Circulating bilirubin levels and risk of colorectal cancer: serological and Mendelian randomization analyses
Seyed Khoei, Nazlisadat ; Jenab, Mazda ; Murphy, Neil ; Banbury, Barbara L. ; Carreras-Torres, Robert ; Viallon, Vivian ; Kühn, Tilman ; Bueno-de-Mesquita, Bas ; Aleksandrova, Krasimira ; Cross, Amanda J. ; Weiderpass, Elisabete ; Stepien, Magdalena ; Bulmer, Andrew ; Tjønneland, Anne ; Boutron-Ruault, Marie Christine ; Severi, Gianluca ; Carbonnel, Franck ; Katzke, Verena ; Boeing, Heiner ; Bergmann, Manuela M. ; Trichopoulou, Antonia ; Karakatsani, Anna ; Martimianaki, Georgia ; Palli, Domenico ; Tagliabue, Giovanna ; Panico, Salvatore ; Tumino, Rosario ; Sacerdote, Carlotta ; Skeie, Guri ; Merino, Susana ; Bonet, Catalina ; Rodríguez-Barranco, Miguel ; Gil, Leire ; Chirlaque, Maria Dolores ; Ardanaz, Eva ; Myte, Robin ; Hultdin, Johan ; Perez-Cornago, Aurora ; Aune, Dagfinn ; Tsilidis, Konstantinos K. ; Albanes, Demetrius ; Baron, John A. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Brenner, Hermann ; Campbell, Peter T. ; Casey, Graham ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chanock, Stephen J. ; Cotterchio, Michelle ; Gallinger, Steven ; Gruber, Stephen B. ; Haile, Robert W. ; Hampe, Jochen ; Hoffmeister, Michael ; Hopper, John L. ; Hsu, Li ; Huyghe, Jeroen R. ; Jenkins, Mark A. ; Joshi, Amit D. ; Kampman, Ellen ; Larsson, Susanna C. ; Marchand, Loic Le; Li, Christopher I. ; Li, Li ; Lindblom, Annika ; Lindor, Noralane M. ; Martín, Vicente ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Ogino, Shuji ; Parfrey, Patrick S. ; Pharoah, Paul D.P. ; Rennert, Gad ; Sakoda, Lori C. ; Schafmayer, Clemens ; Schmit, Stephanie L. ; Schoen, Robert E. ; Slattery, Martha L. ; Thibodeau, Stephen N. ; Ulrich, Cornelia M. ; Duijnhoven, Franzel J.B. van; Weigl, Korbinian ; Weinstein, Stephanie J. ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Zhang, Xuehong ; Ferrari, Pietro ; Anton, Gabriele ; Peters, Annette ; Peters, Ulrike ; Gunter, Marc J. ; Wagner, Karl Heinz ; Freisling, Heinz - \ 2020
BMC Medicine 18 (2020)1. - ISSN 1741-7015 - 1 p.
Anti-oxidants - Bilirubin - Cancer - Colorectal cancer - Mendelian randomization analysis
BACKGROUND: Bilirubin, a byproduct of hemoglobin breakdown and purported anti-oxidant, is thought to be cancer preventive. We conducted complementary serological and Mendelian randomization (MR) analyses to investigate whether alterations in circulating levels of bilirubin are associated with risk of colorectal cancer (CRC). We decided a priori to perform analyses separately in men and women based on suggestive evidence that associations may differ by sex. METHODS: In a case-control study nested in the European Prospective Investigation into Cancer and Nutrition (EPIC), pre-diagnostic unconjugated bilirubin (UCB, the main component of total bilirubin) concentrations were measured by high-performance liquid chromatography in plasma samples of 1386 CRC cases and their individually matched controls. Additionally, 115 single-nucleotide polymorphisms (SNPs) robustly associated (P < 5 × 10-8) with circulating total bilirubin were instrumented in a 2-sample MR to test for a potential causal effect of bilirubin on CRC risk in 52,775 CRC cases and 45,940 matched controls in the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO), the Colon Cancer Family Registry (CCFR), and the Colorectal Transdisciplinary (CORECT) study. RESULTS: The associations between circulating UCB levels and CRC risk differed by sex (Pheterogeneity = 0.008). Among men, higher levels of UCB were positively associated with CRC risk (odds ratio [OR] = 1.19, 95% confidence interval [CI] = 1.04-1.36; per 1-SD increment of log-UCB). In women, an inverse association was observed (OR = 0.86 (0.76-0.97)). In the MR analysis of the main UGT1A1 SNP (rs6431625), genetically predicted higher levels of total bilirubin were associated with a 7% increase in CRC risk in men (OR = 1.07 (1.02-1.12); P = 0.006; per 1-SD increment of total bilirubin), while there was no association in women (OR = 1.01 (0.96-1.06); P = 0.73). Raised bilirubin levels, predicted by instrumental variables excluding rs6431625, were suggestive of an inverse association with CRC in men, but not in women. These differences by sex did not reach formal statistical significance (Pheterogeneity ≥ 0.2). CONCLUSIONS: Additional insight into the relationship between circulating bilirubin and CRC is needed in order to conclude on a potential causal role of bilirubin in CRC development.
Genome-wide Modeling of Polygenic Risk Score in Colorectal Cancer Risk
Thomas, Minta ; Sakoda, Lori C. ; Hoffmeister, Michael ; Rosenthal, Elisabeth A. ; Lee, Jeffrey K. ; Duijnhoven, Franzel J.B. van; Platz, Elizabeth A. ; Wu, Anna H. ; Dampier, Christopher H. ; Chapelle, Albert de la; Wolk, Alicja ; Joshi, Amit D. ; Burnett-Hartman, Andrea ; Gsur, Andrea ; Lindblom, Annika ; Castells, Antoni ; Win, Aung Ko ; Namjou, Bahram ; Guelpen, Bethany Van; Tangen, Catherine M. ; He, Qianchuan ; Li, Christopher I. ; Schafmayer, Clemens ; Joshu, Corinne E. ; Ulrich, Cornelia M. ; Bishop, D.T. ; Buchanan, Daniel D. ; Schaid, Daniel ; Drew, David A. ; Muller, David C. ; Duggan, David ; Crosslin, David R. ; Albanes, Demetrius ; Giovannucci, Edward L. ; Larson, Eric ; Qu, Flora ; Mentch, Frank ; Giles, Graham G. ; Hakonarson, Hakon ; Hampel, Heather ; Stanaway, Ian B. ; Figueiredo, Jane C. ; Huyghe, Jeroen R. ; Minnier, Jessica ; Chang-Claude, Jenny ; Hampe, Jochen ; Harley, John B. ; Visvanathan, Kala ; Curtis, Keith R. ; Offit, Kenneth ; Li, Li ; Marchand, Loic Le; Vodickova, Ludmila ; Gunter, Marc J. ; Jenkins, Mark A. ; Slattery, Martha L. ; Lemire, Mathieu ; Woods, Michael O. ; Song, Mingyang ; Murphy, Neil ; Lindor, Noralane M. ; Dikilitas, Ozan ; Pharoah, Paul D.P. ; Campbell, Peter T. ; Newcomb, Polly A. ; Milne, Roger L. ; MacInnis, Robert J. ; Castellví-Bel, Sergi ; Ogino, Shuji ; Berndt, Sonja I. ; Bézieau, Stéphane ; Thibodeau, Stephen N. ; Gallinger, Steven J. ; Zaidi, Syed H. ; Harrison, Tabitha A. ; Keku, Temitope O. ; Hudson, Thomas J. ; Vymetalkova, Veronika ; Moreno, Victor ; Martín, Vicente ; Arndt, Volker ; Wei, Wei Qi ; Chung, Wendy ; Su, Yu Ru ; Hayes, Richard B. ; White, Emily ; Vodicka, Pavel ; Casey, Graham ; Gruber, Stephen B. ; Schoen, Robert E. ; Chan, Andrew T. ; Potter, John D. ; Brenner, Hermann ; Jarvik, Gail P. ; Corley, Douglas A. ; Peters, Ulrike ; Hsu, Li - \ 2020
American Journal of Human Genetics 107 (2020)3. - ISSN 0002-9297 - p. 432 - 444.
cancer risk prediction - colorectal cancer - machine learning - polygenic risk score
Accurate colorectal cancer (CRC) risk prediction models are critical for identifying individuals at low and high risk of developing CRC, as they can then be offered targeted screening and interventions to address their risks of developing disease (if they are in a high-risk group) and avoid unnecessary screening and interventions (if they are in a low-risk group). As it is likely that thousands of genetic variants contribute to CRC risk, it is clinically important to investigate whether these genetic variants can be used jointly for CRC risk prediction. In this paper, we derived and compared different approaches to generating predictive polygenic risk scores (PRS) from genome-wide association studies (GWASs) including 55,105 CRC-affected case subjects and 65,079 control subjects of European ancestry. We built the PRS in three ways, using (1) 140 previously identified and validated CRC loci; (2) SNP selection based on linkage disequilibrium (LD) clumping followed by machine-learning approaches; and (3) LDpred, a Bayesian approach for genome-wide risk prediction. We tested the PRS in an independent cohort of 101,987 individuals with 1,699 CRC-affected case subjects. The discriminatory accuracy, calculated by the age- and sex-adjusted area under the receiver operating characteristics curve (AUC), was highest for the LDpred-derived PRS (AUC = 0.654) including nearly 1.2 M genetic variants (the proportion of causal genetic variants for CRC assumed to be 0.003), whereas the PRS of the 140 known variants identified from GWASs had the lowest AUC (AUC = 0.629). Based on the LDpred-derived PRS, we are able to identify 30% of individuals without a family history as having risk for CRC similar to those with a family history of CRC, whereas the PRS based on known GWAS variants identified only top 10% as having a similar relative risk. About 90% of these individuals have no family history and would have been considered average risk under current screening guidelines, but might benefit from earlier screening. The developed PRS offers a way for risk-stratified CRC screening and other targeted interventions.
Cumulative Burden of Colorectal Cancer–Associated Genetic Variants Is More Strongly Associated With Early-Onset vs Late-Onset Cancer
Archambault, Alexi N. ; Su, Yu Ru ; Jeon, Jihyoun ; Thomas, Minta ; Lin, Yi ; Conti, David V. ; Win, Aung Ko ; Sakoda, Lori C. ; Lansdorp-Vogelaar, Iris ; Peterse, Elisabeth F.P. ; Zauber, Ann G. ; Duggan, David ; Holowatyj, Andreana N. ; Huyghe, Jeroen R. ; Brenner, Hermann ; Cotterchio, Michelle ; Bézieau, Stéphane ; Schmit, Stephanie L. ; Edlund, Christopher K. ; Southey, Melissa C. ; MacInnis, Robert J. ; Campbell, Peter T. ; Chang-Claude, Jenny ; Slattery, Martha L. ; Chan, Andrew T. ; Joshi, Amit D. ; Song, Mingyang ; Cao, Yin ; Woods, Michael O. ; White, Emily ; Weinstein, Stephanie J. ; Ulrich, Cornelia M. ; Hoffmeister, Michael ; Bien, Stephanie A. ; Harrison, Tabitha A. ; Hampe, Jochen ; Li, Christopher I. ; Schafmayer, Clemens ; Offit, Kenneth ; Pharoah, Paul D. ; Moreno, Victor ; Lindblom, Annika ; Wolk, Alicja ; Wu, Anna H. ; Li, Li ; Gunter, Marc J. ; Gsur, Andrea ; Keku, Temitope O. ; Pearlman, Rachel ; Bishop, D.T. ; Castellví-Bel, Sergi ; Moreira, Leticia ; Vodicka, Pavel ; Kampman, Ellen ; Giles, Graham G. ; Albanes, Demetrius ; Baron, John A. ; Berndt, Sonja I. ; Brezina, Stefanie ; Buch, Stephan ; Buchanan, Daniel D. ; Trichopoulou, Antonia ; Severi, Gianluca ; Chirlaque, María Dolores ; Sánchez, Maria José ; Palli, Domenico ; Kühn, Tilman ; Murphy, Neil ; Cross, Amanda J. ; Burnett-Hartman, Andrea N. ; Chanock, Stephen J. ; Chapelle, Albert de la; Easton, Douglas F. ; Elliott, Faye ; English, Dallas R. ; Feskens, Edith J.M. ; FitzGerald, Liesel M. ; Goodman, Phyllis J. ; Hopper, John L. ; Hudson, Thomas J. ; Hunter, David J. ; Jacobs, Eric J. ; Joshu, Corinne E. ; Küry, Sébastien ; Markowitz, Sanford D. ; Milne, Roger L. ; Platz, Elizabeth A. ; Rennert, Gad ; Rennert, Hedy S. ; Schumacher, Fredrick R. ; Sandler, Robert S. ; Seminara, Daniela ; Tangen, Catherine M. ; Thibodeau, Stephen N. ; Toland, Amanda E. ; Duijnhoven, Franzel J.B. van; Visvanathan, Kala ; Vodickova, Ludmila ; Potter, John D. ; Männistö, Satu ; Weigl, Korbinian ; Figueiredo, Jane ; Martín, Vicente ; Larsson, Susanna C. ; Parfrey, Patrick S. ; Huang, Wen Yi ; Lenz, Heinz Josef ; Castelao, Jose E. ; Gago-Dominguez, Manuela ; Muñoz-Garzón, Victor ; Mancao, Christoph ; Haiman, Christopher A. ; Wilkens, Lynne R. ; Siegel, Erin ; Barry, Elizabeth ; Younghusband, Ban ; Guelpen, Bethany Van; Harlid, Sophia ; Zeleniuch-Jacquotte, Anne ; Liang, Peter S. ; Du, Mengmeng ; Casey, Graham ; Lindor, Noralane M. ; Marchand, Loic Le; Gallinger, Steven J. ; Jenkins, Mark A. ; Newcomb, Polly A. ; Gruber, Stephen B. ; Schoen, Robert E. ; Hampel, Heather ; Corley, Douglas A. ; Hsu, Li ; Peters, Ulrike ; Hayes, Richard B. - \ 2020
Gastroenterology 158 (2020)5. - ISSN 0016-5085 - p. 1274 - 1286.e12.
Colon Cancer - EOCRC - Penetrance - SNP
Background & Aims: Early-onset colorectal cancer (CRC, in persons younger than 50 years old) is increasing in incidence; yet, in the absence of a family history of CRC, this population lacks harmonized recommendations for prevention. We aimed to determine whether a polygenic risk score (PRS) developed from 95 CRC-associated common genetic risk variants was associated with risk for early-onset CRC. Methods: We studied risk for CRC associated with a weighted PRS in 12,197 participants younger than 50 years old vs 95,865 participants 50 years or older. PRS was calculated based on single nucleotide polymorphisms associated with CRC in a large-scale genome-wide association study as of January 2019. Participants were pooled from 3 large consortia that provided clinical and genotyping data: the Colon Cancer Family Registry, the Colorectal Transdisciplinary Study, and the Genetics and Epidemiology of Colorectal Cancer Consortium and were all of genetically defined European descent. Findings were replicated in an independent cohort of 72,573 participants. Results: Overall associations with CRC per standard deviation of PRS were significant for early-onset cancer, and were stronger compared with late-onset cancer (P for interaction = .01); when we compared the highest PRS quartile with the lowest, risk increased 3.7-fold for early-onset CRC (95% CI 3.28–4.24) vs 2.9-fold for late-onset CRC (95% CI 2.80–3.04). This association was strongest for participants without a first-degree family history of CRC (P for interaction = 5.61 × 10–5). When we compared the highest with the lowest quartiles in this group, risk increased 4.3-fold for early-onset CRC (95% CI 3.61–5.01) vs 2.9-fold for late-onset CRC (95% CI 2.70–3.00). Sensitivity analyses were consistent with these findings. Conclusions: In an analysis of associations with CRC per standard deviation of PRS, we found the cumulative burden of CRC-associated common genetic variants to associate with early-onset cancer, and to be more strongly associated with early-onset than late-onset cancer, particularly in the absence of CRC family history. Analyses of PRS, along with environmental and lifestyle risk factors, might identify younger individuals who would benefit from preventive measures.
Circulating Levels of Insulin-like Growth Factor 1 and Insulin-like Growth Factor Binding Protein 3 Associate With Risk of Colorectal Cancer Based on Serologic and Mendelian Randomization Analyses
Murphy, Neil ; Carreras-Torres, Robert ; Song, Mingyang ; Chan, Andrew T. ; Martin, Richard M. ; Papadimitriou, Nikos ; Dimou, Niki ; Tsilidis, Konstantinos K. ; Banbury, Barbara ; Bradbury, Kathryn E. ; Besevic, Jelena ; Rinaldi, Sabina ; Riboli, Elio ; Cross, Amanda J. ; Travis, Ruth C. ; Agnoli, Claudia ; Albanes, Demetrius ; Berndt, Sonja I. ; Bézieau, Stéphane ; Bishop, D.T. ; Brenner, Hermann ; Buchanan, Daniel D. ; Onland-Moret, N.C. ; Burnett-Hartman, Andrea ; Campbell, Peter T. ; Casey, Graham ; Castellví-Bel, Sergi ; Chang-Claude, Jenny ; Chirlaque, María Dolores ; Chapelle, Albert de la; English, Dallas ; Figueiredo, Jane C. ; Gallinger, Steven J. ; Giles, Graham G. ; Gruber, Stephen B. ; Gsur, Andrea ; Hampe, Jochen ; Hampel, Heather ; Harrison, Tabitha A. ; Hoffmeister, Michael ; Hsu, Li ; Huang, Wen Yi ; Huyghe, Jeroen R. ; Jenkins, Mark A. ; Keku, Temitope O. ; Kühn, Tilman ; Kweon, Sun Seog ; Marchand, Loic Le; Li, Christopher I. ; Li, Li ; Lindblom, Annika ; Martín, Vicente ; Milne, Roger L. ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Ogino, Shuji ; Ose, Jennifer ; Perduca, Vittorio ; Phipps, Amanda I. ; Platz, Elizabeth A. ; Potter, John D. ; Qu, Conghui ; Rennert, Gad ; Sakoda, Lori C. ; Schafmayer, Clemens ; Schoen, Robert E. ; Slattery, Martha L. ; Tangen, Catherine M. ; Ulrich, Cornelia M. ; Duijnhoven, Franzel J.B. van; Guelpen, Bethany Van; Visvanathan, Kala ; Vodicka, Pavel ; Vodickova, Ludmila ; Vymetalkova, Veronika ; Wang, Hansong ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Zheng, Wei ; Peters, Ulrike ; Gunter, Marc J. - \ 2020
Gastroenterology 158 (2020)5. - ISSN 0016-5085 - p. 1300 - 1312.e20.
CRC - GWAS - Risk Factors - Signal Transduction
Background & Aims: Human studies examining associations between circulating levels of insulin-like growth factor 1 (IGF1) and insulin-like growth factor binding protein 3 (IGFBP3) and colorectal cancer risk have reported inconsistent results. We conducted complementary serologic and Mendelian randomization (MR) analyses to determine whether alterations in circulating levels of IGF1 or IGFBP3 are associated with colorectal cancer development. Methods: Serum levels of IGF1 were measured in blood samples collected from 397,380 participants from the UK Biobank, from 2006 through 2010. Incident cancer cases and cancer cases recorded first in death certificates were identified through linkage to national cancer and death registries. Complete follow-up was available through March 31, 2016. For the MR analyses, we identified genetic variants associated with circulating levels of IGF1 and IGFBP3. The association of these genetic variants with colorectal cancer was examined with 2-sample MR methods using genome-wide association study consortia data (52,865 cases with colorectal cancer and 46,287 individuals without [controls]) Results: After a median follow-up period of 7.1 years, 2665 cases of colorectal cancer were recorded. In a multivariable-adjusted model, circulating level of IGF1 associated with colorectal cancer risk (hazard ratio per 1 standard deviation increment of IGF1, 1.11; 95% confidence interval [CI] 1.05–1.17). Similar associations were found by sex, follow-up time, and tumor subsite. In the MR analyses, a 1 standard deviation increment in IGF1 level, predicted based on genetic factors, was associated with a higher risk of colorectal cancer risk (odds ratio 1.08; 95% CI 1.03–1.12; P = 3.3 × 10–4). Level of IGFBP3, predicted based on genetic factors, was associated with colorectal cancer risk (odds ratio per 1 standard deviation increment, 1.12; 95% CI 1.06–1.18; P = 4.2 × 10–5). Colorectal cancer risk was associated with only 1 variant in the IGFBP3 gene region (rs11977526), which also associated with anthropometric traits and circulating level of IGF2. Conclusions: In an analysis of blood samples from almost 400,000 participants in the UK Biobank, we found an association between circulating level of IGF1 and colorectal cancer. Using genetic data from 52,865 cases with colorectal cancer and 46,287 controls, a higher level of IGF1, determined by genetic factors, was associated with colorectal cancer. Further studies are needed to determine how this signaling pathway might contribute to colorectal carcinogenesis.
Physical activity and risks of breast and colorectal cancer : a Mendelian randomisation analysis
Papadimitriou, Nikos ; Dimou, Niki ; Tsilidis, Konstantinos K. ; Banbury, Barbara ; Martin, Richard M. ; Lewis, Sarah J. ; Kazmi, Nabila ; Robinson, Timothy M. ; Albanes, Demetrius ; Aleksandrova, Krasimira ; Berndt, Sonja I. ; Timothy Bishop, D. ; Brenner, Hermann ; Buchanan, Daniel D. ; Bueno-de-Mesquita, Bas ; Campbell, Peter T. ; Castellví-Bel, Sergi ; Chan, Andrew T. ; Chang-Claude, Jenny ; Ellingjord-Dale, Merete ; Figueiredo, Jane C. ; Gallinger, Steven J. ; Giles, Graham G. ; Giovannucci, Edward ; Gruber, Stephen B. ; Gsur, Andrea ; Hampe, Jochen ; Hampel, Heather ; Harlid, Sophia ; Harrison, Tabitha A. ; Hoffmeister, Michael ; Hopper, John L. ; Hsu, Li ; María Huerta, José ; Huyghe, Jeroen R. ; Jenkins, Mark A. ; Keku, Temitope O. ; Kühn, Tilman ; Vecchia, Carlo La; Marchand, Loic Le; Li, Christopher I. ; Li, Li ; Lindblom, Annika ; Lindor, Noralane M. ; Lynch, Brigid ; Markowitz, Sanford D. ; Masala, Giovanna ; May, Anne M. ; Milne, Roger ; Monninkhof, Evelyn ; Moreno, Lorena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Perduca, Vittorio ; Pharoah, Paul D.P. ; Platz, Elizabeth A. ; Potter, John D. ; Rennert, Gad ; Riboli, Elio ; Sánchez, Maria Jose ; Schmit, Stephanie L. ; Schoen, Robert E. ; Severi, Gianluca ; Sieri, Sabina ; Slattery, Martha L. ; Song, Mingyang ; Tangen, Catherine M. ; Thibodeau, Stephen N. ; Travis, Ruth C. ; Trichopoulou, Antonia ; Ulrich, Cornelia M. ; Duijnhoven, Franzel J.B. van; Guelpen, Bethany Van; Vodicka, Pavel ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Peters, Ulrike ; Gunter, Marc J. ; Murphy, Neil - \ 2020
Nature Communications 11 (2020)1. - ISSN 2041-1723
Physical activity has been associated with lower risks of breast and colorectal cancer in epidemiological studies; however, it is unknown if these associations are causal or confounded. In two-sample Mendelian randomisation analyses, using summary genetic data from the UK Biobank and GWA consortia, we found that a one standard deviation increment in average acceleration was associated with lower risks of breast cancer (odds ratio [OR]: 0.51, 95% confidence interval [CI]: 0.27 to 0.98, P-value = 0.04) and colorectal cancer (OR: 0.66, 95% CI: 0.48 to 0.90, P-value = 0.01). We found similar magnitude inverse associations for estrogen positive (ER+ve) breast cancer and for colon cancer. Our results support a potentially causal relationship between higher physical activity levels and lower risks of breast cancer and colorectal cancer. Based on these data, the promotion of physical activity is probably an effective strategy in the primary prevention of these commonly diagnosed cancers.
A loop-mediated isothermal amplification (LAMP) assay based on unique markers derived from genotyping by sequencing data for rapid in planta diagnosis of Panama disease caused by Tropical Race 4 in banana
Ordóñez, N. ; Salacinas, M. ; Mendes, O. ; Seidl, M.F. ; Meijer, H.J.G. ; Schoen, C.D. ; Kema, G.H.J. - \ 2019
Plant Pathology 68 (2019)9. - ISSN 0032-0862 - p. 1682 - 1693.
DArTseq - field diagnostic - Fusarium odoratissimum - LAMP - Musa - Tropical Race 4
The socio-economic impact of Fusarium odoratissimum, which is colloquially called tropical race 4 (TR4), is escalating as this fungal pathogen spreads to new banana-growing areas. Hence, the development of simple, reliable and rapid detection technologies is indispensable for implementing quarantine measures. Here, a versatile loop-mediated isothermal amplification (LAMP) assay has been developed that is applicable under field and laboratory conditions. DNA markers unique to TR4 isolates were obtained by diversity arrays technology sequencing (DArTseq), a genotyping by sequencing technology that was conducted on 27 genotypes, comprising 24 previously reported vegetative compatibility groups (VCGs) and three TR4 isolates. The developed LAMP TR4 assay was successfully tested using 22 TR4 isolates and 45 non-target fungal and bacterial isolates, as well as on infected plants under greenhouse and field conditions. The detection limit was 1 pg µL−1 pure TR4 DNA or 102 copies plasmid-localized TR4 unique sequence (SeqA) per reaction, which was not affected by background DNA in complex samples. The LAMP TR4 assay offers a powerful tool for the routine and unambiguous identification of banana plants infected with TR4, contributing to advanced diagnosis in field situations and monitoring of fusarium wilt.
Plasma citrulline concentration, a marker for intestinal functionality, reflects exercise intensity in healthy young men
Kartaram, Shirley ; Mensink, Marco ; Teunis, Marc ; Schoen, Eric ; Witte, Gerrit ; Janssen Duijghuijsen, Lonneke ; Verschuren, Martie ; Mohrmann, Karin ; M'Rabet, Laura ; Knipping, Karen ; Wittink, Harriet ; Helvoort, Ardy van; Garssen, Johan ; Witkamp, Renger ; Pieters, Raymond ; Norren, Klaske van - \ 2019
Clinical Nutrition 38 (2019)5. - ISSN 0261-5614 - p. 2251 - 2258.
Citrulline - Exercise intensity - Glutamine - Intestinal fatty acid binding protein - Intestinal function
Background & aims: Plasma citrulline concentration is considered to be a marker for enterocyte metabolic mass and to reflect its reduction as may occur during intestinal dysfunction. Strenuous exercise can act as a stressor to induce small intestinal injury. Our previous studies suggest that this comprises the intestinal ability to produce citrulline from a glutamine-rich protein bolus. In this study we investigated the effects of different exercise intensities and hydration state on citrulline and iFABP levels following a post-exercise glutamine bolus in healthy young men. Methods: Fifteen healthy young men (20–35 yrs, VO2 max 56.9 ± 3.9 ml kg−1 min−1) performed in a randomly assigned cross-over design, a rest (protocol 1) and four cycle ergometer protocols. The volunteers cycled submaximal at different percentages of their individual pre-assessed maximum workload (Wmax): 70% Wmax in hydrated (protocol 2) and dehydrated state (protocol 3), 50% Wmax (protocol 4) and intermittent 85/55% Wmax in blocks of 2 min (protocol 5). Immediately after 1 h exercise or rest, subjects were given a glutamine bolus with added alanine as an iso-caloric internal standard (7.5 g of each amino acid). Blood samples were collected before, during and after rest or exercise, up to 24 h post onset of the experiment. Amino acids and urea were analysed as metabolic markers, creatine phosphokinase and iFABP as markers of muscle and intestinal damage, respectively. Data were analysed using a multilevel mixed linear statistical model. p values were corrected for multiple testing. Results: Citrulline levels already increased before glutamine supplementation during normal hydrated exercise, while this was not observed in the dehydrated and rest protocols. The low intensity exercise protocol (50% Wmax) showed the highest increase in citrulline levels both during exercise (43.83 μmol/L ± 2.63 (p < 0.001)) and after glutamine consumption (50.54 μmol/L ± 2.62) compared to the rest protocol (28.97 μmol/L ± 1.503 and 41.65 μmol/L ± 1.96, respectively, p < 0.05). However, following strenuous exercise at 70% Wmax in the dehydrated state, citrulline levels did not increase during exercise and less after the glutamine consumption when compared to the resting condition and hydrated protocols. In line with this, serum iFABP levels were the highest with the strenuous dehydrated protocol (1443.72 μmol/L ± 249.9, p < 0.001), followed by the high intensity exercise at 70% Wmax in the hydrated condition. Conclusions: Exercise induces an increase in plasma citrulline, irrespective of a glutamine bolus. The extent to which this occurs is dependent on exercise intensity and the hydration state of the subjects. The same holds true for both the post-exercise increase in citrulline levels following glutamine supplementation and serum iFABP levels. These data indicate that citrulline release during exercise and after an oral glutamine bolus might be dependent on the intestinal health state and therefore on intestinal functionality. Glutamine is known to play a major role in intestinal physiology and the maintenance of gut health and barrier function. Together, this suggests that in clinical practice, a glutamine bolus to increase citrulline levels after exercise might be preferable compared to supplementing citrulline itself. To our knowledge this is the first time that exercise workload-related effects on plasma citrulline are reported in relation to intestinal damage.
|Identification and functional characterisation of host interactions of the potato CC-NB-LRR Rx1
Sukarta, O.C.A. ; Slootweg, E.J. ; Zheng, Qi ; Schoen, Ruben ; Pomp, H. ; Roosien, J. ; Smant, G. ; Goverse, A. - \ 2018
The potato Rx1 is an intracellular Nucleotide-binding Leucine Rich Repeat (NLR) immune receptor with an archetypical N-terminal coiled-coil (CC) domain. It confers extreme resistance against Potato Virus X (PVX) by gene-specific recognition of the viral coat protein (CP). Recent findings point to a role of Rx1 in the nucleus whereby it could directly bind host genetic material, though it remains unclear how this process eventually leads to defence. A possibility is that Rx1 recruits other host factors, for example via the CC domain, which is predicted to act as scaffolds for nuclear signalling. Here, we used the CC domains of Rx1 and the Rx1-like protein Gpa2 (mediates defence against the nematode Globodera pallida) as baits in a Co-IP/MS analysis after cell fractionation to co-purify putative interactors from Nicotiana benthamiana. Five hits (designated Rp01-Rp05) were further prioritized as candidate Rx1/Gpa2 interacting proteins. Similar pull-down experiments confirmed complex formation with the full-length immune receptors in plantae. Interestingly, co-expression of Rp05 alters the subcellular distribution of the Rx1-CC domain, hinting its role in Rx1-function. Transient overexpression experiments confirm that Rp05 could in fact potentiate defense against PVX. Interestingly, however, this occurs independently of Rx1. We substantiated this model by demonstrating that Rp05 could influence HR-responses by other NLR proteins (e.g. Gpa2, Sw5A/B and Mi-1) indicating that it may be a common downstream component in immune signaling. Currently, we focus on elucidating the detailed molecular underpinning of Rp05 function in R-gene mediated resistances using Rx1 as the principal model system.
|Genotyping by sequencing to identify diagnostic regions in Fusarium oxysporum f. sp. cubense Tropical Race 4 and applications in disease epidemiology
Salacinas, Maricar ; Ordonez, N. ; Mendes, O. ; Schoen, C.D. ; Seidl, M.F. ; Meijer, H.J.G. ; Kema, G.H.J. - \ 2018
|Innovative detection methods to support plant health diagnostics
Bonants, P.J.M. ; Houwers, I.M. ; Dullemans, A.M. ; Griekspoor, Y. ; Mendes, O. ; Gent-Pelzer, M.P.E. van; Vlugt, R.A.A. van der; Bergervoet, J.H.W. ; Schoen, C.D. ; Wolf, J.M. van der; Lee, T.A.J. van der - \ 2018
Automated DNA purification and multiplexed lamp assay preparation on a centrifugal microfluidic 'Lab-on-a-Disc' platform
Kinahan, David J. ; Julius, Lourdes A.N. ; Schoen, Cor ; Dreo, Tanja ; Ducree, Jens - \ 2018
In: 2018 IEEE Micro Electro Mechanical Systems, MEMS 2018. - Institute of Electrical and Electronics Engineers Inc. - ISBN 9781538647820 - p. 1134 - 1137.
This work presents a rotational-pulse actuated micro-fluidic cartridge enabling automated detection of plant pathogens on a compact device towards point-of-use monitoring of food safety. This highly integrated 'Lab-on-a-Disc' (LoaD) system first runs the sample over a stationary phase of silica beads, followed by ethanol (EtOH) wash and final elution of DNA. The eluate is then homogenized using 'shake mode' agitation, accurately metered and then mixed with reagents for loop-mediated isothermal amplification (LAMP). We successfully purify plant DNA and demonstrate on-disc quantitative LAMP amplification.
Loop-mediated isothermal amplification (LAMP) shield for Arduino DNA detection
Velders, Aldrik H. ; Schoen, Cor ; Saggiomo, Vittorio - \ 2018
BMC Research Notes 11 (2018). - ISSN 1756-0500
Arduino instruments - Loop mediated isothermal amplification - Nucleic acid detection - Portable
Objective: Loop-mediated isothermal amplification (LAMP) of DNA is gaining relevance as a method to detect nucleic acids, as it is easier, faster, and more powerful than conventional Polymerase Chain Reaction. However, LAMP is still mostly used in laboratory settings, because of the lack of a cheap and easy, one-button device that can perform LAMP experiments. Results: Here we show how to build and program an Arduino shield for a LAMP and detection of DNA. The here described Arduino Shield is cheap, easy to assemble, to program and use, it is battery operated and the detection of DNA is done by naked-eye so that it can be used in field.
Fungal communities including plant pathogens in near surface air are similar across northwestern Europe
Nicolaisen, Mogens ; West, Jonathan S. ; Sapkota, Rumakanta ; Canning, Gail G.M. ; Schoen, Cor ; Justesen, Annemarie F. - \ 2017
Frontiers in Microbiology 8 (2017)SEP. - ISSN 1664-302X
Air sampling - Airborne - Metabarcoding - Plant pathogen - Urban
Information on the diversity of fungal spores in air is limited, and also the content of airborne spores of fungal plant pathogens is understudied. In the present study, a total of 152 air samples were taken from rooftops at urban settings in Slagelse, DK, Wageningen NL, and Rothamsted, UK together with 41 samples from above oilseed rape fields in Rothamsted. Samples were taken during 10-day periods in spring and autumn, each sample representing 1 day of sampling. The fungal content of samples was analyzed by metabarcoding of the fungal internal transcribed sequence 1 (ITS1) and by qPCR for specific fungi. The metabarcoding results demonstrated that season had significant effects on airborne fungal communities. In contrast, location did not have strong effects on the communities, even though locations were separated by up to 900 km. Also, a number of plant pathogens had strikingly similar patterns of abundance at the three locations. Rooftop samples were more diverse than samples taken above fields, probably reflecting greater mixing of air from a range of microenvironments for the rooftop sites. Pathogens that were known to be present in the crop were also found in air samples taken above the field. This paper is one of the first detailed studies of fungal composition in air with the focus on plant pathogens and shows that it is possible to detect a range of pathogens in rooftop air samplers using metabarcoding.
|Highly scalable combinatorial mixing of samples with target-specific primers for rapid pathogen detection on a centrifugal platform
Chung, D.W.Y. ; Kinahan, D.J. ; Schoen, C. ; Dreo, T. ; Ducrée, J. - \ 2016
In: 20th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2016. - Chemical and Biological Microsystems Society - ISBN 9780979806490 - p. 848 - 849.
In application areas such as crop genotyping, plant diagnostics, pharmaceuticals and forensics, screening a large number of M samples for specific responses to a library of N active agents in a time- and cost-efficient manner is of critical importance. Parameters of interest include response of cells to a specific drug compound, identification of specific genes or plant pathogens in crops using DNA markers and DNA traceability for food safety. The cost of reagents as well as the liquid handling ro-botics required to perform the enormous number of pipetting steps severely hamper the proliferation of such key technologies into smaller laboratories.
Development and application of loop-mediated isothermal amplification (LAMP) for detection of Plasmopara viticola
Kong, X. ; Qin, W. ; Xiaoqing, X. ; Kong, F. ; Schoen, C.D. ; Feng, J. ; Wang, Z. ; Zhang, H. - \ 2016
Scientific Reports 6 (2016). - ISSN 2045-2322 - 9 p.
A rapid LAMP (loop-mediated isothermal amplification) detection method was developed on the basis of the ITS sequence of P. viticola, the major causal agent of grape downy mildew. Among the 38 fungal and oomycete species tested, DNA isolated exclusively from P. viticola resulted in a specific product after LAMP amplification. This assay had high sensitivity and was able to detect the presence of less than 33 fg of genomic DNA per 25-μL reaction within 30 min. The infected leaves may produce sporangia that serve as a secondary inoculum. The developed LAMP assay is efficient for estimating the latent infection of grape leaves by P. viticola. When combined with the rapid and simple DNA extraction method, this assay’s total detection time is shortened to approximately one hour; therefore it is suitable for on-site detection of latent infection in the field. The sporangia levels in the air are strongly associated with disease severity. The LAMP method was also demonstrated to be able to estimate the level of sporangia released in the air in a certain period. This assay should make disease forecasting more accurate and rapid and should be helpful in decision-making regarding the control of grape downy mildew.
Multiplex detection and identification of Phytophthora spp. using target-specific primer extension and Luminex xTAG technology
Kostov, K. ; Verstappen, E.C.P. ; Bergervoet, J.H.W. ; Weerdt, M. de; Schoen, C.D. ; Slavov, S. ; Bonants, P.J.M. - \ 2016
Plant Pathology 65 (2016)6. - ISSN 0032-0862 - p. 1008 - 1021.
Detection - Identification - Luminex - Multiplex - Phytophthora - TSPE
There are more than 100 species that belong to the fungus-like genus Phytophthora, many of which can cause severe damage to plants in both natural and agricultural ecosystems. The availability of techniques for detection and identification are crucial for monitoring and control of these pathogens. In recent years, new methods using molecular approaches have been developed. However, the majority of them are designed to detect single Phytophthora species. Techniques that are able to target multiple species in one sample would offer advantages, especially for the assessment of Phytophthora diversity in the environment. This paper describes a multiplex assay for simultaneous detection and identification of 26 members of Phytophthora down to species level and another 22 to clade or subclade level through target-specific primer extension (TSPE) and the Luminex xTAG array detection system. The assay starts with PCR amplification of two genomic regions, ITS and coxI, followed by a multiplex TSPE reaction with clade-, subclade- and species-specific probes. As a result, biotin-dCTP labelled products are generated and subsequently detected through hybridization with a set of anti-TAG coupled, colour-coded paramagnetic beads. The specificity of the method has been tested using DNA extracts from over 400 isolates representing 110 Phytophthora species and subspecies. The sensitivity and robustness have been determined by the use of DNA mixtures, dilution series and environmental samples. Thus the developed technique allows simultaneous identification of multiple Phytophthora species, particularly useful for the detection of these pathogens in environmental samples such as soil, water and plant tissue.
|Nematocure : kennisconcept voor duurzame wering van nematoden in agroproductiesystemen
Overbeek, L.S. van; Elberse, I. ; Korthals, G.W. ; Molendijk, L.P.G. ; Nijhuis, E.H. ; Os, G.J. van; Schoen, C.D. ; Visser, J.H.M. ; Wurff, A.W.G. van der - \ 2015
In: Kennisbasisprogramma Duurzaam Agroketens Wageningen UR - p. 33 - 38.
Plantenziektenkundig laboratorium voor elke glastuinbouwteler : On-site detectie voor snel opsporen pathogenen
Bezemer, J. ; Schoen, C.D. - \ 2015
Onder Glas 12 (2015)3. - p. 24 - 25.
glastuinbouw - groenten - tomaten - afwijkingen, planten - tests - testinstallaties - innovaties - detectie - technieken - greenhouse horticulture - vegetables - tomatoes - plant disorders - tests - test rigs - innovations - detection - techniques
Een teler heeft een virus in de kas, maar hij weet niet welk virus precies? Hij heeft last van een aaltje en wil uitzoeken welk aaltje het is? Zijn de vlekjes veroorzaakt door Botrytis of door meeldauw? Binnenkort zorgen telers zelf voor antwoorden op deze vragen. Snel en goedkoop, in de kas.
Quirky patterns in time-series of estimates of recruitment could be artefacts
Dickey-Collas, M. ; Hintzen, N.T. ; Nash, R.D.M. ; Schoen, P.J. ; Payne, M.R. - \ 2015
ICES Journal of Marine Science 72 (2015)1. - ISSN 1054-3139 - p. 111 - 116.
stock-assessment - marine fishes - assessment models - reference points - atlantic - variability - abundance - sea - populations - management
The accessibility of databases of global or regional stock assessment outputs is leading to an increase in meta-analysis of the dynamics of fish stocks. In most of these analyses, each of the time-series is generally assumed to be directly comparable. However, the approach to stock assessment employed, and the associated modelling assumptions, can have an important influence on the characteristics of each time-series. We explore this idea by investigating recruitment time-series with three different recruitment parameterizations: a stock–recruitment model, a random-walk time-series model, and non-parametric “free” estimation of recruitment. We show that the recruitment time-series is sensitive to model assumptions and this can impact reference points in management, the perception of variability in recruitment and thus undermine meta-analyses. The assumption of the direct comparability of recruitment time-series in databases is therefore not consistent across or within species and stocks. Caution is therefore required as perhaps the characteristics of the time-series of stock dynamics may be determined by the model used to generate them, rather than underlying ecological phenomena. This is especially true when information about cohort abundance is noisy or lacking.
Rapid identification and detection of pathogenic Fungi by padlock probes
Tsui, C.K.M. ; Wang, B. ; Schoen, C.D. ; Hamelin, R.C. - \ 2013
In: Laboratory Protocols in Fungal Biology / Kumar Gupta, Vijai, Tuohy, Maria G., Ayyachamy, Manimaran, Turner, Kevin M., O'Donovan, Anthonia, New York : Springer Science + Business Media (Fungal Biology ) - ISBN 9781461423553 - p. 505 - 517.
Fungi are important pathogens of human diseases, as well as to agricultural crop and trees. Molecular diagnostics can detect diseases early, and improve identification accuracy and follow-up disease management. The use of padlock probe is effective to facilitate these detections and pathogen identification quickly and accurately. In this chapter we describe three diagnostic assays that utilize padlock probes in combination with various technologies for the detection of pathogenic fungi.