1
|
Jiang Y, Thienpont B, Sapuru V, Hite RK, Dittman JS, Sturgis JN, Scheuring S. Membrane-mediated protein interactions drive membrane protein organization. Nat Commun 2022; 13:7373. [PMID: 36450733 PMCID: PMC9712761 DOI: 10.1038/s41467-022-35202-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/22/2022] [Indexed: 12/02/2022] Open
Abstract
The plasma membrane's main constituents, i.e., phospholipids and membrane proteins, are known to be organized in lipid-protein functional domains and supercomplexes. No active membrane-intrinsic process is known to establish membrane organization. Thus, the interplay of thermal fluctuations and the biophysical determinants of membrane-mediated protein interactions must be considered to understand membrane protein organization. Here, we used high-speed atomic force microscopy and kinetic and membrane elastic theory to investigate the behavior of a model membrane protein in oligomerization and assembly in controlled lipid environments. We find that membrane hydrophobic mismatch modulates oligomerization and assembly energetics, and 2D organization. Our experimental and theoretical frameworks reveal how membrane organization can emerge from Brownian diffusion and a minimal set of physical properties of the membrane constituents.
Collapse
Affiliation(s)
- Yining Jiang
- Biochemistry & Structural Biology, Cell & Developmental Biology, and Molecular Biology (BCMB) Program, Weill Cornell Graduate School of Biomedical Sciences, 1300 York Avenue, New York, NY 10065 USA ,grid.5386.8000000041936877XWeill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065 USA
| | - Batiste Thienpont
- grid.5399.60000 0001 2176 4817Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Unité Mixte de Recherche (UMR) 7255, Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université, Marseille, France
| | - Vinay Sapuru
- grid.51462.340000 0001 2171 9952Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA ,Physiology, Biophysics, and Systems Biology (PBSB) Program, Weill Cornell Graduate School of Biomedical Sciences, 1300 York Avenue, New York, NY 10065 USA
| | - Richard K. Hite
- grid.51462.340000 0001 2171 9952Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065 USA
| | - Jeremy S. Dittman
- grid.5386.8000000041936877XWeill Cornell Medicine, Department of Biochemistry, 1300 York Avenue, New York, NY 10065 USA
| | - James N. Sturgis
- grid.5399.60000 0001 2176 4817Laboratoire d’Ingénierie des Systèmes Macromoléculaires (LISM), Unité Mixte de Recherche (UMR) 7255, Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université, Marseille, France
| | - Simon Scheuring
- grid.5386.8000000041936877XWeill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, NY 10065 USA ,grid.5386.8000000041936877XWeill Cornell Medicine, Department of Physiology and Biophysics, 1300 York Avenue, New York, NY 10065 USA ,grid.5386.8000000041936877XKavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853 USA
| |
Collapse
|
2
|
Jiang Y, Thienpont B, Sturgis JN, Dittman J, Scheuring S. Membrane-mediated membrane protein interactions drive membrane protein organization. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
|
3
|
Thienpont B, Sturgis JN. The Influence of Lipids on the Assembly of Aquaporin Z. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
4
|
Heylen L, Thienpont B, Naesens M, Lambrechts D, Sprangers B. The Emerging Role of DNA Methylation in Kidney Transplantation: A Perspective. Am J Transplant 2016; 16:1070-8. [PMID: 26780242 DOI: 10.1111/ajt.13585] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 09/28/2015] [Accepted: 10/14/2015] [Indexed: 01/25/2023]
Abstract
Allograft outcome depends on a range of factors, including donor age, the allo-immune response, ischemia-reperfusion injury, and interstitial fibrosis of the allograft. Changes in the epigenome, and in DNA methylation in particular, have been implicated in each of these processes, in either the kidney or other organ systems. This review provides a primer for DNA methylation analyses and a discussion of the strengths and weaknesses of current studies, but it is also a perspective for future DNA methylation research in kidney transplantation. We present exciting prospects for leveraging DNA methylation analyses as a tool in kidney biology research, and as a diagnostic or prognostic marker for predicting allograft quality and success. Topics discussed include DNA methylation changes in aging and in response to hypoxia and oxidative stress upon ischemia-reperfusion injury. Moreover, emerging evidence suggests that DNA methylation contributes to organ fibrosis and that systemic DNA methylation alterations correlate with the rate of kidney function decline in patients with chronic kidney disease and end-stage renal failure. Monitoring or targeting the epigenome could therefore reveal novel therapeutic approaches in transplantation and open up paths to biomarker discovery and targeted therapy.
Collapse
Affiliation(s)
- L Heylen
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium.,Department of Immunology and Microbiology, KU Leuven, Leuven, Belgium.,Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Leuven, Belgium.,Vesalius Research Center, VIB, Leuven, Belgium
| | - B Thienpont
- Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Leuven, Belgium.,Vesalius Research Center, VIB, Leuven, Belgium
| | - M Naesens
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium.,Department of Immunology and Microbiology, KU Leuven, Leuven, Belgium
| | - D Lambrechts
- Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Leuven, Belgium.,Vesalius Research Center, VIB, Leuven, Belgium
| | - B Sprangers
- Department of Nephrology and Renal Transplantation, University Hospitals Leuven, Leuven, Belgium.,Department of Immunology and Microbiology, KU Leuven, Leuven, Belgium
| |
Collapse
|
5
|
Breckpot J, Thienpont B, Gewillig M, Allegaert K, Vermeesch JR, Devriendt K. Differences in Copy Number Variation between Discordant Monozygotic Twins as a Model for Exploring Chromosomal Mosaicism in Congenital Heart Defects. Mol Syndromol 2012; 2:81-87. [PMID: 22511896 DOI: 10.1159/000335284] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2011] [Indexed: 12/21/2022] Open
Abstract
Studies addressing the role of somatic copy number variation (CNV) in the genesis of congenital heart defects (CHDs) are scarce, as cardiac tissue is difficult to obtain, especially in non-affected individuals. We explored the occurrence of copy number differences in monozygotic (MZ) twins discordant for the presence of a CHD, as an illustrative model for chromosomal mosaicism in CHDs. Array comparative genomic hybridization was performed on peripheral blood-derived DNA obtained from 6 discordant MZ twin pairs and on sex-matched reference samples. To identify CNV differences between both twin members as well as potential CNVs in both twins contributing to the phenotype, DNA from each twin was hybridized against its co-twin, and against a normal control. Three copy number differences in 1 out of 6 MZ twin pairs were detected, confirming the occurrence of somatic CNV events in MZ twins. Further investigation by copy number and (epi)genome sequencing analyses in MZ twins, discordant for the presence of CHDs, is required to improve our knowledge on how postzygotic genetic, environmental and stochastic factors can affect human heart development.
Collapse
Affiliation(s)
- J Breckpot
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | | | | | | | | |
Collapse
|
6
|
Breckpot J, Thienpont B, Arens Y, Tranchevent L, Vermeesch J, Moreau Y, Gewillig M, Devriendt K. Challenges of Interpreting Copy Number Variation in Syndromic and Non-Syndromic Congenital Heart Defects. Cytogenet Genome Res 2011; 135:251-9. [DOI: 10.1159/000331272] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
|
7
|
Balikova I, Lehesjoki AE, de Ravel T, Thienpont B, Chandler K, Clayton-Smith J, Träskelin AL, Fryns JP, Vermeesch J. Deletions in theVPS13B(COH1) gene as a cause of Cohen syndrome. Hum Mutat 2009; 30:E845-54. [DOI: 10.1002/humu.21065] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
8
|
Maas NMC, Van Buggenhout G, Hannes F, Thienpont B, Sanlaville D, Kok K, Midro A, Andrieux J, Anderlid BM, Schoumans J, Hordijk R, Devriendt K, Fryns JP, Vermeesch JR. Genotype-phenotype correlation in 21 patients with Wolf-Hirschhorn syndrome using high resolution array comparative genome hybridisation (CGH). J Med Genet 2007; 45:71-80. [PMID: 17873117 DOI: 10.1136/jmg.2007.052910] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND The Wolf-Hirschhorn syndrome (WHS) is usually caused by terminal deletions of the short arm of chromosome 4 and is phenotypically defined by growth and mental retardation, seizures, and specific craniofacial manifestations. Large variation is observed in phenotypic expression of these features. In order to compare the phenotype with the genotype, we localised the breakpoints of the 4 pter aberrations using a chromosome 4 specific tiling BAC/PAC array. METHODS In total, DNA from 21 patients was analysed, of which 8 had a cytogenetic visible and 13 a submicroscopic deletion. RESULTS AND CONCLUSION In addition to classical terminal deletions sized between 1.9 and 30 Mb, we observed the smallest terminal deletion (1.4 Mb) ever reported in a patient with mild WHS stigmata. In addition, we identified and mapped interstitial deletions in four patients. This study positions the genes causing microcephaly, intrauterine and postnatal growth retardation between 0.3 and 1.4 Mb and further refines the regions causing congenital heart disease, cleft lip and/or palate, oligodontia, and hypospadias.
Collapse
Affiliation(s)
- N M C Maas
- Center for Human Genetics, University Hospital, Catholic University of Leuven, Leuven, Belgium
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
de Ravel TJL, Balikova I, Thienpont B, Hannes F, Maas N, Fryns JP, Devriendt K, Vermeesch JR. Molecular karyotyping of patients with MCA/MR: the blurred boundary between normal and pathogenic variation. Cytogenet Genome Res 2006; 115:225-30. [PMID: 17124404 DOI: 10.1159/000095918] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2006] [Accepted: 05/02/2006] [Indexed: 11/19/2022] Open
Abstract
Molecular karyotyping has revealed that microdeletions/duplications in the human genome are a major cause of multiple congenital anomalies associated with mental retardation (MCA/MR). The identification of a de novo chromosomal imbalance in a patient with MCA/MR is usually considered causal for the phenotype while a chromosomal imbalance inherited from a phenotypically normal parent is considered as a benign variation and not related to the disorder. Around 40% of imbalances in patients with MCA/MR in this series is inherited from a healthy parent and the majority of these appear to be (extremely) rare variants. As some of these contain known disease-causing genes and have also been found to be de novo in MCA/MR patients, this challenges the general view that such familial variants are innocent and of no major phenotypic consequence. Rather, we argue, that human genomes can be tolerant of genomic copy number variations depending on the genetic and environmental background and that different mechanisms play a role in determining whether these chromosomal imbalances manifest themselves.
Collapse
Affiliation(s)
- T J L de Ravel
- Centre for Human Genetics, UZ Gasthuisberg, Leuven, Belgium
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Thienpont B, Gewillig M, Fryns JP, Devriendt K, Vermeesch J. Molecular cytogenetic characterization of a constitutional complex intrachromosomal 4q rearrangement in a patient with multiple congenital anomalies. Cytogenet Genome Res 2006; 114:338-41. [PMID: 16954676 DOI: 10.1159/000094223] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Accepted: 01/09/2006] [Indexed: 01/07/2023] Open
Abstract
Constitutional Complex Chromosomal Rearrangements (CCRs) are very rare. While the vast majority of CCRs involve more than one chromosome, only seven cases describe CCRs with four or more breakpoints within a single chromosome. Here, we present a patient with multiple congenital anomalies and mental retardation. Array Comparative Genomic Hybridisation (array CGH), FISH and Multicolour Banding FISH revealed a de novo complex rearrangement with two deletions, a duplication and an inversion of 4q. This CCR involving at least seven breakpoints is one of the most complex rearrangements of a single chromosome reported thus far. Potential mechanisms generating such complex rearrangements are discussed.
Collapse
Affiliation(s)
- B Thienpont
- Center for Human Genetics, University Hospital Leuven, Leuven, Belgium
| | | | | | | | | |
Collapse
|
11
|
Menten B, Maas N, Thienpont B, Buysse K, Vandesompele J, Melotte C, de Ravel T, Van Vooren S, Balikova I, Backx L, Janssens S, De Paepe A, De Moor B, Moreau Y, Marynen P, Fryns JP, Mortier G, Devriendt K, Speleman F, Vermeesch JR. Emerging patterns of cryptic chromosomal imbalance in patients with idiopathic mental retardation and multiple congenital anomalies: a new series of 140 patients and review of published reports. J Med Genet 2006; 43:625-33. [PMID: 16490798 PMCID: PMC2564583 DOI: 10.1136/jmg.2005.039453] [Citation(s) in RCA: 304] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
BACKGROUND Chromosomal abnormalities are a major cause of mental retardation and multiple congenital anomalies (MCA/MR). Screening for these chromosomal imbalances has mainly been done by standard karyotyping. Previous array CGH studies on selected patients with chromosomal phenotypes and normal karyotypes suggested an incidence of 10-15% of previously unnoticed de novo chromosomal imbalances. OBJECTIVE To report array CGH screening of a series of 140 patients (the largest published so far) with idiopathic MCA/MR but normal karyotype. RESULTS Submicroscopic chromosomal imbalances were detected in 28 of the 140 patients (20%) and included 18 deletions, seven duplications, and three unbalanced translocations. Seventeen of 24 imbalances were confirmed de novo and 19 were assumed to be causal. Excluding subtelomeric imbalances, our study identified 11 clinically relevant interstitial submicroscopic imbalances (8%). Taking this and previously reported studies into consideration, array CGH screening with a resolution of at least 1 Mb has been undertaken on 432 patients with MCA/MR. Most imbalances are non-recurrent and spread across the genome. In at least 8.8% of these patients (38 of 432) de novo intrachromosomal alterations have been identified. CONCLUSIONS Array CGH should be considered an essential aspect of the genetic analysis of patients with MCA/MR. In addition, in the present study three patients were mosaic for a structural chromosome rearrangement. One of these patients had monosomy 7 in as few as 8% of the cells, showing that array CGH allows detection of low grade mosaicisims.
Collapse
Affiliation(s)
- B Menten
- Centre for Medical Genetics, Ghent University, Ghent, Belgium
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Maas N, Thienpont B, Vermeesch JR, Fryns JP. Facial asymmetry, cardiovascular anomalies and adducted thumbs as unusual symptoms in Dubowitz syndrome: a microdeletion/duplication in 13q. Genet Couns 2006; 17:477-9. [PMID: 17375538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
|