1
|
Ye F, Zhang S, Fu Y, Yang L, Zhang G, Wu Y, Pan J, Chen H, Wang X, Ma L, Niu H, Jiang M, Zhang T, Jia D, Wang J, Wang Y, Han X, Guo G. Fast and flexible profiling of chromatin accessibility and total RNA expression in single nuclei using Microwell-seq3. Cell Discov 2024; 10:33. [PMID: 38531851 DOI: 10.1038/s41421-023-00642-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 12/21/2023] [Indexed: 03/28/2024] Open
Abstract
Single cell chromatin accessibility profiling and transcriptome sequencing are the most widely used technologies for single-cell genomics. Here, we present Microwell-seq3, a high-throughput and facile platform for high-sensitivity single-nucleus chromatin accessibility or full-length transcriptome profiling. The method combines a preindexing strategy and a penetrable chip-in-a-tube for single nucleus loading and DNA amplification and therefore does not require specialized equipment. We used Microwell-seq3 to profile chromatin accessibility in more than 200,000 single nuclei and the full-length transcriptome in ~50,000 nuclei from multiple adult mouse tissues. Compared with the existing polyadenylated transcript capture methods, integrative analysis of cell type-specific regulatory elements and total RNA expression uncovered comprehensive cell type heterogeneity in the brain. Gene regulatory networks based on chromatin accessibility profiling provided an improved cell type communication model. Finally, we demonstrated that Microwell-seq3 can identify malignant cells and their specific regulons in spontaneous lung tumors of aged mice. We envision a broad application of Microwell-seq3 in many areas of research.
Collapse
Affiliation(s)
- Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shuang Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yuting Fu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lei Yang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Guodong Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yijun Wu
- Department of Thyroid Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jun Pan
- Department of Thyroid Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Haide Chen
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xinru Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lifeng Ma
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Haofu Niu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Mengmeng Jiang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tingyue Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
| | - Danmei Jia
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yongcheng Wang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoping Han
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang, China.
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang, China.
- Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China.
| |
Collapse
|
2
|
Eissman JM, Archer DB, Mukherjee S, Lee ML, Choi S, Scollard P, Trittschuh EH, Mez JB, Bush WS, Kunkle BW, Naj AC, Gifford KA, Cuccaro ML, Cruchaga C, Pericak‐Vance MA, Farrer LA, Wang L, Schellenberg GD, Mayeux RP, Haines JL, Jefferson AL, Kukull WA, Keene CD, Saykin AJ, Thompson PM, Martin ER, Bennett DA, Barnes LL, Schneider JA, Crane PK, Hohman TJ, Dumitrescu L. Sex-specific genetic architecture of late-life memory performance. Alzheimers Dement 2024; 20:1250-1267. [PMID: 37984853 PMCID: PMC10917043 DOI: 10.1002/alz.13507] [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: 04/04/2023] [Revised: 08/08/2023] [Accepted: 09/07/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Women demonstrate a memory advantage when cognitively healthy yet lose this advantage to men in Alzheimer's disease. However, the genetic underpinnings of this sex difference in memory performance remain unclear. METHODS We conducted the largest sex-aware genetic study on late-life memory to date (Nmales = 11,942; Nfemales = 15,641). Leveraging harmonized memory composite scores from four cohorts of cognitive aging and AD, we performed sex-stratified and sex-interaction genome-wide association studies in 24,216 non-Hispanic White and 3367 non-Hispanic Black participants. RESULTS We identified three sex-specific loci (rs67099044-CBLN2, rs719070-SCHIP1/IQCJ-SCHIP), including an X-chromosome locus (rs5935633-EGL6/TCEANC/OFD1), that associated with memory. Additionally, we identified heparan sulfate signaling as a sex-specific pathway and found sex-specific genetic correlations between memory and cardiovascular, immune, and education traits. DISCUSSION This study showed memory is highly and comparably heritable across sexes, as well as highlighted novel sex-specific genes, pathways, and genetic correlations that related to late-life memory. HIGHLIGHTS Demonstrated the heritable component of late-life memory is similar across sexes. Identified two genetic loci with a sex-interaction with baseline memory. Identified an X-chromosome locus associated with memory decline in females. Highlighted sex-specific candidate genes and pathways associated with memory. Revealed sex-specific shared genetic architecture between memory and complex traits.
Collapse
|
3
|
Takeshita LY, Davidsen PK, Herbert JM, Antczak P, Hesselink MKC, Schrauwen P, Weisnagel SJ, Robbins JM, Gerszten RE, Ghosh S, Sarzynski MA, Bouchard C, Falciani F. Genomics and transcriptomics landscapes associated to changes in insulin sensitivity in response to endurance exercise training. Sci Rep 2021; 11:23314. [PMID: 34857871 PMCID: PMC8639975 DOI: 10.1038/s41598-021-98792-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 08/25/2021] [Indexed: 01/14/2023] Open
Abstract
Despite good adherence to supervised endurance exercise training (EET), some individuals experience no or little improvement in peripheral insulin sensitivity. The genetic and molecular mechanisms underlying this phenomenon are currently not understood. By investigating genome-wide variants associated with baseline and exercise-induced changes (∆) in insulin sensitivity index (Si) in healthy volunteers, we have identified novel candidate genes whose mouse knockouts phenotypes were consistent with a causative effect on Si. An integrative analysis of functional genomic and transcriptomic profiles suggests genetic variants have an aggregate effect on baseline Si and ∆Si, focused around cholinergic signalling, including downstream calcium and chemokine signalling. The identification of calcium regulated MEF2A transcription factor as the most statistically significant candidate driving the transcriptional signature associated to ∆Si further strengthens the relevance of calcium signalling in EET mediated Si response.
Collapse
Affiliation(s)
- Louise Y. Takeshita
- grid.10025.360000 0004 1936 8470Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK
| | - Peter K. Davidsen
- grid.10025.360000 0004 1936 8470Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK
| | - John M. Herbert
- grid.10025.360000 0004 1936 8470Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK
| | - Philipp Antczak
- grid.10025.360000 0004 1936 8470Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK ,grid.411097.a0000 0000 8852 305XCenter for Molecular Medicine Cologne, University Hospital Cologne, 50931 Cologne, Germany
| | - Matthijs K. C. Hesselink
- grid.5012.60000 0001 0481 6099Department of Nutrition and Movement Sciences, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Centre, Maastricht, The Netherlands
| | - Patrick Schrauwen
- grid.5012.60000 0001 0481 6099Department of Nutrition and Movement Sciences, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Centre, Maastricht, The Netherlands
| | - S. John Weisnagel
- grid.23856.3a0000 0004 1936 8390Diabetes Research Unit, Endocrinology and Nephrology Axis, CRCHU de Québec, Université Laval, Québec City, Canada
| | - Jeremy M. Robbins
- grid.239395.70000 0000 9011 8547Division of Cardiovascular Medicine, and Cardiovascular Research Center, Beth Israel Deaconess Medical Center, Boston, MA 02215 USA
| | - Robert E. Gerszten
- grid.239395.70000 0000 9011 8547Division of Cardiovascular Medicine, and Cardiovascular Research Center, Beth Israel Deaconess Medical Center, Boston, MA 02215 USA
| | - Sujoy Ghosh
- grid.428397.30000 0004 0385 0924Centre for Computational Biology and Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Mark A. Sarzynski
- grid.254567.70000 0000 9075 106XDepartment of Exercise Science, Arnold School of Public Health, University of South Carolina, Columbia, SC USA
| | - Claude Bouchard
- grid.250514.70000 0001 2159 6024Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA USA
| | - Francesco Falciani
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
| |
Collapse
|
4
|
Dufresne J, Bowden P, Thavarajah T, Florentinus-Mefailoski A, Chen ZZ, Tucholska M, Norzin T, Ho MT, Phan M, Mohamed N, Ravandi A, Stanton E, Slutsky AS, Dos Santos CC, Romaschin A, Marshall JC, Addison C, Malone S, Heyland D, Scheltens P, Killestein J, Teunissen C, Diamandis EP, Siu KWM, Marshall JG. The plasma peptides of breast versus ovarian cancer. Clin Proteomics 2019; 16:43. [PMID: 31889940 PMCID: PMC6927194 DOI: 10.1186/s12014-019-9262-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
Background There is a need to demonstrate a proof of principle that proteomics has the capacity to analyze plasma from breast cancer versus other diseases and controls in a multisite clinical trial design. The peptides or proteins that show a high observation frequency, and/or precursor intensity, specific to breast cancer plasma might be discovered by comparison to other diseases and matched controls. The endogenous tryptic peptides of breast cancer plasma were compared to ovarian cancer, female normal, sepsis, heart attack, Alzheimer's and multiple sclerosis along with the institution-matched normal and control samples collected directly onto ice. Methods Endogenous tryptic peptides were extracted from individual breast cancer and control EDTA plasma samples in a step gradient of acetonitrile, and collected over preparative C18 for LC-ESI-MS/MS with a set of LTQ XL linear quadrupole ion traps working together in parallel to randomly and independently sample clinical populations. The MS/MS spectra were fit to fully tryptic peptides or phosphopeptides within proteins using the X!TANDEM algorithm. The protein observation frequency was counted using the SEQUEST algorithm after selecting the single best charge state and peptide sequence for each MS/MS spectra. The observation frequency was subsequently tested by Chi Square analysis. The log10 precursor intensity was compared by ANOVA in the R statistical system. Results Peptides and/or phosphopeptides of common plasma proteins such as APOE, C4A, C4B, C3, APOA1, APOC2, APOC4, ITIH3 and ITIH4 showed increased observation frequency and/or precursor intensity in breast cancer. Many cellular proteins also showed large changes in frequency by Chi Square (χ2 > 100, p < 0.0001) in the breast cancer samples such as CPEB1, LTBP4, HIF-1A, IGHE, RAB44, NEFM, C19orf82, SLC35B1, 1D12A, C8orf34, HIF1A, OCLN, EYA1, HLA-DRB1, LARS, PTPDC1, WWC1, ZNF562, PTMA, MGAT1, NDUFA1, NOGOC, OR1E1, OR1E2, CFI, HSA12, GCSH, ELTD1, TBX15, NR2C2, FLJ00045, PDLIM1, GALNT9, ASH2L, PPFIBP1, LRRC4B, SLCO3A1, BHMT2, CS, FAM188B2, LGALS7, SAT2, SFRS8, SLC22A12, WNT9B, SLC2A4, ZNF101, WT1, CCDC47, ERLIN1, SPFH1, EID2, THOC1, DDX47, MREG, PTPRE, EMILIN1, DKFZp779G1236 and MAP3K8 among others. The protein gene symbols with large Chi Square values were significantly enriched in proteins that showed a complex set of previously established functional and structural relationships by STRING analysis. An increase in mean precursor intensity of peptides was observed for QSER1 as well as SLC35B1, IQCJ-SCHIP1, MREG, BHMT2, LGALS7, THOC1, ANXA4, DHDDS, SAT2, PTMA and FYCO1 among others. In contrast, the QSER1 peptide QPKVKAEPPPK was apparently specific to ovarian cancer. Conclusion There was striking agreement between the breast cancer plasma peptides and proteins discovered by LC-ESI-MS/MS with previous biomarkers from tumors, cells lines or body fluids by genetic or biochemical methods. The results indicate that variation in plasma peptides from breast cancer versus ovarian cancer may be directly discovered by LC-ESI-MS/MS that will be a powerful tool for clinical research. It may be possible to use a battery of sensitive and robust linear quadrupole ion traps for random and independent sampling of plasma from a multisite clinical trial.
Collapse
Affiliation(s)
- Jaimie Dufresne
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Pete Bowden
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Thanusi Thavarajah
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Angelique Florentinus-Mefailoski
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Zhuo Zhen Chen
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Monika Tucholska
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Tenzin Norzin
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Margaret Truc Ho
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Morla Phan
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Nargiz Mohamed
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada
| | - Amir Ravandi
- 2Institute of Cardiovascular Sciences, St. Boniface Hospital Research Center, University of Manitoba, Winnipeg, Canada
| | - Eric Stanton
- 3Division of Cardiology, Department of Medicine, McMaster University, Hamilton, Canada
| | - Arthur S Slutsky
- 4St. Michael's Hospital, Keenan Chair in Medicine, Professor of Medicine, Surgery & Biomedical Engineering, University of Toronto, Toronto, Canada
| | - Claudia C Dos Santos
- 5St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - Alexander Romaschin
- 5St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - John C Marshall
- 5St. Michael's Hospital, Keenan Research Centre for Biomedical Science, Toronto, Canada
| | - Christina Addison
- 6Program for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Shawn Malone
- 6Program for Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, Canada
| | - Daren Heyland
- 7Clinical Evaluation Research Unit, Kingston General Hospital, Kingston, Canada
| | - Philip Scheltens
- 8Alzheimer Center, Dept of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Joep Killestein
- 9MS Center, Dept of Neurology, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Charlotte Teunissen
- 10Neurochemistry Lab and Biobank, Dept of Clinical Chemsitry, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | | | - K W M Siu
- 12University of Windsor, Windsor, Canada
| | - John G Marshall
- 1Ryerson Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Faculty of Science, Ryerson University, 350 Victoria St., Toronto, ON Canada.,13International Biobank of Luxembourg (IBBL), Luxembourg Institute of Health (formerly CRP Sante Luxembourg), Strassen, Luxembourg
| |
Collapse
|
5
|
Vallée Marcotte B, Guénard F, Lemieux S, Couture P, Rudkowska I, Calder PC, Minihane AM, Vohl MC. Fine mapping of genome-wide association study signals to identify genetic markers of the plasma triglyceride response to an omega-3 fatty acid supplementation. Am J Clin Nutr 2019; 109:176-185. [PMID: 30624603 PMCID: PMC6358031 DOI: 10.1093/ajcn/nqy298] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/02/2018] [Indexed: 12/13/2022] Open
Abstract
Background Using a genome-wide association study (GWAS) approach, our group previously computed a genetic risk score (GRS) from single nucleotide polymorphisms (SNPs) of 10 loci that affect the plasma triglyceride (TG) response to an omega-3 (n-3) fatty acid (FA) supplementation. Objectives The objective was to compute a novel and more refined GRS using fine mapping to include a large number of genetic variants. Methods A total of 208 participants of the Fatty Acid Sensor (FAS) Study received 5 g fish oil/d, containing 1.9-2.2 g eicosapentaenoic acid and 1.1 g docosahexanoic acid, for 6 wk. Plasma TG concentrations were measured before and after supplementation. Dense genotyping and genotype imputation were used to refine mapping around GWAS hits. A GRS was computed by summing the number of at-risk alleles of tagging SNPs. Analyses were replicated in samples of the FINGEN study. Results A total of 31 tagging SNPs associated with the TG response were used for GRS calculation in the FAS study. In a general linear model adjusted for age, sex, and body mass index, the GRS explained 49.73% of TG response variance (P < 0.0001). Nonresponders to the n-3 FA supplementation had a higher GRS than did responders. In the FINGEN replication study, the GRS explained 3.67% of TG response variance (P = 0.0006). Conclusions Fine mapping proved to be effective to refine the previous GRS. Carrying increasing numbers of at-risk alleles of 31 SNPs confers a higher risk of being nonresponsive to n-3 FAs. The genetic profile therefore appears to be an important determinant of the plasma TG response to an n-3 FA supplementation and could be used to target those most likely to gain clinical benefit. This trial was registered at http://www.clinicaltrials.gov as NCT01343342.
Collapse
Affiliation(s)
| | - Frédéric Guénard
- Institute of Nutrition and Functional Foods, Laval University, Quebec City, Quebec, Canada
| | - Simone Lemieux
- Institute of Nutrition and Functional Foods, Laval University, Quebec City, Quebec, Canada
| | - Patrick Couture
- Institute of Nutrition and Functional Foods, Laval University, Quebec City, Quebec, Canada,CHU de Québec Research Center–Endocrinology and Nephrology, Quebec City, Quebec, Canada
| | - Iwona Rudkowska
- CHU de Québec Research Center–Endocrinology and Nephrology, Quebec City, Quebec, Canada
| | - Philip C Calder
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom,NIHR Southampton Biomedical Research Center, University Hospital Southampton NHS Foundation Trust and University of Southampton, Southampton, United Kingdom
| | | | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods, Laval University, Quebec City, Quebec, Canada,Address correspondence to M-CV (e-mail: )
| |
Collapse
|
6
|
Elsaid MF, Chalhoub N, Ben-Omran T, Kamel H, Al Mureikhi M, Ibrahim K, Elizabeth Ross M, Abdel Aleem AK. Homozygous nonsense mutation in SCHIP1/IQCJ-SCHIP1 causes a neurodevelopmental brain malformation syndrome. Clin Genet 2017; 93:387-391. [PMID: 28787085 DOI: 10.1111/cge.13122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/18/2017] [Accepted: 08/03/2017] [Indexed: 12/11/2022]
Abstract
We report a consanguineous Arab family with 3 affected siblings who display a disorder of global developmental delay, learning difficulties, facial dysmorphism, hearing impairments, and cataract. The clinical phenotype was associated with characteristic brain magnetic resonance imaging (MRI) features of axonal guidance defects involving anterior commissure agenesis as well as scattered areas of polymicrogyria-cobblestone complex. Whole genome sequencing revealed a novel nonsense mutation (159609921C>T) that segregated in the family consistent in an autosomal recessive pattern. This mutation located in the C-terminal region shared by the Schwanomin-Interacting Protein1 (SCHIP1) isoforms including the IQCJ-SCHIP1. The in vitro expression of SCHIP1 and IQCJ-SCHIP1 truncated mutant isoforms (NM_001197109.1; p.R209* and NM_001197114.1; p.R501*, respectively) were markedly reduced as compared to their full-length versions suggesting protein stability/folding impairment. The pathogenic nature of this mutation is supported by a previously reported mouse knockout of Schip1 isoforms, which phenocopied the human axon guidance abnormality. This is the first report of a SCHIP1/IQCJ-SCHIP1 point mutation in humans associated with a neurological-developmental phenotype.
Collapse
Affiliation(s)
- M F Elsaid
- Department of Neuropediatrics, Hamad Medical Corporation, Doha, Qatar
| | - N Chalhoub
- Neurogenetics Lab, Weill Cornell Medicine, Doha, Qatar
| | - T Ben-Omran
- Department of Clinical and Metabolic Genetics, Hamad Medical Corporation, Doha, Qatar
| | - H Kamel
- Department of Radiology, Hamad Medical Corporation, Doha, Qatar
| | - M Al Mureikhi
- Department of Clinical and Metabolic Genetics, Hamad Medical Corporation, Doha, Qatar
| | - K Ibrahim
- Department of Neuropediatrics, Hamad Medical Corporation, Doha, Qatar
| | - M Elizabeth Ross
- BMRI Center for Neurogenetics and Department of Neurology, Weill Cornell Medicine, NY, New York
| | - A K Abdel Aleem
- Neurogenetics Lab, Weill Cornell Medicine, Doha, Qatar.,BMRI Center for Neurogenetics and Department of Neurology, Weill Cornell Medicine, NY, New York
| |
Collapse
|
7
|
Vallée Marcotte B, Guénard F, Cormier H, Lemieux S, Couture P, Rudkowska I, Vohl MC. Plasma Triglyceride Levels May Be Modulated by Gene Expression of IQCJ, NXPH1, PHF17 and MYB in Humans. Int J Mol Sci 2017; 18:ijms18020257. [PMID: 28134766 PMCID: PMC5343793 DOI: 10.3390/ijms18020257] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/12/2017] [Accepted: 01/17/2017] [Indexed: 02/07/2023] Open
Abstract
A genome-wide association study (GWAS) by our group identified loci associated with the plasma triglyceride (TG) response to ω-3 fatty acid (FA) supplementation in IQCJ, NXPH1, PHF17 and MYB. Our aim is to investigate potential mechanisms underlying the associations between single nucleotide polymorphisms (SNPs) in the four genes and TG levels following ω-3 FA supplementation. 208 subjects received 3 g/day of ω-3 FA (1.9–2.2 g of EPA and 1.1 g of docosahexaenoic acid (DHA)) for six weeks. Plasma TG were measured before and after the intervention. 67 SNPs were selected to increase the density of markers near GWAS hits. Genome-wide expression and methylation analyses were conducted on respectively 30 and 35 participants’ blood sample together with in silico analyses. Two SNPs of IQCJ showed different affinities to splice sites depending on alleles. Expression levels were influenced by genotype for one SNP in NXPH1 and one in MYB. Associations between 12 tagged SNPs of IQCJ, 26 of NXPH1, seven of PHF17 and four of MYB and gene-specific CpG site methylation levels were found. The response of plasma TG to ω-3 FA supplementation may be modulated by the effect of DNA methylation on expression levels of genes revealed by GWAS.
Collapse
Affiliation(s)
- Bastien Vallée Marcotte
- Institute of Nutrition and Functional Foods (INAF), Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
| | - Frédéric Guénard
- Institute of Nutrition and Functional Foods (INAF), Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
| | - Hubert Cormier
- Institute of Nutrition and Functional Foods (INAF), Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
| | - Simone Lemieux
- Institute of Nutrition and Functional Foods (INAF), Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
| | - Patrick Couture
- Institute of Nutrition and Functional Foods (INAF), Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
- CHU de Québec Research Center-Endocrinology and Nephrology, 2705 Laurier Blvd, Quebec, QC G1V 4G2, Canada.
| | - Iwona Rudkowska
- CHU de Québec Research Center-Endocrinology and Nephrology, 2705 Laurier Blvd, Quebec, QC G1V 4G2, Canada.
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
- CHU de Québec Research Center-Endocrinology and Nephrology, 2705 Laurier Blvd, Quebec, QC G1V 4G2, Canada.
| |
Collapse
|
8
|
Martin PM, Cifuentes-Diaz C, Devaux J, Garcia M, Bureau J, Thomasseau S, Klingler E, Girault JA, Goutebroze L. Schwannomin-interacting Protein 1 Isoform IQCJ-SCHIP1 Is a Multipartner Ankyrin- and Spectrin-binding Protein Involved in the Organization of Nodes of Ranvier. J Biol Chem 2016; 292:2441-2456. [PMID: 27979964 DOI: 10.1074/jbc.m116.758029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/14/2016] [Indexed: 11/06/2022] Open
Abstract
The nodes of Ranvier are essential regions for action potential conduction in myelinated fibers. They are enriched in multimolecular complexes composed of voltage-gated Nav and Kv7 channels associated with cell adhesion molecules. Cytoskeletal proteins ankyrin-G (AnkG) and βIV-spectrin control the organization of these complexes and provide mechanical support to the plasma membrane. IQCJ-SCHIP1 is a cytoplasmic protein present in axon initial segments and nodes of Ranvier. It interacts with AnkG and is absent from nodes and axon initial segments of βIV-spectrin and AnkG mutant mice. Here, we show that IQCJ-SCHIP1 also interacts with βIV-spectrin and Kv7.2/3 channels and self-associates, suggesting a scaffolding role in organizing nodal proteins. IQCJ-SCHIP1 binding requires a βIV-spectrin-specific domain and Kv7 channel 1-5-10 calmodulin-binding motifs. We then investigate the role of IQCJ-SCHIP1 in vivo by studying peripheral myelinated fibers in Schip1 knock-out mutant mice. The major nodal proteins are normally enriched at nodes in these mice, indicating that IQCJ-SCHIP1 is not required for their nodal accumulation. However, morphometric and ultrastructural analyses show an altered shape of nodes similar to that observed in βIV-spectrin mutant mice, revealing that IQCJ-SCHIP1 contributes to nodal membrane-associated cytoskeleton organization, likely through its interactions with the AnkG/βIV-spectrin network. Our work reveals that IQCJ-SCHIP1 interacts with several major nodal proteins, and we suggest that it contributes to a higher organizational level of the AnkG/βIV-spectrin network critical for node integrity.
Collapse
Affiliation(s)
- Pierre-Marie Martin
- From INSERM, UMR-S 839, F-75005 Paris.,the Université Pierre et Marie Curie (UPMC)-Sorbonne Universités, UMR-S 839, 75005 Paris.,the Institut du Fer à Moulin, 75005 Paris, and
| | - Carmen Cifuentes-Diaz
- From INSERM, UMR-S 839, F-75005 Paris.,the Université Pierre et Marie Curie (UPMC)-Sorbonne Universités, UMR-S 839, 75005 Paris.,the Institut du Fer à Moulin, 75005 Paris, and
| | - Jérôme Devaux
- the Aix Marseille University, CNRS, CRN2M, 13344 Marseille, France
| | - Marta Garcia
- From INSERM, UMR-S 839, F-75005 Paris.,the Université Pierre et Marie Curie (UPMC)-Sorbonne Universités, UMR-S 839, 75005 Paris.,the Institut du Fer à Moulin, 75005 Paris, and
| | - Jocelyne Bureau
- From INSERM, UMR-S 839, F-75005 Paris.,the Université Pierre et Marie Curie (UPMC)-Sorbonne Universités, UMR-S 839, 75005 Paris.,the Institut du Fer à Moulin, 75005 Paris, and
| | - Sylvie Thomasseau
- From INSERM, UMR-S 839, F-75005 Paris.,the Université Pierre et Marie Curie (UPMC)-Sorbonne Universités, UMR-S 839, 75005 Paris.,the Institut du Fer à Moulin, 75005 Paris, and
| | - Esther Klingler
- From INSERM, UMR-S 839, F-75005 Paris.,the Université Pierre et Marie Curie (UPMC)-Sorbonne Universités, UMR-S 839, 75005 Paris.,the Institut du Fer à Moulin, 75005 Paris, and
| | - Jean-Antoine Girault
- From INSERM, UMR-S 839, F-75005 Paris.,the Université Pierre et Marie Curie (UPMC)-Sorbonne Universités, UMR-S 839, 75005 Paris.,the Institut du Fer à Moulin, 75005 Paris, and
| | - Laurence Goutebroze
- the Université Pierre et Marie Curie (UPMC)-Sorbonne Universités, UMR-S 839, 75005 Paris, .,the Institut du Fer à Moulin, 75005 Paris, and
| |
Collapse
|
9
|
Vallée Marcotte B, Cormier H, Guénard F, Rudkowska I, Lemieux S, Couture P, Vohl MC. Novel Genetic Loci Associated with the Plasma Triglyceride Response to an Omega-3 Fatty Acid Supplementation. JOURNAL OF NUTRIGENETICS AND NUTRIGENOMICS 2016; 9:1-11. [PMID: 27160456 DOI: 10.1159/000446024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/07/2016] [Indexed: 11/19/2022]
Abstract
BACKGROUND A recent genome-wide association study (GWAS) by our group identified 13 loci associated with the plasma triglyceride (TG) response to omega-3 (n-3) fatty acid (FA) supplementation. This study aimed to test whether single-nucleotide polymorphisms (SNPs) within the IQCJ, NXPH1, PHF17 and MYB genes are associated with the plasma TG response to an n-3 FA supplementation. METHODS A total of 208 subjects followed a 6-week n-3 FA supplementation of 5 g/day of fish oil (1.9-2.2 g of eicosapentaenoic acid and 1.1 g of docosahexaenoic acid). Measurements of plasma lipids were made before and after the supplementation. Sixty-seven tagged SNPs were selected to increase the density of markers near GWAS hits. RESULTS In a repeated model, independent effects of the genotype and the gene-supplementation interaction were associated with plasma TG. Genotype effects were observed with two SNPs of NXPH1, and gene-diet interactions were observed with ten SNPs of IQCJ, four SNPs of NXPH1 and three SNPs of MYB. Positive and negative responders showed different genotype frequencies with nine SNPs of IQCJ, two SNPs of NXPH1 and two SNPs of MYB. CONCLUSION Fine mapping in GWAS-associated loci allowed the identification of SNPs partly explaining the large interindividual variability observed in plasma TG levels in response to an n-3 FA supplementation.
Collapse
|
10
|
Papandréou MJ, Vacher H, Fache MP, Klingler E, Rueda-Boroni F, Ferracci G, Debarnot C, Pipéroglou C, Garcia Del Caño G, Goutebroze L, Dargent B. CK2-regulated schwannomin-interacting protein IQCJ-SCHIP-1 association with AnkG contributes to the maintenance of the axon initial segment. J Neurochem 2015; 134:527-37. [PMID: 25950943 DOI: 10.1111/jnc.13158] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 04/14/2015] [Accepted: 05/04/2015] [Indexed: 11/30/2022]
Abstract
The axon initial segment (AIS) plays a central role in electrogenesis and in the maintenance of neuronal polarity. Its molecular organization is dependent on the scaffolding protein ankyrin (Ank) G and is regulated by kinases. For example, the phosphorylation of voltage-gated sodium channels by the protein kinase CK2 regulates their interaction with AnkG and, consequently, their accumulation at the AIS. We previously showed that IQ motif containing J-Schwannomin-Interacting Protein 1 (IQCJ-SCHIP-1), an isoform of the SCHIP-1, accumulated at the AIS in vivo. Here, we analyzed the molecular mechanisms involved in IQCJ-SCHIP-1-specific axonal location. We showed that IQCJ-SCHIP-1 accumulation in the AIS of cultured hippocampal neurons depended on AnkG expression. Pull-down assays and surface plasmon resonance analysis demonstrated that AnkG binds to CK2-phosphorylated IQCJ-SCHIP-1 but not to the non-phosphorylated protein. Surface plasmon resonance approaches using IQCJ-SCHIP-1, SCHIP-1a, another SCHIP-1 isoform, and their C-terminus tail mutants revealed that a segment including multiple CK2-phosphorylatable sites was directly involved in the interaction with AnkG. Pharmacological inhibition of CK2 diminished both IQCJ-SCHIP-1 and AnkG accumulation in the AIS. Silencing SCHIP-1 expression reduced AnkG cluster at the AIS. Finally, over-expression of IQCJ-SCHIP-1 decreased AnkG concentration at the AIS, whereas a mutant deleted of the CK2-regulated AnkG interaction site did not. Our study reveals that CK2-regulated IQJC-SCHIP-1 association with AnkG contributes to AIS maintenance. The axon initial segment (AIS) organization depends on ankyrin (Ank) G and kinases. Here we showed that AnkG binds to CK2-phosphorylated IQCJ-SCHIP-1, in a segment including 12 CK2-phosphorylatable sites. In cultured neurons, either pharmacological inhibition of CK2 or IQCJ-SCHIP-1 silencing reduced AnkG clustering. Overexpressed IQCJ-SCHIP-1 decreased AnkG concentration at the AIS whereas a mutant deleted of the CK2-regulated AnkG interaction site did not. Thus, CK2-regulated IQJC-SCHIP-1 association with AnkG contributes to AIS maintenance.
Collapse
Affiliation(s)
| | - Hélène Vacher
- CRN2M-UMR7286, Aix Marseille Université, CNRS, Marseille, France
| | | | - Esther Klingler
- Institut du Fer à Moulin, Inserm, UMR-S 839, Université Pierre et Marie-Curie, Paris, France
| | | | | | - Claire Debarnot
- CRN2M-UMR7286, Aix Marseille Université, CNRS, Marseille, France
| | | | - Gontzal Garcia Del Caño
- CRN2M-UMR7286, Aix Marseille Université, CNRS, Marseille, France.,Department of Neurosciences, University of the Basque Country, Vitoria-Gasteiz, Spain
| | - Laurence Goutebroze
- Institut du Fer à Moulin, Inserm, UMR-S 839, Université Pierre et Marie-Curie, Paris, France
| | | |
Collapse
|
11
|
Nacu S, Yuan W, Kan Z, Bhatt D, Rivers CS, Stinson J, Peters BA, Modrusan Z, Jung K, Seshagiri S, Wu TD. Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples. BMC Med Genomics 2011; 4:11. [PMID: 21261984 PMCID: PMC3041646 DOI: 10.1186/1755-8794-4-11] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 01/24/2011] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs), have been estimated using expressed sequence tag (EST) libraries to involve 4-6% of all genes. Deep transcriptional sequencing (RNA-Seq) now makes it possible to study the occurrence and expression levels of TICs in individual samples across the genome. METHODS We performed single-end RNA-Seq on three human prostate adenocarcinoma samples and their corresponding normal tissues, as well as brain and universal reference samples. We developed two bioinformatics methods to specifically identify TIC events: a targeted alignment method using artificial exon-exon junctions within 200,000 bp from adjacent genes, and genomic alignment allowing splicing within individual reads. We performed further experimental verification and characterization of selected TIC and fusion events using quantitative RT-PCR and comparative genomic hybridization microarrays. RESULTS Targeted alignment against artificial exon-exon junctions yielded 339 distinct TIC events, including 32 gene pairs with multiple isoforms. The false discovery rate was estimated to be 1.5%. Spliced alignment to the genome was less sensitive, finding only 18% of those found by targeted alignment in 33-nt reads and 59% of those in 50-nt reads. However, spliced alignment revealed 30 cases of TICs with intervening exons, in addition to distant inversions, scrambled genes, and translocations. Our findings increase the catalog of observed TIC gene pairs by 66%.We verified 6 of 6 predicted TICs in all prostate samples, and 2 of 5 predicted novel distant gene fusions, both private events among 54 prostate tumor samples tested. Expression of TICs correlates with that of the upstream gene, which can explain the prostate-specific pattern of some TIC events and the restriction of the SLC45A3-ELK4 e4-e2 TIC to ERG-negative prostate samples, as confirmed in 20 matched prostate tumor and normal samples and 9 lung cancer cell lines. CONCLUSIONS Deep transcriptional sequencing and analysis with targeted and spliced alignment methods can effectively identify TIC events across the genome in individual tissues. Prostate and reference samples exhibit a wide range of TIC events, involving more genes than estimated previously using ESTs. Tissue specificity of TIC events is correlated with expression patterns of the upstream gene. Some TIC events, such as MSMB-NCOA4, may play functional roles in cancer.
Collapse
Affiliation(s)
- Serban Nacu
- Department of Bioinformatics and Molecular Biology, Genentech, Inc, South San Francisco, California 94080, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Martin PM, Cifuentes-Diaz C, Garcia M, Goutebroze L, Girault JA. [Axon and Schwann cells... so far away, so close]. Rev Neurol (Paris) 2008; 164:1057-62. [PMID: 19041107 DOI: 10.1016/j.neurol.2008.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Myelination was a major step in the evolution of the nervous system. Appearing first in jaw fish, myelination allows the fast and secure propagation of action potentials at a low energetic cost, and without exaggerated increase in axonal diameter. In the peripheral nervous system of mammals, myelination results from the tight interactions between Schwann cells and axons, leading to the formation of highly differentiated domains along the axon. The molecular determinants of these interactions are starting to be well identified. Their understanding provides a precise framework to interpret the defects, which occur in pathological circumstances. This review summarizes the present state of knowledge concerning axoglial interactions in peripheral nerves.
Collapse
Affiliation(s)
- P-M Martin
- Inserm UMR-S 839, institut du Fer-à-Moulin, 17, rue du Fer-à-Moulin, 75005 Paris, France
| | | | | | | | | |
Collapse
|
13
|
Schwannomin-interacting protein-1 isoform IQCJ-SCHIP-1 is a late component of nodes of Ranvier and axon initial segments. J Neurosci 2008; 28:6111-7. [PMID: 18550753 DOI: 10.1523/jneurosci.1044-08.2008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Axon initial segments (AISs) and nodes of Ranvier (NRs) are essential regions for saltatory conduction of the action potential along the axon. These two domains are enriched in similar multimolecular complexes, which include voltage-gated sodium channels (Na(v)), NF186 (neurofascin 186), NrCAM (neuron glia-related cell adhesion molecule), and cytoskeleton linkers ankyrin G (AnkG) and betaIV-spectrin. Identification of novel members of these complexes is critical to better understand their formation, function, and maintenance. Here we report that IQCJ-SCHIP-1, a recently identified isoform of schwannomin-interacting protein-1 (SCHIP-1), is a novel component of both AISs and NRs in the central and peripheral nervous systems. We show that IQCJ-SCHIP-1 binds calmodulin in the absence of Ca(2+) and is highly enriched at AISs and NRs. IQCJ-SCHIP-1 accumulation at AISs and NRs is a late event, suggesting that IQCJ-SCHIP-1 is likely to play a role in mature AISs and NRs rather than during their formation. IQCJ-SCHIP-1 was not detected at AISs in the absence of AnkG and interacted in vitro with this protein. IQCJ-SCHIP-1 was also absent from central NRs and AISs of quivering mice, which have a mutation of betaIV-spectrin. We suggest that IQCJ-SCHIP-1 might participate, along with AnkG and betaIV-spectrin, in the stabilization or function of the multimolecular complexes of AISs and NRs, possibly by participating in Ca(2+)-mediated responses.
Collapse
|
14
|
Scoles DR. The merlin interacting proteins reveal multiple targets for NF2 therapy. Biochim Biophys Acta Rev Cancer 2007; 1785:32-54. [PMID: 17980164 DOI: 10.1016/j.bbcan.2007.10.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Revised: 09/29/2007] [Accepted: 10/03/2007] [Indexed: 01/20/2023]
Abstract
The neurofibromatosis 2 (NF2) tumor suppressor protein merlin is commonly mutated in human benign brain tumors. The gene altered in NF2 was located on human chromosome 22q12 in 1993 and the encoded protein named merlin and schwannomin. Merlin has homology to ERM family proteins, ezrin, radixin, and moesin, within the protein 4.1 superfamily. In efforts to determine merlin function several groups have discovered 34 merlin interacting proteins, including ezrin, radixin, moesin, CD44, layilin, paxillin, actin, N-WASP, betaII-spectrin, microtubules, TRBP, eIF3c, PIKE, NHERF, MAP, RalGDS, RhoGDI, EG1/magicin, HEI10, HRS, syntenin, caspr/paranodin, DCC, NGB, CRM1/exportin, SCHIP1, MYPT-1-PP1delta, RIbeta, PKA, PAK (three types), calpain and Drosophila expanded. Many of the proteins that interact with the merlin N-terminal domain also bind ezrin, while other merlin interacting proteins do not bind other members of the ERM family. Merlin also interacts with itself. This review describes these proteins, their possible roles in NF2, and the resultant hypothesized merlin functions. Review of all of the merlin interacting proteins and functional consequences of losses of these interactions reveals multiple merlin actions in PI3-kinase, MAP kinase and small GTPase signaling pathways that might be targeted to inhibit the proliferation of NF2 tumors.
Collapse
Affiliation(s)
- Daniel R Scoles
- Women's Cancer Research Institute, CSMC Burns and Allen Research Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA.
| |
Collapse
|