The major goals of my research program are to make a contribution in delineating the inherited and somatic genetic factors together with nutritional factors and their molecular mechanisms that cause the initiation and progression of colorectal cancer (CRC). This is the principal disease on which my research is focused, but my work plans also includes similar in progress projects in breast cancer, liver cancer, pancreatic cancer, and inflammatory bowel disease.
The separate project themes in my cancer biomarker and genetic / nutritional cancer epidemiology research program are described below.
1. Genetic and Nutritional Epidemiology of Cancer
2. Familial Colorectal Cancer Genetics
3. Cancer Biomarkers for Detection, Prediction, and Prognosis
4. Infectious Agents and Colorectal Cancer
5. Metabolomics & Proteomics
1. Genetic and Nutritional Epidemiology of Cancer (Colorectal, Breast, Liver, Pancreas, and Prostate)
Studies are in progress and planned for the next few years investigating the effects of oxidative stress exposures, nutritional / dietary factors and potential chemopreventive agents such as Selenium (Se) Vitamin D, Advanced Glycation End Products, Zinc, and Copper on the development and clinical outcome analyses of CRC and other cancer sites such as breast, liver, pancreas and prostate using large cancer case control and prospective cohorts from several European collaborators (principally Dr Mazda Jenab & EPIC colleagues, IARC, Lyon and Prof Pavel Vodicka & Dr Pavel Soucek, Prague, Czech Republic). These studies will be further integrated with analyses of nutritional biomarkers, genetic variation, gene expression, epigenetic markers, micro RNA profiling, and metabolomic profiling of these pathways.
Cancer Risk: The Influence of Selenoprotein Gene Variants and Blood Selenium Status
The essential micronutrient selenium (Se) is incorporated as the amino acid selenocysteine in 25 functional selenoproteins implicated in cell protection from oxidative stress, redox control and inflammatory response. Previously, together with Professor John Hesketh at Newcastle University (England) we showed for the first time modification of CRC risk with functional variants of several selenoprotein pathway genes (Meplan et al, 2010). We recently published the largest prospective study of Se status (using the two markers of Se and Selenoprotein P) and the association with CRC, within the European Prospective Investigation of Cancer and Nutrition Cohort (EPIC). This work showed that Se status is associated with CRC risk (Hughes et al, 2015 Int J Cancer 136:1149-61. PMID: 25042282). We are currently pursuing this work (via a grant I was awarded as PI by the Irish Health Research Board) in collaboration with Dr Mazda Jenab (IARC, Lyon, France) by a systems biology approach examining variation in genes involved in Se metabolism using the large EPIC nested CRC cohort, comprising 1450 cases matched to an equal number of controls. We are also examine interaction between Se status and genetic variation. We have also recently conducted in EPIC a similar study of Liver cancer and Se status (in review, American Journal of Clinical Nutrition), and have new grants from the HRB (2016-2019) to examine the interaction of Se status and genetics in breast cancer risk and from the WCRF (2016-2019) to examine the interaction of Se status and genetics in advanced prostate cancer risk.
2. Familial Colorectal Cancer Genetics
I collaborate with Michael Farrell, clinical genetics counsellor, and Dr David Gallagher, medical oncologist, in the Mater Private hospital in Dublin, on the genotype and phenotype interactions in Lynch syndrome (LS) CRC families. LS is an inherited predisposition to a range of cancers, notably uterine cancer in females and colorectal cancer (CRC) in both sexes, caused by mutated mismatch repair (MMR) genes.
Genetic counselling of at-risk individuals is based on identification of the deleterious germline MMR gene mutation in an appropriate family member who has developed cancer. Approximately 25% of mismatch repair (MMR) variants are exonic nucleotide substitutions. Some result in the substitution of one amino acid for another in the protein sequence, so-called missense variants, while others are silent. The interpretation of the effect of missense and silent variants as deleterious or neutral is challenging. These variants are termed ‘variants of uncertain significance’ or VUS. Pre-symptomatic testing for clinical use is not recommended for relatives of individuals with these variants. These relatives, including non-carriers, are considered at high-risk as long as the contribution of the variant to disease causation cannot be determined.
We have previously published two studies in the journal Familial Cancer that use a multivariate approach to detail the likely deleterious effect of particular missense variants in these MMR genes (Farrell et al 2012; Farrell et al 2013). Our integrative strategy is required to adequately assess the clinical significance of a VUS, especially in the absence of segregation data from multiple families harbouring the same base pair substitution.
3. Cancer Biomarkers for Detection, Prediction, and Prognosis
The program over the next few years will progress and expand ongoing investigations of potential genetic, epigenetic, protein and biochemical markers for early detection of advanced adenomas and CRCs, as well as markers of prognosis and therapy response in CRC.
• Epigenetics –TFAP2E gene hypermethylation and CRC: In collaboration with Dr Marc Taenzer within the group of Prof. Matthias Ebert (Technical University, Munich and University Hospital Mannheim) we recently published in the New England Journal of Medicine that TFAP2E gene hypermethylation was associated with clinical non-responsiveness to chemotherapy in CRC (Ebert et al 2012). We wish to further test genetic variation in the TFAP2E and DKK pathways genes for association with disease risk, clinical outcome and epidemiological risk factors using EPIC, Czech, German and Irish CRC cohorts. I am also currently working on other methylation targets for CRC screening and prognosis with Dr Taenzer.
• DNA Markers: A CRC detection biomarker system in commercial development is the Randox (a diagnostic company based in Northern Ireland) RanplexCRCTM mutation biochip. They have a stool DNA CRC screening assay for 28 mutations in 4 genes (APC, P53, KRAS, and BRAF) involved in CRC initiation and progression. They also have a version specifically to aid in the selection of patients for anti-EGFR therapy. This biochip rapidly detects (3 hours) 20 point mutations within the genes KRAS, BRAF and PIK3CA from tissue DNA (fresh frozen biopsies or formalin fixed tissue). I am collaborating with Randox to use these assays to type DNA from stool samples from Irish patients, and on adenoma and CRC tissue DNA. We see increased efficacy of this technique compared to Sanger sequencing and pyrosequencing (manuscript in progress and then future validation screening work in next 2 years).
• miRNA Markers: In collaboration with Prof Martin Clynes (Dublin City University) we have profiled serum to define miRNAs (Taqman arrays) differently expressed between adenoma and cancer stages, and from healthy controls (see Aherne et al, 2015 BMC Cancer 15:329).
4. Infectious Agents and Colorectal Cancer
An estimated 15% or more of the cancer burden worldwide is attributable to known infectious agents. I have also recently started working on infectious agent biomarkers and CRC carcinogenesis (see for example Flanagan et al 2014 Eur J Clin Microbiol Infect Dis. 33:1381-1390). Some of this work is in collaboration with Dr Massimo Tommasino, head of the Infections and Cancer Biology Group, IARC, Lyon and Dr Michael Pawlita of the German Cancer Research Centre in Heidelberg.
A study of the bacterium (Fusobacterium nucleatum, Fn) provided further new evidence that this common gut bacterium is involved in CRC (Flanagan et al 2014 Eur J Clin Microbiol Infect Dis. 33:1381-1390 PMID: 25042282). The manuscript describes the presence of the Fn in tissue and stool samples from patients with CRC and colorectal adenomas (CRA). It confirms in European patients previous observations from North America that Fn is found more abundantly in disease biopsy samples of CRC patients compared to the matched normal biopsies. The research further showed that Fn infection levels may be associated with both adenoma progression from early to advanced stages and the transition from adenoma to cancer. Potentially the most important new finding of the study was the association observed between Fn infection and CRC prognosis. Cancer patients with low bacterial levels had a significantly longer overall survival time than patients with moderate and high levels of the bacterium. Finally, the study also showed that stool screening for Fn is a potential biomarker indicating the presence of colorectal neoplasia, but that this needs tested in a large study.
I am working with Prof Micheal Pawlita, German Cancer Research Centre, Heidelberg, Germany and Dr Massimo Tommasino, head of the Infections and Cancer Biology Group, IARC, Lyon to use LUMINEX high throughout DNA tissue and serological typing of 100s of infectious agents (bacterial and viral) in large case-control cohort screens. This will allow a unique and innovative analysis in the next 2 years to incorporate data on infectious status, immune status and nutritional exposures to my cohort studies on cancer risk and outcomes, and host genetic / nutritional status susceptibility to infection. I also plan to examine microbial / immune tumour microenvironment in ex-vivo ‘sponge’ tissue models of CRC.
5. Metabolomics & Proteomics
In collaboration with Prof Martin Clynes (Dublin City University) and Dr Paul Dowling (Maynooth University) we used combined proteomic and metabolomic approaches to define metabolite biomarker signals in CRC patients (Dowling et al, 2015 Clin Chim Acta. 441:133-41 PMID: 25540887).
In collaboration with Dr Mazda Jenab and Dr Augustin Scalbert (IARC) we are currently using quantitative tandem mass spectrometry with a targeted metabolomic metabolite kit (Biocrates, Germany) to try to locate metabolite biomarkers of the adenoma to CRC progression. We are examining a large number of serum samples from Ireland and the Czech Republic and in the future wish to examine matched sets of disease+normal tissue pairs from patients with CRCs and CRAs (this will be in collaboration with Dr James Kinross, Imperial College London).
Publications (listed by research area topic)
Colorectal cancer: screening, biomarkers, nutrition, epidemiology, infectious agents, familial genetics
• Václavíková R, Hughes DJ, Souček P (2015) Microsomal Epoxide Hydrolase 1 (EPHX1): Gene, Structure, Function, and Role in Human Disease. Gene Jul 24. doi: 10.1016/j.gene.2015.07.071. [Epub ahead of print]. PMID: 26216302
• Aherne ST, Madden SF, Hughes DJ, Pardini B, Naccarati A, Levy M, Vodicka P, Neary P, Dowling P, Clynes M (2015) Circulating miRNAs miR-34a and miR-150 associated with colorectal cancer progression. BMC Cancer 15:329. Published 30 April 2015, PMID: 25924769.
• Hughes DJ, Fedirko V, Jenab M, Schomburg L, Méplan C, Freisling H, Bueno de Mesquita HB, Hybsier S, Becker NP, Czuban M, Tjønneland A, Outzen M, Boutron-Ruault MC, Racine A, Bastide N, Kühn T, Kaaks R, Trichopoulos D, Trichopoulou A, Lagiou P, Panico S, Peeters PH, Weiderpass E, Skeie G, Dagrun E, Chirlaque MD, Sánchez MJ, Ardanaz E, Ljuslinder I, Wennberg M, Bradbury KE, Vineis P, Naccarati A, Palli D, Boeing H, Overvad K, Dorronsoro M, Jakszyn P, Cross AJ, Ramón Quirós J, Stepien M, Kong SY, Duarte-Salles T, Riboli E, Hesketh JE (2015) Selenium Status is Associated with Colorectal Cancer risk in the European Prospective Investigation of Cancer and Nutrition Cohort. Int J Cancer. Mar 1;136(5):1149-61. PMID: 25042282
• Hughes DJ, Fedirko V, Jones JS, Méplan C, Schomburg L, Hybsier S, Riboli E, Hesketh J, Jenab M (on behalf of EPIC Group) (2015) Association of selenoprotein and selenium pathway genetic variations with colorectal cancer risk and interaction with selenium status. In Book: Global Advances in Selenium Research from Theory to Application, pp 53-54 (editors Banuelos GS, Lin ZQ, Moraes MF, Guilherme LRG & dos Reis AR), Taylor & Francis, London, UK
• Dowling P, Hughes DJ, Larkin AM, Meiller J, Henry M, Meleady P, Lynch V, Pardini B, Naccarati A, Levy M, Vodicka P, Neary P, Clynes M (2015) Elevated levels of 14-3-3 proteins, serotonin, gamma enolase and pyruvate kinase identified in clinical samples from patients diagnosed with colorectal cancer. Clin Chim Acta. Feb 20;441:133-41. PMID: 25540887
• Flanagan L, Schmid J, Neary P, Ebert MP, Soucek P, Kunicka T, Liska V, Bruha J, Dezeeuw N, Tommasino M, Jenab M, Prehn JH, Hughes DJ (2014) Fusobacterium nucleatum associates with stages of colorectal neoplasia development, colorectal cancer and disease outcome. Eur J Clin Microbiol Infect Dis. Aug;33(8), 1381-1390. PMID:24599709
• Kelley L, Swan N, Hughes DJ (2013). An analysis of the duplicate testing strategy of an Irish immunochemical FOBT colorectal cancer screening programme. Colorectal Disease, 15, e512–e521. PMID: 23746062
•Farrell MP, Hughes DJ, Drost M, Wallace AJ, Cummins RJ, Fletcher TA, Meany MA,Kay EW, de Wind N, Power DG, Andrews EJ, Green AJ, Gallagher DJ (2013). Multivariate analysis of MLH1 c.1664T>C (p.Leu555Pro) mismatch repair gene variant demonstrates its pathogenicity. Familial Cancer, 12, 741-747. PMID: 23712482
• Ebert MPA, Tänzer M, Balluff B, Burgermeister E, Kretzschmar AK, Hughes DJ, Tetzner R, Lofton-Day C, Rosenberg R, Reinacher-Schick A, Schulmann K, Hofheinz R, Röcken C, Keller G, Langer R, Stöhlmacher J, Schuster T, Ströbel P, Schmid R (2012). TFAP2E/DKK4 and Chemoresistance in Colorectal Cancer. New England Journal of Medicine, 366, 44-53. PMID:22216841
• Farrell MP, Hughes DJ, Berry IR, et al, Daly PA (2012) Clinical correlation and molecular evaluation confirm that the hMLH1 p.R182G (c.544a/g) mutation is pathogenic and causes lynch syndrome. Familial Cancer 11(3):509-518. PMID: 22773173
• Hughes DJ, Soucek P, Hlavatá I, Pardini B, Naccarati A, Vodickova L, Jenab M, and Vodicka P (2011) Variation in the Vitamin D receptor gene is not associated with Colorectal Cancer Risk in the Czech Republic. Journal of Gastrointestinal Cancer 42, 149-154. PMID: 20585998
• Hughes DJ, Hlavatá I, Soucek P, Pardini B, Naccarati A, Vodickova L, O’Morain C, and Vodicka P (2011) Ornithine Decarboxylase G316A Genotype and Colorectal Cancer Risk. Colorectal Disease 13, 860-864. PMID: 20456464
• Méplan C, Hughes DJ, Pardini B, Naccareti A, Soucek P, Vodickova L, Hlavata I, Vrana D, Vodicka P and Hesketh J (2010) Genetic Variants in Selenoprotein Genes Increase Risk of Colorectal Cancer. Carcinogenesis, Jun;31(6):1074-9. PMID: 20378690.
Gastrointestinal disease genetics
• Hughes DJ, McManus R, Neary P, O’Morain C, O’Sullivan M (2011) Common Variation in the Vitamin D Receptor Gene and Risk of Inflammatory Bowel Disease in an Irish Case-Control Study. Eur J Gastroenterol Hepatol 23, 807-812. PMID:21818054
• Murphy G, Thornton J, McManus R, Swan N, Ryan B, O’Morain CA, Hughes DJ, O’Sullivan M (2009) Association of gastric disease with polymorphisms in the inflammatory related genes IL-1B, IL-1RN, IL-10, TNF and TLR4. Eur J Gastroenterol Hepatol 21, 630–635. PMID: 19295440
Renal cancer genetics
• Morris MR, Hughes DJ, Tian YM, Ricketts CJ, Lau KW, Gentle D, Shuib S, Serrano-Fernandez P, Lubinski J, Wiesener MS, Pugh CW, Latif F, Ratcliffe PJ, Maher ER (2009) Mutation analysis of hypoxia-inducible factors HIF1A and HIF2A in renal cell carcinoma. Anticancer Res 29, 4337-43. PMID: 20032376
Breast cancer genetic epidemiology, familial genetics
• Hughes DJ (2008) Use of Association Studies to Define Genetic Modifiers of Breast Cancer Risk in BRCA1 and BRCA2 Mutation Carriers. Familial Cancer 7, 233-244. PMID: 18283561
• Sinilnikova OM, Antoniou AC, Simard J, Healey S, Léoné M, et al, Hughes DJ, et al, Easton D, Chenevix-Trench G, Stoppa-Lyonnet D, on behalf of CIMBA (2009) The TP53 Arg72Pro and MDM2 309G/T polymorphisms are not associated with breast cancer risk in BRCA1 and BRCA2 mutation carriers. British J Cancer 101, 1456–1460. PMID: 19707196
• Antoniou AC, Sinilnikova OM, Simard J, Léoné M, Dumont M, Neuhausen SL, Struewing JP, Stoppa Lyonnet D, Barjhoux L, Hughes DJ, et al, Couch F, Easton DF and Chenevix-Trench G on behalf of CIMBA (2007). RAD51 135G/C modifies breast cancer risk among BRCA2 mutation carriers: Results from a combined analysis of 19 studies. Am J Hum Genet 81, 1186-1200. PMID: 17999359
• Cox A, Dunning AM, Garcia-Closas M, Balasubramanian S, Reed MW, Pooley KA, et al, Sangrajrang S, Hughes D, Odefrey F, et al, Pharoah PD, Easton DF; on behalf of the Breast Cancer Association Consortium (2007) A common coding variant in CASP8 is associated with breast cancer risk. Nature Genetics 39, 352-8. PMID: 17293864
• Couch FJ, Antoniou AC, Sinilnikova O, Vierkant RA, Pankratz VS, Fredericksen ZS, Stoppa-Lyonnet D, Coupier I, Hughes D, et al, Easton DF, Chenevix-Trench G on behalf of the Consortium of Investigators of Modifiers of BRCA1/2 (2007) AURKA F31I Polymorphism and Breast Cancer Risk in BRCA1 and BRCA2 Mutation Carriers: A CIMBA study. Cancer Epi Bio Prev 16, 1416-21. PMID: 17627006
• Sinilnikova OM, McKay JD, Tavtigian SV, Canzian F, DeSilva D, Biessy C, Monnier S, Dossus L, Boillot C, Gioia L, Hughes DJ, et al, Kaaks R (2007) Haplotype-Based Analysis of Common Variation in the Acetyl-CoA Carboxylase alpha Gene and Breast Cancer Risk: a Case-Control Study Nested within the European Prospective Investigation into Cancer and Nutrition. Cancer Epi Bio Prev 16, 409-15. PMID: 17372234
• Chenevix-Trench G, Milne RL, Antoniou AC, et al* (2007) An international initiative to identify genetic modifiers of cancer risk in BRCA1 and BRCA2 mutation carriers: the Consortium of Investigators of Modifiers of BRCA1 and BRCA2 (CIMBA). Breast Cancer Res 9, 104. (*CIMBA co-author)
• The Breast Cancer Association Consortium (BCAC) (2006) Commonly Studied Single-Nucleotide Polymorphisms and Breast Cancer: Results from the Breast Cancer Association Consortium. Journal of the National Cancer Institute 98, 1382-96. PMID: 17018785
• Hughes DJ, Sophie M. Ginolhac, Isabelle Coupier, Laure Barjhoux, Valérie Gaborieau, et al, Olga M. Sinilnikova (2005) Modification of breast cancer risk in BRCA1 and BRCA2 mutation carriers with polyglutamine repeat length in the AIB1 gene. Int J Cancer 117;230-233. PMID: 15900600
• Hughes D, Ginolhac SM, Coupier I, Corbex M, et al, Sinilnikova OM (2005) Common BRCA2 variants and modification of breast and ovarian cancer risk in BRCA1 mutation carriers. Cancer Epi Bio Prev 14;265-267. PMID: 15668505
• Coupier I, Cousin PY, Hughes D, Legoix-Né P, Trehin A, Sinilnikova O, Stoppa-Lyonnet D (2005) BAP1 and breast cancer risk. Familial Cancer 4 ;273-7. PMID: 16341802
• Sinilnikova OM, Ginolhac SM, Magnard C, Léoné M, Anczukow O, Hughes D, Moreau K, Thompson D, Gaborieau V, Hall J, Gérard JP, Bonadona V, Lasset C, Goldgar DE, Joulin V, Dalla Venezia N, Lenoir GM (2004) Acetyl-CoA Carboxylase α Gene and Breast Cancer Susceptibility. Carcinogenesis 25;2417-2424. PMID: 15333468
Circulating tumour cells
• Commission written solely by Hughes DJ for Rarecells company – Paterlini-Brechot P (2011) Organ-specific markers in circulating tumor cell screening: an early indicator of metastasis-capable malignancy. Invited Review. Future Oncology 7, 849-871. PMID:21732757
• The C. elegans Sequencing Consortium* (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2012-8 PMID:9851916. *member
Cystic fibrosis genetics
• Hughes D, Dörk T, Sthurmann M, Graham C (2001) Mutation and haplotype analysis of the CFTR gene in atypically mild cystic fibrosis patients from Northern Ireland. J Med Genet 38: 136-139. PMID: 11288718
• Estivill X, Bancells C, Ramos C, Biomed Cystic Fibrosis Genetic Analysis Consortium* (1997) Geographic distribution and regional origin of 272 cystic fibrosis mutations in European populations. Hum Mutation 10: 135–54. PMID: 9259197. *I was a contributing member
• Hughes D, Hill A, Macek M Jr, Redmond A, Nevin N, Graham C (1996) Mutation Characterization of the CFTR Gene in 206 Northern Irish CF Families: 30 Mutations, Two of which are Novel, Account for 94% of CF Chromosomes. Human Mutation 8: 340-347. PMID: 8956039
• Hughes D, Wallace A, Taylor J, Tassabehji M, McMahon R, Hill A, Nevin N, Graham C (1996) Fluorescent Multiplex Microsatellites used to Define Haplotypes Associated with 75 CFTR Mutations from the UK on 437 CF Chromosomes. Human Mutation 8: 229-235. PMID: 8889582
• Hughes D, Hill A, Redmond A, Nevin N, Graham C (1995) Fluorescent Multiplex Microsatellites used to identify Haplotype Associations with 15 CFTR Mutations in 124 Northern Irish CF Families. Human Genetics 95: 462-464. PMID: 7535745
• The Cystic Fibrosis Genetic Analysis Consortium* (1994) Population variation of common cystic fibrosis mutations. Human Mutation 4: 167-177. PMID:7530552. *contributor / member
Immune function genetics
• Williams F, Hughes D, Middleton D (1994) A new HLA-DRB1*11 allele (DRB1*1109) differing at codons 32, 34 and 37. Tissue Antigens 44: 63-64. PMID: 7974472
• Middleton D, Hughes D, Trainor F, Graham C, Savage D (1994) An HLA-DRB*04 first domain sequence (DRB1*0416) which differs from HLA-DRB1*0401 at codon 59. Tissue Antigens 43: 44-46. PMID: 8023318
• Middleton D, Hughes D, Williams F, Graham C, Martin J, Savage D (1993) A new DRB1 allele DRB1*1107 a combination of DRB1*11 and DRB1*03. Tissue Antigens 42:160-3. PMID: 8284792
Neurological disease genetics
• Mullan M, Bennett C, Figueredo C, Hughes D, et al. (1995) Clinical features of early onset, familial Alzheimer’s disease linked to chromosome 14. American Journal of Medical Genetics 60: 44-52. PMID:7485234
• Hughes D, Brown J, Hardy J, Chartier-Harlin MC (1992) A polymorphic dinucleotide repeat in intron 2 of the human cystatin-C gene. Human Molecular Genetics 1: 143. PMID:1301159
• Fidani L, Rooke K, Chartier-Harlin MC, Hughes D, Tanzi R, Mullan M, Roques P, Hardy J, Goate A (1992) Screening for mutations in the open reading frame and promoter of the beta -amyloid precursor protein gene in familial Alzheimer’s disease: Identification of a further family with APP717 Val/Ile. Human Molecular Genetics 1: 165-168. PMID:1303172
• Chartier-Harlin MC, Crawford F, Houlden H, Warren A, Hughes D, Fidani L, Goate A, Rossor M, Roques P, Hardy J, Mullan M (1991) Mutations at codon 717 of the amyloid precursor protein gene cause Alzheimer’s disease. Nature 353: 844-846. PMID:1944558
• Crawford F, Hardy J, Mullan M, Goate A, Hughes D, Fidani L, Roques P, Rossor M, Chartier-Harlin MC (1991) Sequencing of codon 16 and 17 of the B-amyloid precursor protein gene in 14 families with early onset Alzheimer’s disease fails to reveal mutations in the B-amyloid sequence. Neuroscience Letters 133: 1-2. PMID:1791986