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17 results on '"Bruggeling, Carlijn E"'

1. The human gut microbiome and health inequities

Author

Amato, Katherine R., Arrieta, Marie-Claire, Azad, Meghan B., Bailey, Michael T., Broussard, Josiane L., Bruggeling, Carlijn E., Claud, Erika C., Costello, Elizabeth K., Davenport, Emily R., Dutilh, Bas E., Ewald, Holly A. Swain, Ewald, Paul, Hanlon, Erin C., Julion, Wrenetha, Keshavarzian, Ali, Maurice, Corinne F., Miller, Gregory E., Preidis, Geoffrey A., Segurel, Laure, Singer, Burton, Subramanian, Sathish, Zhao, Liping, and Kuzawa, Christopher W.

Published
2021

2. Bacterial oncotraits rather than spatial organization are associated with dysplasia in ulcerative colitis

Author

Bruggeling, Carlijn E, primary, te Groen, Maarten, additional, Garza, Daniel R, additional, van Heeckeren tot Overlaer, Famke, additional, Krekels, Joyce P M, additional, Sulaiman, Basma-Chick, additional, Karel, Davy, additional, Rulof, Athreyu, additional, Schaaphok, Anne R, additional, Hornikx, Daniel L A H, additional, Nagtegaal, Iris D, additional, Dutilh, Bas E, additional, Hoentjen, Frank, additional, and Boleij, Annemarie, additional

Published
2023
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3. Bacterial Oncotraits Rather than Spatial Organization Are Associated with Dysplasia in Ulcerative Colitis

Author

Bruggeling, Carlijn E, Te Groen, Maarten, Garza, Daniel R, van Heeckeren Tot Overlaer, Famke, Krekels, Joyce P M, Sulaiman, Basma-Chick, Karel, Davy, Rulof, Athreyu, Schaaphok, Anne R, Hornikx, Daniel L A H, Nagtegaal, Iris D, Dutilh, Bas E, Hoentjen, Frank, Boleij, Annemarie, Bruggeling, Carlijn E, Te Groen, Maarten, Garza, Daniel R, van Heeckeren Tot Overlaer, Famke, Krekels, Joyce P M, Sulaiman, Basma-Chick, Karel, Davy, Rulof, Athreyu, Schaaphok, Anne R, Hornikx, Daniel L A H, Nagtegaal, Iris D, Dutilh, Bas E, Hoentjen, Frank, and Boleij, Annemarie

Abstract

Background and Aims: Colonic bacterial biofilms are frequently present in ulcerative colitis [UC] and may increase dysplasia risk through pathogens expressing oncotraits. This prospective cohort study aimed to determine [1] the association of oncotraits and longitudinal biofilm presence with dysplasia risk in UC, and [2] the relation of bacterial composition with biofilms and dysplasia risk. Methods: Faeces and left- and right-sided colonic biopsies were collected from 80 UC patients and 35 controls. Oncotraits [FadA of Fusobacterium, BFT of Bacteroides fragilis, colibactin [ClbB] and Intimin [Eae] of Escherichia coli] were assessed in faecal DNA with multiplex quantitative polymerase chain reaction [qPCR]. Biopsies were screened for biofilms [n=873] with 16S rRNA fluorescent in situ hybridiation. Shotgun metagenomic sequencing [n=265], and ki67-immunohistochemistry were performed. Associations were determined with a mixed-effects regression model. Results: Biofilms were highly prevalent in UC patients [90.8%] with a median persistence of 3 years (interquartile range [IQR] 2-5 years). Biofilm-positive biopsies showed increased epithelial hypertrophy [p=0.025] and a reduced Shannon diversity independent of disease status [p=0.015], but were not significantly associated with dysplasia in UC: adjusted odds ratio [aOR] 1.45, 95% confidence interval [CI] 0.63-3.40. In contrast, ClbB independently associated with dysplasia [aOR 7.16, 95% CI 1.75-29.28], and FadA and Fusobacteriales were associated with a decreased dysplasia risk in UC [aOR 0.23, 95% CI 0.06-0.83, p<0.01]. Conclusions: Biofilms are a hallmark of UC; however, because of their high prevalence are a poor biomarker for dysplasia. In contrast, colibactin presence and FadA absence independently associate with dysplasia in UC and might therefore be valuable biomarkers for future risk stratification and intervention strategies.

Published
2023

4. Bacterial Oncotraits Rather than Spatial Organization Are Associated with Dysplasia in Ulcerative Colitis

Author

Theoretical Biology and Bioinformatics, Sub Bioinformatics, Bruggeling, Carlijn E, Te Groen, Maarten, Garza, Daniel R, van Heeckeren Tot Overlaer, Famke, Krekels, Joyce P M, Sulaiman, Basma-Chick, Karel, Davy, Rulof, Athreyu, Schaaphok, Anne R, Hornikx, Daniel L A H, Nagtegaal, Iris D, Dutilh, Bas E, Hoentjen, Frank, Boleij, Annemarie, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Bruggeling, Carlijn E, Te Groen, Maarten, Garza, Daniel R, van Heeckeren Tot Overlaer, Famke, Krekels, Joyce P M, Sulaiman, Basma-Chick, Karel, Davy, Rulof, Athreyu, Schaaphok, Anne R, Hornikx, Daniel L A H, Nagtegaal, Iris D, Dutilh, Bas E, Hoentjen, Frank, and Boleij, Annemarie

Published
2023

5. BACTERIAL ONCOTRAITS BUT NOT BIOFILMS ARE ASSOCIATED WITH DYSPLASIA IN ULCERATIVE COLITIS

Author

Bruggeling, Carlijn E., primary, te Groen, Maarten, additional, Garza, Daniel R., additional, van Heeckeren tot Overlaer, Famke, additional, Krekels, Joyce P.M., additional, Sulaiman, Basma-Chick, additional, Karel, Davy, additional, Rulof, Athreyu, additional, Schaaphok, Anne R., additional, Hornikx, Daniel L.A.H., additional, Nagtegaal, Iris D., additional, Dutilh, Bas E., additional, Hoentjen, Frank, additional, and Boleij, Annemarie, additional

Published
2022
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7. The human gut microbiome and health inequities

Author

Amato, Katherine R, Arrieta, Marie-Claire, Azad, Meghan B, Bailey, Michael T, Broussard, Josiane L, Bruggeling, Carlijn E, Claud, Erika C, Costello, Elizabeth K, Davenport, Emily R, Dutilh, Bas E, Swain Ewald, Holly A, Ewald, Paul, Hanlon, Erin C, Julion, Wrenetha, Keshavarzian, Ali, Maurice, Corinne F, Miller, Gregory E, Preidis, Geoffrey A, Segurel, Laure, Singer, Burton, Subramanian, Sathish, Zhao, Liping, Kuzawa, Christopher W, Amato, Katherine R, Arrieta, Marie-Claire, Azad, Meghan B, Bailey, Michael T, Broussard, Josiane L, Bruggeling, Carlijn E, Claud, Erika C, Costello, Elizabeth K, Davenport, Emily R, Dutilh, Bas E, Swain Ewald, Holly A, Ewald, Paul, Hanlon, Erin C, Julion, Wrenetha, Keshavarzian, Ali, Maurice, Corinne F, Miller, Gregory E, Preidis, Geoffrey A, Segurel, Laure, Singer, Burton, Subramanian, Sathish, Zhao, Liping, and Kuzawa, Christopher W

Abstract

Individuals who are minoritized as a result of race, sexual identity, gender, or socioeconomic status experience a higher prevalence of many diseases. Understanding the biological processes that cause and maintain these socially driven health inequities is essential for addressing them. The gut microbiome is strongly shaped by host environments and affects host metabolic, immune, and neuroendocrine functions, making it an important pathway by which differences in experiences caused by social, political, and economic forces could contribute to health inequities. Nevertheless, few studies have directly integrated the gut microbiome into investigations of health inequities. Here, we argue that accounting for host-gut microbe interactions will improve understanding and management of health inequities, and that health policy must begin to consider the microbiome as an important pathway linking environments to population health.

Published
2021

8. Optimized bacterial DNA isolation method for microbiome analysis of human tissues

Author

Theoretical Biology and Bioinformatics, Sub Bioinformatics, Bruggeling, Carlijn E, Garza, Daniel R, Achouiti, Soumia, Mes, Wouter, Dutilh, Bas E, Boleij, Annemarie, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Bruggeling, Carlijn E, Garza, Daniel R, Achouiti, Soumia, Mes, Wouter, Dutilh, Bas E, and Boleij, Annemarie

Published
2021

9. The human gut microbiome and health inequities

Author

Theoretical Biology and Bioinformatics, Sub Bioinformatics, Amato, Katherine R, Arrieta, Marie-Claire, Azad, Meghan B, Bailey, Michael T, Broussard, Josiane L, Bruggeling, Carlijn E, Claud, Erika C, Costello, Elizabeth K, Davenport, Emily R, Dutilh, Bas E, Swain Ewald, Holly A, Ewald, Paul, Hanlon, Erin C, Julion, Wrenetha, Keshavarzian, Ali, Maurice, Corinne F, Miller, Gregory E, Preidis, Geoffrey A, Segurel, Laure, Singer, Burton, Subramanian, Sathish, Zhao, Liping, Kuzawa, Christopher W, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Amato, Katherine R, Arrieta, Marie-Claire, Azad, Meghan B, Bailey, Michael T, Broussard, Josiane L, Bruggeling, Carlijn E, Claud, Erika C, Costello, Elizabeth K, Davenport, Emily R, Dutilh, Bas E, Swain Ewald, Holly A, Ewald, Paul, Hanlon, Erin C, Julion, Wrenetha, Keshavarzian, Ali, Maurice, Corinne F, Miller, Gregory E, Preidis, Geoffrey A, Segurel, Laure, Singer, Burton, Subramanian, Sathish, Zhao, Liping, and Kuzawa, Christopher W

Published
2021

10. Microsatellite instability screening in colorectal adenomas to detect Lynch syndrome patients?: A systematic review and meta-analysis

Author

Dabir, Parag D, Bruggeling, Carlijn E, van der Post, Rachel S, Dutilh, Bas E, Hoogerbrugge, Nicoline, Ligtenberg, Marjolijn J L, Boleij, Annemarie, Nagtegaal, Iris D, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Sub Bioinformatics, and Theoretical Biology and Bioinformatics

Subjects
POLYPS, Male, endocrine system diseases, Colorectal cancer, Review Article, HEREDITARY, Gastroenterology, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], Genetics (clinical), Brain Neoplasms, Middle Aged, CANCER, Lynch syndrome, DEFICIENCY, Meta-analysis, HIGH-GRADE DYSPLASIA, Cohort, YOUNG-PATIENTS, Colorectal Neoplasms, Hereditary Nonpolyposis/diagnosis, Female, Microsatellite Instability, DNA mismatch repair, Biomarkers, Tumor/genetics, Colorectal Neoplasms, EXPRESSION, Adult, Adenoma, medicine.medical_specialty, Coronacrisis-Taverne, Adenoma/diagnosis, Context (language use), Rare cancers Radboud Institute for Molecular Life Sciences [Radboudumc 9], Neoplastic Syndromes, Hereditary, Internal medicine, Biomarkers, Tumor, Genetics, medicine, Humans, GERMLINE MUTATION, business.industry, SERRATED LESIONS, Comment, Microsatellite instability, medicine.disease, Colorectal Neoplasms, Hereditary Nonpolyposis, digestive system diseases, stomatognathic diseases, MISMATCH REPAIR PROTEINS, business
Abstract

Contains fulltext : 218215pub.pdf (Publisher’s version ) (Closed access) The colorectal cancer spectrum has changed due to population screening programs, with a shift toward adenomas and early cancers. Whether it would be a feasible option to test these adenomas for detection of Lynch syndrome (LS) patients is unclear. Through meta-analysis and systematic review, risk factors for DNA mismatch repair deficiency (dMMR) and microsatellite instability (MSI) in adenomas were identified in LS and unselected patient cohorts. Data were extracted for patient age and MMR variant together with adenoma type, grade, size, and location. A total of 41 studies were included, and contained more than 519 LS patients and 1698 unselected patients with 1142 and 2213 adenomas respectively. dMMR/MSI was present in 69.5% of conventional adenomas in LS patients, compared with 2.8% in unselected patients. In the LS cohort, dMMR/MSI was more frequently present in patients older than 60 years (82% versus 54%). dMMR/MSI was also more common in villous adenomas (84%), adenomas over 1 cm (81%), and adenomas with high grade dysplasia (88%). No significant differences were observed for dMMR/MSI in relation to MMR variants and location of adenomas. In the context of screening, we conclude that detection of dMMR/MSI in conventional adenomas of unselected patients is uncommon and might be considered as indication for LS testing. Within the LS cohort, 69.5% of LS patients could have been detected through dMMR/MSI screening of their conventional adenomas.

Published
2020

11. Microsatellite instability screening in colorectal adenomas to detect Lynch syndrome patients?: A systematic review and meta-analysis

Author

Sub Bioinformatics, Theoretical Biology and Bioinformatics, Dabir, Parag D, Bruggeling, Carlijn E, van der Post, Rachel S, Dutilh, Bas E, Hoogerbrugge, Nicoline, Ligtenberg, Marjolijn J L, Boleij, Annemarie, Nagtegaal, Iris D, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Dabir, Parag D, Bruggeling, Carlijn E, van der Post, Rachel S, Dutilh, Bas E, Hoogerbrugge, Nicoline, Ligtenberg, Marjolijn J L, Boleij, Annemarie, and Nagtegaal, Iris D

Published
2020

12. The human gutmicrobiome and health inequities.

Author

Amato, Katherine R., Arrieta, Marie-Claire, Azad, Meghan B., Bailey, Michael T., Broussard, Josiane L., Bruggeling, Carlijn E., Claud, Erika C., Costello, Elizabeth K., Davenport, Emily R., Dutilh, Bas E., Ewald, Holly A. Swain, Ewald, Paul, Hanlon, Erin C., Julion, Wrenetha, Keshavarzian, Ali, Maurice, Corinne F., Miller, Gregory E., Preidis, Geoffrey A., Segurel, Laure, and Singer, Burton

Subjects
HEALTH equity, GUT microbiome, HEALTH policy, POPULATION health, GENDER
Abstract

Individuals who are minoritized as a result of race, sexual identity, gender, or socioeconomic status experience a higher prevalence of many diseases. Understanding the biological processes that cause and maintain these socially driven health inequities is essential for addressing them. The gut microbiome is strongly shaped by host environments and affects host metabolic, immune, and neuroendocrine functions, making it an important pathway by which differences in experiences caused by social, political, and economic forces could contribute to health inequities. Nevertheless, few studies have directly integrated the gut microbiome into investigations of health inequities. Here, we argue that accounting for host-gut microbe interactions will improve understanding and management of health inequities, and that health policy must begin to consider the microbiome as an important pathway linking environments to population health. [ABSTRACT FROM AUTHOR]

Published
2021
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14. CRISPR/Cas9-Mediated Genome Editing of Herpesviruses Limits Productive and Latent Infections

Author

van Diemen, Ferdy R., Kruse, Elisabeth M., Hooykaas, Marjolein J G, Bruggeling, Carlijn E., Schürch, Anita C., van Ham, Petra M., Imhof, Saskia M., Nijhuis, Monique, Wiertz, Emmanuel J H J, Lebbink, Robert Jan, van Diemen, Ferdy R., Kruse, Elisabeth M., Hooykaas, Marjolein J G, Bruggeling, Carlijn E., Schürch, Anita C., van Ham, Petra M., Imhof, Saskia M., Nijhuis, Monique, Wiertz, Emmanuel J H J, and Lebbink, Robert Jan

Published
2016

15. CRISPR/Cas9-Mediated Genome Editing of Herpesviruses Limits Productive and Latent Infections

Author

MMB Research line 3a, Infection & Immunity, MMB, MS Oogheelkunde, van Diemen, Ferdy R., Kruse, Elisabeth M., Hooykaas, Marjolein J G, Bruggeling, Carlijn E., Schürch, Anita C., van Ham, Petra M., Imhof, Saskia M., Nijhuis, Monique, Wiertz, Emmanuel J H J, Lebbink, Robert Jan, MMB Research line 3a, Infection & Immunity, MMB, MS Oogheelkunde, van Diemen, Ferdy R., Kruse, Elisabeth M., Hooykaas, Marjolein J G, Bruggeling, Carlijn E., Schürch, Anita C., van Ham, Petra M., Imhof, Saskia M., Nijhuis, Monique, Wiertz, Emmanuel J H J, and Lebbink, Robert Jan

Published
2016

17. Microsatellite instability screening in colorectal adenomas to detect Lynch syndrome patients? A systematic review and meta-analysis.

Author

Dabir PD, Bruggeling CE, van der Post RS, Dutilh BE, Hoogerbrugge N, Ligtenberg MJL, Boleij A, and Nagtegaal ID

Subjects
Adenoma diagnosis, Adult, Colorectal Neoplasms, Hereditary Nonpolyposis diagnosis, Female, Humans, Male, Middle Aged, Adenoma genetics, Biomarkers, Tumor genetics, Colorectal Neoplasms, Hereditary Nonpolyposis genetics, Microsatellite Instability
Abstract

The colorectal cancer spectrum has changed due to population screening programs, with a shift toward adenomas and early cancers. Whether it would be a feasible option to test these adenomas for detection of Lynch syndrome (LS) patients is unclear. Through meta-analysis and systematic review, risk factors for DNA mismatch repair deficiency (dMMR) and microsatellite instability (MSI) in adenomas were identified in LS and unselected patient cohorts. Data were extracted for patient age and MMR variant together with adenoma type, grade, size, and location. A total of 41 studies were included, and contained more than 519 LS patients and 1698 unselected patients with 1142 and 2213 adenomas respectively. dMMR/MSI was present in 69.5% of conventional adenomas in LS patients, compared with 2.8% in unselected patients. In the LS cohort, dMMR/MSI was more frequently present in patients older than 60 years (82% versus 54%). dMMR/MSI was also more common in villous adenomas (84%), adenomas over 1 cm (81%), and adenomas with high grade dysplasia (88%). No significant differences were observed for dMMR/MSI in relation to MMR variants and location of adenomas. In the context of screening, we conclude that detection of dMMR/MSI in conventional adenomas of unselected patients is uncommon and might be considered as indication for LS testing. Within the LS cohort, 69.5% of LS patients could have been detected through dMMR/MSI screening of their conventional adenomas.

Published
2020
Full Text
View/download PDF

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