1
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Burnim AA, Dufault-Thompson K, Jiang X. The three-sided right-handed β-helix is a versatile fold for glycan interactions. Glycobiology 2024; 34:cwae037. [PMID: 38767844 PMCID: PMC11129586 DOI: 10.1093/glycob/cwae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024] Open
Abstract
Interactions between proteins and glycans are critical to various biological processes. With databases of carbohydrate-interacting proteins and increasing amounts of structural data, the three-sided right-handed β-helix (RHBH) has emerged as a significant structural fold for glycan interactions. In this review, we provide an overview of the sequence, mechanistic, and structural features that enable the RHBH to interact with glycans. The RHBH is a prevalent fold that exists in eukaryotes, prokaryotes, and viruses associated with adhesin and carbohydrate-active enzyme (CAZyme) functions. An evolutionary trajectory analysis on structurally characterized RHBH-containing proteins shows that they likely evolved from carbohydrate-binding proteins with their carbohydrate-degrading activities evolving later. By examining three polysaccharide lyase and three glycoside hydrolase structures, we provide a detailed view of the modes of glycan binding in RHBH proteins. The 3-dimensional shape of the RHBH creates an electrostatically and spatially favorable glycan binding surface that allows for extensive hydrogen bonding interactions, leading to favorable and stable glycan binding. The RHBH is observed to be an adaptable domain capable of being modified with loop insertions and charge inversions to accommodate heterogeneous and flexible glycans and diverse reaction mechanisms. Understanding this prevalent protein fold can advance our knowledge of glycan binding in biological systems and help guide the efficient design and utilization of RHBH-containing proteins in glycobiology research.
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Affiliation(s)
- Audrey A Burnim
- National Library of Medicine, National Institutes of Health, Building 38A, Room 6N607, 8600 Rockville Pike, Bethesda, MD 20894 United States
| | - Keith Dufault-Thompson
- National Library of Medicine, National Institutes of Health, Building 38A, Room 6N607, 8600 Rockville Pike, Bethesda, MD 20894 United States
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health, Building 38A, Room 6N607, 8600 Rockville Pike, Bethesda, MD 20894 United States
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2
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Redfield SE, De-la-Torre P, Zamani M, Wang H, Khan H, Morris T, Shariati G, Karimi M, Kenna MA, Seo GH, Xu H, Lu W, Naz S, Galehdari H, Indzhykulian AA, Shearer AE, Vona B. PKHD1L1, a gene involved in the stereocilia coat, causes autosomal recessive nonsyndromic hearing loss. Hum Genet 2024; 143:311-329. [PMID: 38459354 PMCID: PMC11043200 DOI: 10.1007/s00439-024-02649-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/21/2024] [Indexed: 03/10/2024]
Abstract
Identification of genes associated with nonsyndromic hearing loss is a crucial endeavor given the substantial number of individuals who remain without a diagnosis after even the most advanced genetic testing. PKHD1L1 was established as necessary for the formation of the cochlear hair-cell stereociliary coat and causes hearing loss in mice and zebrafish when mutated. We sought to determine if biallelic variants in PKHD1L1 also cause hearing loss in humans. Exome sequencing was performed on DNA of four families segregating autosomal recessive nonsyndromic sensorineural hearing loss. Compound heterozygous p.[(Gly129Ser)];p.[(Gly1314Val)] and p.[(Gly605Arg)];p[(Leu2818TyrfsTer5)], homozygous missense p.(His2479Gln) and nonsense p.(Arg3381Ter) variants were identified in PKHD1L1 that were predicted to be damaging using in silico pathogenicity prediction methods. In vitro functional analysis of two missense variants was performed using purified recombinant PKHD1L1 protein fragments. We then evaluated protein thermodynamic stability with and without the missense variants found in one of the families and performed a minigene splicing assay for another variant. In silico molecular modeling using AlphaFold2 and protein sequence alignment analysis were carried out to further explore potential variant effects on structure. In vitro functional assessment indicated that both engineered PKHD1L1 p.(Gly129Ser) and p.(Gly1314Val) mutant constructs significantly reduced the folding and structural stabilities of the expressed protein fragments, providing further evidence to support pathogenicity of these variants. Minigene assay of the c.1813G>A p.(Gly605Arg) variant, located at the boundary of exon 17, revealed exon skipping leading to an in-frame deletion of 48 amino acids. In silico molecular modeling exposed key structural features that might suggest PKHD1L1 protein destabilization. Multiple lines of evidence collectively associate PKHD1L1 with nonsyndromic mild-moderate to severe sensorineural hearing loss. PKHD1L1 testing in individuals with mild-moderate hearing loss may identify further affected families.
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Affiliation(s)
- Shelby E Redfield
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, 300 Longwood Avenue, BCH-3129, Boston, MA, 02115, USA
| | - Pedro De-la-Torre
- Mass Eye and Ear, Eaton Peabody Laboratories, Boston, MA, USA
- Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
| | - Hanjun Wang
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, No. 40 Daxuebei Road, Zhengzhou, 450052, China
| | - Hina Khan
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Tyler Morris
- Mass Eye and Ear, Eaton Peabody Laboratories, Boston, MA, USA
| | - Gholamreza Shariati
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Majid Karimi
- Khuzestan Cochlear Implantation Center (Tabassom), Ahvaz, Iran
| | - Margaret A Kenna
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, 300 Longwood Avenue, BCH-3129, Boston, MA, 02115, USA
- Mass Eye and Ear, Eaton Peabody Laboratories, Boston, MA, USA
| | | | - Hongen Xu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, No. 40 Daxuebei Road, Zhengzhou, 450052, China
| | - Wei Lu
- Department of Otorhinolaryngology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jian-She Road, Zhengzhou, 450052, China
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Artur A Indzhykulian
- Mass Eye and Ear, Eaton Peabody Laboratories, Boston, MA, USA.
- Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA.
| | - A Eliot Shearer
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, 300 Longwood Avenue, BCH-3129, Boston, MA, 02115, USA.
- Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA.
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, 37073, Göttingen, Germany.
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075, Göttingen, Germany.
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3
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Bannell TAK, Cockburn JJB. The molecular structure and function of fibrocystin, the key gene product implicated in autosomal recessive polycystic kidney disease (ARPKD). Ann Hum Genet 2024; 88:58-75. [PMID: 37905714 DOI: 10.1111/ahg.12535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/14/2023] [Accepted: 10/03/2023] [Indexed: 11/02/2023]
Abstract
Autosomal recessive polycystic kidney disease is an early onset inherited hepatorenal disorder affecting around 1 in 20,000 births with no approved specific therapies. The disease is almost always caused by variations in the polycystic kidney and hepatic disease 1 gene, which encodes fibrocystin (FC), a very large, single-pass transmembrane glycoprotein found in primary cilia, urine and urinary exosomes. By comparison to proteins involved in autosomal dominant PKD, our structural and molecular understanding of FC has lagged far behind such that there are no published experimentally determined structures of any part of the protein. Bioinformatics analyses predict that the ectodomain contains a long chain of immunoglobulin-like plexin-transcription factor domains, a protective antigen 14 domain, a tandem G8-TMEM2 homology region and a sperm protein, enterokinase and agrin domain. Here we review current knowledge on the molecular function of the protein from a structural perspective.
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Affiliation(s)
- Travis A K Bannell
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Joseph J B Cockburn
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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4
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Kang JY, Yang J, Lee H, Park S, Gil M, Kim KE. Systematic Multiomic Analysis of PKHD1L1 Gene Expression and Its Role as a Predicting Biomarker for Immune Cell Infiltration in Skin Cutaneous Melanoma and Lung Adenocarcinoma. Int J Mol Sci 2023; 25:359. [PMID: 38203530 PMCID: PMC10778817 DOI: 10.3390/ijms25010359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/16/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
The identification of genetic factors that regulate the cancer immune microenvironment is important for understanding the mechanism of tumor progression and establishing an effective treatment strategy. Polycystic kidney and hepatic disease 1-like protein 1 (PKHD1L1) is a large transmembrane protein that is highly expressed in immune cells; however, its association with tumor progression remains unclear. Here, we systematically analyzed the clinical relevance of PKHD1L1 in the tumor microenvironment in multiple cancer types using various bioinformatic tools. We found that the PKHD1L1 mRNA expression levels were significantly lower in skin cutaneous melanoma (SKCM) and lung adenocarcinoma (LUAD) than in normal tissues. The decreased expression of PKHD1L1 was significantly associated with unfavorable overall survival (OS) in SKCM and LUAD. Additionally, PKHD1L1 expression was positively correlated with the levels of infiltrating B cells, cluster of differentiation (CD)-8+ T cells, and natural killer (NK) cells, suggesting that the infiltration of immune cells could be associated with a good prognosis due to increased PKHD1L1 expression. Gene ontology (GO) analysis also revealed the relationship between PKHD1L1-co-altered genes and the activation of lymphocytes, including B and T cells. Collectively, this study shows that PKHD1L1 expression is positively correlated with a good prognosis via the induction of immune infiltration, suggesting that PKHD1L1 has potential prognostic value in SKCM and LUAD.
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Affiliation(s)
- Ji Young Kang
- Department of Health Industry, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (J.Y.K.); (M.G.)
| | - Jisun Yang
- Department of Cosmetic Sciences, Sookmyung Women’s University, Seoul 04310, Republic of Korea;
| | - Haeryung Lee
- Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (H.L.); (S.P.)
| | - Soochul Park
- Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (H.L.); (S.P.)
| | - Minchan Gil
- Department of Health Industry, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (J.Y.K.); (M.G.)
| | - Kyung Eun Kim
- Department of Health Industry, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (J.Y.K.); (M.G.)
- Department of Cosmetic Sciences, Sookmyung Women’s University, Seoul 04310, Republic of Korea;
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5
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Redfield SE, De-la-Torre P, Zamani M, Wang H, Khan H, Morris T, Shariati G, Karimi M, Kenna MA, Seo GH, Xu H, Lu W, Naz S, Galehdari H, Indzhykulian AA, Shearer AE, Vona B. PKHD1L1, A Gene Involved in the Stereocilia Coat, Causes Autosomal Recessive Nonsyndromic Hearing Loss. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.08.23296081. [PMID: 37873491 PMCID: PMC10593026 DOI: 10.1101/2023.10.08.23296081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Identification of genes associated with nonsyndromic hearing loss is a crucial endeavor given the substantial number of individuals who remain without a diagnosis after even the most advanced genetic testing. PKHD1L1 was established as necessary for the formation of the cochlear hair-cell stereociliary coat and causes hearing loss in mice and zebrafish when mutated. We sought to determine if biallelic variants in PKHD1L1 also cause hearing loss in humans. Exome sequencing was performed on DNA of four families segregating autosomal recessive nonsyndromic sensorineural hearing loss. Compound heterozygous p.[(Gly129Ser)];p.[(Gly1314Val)] and p.[(Gly605Arg)];p[(Leu2818TyrfsTer5)], homozygous missense p.(His2479Gln) and nonsense p.(Arg3381Ter) variants were identified in PKHD1L1 that were predicted to be damaging using in silico pathogenicity prediction methods. In vitro functional analysis of two missense variants was performed using purified recombinant PKHD1L1 protein fragments. We then evaluated protein thermodynamic stability with and without the missense variants found in one of the families and performed a minigene splicing assay for another variant. In silico molecular modelling using AlphaFold2 and protein sequence alignment analysis were carried out to further explore potential variant effects on structure. In vitro functional assessment indicated that both engineered PKHD1L1 p.(Gly129Ser) and p.(Gly1314Val) mutant constructs significantly reduced the folding and structural stabilities of the expressed protein fragments, providing further evidence to support pathogenicity of these variants. Minigene assay of the c.1813G>A p.(Gly605Arg) variant, located at the boundary of exon 17, revealed exon skipping leading to an in-frame deletion of 48 amino acids. In silico molecular modelling exposed key structural features that might suggest PKHD1L1 protein destabilization. Multiple lines of evidence collectively associate PKHD1L1 with nonsyndromic mild-moderate to severe sensorineural hearing loss. PKHD1L1 testing in individuals with mild-moderate hearing loss may identify further affected families.
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Affiliation(s)
- Shelby E. Redfield
- Department of Otolaryngology and Communication Enhancement, Boston Children’s Hospital, 300 Longwood Avenue, BCH-3129, Boston, MA 02115, USA
| | - Pedro De-la-Torre
- Mass Eye and Ear, Eaton Peabody Laboratories, Boston, Massachusetts, USA
- Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
| | - Hanjun Wang
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, No. 40 Daxuebei Road, Zhengzhou, 450052, China
| | - Hina Khan
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Tyler Morris
- Mass Eye and Ear, Eaton Peabody Laboratories, Boston, Massachusetts, USA
| | - Gholamreza Shariati
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz, Iran
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Majid Karimi
- Khuzestan Cochlear Implantation Center (Tabassom), Ahvaz, Iran
| | - Margaret A. Kenna
- Department of Otolaryngology and Communication Enhancement, Boston Children’s Hospital, 300 Longwood Avenue, BCH-3129, Boston, MA 02115, USA
- Mass Eye and Ear, Eaton Peabody Laboratories, Boston, Massachusetts, USA
| | | | - Hongen Xu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, No. 40 Daxuebei Road, Zhengzhou, 450052, China
| | - Wei Lu
- Department of Otorhinolaryngology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jian-she Road, Zhengzhou, 450052, China
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Artur A. Indzhykulian
- Mass Eye and Ear, Eaton Peabody Laboratories, Boston, Massachusetts, USA
- Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - A. Eliot Shearer
- Department of Otolaryngology and Communication Enhancement, Boston Children’s Hospital, 300 Longwood Avenue, BCH-3129, Boston, MA 02115, USA
- Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany
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6
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Harafuji N, Yang C, Wu M, Thiruvengadam G, Gordish-Dressman H, Thompson RG, Bell PD, Rosenberg AZ, Dafinger C, Liebau MC, Bebok Z, Caldovic L, Guay-Woodford LM. Differential regulation of MYC expression by PKHD1/Pkhd1 in human and mouse kidneys: phenotypic implications for recessive polycystic kidney disease. Front Cell Dev Biol 2023; 11:1270980. [PMID: 38125876 PMCID: PMC10731465 DOI: 10.3389/fcell.2023.1270980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/30/2023] [Indexed: 12/23/2023] Open
Abstract
Autosomal recessive polycystic kidney disease (ARPKD; MIM#263200) is a severe, hereditary, hepato-renal fibrocystic disorder that leads to early childhood morbidity and mortality. Typical forms of ARPKD are caused by pathogenic variants in the PKHD1 gene, which encodes the fibrocystin/polyductin (FPC) protein. MYC overexpression has been proposed as a driver of renal cystogenesis, but little is known about MYC expression in recessive PKD. In the current study, we provide the first evidence that MYC is overexpressed in kidneys from ARPKD patients and confirm that MYC is upregulated in cystic kidneys from cpk mutant mice. In contrast, renal MYC expression levels were not altered in several Pkhd1 mutant mice that lack a significant cystic kidney phenotype. We leveraged previous observations that the carboxy-terminus of mouse FPC (FPC-CTD) is proteolytically cleaved through Notch-like processing, translocates to the nucleus, and binds to double stranded DNA, to examine whether the FPC-CTD plays a role in regulating MYC/Myc transcription. Using immunofluorescence, reporter gene assays, and ChIP, we demonstrate that both human and mouse FPC-CTD can localize to the nucleus, bind to the MYC/Myc P1 promoter, and activate MYC/Myc expression. Interestingly, we observed species-specific differences in FPC-CTD intracellular trafficking. Furthermore, our informatic analyses revealed limited sequence identity of FPC-CTD across vertebrate phyla and database queries identified temporal differences in PKHD1/Pkhd1 and CYS1/Cys1 expression patterns in mouse and human kidneys. Given that cystin, the Cys1 gene product, is a negative regulator of Myc transcription, these temporal differences in gene expression could contribute to the relative renoprotection from cystogenesis in Pkhd1-deficient mice. Taken together, our findings provide new mechanistic insights into differential mFPC-CTD and hFPC-CTD regulation of MYC expression in renal epithelial cells, which may illuminate the basis for the phenotypic disparities between human patients with PKHD1 pathogenic variants and Pkhd1-mutant mice.
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Affiliation(s)
- Naoe Harafuji
- Center for Translational Research, Children’s National Hospital, Washington, DC, United States
| | - Chaozhe Yang
- Center for Translational Research, Children’s National Hospital, Washington, DC, United States
| | - Maoqing Wu
- Center for Translational Research, Children’s National Hospital, Washington, DC, United States
| | - Girija Thiruvengadam
- Center for Translational Research, Children’s National Hospital, Washington, DC, United States
| | | | - R. Griffin Thompson
- Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - P. Darwin Bell
- Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Avi Z. Rosenberg
- Department of Pathology, Johns Hopkins University, Baltimore, MD, United States
| | - Claudia Dafinger
- Department of Pediatrics and Center for Molecular Medicine, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Max C. Liebau
- Department of Pediatrics, Center for Family Health, Center for Rare Diseases and Center for Molecular Medicine, Medical Faculty and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Zsuzsanna Bebok
- Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ljubica Caldovic
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, United States
- Department of Genomics and Precision Medicine, School of Medical and Health Sciences, The George Washington University, Washington, DC, United States
| | - Lisa M. Guay-Woodford
- Center for Translational Research, Children’s National Hospital, Washington, DC, United States
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, United States
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7
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Makrogkikas S, Cheng RK, Lu H, Roy S. A conserved function of Pkhd1l1, a mammalian hair cell stereociliary coat protein, in regulating hearing in zebrafish. J Neurogenet 2023; 37:85-92. [PMID: 36960824 DOI: 10.1080/01677063.2023.2187792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/02/2023] [Indexed: 03/25/2023]
Abstract
Pkhd1l1 is predicted to encode a very large type-I transmembrane protein, but its function has largely remained obscure. Recently, it was shown that Pkhdl1l1 is a component of the coat that decorates stereocilia of outer hair cells in the mouse ear. Consistent with this localization, conditional deletion of Pkhd1l1 specifically from hair cells, was associated with progressive hearing loss. In the zebrafish, there are two paralogous pkhd1l1 genes - pkhd1l1α and pkhd1l1β. Using CRISPR-Cas9 mediated gene editing, we generated loss-of-function alleles for both and show that the double mutants exhibit nonsense-mediated-decay (NMD) of the RNAs. With behavioural assays, we demonstrate that zebrafish pkhd1l1 genes also regulate hearing; however, in contrast to Pkhd1l1 mutant mice, which develop progressive hearing loss, the double mutant zebrafish exhibited statistically significant hearing loss even from the larval stage. Our data highlight a conserved function of Pkhd1l1 in hearing and based on these findings from animal models, we postulate that PKHD1L1 could be a candidate gene for sensorineural hearing loss (SNHL) in humans.
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Affiliation(s)
- Stylianos Makrogkikas
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ruey-Kuang Cheng
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Hao Lu
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Sudipto Roy
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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8
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Yu J, Wang G, Chen Z, Wan L, Zhou J, Cai J, Liu X, Wang Y. Deficit of PKHD1L1 in the dentate gyrus increases seizure susceptibility in mice. Hum Mol Genet 2023; 32:506-519. [PMID: 36067019 DOI: 10.1093/hmg/ddac220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 01/24/2023] Open
Abstract
Epilepsy is a chronic neurological disorder featuring recurrent, unprovoked seizures, which affect more than 65 million people worldwide. Here, we discover that the PKHD1L1, which is encoded by polycystic kidney and hepatic disease1-like 1 (Pkhd1l1), wildly distributes in neurons in the central nervous system (CNS) of mice. Disruption of PKHD1L1 in the dentate gyrus region of the hippocampus leads to increased susceptibility to pentylenetetrazol-induced seizures in mice. The disturbance of PKHD1L1 leads to the overactivation of the mitogen-activated protein kinase (MAPK)/extracellular regulated kinase (ERK)-Calpain pathway, which is accompanied by remarkable degradation of cytoplasmic potassium chloride co-transporter 2 (KCC2) level together with the impaired expression and function of membrane KCC2. However, the reduction of membrane KCC2 is associated with the damaged inhibitory ability of the vital GABA receptors, which ultimately leads to the significantly increased susceptibility to epileptic seizures. Our data, thus, indicate for the first time that Pkhd1l1, a newly discovered polycystic kidney disease (PKD) association gene, is required in neurons to maintain neuronal excitability by regulation of KCC2 expression in CNS. A new mechanism of the clinical association between genetic PKD and seizures has been built, which could be a potential therapeutic target for treating PKD-related seizures.
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Affiliation(s)
- Jiangning Yu
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Biological Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Guoxiang Wang
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Biological Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zhiyun Chen
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Biological Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Li Wan
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Biological Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China.,Rehabilitation Center, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen 518035, China
| | - Jing Zhou
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Biological Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China.,Rehabilitation Center, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen 518035, China
| | - Jingyi Cai
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Biological Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xu Liu
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Biological Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yun Wang
- Department of Neurology, Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Biological Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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9
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Wang D, Chen X, Du Y, Li X, Ying L, Lu Y, Shen B, Gao X, Yi X, Xia X, Sui X, Shu Y. Associations of HER2 Mutation With Immune-Related Features and Immunotherapy Outcomes in Solid Tumors. Front Immunol 2022; 13:799988. [PMID: 35281032 PMCID: PMC8905508 DOI: 10.3389/fimmu.2022.799988] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/03/2022] [Indexed: 12/11/2022] Open
Abstract
Background HER2 is one of the most extensively studied oncogenes in solid tumors. However, the association between tumor microenvironment (TME) and HER2 mutation remains elusive, and there are no specific therapies for HER2-mutated tumors. Immune checkpoint inhibitors (ICIs) have been approved for some tumor subgroups that lack targeted therapies, while their effects are still unclear in HER2-mutated tumors. We examined whether HER2 mutation impacts treatment outcomes of ICIs in solid tumors via its association with anticancer immunity. Methods Multi-omics data of solid tumors from The Cancer Genome Atlas (TCGA), the Asian Cancer Research Group and the Affiliated Hospital of Jiangsu University were used to analyze the association between HER2 mutations and tumor features. Data of patients with multiple microsatellite-stable solid tumors, who were treated by ICIs including antibodies against programmed cell death-1 (PD-1), programmed cell death ligand-1 (PD-L1), or cytotoxic T lymphocyte-associated protein 4 (CTLA-4) in eight studies, were collected to investigate the effects of HER2 mutations on immunotherapy outcomes. Results The mutation rate of HER2 varied in solid tumors of TCGA, with an overall incidence of 3.13%, ranged from 0.39% to 12.2%. Concurrent HER2 mutations and amplifications were rare (0.26%). HER2 mutation was not associated with HER2 protein expression but was positively associated with microsatellite instability, tumor mutation and neoantigen burdens, infiltrating antitumor immune cells, and signal activities of antitumor immunity. Of 321 ICI-treated patients, 18 carried HER2 mutations (5.6%) and showed improved objective response rates compared with those with HER2 wild-type (44.4% vs. 25.7%, p=0.081), especially in the anti-PD-1/anti-PD-L1 subgroup (62.5% vs. 28.4%, p=0.04). Heterogeneity was observed among tumor types. Patients with HER2 mutations also had superior overall survival than those with HER2 wild-type (HR=0.47, 95%CI: 0.23-0.97, p=0.04), especially in the presence of co-mutations in ABCA1 (HR = 0.23, 95% CI: 0.07-0.73, p=0.013), CELSR1 (HR = 0.24, 95% CI: 0.08-0.77, p=0.016), LRP2 (HR = 0.24, 95% CI: 0.07-0.74, p=0.014), or PKHD1L1 (HR = 0.2, 95% CI: 0.05-0.8, p=0.023). Conclusions HER2 mutations may improve the TME to favor immunotherapy. A prospective basket trial is needed to further investigate the impacts of HER2 mutations on immunotherapy outcomes in solid tumors.
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Affiliation(s)
- Deqiang Wang
- Department of Medical Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Xiaofeng Chen
- Department of Medical Oncology, Jiangsu Province Hospital, Nanjing, China
| | - Yian Du
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Xiaoqin Li
- Department of Medical Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Leqian Ying
- Department of Medical Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yi Lu
- Department of Medical Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Bo Shen
- Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Xuan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Shenzhen Clinical Laboratory, GenePlus, Shenzhen, China
| | - Xin Yi
- Beijing Institute, GenePlus, Beijing, China
| | | | - Xinbing Sui
- Department of Medical Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang, China.,School of Pharmacy, Hangzhou Normal University, Hangzhou, China
| | - Yongqian Shu
- Department of Medical Oncology, Jiangsu Province Hospital, Nanjing, China
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10
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Cordido A, Vizoso-Gonzalez M, Garcia-Gonzalez MA. Molecular Pathophysiology of Autosomal Recessive Polycystic Kidney Disease. Int J Mol Sci 2021; 22:6523. [PMID: 34204582 PMCID: PMC8235086 DOI: 10.3390/ijms22126523] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/19/2022] Open
Abstract
Autosomal recessive polycystic kidney disease (ARPKD) is a rare disorder and one of the most severe forms of polycystic kidney disease, leading to end-stage renal disease (ESRD) in childhood. PKHD1 is the gene that is responsible for the vast majority of ARPKD. However, some cases have been related to a new gene that was recently identified (DZIP1L gene), as well as several ciliary genes that can mimic a ARPKD-like phenotypic spectrum. In addition, a number of molecular pathways involved in the ARPKD pathogenesis and progression were elucidated using cellular and animal models. However, the function of the ARPKD proteins and the molecular mechanism of the disease currently remain incompletely understood. Here, we review the clinics, treatment, genetics, and molecular basis of ARPKD, highlighting the most recent findings in the field.
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Affiliation(s)
- Adrian Cordido
- Grupo de Xenética e Bioloxía do Desenvolvemento das Enfermidades Renais, Laboratorio de Nefroloxía (No. 11), Instituto de Investigación Sanitaria de Santiago (IDIS), Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain; (A.C.); (M.V.-G.)
- Grupo de Medicina Xenómica, Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain
| | - Marta Vizoso-Gonzalez
- Grupo de Xenética e Bioloxía do Desenvolvemento das Enfermidades Renais, Laboratorio de Nefroloxía (No. 11), Instituto de Investigación Sanitaria de Santiago (IDIS), Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain; (A.C.); (M.V.-G.)
- Grupo de Medicina Xenómica, Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain
| | - Miguel A. Garcia-Gonzalez
- Grupo de Xenética e Bioloxía do Desenvolvemento das Enfermidades Renais, Laboratorio de Nefroloxía (No. 11), Instituto de Investigación Sanitaria de Santiago (IDIS), Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain; (A.C.); (M.V.-G.)
- Grupo de Medicina Xenómica, Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain
- Fundación Publica Galega de Medicina Xenómica-SERGAS, Complexo Hospitalario de Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain
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11
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Zimmerman KA, Hopp K, Mrug M. Role of chemokines, innate and adaptive immunity. Cell Signal 2020; 73:109647. [PMID: 32325183 DOI: 10.1016/j.cellsig.2020.109647] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/16/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023]
Abstract
Polycystic Kidney Disease (PKD) triggers a robust immune system response including changes in both innate and adaptive immunity. These changes involve immune cells (e.g., macrophages and T cells) as well as cytokines and chemokines (e.g., MCP-1) that regulate the production, differentiation, homing, and various functions of these cells. This review is focused on the role of the immune system and its associated factors in the pathogenesis of PKDs as evidenced by data from cell-based systems, animal models, and PKD patients. It also highlights relevant pre-clinical and clinical studies that point to specific immune system components as promising candidates for the development of prognostic biomarkers and therapeutic strategies to improve PKD outcomes.
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Affiliation(s)
- Kurt A Zimmerman
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Division of Nephrology, Department of Internal Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Katharina Hopp
- Department of Medicine, Division of Renal Diseases and Hypertension, Polycystic Kidney Disease Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michal Mrug
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Department of Veterans Affairs Medical Center, Birmingham, AL 35233, USA.
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12
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Lea WA, McGreal K, Sharma M, Parnell SC, Zelenchuk L, Charlesworth MC, Madden BJ, Johnson KL, McCormick DJ, Hogan MC, Ward CJ. Analysis of the polycystin complex (PCC) in human urinary exosome-like vesicles (ELVs). Sci Rep 2020; 10:1500. [PMID: 32001768 PMCID: PMC6992733 DOI: 10.1038/s41598-020-58087-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 01/05/2020] [Indexed: 12/21/2022] Open
Abstract
The polycystin-1 (PC1), polycystin-2 (PC2) and fibrocystin proteins, the respective products of the PKD1, PKD2 and PKHD1 genes, are abundant in urinary exosome-like vesicles (ELVs) where they form the polycystin complex (PCC). ELVs are 100 nm diameter membrane vesicles shed into the urine by the cells lining the nephron. Using MS/MS analysis of ELVs from individuals with PKD1 mutations and controls, we show that in addition to the well-described GPS/GAIN cleavage event in PC1 at 3048 aa and the proprotein convertase cleavage (PPC) event in fibrocystin at 3616 aa, there are multiple other cleavage events in these proteins. The C-terminal 11 transmembrane portion of PC1 undergoes three cleavage events in vivo. The absence of peptides from the C-terminal cytoplasmic tail of fibrocystin implies a cleavage event close to its single TM domain prior to loading onto the ELVs. There is also evidence that the C-terminal tail of PC2 is also cleaved in ELVs. Native gel analysis of the PCC shows that the entire complex is > 2 MDa in size and that N-terminal GPS/GAIN cleaved PC1 and PPC cleaved fibrocystin ectodomains can be released under non-reducing conditions and resolve at 300 kDa. This paper shows that the three major human cystogene proteins are detectable in human urinary ELVs and that all three undergo post-translational proteolytic processing. Human urinary ELVs may be a useful source of material in the search for proteins that interact with the PCC.
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Affiliation(s)
- Wendy A Lea
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Kerri McGreal
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Madhulika Sharma
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Stephen C Parnell
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Lesya Zelenchuk
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - M Cristine Charlesworth
- Mayo Proteomic Core, Medical Sciences Building, Ms 3-121, Mayo Clinic, 200 First Street, SW Rochester, MN, 55905, USA
| | - Benjamin J Madden
- Mayo Proteomic Core, Medical Sciences Building, Ms 3-121, Mayo Clinic, 200 First Street, SW Rochester, MN, 55905, USA
| | - Kenneth L Johnson
- Mayo Proteomic Core, Medical Sciences Building, Ms 3-121, Mayo Clinic, 200 First Street, SW Rochester, MN, 55905, USA
| | - Daniel J McCormick
- Mayo Proteomic Core, Medical Sciences Building, Ms 3-121, Mayo Clinic, 200 First Street, SW Rochester, MN, 55905, USA
| | - Marie C Hogan
- Division of Nephrology, Department of Internal Medicine, Mayo Clinic, Rochester, USA
| | - Christopher J Ward
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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13
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NF1 patient missense variants predict a role for ATM in modifying neurofibroma initiation. Acta Neuropathol 2020; 139:157-174. [PMID: 31664505 DOI: 10.1007/s00401-019-02086-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 01/01/2023]
Abstract
In Neurofibromatosis type 1, NF1 gene mutations in Schwann cells (SC) drive benign plexiform neurofibroma (PNF), and no additional SC changes explain patient-to-patient variability in tumor number. Evidence from twin studies suggests that variable expressivity might be caused by unidentified modifier genes. Whole exome sequencing of SC and fibroblast DNA from the same resected PNFs confirmed biallelic SC NF1 mutations; non-NF1 somatic SC variants were variable and present at low read number. We identified frequent germline variants as possible neurofibroma modifier genes. Genes harboring variants were validated in two additional cohorts of NF1 patients and by variant burden test. Genes including CUBN, CELSR2, COL14A1, ATR and ATM also showed decreased gene expression in some neurofibromas. ATM-relevant DNA repair defects were also present in a subset of neurofibromas with ATM variants, and in some neurofibroma SC. Heterozygous ATM G2023R or homozygous S707P variants reduced ATM protein expression in heterologous cells. In mice, genetic Atm heterozygosity promoted Schwann cell precursor self-renewal and increased tumor formation in vivo, suggesting that ATM variants contribute to neurofibroma initiation. We identify germline variants, rare in the general population, overrepresented in NF1 patients with neurofibromas. ATM and other identified genes are candidate modifiers of PNF pathogenesis.
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14
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PKHD1L1 is a coat protein of hair-cell stereocilia and is required for normal hearing. Nat Commun 2019; 10:3801. [PMID: 31444330 PMCID: PMC6707252 DOI: 10.1038/s41467-019-11712-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/28/2019] [Indexed: 12/18/2022] Open
Abstract
The bundle of stereocilia on inner ear hair cells responds to subnanometer deflections produced by sound or head movement. Stereocilia are interconnected by a variety of links and also carry an electron-dense surface coat. The coat may contribute to stereocilia adhesion or protect from stereocilia fusion, but its molecular identity remains unknown. From a database of hair-cell-enriched translated proteins, we identify Polycystic Kidney and Hepatic Disease 1-Like 1 (PKHD1L1), a large, mostly extracellular protein of 4249 amino acids with a single transmembrane domain. Using serial immunogold scanning electron microscopy, we show that PKHD1L1 is expressed at the tips of stereocilia, especially in the high-frequency regions of the cochlea. PKHD1L1-deficient mice lack the surface coat at the upper but not lower regions of stereocilia, and they develop progressive hearing loss. We conclude that PKHD1L1 is a component of the surface coat and is required for normal hearing in mice. There is little known about the function or molecular identity of the electron-dense stereocilia coat, which is transiently present at the surface of stereocilia. In this study authors screened a database of hair-cell-enriched translated proteins to identify the expression of Polycystic Kidney and Hepatic Disease 1-Like 1 (PKHD1L1), a large, mostly extracellular protein, and show that it forms the coat at the tips of stereocilia and is required for normal hearing in mice
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15
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Zheng C, Quan R, Xia EJ, Bhandari A, Zhang X. Original tumour suppressor gene polycystic kidney and hepatic disease 1-like 1 is associated with thyroid cancer cell progression. Oncol Lett 2019; 18:3227-3235. [PMID: 31452800 PMCID: PMC6676403 DOI: 10.3892/ol.2019.10632] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 06/13/2019] [Indexed: 02/03/2023] Open
Abstract
In recent decades, thyroid cancer (TC) has become one of the most common endocrine malignancies. Next-generation sequencing of paired TC and adjacent healthy thyroid tissues demonstrated that polycystic kidney and hepatic disease 1-like 1 (PKHD1L1) may serve as a tumour suppressor gene in thyroid cancer. However, the function of PKHD1L1 in thyroid cancer is still unknown. To validate the results of whole-transcriptome resequencing, the expression levels of PKHD1L1 were evaluated in 58 pairs of papillary thyroid cancer (PTC) tissue samples and three thyroid cancer cell lines. In addition, The Cancer Genome Atlas (TCGA) data were used to analyse the relationship between PKHD1L1 and patient clinicopathological features. Cell Counting Kit-8, colony formation, migration and invasion assays were performed to assess the effects of PKHD1L1 knockdown in three TC cell lines. PKHD1L1 expression was significantly lower in thyroid carcinoma compared with that in matched normal tissue, and this result was consistent with that in TCGA cohort. TCGA data demonstrated that PKHD1L1 downregulation was associated with a number of aggressive clinicopathological features, such as histological type, lymph node metastasis (LNM), distant metastasis, tumour size and clinical stage. Logistic regression analysis of data from patients with PTC revealed that PKHD1L1 expression, histological type, age and tumour size were independent high-risk factors for LNM. The PKHD1L1 biological function was investigated in the three TC cell lines: TPC-1, KTC1 and BCPAP. A loss of function experiment demonstrated that PKHD1L1 knockdown promoted cell proliferation, colony formation and cell invasion in TC cell lines. In conclusion, PKHD1L1 may be a tumour suppressor gene associated with PC, and may be a potential therapeutic target in the future.
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Affiliation(s)
- Chen Zheng
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Ruida Quan
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Er-Jie Xia
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Adheesh Bhandari
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Xiaohua Zhang
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
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16
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de Stephanis L, Mangolini A, Servello M, Harris PC, Dell'Atti L, Pinton P, Aguiari G. MicroRNA501-5p induces p53 proteasome degradation through the activation of the mTOR/MDM2 pathway in ADPKD cells. J Cell Physiol 2018; 233:6911-6924. [PMID: 29323708 DOI: 10.1002/jcp.26473] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 01/05/2018] [Indexed: 01/01/2023]
Abstract
Cell proliferation and apoptosis are typical hallmarks of autosomal dominant polycystic kidney disease (ADPKD) and cause the development of kidney cysts that lead to end-stage renal disease (ESRD). Many factors, impaired by polycystin complex loss of function, may promote these biological processes, including cAMP, mTOR, and EGFR signaling pathways. In addition, microRNAs (miRs) may also regulate the ADPKD related signaling network and their dysregulation contributes to disease progression. However, the role of miRs in ADPKD pathogenesis has not been fully understood, but also the function of p53 is quite obscure, especially its regulatory contribution on cell proliferation and apoptosis. Here, we describe for the first time that miR501-5p, upregulated in ADPKD cells and tissues, induces the activation of mTOR kinase by PTEN and TSC1 gene repression. The increased activity of mTOR kinase enhances the expression of E3 ubiquitin ligase MDM2 that in turn promotes p53 ubiquitination, leading to its degradation by proteasome machinery in a network involving p70S6K. Moreover, the overexpression of miR501-5p stimulates cell proliferation in kidney cells by the inhibition of p53 function in a mechanism driven by mTOR signaling. In fact, the downregulation of this miR as well as the pharmacological treatment with proteasome and mTOR inhibitors in ADPKD cells reduces cell growth by the activation of apoptosis. Consequently, the stimulation of cell death in ADPKD cells may occur through the inhibition of mTOR/MDM2 signaling and the restoring of p53 function. The data presented here confirm that the impaired mTOR signaling plays an important role in ADPKD.
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Affiliation(s)
- Lucia de Stephanis
- Department of Biomedical and Surgical Specialty Sciences, University of Ferrara, Ferrara, Italy
| | | | - Miriam Servello
- Department of Biomedical and Surgical Specialty Sciences, University of Ferrara, Ferrara, Italy.,Unit of Urology, St. Anna Hospital, Ferrara, Italy
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic College of Medicine, Rochester, Minnesota
| | | | - Paolo Pinton
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Gianluca Aguiari
- Department of Biomedical and Surgical Specialty Sciences, University of Ferrara, Ferrara, Italy
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17
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Evidence of positive selection towards Zebuine haplotypes in the BoLA region of Brangus cattle. Animal 2017; 12:215-223. [PMID: 28707606 DOI: 10.1017/s1751731117001380] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Brangus breed was developed to combine the superior characteristics of both of its founder breeds, Angus and Brahman. It combines the high adaptability to tropical and subtropical environments, disease resistance, and overall hardiness of Zebu cattle with the reproductive potential and carcass quality of Angus. It is known that the major histocompatibility complex (MHC, also known as bovine leucocyte antigen: BoLA), located on chromosome 23, encodes several genes involved in the adaptive immune response and may be responsible for adaptation to harsh environments. The objective of this work was to evaluate whether the local breed ancestry percentages in the BoLA locus of a Brangus population diverged from the estimated genome-wide proportions and to identify signatures of positive selection in this genomic region. For this, 167 animals (100 Brangus, 45 Angus and 22 Brahman) were genotyped using a high-density single nucleotide polymorphism array. The local ancestry analysis showed that more than half of the haplotypes (55.0%) shared a Brahman origin. This value was significantly different from the global genome-wide proportion estimated by cluster analysis (34.7% Brahman), and the proportion expected by pedigree (37.5% Brahman). The analysis of selection signatures by genetic differentiation (F st ) and extended haplotype homozygosity-based methods (iHS and Rsb) revealed 10 and seven candidate regions, respectively. The analysis of the genes located within these candidate regions showed mainly genes involved in immune response-related pathway, while other genes and pathways were also observed (cell surface signalling pathways, membrane proteins and ion-binding proteins). Our results suggest that the BoLA region of Brangus cattle may have been enriched with Brahman haplotypes as a consequence of selection processes to promote adaptation to subtropical environments.
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18
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De Angelis JE, Lagendijk AK, Chen H, Tromp A, Bower NI, Tunny KA, Brooks AJ, Bakkers J, Francois M, Yap AS, Simons C, Wicking C, Hogan BM, Smith KA. Tmem2 Regulates Embryonic Vegf Signaling by Controlling Hyaluronic Acid Turnover. Dev Cell 2017; 40:123-136. [PMID: 28118600 DOI: 10.1016/j.devcel.2016.12.017] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 10/18/2016] [Accepted: 12/16/2016] [Indexed: 11/28/2022]
Abstract
Angiogenesis is responsible for tissue vascularization during development, as well as in pathological contexts, including cancer and ischemia. Vascular endothelial growth factors (VEGFs) regulate angiogenesis by acting through VEGF receptors to induce endothelial cell signaling. VEGF is processed in the extracellular matrix (ECM), but the complexity of ECM control of VEGF signaling and angiogenesis remains far from understood. In a forward genetic screen, we identified angiogenesis defects in tmem2 zebrafish mutants that lack both arterial and venous Vegf/Vegfr/Erk signaling. Strikingly, tmem2 mutants display increased hyaluronic acid (HA) surrounding developing vessels. Angiogenesis in tmem2 mutants was rescued, or restored after failed sprouting, by degrading this increased HA. Furthermore, oligomerized HA or overexpression of Vegfc rescued angiogenesis in tmem2 mutants. Based on these data, and the known structure of Tmem2, we find that Tmem2 regulates HA turnover to promote normal Vegf signaling during developmental angiogenesis.
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Affiliation(s)
- Jessica E De Angelis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Anne K Lagendijk
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Huijun Chen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alisha Tromp
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Neil I Bower
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kathryn A Tunny
- Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Andrew J Brooks
- Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jeroen Bakkers
- Department of Cardiac Development and Genetics, Hubrecht Institute, University Medical Centre Utrecht, Utrecht 3584 CT, the Netherlands; Department of Medical Physiology, University Medical Centre Utrecht, Utrecht 3584 EA, the Netherlands
| | - Mathias Francois
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alpha S Yap
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Cas Simons
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Carol Wicking
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Benjamin M Hogan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Kelly A Smith
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
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Erdman VV, Karimov DD, Nasibullin TR, Timasheva IR, Tuktarova IA, Mustafina OE. The role of Alu polymorphism of PLAT, PKHD1L1, STK38L, and TEAD1 genes in development of a longevity trait. ADVANCES IN GERONTOLOGY 2017. [DOI: 10.1134/s2079057017020059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Porsch RM, Merello E, De Marco P, Cheng G, Rodriguez L, So M, Sham PC, Tam PK, Capra V, Cherny SS, Garcia-Barcelo MM, Campbell DD. Sacral agenesis: a pilot whole exome sequencing and copy number study. BMC MEDICAL GENETICS 2016; 17:98. [PMID: 28007035 PMCID: PMC5178083 DOI: 10.1186/s12881-016-0359-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 12/02/2016] [Indexed: 12/30/2022]
Abstract
Background Caudal regression syndrome (CRS) or sacral agenesis is a rare congenital disorder characterized by a constellation of congenital caudal anomalies affecting the caudal spine and spinal cord, the hindgut, the urogenital system, and the lower limbs. CRS is a complex condition, attributed to an abnormal development of the caudal mesoderm, likely caused by the effect of interacting genetic and environmental factors. A well-known risk factor is maternal type 1 diabetes. Method Whole exome sequencing and copy number variation (CNV) analyses were conducted on 4 Caucasian trios to identify de novo and inherited rare mutations. Results In this pilot study, exome sequencing and copy number variation (CNV) analyses implicate a number of candidate genes, including SPTBN5, MORN1, ZNF330, CLTCL1 and PDZD2. De novo mutations were found in SPTBN5, MORN1 and ZNF330 and inherited predicted damaging mutations in PDZD2 (homozygous) and CLTCL1 (compound heterozygous). Importantly, predicted damaging mutations in PTEN (heterozygous), in its direct regulator GLTSCR2 (compound heterozygous) and in VANGL1 (heterozygous) were identified. These genes had previously been linked with the CRS phenotype. Two CNV deletions, one de novo (chr3q13.13) and one homozygous (chr8p23.2), were detected in one of our CRS patients. These deletions overlapped with CNVs previously reported in patients with similar phenotype. Conclusion Despite the genetic diversity and the complexity of the phenotype, this pilot study identified genetic features common across CRS patients. Electronic supplementary material The online version of this article (doi:10.1186/s12881-016-0359-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robert M Porsch
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | | | | | - Guo Cheng
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | | | - Manting So
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Pak C Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR.,Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR.,Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR.,State Key Laboratory of Brain and Cognitive Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Paul K Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR.,Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | | | - Stacey S Cherny
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR.,Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR.,State Key Laboratory of Brain and Cognitive Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Maria-Mercè Garcia-Barcelo
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR. .,Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR. .,The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam, Hong Kong, People's Republic of China.
| | - Desmond D Campbell
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR. .,Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR.
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21
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Identification of Gene Mutations and Fusion Genes in Patients with Sézary Syndrome. J Invest Dermatol 2016; 136:1490-1499. [DOI: 10.1016/j.jid.2016.03.024] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/07/2016] [Accepted: 03/11/2016] [Indexed: 12/12/2022]
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Lessard S, Manning AK, Low-Kam C, Auer PL, Giri A, Graff M, Schurmann C, Yaghootkar H, Luan J, Esko T, Karaderi T, Bottinger EP, Lu Y, Carlson C, Caulfield M, Dubé MP, Jackson RD, Kooperberg C, McKnight B, Mongrain I, Peters U, Reiner AP, Rhainds D, Sotoodehnia N, Hirschhorn JN, Scott RA, Munroe PB, Frayling TM, Loos RJF, North KE, Edwards TL, Tardif JC, Lindgren CM, Lettre G. Testing the role of predicted gene knockouts in human anthropometric trait variation. Hum Mol Genet 2016; 25:2082-2092. [PMID: 26908616 PMCID: PMC5062577 DOI: 10.1093/hmg/ddw055] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/15/2016] [Indexed: 11/12/2022] Open
Abstract
Although the role of complete gene inactivation by two loss-of-function mutations inherited in trans is well-established in recessive Mendelian diseases, we have not yet explored how such gene knockouts (KOs) could influence complex human phenotypes. Here, we developed a statistical framework to test the association between gene KOs and quantitative human traits. Our method is flexible, publicly available, and compatible with common genotype format files (e.g. PLINK and vcf). We characterized gene KOs in 4498 participants from the NHLBI Exome Sequence Project (ESP) sequenced at high coverage (>100×), 1976 French Canadians from the Montreal Heart Institute Biobank sequenced at low coverage (5.7×), and >100 000 participants from the Genetic Investigation of ANthropometric Traits (GIANT) Consortium genotyped on an exome array. We tested associations between gene KOs and three anthropometric traits: body mass index (BMI), height and BMI-adjusted waist-to-hip ratio (WHR). Despite our large sample size and multiple datasets available, we could not detect robust associations between specific gene KOs and quantitative anthropometric traits. Our results highlight several limitations and challenges for future gene KO studies in humans, in particular when there is no prior knowledge on the phenotypes that might be affected by the tested gene KOs. They also suggest that gene KOs identified with current DNA sequencing methodologies probably do not strongly influence normal variation in BMI, height, and WHR in the general human population.
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Affiliation(s)
- Samuel Lessard
- Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Alisa K Manning
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA 02142, USA Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA 02114, USA Department of Medicine and
| | - Cécile Low-Kam
- Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Paul L Auer
- School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI 53201-0413, USA
| | - Ayush Giri
- Division of Epidemiology, Institute for Medicine and Public Health and
| | - Mariaelisa Graff
- University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine and The Mindich Child Health and Development Institute, the Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hanieh Yaghootkar
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Jian'an Luan
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Tonu Esko
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA 02142, USA Estonian Genome Center, University of Tartu, Tartu, Estonia Division of Endocrinology, Genetics and Basic and Translational Obesity Research, Children's Hospital Boston, Boston, MA 02115, USA
| | - Tugce Karaderi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | | | | | | | | | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine and
| | - Chris Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Mark Caulfield
- Clinical Pharmacology, William Harvey Research Institute and NIHR Barts Cardiovascular Biomedical Research Unit, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Marie-Pierre Dubé
- Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, Ohio State University, Columbus, OH 43210, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Ian Mongrain
- Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - David Rhainds
- Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Nona Sotoodehnia
- Division of Cardiology, Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98195-6422, USA
| | - Joel N Hirschhorn
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA 02142, USA Department of Genetics, Harvard Medical School, Boston, MA 02115, USA Division of Endocrinology, Genetics and Basic and Translational Obesity Research, Children's Hospital Boston, Boston, MA 02115, USA
| | - Robert A Scott
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Patricia B Munroe
- Clinical Pharmacology, William Harvey Research Institute and NIHR Barts Cardiovascular Biomedical Research Unit, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine and The Mindich Child Health and Development Institute, the Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kari E North
- University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
| | - Todd L Edwards
- Division of Epidemiology, Institute for Medicine and Public Health and Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Jean-Claude Tardif
- Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Cecilia M Lindgren
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA 02142, USA Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK The Big Data Institute, University of Oxford, Oxford, UK
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
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Xu Y, Xiao B, Jiang WT, Wang L, Gen HQ, Chen YW, Sun Y, Ji X. A novel mutation identified in PKHD1 by targeted exome sequencing: guiding prenatal diagnosis for an ARPKD family. Gene 2014; 551:33-8. [PMID: 25153916 DOI: 10.1016/j.gene.2014.08.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 08/14/2014] [Accepted: 08/18/2014] [Indexed: 01/24/2023]
Abstract
Autosomal recessive polycystic kidney disease (ARPKD) is a rare hereditary renal cystic disease involving multiple organs, mainly the kidney and liver. Parents who had an affected child with ARPKD are in strong demand for an early and reliable prenatal diagnosis to guide the future pregnancies. Here we provide an example of prenatal diagnosis of an ARPKD family where traditional antenatal ultrasound examinations failed to produce conclusive results till 26th week of gestation. Compound heterozygous mutations c.274C>T (p.Arg92Trp) and c.9059T>C (p.Leu3020Pro) were identified using targeted exome sequencing in the patient and confirmed by Sanger sequencing. Further, the mother and father were revealed to be carriers of heterozygous c.274C>T and c.9059T>C mutations, respectively. Molecular prenatal diagnosis was performed for the current pregnancy by direct sequencing plus linkage analysis. Two mutations identified in the patient were both found in the fetus. In conclusion, compound heterozygous PKHD1 mutations were elucidated to be the molecular basis of the patient with ARPKD. The newly identified c.9059T>C mutation in the patient expands mutation spectrum in PKHD1 gene. For those ultrasound failed to provide clear diagnosis, we propose the new prenatal diagnosis procedure: first, screening underlying mutations in PKHD1 gene in the proband by targeted exome sequencing; then detecting causative mutations by direct sequencing in the fetal DNA and confirming results by linkage analysis.
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Affiliation(s)
- Yan Xu
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Bing Xiao
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Wen-Ting Jiang
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Lei Wang
- Department of Pediatric Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong-Quan Gen
- Department of urinary Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying-Wei Chen
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Yu Sun
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Xing Ji
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China.
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Mathieu-Rivet E, Scholz M, Arias C, Dardelle F, Schulze S, Le Mauff F, Teo G, Hochmal AK, Blanco-Rivero A, Loutelier-Bourhis C, Kiefer-Meyer MC, Fufezan C, Burel C, Lerouge P, Martinez F, Bardor M, Hippler M. Exploring the N-glycosylation pathway in Chlamydomonas reinhardtii unravels novel complex structures. Mol Cell Proteomics 2013; 12:3160-83. [PMID: 23912651 PMCID: PMC3820931 DOI: 10.1074/mcp.m113.028191] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 08/01/2013] [Indexed: 01/13/2023] Open
Abstract
Chlamydomonas reinhardtii is a green unicellular eukaryotic model organism for studying relevant biological and biotechnological questions. The availability of genomic resources and the growing interest in C. reinhardtii as an emerging cell factory for the industrial production of biopharmaceuticals require an in-depth analysis of protein N-glycosylation in this organism. Accordingly, we used a comprehensive approach including genomic, glycomic, and glycoproteomic techniques to unravel the N-glycosylation pathway of C. reinhardtii. Using mass-spectrometry-based approaches, we found that both endogenous soluble and membrane-bound proteins carry predominantly oligomannosides ranging from Man-2 to Man-5. In addition, minor complex N-linked glycans were identified as being composed of partially 6-O-methylated Man-3 to Man-5 carrying one or two xylose residues. These findings were supported by results from a glycoproteomic approach that led to the identification of 86 glycoproteins. Here, a combination of in-source collision-induced dissodiation (CID) for glycan fragmentation followed by mass tag-triggered CID for peptide sequencing and PNGase F treatment of glycopeptides in the presence of (18)O-labeled water in conjunction with CID mass spectrometric analyses were employed. In conclusion, our data support the notion that the biosynthesis and maturation of N-linked glycans in the endoplasmic reticulum and Golgi apparatus occur via a GnT I-independent pathway yielding novel complex N-linked glycans that maturate differently from their counterparts in land plants.
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Affiliation(s)
- Elodie Mathieu-Rivet
- From the ‡Université de Rouen, Laboratoire Glyco-MEV, EA 4358, Institut de Recherche et d'Innovation Biomédicale (IRIB), 76821 Mont-Saint-Aignan Cedex, France
| | - Martin Scholz
- ¶Institute of Plant Biology and Biotechnology, Schlossplatz 8, University of Münster, D-48143, Germany
| | - Carolina Arias
- ‖Comisión Docente de Fisiología Vegetal, Departamento de Biología, Edificio de Biología Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Flavien Dardelle
- From the ‡Université de Rouen, Laboratoire Glyco-MEV, EA 4358, Institut de Recherche et d'Innovation Biomédicale (IRIB), 76821 Mont-Saint-Aignan Cedex, France
| | - Stefan Schulze
- ¶Institute of Plant Biology and Biotechnology, Schlossplatz 8, University of Münster, D-48143, Germany
| | - François Le Mauff
- ‡‡Bioprocessing Technology Institute, Agency for Science Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, Singapore, 138668
| | - Gavin Teo
- ‡‡Bioprocessing Technology Institute, Agency for Science Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, Singapore, 138668
| | - Ana Karina Hochmal
- ¶Institute of Plant Biology and Biotechnology, Schlossplatz 8, University of Münster, D-48143, Germany
| | - Amaya Blanco-Rivero
- ‖Comisión Docente de Fisiología Vegetal, Departamento de Biología, Edificio de Biología Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Corinne Loutelier-Bourhis
- §§Université de Rouen, Laboratoire COBRA UMR 6014 & FR 3038, INSA de Rouen, 1 Rue Tesnière, 76821 Mont St Aignan Cedex, France
| | - Marie-Christine Kiefer-Meyer
- From the ‡Université de Rouen, Laboratoire Glyco-MEV, EA 4358, Institut de Recherche et d'Innovation Biomédicale (IRIB), 76821 Mont-Saint-Aignan Cedex, France
| | - Christian Fufezan
- ¶Institute of Plant Biology and Biotechnology, Schlossplatz 8, University of Münster, D-48143, Germany
| | - Carole Burel
- From the ‡Université de Rouen, Laboratoire Glyco-MEV, EA 4358, Institut de Recherche et d'Innovation Biomédicale (IRIB), 76821 Mont-Saint-Aignan Cedex, France
| | - Patrice Lerouge
- From the ‡Université de Rouen, Laboratoire Glyco-MEV, EA 4358, Institut de Recherche et d'Innovation Biomédicale (IRIB), 76821 Mont-Saint-Aignan Cedex, France
| | - Flor Martinez
- ‖Comisión Docente de Fisiología Vegetal, Departamento de Biología, Edificio de Biología Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Muriel Bardor
- From the ‡Université de Rouen, Laboratoire Glyco-MEV, EA 4358, Institut de Recherche et d'Innovation Biomédicale (IRIB), 76821 Mont-Saint-Aignan Cedex, France
| | - Michael Hippler
- ¶Institute of Plant Biology and Biotechnology, Schlossplatz 8, University of Münster, D-48143, Germany
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Inferring polymorphism-induced regulatory gene networks active in human lymphocyte cell lines by weighted linear mixed model analysis of multiple RNA-Seq datasets. PLoS One 2013; 8:e78868. [PMID: 24205334 PMCID: PMC3813575 DOI: 10.1371/journal.pone.0078868] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 09/18/2013] [Indexed: 11/21/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) contribute to the between-individual expression variation of many genes. A regulatory (trait-associated) SNP is usually located near or within a (host) gene, possibly influencing the gene’s transcription or/and post-transcriptional modification. But its targets may also include genes that are physically farther away from it. A heuristic explanation of such multiple-target interferences is that the host gene transfers the SNP genotypic effects to the distant gene(s) by a transcriptional or signaling cascade. These connections between the host genes (regulators) and the distant genes (targets) make the genetic analysis of gene expression traits a promising approach for identifying unknown regulatory relationships. In this study, through a mixed model analysis of multi-source digital expression profiling for 140 human lymphocyte cell lines (LCLs) and the genotypes distributed by the international HapMap project, we identified 45 thousands of potential SNP-induced regulatory relationships among genes (the significance level for the underlying associations between expression traits and SNP genotypes was set at FDR < 0.01). We grouped the identified relationships into four classes (paradigms) according to the two different mechanisms by which the regulatory SNPs affect their cis- and trans- regulated genes, modifying mRNA level or altering transcript splicing patterns. We further organized the relationships in each class into a set of network modules with the cis- regulated genes as hubs. We found that the target genes in a network module were often characterized by significant functional similarity, and the distributions of the target genes in three out of the four networks roughly resemble a power-law, a typical pattern of gene networks obtained from mutation experiments. By two case studies, we also demonstrated that significant biological insights can be inferred from the identified network modules.
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Dheilly NM, Haynes PA, Raftos DA, Nair SV. Time course proteomic profiling of cellular responses to immunological challenge in the sea urchin, Heliocidaris erythrogramma. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2012; 37:243-56. [PMID: 22446733 DOI: 10.1016/j.dci.2012.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 02/09/2012] [Accepted: 03/12/2012] [Indexed: 05/20/2023]
Abstract
Genome sequences and high diversity cDNA arrays have provided a detailed molecular understanding of immune responses in a number of invertebrates, including sea urchins. However, complementary analyses have not been undertaken at the level of proteins. Here, we use shotgun proteomics to describe changes in the abundance of proteins from coelomocytes of sea urchins after immunological challenge and wounding. The relative abundance of 345 reproducibly identified proteins were measured 6, 24 and 48 h after injection. Significant changes in the relative abundance of 188 proteins were detected. These included pathogen-binding proteins, such as the complement component C3 and scavenger receptor cysteine rich proteins, as well as proteins responsible for cytoskeletal remodeling, endocytosis and intracellular signaling. An initial systemic reaction to wounding was followed by a more specific response to immunological challenge involving proteins such as apolipophorin, dual oxidase, fibrocystin L, aminopeptidase N and α-2-macroglobulin.
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Affiliation(s)
- Nolwenn M Dheilly
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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Smith KA, Lagendijk AK, Courtney AD, Chen H, Paterson S, Hogan BM, Wicking C, Bakkers J. Transmembrane protein 2 (Tmem2) is required to regionally restrict atrioventricular canal boundary and endocardial cushion development. Development 2011; 138:4193-8. [PMID: 21896629 DOI: 10.1242/dev.065375] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The atrioventricular canal (AVC) physically separates the atrial and ventricular chambers of the heart and plays a crucial role in the development of the valves and septa. Defects in AVC development result in aberrant heart morphogenesis and are a significant cause of congenital heart malformations. We have used a forward genetic screen in zebrafish to identify novel regulators of cardiac morphogenesis. We isolated a mutant, named wickham (wkm), that was indistinguishable from siblings at the linear heart tube stage but exhibited a specific loss of cardiac looping at later developmental stages. Positional cloning revealed that the wkm locus encodes transmembrane protein 2 (Tmem2), a single-pass transmembrane protein of previously unknown function. Expression analysis demonstrated myocardial and endocardial expression of tmem2 in zebrafish and conserved expression in the endocardium of mouse embryos. Detailed phenotypic analysis of the wkm mutant identified an expansion of expression of known myocardial and endocardial AVC markers, including bmp4 and has2. By contrast, a reduction in the expression of spp1, a marker of the maturing valvular primordia, was observed, suggesting that an expansion of immature AVC is detrimental to later valve maturation. Finally, we show that immature AVC expansion in wkm mutants is rescued by depleting Bmp4, indicating that Tmem2 restricts bmp4 expression to delimit the AVC primordium during cardiac development.
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Affiliation(s)
- Kelly A Smith
- Hubrecht Institute, KNAW and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands.
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Epidermal growth factor-mediated proliferation and sodium transport in normal and PKD epithelial cells. Biochim Biophys Acta Mol Basis Dis 2010; 1812:1301-13. [PMID: 20959142 DOI: 10.1016/j.bbadis.2010.10.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 09/30/2010] [Accepted: 10/11/2010] [Indexed: 02/07/2023]
Abstract
Members of the epidermal growth factor (EGF) family bind to ErbB (EGFR) family receptors which play an important role in the regulation of various fundamental cell processes including cell proliferation and differentiation. The normal rodent kidney has been shown to express at least three members of the ErbB receptor family and is a major site of EGF ligand synthesis. Polycystic kidney disease (PKD) is a group of diseases caused by mutations in single genes and is characterized by enlarged kidneys due to the formation of multiple cysts in both kidneys. Tubule cells proliferate, causing segmental dilation, in association with the abnormal deposition of several proteins. One of the first abnormalities described in cell biological studies of PKD pathogenesis was the abnormal mislocalization of the EGFR in cyst lining epithelial cells. The kidney collecting duct (CD) is predominantly an absorptive epithelium where electrogenic Na(+) entry is mediated by the epithelial Na(+) channel (ENaC). ENaC-mediated sodium absorption represents an important ion transport pathway in the CD that might be involved in the development of PKD. A role for EGF in the regulation of ENaC-mediated sodium absorption has been proposed. However, several investigations have reported contradictory results indicating opposite effects of EGF and its related factors on ENaC activity and sodium transport. Recent advances in understanding how proteins in the EGF family regulate the proliferation and sodium transport in normal and PKD epithelial cells are discussed here. This article is part of a Special Issue entitled: Polycystic Kidney Disease.
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Harris PC. 2008 Homer W. Smith Award: Insights into the Pathogenesis of Polycystic Kidney Disease from Gene Discovery. J Am Soc Nephrol 2009; 20:1188-98. [DOI: 10.1681/asn.2009010014] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Sabates-Bellver J, Van der Flier LG, de Palo M, Cattaneo E, Maake C, Rehrauer H, Laczko E, Kurowski MA, Bujnicki JM, Menigatti M, Luz J, Ranalli TV, Gomes V, Pastorelli A, Faggiani R, Anti M, Jiricny J, Clevers H, Marra G. Transcriptome profile of human colorectal adenomas. Mol Cancer Res 2008; 5:1263-75. [PMID: 18171984 DOI: 10.1158/1541-7786.mcr-07-0267] [Citation(s) in RCA: 376] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Colorectal cancers are believed to arise predominantly from adenomas. Although these precancerous lesions have been subjected to extensive clinical, pathologic, and molecular analyses, little is currently known about the global gene expression changes accompanying their formation. To characterize the molecular processes underlying the transformation of normal colonic epithelium, we compared the transcriptomes of 32 prospectively collected adenomas with those of normal mucosa from the same individuals. Important differences emerged not only between the expression profiles of normal and adenomatous tissues but also between those of small and large adenomas. A key feature of the transformation process was the remodeling of the Wnt pathway reflected in patent overexpression and underexpression of 78 known components of this signaling cascade. The expression of 19 Wnt targets was closely correlated with clear up-regulation of KIAA1199, whose function is currently unknown. In normal mucosa, KIAA1199 expression was confined to cells in the lower portion of intestinal crypts, where Wnt signaling is physiologically active, but it was markedly increased in all adenomas, where it was expressed in most of the epithelial cells, and in colon cancer cell lines, it was markedly reduced by inactivation of the beta-catenin/T-cell factor(s) transcription complex, the pivotal mediator of Wnt signaling. Our transcriptomic profiles of normal colonic mucosa and colorectal adenomas shed new light on the early stages of colorectal tumorigenesis and identified KIAA1199 as a novel target of the Wnt signaling pathway and a putative marker of colorectal adenomatous transformation.
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Affiliation(s)
- Jacob Sabates-Bellver
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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31
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Gallagher AR, Esquivel EL, Briere TS, Tian X, Mitobe M, Menezes LF, Markowitz GS, Jain D, Onuchic LF, Somlo S. Biliary and pancreatic dysgenesis in mice harboring a mutation in Pkhd1. THE AMERICAN JOURNAL OF PATHOLOGY 2008; 172:417-29. [PMID: 18202188 DOI: 10.2353/ajpath.2008.070381] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Autosomal recessive polycystic kidney disease is a hereditary fibrocystic disease that involves the kidneys and the biliary tract. Mutations in the PKHD1 gene are responsible for typical forms of autosomal recessive polycystic kidney disease. We have generated a mouse model with targeted mutation of Pkhd1 by disrupting exon 4, resulting in a mutant transcript with deletion of 66 codons and expression at approximately 30% of wild-type levels. Pkhd1(del4/del4) mice develop intrahepatic bile duct proliferation with progressive cyst formation and associated periportal fibrosis. In addition, these mice exhibit extrahepatic manifestations, including pancreatic cysts, splenomegaly, and common bile duct dilation. The kidneys are unaffected both histologically and functionally. Fibrocystin is expressed in the apical membranes and cilia of bile ducts and distal nephron segments but is absent from the proximal tubule. This pattern is unchanged in orthologous models of autosomal dominant polycystic kidney disease due to mutation in Pkd1 or Pkd2. Mutant fibrocystin in Pkhd1(del4/del4) mice also retains this expression pattern. The hypomorphic Pkhd1(del4/del4) mouse model provides evidence that reduced functional levels of fibrocystin are sufficient for cystogenesis and fibrosis in the liver and pancreas, but not the kidney, and supports the hypothesis of species-dependent differences in susceptibility of tissues to Pkhd1 mutations.
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Affiliation(s)
- Anna-Rachel Gallagher
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
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Menezes LF, Onuchic LF. Molecular and cellular pathogenesis of autosomal recessive polycystic kidney disease. Braz J Med Biol Res 2007; 39:1537-48. [PMID: 17160262 DOI: 10.1590/s0100-879x2006001200004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Accepted: 08/29/2006] [Indexed: 11/22/2022] Open
Abstract
Autosomal recessive polycystic kidney disease (ARPKD) is an inherited disease characterized by a malformation complex which includes cystically dilated tubules in the kidneys and ductal plate malformation in the liver. The disorder is observed primarily in infancy and childhood, being responsible for significant pediatric morbidity and mortality. All typical forms of ARPKD are caused by mutations in a single gene, PKHD1 (polycystic kidney and hepatic disease 1). This gene has a minimum of 86 exons, assembled into multiple differentially spliced transcripts and has its highest level of expression in kidney, pancreas and liver. Mutational analyses revealed that all patients with both mutations associated with truncation of the longest open reading frame-encoded protein displayed the severe phenotype. This product, polyductin, is a 4,074-amino acid protein expressed in the cytoplasm, plasma membrane and primary apical cilia, a structure that has been implicated in the pathogenesis of different polycystic kidney diseases. In fact, cholangiocytes isolated from an ARPKD rat model develop shorter and dysmorphic cilia, suggesting polyductin to be important for normal ciliary morphology. Polyductin seems also to participate in tubule morphogenesis and cell mitotic orientation along the tubular axis. The recent advances in the understanding of in vitro and animal models of polycystic kidney diseases have shed light on the molecular and cellular mechanisms of cyst formation and progression, allowing the initiation of therapeutic strategy designing and promising perspectives for ARPKD patients. It is notable that vasopressin V2 receptor antagonists can inhibit/halt the renal cystic disease progression in an orthologous rat model of human ARPKD.
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Affiliation(s)
- L F Menezes
- Disciplina de Nefrologia, Departamento de Clínica Médica, Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Arnaldo 455, Sala 3310, 01246-903 São Paulo, SP, Brazil.
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Sweeney WE, Avner ED. Molecular and cellular pathophysiology of autosomal recessive polycystic kidney disease (ARPKD). Cell Tissue Res 2006; 326:671-85. [PMID: 16767405 DOI: 10.1007/s00441-006-0226-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Accepted: 04/20/2006] [Indexed: 12/19/2022]
Abstract
Autosomal recessive polycystic kidney disease (ARPKD) belongs to a group of congenital hepatorenal fibrocystic syndromes characterized by dual renal and hepatic involvement of variable severity. Despite the wide clinical spectrum of ARPKD (MIM 263200), genetic linkage studies indicate that mutations at a single locus, PKHD1 (polycystic kidney and hepatic disease 1), located on human chromosome region 6p21.1-p12, are responsible for all phenotypes of ARPKD. Identification of cystic disease genes and their encoded proteins has provided investigators with critical tools to begin to unravel the molecular and cellular mechanisms of PKD. PKD cystic epithelia share common phenotypic abnormalities despite the different genetic mutations that underlie the disease. Recent studies have shown that many cyst-causing proteins are expressed in multimeric complexes at distinct subcellular locations within epithelia. This co-expression of cystoproteins suggests that cyst formation, regardless of the underlying disease gene, results from perturbations in convergent and/or integrated signal transduction pathways. To date, no specific therapies are in clinical use for ameliorating cyst growth in ARPKD. However, studies noted in this review suggest that therapeutic targeting of the cAMP and epidermal growth factor receptor (EGFR)-axis abnormalities in cystic epithelia may translate into effective therapies for ARPKD and, by analogy, autosomal dominant polycystic kidney disease (ADPKD). A particularly promising approach appears to be the targeting of downstream intermediates of both the cAMP and EGFR axis. This review focuses on ARPKD and presents a concise summary of the current understanding of the molecular genetics and cellular pathophysiology of this disease. It also highlights phenotypic and mechanistic similarities between ARPKD and ADPKD.
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Affiliation(s)
- William E Sweeney
- Children's Research Institute, Children's Hospital Health System of Wisconsin, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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Adeva M, El-Youssef M, Rossetti S, Kamath PS, Kubly V, Consugar MB, Milliner DM, King BF, Torres VE, Harris PC. Clinical and molecular characterization defines a broadened spectrum of autosomal recessive polycystic kidney disease (ARPKD). Medicine (Baltimore) 2006; 85:1-21. [PMID: 16523049 DOI: 10.1097/01.md.0000200165.90373.9a] [Citation(s) in RCA: 148] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The autosomal recessive form of polycystic kidney disease (ARPKD) is generally considered an infantile disorder with the typical presentation of greatly enlarged echogenic kidneys detected in utero or within the neonatal period, often resulting in neonatal demise. However, there is an increasing realization that survivors often thrive into adulthood with complications of the ductal plate malformation, manifesting as congenital hepatic fibrosis and Caroli disease, becoming prominent. Previous natural history studies have concentrated almost exclusively on the infantile presenting group. However, developments in understanding the genetic basis of ARPKD, through identification of the disease gene, PKHD1, have allowed exploration of the etiology in patients with ARPKD-like disease or congenital hepatic fibrosis presenting later in childhood or as adults. In the current study we retrospectively reviewed the clinical records, and where possible performed PKHD1 mutation screening, in patients diagnosed with ARPKD or congenital hepatic fibrosis at the Mayo Clinic, Rochester, MN, from 1961 to 2004. Of a total of 133 cases reviewed, 65 were considered to meet the diagnostic criteria with an average duration of follow-up of 8.6 +/- 6.4 years. Fifty-five cases had ARPKD and 10 had isolated congenital hepatic fibrosis with no or minimal renal involvement. The patients were analyzed as 3 groups categorized by the age at diagnosis; <1 years (n = 22), 1-20 years (n = 23), and >20 years (n = 20). The presenting feature in the neonates was typically associated with renal enlargement, but in the older groups, more often involved manifestations of liver disease, including hepatosplenomegaly, hypersplenism, variceal bleeding, and cholangitis. During follow-up, 22 patients had renal insufficiency and 8 developed end-stage renal disease (ESRD), most from the neonatal group. Liver disease was evident on follow-up in all diagnostic groups but particularly prevalent in those diagnosed later in life. A total of 12 patients died, 6 in the neonatal period, but 86% of patients were alive at 40 years of age. The likelihood of being alive without ESRD differed significantly between the diagnostic groups with 36%, 80%, and 88% survival in the 3 diagnostic groups, respectively, 20 years after the diagnosis. Considerable evidence of intrafamilial phenotype variability was observed. Mutation analysis was performed in 31 families and at least 1 mutation was detected in 25 (81%), with 76% of mutant alleles detected in those cases. Consistent with the relatively mild disease manifestations in this population, the majority of changes were missense (79%) and no case had 2 truncating changes. Mutations were detected in all diagnostic groups, indicating that congenital hepatic fibrosis with minimal kidney involvement can result from PKHD1 mutation. The finding of 6 cases with no detected mutations may represent missed mutations or possible evidence of genetic heterogeneity. The current study indicates a broadened spectrum for the ARPKD phenotype and that later presenting cases with predominant liver disease should be considered part of ARPKD.
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Affiliation(s)
- Magdalena Adeva
- From Divisions of Nephrology (MA, SR, VK, MC, DMM, VET, PCH), Gastroenterology and Hepatology (ME-Y, PSK), and Radiology (BFK), Mayo Clinic College of Medicine, Rochester, Minnesota
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Nagano J, Kitamura K, Hujer KM, Ward CJ, Bram RJ, Hopfer U, Tomita K, Huang C, Miller RT. Fibrocystin interacts with CAML, a protein involved in Ca2+ signaling. Biochem Biophys Res Commun 2005; 338:880-9. [PMID: 16243292 DOI: 10.1016/j.bbrc.2005.10.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2005] [Accepted: 10/05/2005] [Indexed: 11/30/2022]
Abstract
The predicted structure of the autosomal recessive polycystic kidney disease protein, fibrocystin, suggests that it may function as a receptor, but its function remains unknown. To understand its function, we searched for proteins that interact with the intracellular C-terminus of fibrocystin using the yeast two-hybrid system. From the screening, we found calcium modulating cyclophilin ligand (CAML), a protein involved in Ca(2+) signaling. Immunofluorescent analysis showed that both proteins are co-localized in the apical membrane, primary cilia, and the basal body of cells derived from the distal nephron Epitope-tagged expression constructs of both proteins were co-immunoprecipitated from COS7 cells. The intracellular C-terminus of fibrocystin interacts with CAML, a protein with an intracellular distribution that is similar to that of PKD2. Fibrocystin may participate in regulation of intracellular Ca(2+) in the distal nephron in a manner similar to PKD1 and PKD2 that are involved in autosomal dominant polycystic kidney disease.
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Affiliation(s)
- Junko Nagano
- Division of Nephrology, Department of Medicine, Case Western Reserve University, Lois Stokes Veterans Affairs Medical Center, Cleveland, OH, USA
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Risinger JI, Maxwell GL, Chandramouli GVR, Aprelikova O, Litzi T, Umar A, Berchuck A, Barrett JC. Gene Expression Profiling of Microsatellite Unstable and Microsatellite Stable Endometrial Cancers Indicates Distinct Pathways of Aberrant Signaling. Cancer Res 2005; 65:5031-7. [PMID: 15958545 DOI: 10.1158/0008-5472.can-04-0850] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microsatellite instability (MSI) is a molecular phenotype present in approximately 25% of endometrial cancers. We examined the global gene expression profiles of early-stage endometrioid endometrial cancers with and without the MSI phenotype to test the hypothesis that MSI phenotype may determine a unique molecular signature among otherwise similar cancers. Unsupervised principal component analysis of the expression data from these cases indicated two distinct groupings of cancers based on MSI phenotype. A relatively small number of array features (392) at high statistical value (P < 0.001) were identified that drive the instability signature in these cancers; 109 of these transcripts differed by at least 2-fold. These data identify distinct gene expression profiles for MSI and microsatellite stable (MSS) cancers, which suggest that cancers with MSI develop in part by different mechanisms from their similar stable counterparts. In particular, we found evidence that two members of the secreted frizzled related protein family (SFRP1 and SFRP4) were more frequently down-regulated in MSI cancers as compared with MSS cancers. Down-regulation was accompanied by promoter hypermethylation for SFRP1. SFRP1 was hypermethylated in 8 of 12 MSI cancers whereas only 3 of 16 MSS cancers were methylated. The WNT target fibroblast growth factor 18 was found to be up-regulated in MSI cancers. These data classify histologically similar endometrioid endometrial cancers into two distinct groupings with implications affecting therapy and prevention.
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Affiliation(s)
- John I Risinger
- Laboratory of Biosystems and Cancer, National Cancer Institute, Bethesda, Maryland, USA.
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Menezes LFC, Cai Y, Nagasawa Y, Silva AMG, Watkins ML, Da Silva AM, Somlo S, Guay-Woodford LM, Germino GG, Onuchic LF. Polyductin, the PKHD1 gene product, comprises isoforms expressed in plasma membrane, primary cilium, and cytoplasm. Kidney Int 2004; 66:1345-55. [PMID: 15458427 DOI: 10.1111/j.1523-1755.2004.00844.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND PKHD1, the autosomal-recessive polycystic kidney disease (ARPKD) gene, encodes multiple alternatively spliced transcripts predicted to generate membrane-bound and secreted proteins. The longest open reading frame encodes polyductin (fibrocystin), a putative 4074 amino acid protein with a single transmembrane domain and an intracellular C-terminus. METHODS To characterize the PKHD1 products and their expression profile, we raised polyclonal antibodies against different portions of polyductin and analyzed different organs using various methods. RESULTS Western blot analyses demonstrated specific bands of >440 kD in human adult kidney, liver, and pancreas and approximately 230 kD in kidney and liver, predominantly observed in membrane fractions. The >440-kD putative membrane protein was immunoprecipitated from kidney and subsequently detected by Western blotting using two distinct antisera. An additional product of approximately 140 kD was specifically recognized by affinity-purified antisera predominantly in soluble fractions. Immunohistochemistry studies revealed specific staining in cortical and medullary collecting ducts and thick ascending limbs of Henle (TALH). Serial sections were stained with antibodies against aquaporin-2 and Tamm-Horsfall protein to confirm the nephron segment localization. Positive staining was also detected in biliary and pancreatic duct epithelia. Analyses of mouse developing tissues showed specific staining in the ureteric bud branches, intra- and extrahepatic biliary ducts, pancreatic ducts, and salivary glands. Immunofluorescence studies in inner medullary collecting duct cultured cells and immunoelectron microscopy analysis of medullary collecting ducts demonstrated that the protein localizes to the primary cilium. Positive signal was also detected in the apical membrane and in cytoplasm. CONCLUSION The results indicate that polyductin is part of the group of polycystic kidney disease (PKD)-related proteins expressed in primary apical cilia. Our data also suggest that, in addition to its likely involvement in cilia function, polyductin probably serves in other subcellular functional roles. The detection of three different products using two antisera, with evidence for distinct subcellular localizations, suggests that PKHD1 encodes membrane-bound and soluble isoforms.
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Affiliation(s)
- Luís F C Menezes
- Department of Medicine, University of São Paulo School of Medicine, São Paulo, Brazil
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Zhang MZ, Mai W, Li C, Cho SY, Hao C, Moeckel G, Zhao R, Kim I, Wang J, Xiong H, Wang H, Sato Y, Wu Y, Nakanuma Y, Lilova M, Pei Y, Harris RC, Li S, Coffey RJ, Sun L, Wu D, Chen XZ, Breyer MD, Zhao ZJ, McKanna JA, Wu G. PKHD1 protein encoded by the gene for autosomal recessive polycystic kidney disease associates with basal bodies and primary cilia in renal epithelial cells. Proc Natl Acad Sci U S A 2004; 101:2311-6. [PMID: 14983006 PMCID: PMC356947 DOI: 10.1073/pnas.0400073101] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mutations of the polycystic kidney and hepatic disease 1 (PKHD1) gene have been shown to cause autosomal recessive polycystic kidney disease (ARPKD), but the cellular functions of the gene product (PKHD1) remain uncharacterized. To illuminate its properties, the spatial and temporal expression patterns of PKHD1 were determined in mouse, rat, and human tissues by using polyclonal Abs and mAbs recognizing various specific regions of the gene product. During embryogenesis, PKHD1 is widely expressed in epithelial derivatives, including neural tubules, gut, pulmonary bronchi, and hepatic cells. In the kidneys of the pck rats, the rat model of which is genetically homologous to human ARPKD, the level of PKHD1 was significantly reduced but not completely absent. In cultured renal cells, the PKHD1 gene product colocalized with polycystin-2, the gene product of autosomal dominant polycystic disease type 2, at the basal bodies of primary cilia. Immunoreactive PKHD1 localized predominantly at the apical domain of polarized epithelial cells, suggesting it may be involved in the tubulogenesis and/or maintenance of duct-lumen architecture. Reduced PKHD1 levels in pck rat kidneys and its colocalization with polycystins may underlie the pathogenic basis for cystogenesis in polycystic kidney diseases.
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Affiliation(s)
- Ming-Zhi Zhang
- Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA
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Rossetti S, Torra R, Coto E, Consugar M, Kubly V, Málaga S, Navarro M, El-Youssef M, Torres VE, Harris PC. A complete mutation screen of PKHD1 in autosomal-recessive polycystic kidney disease (ARPKD) pedigrees. Kidney Int 2003; 64:391-403. [PMID: 12846734 DOI: 10.1046/j.1523-1755.2003.00111.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Autosomal-recessive polycystic kidney disease (ARPKD) is an important neonatal nephropathy characterized by fusiform dilation of collecting ducts, congenital hepatic fibrosis, and in some cases Caroli's disease. The ARPKD gene, PKHD1, has recently been identified. Herein we describe an effective method for PKHD1 mutation screening and the results from analysis of a novel ARPKD cohort. METHODS The coding region of PKHD1 was amplified as 79 fragments and analyzed for base pair changes by denaturing high-performance liquid chromatography (DHPLC). Forty-seven ARPKD and 14 pedigrees with congenital hepatic fibrosis and/or Caroli's disease, were screened for PKHD1 mutations. RESULTS Thirty-three different mutations were detected on 57 alleles (51.1% ARPKD, 32.1% congenital hepatic fibrosis/Caroli's disease). In the 22 pedigrees where both mutations were identified, two were homozygous for 9689delA and the remainder were compound heterozygotes; a combination of truncating, missense and splicing changes. Patients with two truncating mutations all died in the perinatal period. Two frequent truncating mutations were identified: 9689delA (9 alleles) and 5896insA (8 alleles) plus some more common missense changes; haplotype analysis indicated most were ancestral mutations. CONCLUSION DHPLC has been established as a rapid mutation screening method for ARPKD. The mutation detection rate was high in severely affected patients (85%), lower in those with moderate ARPKD (41.9%), and low, but significant, in adults with congenital hepatic fibrosis/Caroli's disease (32.1%). The prospects for gene-based diagnostics are complicated by the large gene size, marked allelic heterogeneity, and clinical diversity of the ARPKD phenotype. Identification of some common mutations, especially in specific populations, will aid mutation screening.
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Affiliation(s)
- Sandro Rossetti
- Division of Nephrology, Mayo Clinic, Rochester, Minnesota 55905, USA
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