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      Hnf1b haploinsufficiency differentially affects developmental target genes in a new renal cysts and diabetes mouse model

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          ABSTRACT

          Heterozygous mutations in HNF1B cause the complex syndrome renal cysts and diabetes (RCAD), characterized by developmental abnormalities of the kidneys, genital tracts and pancreas, and a variety of renal, pancreas and liver dysfunctions. The pathogenesis underlying this syndrome remains unclear as mice with heterozygous null mutations have no phenotype, while constitutive/conditional Hnf1b ablation leads to more severe phenotypes. We generated a novel mouse model carrying an identified human mutation at the intron-2 splice donor site. Unlike heterozygous mice previously characterized, mice heterozygous for the splicing mutation exhibited decreased HNF1B protein levels and bilateral renal cysts from embryonic day 15, originated from glomeruli, early proximal tubules (PTs) and intermediate nephron segments, concurrently with delayed PT differentiation, hydronephrosis and rare genital tract anomalies. Consistently, mRNA sequencing showed that most downregulated genes in embryonic kidneys were primarily expressed in early PTs and the loop of Henle and involved in ion/drug transport, organic acid and lipid metabolic processes, while the expression of previously identified targets upon Hnf1b ablation, including cystic disease genes, was weakly or not affected. Postnatal analyses revealed renal abnormalities, ranging from glomerular cysts to hydronephrosis and, rarely, multicystic dysplasia. Urinary proteomics uncovered a particular profile predictive of progressive decline in kidney function and fibrosis, and displayed common features with a recently reported urine proteome in an RCAD pediatric cohort. Altogether, our results show that reduced HNF1B levels lead to developmental disease phenotypes associated with the deregulation of a subset of HNF1B targets. They further suggest that this model represents a unique clinical/pathological viable model of the RCAD disease.

          Abstract

          Summary: A novel established mouse model carrying a heterozygous splicing human mutation in the Hnf1b gene exhibits phenotypes similar to those of patients with renal cysts and diabetes disease.

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          Most cited references74

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          ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

          ToppGene Suite (http://toppgene.cchmc.org; this web site is free and open to all users and does not require a login to access) is a one-stop portal for (i) gene list functional enrichment, (ii) candidate gene prioritization using either functional annotations or network analysis and (iii) identification and prioritization of novel disease candidate genes in the interactome. Functional annotation-based disease candidate gene prioritization uses a fuzzy-based similarity measure to compute the similarity between any two genes based on semantic annotations. The similarity scores from individual features are combined into an overall score using statistical meta-analysis. A P-value of each annotation of a test gene is derived by random sampling of the whole genome. The protein–protein interaction network (PPIN)-based disease candidate gene prioritization uses social and Web networks analysis algorithms (extended versions of the PageRank and HITS algorithms, and the K-Step Markov method). We demonstrate the utility of ToppGene Suite using 20 recently reported GWAS-based gene–disease associations (including novel disease genes) representing five diseases. ToppGene ranked 19 of 20 (95%) candidate genes within the top 20%, while ToppNet ranked 12 of 16 (75%) candidate genes among the top 20%.
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            Noise in protein expression scales with natural protein abundance.

            Noise in gene expression is generated at multiple levels, such as transcription and translation, chromatin remodeling and pathway-specific regulation. Studies of individual promoters have suggested different dominating noise sources, raising the question of whether a general trend exists across a large number of genes and conditions. We examined the variation in the expression levels of 43 Saccharomyces cerevisiae proteins, in cells grown under 11 experimental conditions. For all classes of genes and under all conditions, the expression variance was approximately proportional to the mean; the same scaling was observed at steady state and during the transient responses to the perturbations. Theoretical analysis suggests that this scaling behavior reflects variability in mRNA copy number, resulting from random 'birth and death' of mRNA molecules or from promoter fluctuations. Deviation of coexpressed genes from this general trend, including high noise in stress-related genes and low noise in proteasomal genes, may indicate fluctuations in pathway-specific regulators or a differential activation pattern of the underlying gene promoters.
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              The Rd8 mutation of the Crb1 gene is present in vendor lines of C57BL/6N mice and embryonic stem cells, and confounds ocular induced mutant phenotypes.

              We noted an unexpected inheritance pattern of lesions in several strains of gene-manipulated mice with ocular phenotypes. The lesions, which appeared at various stages of backcross to C57BL/6, bore resemblance to the rd8 retinal degeneration phenotype. We set out to examine the prevalence of this mutation in induced mutant mouse lines, vendor C57BL/6 mice and in widely used embryonic stem cells. Ocular lesions were evaluated by fundus examination and histopathology. Detection of the rd8 mutation at the genetic level was performed by PCR with appropriate primers. Data were confirmed by DNA sequencing in selected cases. Analysis of several induced mutant mouse lines with ocular disease phenotypes revealed that the disease was associated 100% with the presence of the rd8 mutation in the Crb1 gene rather than with the gene of interest. DNA analysis of C57BL/6 mice from common commercial vendors demonstrated the presence of the rd8 mutation in homozygous form in all C57BL/6N substrains, but not in the C57BL/6J substrain. A series of commercially available embryonic stem cells of C57BL/6N origin and C57BL/6N mouse lines used to generate ES cells also contained the rd8 mutation. Affected mice displayed ocular lesions typical of rd8, which were detectable by funduscopy and histopathology as early as 6 weeks of age. These findings identify the presence of the rd8 mutation in the C57BL/6N mouse substrain used widely to produce transgenic and knockout mice. The results have grave implications for the vision research community who develop mouse lines to study eye disease, as presence of rd8 can produce significant disease phenotypes unrelated to the gene or genes of interest. It is suggested that researchers screen for rd8 if their mouse lines were generated on the C57BL/6N background, bear resemblance to the rd8 phenotype, or are of indeterminate origin.
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                Author and article information

                Journal
                Dis Model Mech
                Dis Model Mech
                DMM
                dmm
                Disease Models & Mechanisms
                The Company of Biologists Ltd
                1754-8403
                1754-8411
                1 May 2021
                4 May 2021
                4 May 2021
                : 14
                : 5
                : dmm047498
                Affiliations
                [1 ]Sorbonne Université, CNRS, Institut de Biologie Paris Seine , Laboratoire de Biologie du Développement, IBPS, UMR7622 , F-75005 Paris, France
                [2 ]Mosaiques Diagnostics , 30659 Hannover, Germany
                [3 ]Department of Pediatric Nephrology, Hannover Medical School , 30625 Hannover, Germany
                [4 ]Biomedical Sciences Research Center Alexander Fleming , Institute for Fundamental Biomedical Science, 16672 Athens, Greece
                [5 ]Sorbonne Université, Université Paris Descartes, UMRS 1138, CNRS, ERL 8228, Centre de Recherche des Cordeliers , F-75006 Paris, France
                Author notes
                [*]

                Present address: Centre de Recherche Institut Curie, 75005 Paris, France.

                [‡]

                Present address: Cepton Strategies 11 rue Lincoln, 75008 Paris, France.

                [§]

                These authors contributed equally to this work

                []Author for correspondence ( silvia.cereghini@ 123456upmc.fr )

                Handling Editor: Monica J. Justice

                Author information
                http://orcid.org/0000-0001-9848-2885
                http://orcid.org/0000-0003-1698-7295
                http://orcid.org/0000-0002-1562-089X
                Article
                DMM047498
                10.1242/dmm.047498
                8126479
                33737325
                3f8a8266-d633-4916-be71-7161ba821b77
                © 2021. Published by The Company of Biologists Ltd

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.

                History
                : 16 September 2020
                : 9 March 2021
                Funding
                Funded by: GIS-Institut des Maladies Rares, http://dx.doi.org/10.13039/501100006587;
                Funded by: Institut Clinique de la Souris;
                Funded by: Agence National de la Recherche;
                Award ID: Blan06-2_139420
                Funded by: Institut National de la Santé et de la Recherche Médicale, http://dx.doi.org/10.13039/501100001677;
                Funded by: Seventh Framework Programme, http://dx.doi.org/10.13039/100011102;
                Award ID: 238821
                Funded by: Horizon 2020, http://dx.doi.org/10.13039/100010661;
                Award ID: 642937
                Funded by: Centre National de la Recherche Scientifique, http://dx.doi.org/10.13039/501100004794;
                Funded by: Sorbonne Université;
                Funded by: Innovative Training Network RENALTRACT;
                Award ID: MSCA-ITN-2014-642937
                Categories
                Developmental Disorders
                Metabolic Disorders
                Research Article

                Molecular medicine
                hnf1b transcription factor,rcad syndrome,gene dosage,glomerular and proximal tubule cysts,mouse models,transcriptomics

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