, Rayner E, Kartsonaki C, Cross W, Kovac M, Ulahannan D, Palles C, Gillies RS, MacGregor? TP, Church D, Maynard ND, Buffa F, Cazier JB, Graham TA, Wang LM, Sharma RA, Middleton M, Tomlinson I. Differential clonal evolution in oesophageal cancers in response to neo-adjuvant chemotherapy. Nat Commun. 711111. (2016)
  • Raducu M, Fung E, Serres S, Infante P, Barberis A, Fischer R, Bristow C, Thézénas ML, Finta C, Christianson JC, Buffa FM, Kessler BM, Sibson NR, Di Marcotullio L, Toftgård R, D'Angiolella V. SCF (Fbxl17) ubiquitylation of Sufu regulates Hedgehog signaling and medulloblastoma development. EMBO J. 35(13)1400-16. (2016)
  • Chen L, Zeng X, Kleibeuker E, Buffa F, Barberis A, Leek RD, Roxanis I, Zhang W, Worth A, Beech JS, Harris AL, Cai S. Paracrine effect of GTP cyclohydrolase and angiopoietin-1 interaction in stromal fibroblasts on tumor Tie2 activation and breast cancer growth. Oncotarget. 7(8)9353-67. (2016)
  • Frago S, Nicholls RD, Strickland M, Hughes J, Williams C, Garner L, Surakhy M, Maclean R, Rezgui D, Prince SN, Zaccheo OJ, Ebner D, Sanegre S, Yu S, Buffa FM, Crump MP, Hassan AB. Functional evolution of IGF2IGF2R domain 11 binding generates novel structural interactions and a specific IGF2 antagonist. Proc Natl Acad Sci U S A. 113(20)E2766-75. (2016)
  • Yang J, AlTahan? A, Jones DT, Buffa FM, Bridges E, Interiano RB, Qu C, Vogt N, Li JL, Baban D, Ragoussis J, Nicholson R, Davidoff AM, Harris AL. Estrogen receptor-α directly regulates the hypoxia-inducible factor 1 pathway associated with antiestrogen response in breast cancer. Proc Natl Acad Sci U S A. 112(49)15172-7. (2015)
  • Gee HE, Buffa FM, Harris AL, Toohey JM, Carroll SL, Cooper CL, Beith J, McNeil? C, Carmalt H, Mak C, Warrier S, Holliday A, Selinger C, Beckers R, Kennedy C, Graham P, Swarbrick A, Millar EK, O'Toole SA, Molloy T. MicroRNA?-Related DNA Repair/Cell-Cycle Genes Independently Associated With Relapse After Radiation Therapy for Early Breast Cancer. Int J Radiat Oncol Biol Phys. (2015) 93(5)1104-14.
  • Vlahov N, Scrace S, Soto MS, Grawenda AM, Bradley L, Pankova D, Papaspyropoulos A, Yee KS, Buffa F, Goding CR, Timpson P, Sibson N, O'Neill E. Alternate RASSF1 Transcripts Control SRC Activity, E-Cadherin Contacts, and YAP-Mediated Invasion. Curr Biol. (2015) 25(23)3019-34.
  • Leszczynska KB, Foskolou IP, Abraham AG, Anbalagan S, Tellier C, Haider S, Span PN, O'Neill EE, Buffa FM, Hammond EM. Hypoxia-induced p53 modulates both apoptosis and radiosensitivity via AKT. J Clin Invest. (2015) 125(6)2385-98.
  • Masca NG, Hensor EM, Cornelius VR, Buffa FM, Marriott HM, Eales JM, Messenger MP, Anderson AE, Boot C, Bunce C, Goldin RD, Harris J, Hinchliffe RF, Junaid H, Kingston S, Martin-Ruiz C, Nelson CP, Peacock J, Seed PT, Shinkins B, Staples KJ, Toombs J, Wright AK, Teare MD. RIPOSTE a framework for improving the design and analysis of laboratory-based research. Elife. (2015) 4. doi 10.7554/eLife.05519.
  • Ledaki I, McIntyre? A, Wigfield S, Buffa F, McGowan? S, Baban D, Li JL, Harris AL. Carbonic anhydrase IX induction defines a heterogeneous cancer cell response to hypoxia and mediates stem cell-like properties and sensitivity to HDAC inhibition. Oncotarget (2015) 6(23)19413-27.
  • Tiwana GS, Prevo R, Buffa FM, Yu S, Ebner DV, Howarth A, Folkes LK, Budwal B, Chu KY, Durrant L, Muschel RJ, McKenna? WG, Higgins GS. Identification of vitamin B1 metabolism as a tumor-specific radiosensitizing pathway using a high-throughput colony formation screen.. Oncotarget (2015) 65978-89.
  • Petersen I, Desmedt C, Harris A, Buffa F, Kollek R. Informed consent, biobank research, and locality perceptions of breast cancer patients in European countries. J Empir Res Hum Res Ethics. 948-55 (2014)
  • Leung WY, Roxanis I, Sheldon H, Buffa FM, Li JL, Harris AL, Kong A. Combining lapatinib and pertuzumab to overcome lapatinib resistance due to NRG1-mediated signalling in HER2-amplified breast cancer. Oncotarget (2015) 6(8)5678-94.
  • Valli A, Rodriguez M, Moutsianas L, Fischer R, Fedele V, Huang HL, Van Stiphout R, Jones D, Mccarthy M, Vinaxia M, Igarashi K, Sato M, Soga T, Buffa F, Mccullagh J, Yanes O, Harris A, Kessler B. Hypoxia induces a lipogenic cancer cell phenotype via HIF1α-dependent and -independent pathways. Oncotarget (2015) 6(4)1920-41
  • Choudhry H, Albukhari A, Morotti M, Hider S, Moralli D, Smythies J, Schödel J, Green CM, Camps C, Buffa F, Ratcliffe P, Ragoussis J, Harris AL, Mole DR. Tumor hypoxia induces nuclear paraspeckle formation through HIF-2α dependent transcriptional activation of NEAT1 leading to cancer cell survival. Oncogene (2015) 34(34)4482-90.
  • Pettersen EO, Ebbesen P, Gieling RG, Williams KJ, Dubois L, Lambin P, Ward C, Meehan J, Kunkler IH, Langdon SP, Ree AH, Flatmark K, Lyng H, Calzada MJ, Peso LD, Landazuri MO, Görlach A, Flamm H, Kieninger J, Urban G, Weltin A, Singleton DC, Haider S, Buffa FM, Harris AL, Scozzafava A, Supuran CT, Moser I, Jobst G, Busk M, Toustrup K, Overgaard J, Alsner J, Pouyssegur J, Chiche J, Mazure N, Marchiq I, Parks S, Ahmed A, Ashcroft M, Pastorekova S, Cao Y, Rouschop KM, Wouters BG, Koritzinsky M, Mujcic H, Cojocari D. Targeting tumour hypoxia to prevent cancer metastasis. From biology, biosensing and technology to drug development the METOXIA consortium. J Enzyme Inhib Med Chem (2015) 30689-721.
  • van den Beucken T, Koch E, Chu K, Rupaimoole R, Prickaerts P, Adriaens M, Voncken JW, Harris AL, Buffa FM, Haider S, Starmans MH, Yao CQ, Ivan M, Ivan C, Pecot CV, Boutros PC, Sood AK, Koritzinsky M, Wouters BG. Hypoxia promotes stem cell phenotypes and poor prognosis through epigenetic regulation of DICER. Nat Commun. 55203 (2014)
  • Bensaad K, Favaro E, Lewis CA, Peck B, Lord S, Collins JM, Pinnick KE, Wigfield S, Buffa FM, Li JL, Zhang Q, Wakelam MJ, Karpe F, Schulze A, Harris AL. Fatty Acid Uptake and Lipid Storage Induced by HIF-1α Contribute to Cell Growth and Survival after Hypoxia-Reoxygenation. Cell Rep. 9(1)349-65 (2014)
  • Generali D, Buffa FM (joint first), Deb S, Cummings M, Reid LE, Taylor M, Andreis D, Allevi G, Ferrero G, Byrne D, Martinotti M, Bottini A, Harris AL, Lakhani SR, Fox SB. COX-2 expression is predictive for early relapse and aromatase inhibitor resistance in patients with ductal carcinoma in situ of the breast, and is a target for treatment. Br J Cancer. 111(1)46-54 (2014)
  • Camps C, Saini HK, Mole DR, Choudhry H, Reczko M, Guerra-Assunção JA, Tian YM, Buffa FM, Harris AL, Hatzigeorgiou AG, Enright AJ, Ragoussis J. Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia. Mol Cancer. 13(1)28. (2014)
  • Airley RE, McHugh? P, Evans AR, Harris B, Winchester L, Buffa FM, Al-Tameemi W, Leek R, Harris AL. Role of carbohydrate response element-binding protein (ChREBP?) in generating an aerobic metabolic phenotype and in breast cancer progression. Br J Cancer. 110(3)715-23 (2014).
  • Eustace A, Mani N, Span PN, Irlam JJ, Taylor J, Betts GN, Denley H, Miller CJ, Homer JJ, Rojas AM, Hoskin PJ, Buffa FM, Harris AL, Kaanders JH, West CM. A 26-gene hypoxia signature predicts benefit from hypoxia-modifying therapy in laryngeal cancer but not bladder cancer. Clin Cancer Res. 194879-88 (2013)
  • Blick C, Ramachandran A, Wigfield S, McCormick? R, Jubb A, Buffa FM, Turley H, Knowles MA, Cranston D, Catto J, Harris AL. Hypoxia regulates FGFR3 expression via HIF-1α and miR-100 and contributes to cell survival in non-muscle invasive bladder cancer. Br J Cancer. 10950-9 (2013)
  • Kumar K, Wigfield S, Gee HE, Devlin CM, Singleton D, Li JL, Buffa F, Huffman M, Sinn AL, Silver J, Turley H, Leek R, Harris AL, Ivan M. Dichloroacetate reverses the hypoxic adaptation to bevacizumab and enhances its antitumor effects in mouse xenografts. J Mol Med 91749-58 (2013)
  • Ramachandran A, Betts G, Bhana S, Helme G, Blick C, Moller-Levet C, Saunders E, Valentine H, Pepper S, Miller CJ, Buffa F, Harris AL, West CM. An in vivo hypoxia metagene identifies the novel hypoxia inducible factor target gene SLCO1B3. Eur J Cancer. 491741-51 (2013)
  • Betts GN, Eustace A, Patiar S, Valentine HR, Irlam J, Ramachandran A, Merve A, Homer JJ, Möller-Levet C, Buffa FM, Hall G, Miller CJ, Harris AL, West CM. Prospective technical validation and assessment of intra-tumour heterogeneity of a low density array hypoxia gene profile in head and neck squamous cell carcinoma. Eur J Cancer 49156-65 (2012)
  • Favaro E, Bensaad K, Chong MG, Tennant DA, Ferguson DJ, Snell C, Steers G, Turley H, Li JL, Günther UL, Buffa FM, McIntyre? A, Harris AL. Glucose utilization via glycogen phosphorylase sustains proliferation and prevents premature senescence in cancer cells. Cell Metab. 16751-64. (2012)
  • Jones DT, Lechertier T, Mitter R, Herbert JM, Bicknell R, Jones JL, Li JL, Buffa F, Harris AL, Hodivala-Dilke K. Gene expression analysis in human breast cancer associated blood vessels. PLos One 7e44294 (2012)
  • Yang J, Staples O, Thomas LW, Briston T, Robson M, Poon E, Simões ML, El-Emir E, Buffa FM, Ahmed A, Annear NP, Shukla D, Pedley B, Maxwell PH, Harris AL, Ashcroft M. Human CHCHD4 mitochondrial proteins regulate cellular oxygen consumption rate and metabolism and provide a critical role in hypoxia signaling and tumor progression. J Clin Invest 122600-11 (2012)
  • Pike LR, Singleton DC, Buffa F, Abramczyk O, Phadwal K, Li JL, Simon AK, Murray J, Harris A. ULK1Transcriptional regulation by ATF4 contributes to cancer cell survival. Biochem J. 449389-400 (2012)
  • Coutts AS, Pires IM, Weston L, Buffa FM, Milani M, Li JL, Harris AL, Hammond EM, La Thangue NB. Hypoxia-driven cell motility reflects the interplay between JMY and HIF-1α. Oncogene. 304835-42 (2011)
  • Gee HE, Buffa FM, Camps C, Ramachandran A, Leek R, Taylor M, Patil M, Sheldon H, Betts G, Homer J, West C, Ragoussis J, Harris AL. The small-nucleolar RNAs commonly used for microRNA normalisation correlate with tumour pathology and prognosis. Br J Cancer. 1041168-77 (2011)
  • Church DN, Phillips BR, Stuckey DJ, Barnes DJ, Buffa FM, Manek S, Clarke K, Harris AL, Carter EJ, Hassan AB. Igf2 ligand dependency of Pten(+/-) developmental and tumour phenotypes in the mouse. Oncogene 313635-46 (2011)
  • Rossi S, Christ-Neumann M, Rüping S, Buffa F, Wegener D, McVie? G, Coveney P, Graf N, Delorenzi M. p-Medicine From data sharing and integration via VPH models to personalized medicine. Ecancermedicalscience. 5218 (2011)
  • Martin L, Anguita A, Graf N, Tsiknakis M, Brochhausen M, Rüping S, Bucur A, Sfakianakis S, Sengstag T, Buffa F, Stenzhorn H. ACGT advancing clinico-genomic trials on cancer - four years of experience. Health Technol Inform. 169734-8 (2011)
  • Ghazoui Z, Buffa FM, Dunbier AK, Anderson H, Dexter T, Detre S, Salter J, Smith IE, Harris AL, Dowsett M. Close and stable relationship between proliferation and a hypoxia metagene in aromatase inhibitor treated ER-positive breast cancer. Clin Cancer Res. 173005-12 (2011)
  • Mehta S, Hughes NP, Buffa FM, Li SP, Adams RF, Adwani A, Taylor NJ, Levitt NC, Padhani AR, Makris A, Harris AL. Assessing early therapeutic response to bevacizumab in primary breast cancer using magnetic resonance imaging and gene expression profiles. J Natl Cancer Inst Monogr. 4371-4 (2011)

Reviews, Opinions and Editorials in peer-reviewed journals (Selected)

  • Harris BHL, Macaulay VM, Harris DA, Klenerman P, Karpe F, Lord SR, Harris AL, Buffa FM (corresponding). Obesity: a perfect storm for carcinogenesis. Cancer Metastasis Rev. 41(3):491-515. doi: 10.1007/s10555-022-10046-2 (2022)
  • Ke M, Elshenawy B, Sheldon H, Arora A, Buffa FM (corresponding). Single cell RNA-sequencing: A powerful yet still challenging technology to study cellular heterogeneity. Bioessays. 44(11):e2200084. doi: 10.1002/bies.202200084 (2022)
  • Pasqualetti F, Rizzo M, Franceschi S, Lessi F, Paiar F, Buffa FM. New perspectives in liquid biopsy for glioma patients. Curr Opin Oncol. 34(6):705-712. doi: 10.1097/CCO.0000000000000902 (2022). Dhawan A, Buffa FM (corresponding). Machine Learning Using Gene-Sets to Infer miRNA Function. Adv Exp Med Biol. 2022;1385:229-240. doi: 10.1007/978-3-031-08356-3_8.
  • Pasqualetti F, Barberis A, Zanotti S, Montemurro N, De Salvo GL, Soffietti R, Mazzanti CM, Ius T, Caffo M, Paiar F, Bocci G, Lombardi G, Harris AL, Buffa FM. The impact of survivorship bias in glioblastoma research. Crit Rev Oncol Hematol. 2023 Aug;188:104065. doi: 10.1016/j.critrevonc.2023.104065.
  • Victori P, Buffa FM (corresponding). The many faces of mathematical modelling in oncology. Br J Radiol. 92(1093): 20180856. doi: 10.1259/bjr.20180856 (2019)
  • O'Cathail SM, Buffa FM (corresponding). Science in Focus: Bioinformatics Part 1 - Lost in Translation. Clin Oncol (R Coll Radiol). 2019 Jun;31(6):337-340. doi: 10.1016/j.clon.2019.03.043. Epub 2019 Apr 8. PubMed? PMID: 30975523.
  • Harris BH, Barberis A, West CM, Buffa FM (corresponding). Gene Expression Signatures as Biomarkers of Tumour Hypoxia. Clin Oncol (2015) 27(10)547-60.
  • Favaro E, Lord S, Harris AL, Buffa FM (corresponding). Gene expression and hypoxia in breast cancer. Genome Medicine 3(8)55 (2011)
  • McCormick? R, Buffa FM, Ragoussis J, Harris AL. The role of hypoxia regulated microRNAs in cancer. Curr Top Microbiol Immunol 34547-70 (2010)
  • Jubb AM, Buffa FM (joint first), Harris AL. Assessment of tumor hypoxia for prediction of response to therapy and cancer prognosis. J Cell Mol Med 1418-29 (2009)
  • Bentzen SM, Buffa FM, Wilson G. Multiple biomarker tissue microarrays Bioinformatics and practical approaches. Cancer and Metastasis Review 27(3)481-94 (2008)

Book chapters

  • Buffa FM and Harris AL. Diagnostic and prognostic biomarkers, Cancer Systems Biology, Bioinformatics and Medicine Research and Clinical Applications. Eds F. Marcus and A. Cesario. Springer (2011)
  • Buffa FM. Fundamental Radiobiology and its Application to Radiation Oncology. NATO Science for Peace and Security B Physics and Biophysics. Springer 2009 ISBN 978-90-481-3095-5
Buffa Lab Buffa Lab Researcher Research program Contact the researcher