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Tang L, Swedlund B, Dupont S, Harland C, Costa Monteiro Moreira G, Durkin K, Artesi M, Mullaart E, Sartelet A, Karim L, Coppieters W, Georges M, Charlier C. GWAS reveals determinants of mobilization rate and dynamics of an active endogenous retrovirus of cattle. Nat Commun 2024; 15:2154. [PMID: 38461177 PMCID: PMC10924933 DOI: 10.1038/s41467-024-46434-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/22/2024] [Indexed: 03/11/2024] Open
Abstract
Five to ten percent of mammalian genomes is occupied by multiple clades of endogenous retroviruses (ERVs), that may count thousands of members. New ERV clades arise by retroviral infection of the germline followed by expansion by reinfection and/or retrotransposition. ERV mobilization is a source of deleterious variation, driving the emergence of ERV silencing mechanisms, leaving "DNA fossils". Here we show that the ERVK[2-1-LTR] clade is still active in the bovine and a source of disease-causing alleles. We develop a method to measure the rate of ERVK[2-1-LTR] mobilization, finding an average of 1 per ~150 sperm cells, with >10-fold difference between animals. We perform a genome-wide association study and identify eight loci affecting ERVK[2-1-LTR] mobilization. We provide evidence that polymorphic ERVK[2-1-LTR] elements in four of these loci cause the association. We generate a catalogue of full length ERVK[2-1-LTR] elements, and show that it comprises 15% of C-type autonomous elements, and 85% of D-type non-autonomous elements lacking functional genes. We show that >25% of the variance of mobilization rate is determined by the number of C-type elements, yet that de novo insertions are dominated by D-type elements. We propose that D-type elements act as parasite-of-parasite gene drives that may contribute to the observed demise of ERV elements.
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Affiliation(s)
- Lijing Tang
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
| | - Benjamin Swedlund
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Sébastien Dupont
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Chad Harland
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- Livestock Improvement Corporation, Hamilton, New Zealand
| | | | - Keith Durkin
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- Laboratory of Human Genetics, GIGA & Faculty of Medicine, University of Liège, Liège, Belgium
| | - Maria Artesi
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- Laboratory of Human Genetics, GIGA & Faculty of Medicine, University of Liège, Liège, Belgium
| | | | - Arnaud Sartelet
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- Comparative Veterinary Medicine, FARAH & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Latifa Karim
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- Genomics core facility, GIGA, University of Liège, Liège, Belgium
| | - Wouter Coppieters
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- Genomics core facility, GIGA, University of Liège, Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
| | - Carole Charlier
- Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
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Lee YL, Bouwman AC, Harland C, Bosse M, Costa Monteiro Moreira G, Veerkamp RF, Mullaart E, Cambisano N, Groenen MAM, Karim L, Coppieters W, Georges M, Charlier C. The rate of de novo structural variation is increased in in vitro-produced offspring and preferentially affects the paternal genome. Genome Res 2023; 33:1455-1464. [PMID: 37793781 PMCID: PMC10620045 DOI: 10.1101/gr.277884.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/08/2023] [Indexed: 10/06/2023]
Abstract
Assisted reproductive technologies (ARTs), including in vitro maturation and fertilization (IVF), are increasingly used in human and animal reproduction. Whether these technologies directly affect the rate of de novo mutation (DNM), and to what extent, has been a matter of debate. Here we take advantage of domestic cattle, characterized by complex pedigrees that are ideally suited to detect DNMs and by the systematic use of ART, to study the rate of de novo structural variation (dnSV) in this species and how it is impacted by IVF. By exploiting features of associated de novo point mutations (dnPMs) and dnSVs in clustered DNMs, we provide strong evidence that (1) IVF increases the rate of dnSV approximately fivefold, and (2) the corresponding mutations occur during the very early stages of embryonic development (one- and two-cell stage), yet primarily affect the paternal genome.
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Affiliation(s)
- Young-Lim Lee
- Unit of Animal Genomics, GIGA-R, Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium;
- Wageningen University and Research, Animal Breeding, and Genomics, 6708 WG Wageningen, The Netherlands
| | - Aniek C Bouwman
- Wageningen University and Research, Animal Breeding, and Genomics, 6708 WG Wageningen, The Netherlands
| | - Chad Harland
- Unit of Animal Genomics, GIGA-R, Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
- Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - Mirte Bosse
- Wageningen University and Research, Animal Breeding, and Genomics, 6708 WG Wageningen, The Netherlands
| | | | - Roel F Veerkamp
- Wageningen University and Research, Animal Breeding, and Genomics, 6708 WG Wageningen, The Netherlands
| | | | - Nadine Cambisano
- GIGA Genomics Platform, GIGA Institute, University of Liège, B-4000 Liège, Belgium
| | - Martien A M Groenen
- Wageningen University and Research, Animal Breeding, and Genomics, 6708 WG Wageningen, The Netherlands
| | - Latifa Karim
- GIGA Genomics Platform, GIGA Institute, University of Liège, B-4000 Liège, Belgium
| | - Wouter Coppieters
- Unit of Animal Genomics, GIGA-R, Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
- GIGA Genomics Platform, GIGA Institute, University of Liège, B-4000 Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R, Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium;
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R, Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium;
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Lee YL, Bosse M, Takeda H, Moreira GCM, Karim L, Druet T, Oget-Ebrad C, Coppieters W, Veerkamp RF, Groenen MAM, Georges M, Bouwman AC, Charlier C. High-resolution structural variants catalogue in a large-scale whole genome sequenced bovine family cohort data. BMC Genomics 2023; 24:225. [PMID: 37127590 PMCID: PMC10152703 DOI: 10.1186/s12864-023-09259-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 03/20/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Structural variants (SVs) are chromosomal segments that differ between genomes, such as deletions, duplications, insertions, inversions and translocations. The genomics revolution enabled the discovery of sub-microscopic SVs via array and whole-genome sequencing (WGS) data, paving the way to unravel the functional impact of SVs. Recent human expression QTL mapping studies demonstrated that SVs play a disproportionally large role in altering gene expression, underlining the importance of including SVs in genetic analyses. Therefore, this study aimed to generate and explore a high-quality bovine SV catalogue exploiting a unique cattle family cohort data (total 266 samples, forming 127 trios). RESULTS We curated 13,731 SVs segregating in the population, consisting of 12,201 deletions, 1,509 duplications, and 21 multi-allelic CNVs (> 50-bp). Of these, we validated a subset of copy number variants (CNVs) utilising a direct genotyping approach in an independent cohort, indicating that at least 62% of the CNVs are true variants, segregating in the population. Among gene-disrupting SVs, we prioritised two likely high impact duplications, encompassing ORM1 and POPDC3 genes, respectively. Liver expression QTL mapping results revealed that these duplications are likely causing altered gene expression, confirming the functional importance of SVs. Although most of the accurately genotyped CNVs are tagged by single nucleotide polymorphisms (SNPs) ascertained in WGS data, most CNVs were not captured by individual SNPs obtained from a 50K genotyping array. CONCLUSION We generated a high-quality SV catalogue exploiting unique whole genome sequenced bovine family cohort data. Two high impact duplications upregulating the ORM1 and POPDC3 are putative candidates for postpartum feed intake and hoof health traits, thus warranting further investigation. Generally, CNVs were in low LD with SNPs on the 50K array. Hence, it remains crucial to incorporate CNVs via means other than tagging SNPs, such as investigation of tagging haplotypes, direct imputation of CNVs, or direct genotyping as done in the current study. The SV catalogue and the custom genotyping array generated in the current study will serve as valuable resources accelerating utilisation of full spectrum of genetic variants in bovine genomes.
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Affiliation(s)
- Young-Lim Lee
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, the Netherlands.
- Unit of Animal Genomics, Faculty of Veterinary Medicine, GIGA-R &, University of Liège, Liège, Belgium.
| | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, the Netherlands
| | - Haruko Takeda
- Unit of Animal Genomics, Faculty of Veterinary Medicine, GIGA-R &, University of Liège, Liège, Belgium
| | | | - Latifa Karim
- GIGA Institute, GIGA Genomics Platform, University of Liège, Liège, Belgium
| | - Tom Druet
- Unit of Animal Genomics, Faculty of Veterinary Medicine, GIGA-R &, University of Liège, Liège, Belgium
| | - Claire Oget-Ebrad
- Unit of Animal Genomics, Faculty of Veterinary Medicine, GIGA-R &, University of Liège, Liège, Belgium
| | - Wouter Coppieters
- Unit of Animal Genomics, Faculty of Veterinary Medicine, GIGA-R &, University of Liège, Liège, Belgium
- GIGA Institute, GIGA Genomics Platform, University of Liège, Liège, Belgium
| | - Roel F Veerkamp
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, the Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, the Netherlands
| | - Michel Georges
- Unit of Animal Genomics, Faculty of Veterinary Medicine, GIGA-R &, University of Liège, Liège, Belgium
| | - Aniek C Bouwman
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, the Netherlands
| | - Carole Charlier
- Unit of Animal Genomics, Faculty of Veterinary Medicine, GIGA-R &, University of Liège, Liège, Belgium
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4
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Hoogstrate Y, Draaisma K, Ghisai SA, van Hijfte L, Barin N, de Heer I, Coppieters W, van den Bosch TPP, Bolleboom A, Gao Z, Vincent AJPE, Karim L, Deckers M, Taphoorn MJB, Kerkhof M, Weyerbrock A, Sanson M, Hoeben A, Lukacova S, Lombardi G, Leenstra S, Hanse M, Fleischeuer REM, Watts C, Angelopoulos N, Gorlia T, Golfinopoulos V, Bours V, van den Bent MJ, Robe PA, French PJ. Transcriptome analysis reveals tumor microenvironment changes in glioblastoma. Cancer Cell 2023; 41:678-692.e7. [PMID: 36898379 DOI: 10.1016/j.ccell.2023.02.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/20/2022] [Accepted: 02/14/2023] [Indexed: 03/12/2023]
Abstract
A better understanding of transcriptional evolution of IDH-wild-type glioblastoma may be crucial for treatment optimization. Here, we perform RNA sequencing (RNA-seq) (n = 322 test, n = 245 validation) on paired primary-recurrent glioblastoma resections of patients treated with the current standard of care. Transcriptional subtypes form an interconnected continuum in a two-dimensional space. Recurrent tumors show preferential mesenchymal progression. Over time, hallmark glioblastoma genes are not significantly altered. Instead, tumor purity decreases over time and is accompanied by co-increases in neuron and oligodendrocyte marker genes and, independently, tumor-associated macrophages. A decrease is observed in endothelial marker genes. These composition changes are confirmed by single-cell RNA-seq and immunohistochemistry. An extracellular matrix-associated gene set increases at recurrence and bulk, single-cell RNA, and immunohistochemistry indicate it is expressed mainly by pericytes. This signature is associated with significantly worse survival at recurrence. Our data demonstrate that glioblastomas evolve mainly by microenvironment (re-)organization rather than molecular evolution of tumor cells.
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Affiliation(s)
- Youri Hoogstrate
- Department of Neurology, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands.
| | - Kaspar Draaisma
- Department of Neurosurgery, UMC Utrecht, 3584CX Utrecht, the Netherlands
| | - Santoesha A Ghisai
- Department of Neurology, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands
| | - Levi van Hijfte
- Department of Neurology, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands; Laboratory of Tumor Immunology, Department of Medical Oncology, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands
| | - Nastaran Barin
- Department of Neurology, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands; Department of Precision and Microsystems Engineering, Delft University of Technology, 2628CD Delft, the Netherlands
| | - Iris de Heer
- Department of Neurology, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands
| | - Wouter Coppieters
- Genomics Platform, GIGA Institute, Université de Liège, 4000 Liège, Belgium
| | | | - Anne Bolleboom
- Deparment of Neuroscience, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands; Department of Neurosurgery, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands
| | - Zhenyu Gao
- Deparment of Neuroscience, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands
| | - Arnaud J P E Vincent
- Department of Neurosurgery, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands
| | - Latifa Karim
- Genomics Platform, GIGA Institute, Université de Liège, 4000 Liège, Belgium
| | - Manon Deckers
- Genomics Platform, GIGA Institute, Université de Liège, 4000 Liège, Belgium
| | - Martin J B Taphoorn
- Department of Neurology, Haaglanden Medical Center, 2512VA The Hague, the Netherlands; Department of Neurology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Melissa Kerkhof
- Department of Neurology, Haaglanden Medical Center, 2512VA The Hague, the Netherlands
| | - Astrid Weyerbrock
- Department of Neurosurgery, Medical Center - University of Freiburg, 79106 Freiburg, Germany; Faculty of Medicine, University of Freiburg, 79085 Freiburg, Germany
| | - Marc Sanson
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Ann Hoeben
- Department of Internal Medicine, Division of Medical Oncology, GROW, Maastricht University Medical Center, 6229ER Maastricht, the Netherlands
| | - Slávka Lukacova
- Department of Oncology, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Giuseppe Lombardi
- Department of Oncology, Oncology 1, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy
| | - Sieger Leenstra
- Department of Neurosurgery, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands
| | - Monique Hanse
- Department of Neurology, Catharina Hospital, 5623EJ Eindhoven, the Netherlands
| | - Ruth E M Fleischeuer
- Department of Pathology, Elisabeth-TweeSteden Hospital, 5042AD Tilburg, the Netherlands
| | - Colin Watts
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, B15 2SY Birmingham, UK
| | - Nicos Angelopoulos
- Systems Immunity Research Institute, Medical School, Cardiff University, CF14 4XN Cardiff, UK
| | | | | | - Vincent Bours
- Université de Liège, Department of Human Genetics, 4000 Liège, Belgium
| | | | - Pierre A Robe
- Department of Neurosurgery, UMC Utrecht, 3584CX Utrecht, the Netherlands; Université de Liège, Department of Human Genetics, 4000 Liège, Belgium
| | - Pim J French
- Department of Neurology, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands.
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Georges A, Lavergne A, Mandai M, Lepiemme F, Karim L, Demeulenaere L, Aguilar D, Schyns M, Nguyen L, Rakic JM, Takahashi M, Georges M, Takeda H. Comparing the transcriptome of developing native and iPSC-derived mouse retinae by single cell RNA sequencing. Sci Rep 2023; 13:1223. [PMID: 36681719 PMCID: PMC9867755 DOI: 10.1038/s41598-023-28429-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
We report the generation and analysis of single-cell RNA-Seq data (> 38,000 cells) from mouse native retinae and induced pluripotent stem cell (iPSC)-derived retinal organoids at four matched stages of development spanning the emergence of the major retinal cell types. We combine information from temporal sampling, visualization of 3D UMAP manifolds, pseudo-time and RNA velocity analyses, to show that iPSC-derived 3D retinal organoids broadly recapitulate the native developmental trajectories. However, we observe relaxation of spatial and temporal transcriptome control, premature emergence and dominance of photoreceptor precursor cells, and susceptibility of dynamically regulated pathways and transcription factors to culture conditions in retinal organoids. We demonstrate that genes causing human retinopathies are enriched in cell-type specifying genes and identify a subset of disease-causing genes with expression profiles that are highly conserved between human retinae and murine retinal organoids. This study provides a resource to the community that will be useful to assess and further improve protocols for ex vivo recapitulation and study of retinal development.
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Affiliation(s)
- Anouk Georges
- GIGA Stem Cells, GIGA Institute, University of Liège, Liège, Belgium
- Department of Ophthalmology, Faculty of Medicine and CHU University Hospital, University of Liège, Liège, Belgium
| | - Arnaud Lavergne
- GIGA Bioinformatics Platform, GIGA Institute, University of Liège, Liège, Belgium
| | - Michiko Mandai
- Laboratory for Retinal Regeneration, Center for Developmental Biology, RIKEN, Kobe, Japan
| | - Fanny Lepiemme
- GIGA Stem Cells, GIGA Institute, University of Liège, Liège, Belgium
| | - Latifa Karim
- GIGA Genomics Platform, GIGA Institute, University of Liège, Liège, Belgium
| | - Loic Demeulenaere
- Unit of Animal Genomics, GIGA Institute, University of Liège, Liège, Belgium
| | - Diego Aguilar
- Unit of Animal Genomics, GIGA Institute, University of Liège, Liège, Belgium
| | - Michael Schyns
- Digital Business, HEC Management School, University of Liège, Liège, Belgium
| | - Laurent Nguyen
- GIGA Stem Cells, GIGA Institute, University of Liège, Liège, Belgium
| | - Jean-Marie Rakic
- Department of Ophthalmology, Faculty of Medicine and CHU University Hospital, University of Liège, Liège, Belgium
| | - Masayo Takahashi
- Laboratory for Retinal Regeneration, Center for Biosystems Dynamics Research, RIKEN, Kobe, Japan
| | - Michel Georges
- Unit of Animal Genomics, GIGA Institute, University of Liège, Liège, Belgium.
| | - Haruko Takeda
- Unit of Animal Genomics, GIGA Institute, University of Liège, Liège, Belgium
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6
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Deflandre B, Stulanovic N, Planckaert S, Anderssen S, Bonometti B, Karim L, Coppieters W, Devreese B, Rigali S. The virulome of Streptomyces scabiei in response to cello-oligosaccharide elicitors. Microb Genom 2022; 8. [PMID: 35040428 PMCID: PMC8914351 DOI: 10.1099/mgen.0.000760] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The development of spots or lesions symptomatic of common scab on root and tuber crops is caused by few pathogenic Streptomyces with Streptomyces scabiei 87–22 as the model species. Thaxtomin phytotoxins are the primary virulence determinants, mainly acting by impairing cellulose synthesis, and their production in S. scabiei is in turn boosted by cello-oligosaccharides released from host plants. In this work we aimed to determine which molecules and which biosynthetic gene clusters (BGCs) of the specialized metabolism of S. scabiei 87–22 show a production and/or a transcriptional response to cello-oligosaccharides. Comparative metabolomic analyses revealed that molecules of the virulome of S. scabiei induced by cellobiose and cellotriose include (i) thaxtomin and concanamycin phytotoxins, (ii) desferrioxamines, scabichelin and turgichelin siderophores in order to acquire iron essential for housekeeping functions, (iii) ectoine for protection against osmotic shock once inside the host, and (iv) bottromycin and concanamycin antimicrobials possibly to prevent other microorganisms from colonizing the same niche. Importantly, both cello-oligosaccharides reduced the production of the spore germination inhibitors germicidins thereby giving the ‘green light’ to escape dormancy and trigger the onset of the pathogenic lifestyle. For most metabolites - either with induced or reduced production - cellotriose was revealed to be a slightly stronger elicitor compared to cellobiose, supporting an earlier hypothesis which suggested the trisaccharide was the real trigger for virulence released from the plant cell wall through the action of thaxtomins. Interestingly, except for thaxtomins, none of these BGCs’ expression seems to be under direct control of the cellulose utilization repressor CebR suggesting the existence of a yet unknown mechanism for switching on the virulome. Finally, a transcriptomic analysis revealed nine additional cryptic BGCs that have their expression awakened by cello-oligosaccharides, suggesting that other and yet to be discovered metabolites could be part of the virulome of S. scabiei.
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Affiliation(s)
- Benoit Deflandre
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
| | - Nudzejma Stulanovic
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
| | - Sören Planckaert
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, B-9000, Ghent, Belgium
| | - Sinaeda Anderssen
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
| | - Beatrice Bonometti
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
| | - Latifa Karim
- Genomics Platform, GIGA, University of Liège, B-4000, Liège, Belgium
| | - Wouter Coppieters
- Genomics Platform, GIGA, University of Liège, B-4000, Liège, Belgium
| | - Bart Devreese
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, B-9000, Ghent, Belgium
| | - Sébastien Rigali
- InBioS-Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, B-4000, Liège, Belgium
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7
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Lee YL, Takeda H, Costa Monteiro Moreira G, Karim L, Mullaart E, Coppieters W, Appeltant R, Veerkamp RF, Groenen MAM, Georges M, Bosse M, Druet T, Bouwman AC, Charlier C. A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle. PLoS Genet 2021; 17:e1009331. [PMID: 34288907 PMCID: PMC8328317 DOI: 10.1371/journal.pgen.1009331] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 08/02/2021] [Accepted: 06/08/2021] [Indexed: 12/24/2022] Open
Abstract
Clinical mastitis (CM) is an inflammatory disease occurring in the mammary glands of lactating cows. CM is under genetic control, and a prominent CM resistance QTL located on chromosome 6 was reported in various dairy cattle breeds. Nevertheless, the biological mechanism underpinning this QTL has been lacking. Herein, we mapped, fine-mapped, and discovered the putative causal variant underlying this CM resistance QTL in the Dutch dairy cattle population. We identified a ~12 kb multi-allelic copy number variant (CNV), that is in perfect linkage disequilibrium with a lead SNP, as a promising candidate variant. By implementing a fine-mapping and through expression QTL mapping, we showed that the group-specific component gene (GC), a gene encoding a vitamin D binding protein, is an excellent candidate causal gene for the QTL. The multiplicated alleles are associated with increased GC expression and low CM resistance. Ample evidence from functional genomics data supports the presence of an enhancer within this CNV, which would exert cis-regulatory effect on GC. We observed that strong positive selection swept the region near the CNV, and haplotypes associated with the multiplicated allele were strongly selected for. Moreover, the multiplicated allele showed pleiotropic effects for increased milk yield and reduced fertility, hinting that a shared underlying biology for these effects may revolve around the vitamin D pathway. These findings together suggest a putative causal variant of a CM resistance QTL, where a cis-regulatory element located within a CNV can alter gene expression and affect multiple economically important traits.
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Affiliation(s)
- Young-Lim Lee
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, the Netherlands
| | - Haruko Takeda
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | | | - Latifa Karim
- GIGA Genomics Platform, GIGA Institute, University of Liège, Liège, Belgium
| | | | - Wouter Coppieters
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- GIGA Genomics Platform, GIGA Institute, University of Liège, Liège, Belgium
| | | | - Ruth Appeltant
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Roel F. Veerkamp
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, the Netherlands
| | - Martien A. M. Groenen
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, the Netherlands
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Mirte Bosse
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, the Netherlands
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Aniek C. Bouwman
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, the Netherlands
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
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8
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Payen VL, Lavergne A, Alevra Sarika N, Colonval M, Karim L, Deckers M, Najimi M, Coppieters W, Charloteaux B, Sokal EM, El Taghdouini A. Single-cell RNA sequencing of human liver reveals hepatic stellate cell heterogeneity. JHEP Rep 2021; 3:100278. [PMID: 34027339 PMCID: PMC8121977 DOI: 10.1016/j.jhepr.2021.100278] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 02/11/2021] [Accepted: 02/28/2021] [Indexed: 02/07/2023] Open
Abstract
Background & Aims The multiple vital functions of the human liver are performed by highly specialised parenchymal and non-parenchymal cells organised in complex collaborative sinusoidal units. Although crucial for homeostasis, the cellular make-up of the human liver remains to be fully elucidated. Here, single-cell RNA-sequencing was used to unravel the heterogeneity of human liver cells, in particular of hepatocytes (HEPs) and hepatic stellate cells (HSCs). Method The transcriptome of ~25,000 freshly isolated human liver cells was profiled using droplet-based RNA-sequencing. Recently published data sets and RNA in situ hybridisation were integrated to validate and locate newly identified cell populations. Results In total, 22 cell populations were annotated that reflected the heterogeneity of human parenchymal and non-parenchymal liver cells. More than 20,000 HEPs were ordered along the portocentral axis to confirm known, and reveal previously undescribed, zonated liver functions. The existence of 2 subpopulations of human HSCs with unique gene expression signatures and distinct intralobular localisation was revealed (i.e. portal and central vein-concentrated GPC3+ HSCs and perisinusoidally located DBH+ HSCs). In particular, these data suggest that, although both subpopulations collaborate in the production and organisation of extracellular matrix, GPC3+ HSCs specifically express genes involved in the metabolism of glycosaminoglycans, whereas DBH+ HSCs display a gene signature that is reminiscent of antigen-presenting cells. Conclusions This study highlights metabolic zonation as a key determinant of HEP transcriptomic heterogeneity and, for the first time, outlines the existence of heterogeneous HSC subpopulations in the human liver. These findings call for further research on the functional implications of liver cell heterogeneity in health and disease. Lay summary This study resolves the cellular landscape of the human liver in an unbiased manner and at high resolution to provide new insights into human liver cell biology. The results highlight the physiological heterogeneity of human hepatic stellate cells. A cell atlas from the near-native transcriptome of >25,000 human liver cells is presented. Hepatocytes were ordered along the portocentral axis to reveal previously undescribed gene expression patterns and zonated liver functions. Two subpopulations of human hepatic stellate cells (HSCs) are reported, characterised by different spatial distribution in the native tissue. Characteristic gene signatures of HSC subpopulations are suggestive of far-reaching functional differences.
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Key Words
- BSA, bovine serum albumin
- CC, cholangiocyte
- CV, central vein
- DEG, differentially expressed gene
- EC, endothelial cell
- ECM, extracellular matrix
- Extracellular matrix
- FFPE, formaldehyde-fixed paraffin embedded
- GAG, glycosaminoglycan
- GEO, Gene Expression Omnibus
- GO, gene ontology
- HEP, hepatocyte
- HLA, human leukocyte antigen
- HRP, horseradish peroxidase
- HSC, hepatic stellate cell
- Hepatocyte
- ISH, in situ hybridisation
- KLR, killer lectin-like receptor
- LP, lymphoid cell
- Liver cell atlas
- MP, macrophage
- MZ, midzonal
- PC, pericentral
- PP, periportal
- PV, portal vein
- TBS, Tris buffered saline
- TSA, tyramide signal amplification
- UMAP, uniform manifold approximation and projection
- UMI, unique molecular identifier
- VIM, vimentin
- Zonation
- scRNA-seq, single-cell RNA-sequencing
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Affiliation(s)
- Valéry L. Payen
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
- Laboratory of Advanced Drug Delivery and Biomaterials (ADDB), LDRI Institute, Université catholique de Louvain, Brussels, Belgium
| | - Arnaud Lavergne
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | - Niki Alevra Sarika
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
- Laboratory of Advanced Drug Delivery and Biomaterials (ADDB), LDRI Institute, Université catholique de Louvain, Brussels, Belgium
| | - Megan Colonval
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | - Latifa Karim
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | - Manon Deckers
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | - Mustapha Najimi
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
| | - Wouter Coppieters
- Genomics Platform, GIGA Institute, Université de Liège, Liège, Belgium
| | | | - Etienne M. Sokal
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
- Corresponding authors. Address: Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Avenue Mounier 52 Box B1.52.03, 1200 Brussels, Belgium.
| | - Adil El Taghdouini
- Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Brussels, Belgium
- Corresponding authors. Address: Laboratory of Pediatric Hepatology and Cell Therapy (PEDI), IREC Institute, Université catholique de Louvain, Avenue Mounier 52 Box B1.52.03, 1200 Brussels, Belgium.
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Coppieters W, Karim L, Georges M. SNP-based quantitative deconvolution of biological mixtures: application to the detection of cows with subclinical mastitis by whole-genome sequencing of tank milk. Genome Res 2020; 30:1201-1207. [PMID: 32591360 PMCID: PMC7462076 DOI: 10.1101/gr.256172.119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 06/19/2020] [Indexed: 11/25/2022]
Abstract
Biological products of importance in food (e.g., milk) and medical (e.g., donor blood-derived products) sciences often correspond to mixtures of samples contributed by multiple individuals. Identifying which individuals contributed to the mixture and in what proportions may be of interest in several circumstances. We herein present a method that allows to do this by shallow whole-genome sequencing of the DNA in mixed samples from hundreds of donors. We show the efficacy of the approach for the detection of cows with subclinical mastitis by analysis of farms' tank mixtures containing milk from as many as 500 cows.
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Affiliation(s)
| | - Latifa Karim
- Genomics Platform, GIGA Institute, University of Liège
| | - Michel Georges
- Unit of Animal Genomics, GIGA Institute & Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
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10
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Artesi M, Tamma N, Deckers M, Karim L, Coppieters W, Van den Broeke A, Georges M, Charlier C, Durkin K. Colour‐sidedness in Gloucester cattle is associated with a complex structural variant impacting regulatory elements downstream of KIT. Anim Genet 2020; 51:461-465. [DOI: 10.1111/age.12932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2020] [Indexed: 11/27/2022]
Affiliation(s)
- M. Artesi
- Unit of Animal Genomics GIGA Institute University of Liège 1, avenue de l’hôpital Liège4000Belgium
| | - N. Tamma
- Unit of Animal Genomics GIGA Institute University of Liège 1, avenue de l’hôpital Liège4000Belgium
| | - M. Deckers
- Unit of Animal Genomics GIGA Institute University of Liège 1, avenue de l’hôpital Liège4000Belgium
| | - L. Karim
- Unit of Animal Genomics GIGA Institute University of Liège 1, avenue de l’hôpital Liège4000Belgium
| | - W. Coppieters
- Unit of Animal Genomics GIGA Institute University of Liège 1, avenue de l’hôpital Liège4000Belgium
| | - A. Van den Broeke
- Unit of Animal Genomics GIGA Institute University of Liège 1, avenue de l’hôpital Liège4000Belgium
- Laboratory of Experimental Hematology Institut Jules Bordet Université Libre de Bruxelles Boulevard de Waterloo 121 Brussels 1000 Belgium
| | - M. Georges
- Unit of Animal Genomics GIGA Institute University of Liège 1, avenue de l’hôpital Liège4000Belgium
| | - C. Charlier
- Unit of Animal Genomics GIGA Institute University of Liège 1, avenue de l’hôpital Liège4000Belgium
| | - K. Durkin
- Unit of Animal Genomics GIGA Institute University of Liège 1, avenue de l’hôpital Liège4000Belgium
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11
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Debode F, Hulin J, Charloteaux B, Coppieters W, Hanikenne M, Karim L, Berben G. Detection and identification of transgenic events by next generation sequencing combined with enrichment technologies. Sci Rep 2019; 9:15595. [PMID: 31666537 PMCID: PMC6821802 DOI: 10.1038/s41598-019-51668-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 09/20/2019] [Indexed: 12/12/2022] Open
Abstract
Next generation sequencing (NGS) is a promising tool for analysing the quality and safety of food and feed products. The detection and identification of genetically modified organisms (GMOs) is complex, as the diversity of transgenic events and types of structural elements introduced in plants continue to increase. In this paper, we show how a strategy that combines enrichment technologies with NGS can be used to detect a large panel of structural elements and partially or completely reconstruct the new sequence inserted into the plant genome in a single analysis, even at low GMO percentages. The strategy of enriching sequences of interest makes the approach applicable even to mixed products, which was not possible before due to insufficient coverage of the different genomes present. This approach is also the first step towards a more complete characterisation of agrifood products in a single analysis.
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Affiliation(s)
- Frédéric Debode
- Walloon Agricultural Research Center (CRA-W), Unit Traceability and Authentication, chaussée de Namur 24, 5030, Gembloux, Belgium.
| | - Julie Hulin
- Walloon Agricultural Research Center (CRA-W), Unit Traceability and Authentication, chaussée de Namur 24, 5030, Gembloux, Belgium
| | - Benoît Charloteaux
- University of Liège, GIGA - Genomics Platform, B34, 4000, Liège (Sart Tilman), Belgium
| | - Wouter Coppieters
- University of Liège, GIGA - Genomics Platform, B34, 4000, Liège (Sart Tilman), Belgium
| | - Marc Hanikenne
- University of Liège, InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, Chemin de la Vallée, 4, B22, 4000, Liège (Sart Tilman), Belgium
| | - Latifa Karim
- University of Liège, GIGA - Genomics Platform, B34, 4000, Liège (Sart Tilman), Belgium
| | - Gilbert Berben
- Walloon Agricultural Research Center (CRA-W), Unit Traceability and Authentication, chaussée de Namur 24, 5030, Gembloux, Belgium
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12
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Amininejad L, Charloteaux B, Theatre E, Liefferinckx C, Dmitrieva J, Hayard P, Muls V, Maisin JM, Schapira M, Ghislain JM, Closset P, Talib M, Abramowicz M, Momozawa Y, Deffontaine V, Crins F, Mni M, Karim L, Cambisano N, Ornemese S, Zucchi A, Minsart C, Deviere J, Hugot JP, De Vos M, Louis E, Vermeire S, Van Gossum A, Coppieters W, Twizere JC, Georges M, Franchimont D. Analysis of Genes Associated With Monogenic Primary Immunodeficiency Identifies Rare Variants in XIAP in Patients With Crohn's Disease. Gastroenterology 2018; 154:2165-2177. [PMID: 29501442 DOI: 10.1053/j.gastro.2018.02.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 02/15/2018] [Accepted: 02/17/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS A few rare monogenic primary immunodeficiencies (PIDs) are characterized by chronic intestinal inflammation that resembles Crohn's disease (CD). We investigated whether 23 genes associated with 10 of these monogenic disorders contain common, low-frequency, or rare variants that increase risk for CD. METHODS Common and low frequency variants in 1 Mb loci centered on the candidate genes were analyzed using meta-data corresponding to genotypes of approximately 17,000 patients with CD or without CD (controls) in Europe. The contribution of rare variants was assessed by high-throughput sequencing of 4750 individuals, including 660 early-onset and/or familial cases among the 2390 patients with CD. Variants were expressed from vectors in SW480 or HeLa cells and functions of their products were analyzed in immunofluorescence, luciferase, immunoprecipitation, and immunoblot assays. RESULTS We reproduced the association of the interleukin 10 locus with CD (P = .007), although none of the significantly associated variants modified the coding sequence of interleukin 10. We found XIAP to be significantly enriched for rare coding mutations in patients with CD vs controls (P = .02). We identified 4 previously unreported missense variants associated with CD. Variants in XIAP cause the PID X-linked lymphoproliferative disease type 2, yet none of the carriers of these variants had all the clinical features of X-linked lymphoproliferative disease type 2. Identified XIAP variants S123N, R233Q, and P257A were associated with an impaired activation of NOD2 signaling after muramyl dipeptide stimulation. CONCLUSIONS In a systematic analysis of variants in 23 PID-associated genes, we confirmed the association of variants in XIAP with CD. Further screenings for CD-associated variants and analyses of their functions could increase our understanding of the relationship between PID-associated genes and CD pathogenesis.
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Affiliation(s)
- Leila Amininejad
- Department of Gastroenterology, Hepatopancreatology and Digestive Oncology and Laboratory of Experimental Gastroenterology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Benoit Charloteaux
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium
| | - Emilie Theatre
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium
| | - Claire Liefferinckx
- Department of Gastroenterology, Hepatopancreatology and Digestive Oncology and Laboratory of Experimental Gastroenterology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Julia Dmitrieva
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium
| | - Pierre Hayard
- Department of Gastroenterology Charleroi University Hospital, Charleroi, Belgium
| | - Vincianne Muls
- Department of Gastroenterology, Saint Pierre Hospital, Brussels, Belgium
| | - Jean-Marc Maisin
- Department of Gastroenterology, Jolimont Hospital, La Louvière, Belgium
| | - Michael Schapira
- Department of Gastroenterology, Jolimont Hospital, La Louvière, Belgium
| | | | - Pierre Closset
- Department of Gastroenterology, Ixelles Hospital, Brussels, Belgium
| | - Mehdi Talib
- Department of Gastroenterology, Brugmann Hospital, Brussels, Belgium
| | - Marc Abramowicz
- Department of Human genetics, Erasme hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Yukihide Momozawa
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium
| | - Valerie Deffontaine
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium
| | - François Crins
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium
| | - Myriam Mni
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium
| | - Latifa Karim
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium; Groupe Interdisciplinaire de Génoprotéomique Appliquée Genomics Platform, University of Liège, Liège, Belgium
| | - Nadine Cambisano
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium; Groupe Interdisciplinaire de Génoprotéomique Appliquée Genomics Platform, University of Liège, Liège, Belgium
| | - Sandra Ornemese
- Grappe Interdisciplinaire de Génoprotéomique Appliquée Imaging Platform, University of Liège, Liège, Belgium
| | - Alessandro Zucchi
- Laboratory of Parasitology, Université Libre de Bruxelles, Brussels, Belgium
| | - Charlotte Minsart
- Department of Gastroenterology, Hepatopancreatology and Digestive Oncology and Laboratory of Experimental Gastroenterology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Jacques Deviere
- Department of Gastroenterology, Hepatopancreatology and Digestive Oncology and Laboratory of Experimental Gastroenterology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean-Pierre Hugot
- Institut National de la Santé et de la Recherche Médicale U843, Hôpital Robert Debré, Paris, France
| | - Martine De Vos
- Department of Gastroenterology and Hepatology, Ghent University Hospital, Ghent, Belgium
| | - Edouard Louis
- Department of Gastroenterology, Sart Tilman Hospital, University of Liège, Liège, Belgium
| | - Severine Vermeire
- Department of Clinical and Experimental Medecine, Gastroenterology Section, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Andre Van Gossum
- Department of Gastroenterology, Hepatopancreatology and Digestive Oncology and Laboratory of Experimental Gastroenterology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Wouter Coppieters
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium; Groupe Interdisciplinaire de Génoprotéomique Appliquée Genomics Platform, University of Liège, Liège, Belgium
| | - Jean-Claude Twizere
- Laboratory of Protein Signalling and Interactions, Groupe Interdisciplinaire de Génoprotéomique Appliquée, University of Liège, Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée and Faculty of Veterinary Medecine, University of Liège, Liège, Belgium
| | - Denis Franchimont
- Department of Gastroenterology, Hepatopancreatology and Digestive Oncology and Laboratory of Experimental Gastroenterology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium.
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Adam D, Maciejewska M, Naômé A, Martinet L, Coppieters W, Karim L, Baurain D, Rigali S. Isolation, Characterization, and Antibacterial Activity of Hard-to-Culture Actinobacteria from Cave Moonmilk Deposits. Antibiotics (Basel) 2018; 7:antibiotics7020028. [PMID: 29565274 PMCID: PMC6023089 DOI: 10.3390/antibiotics7020028] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 11/16/2022] Open
Abstract
Cave moonmilk deposits host an abundant and diverse actinobacterial population that has a great potential for producing novel natural bioactive compounds. In our previous attempt to isolate culturable moonmilk-dwelling Actinobacteria, only Streptomyces species were recovered, whereas a metagenetic study of the same deposits revealed a complex actinobacterial community including 46 actinobacterial genera in addition to streptomycetes. In this work, we applied the rehydration-centrifugation method to lessen the occurrence of filamentous species and tested a series of strategies to achieve the isolation of hard-to-culture and rare Actinobacteria from the moonmilk deposits of the cave “Grotte des Collemboles”. From the “tips and tricks” that were tested, separate autoclaving of the components of the International Streptomyces Project (ISP) medium number 5 (ISP5) medium, prolonged incubation time, and dilution of the moonmilk suspension were found to most effectively improve colony forming units. Taxonomic analyses of the 40 isolates revealed new representatives of the Agromyces, Amycolatopsis, Kocuria, Micrococcus, Micromonospora, Nocardia, and Rhodococcus species, as well as additional new streptomycetes. The applied methodologies allowed the isolation of strains associated with both the least and most abundant moonmilk-dwelling actinobacterial operational taxonomic units. Finally, bioactivity screenings revealed that some isolates displayed high antibacterial activities, and genome mining uncovered a strong potential for the production of natural compounds.
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Affiliation(s)
- Delphine Adam
- Integrative Biological Sciences (InBioS), Center for Protein Engineering, Liège University, B-4000 Liège, Belgium.
| | - Marta Maciejewska
- Integrative Biological Sciences (InBioS), Center for Protein Engineering, Liège University, B-4000 Liège, Belgium.
| | - Aymeric Naômé
- Integrative Biological Sciences (InBioS), Center for Protein Engineering, Liège University, B-4000 Liège, Belgium.
| | - Loïc Martinet
- Integrative Biological Sciences (InBioS), Center for Protein Engineering, Liège University, B-4000 Liège, Belgium.
| | - Wouter Coppieters
- Genomics Platform, GIGA (Grappe Interdisciplinaire de Génoprotéomique Appliquée), University of Liège (B34), B-4000 Liège, Belgium.
| | - Latifa Karim
- Genomics Platform, GIGA (Grappe Interdisciplinaire de Génoprotéomique Appliquée), University of Liège (B34), B-4000 Liège, Belgium.
| | - Denis Baurain
- Integrative Biological Sciences (InBioS), PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, B-4000 Liège, Belgium.
| | - Sébastien Rigali
- Integrative Biological Sciences (InBioS), Center for Protein Engineering, Liège University, B-4000 Liège, Belgium.
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Wenric S, ElGuendi S, Caberg JH, Bezzaou W, Fasquelle C, Charloteaux B, Karim L, Hennuy B, Frères P, Collignon J, Boukerroucha M, Schroeder H, Olivier F, Jossa V, Jerusalem G, Josse C, Bours V. Transcriptome-wide analysis of natural antisense transcripts shows their potential role in breast cancer. Sci Rep 2017; 7:17452. [PMID: 29234122 PMCID: PMC5727077 DOI: 10.1038/s41598-017-17811-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/01/2017] [Indexed: 01/20/2023] Open
Abstract
Non-coding RNAs (ncRNA) represent 1/5 of the mammalian transcript number, and 90% of the genome length is transcribed. Many ncRNAs play a role in cancer. Among them, non-coding natural antisense transcripts (ncNAT) are RNA sequences that are complementary and overlapping to those of either protein-coding (PCT) or non-coding transcripts. Several ncNATs were described as regulating protein coding gene expression on the same loci, and they are expected to act more frequently in cis compared to other ncRNAs that commonly function in trans. In this work, 22 breast cancers expressing estrogen receptors and their paired adjacent non-malignant tissues were analyzed by strand-specific RNA sequencing. To highlight ncNATs potentially playing a role in protein coding gene regulations that occur in breast cancer, three different data analysis methods were used: differential expression analysis of ncNATs between tumor and non-malignant tissues, differential correlation analysis of paired ncNAT/PCT between tumor and non-malignant tissues, and ncNAT/PCT read count ratio variation between tumor and non-malignant tissues. Each of these methods yielded lists of ncNAT/PCT pairs that were enriched in survival-associated genes. This work highlights ncNAT lists that display potential to affect the expression of protein-coding genes involved in breast cancer pathology.
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Affiliation(s)
- Stephane Wenric
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liege, Belgium.,University Hospital (CHU), Department of Medical Oncology, Liege, Belgium
| | - Sonia ElGuendi
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liege, Belgium
| | | | - Warda Bezzaou
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liege, Belgium
| | - Corinne Fasquelle
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liege, Belgium
| | | | - Latifa Karim
- University of Liège, GIGA-Genomics Platform, Liege, Belgium
| | - Benoit Hennuy
- University of Liège, GIGA-Genomics Platform, Liege, Belgium
| | - Pierre Frères
- University Hospital (CHU), Department of Medical Oncology, Liege, Belgium
| | - Joëlle Collignon
- University Hospital (CHU), Department of Medical Oncology, Liege, Belgium
| | | | - Hélène Schroeder
- University Hospital (CHU), Department of Medical Oncology, Liege, Belgium
| | - Fabrice Olivier
- University Hospital (CHU), Department of Medical Oncology, Liege, Belgium
| | - Véronique Jossa
- Clinique Saint-Vincent (CHC), Department of Pathology, Liege, Belgium
| | - Guy Jerusalem
- University Hospital (CHU), Department of Medical Oncology, Liege, Belgium
| | - Claire Josse
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liege, Belgium. .,University Hospital (CHU), Department of Medical Oncology, Liege, Belgium.
| | - Vincent Bours
- University of Liège, GIGA-Research, Laboratory of Human Genetics, Liege, Belgium.,University Hospital (CHU), Center of Genetics, Liege, Belgium
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15
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El Guendi S, Wenric S, Charloteaux B, Karim L, Hennuy B, Bezzaou W, Boukerroucha M, Jerusalem G, Josse C, Bours V. Study of the role played by natural antisens transcripts (NAT) in breast cancer through the regulation of the expression of their paired protein coding genes. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx143.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Vohra RS, Pasquali S, Kirkham AJ, Marriott P, Johnstone M, Spreadborough P, Alderson D, Griffiths EA, Fenwick S, Elmasry M, Nunes Q, Kennedy D, Basit Khan R, Khan MAS, Magee CJ, Jones SM, Mason D, Parappally CP, Mathur P, Saunders M, Jamel S, Ul Haque S, Zafar S, Shiwani MH, Samuel N, Dar F, Jackson A, Lovett B, Dindyal S, Winter H, Fletcher T, Rahman S, Wheatley K, Nieto T, Ayaani S, Youssef H, Nijjar RS, Watkin H, Naumann D, Emeshi S, Sarmah PB, Lee K, Joji N, Heath J, Teasdale RL, Weerasinghe C, Needham PJ, Welbourn H, Forster L, Finch D, Blazeby JM, Robb W, McNair AGK, Hrycaiczuk A, Charalabopoulos A, Kadirkamanathan S, Tang CB, Jayanthi NVG, Noor N, Dobbins B, Cockbain AJ, Nilsen-Nunn A, Siqueira J, Pellen M, Cowley JB, Ho WM, Miu V, White TJ, Hodgkins KA, Kinghorn A, Tutton MG, Al-Abed YA, Menzies D, Ahmad A, Reed J, Khan S, Monk D, Vitone LJ, Murtaza G, Joel A, Brennan S, Shier D, Zhang C, Yoganathan T, Robinson SJ, McCallum IJD, Jones MJ, Elsayed M, Tuck L, Wayman J, Carney K, Aroori S, Hosie KB, Kimble A, Bunting DM, Fawole AS, Basheer M, Dave RV, Sarveswaran J, Jones E, Kendal C, Tilston MP, Gough M, Wallace T, Singh S, Downing J, Mockford KA, Issa E, Shah N, Chauhan N, Wilson TR, Forouzanfar A, Wild JRL, Nofal E, Bunnell C, Madbak K, Rao STV, Devoto L, Siddiqi N, Khawaja Z, Hewes JC, Gould L, Chambers A, Urriza Rodriguez D, Sen G, Robinson S, Carney K, Bartlett F, Rae DM, Stevenson TEJ, Sarvananthan K, Dwerryhouse SJ, Higgs SM, Old OJ, Hardy TJ, Shah R, Hornby ST, Keogh K, Frank L, Al-Akash M, Upchurch EA, Frame RJ, Hughes M, Jelley C, Weaver S, Roy S, Sillo TO, Galanopoulos G, Cuming T, Cunha P, Tayeh S, Kaptanis S, Heshaishi M, Eisawi A, Abayomi M, Ngu WS, Fleming K, Singh Bajwa D, Chitre V, Aryal K, Ferris P, Silva M, Lammy S, Mohamed S, Khawaja A, Hussain A, Ghazanfar MA, Bellini MI, Ebdewi H, Elshaer M, Gravante G, Drake B, Ogedegbe A, Mukherjee D, Arhi C, Giwa Nusrat Iqbal L, Watson NF, Kumar Aggarwal S, Orchard P, Villatoro E, Willson PD, Wa K, Mok J, Woodman T, Deguara J, Garcea G, Babu BI, Dennison AR, Malde D, Lloyd D, Satheesan S, Al-Taan O, Boddy A, Slavin JP, Jones RP, Ballance L, Gerakopoulos S, Jambulingam P, Mansour S, Sakai N, Acharya V, Sadat MM, Karim L, Larkin D, Amin K, Khan A, Law J, Jamdar S, Smith SR, Sampat K, M O'shea K, Manu M, Asprou FM, Malik NS, Chang J, Johnstone M, Lewis M, Roberts GP, Karavadra B, Photi E, Hewes J, Gould L, Chambers A, Rodriguez D, O'Reilly DA, Rate AJ, Sekhar H, Henderson LT, Starmer BZ, Coe PO, Tolofari S, Barrie J, Bashir G, Sloane J, Madanipour S, Halkias C, Trevatt AEJ, Borowski DW, Hornsby J, Courtney MJ, Virupaksha S, Seymour K, Robinson S, Hawkins H, Bawa S, Gallagher PV, Reid A, Wood P, Finch JG, Parmar J, Stirland E, Gardner-Thorpe J, Al-Muhktar A, Peterson M, Majeed A, Bajwa FM, Martin J, Choy A, Tsang A, Pore N, Andrew DR, Al-Khyatt W, Taylor C, Bhandari S, Chambers A, Subramanium D, Toh SKC, Carter NC, Mercer SJ, Knight B, Tate S, Pearce B, Wainwright D, Vijay V, Alagaratnam S, Sinha S, Khan S, El-Hasani SS, Hussain AA, Bhattacharya V, Kansal N, Fasih T, Jackson C, Siddiqui MN, Chishti IA, Fordham IJ, Siddiqui Z, Bausbacher H, Geogloma I, Gurung K, Tsavellas G, Basynat P, Kiran Shrestha A, Basu S, Chhabra Mohan Harilingam A, Rabie M, Akhtar M, Kumar P, Jafferbhoy SF, Hussain N, Raza S, Haque M, Alam I, Aseem R, Patel S, Asad M, Booth MI, Ball WR, Wood CPJ, Pinho-Gomes AC, Kausar A, Rami Obeidallah M, Varghase J, Lodhia J, Bradley D, Rengifo C, Lindsay D, Gopalswamy S, Finlay I, Wardle S, Bullen N, Iftikhar SY, Awan A, Ahmed J, Leeder P, Fusai G, Bond-Smith G, Psica A, Puri Y, Hou D, Noble F, Szentpali K, Broadhurst J, Date R, Hossack MR, Li Goh Y, Turner P, Shetty V, Riera M, Macano CAW, Sukha A, Preston SR, Hoban JR, Puntis DJ, Williams SV, Krysztopik R, Kynaston J, Batt J, Doe M, Goscimski A, Jones GH, Smith SR, Hall C, Carty N, Ahmed J, Panteleimonitis S, Gunasekera RT, Sheel ARG, Lennon H, Hindley C, Reddy M, Kenny R, Elkheir N, McGlone ER, Rajaganeshan R, Hancorn K, Hargreaves A, Prasad R, Longbotham DA, Vijayanand D, Wijetunga I, Ziprin P, Nicolay CR, Yeldham G, Read E, Gossage JA, Rolph RC, Ebied H, Phull M, Khan MA, Popplewell M, Kyriakidis D, Hussain A, Henley N, Packer JR, Derbyshire L, Porter J, Appleton S, Farouk M, Basra M, Jennings NA, Ali S, Kanakala V, Ali H, Lane R, Dickson-Lowe R, Zarsadias P, Mirza D, Puig S, Al Amari K, Vijayan D, Sutcliffe R, Marudanayagam R, Hamady Z, Prasad AR, Patel A, Durkin D, Kaur P, Bowen L, Byrne JP, Pearson KL, Delisle TG, Davies J, Tomlinson MA, Johnpulle MA, Slawinski C, Macdonald A, Nicholson J, Newton K, Mbuvi J, Farooq A, Sidhartha Mothe B, Zafrani Z, Brett D, Francombe J, Spreadborough P, Barnes J, Cheung M, Al-Bahrani AZ, Preziosi G, Urbonas T, Alberts J, Mallik M, Patel K, Segaran A, Doulias T, Sufi PA, Yao C, Pollock S, Manzelli A, Wajed S, Kourkulos M, Pezzuto R, Wadley M, Hamilton E, Jaunoo S, Padwick R, Sayegh M, Newton RC, Hebbar M, Farag SF, Spearman J, Hamdan MF, D'Costa C, Blane C, Giles M, Peter MB, Hirst NA, Hossain T, Pannu A, El-Dhuwaib Y, Morrison TEM, Taylor GW, Thompson RLE, McCune K, Loughlin P, Lawther R, Byrnes CK, Simpson DJ, Mawhinney A, Warren C, McKay D, McIlmunn C, Martin S, MacArtney M, Diamond T, Davey P, Jones C, Clements JM, Digney R, Chan WM, McCain S, Gull S, Janeczko A, Dorrian E, Harris A, Dawson S, Johnston D, McAree B, Ghareeb E, Thomas G, Connelly M, McKenzie S, Cieplucha K, Spence G, Campbell W, Hooks G, Bradley N, Hill ADK, Cassidy JT, Boland M, Burke P, Nally DM, Hill ADK, Khogali E, Shabo W, Iskandar E, McEntee GP, O'Neill MA, Peirce C, Lyons EM, O'Sullivan AW, Thakkar R, Carroll P, Ivanovski I, Balfe P, Lee M, Winter DC, Kelly ME, Hoti E, Maguire D, Karunakaran P, Geoghegan JG, Martin ST, McDermott F, Cross KS, Cooke F, Zeeshan S, Murphy JO, Mealy K, Mohan HM, Nedujchelyn Y, Fahad Ullah M, Ahmed I, Giovinazzo F, Milburn J, Prince S, Brooke E, Buchan J, Khalil AM, Vaughan EM, Ramage MI, Aldridge RC, Gibson S, Nicholson GA, Vass DG, Grant AJ, Holroyd DJ, Jones MA, Sutton CMLR, O'Dwyer P, Nilsson F, Weber B, Williamson TK, Lalla K, Bryant A, Carter CR, Forrest CR, Hunter DI, Nassar AH, Orizu MN, Knight K, Qandeel H, Suttie S, Belding R, McClarey A, Boyd AT, Guthrie GJK, Lim PJ, Luhmann A, Watson AJM, Richards CH, Nicol L, Madurska M, Harrison E, Boyce KM, Roebuck A, Ferguson G, Pati P, Wilson MSJ, Dalgaty F, Fothergill L, Driscoll PJ, Mozolowski KL, Banwell V, Bennett SP, Rogers PN, Skelly BL, Rutherford CL, Mirza AK, Lazim T, Lim HCC, Duke D, Ahmed T, Beasley WD, Wilkinson MD, Maharaj G, Malcolm C, Brown TH, Shingler GM, Mowbray N, Radwan R, Morcous P, Wood S, Kadhim A, Stewart DJ, Baker AL, Tanner N, Shenoy H, Hafiz S, Marchi JA, Singh-Ranger D, Hisham E, Ainley P, O'Neill S, Terrace J, Napetti S, Hopwood B, Rhys T, Downing J, Kanavati O, Coats M, Aleksandrov D, Kallaway C, Yahya S, Weber B, Templeton A, Trotter M, Lo C, Dhillon A, Heywood N, Aawsaj Y, Hamdan A, Reece-Bolton O, McGuigan A, Shahin Y, Ali A, Luther A, Nicholson JA, Rajendran I, Boal M, Ritchie J. Population-based cohort study of variation in the use of emergency cholecystectomy for benign gallbladder diseases. Br J Surg 2016; 103:1716-1726. [PMID: 27748962 DOI: 10.1002/bjs.10288] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/21/2016] [Accepted: 07/06/2016] [Indexed: 01/05/2023]
Abstract
Abstract
Background
The aims of this prospective population-based cohort study were to identify the patient and hospital characteristics associated with emergency cholecystectomy, and the influences of these in determining variations between hospitals.
Methods
Data were collected for consecutive patients undergoing cholecystectomy in acute UK and Irish hospitals between 1 March and 1 May 2014. Potential explanatory variables influencing the performance of emergency cholecystectomy were analysed by means of multilevel, multivariable logistic regression modelling using a two-level hierarchical structure with patients (level 1) nested within hospitals (level 2).
Results
Data were collected on 4744 cholecystectomies from 165 hospitals. Increasing age, lower ASA fitness grade, biliary colic, the need for further imaging (magnetic retrograde cholangiopancreatography), endoscopic interventions (endoscopic retrograde cholangiopancreatography) and admission to a non-biliary centre significantly reduced the likelihood of an emergency cholecystectomy being performed. The multilevel model was used to calculate the probability of receiving an emergency cholecystectomy for a woman aged 40 years or over with an ASA grade of I or II and a BMI of at least 25·0 kg/m2, who presented with acute cholecystitis with an ultrasound scan showing a thick-walled gallbladder and a normal common bile duct. The mean predicted probability of receiving an emergency cholecystectomy was 0·52 (95 per cent c.i. 0·45 to 0·57). The predicted probabilities ranged from 0·02 to 0·95 across the 165 hospitals, demonstrating significant variation between hospitals.
Conclusion
Patients with similar characteristics presenting to different hospitals with acute gallbladder pathology do not receive comparable care.
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Affiliation(s)
| | - R S Vohra
- Trent Oesophago-Gastric Unit, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - S Pasquali
- Surgical Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - A J Kirkham
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, UK
| | - P Marriott
- West Midlands Research Collaborative, Academic Department of Surgery, University of Birmingham, Birmingham, UK
| | - M Johnstone
- West Midlands Research Collaborative, Academic Department of Surgery, University of Birmingham, Birmingham, UK
| | - P Spreadborough
- West Midlands Research Collaborative, Academic Department of Surgery, University of Birmingham, Birmingham, UK
| | - D Alderson
- Academic Department of Surgery, University of Birmingham, Birmingham, UK
| | - E A Griffiths
- Department of Upper Gastrointestinal Surgery, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - S Fenwick
- Aintree University Hospital NHS Foundation Trust
| | - M Elmasry
- Aintree University Hospital NHS Foundation Trust
| | - Q Nunes
- Aintree University Hospital NHS Foundation Trust
| | - D Kennedy
- Aintree University Hospital NHS Foundation Trust
| | | | | | | | | | - D Mason
- Wirral University Teaching Hospital
| | | | | | | | - S Jamel
- Barnet and Chase Farm Hospital
| | | | - S Zafar
- Barnet and Chase Farm Hospital
| | | | - N Samuel
- Barnsley District General Hospital
| | - F Dar
- Barnsley District General Hospital
| | | | | | | | | | | | | | - K Wheatley
- Sandwell and West Birmingham Hospitals NHS Trust
| | - T Nieto
- Sandwell and West Birmingham Hospitals NHS Trust
| | - S Ayaani
- Sandwell and West Birmingham Hospitals NHS Trust
| | - H Youssef
- Heart of England Foundation NHS Trust
| | | | - H Watkin
- Heart of England Foundation NHS Trust
| | - D Naumann
- Heart of England Foundation NHS Trust
| | - S Emeshi
- Heart of England Foundation NHS Trust
| | | | - K Lee
- Heart of England Foundation NHS Trust
| | - N Joji
- Heart of England Foundation NHS Trust
| | - J Heath
- Blackpool Teaching Hospitals NHS Foundation Trust
| | - R L Teasdale
- Blackpool Teaching Hospitals NHS Foundation Trust
| | | | - P J Needham
- Bradford Teaching Hospitals NHS Foundation Trust
| | - H Welbourn
- Bradford Teaching Hospitals NHS Foundation Trust
| | - L Forster
- Bradford Teaching Hospitals NHS Foundation Trust
| | - D Finch
- Bradford Teaching Hospitals NHS Foundation Trust
| | | | - W Robb
- University Hospitals Bristol NHS Trust
| | | | | | | | | | | | | | | | - B Dobbins
- Calderdale and Huddersfield NHS Trust
| | | | | | | | - M Pellen
- Hull and East Yorkshire NHS Trust
| | | | - W-M Ho
- Hull and East Yorkshire NHS Trust
| | - V Miu
- Hull and East Yorkshire NHS Trust
| | - T J White
- Chesterfield Royal Hospital NHS Foundation Trust
| | - K A Hodgkins
- Chesterfield Royal Hospital NHS Foundation Trust
| | - A Kinghorn
- Chesterfield Royal Hospital NHS Foundation Trust
| | - M G Tutton
- Colchester Hospital University NHS Foundation Trust
| | - Y A Al-Abed
- Colchester Hospital University NHS Foundation Trust
| | - D Menzies
- Colchester Hospital University NHS Foundation Trust
| | - A Ahmad
- Colchester Hospital University NHS Foundation Trust
| | - J Reed
- Colchester Hospital University NHS Foundation Trust
| | - S Khan
- Colchester Hospital University NHS Foundation Trust
| | - D Monk
- Countess of Chester NHS Foundation Trust
| | - L J Vitone
- Countess of Chester NHS Foundation Trust
| | - G Murtaza
- Countess of Chester NHS Foundation Trust
| | - A Joel
- Countess of Chester NHS Foundation Trust
| | | | - D Shier
- Croydon Health Services NHS Trust
| | - C Zhang
- Croydon Health Services NHS Trust
| | | | | | | | - M J Jones
- North Cumbria University Hospitals Trust
| | - M Elsayed
- North Cumbria University Hospitals Trust
| | - L Tuck
- North Cumbria University Hospitals Trust
| | - J Wayman
- North Cumbria University Hospitals Trust
| | - K Carney
- North Cumbria University Hospitals Trust
| | | | | | | | | | | | | | | | | | | | | | - M P Tilston
- Northern Lincolnshire and Goole NHS Foundation Trust
| | - M Gough
- Northern Lincolnshire and Goole NHS Foundation Trust
| | - T Wallace
- Northern Lincolnshire and Goole NHS Foundation Trust
| | - S Singh
- Northern Lincolnshire and Goole NHS Foundation Trust
| | - J Downing
- Northern Lincolnshire and Goole NHS Foundation Trust
| | - K A Mockford
- Northern Lincolnshire and Goole NHS Foundation Trust
| | - E Issa
- Northern Lincolnshire and Goole NHS Foundation Trust
| | - N Shah
- Northern Lincolnshire and Goole NHS Foundation Trust
| | - N Chauhan
- Northern Lincolnshire and Goole NHS Foundation Trust
| | - T R Wilson
- Doncaster and Bassetlaw Hospitals NHS Foundation Trust
| | - A Forouzanfar
- Doncaster and Bassetlaw Hospitals NHS Foundation Trust
| | - J R L Wild
- Doncaster and Bassetlaw Hospitals NHS Foundation Trust
| | - E Nofal
- Doncaster and Bassetlaw Hospitals NHS Foundation Trust
| | - C Bunnell
- Doncaster and Bassetlaw Hospitals NHS Foundation Trust
| | - K Madbak
- Doncaster and Bassetlaw Hospitals NHS Foundation Trust
| | - S T V Rao
- Dorset County Hospital NHS Foundation Trust
| | - L Devoto
- Dorset County Hospital NHS Foundation Trust
| | - N Siddiqi
- Dorset County Hospital NHS Foundation Trust
| | - Z Khawaja
- Dorset County Hospital NHS Foundation Trust
| | | | | | | | | | | | | | | | | | - D M Rae
- Frimley Park Hospital NHS Trust
| | | | | | | | | | - O J Old
- Gloucestershire Hospitals NHS Trust
| | | | - R Shah
- Gloucestershire Hospitals NHS Trust
| | | | - K Keogh
- Gloucestershire Hospitals NHS Trust
| | - L Frank
- Gloucestershire Hospitals NHS Trust
| | - M Al-Akash
- Great Western Hospitals NHS Foundation Trust
| | | | - R J Frame
- Harrogate and District NHS Foundation Trust
| | - M Hughes
- Harrogate and District NHS Foundation Trust
| | - C Jelley
- Harrogate and District NHS Foundation Trust
| | | | | | | | | | - T Cuming
- Homerton University Hospital NHS Trust
| | - P Cunha
- Homerton University Hospital NHS Trust
| | - S Tayeh
- Homerton University Hospital NHS Trust
| | | | | | - A Eisawi
- Tees Hospitals NHS Foundation Trust
| | | | - W S Ngu
- Tees Hospitals NHS Foundation Trust
| | | | | | - V Chitre
- Paget University Hospitals NHS Foundation Trust
| | - K Aryal
- Paget University Hospitals NHS Foundation Trust
| | - P Ferris
- Paget University Hospitals NHS Foundation Trust
| | | | | | | | | | | | | | | | - H Ebdewi
- Kettering General Hospital NHS Foundation Trust
| | - M Elshaer
- Kettering General Hospital NHS Foundation Trust
| | - G Gravante
- Kettering General Hospital NHS Foundation Trust
| | - B Drake
- Kettering General Hospital NHS Foundation Trust
| | - A Ogedegbe
- Barking, Havering and Redbridge University Hospitals NHS Trust
| | - D Mukherjee
- Barking, Havering and Redbridge University Hospitals NHS Trust
| | - C Arhi
- Barking, Havering and Redbridge University Hospitals NHS Trust
| | | | | | | | | | | | | | - K Wa
- Kingston Hospital NHS Foundation Trust
| | - J Mok
- Kingston Hospital NHS Foundation Trust
| | - T Woodman
- Kingston Hospital NHS Foundation Trust
| | - J Deguara
- Kingston Hospital NHS Foundation Trust
| | - G Garcea
- University Hospitals of Leicester NHS Trust
| | - B I Babu
- University Hospitals of Leicester NHS Trust
| | | | - D Malde
- University Hospitals of Leicester NHS Trust
| | - D Lloyd
- University Hospitals of Leicester NHS Trust
| | | | - O Al-Taan
- University Hospitals of Leicester NHS Trust
| | - A Boddy
- University Hospitals of Leicester NHS Trust
| | - J P Slavin
- Leighton Hospital, Mid Cheshire Hospitals NHS Foundation Trust
| | - R P Jones
- Leighton Hospital, Mid Cheshire Hospitals NHS Foundation Trust
| | - L Ballance
- Leighton Hospital, Mid Cheshire Hospitals NHS Foundation Trust
| | - S Gerakopoulos
- Leighton Hospital, Mid Cheshire Hospitals NHS Foundation Trust
| | - P Jambulingam
- Luton and Dunstable University Hospital NHS Foundation Trust
| | - S Mansour
- Luton and Dunstable University Hospital NHS Foundation Trust
| | - N Sakai
- Luton and Dunstable University Hospital NHS Foundation Trust
| | - V Acharya
- Luton and Dunstable University Hospital NHS Foundation Trust
| | - M M Sadat
- Macclesfield District General Hospital
| | - L Karim
- Macclesfield District General Hospital
| | - D Larkin
- Macclesfield District General Hospital
| | - K Amin
- Macclesfield District General Hospital
| | - A Khan
- Central Manchester NHS Foundation Trust
| | - J Law
- Central Manchester NHS Foundation Trust
| | - S Jamdar
- Central Manchester NHS Foundation Trust
| | - S R Smith
- Central Manchester NHS Foundation Trust
| | - K Sampat
- Central Manchester NHS Foundation Trust
| | | | - M Manu
- Royal Wolverhampton Hospitals NHS Trust
| | | | - N S Malik
- Royal Wolverhampton Hospitals NHS Trust
| | - J Chang
- Royal Wolverhampton Hospitals NHS Trust
| | | | - M Lewis
- Norfolk and Norwich University Hospitals NHS Foundation Trust
| | - G P Roberts
- Norfolk and Norwich University Hospitals NHS Foundation Trust
| | - B Karavadra
- Norfolk and Norwich University Hospitals NHS Foundation Trust
| | - E Photi
- Norfolk and Norwich University Hospitals NHS Foundation Trust
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - J Hornsby
- North Tees and Hartlepool NHS Foundation Trust
| | | | | | - K Seymour
- Northumbria Healthcare NHS Foundation Trust
| | - S Robinson
- Northumbria Healthcare NHS Foundation Trust
| | - H Hawkins
- Northumbria Healthcare NHS Foundation Trust
| | - S Bawa
- Northumbria Healthcare NHS Foundation Trust
| | | | - A Reid
- Northumbria Healthcare NHS Foundation Trust
| | - P Wood
- Northumbria Healthcare NHS Foundation Trust
| | - J G Finch
- Northampton General Hospital NHS Trust
| | - J Parmar
- Northampton General Hospital NHS Trust
| | | | | | - A Al-Muhktar
- Sheffield Teaching Hospitals NHS Foundation Trust
| | - M Peterson
- Sheffield Teaching Hospitals NHS Foundation Trust
| | - A Majeed
- Sheffield Teaching Hospitals NHS Foundation Trust
| | | | | | - A Choy
- Peterborough City Hospital
| | | | - N Pore
- United Lincolnshire Hospitals NHS Trust
| | | | | | - C Taylor
- United Lincolnshire Hospitals NHS Trust
| | | | | | | | | | | | | | | | - S Tate
- Portsmouth Hospitals NHS Trust
| | | | | | - V Vijay
- The Princess Alexandra Hospital NHS Trust
| | | | - S Sinha
- The Princess Alexandra Hospital NHS Trust
| | - S Khan
- The Princess Alexandra Hospital NHS Trust
| | | | - A A Hussain
- King's College Hospital NHS Foundation Trust
| | | | - N Kansal
- Gateshead Health NHS Foundation Trust
| | - T Fasih
- Gateshead Health NHS Foundation Trust
| | - C Jackson
- Gateshead Health NHS Foundation Trust
| | | | | | | | | | | | | | - K Gurung
- Queen Elizabeth Hospital NHS Trust
| | - G Tsavellas
- East Kent Hospitals University NHS Foundation Trust
| | - P Basynat
- East Kent Hospitals University NHS Foundation Trust
| | | | - S Basu
- East Kent Hospitals University NHS Foundation Trust
| | | | - M Rabie
- East Kent Hospitals University NHS Foundation Trust
| | - M Akhtar
- East Kent Hospitals University NHS Foundation Trust
| | - P Kumar
- Burton Hospitals NHS Foundation Trust
| | | | - N Hussain
- Burton Hospitals NHS Foundation Trust
| | - S Raza
- Burton Hospitals NHS Foundation Trust
| | - M Haque
- Royal Albert Edward Infirmary, Wigan Wrightington and Leigh NHS Trust
| | - I Alam
- Royal Albert Edward Infirmary, Wigan Wrightington and Leigh NHS Trust
| | - R Aseem
- Royal Albert Edward Infirmary, Wigan Wrightington and Leigh NHS Trust
| | - S Patel
- Royal Albert Edward Infirmary, Wigan Wrightington and Leigh NHS Trust
| | - M Asad
- Royal Albert Edward Infirmary, Wigan Wrightington and Leigh NHS Trust
| | - M I Booth
- Royal Berkshire NHS Foundation Trust
| | - W R Ball
- Royal Berkshire NHS Foundation Trust
| | | | | | | | | | - J Varghase
- Royal Bolton Hospital NHS Foundation Trust
| | - J Lodhia
- Royal Bolton Hospital NHS Foundation Trust
| | - D Bradley
- Royal Bolton Hospital NHS Foundation Trust
| | - C Rengifo
- Royal Bolton Hospital NHS Foundation Trust
| | - D Lindsay
- Royal Bolton Hospital NHS Foundation Trust
| | | | | | | | | | | | - A Awan
- Royal Derby NHS Foundation Trust
| | - J Ahmed
- Royal Derby NHS Foundation Trust
| | - P Leeder
- Royal Derby NHS Foundation Trust
| | | | | | | | | | - D Hou
- Hampshire Hospital NHS Foundation Trust
| | - F Noble
- Hampshire Hospital NHS Foundation Trust
| | | | | | - R Date
- Lancashire Teaching Hospitals NHS Foundation Trust
| | - M R Hossack
- Lancashire Teaching Hospitals NHS Foundation Trust
| | - Y Li Goh
- Lancashire Teaching Hospitals NHS Foundation Trust
| | - P Turner
- Lancashire Teaching Hospitals NHS Foundation Trust
| | - V Shetty
- Lancashire Teaching Hospitals NHS Foundation Trust
| | | | | | | | - S R Preston
- Royal Surrey County Hospital NHS Foundation Trust
| | - J R Hoban
- Royal Surrey County Hospital NHS Foundation Trust
| | - D J Puntis
- Royal Surrey County Hospital NHS Foundation Trust
| | - S V Williams
- Royal Surrey County Hospital NHS Foundation Trust
| | | | | | - J Batt
- Royal United Hospital Bath NHS Trust
| | - M Doe
- Royal United Hospital Bath NHS Trust
| | | | | | | | - C Hall
- Salford Royal NHS Foundation Trust
| | - N Carty
- Salisbury Hospital Foundation Trust
| | - J Ahmed
- Salisbury Hospital Foundation Trust
| | | | | | | | - H Lennon
- Southport and Ormskirk Hospital NHS Trust
| | - C Hindley
- Southport and Ormskirk Hospital NHS Trust
| | - M Reddy
- St George's Healthcare NHS Trust
| | - R Kenny
- St George's Healthcare NHS Trust
| | | | | | | | - K Hancorn
- St Helens and Knowsley Teaching Hospitals NHS Trust
| | - A Hargreaves
- St Helens and Knowsley Teaching Hospitals NHS Trust
| | | | | | | | | | - P Ziprin
- Imperial College Healthcare NHS Trust
| | | | - G Yeldham
- Imperial College Healthcare NHS Trust
| | - E Read
- Imperial College Healthcare NHS Trust
| | | | | | | | | | - M A Khan
- Mid Staffordshire NHS Foundation Trust
| | | | | | - A Hussain
- Mid Staffordshire NHS Foundation Trust
| | | | | | | | | | | | | | | | | | - S Ali
- City Hospitals Sunderland NHS Foundation Trust
| | - V Kanakala
- City Hospitals Sunderland NHS Foundation Trust
| | - H Ali
- Tunbridge Wells and Maidstone NHS Trust
| | - R Lane
- Tunbridge Wells and Maidstone NHS Trust
| | | | | | - D Mirza
- University Hospital Birmingham NHS Foundation Trust
| | - S Puig
- University Hospital Birmingham NHS Foundation Trust
| | - K Al Amari
- University Hospital Birmingham NHS Foundation Trust
| | - D Vijayan
- University Hospital Birmingham NHS Foundation Trust
| | - R Sutcliffe
- University Hospital Birmingham NHS Foundation Trust
| | | | - Z Hamady
- University Hospital Coventry and Warwickshire NHS Trust
| | - A R Prasad
- University Hospital Coventry and Warwickshire NHS Trust
| | - A Patel
- University Hospital Coventry and Warwickshire NHS Trust
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- University Hospital of North Staffordshire NHS Trust
| | - P Kaur
- University Hospital of North Staffordshire NHS Trust
| | - L Bowen
- University Hospital of North Staffordshire NHS Trust
| | - J P Byrne
- University Hospital Southampton NHS Foundation Trust
| | - K L Pearson
- University Hospital Southampton NHS Foundation Trust
| | - T G Delisle
- University Hospital Southampton NHS Foundation Trust
| | - J Davies
- University Hospital Southampton NHS Foundation Trust
| | | | | | | | - A Macdonald
- University Hospital South Manchester NHS Foundation Trust
| | - J Nicholson
- University Hospital South Manchester NHS Foundation Trust
| | - K Newton
- University Hospital South Manchester NHS Foundation Trust
| | - J Mbuvi
- University Hospital South Manchester NHS Foundation Trust
| | - A Farooq
- Warrington and Halton Hospitals NHS Trust
| | | | - Z Zafrani
- Warrington and Halton Hospitals NHS Trust
| | - D Brett
- Warrington and Halton Hospitals NHS Trust
| | | | | | - J Barnes
- South Warwickshire NHS Foundation Trust
| | - M Cheung
- South Warwickshire NHS Foundation Trust
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- Worcestershire Acute Hospitals NHS Trust
| | - E Hamilton
- Worcestershire Acute Hospitals NHS Trust
| | - S Jaunoo
- Worcestershire Acute Hospitals NHS Trust
| | - R Padwick
- Worcestershire Acute Hospitals NHS Trust
| | - M Sayegh
- Western Sussex Hospitals NHS Foundation Trust
| | - R C Newton
- Western Sussex Hospitals NHS Foundation Trust
| | - M Hebbar
- Western Sussex Hospitals NHS Foundation Trust
| | - S F Farag
- Western Sussex Hospitals NHS Foundation Trust
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- Yeovil District Hospital NHS Trust
| | - M Giles
- York Teaching Hospital NHS Foundation Trust
| | - M B Peter
- York Teaching Hospital NHS Foundation Trust
| | - N A Hirst
- York Teaching Hospital NHS Foundation Trust
| | - T Hossain
- York Teaching Hospital NHS Foundation Trust
| | - A Pannu
- York Teaching Hospital NHS Foundation Trust
| | | | | | - G W Taylor
- York Teaching Hospital NHS Foundation Trust
| | | | | | | | | | | | | | | | | | | | | | | | | | - T Diamond
- Belfast City Hospital, Mater Infirmorum Hospital Belfast and Royal Victoria Hospital
| | - P Davey
- Belfast City Hospital, Mater Infirmorum Hospital Belfast and Royal Victoria Hospital
| | - C Jones
- Belfast City Hospital, Mater Infirmorum Hospital Belfast and Royal Victoria Hospital
| | - J M Clements
- Belfast City Hospital, Mater Infirmorum Hospital Belfast and Royal Victoria Hospital
| | - R Digney
- Belfast City Hospital, Mater Infirmorum Hospital Belfast and Royal Victoria Hospital
| | - W M Chan
- Belfast City Hospital, Mater Infirmorum Hospital Belfast and Royal Victoria Hospital
| | - S McCain
- Belfast City Hospital, Mater Infirmorum Hospital Belfast and Royal Victoria Hospital
| | - S Gull
- Belfast City Hospital, Mater Infirmorum Hospital Belfast and Royal Victoria Hospital
| | - A Janeczko
- Belfast City Hospital, Mater Infirmorum Hospital Belfast and Royal Victoria Hospital
| | - E Dorrian
- Belfast City Hospital, Mater Infirmorum Hospital Belfast and Royal Victoria Hospital
| | - A Harris
- Belfast City Hospital, Mater Infirmorum Hospital Belfast and Royal Victoria Hospital
| | - S Dawson
- Belfast City Hospital, Mater Infirmorum Hospital Belfast and Royal Victoria Hospital
| | - D Johnston
- Belfast City Hospital, Mater Infirmorum Hospital Belfast and Royal Victoria Hospital
| | - B McAree
- Belfast City Hospital, Mater Infirmorum Hospital Belfast and Royal Victoria Hospital
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- University Hospital Limerick
| | | | - A D K Hill
- Louth County Hospital and Our Lady of Lourdes Hospital
| | - E Khogali
- Louth County Hospital and Our Lady of Lourdes Hospital
| | - W Shabo
- Louth County Hospital and Our Lady of Lourdes Hospital
| | - E Iskandar
- Louth County Hospital and Our Lady of Lourdes Hospital
| | | | | | | | | | | | | | | | | | - P Balfe
- St Luke's General Hospital Kilkenny
| | - M Lee
- St Luke's General Hospital Kilkenny
| | - D C Winter
- St Vincent's University and Private Hospitals, Dublin
| | - M E Kelly
- St Vincent's University and Private Hospitals, Dublin
| | - E Hoti
- St Vincent's University and Private Hospitals, Dublin
| | - D Maguire
- St Vincent's University and Private Hospitals, Dublin
| | - P Karunakaran
- St Vincent's University and Private Hospitals, Dublin
| | - J G Geoghegan
- St Vincent's University and Private Hospitals, Dublin
| | - S T Martin
- St Vincent's University and Private Hospitals, Dublin
| | - F McDermott
- St Vincent's University and Private Hospitals, Dublin
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - S Gibson
- Crosshouse Hospital, Ayrshire and Arran
| | | | - D G Vass
- Crosshouse Hospital, Ayrshire and Arran
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - H C C Lim
- Glangwili General and Prince Philip Hospital
| | - D Duke
- Glangwili General and Prince Philip Hospital
| | - T Ahmed
- Glangwili General and Prince Philip Hospital
| | - W D Beasley
- Glangwili General and Prince Philip Hospital
| | | | - G Maharaj
- Glangwili General and Prince Philip Hospital
| | - C Malcolm
- Glangwili General and Prince Philip Hospital
| | | | | | | | - R Radwan
- Morriston and Singleton Hospitals
| | | | - S Wood
- Princess of Wales Hospital
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Charlier C, Li W, Harland C, Littlejohn M, Coppieters W, Creagh F, Davis S, Druet T, Faux P, Guillaume F, Karim L, Keehan M, Kadri NK, Tamma N, Spelman R, Georges M. NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock. Genome Res 2016; 26:1333-1341. [PMID: 27646536 PMCID: PMC5052051 DOI: 10.1101/gr.207076.116] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/19/2016] [Indexed: 01/20/2023]
Abstract
We herein report the result of a large-scale, next generation sequencing (NGS)-based screen for embryonic lethal (EL) mutations in Belgian beef and New Zealand dairy cattle. We estimated by simulation that cattle might carry, on average, ∼0.5 recessive EL mutations. We mined exome sequence data from >600 animals, and identified 1377 stop-gain, 3139 frame-shift, 1341 splice-site, 22,939 disruptive missense, 62,399 benign missense, and 92,163 synonymous variants. We show that cattle have a comparable load of loss-of-function (LoF) variants (defined as stop-gain, frame-shift, or splice-site variants) as humans despite having a more variable exome. We genotyped >40,000 animals for up to 296 LoF and 3483 disruptive missense, breed-specific variants. We identified candidate EL mutations based on the observation of a significant depletion in homozygotes. We estimated the proportion of EL mutations at 15% of tested LoF and 6% of tested disruptive missense variants. We confirmed the EL nature of nine candidate variants by genotyping 200 carrier × carrier trios, and demonstrating the absence of homozygous offspring. The nine identified EL mutations segregate at frequencies ranging from 1.2% to 6.6% in the studied populations and collectively account for the mortality of ∼0.6% of conceptuses. We show that EL mutations preferentially affect gene products fulfilling basic cellular functions. The resulting information will be useful to avoid at-risk matings, thereby improving fertility.
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Affiliation(s)
- Carole Charlier
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - Wanbo Li
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, P.R. China
| | - Chad Harland
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium; Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Mathew Littlejohn
- Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Wouter Coppieters
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium; Genomics Platform, GIGA, University of Liège (B34), 4000-Liège, Belgium
| | - Frances Creagh
- Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Steve Davis
- Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - Pierre Faux
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - François Guillaume
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - Latifa Karim
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium; Genomics Platform, GIGA, University of Liège (B34), 4000-Liège, Belgium
| | - Mike Keehan
- Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Naveen Kumar Kadri
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - Nico Tamma
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - Richard Spelman
- Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
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18
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Sartelet A, Harland C, Tamma N, Karim L, Bayrou C, Li W, Ahariz N, Coppieters W, Georges M, Charlier C. A stop-gain in the laminin, alpha 3 gene causes recessive junctional epidermolysis bullosa in Belgian Blue cattle. Anim Genet 2015; 46:566-70. [PMID: 26370913 DOI: 10.1111/age.12342] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2015] [Indexed: 01/15/2023]
Abstract
Four newborn purebred Belgian Blue calves presenting a severe form of epidermolysis bullosa were recently referred to our heredo-surveillance platform. SNP array genotyping followed by autozygosity mapping located the causative gene in a 8.3-Mb interval on bovine chromosome 24. Combining information from (i) whole-genome sequencing of an affected calf, (ii) transcriptomic data from a panel of tissues and (iii) a list of functionally ranked positional candidates pinpointed a private G to A nucleotide substitution in the LAMA3 gene that creates a premature stop codon (p.Arg2609*) in exon 60, truncating 22% of the corresponding protein. The LAMA3 gene encodes the alpha 3 subunit of the heterotrimeric laminin-332, a key constituent of the lamina lucida that is part of the skin basement membrane connecting epidermis and dermis layers. Homozygous loss-of-function mutations in this gene are known to cause severe junctional epidermolysis bullosa in human, mice, horse, sheep and dog. Overall, our data strongly support the causality of the identified gene and mutation.
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Affiliation(s)
- Arnaud Sartelet
- Bovine Clinic, FARAH and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Chad Harland
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Nico Tamma
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Latifa Karim
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.,GIGA-Genomic platform, University of Liège, Liège, Belgium
| | - Calixte Bayrou
- Department of Pathology, FARAH and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Wanbo Li
- Bovine Clinic, FARAH and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Naima Ahariz
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.,GIGA-Genomic platform, University of Liège, Liège, Belgium
| | - Wouter Coppieters
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.,GIGA-Genomic platform, University of Liège, Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
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19
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Sartelet A, Li W, Pailhoux E, Richard C, Tamma N, Karim L, Fasquelle C, Druet T, Coppieters W, Georges M, Charlier C. Genome-wide next-generation DNA and RNA sequencing reveals a mutation that perturbs splicing of the phosphatidylinositol glycan anchor biosynthesis class H gene (PIGH) and causes arthrogryposis in Belgian Blue cattle. BMC Genomics 2015; 16:316. [PMID: 25895751 PMCID: PMC4404575 DOI: 10.1186/s12864-015-1528-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 04/13/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cattle populations are characterized by regular outburst of genetic defects as a result of the extensive use of elite sires. The causative genes and mutations can nowadays be rapidly identified by means of genome-wide association studies combined with next generation DNA sequencing, provided that the causative mutations are conventional loss-of-function variants. We show in this work how the combined use of next generation DNA and RNA sequencing allows for the rapid identification of otherwise difficult to identify splice-site variants. RESULTS We report the use of haplotype-based association mapping to identify a locus on bovine chromosome 10 that underlies autosomal recessive arthrogryposis in Belgian Blue Cattle. We identify 31 candidate mutations by resequencing the genome of four cases and 15 controls at ~10-fold depth. By analyzing RNA-Seq data from a carrier fetus, we observe skipping of the second exon of the PIGH gene, which we confirm by RT-PCR to be fully penetrant in tissues from affected calves. We identify - amongst the 31 candidate variants - a C-to-G transversion in the first intron of the PIGH gene (c211-10C > G) that is predicted to affect its acceptor splice-site. The resulting PIGH protein is likely to be non-functional as it lacks essential domains, and hence to cause arthrogryposis. CONCLUSIONS This work illustrates how the growing arsenal of genome exploration tools continues to accelerate the identification of an even broader range of disease causing mutations, therefore improving the management and control of genetic defects in livestock.
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Affiliation(s)
- Arnaud Sartelet
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Wanbo Li
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Eric Pailhoux
- INRA, UMR 1198, Biologie du Développement et Reproduction, F-78350, Jouy-en-Josas, France.
| | - Christophe Richard
- INRA, UMR 1198, Biologie du Développement et Reproduction, F-78350, Jouy-en-Josas, France.
| | - Nico Tamma
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Latifa Karim
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
- GIGA Genomic Platform, GIGA, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Corinne Fasquelle
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Tom Druet
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Wouter Coppieters
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
- GIGA Genomic Platform, GIGA, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Michel Georges
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Carole Charlier
- GIGA-R & Department of Animal Sciences, Unit of Animal Genomics, Faculty of Veterinary Medicine, University of Liège, Avenue de l'Hôpital 1, 4000, Liège, Belgium.
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20
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Devlin MJ, Van Vliet M, Motyl K, Karim L, Brooks DJ, Louis L, Conlon C, Rosen CJ, Bouxsein ML. Early-onset type 2 diabetes impairs skeletal acquisition in the male TALLYHO/JngJ mouse. Endocrinology 2014; 155:3806-16. [PMID: 25051433 PMCID: PMC4164927 DOI: 10.1210/en.2014-1041] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Type 2 diabetes (T2D) incidence in adolescents is rising and may interfere with peak bone mass acquisition. We tested the effects of early-onset T2D on bone mass, microarchitecture, and strength in the TALLYHO/JngJ mouse, which develops T2D by 8 weeks of age. We assessed metabolism and skeletal acquisition in male TALLYHO/JngJ and SWR/J controls (n = 8-10/group) from 4 weeks to 8 and 17 weeks of age. Tallyho mice were obese; had an approximately 2-fold higher leptin and percentage body fat; and had lower bone mineral density vs SWR at all time points (P < .03 for all). Tallyho had severe deficits in distal femur trabecular bone volume fraction (-54%), trabecular number (-27%), and connectivity density (-82%) (P < .01 for all). Bone formation was higher in Tallyho mice at 8 weeks but lower by 17 weeks of age vs SWR despite similar numbers of osteoblasts. Bone marrow adiposity was 7- to 50-fold higher in Tallyho vs SWR. In vitro, primary bone marrow stromal cell differentiation into osteoblast and adipocyte lineages was similar in SWR and Tallyho, suggesting skeletal deficits were not due to intrinsic defects in Tallyho bone-forming cells. These data suggest the Tallyho mouse might be a useful model to study the skeletal effects of adolescent T2D.
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Affiliation(s)
- M J Devlin
- Department of Anthropology (M.J.D.), University of Michigan, Ann Arbor, Michigan 48104; Center for Advanced Orthopedic Studies (M.J.D., M.V.V., L.K., D.J.B., L.L., C.C., M.L.B.), Beth Israel Deaconess Medical Center, and Harvard Medical School (M.L.B.), Boston, Massachusetts 02215; and Maine Medical Center Research Institute (K.M., C.J.R.), Scarborough, Maine 04074
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21
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Kadri NK, Sahana G, Charlier C, Iso-Touru T, Guldbrandtsen B, Karim L, Nielsen US, Panitz F, Aamand GP, Schulman N, Georges M, Vilkki J, Lund MS, Druet T. A 660-Kb deletion with antagonistic effects on fertility and milk production segregates at high frequency in Nordic Red cattle: additional evidence for the common occurrence of balancing selection in livestock. PLoS Genet 2014; 10:e1004049. [PMID: 24391517 PMCID: PMC3879169 DOI: 10.1371/journal.pgen.1004049] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 11/04/2013] [Indexed: 12/02/2022] Open
Abstract
In dairy cattle, the widespread use of artificial insemination has resulted in increased selection intensity, which has led to spectacular increase in productivity. However, cow fertility has concomitantly severely declined. It is generally assumed that this reduction is primarily due to the negative energy balance of high-producing cows at the peak of lactation. We herein describe the fine-mapping of a major fertility QTL in Nordic Red cattle, and identify a 660-kb deletion encompassing four genes as the causative variant. We show that the deletion is a recessive embryonically lethal mutation. This probably results from the loss of RNASEH2B, which is known to cause embryonic death in mice. Despite its dramatic effect on fertility, 13%, 23% and 32% of the animals carry the deletion in Danish, Swedish and Finnish Red Cattle, respectively. To explain this, we searched for favorable effects on other traits and found that the deletion has strong positive effects on milk yield. This study demonstrates that embryonic lethal mutations account for a non-negligible fraction of the decline in fertility of domestic cattle, and that associated positive effects on milk yield may account for part of the negative genetic correlation. Our study adds to the evidence that structural variants contribute to animal phenotypic variation, and that balancing selection might be more common in livestock species than previously appreciated. We report the identification of a large deletion encompassing four genes and the demonstration of its negative effect on fertility in Nordic Red dairy cattle. We show that this deletion is recessively lethal (homozygous embryos die) and therefore, when carrier cows are mated to carrier bulls, there is a high risk of embryonic mortality. As a result, chances of insemination failure are higher for such matings. Surprisingly, despite its negative effect, the deletion is frequent in Nordic Red cattle. We show that this high frequency may be a consequence of the fact that the deletion is associated with increased milk production and therefore selected for. Due to increased levels of inbreeding resulting from the widespread use of artificial insemination, such recessive lethal alleles may account for a non-negligible fraction of the reduction in fertility observed in cattle.
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Affiliation(s)
- Naveen Kumar Kadri
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
- * E-mail: (GS); (TD)
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | - Terhi Iso-Touru
- MTT Agrifood Research Finland, Biotechnology and Food Research, Jokioinen, Finland
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Latifa Karim
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | | | - Frank Panitz
- Molecular Genetics and Systems Biology, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | | | - Nina Schulman
- MTT Agrifood Research Finland, Biotechnology and Food Research, Jokioinen, Finland
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | - Johanna Vilkki
- MTT Agrifood Research Finland, Biotechnology and Food Research, Jokioinen, Finland
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
- * E-mail: (GS); (TD)
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22
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Georges A, Cambisano N, Ahariz N, Karim L, Georges M. A genome scan conducted in a multigenerational pedigree with convergent strabismus supports a complex genetic determinism. PLoS One 2014; 8:e83574. [PMID: 24376720 PMCID: PMC3871668 DOI: 10.1371/journal.pone.0083574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 11/06/2013] [Indexed: 11/26/2022] Open
Abstract
A genome-wide linkage scan was conducted in a Northern-European multigenerational pedigree with nine of 40 related members affected with concomitant strabismus. Twenty-seven members of the pedigree including all affected individuals were genotyped using a SNP array interrogating > 300,000 common SNPs. We conducted parametric and non-parametric linkage analyses assuming segregation of an autosomal dominant mutation, yet allowing for incomplete penetrance and phenocopies. We detected two chromosome regions with near-suggestive evidence for linkage, respectively on chromosomes 8 and 18. The chromosome 8 linkage implied a penetrance of 0.80 and a rate of phenocopy of 0.11, while the chromosome 18 linkage implied a penetrance of 0.64 and a rate of phenocopy of 0. Our analysis excludes a simple genetic determinism of strabismus in this pedigree.
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Affiliation(s)
- Anouk Georges
- Department of Ophtalmology, Faculty of Medicine, University of Liège (CHU), Liège, Belgium
| | - Nadine Cambisano
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | - Naïma Ahariz
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | - Latifa Karim
- GIGA-R Genotranscriptomics Core Faclity, University of Liège (B34), Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
- * E-mail:
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23
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Gerards M, Kamps R, van Oevelen J, Boesten I, Jongen E, de Koning B, Scholte HR, de Angst I, Schoonderwoerd K, Sefiani A, Ratbi I, Coppieters W, Karim L, de Coo R, van den Bosch B, Smeets H. Exome sequencing reveals a novel Moroccan founder mutation inSLC19A3as a new cause of early-childhood fatal Leigh syndrome. Brain 2013; 136:882-90. [DOI: 10.1093/brain/awt013] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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24
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Charlier C, Agerholm JS, Coppieters W, Karlskov-Mortensen P, Li W, de Jong G, Fasquelle C, Karim L, Cirera S, Cambisano N, Ahariz N, Mullaart E, Georges M, Fredholm M. A deletion in the bovine FANCI gene compromises fertility by causing fetal death and brachyspina. PLoS One 2012; 7:e43085. [PMID: 22952632 PMCID: PMC3430679 DOI: 10.1371/journal.pone.0043085] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/16/2012] [Indexed: 11/18/2022] Open
Abstract
Fertility is one of the most important traits in dairy cattle, and has been steadily declining over the last decades. We herein use state-of-the-art genomic tools, including high-throughput SNP genotyping and next-generation sequencing, to identify a 3.3 Kb deletion in the FANCI gene causing the brachyspina syndrome (BS), a rare recessive genetic defect in Holstein dairy cattle. We determine that despite the very low incidence of BS (<1/100,000), carrier frequency is as high as 7.4% in the Holstein breed. We demonstrate that this apparent discrepancy is likely due to the fact that a large proportion of homozygous mutant calves die during pregnancy. We postulate that several other embryonic lethals may segregate in livestock and significantly compromise fertility, and propose a genotype-driven screening strategy to detect the corresponding deleterious mutations.
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Affiliation(s)
- Carole Charlier
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
- * E-mail: (CC); (MF)
| | - Jorgen Steen Agerholm
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Wouter Coppieters
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
- GIGA-R Genotranscriptomics Core Facility, University of Liège (B34), Liège, Belgium
| | - Peter Karlskov-Mortensen
- Division of Genetics and Bioinformatics, Department of Animal and Veterinary Basic Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Wanbo Li
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | | | - Corinne Fasquelle
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | - Latifa Karim
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
- GIGA-R Genotranscriptomics Core Facility, University of Liège (B34), Liège, Belgium
| | - Susanna Cirera
- Division of Genetics and Bioinformatics, Department of Animal and Veterinary Basic Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Nadine Cambisano
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | - Naima Ahariz
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | | | - Michel Georges
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
| | - Merete Fredholm
- Division of Genetics and Bioinformatics, Department of Animal and Veterinary Basic Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail: (CC); (MF)
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25
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Durkin K, Coppieters W, Drögemüller C, Ahariz N, Cambisano N, Druet T, Fasquelle C, Haile A, Horin P, Huang L, Kamatani Y, Karim L, Lathrop M, Moser S, Oldenbroek K, Rieder S, Sartelet A, Sölkner J, Stålhammar H, Zelenika D, Zhang Z, Leeb T, Georges M, Charlier C. Serial translocation by means of circular intermediates underlies colour sidedness in cattle. Nature 2012; 482:81-4. [PMID: 22297974 DOI: 10.1038/nature10757] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Accepted: 12/05/2011] [Indexed: 11/09/2022]
Abstract
Colour sidedness is a dominantly inherited phenotype of cattle characterized by the polarization of pigmented sectors on the flanks, snout and ear tips. It is also referred to as 'lineback' or 'witrik' (which means white back), as colour-sided animals typically display a white band along their spine. Colour sidedness is documented at least since the Middle Ages and is presently segregating in several cattle breeds around the globe, including in Belgian blue and brown Swiss. Here we report that colour sidedness is determined by a first allele on chromosome 29 (Cs(29)), which results from the translocation of a 492-kilobase chromosome 6 segment encompassing KIT to chromosome 29, and a second allele on chromosome 6 (Cs(6)), derived from the first by repatriation of fused 575-kilobase chromosome 6 and 29 sequences to the KIT locus. We provide evidence that both translocation events involved circular intermediates. This is the first example, to our knowledge, of a phenotype determined by homologous yet non-syntenic alleles that result from a novel copy-number-variant-generating mechanism.
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Affiliation(s)
- Keith Durkin
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, 4000-Liège (Sart Tilman), Belgium
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26
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Karim L, Takeda H, Lin L, Druet T, Arias JAC, Baurain D, Cambisano N, Davis SR, Farnir F, Grisart B, Harris BL, Keehan MD, Littlejohn MD, Spelman RJ, Georges M, Coppieters W. Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Nat Genet 2011; 43:405-13. [PMID: 21516082 DOI: 10.1038/ng.814] [Citation(s) in RCA: 234] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 03/30/2011] [Indexed: 12/16/2022]
Abstract
We report mapping of a quantitative trait locus (QTL) with a major effect on bovine stature to a ∼780-kb interval using a Hidden Markov Model-based approach that simultaneously exploits linkage and linkage disequilibrium. We re-sequenced the interval in six sires with known QTL genotype and identified 13 clustered candidate quantitative trait nucleotides (QTNs) out of >9,572 discovered variants. We eliminated five candidate QTNs by studying the phenotypic effect of a recombinant haplotype identified in a breed diversity panel. We show that the QTL influences fetal expression of seven of the nine genes mapping to the ∼780-kb interval. We further show that two of the eight candidate QTNs, mapping to the PLAG1-CHCHD7 intergenic region, influence bidirectional promoter strength and affect binding of nuclear factors. By performing expression QTL analyses, we identified a splice site variant in CHCHD7 and exploited this naturally occurring null allele to exclude CHCHD7 as single causative gene.
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Affiliation(s)
- Latifa Karim
- Unit of Animal Genomics, Interdisciplinary Institute of Applied Genomics (GIGA-R) and Faculty of Veterinary Medicine, University of Liège (B34), Liège, Belgium
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27
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Rahmane L, Mazzouz H, Chaikhy A, Karim L, Essalim K, Adraoui A, El Kettani A, Lahbil D, Lamari H, Zaghloul K, Amraoui A. 364 Les facteurs influençant la survenue de l’inflammation en post-chirurgie de la cataracte chez l’enfant : une série de 109 yeux. J Fr Ophtalmol 2009. [DOI: 10.1016/s0181-5512(09)73488-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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28
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Adraoui A, Rahmane L, Maarif H, Chaikhy A, Karim L, Allali B, Lahbil D, Elkettani A, Lamari H, Amraoui A, Zaghloul K. 556 Exophtalmie révélant une actinomycose orbitaire : à propos de 2 cas. J Fr Ophtalmol 2009. [DOI: 10.1016/s0181-5512(09)73680-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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Aderdour S, Karim L, Lahbil D, Elkettani A, Lamari H, Rais L, Zaghloul K, Amraoui A. 398 Cataracte du sujet jeune associée à une épilepsie : à propos de 3 cas. J Fr Ophtalmol 2008. [DOI: 10.1016/s0181-5512(08)70996-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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30
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Grisart B, Farnir F, Karim L, Cambisano N, Kim JJ, Kvasz A, Mni M, Simon P, Frère JM, Coppieters W, Georges M. Genetic and functional confirmation of the causality of the DGAT1 K232A quantitative trait nucleotide in affecting milk yield and composition. Proc Natl Acad Sci U S A 2004; 101:2398-403. [PMID: 14983021 PMCID: PMC356962 DOI: 10.1073/pnas.0308518100] [Citation(s) in RCA: 265] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We recently used a positional cloning approach to identify a nonconservative lysine to alanine substitution (K232A) in the bovine DGAT1 gene that was proposed to be the causative quantitative trait nucleotide underlying a quantitative trait locus (QTL) affecting milk fat composition, previously mapped to the centromeric end of bovine chromosome 14. We herein generate genetic and functional data that confirm the causality of the DGAT1 K232A mutation. We have constructed a high-density single-nucleotide polymorphism map of the 3.8-centimorgan BULGE30-BULGE9 interval containing the QTL and show that the association with milk fat percentage maximizes at the DGAT1 gene. We provide evidence that the K allele has undergone a selective sweep. By using a baculovirus expression system, we have expressed both DGAT1 alleles in Sf9 cells and show that the K allele, causing an increase in milk fat percentage in the live animal, is characterized by a higher Vmax in producing triglycerides than the A allele.
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Affiliation(s)
- Bernard Grisart
- Department of Genetics, Faculty of Veterinary Medicine, University of Liège (B43), 20 Boulevard de Colonster, 4000 Liège (Sart Tilman), Belgium
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31
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Blott S, Kim JJ, Moisio S, Schmidt-Küntzel A, Cornet A, Berzi P, Cambisano N, Ford C, Grisart B, Johnson D, Karim L, Simon P, Snell R, Spelman R, Wong J, Vilkki J, Georges M, Farnir F, Coppieters W. Molecular dissection of a quantitative trait locus: a phenylalanine-to-tyrosine substitution in the transmembrane domain of the bovine growth hormone receptor is associated with a major effect on milk yield and composition. Genetics 2003; 163:253-66. [PMID: 12586713 PMCID: PMC1462408 DOI: 10.1093/genetics/163.1.253] [Citation(s) in RCA: 268] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We herein report on our efforts to improve the mapping resolution of a QTL with major effect on milk yield and composition that was previously mapped to bovine chromosome 20. By using a denser chromosome 20 marker map and by exploiting linkage disequilibrium using two distinct approaches, we provide strong evidence that a chromosome segment including the gene coding for the growth hormone receptor accounts for at least part of the chromosome 20 QTL effect. By sequencing individuals with known QTL genotype, we identify an F to Y substitution in the transmembrane domain of the growth hormone receptor gene that is associated with a strong effect on milk yield and composition in the general population.
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Affiliation(s)
- Sarah Blott
- Department of Genetics, Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
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32
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Farnir F, Grisart B, Coppieters W, Riquet J, Berzi P, Cambisano N, Karim L, Mni M, Moisio S, Simon P, Wagenaar D, Vilkki J, Georges M. Simultaneous mining of linkage and linkage disequilibrium to fine map quantitative trait loci in outbred half-sib pedigrees: revisiting the location of a quantitative trait locus with major effect on milk production on bovine chromosome 14. Genetics 2002; 161:275-87. [PMID: 12019241 PMCID: PMC1462117 DOI: 10.1093/genetics/161.1.275] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A maximum-likelihood QTL mapping method that simultaneously exploits linkage and linkage disequilibrium and that is applicable in outbred half-sib pedigrees is described. The method is applied to fine map a QTL with major effect on milk fat content in a 3-cM marker interval on proximal BTA14. This proximal location is confirmed by applying a haplotype-based association method referred to as recombinant ancestral haplotype analysis. The origin of the discrepancy between the QTL position derived in this work and that of a previous analysis is examined and shown to be due to the existence of distinct marker haplotypes associated with QTL alleles having large substitution effects.
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Affiliation(s)
- Frédéric Farnir
- Department of Genetics, Faculty of Veterinary Medicine, University of Liège (B43), 4000-Liège, Belgium
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33
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Grisart B, Coppieters W, Farnir F, Karim L, Ford C, Berzi P, Cambisano N, Mni M, Reid S, Simon P, Spelman R, Georges M, Snell R. Positional candidate cloning of a QTL in dairy cattle: identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield and composition. Genome Res 2002; 12:222-31. [PMID: 11827942 DOI: 10.1101/gr.224202] [Citation(s) in RCA: 670] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We recently mapped a quantitative trait locus (QTL) with a major effect on milk composition--particularly fat content--to the centromeric end of bovine chromosome 14. We subsequently exploited linkage disequilibrium to refine the map position of this QTL to a 3-cM chromosome interval bounded by microsatellite markers BULGE13 and BULGE09. We herein report the positional candidate cloning of this QTL, involving (1) the construction of a BAC contig spanning the corresponding marker interval, (2) the demonstration that a very strong candidate gene, acylCoA:diacylglycerol acyltransferase (DGAT1), maps to that contig, and (3) the identification of a nonconservative K232A substitution in the DGAT1 gene with a major effect on milk fat content and other milk characteristics.
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Affiliation(s)
- Bernard Grisart
- Department of Genetics, Faculty of Veterinary Medicine, University of Liège (B43), 4000-Liège, Belgium
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34
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Charlier C, Segers K, Wagenaar D, Karim L, Berghmans S, Jaillon O, Shay T, Weissenbach J, Cockett N, Gyapay G, Georges M. Human-ovine comparative sequencing of a 250-kb imprinted domain encompassing the callipyge (clpg) locus and identification of six imprinted transcripts: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8. Genome Res 2001; 11:850-62. [PMID: 11337479 PMCID: PMC311092 DOI: 10.1101/gr.172701] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Two ovine BAC clones and a connecting long-range PCR product, jointly spanning approximately 250 kb and representing most of the MULGE5-OY3 marker interval known to contain the clpg locus, were completely sequenced. The resulting genomic sequence was aligned with its human ortholog and extensively annotated. Six transcripts, four of which were novel, were predicted to originate from within the analyzed region and their existence confirmed experimentally: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8. RT-PCR experiments performed on a range of tissues sampled from an 8-wk-old animal demonstrated the preferential expression of all six transcripts in skeletal muscle, which suggests that they are under control of common regulatory elements. The six transcripts were also shown to be subject to parental imprinting: DLK1, DAT, and PEG11 were shown to be paternally expressed and GTL2, antiPEG11, and MEG8 to be maternally expressed.
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Affiliation(s)
- C Charlier
- Department of Genetics, Faculty of Veterinary Medicine, University of Liège (B43), 4000-Liège, Belgium
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35
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Charlier C, Segers K, Karim L, Shay T, Gyapay G, Cockett N, Georges M. The callipyge mutation enhances the expression of coregulated imprinted genes in cis without affecting their imprinting status. Nat Genet 2001; 27:367-9. [PMID: 11279514 DOI: 10.1038/86856] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The callipyge (CLPG) phenotype (from kappa(alpha)lambda(iota), "beautiful," and pi(iota)gamma(epsilon), "buttocks") described in sheep is an inherited muscular hypertrophy that is subject to an unusual parent-of-origin effect referred to as polar overdominance: only heterozygous individuals having inherited the CLPG mutation from their sire exhibit the muscular hypertrophy. The callipyge (clpg) locus was mapped to a chromosome segment of approximately 400 kb (refs. 2-4), which was shown to contain four genes (DLK1, GTL2, PEG11 and MEG8) that are preferentially expressed in skeletal muscle and subject to parental imprinting in this tissue. Here we describe the effect of the CLPG mutation on the expression of these four genes, and demonstrate that callipyge individuals have a unique expression profile that may account for the observed polar overdominance.
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Affiliation(s)
- C Charlier
- Department of Genetics, Faculty of Veterinary Medicine, University of Liège (B43), Liège, Belgium
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36
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Karim L, Coppieters W, Grobet L, Valentini A, Georges M. Convenient genotyping of six myostatin mutations causing double-muscling in cattle using a multiplex oligonucleotide ligation assay. Anim Genet 2000; 31:396-9. [PMID: 11167526 DOI: 10.1046/j.1365-2052.2000.00684.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We herein describe a procedure that allows for simultaneous genotyping of six loss-of-function mutations in the bovine myostatin gene associated with the double-muscling phenotype. The proposed method relies on a multiplex oligonucleotide ligation assay and detection of the fluorescently labelled products using automatic sequencers.
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Affiliation(s)
- L Karim
- Department of Genetics, Faculty of Veterinary Medicine, University of Liège, Belgium
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37
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Farnir F, Coppieters W, Arranz JJ, Berzi P, Cambisano N, Grisart B, Karim L, Marcq F, Moreau L, Mni M, Nezer C, Simon P, Vanmanshoven P, Wagenaar D, Georges M. Extensive genome-wide linkage disequilibrium in cattle. Genome Res 2000; 10:220-7. [PMID: 10673279 DOI: 10.1101/gr.10.2.220] [Citation(s) in RCA: 252] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A genome-wide linkage disequilibrium (LD) map was generated using microsatellite genotypes (284 autosomal microsatellite loci) of 581 gametes sampled from the dutch black-and-white dairy cattle population. LD was measured between all marker pairs, both syntenic and nonsyntenic. Analysis of syntenic pairs revealed surprisingly high levels of LD that, although more pronounced for closely linked marker pairs, extended over several tens of centimorgan. In addition, significant gametic associations were also shown to be very common between nonsyntenic loci. Simulations using the known genealogies of the studied sample indicate that random drift alone is likely to account for most of the observed disequilibrium. No clear evidence was obtained for a direct effect of selection ("Bulmer effect"). The observation of long range disequilibrium between syntenic loci using low-density marker maps indicates that LD mapping has the potential to be very effective in livestock populations. The frequent occurrence of gametic associations between nonsyntenic loci, however, encourages the combined use of linkage and linkage disequilibrium methods to avoid false positive results when mapping genes in livestock.
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Affiliation(s)
- F Farnir
- Department of Genetics, Faculty of Veterinary Medicine, University of Liège (B43), 4000-Liège, Belgium
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38
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Abstract
BACKGROUND This study investigates the rate of cerebral blood flow (rCBF) in Arab patients wth depression. METHODS Forty-four patients with DSM-III-R major depressive disorders were studied at rest using single photon emission computerized tomography (SPECT) with 99m Tc-HMPAO in comparison with 20 normal controls. All patients were assessed using the Hamilton Rating Scale for Depression (HRSD). RESULTS The depressed group showed greater rCBF in left and right posterior frontal and parietal cortical regions than normal controls. Within the depressed group, patients with the least severe illness (HRSD < 20) had significantly lower rCBF than normal controls, whilst those with moderately severe (HRSD 20-29) and severe (HRSD > 30) had significantly greater rCBF in most cortical regions than normal controls. Symptom scores, derived from the HRSD were predicted by rCBF principally increased rCBF in the left frontal cortex. CONCLUSIONS These results suggest a generalized cerebral activation principally in the frontal cortex which is in contrast to the results of most previous studies but more in line with the results of studies of induced affect and some studies of depression subsyndromes.
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Affiliation(s)
- M T Abou-Saleh
- Department of Psychiatry and Behavioural Sciences, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain
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39
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Riquet J, Coppieters W, Cambisano N, Arranz JJ, Berzi P, Davis SK, Grisart B, Farnir F, Karim L, Mni M, Simon P, Taylor JF, Vanmanshoven P, Wagenaar D, Womack JE, Georges M. Fine-mapping of quantitative trait loci by identity by descent in outbred populations: application to milk production in dairy cattle. Proc Natl Acad Sci U S A 1999; 96:9252-7. [PMID: 10430929 PMCID: PMC17766 DOI: 10.1073/pnas.96.16.9252] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We previously mapped a quantitative trait locus (QTL) affecting milk production to bovine chromosome 14. To refine the map position of this QTL, we have increased the density of the genetic map of BTA14q11-16 by addition of nine microsatellites and three single nucleotide polymorphisms. Fine-mapping of the QTL was accomplished by a two-tiered approach. In the first phase, we identified seven sires heterozygous "Qq" for the QTL by marker-assisted segregation analysis in a Holstein-Friesian pedigree comprising 1,158 individuals. In a second phase, we genotyped the seven selected sires for the newly developed high-density marker map and searched for a shared haplotype flanking an hypothetical, identical-by-descent QTL allele with large substitution effect. The seven chromosomes increasing milk fat percentage were indeed shown to carry a common chromosome segment with an estimated size of 5 cM predicted to contain the studied QTL. The same haplotype was shown to be associated with increased fat percentage in the general population as well, providing additional support in favor of the location of the QTL within the corresponding interval.
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Affiliation(s)
- J Riquet
- Department of Genetics, Faculty of Veterinary Medicine, University of Liège (B43), 20 Bd de Colonster, 4000-Liège, Belgium
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40
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Abstract
Plasma tryptophan and other putative amino acids, cortisol, folate and vitamin B12 and urinary biopterin (B) and neopterins (N) were measured in three groups of women: 62 women in the early postpartum period, 23 pregnant and 38 non-gravid controls. Sixty-two postpartum women were screened for depression by the Edinburgh postnatal depression scale (EPDS) on day 7 after delivery. Postpartum women had significantly lower tryptophan, vitamin B12 and significantly greater levels of cortisol, folate, neopterins and biopterins than controls. Comparisons between women who were classified on the EPDS as cases and non-cases revealed only a statistically significant difference for lower N:B (P<0.01) and lower folate (P<0.01) ratio in cases than non-cases. Multiple regression analysis showed a significant contribution for low tryptophan to increased EPDS which also showed significant correlations with low methionine, low tyrosine, low N:B ratio and high vitamin B12.
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Affiliation(s)
- M T Abou-Saleh
- Department of Psychiatry and Behavioural Sciences, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain
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41
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Nezer C, Moreau L, Brouwers B, Coppieters W, Detilleux J, Hanset R, Karim L, Kvasz A, Leroy P, Georges M. An imprinted QTL with major effect on muscle mass and fat deposition maps to the IGF2 locus in pigs. Nat Genet 1999; 21:155-6. [PMID: 9988262 DOI: 10.1038/5935] [Citation(s) in RCA: 256] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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42
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Abstract
Plasma cortisol, prolactin, oestrogen, progesterone, thyroxine, thyrotrophin (TSH) were collected from 23 pregnant, 70 postpartum women at 7 days postpartum, and 38 non-gravid controls. Sixty two postpartum women were screened for depression by the Edinburgh Postnatal Depression Scale (EPDS) on day 7 after delivery and 34 of them were assessed by the Present State Examination (PSE) at 8 +/- 2 weeks after delivery. Postpartum women had a significantly greater level of cortisol, prolactin, thyroxine and oestrogen than non-puerperal women. Postpartum women with current depression (EPDS > or = 11) had significantly lower plasma prolactin levels than those without depression and those who developed depression within 6-10 weeks after delivery (PSE level > or = 5) had significantly lower plasma prolactin and significantly greater progesterone levels than those who were not depressed. There were significant correlations between age and plasma cortisol and prolactin levels. Higher thyroxine levels predicted greater severity of concurrent symptoms of depression (total EPDS score) whilst higher progesterone and lower prolactin levels predicted the occurrence of depression (total PSE score) 6-10 weeks after delivery. Women who breastfed had significantly lower EPDS and total PSE scores and higher plasma prolactin levels than those who did not breastfed their infants whilst women who had previous episodes of depression had significantly greater EPDS and PSE scores, lower prolactin and higher TSH levels than those who had not suffered from previous episodes of depression.
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Affiliation(s)
- M T Abou-Saleh
- Department of Psychiatry & Behavioural Sciences, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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Coppieters W, Riquet J, Arranz JJ, Berzi P, Cambisano N, Grisart B, Karim L, Marcq F, Moreau L, Nezer C, Simon P, Vanmanshoven P, Wagenaar D, Georges M. A QTL with major effect on milk yield and composition maps to bovine chromosome 14. Mamm Genome 1998; 9:540-4. [PMID: 9657851 DOI: 10.1007/s003359900815] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A whole genome scan was undertaken in a granddaughter design comprising 1158 progeny-tested bulls in order to map QTL influencing milk yield and composition. In this paper we report the identification of a locus on the centromeric end of bovine Chromosome (Chr) 14, with major effect on fat and protein percentage as well as milk yield. The genuine nature of this QTL was verified using the grand2-daughter design, that is, by tracing the segregating QTL alleles from heterozygous grandsires to their maternal grandsons and confirming the predicted QTL allele substitution effect.
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Affiliation(s)
- W Coppieters
- Department of Genetics, Faculty of Veterinary Medicine, University of Liège, Belgium
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Arranz JJ, Coppieters W, Berzi P, Cambisano N, Grisart B, Karim L, Marcq F, Moreau L, Mezer C, Riquet J, Simon P, Vanmanshoven P, Wagenaar D, Georges M. A QTL affecting milk yield and composition maps to bovine chromosome 20: a confirmation. Anim Genet 1998; 29:107-15. [PMID: 9699270 DOI: 10.1046/j.1365-2052.1998.00307.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
As part of a whole genome scan undertaken to detect quantitative trait loci (QTL) affecting milk yield and composition, we have genotyped a granddaughter design comprising 1152 sons for six microsatellite markers spanning bovine chromosome 20. An analysis performed across families provided strong evidence (experiment-wise P-values < 0.01) for the presence of a QTL affecting primarily protein percentage towards the telomeric end of the chromosome. A founder sire, shown in a previous study to segregate for a similar QTL in the corresponding chromosome region, was characterized by 29 and 57 sons and maternal grandsons, respectively, in the present design. Sorting corresponding sons and grandsons by paternal or grandpaternal allele provided significant evidence for the segregation of a QTL on chromosome 20. Altogether these results confirm the location of a QTL affecting milk production on bovine chromosome 20.
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Affiliation(s)
- J J Arranz
- Department of Genetics, Faculty of Veterinary Medicine, University of Liège, Belgium
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Abstract
The available literature indicates that anorexia nervosa is rare in Arab culture. We report 5 cases of anorexia nervosa: 3 female and 2 male patients. Two are UAE nationals, 2 are Omanis, and 1 is Sudanese. The occurrence of these cases is discussed in the context of sociocultural changes and the increasing westernization of the UAE society.
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Affiliation(s)
- M T Abou-Saleh
- Department of Psychiatry and Behavioural Sciences, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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Spelman RJ, Coppieters W, Karim L, van Arendonk JA, Bovenhuis H. Quantitative trait loci analysis for five milk production traits on chromosome six in the Dutch Holstein-Friesian population. Genetics 1996; 144:1799-808. [PMID: 8978065 PMCID: PMC1207729 DOI: 10.1093/genetics/144.4.1799] [Citation(s) in RCA: 135] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Twenty Dutch Holstein-Friesian families, with a total of 715 sires, were evaluated in a granddaughter experiment design for marker-QTL associations. Five traits-milk, fat and protein yield and fat and protein percent-were analyzed. Across-family analysis was undertaken using multimarker regression principles. One and two QTL models were fitted. Critical values for the test statistic were calculated empirically by permuting the data. Individual trait distributions of permuted test statistics differed and, thus distributions, had to be calculated for each trait. Experimentwise critical values, which account for evaluating marker-QTL associations on all 29 autosomal-bovine chromosomes and for five traits, were calculated. A QTL for protein percent was identified in one, and two QTL models and was significant at the 1 and 2% level, respectively. Extending the multimarker regression approach to an analysis including two QTL was limited by families not being informative at all markers, which resulted in singularity. Below average heterozygosity for the first and last marker lowered information content for the first and last marker bracket. Highly informative markers at the ends of the mapped chromosome would overcome the decrease in information content in the first and last marker bracket and singularity for the two QTL model.
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Affiliation(s)
- R J Spelman
- Department of Animal Breeding, Wageningen Institute of Animal Sciences, Wageningen Agricultural University, The Netherlands.
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Affiliation(s)
- M T Abou-Saleh
- Department of Psychiatry and Behavioral Sciences, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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Abstract
This open prospective study was undertaken to determine the efficacy and safety of a fixed dose (6 mg) of risperidone in psychotic patients. Hospital in-patients who fulfilled DSM-111-R criteria for schizophrenia, schizoaffective and bipolar disorders were eligible for entry into the study (n = 15). Patients who were on other antipsychotics had a washout period of 1 week before they were started on the drug. A fixed dose of risperidone was administered (6 mg). The Brief Psychiatric Rating Scale (BPRS), Negative Symptom Rating Scale (NSRS) and Abnormal Involuntary Movement Scale were used to measure psychopathology and extrapyramidal side-effects. Five patients dropped out of the study. Two patients became very agitated and potentially aggressive, one patient became very restless and did not respond to benzodiazepines, and one dropped out because of restlessness that did not respond to clonazepam. Of the 10 patients who completed the study, 50 per cent reduction on BPRS and NSRS was achieved by five and six patients respectively. There was a marginally significant trend towards a greater reduction in the magnitude of negative symptoms. Four patients required treatment with anticholinergic drugs. Risperidone was effective in resistent psychotic patients, but agitated and impulsive psychotic patients with positive symptoms may not be best candidates for treatment with risperidone. On average, negative symptoms respond better than positive symptoms.
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Affiliation(s)
- T K Daradkeh
- Department of Psychiatry and Behavioural Sciences, Faculty of Medicine and Health Sciences, Al Ain, United Arab Emirates
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Abstract
To investigate the predictors of employment status of patients with DSM-III-R diagnosis, 55 patients were selected by a simple random technique from the main psychiatric clinic in Al Ain, United Arab Emirates. Structured and formal assessments were carried out to extract the potential predictors of outcome of schizophrenia. Logistic regression model revealed that being married, absence of schizoid personality, free or with minimum symptoms of the illness, later age of onset, and higher educational attainment were the most significant predictors of employment outcome. The implications of the results of this study are discussed in the text.
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Affiliation(s)
- T K Daradkeh
- Department of Psychiatry, Faculty of Medicine & Health Sciences, UAE University, Al Ain
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