1
|
Chari T, Gorin G, Pachter L. Stochastic Modeling of Biophysical Responses to Perturbation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.04.602131. [PMID: 39005347 PMCID: PMC11245117 DOI: 10.1101/2024.07.04.602131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Recent advances in high-throughput, multi-condition experiments allow for genome-wide investigation of how perturbations affect transcription and translation in the cell across multiple biological entities or modalities, from chromatin and mRNA information to protein production and spatial morphology. This presents an unprecedented opportunity to unravel how the processes of DNA and RNA regulation direct cell fate determination and disease response. Most methods designed for analyzing large-scale perturbation data focus on the observational outcomes, e.g., expression; however, many potential transcriptional mechanisms, such as transcriptional bursting or splicing dynamics, can underlie these complex and noisy observations. In this analysis, we demonstrate how a stochastic biophysical modeling approach to interpreting high-throughout perturbation data enables deeper investigation of the 'how' behind such molecular measurements. Our approach takes advantage of modalities already present in data produced with current technologies, such as nascent and mature mRNA measurements, to illuminate transcriptional dynamics induced by perturbation, predict kinetic behaviors in new perturbation settings, and uncover novel populations of cells with distinct kinetic responses to perturbation.
Collapse
Affiliation(s)
- Tara Chari
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | | | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, California
| |
Collapse
|
2
|
Xie J, Herr S, Ma D, Wu S, Zhao H, Sun S, Ma Z, Chan MYL, Li K, Yang Y, Huang F, Shi R, Yuan C. Acute Transcriptomic and Epigenetic Alterations at T12 After Rat T10 Spinal Cord Contusive Injury. Mol Neurobiol 2023; 60:2937-2953. [PMID: 36750527 DOI: 10.1007/s12035-023-03250-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 01/19/2023] [Indexed: 02/09/2023]
Abstract
Spinal cord injury is a severely debilitating condition affecting a significant population in the USA. Spinal cord injury patients often have increased risk of developing persistent neuropathic pain and other neurodegenerative conditions beyond the primary lesion center later in their life. The molecular mechanism conferring to the "latent" damages at distal tissues, however, remains elusive. Here, we studied molecular changes conferring abnormal functionality at distal spinal cord (T12) beyond the lesion center (T10) by combining next-generation sequencing (RNA- and bisulfite sequencing), super-resolution microscopy, and immunofluorescence staining at 7 days post injury. We observed significant transcriptomic changes primarily enriched in neuroinflammation and synaptogenesis associated pathways. Transcription factors (TFs) that regulate neurogenesis and neuron plasticity, including Egr1, Klf4, and Myc, are significantly upregulated. Along with global changes in chromatin arrangements and DNA methylation, including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), bisulfite sequencing further reveals the involvement of DNA methylation changes in regulating cytokine, growth factor, and ion channel expression. Collectively, our results pave the way towards understanding transcriptomic and epigenomic mechanism in conferring long-term disease risks at distal tissues away from the primary lesion center and shed light on potential molecular targets that govern the regulatory mechanism at distal spinal cord tissues.
Collapse
Affiliation(s)
- Junkai Xie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA
| | - Seth Herr
- Center for Paralysis Research, Purdue University, West Lafayette, IN, USA
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, USA
| | - Donghan Ma
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Shichen Wu
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA
| | - Han Zhao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA
| | - Siyuan Sun
- Center for Paralysis Research, Purdue University, West Lafayette, IN, USA
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, USA
| | - Zhixiong Ma
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA
| | - Matthew Yan-Lok Chan
- Agriculture and Biological Engineering, Purdue University, West Lafayette, IN, USA
| | - Katherine Li
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA
| | - Yang Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Fang Huang
- Agriculture and Biological Engineering, Purdue University, West Lafayette, IN, USA
| | - Riyi Shi
- Center for Paralysis Research, Purdue University, West Lafayette, IN, USA.
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN, USA.
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA.
- Purdue Center of Cancer Research, Purdue University, West Lafayette, IN, USA.
| |
Collapse
|
3
|
Xu A, Xu XN, Luo Z, Huang X, Gong RQ, Fu DY. Identification of prognostic cancer-associated fibroblast markers in luminal breast cancer using weighted gene co-expression network analysis. Front Oncol 2023; 13:1191660. [PMID: 37207166 PMCID: PMC10191114 DOI: 10.3389/fonc.2023.1191660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023] Open
Abstract
Background Cancer-associated fibroblasts (CAFs) play a pivotal role in cancer progression and are known to mediate endocrine and chemotherapy resistance through paracrine signaling. Additionally, they directly influence the expression and growth dependence of ER in Luminal breast cancer (LBC). This study aims to investigate stromal CAF-related factors and develop a CAF-related classifier to predict the prognosis and therapeutic outcomes in LBC. Methods The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were utilized to obtain mRNA expression and clinical information from 694 and 101 LBC samples, respectively. CAF infiltrations were determined by estimating the proportion of immune and cancer cells (EPIC) method, while stromal scores were calculated using the Estimation of STromal and Immune cells in MAlignant Tumors using Expression data (ESTIMATE) algorithm. Weighted gene co-expression network analysis (WGCNA) was used to identify stromal CAF-related genes. A CAF risk signature was developed through univariate and least absolute shrinkage and selection operator method (LASSO) Cox regression model. The Spearman test was used to evaluate the correlation between CAF risk score, CAF markers, and CAF infiltrations estimated through EPIC, xCell, microenvironment cell populations-counter (MCP-counter), and Tumor Immune Dysfunction and Exclusion (TIDE) algorithms. The TIDE algorithm was further utilized to assess the response to immunotherapy. Additionally, Gene set enrichment analysis (GSEA) was applied to elucidate the molecular mechanisms underlying the findings. Results We constructed a 5-gene prognostic model consisting of RIN2, THBS1, IL1R1, RAB31, and COL11A1 for CAF. Using the median CAF risk score as the cutoff, we classified LBC patients into high- and low-CAF-risk groups and found that those in the high-risk group had a significantly worse prognosis. Spearman correlation analyses demonstrated a strong positive correlation between the CAF risk score and stromal and CAF infiltrations, with the five model genes showing positive correlations with CAF markers. In addition, the TIDE analysis revealed that high-CAF-risk patients were less likely to respond to immunotherapy. Gene set enrichment analysis (GSEA) identified significant enrichment of ECM receptor interaction, regulation of actin cytoskeleton, epithelial-mesenchymal transition (EMT), and TGF-β signaling pathway gene sets in the high-CAF-risk group patients. Conclusion The five-gene prognostic CAF signature presented in this study was not only reliable for predicting prognosis in LBC patients, but it was also effective in estimating clinical immunotherapy response. These findings have significant clinical implications, as the signature may guide tailored anti-CAF therapy in combination with immunotherapy for LBC patients.
Collapse
Affiliation(s)
- An Xu
- Medical College of Yangzhou University, Yangzhou, Jiangsu, China
| | - Xiang-Nan Xu
- Department of Thyroid and Breast Surgery, Northern Jiangsu People’s Hospital, Yangzhou, Jiangsu, China
| | - Zhou Luo
- Department of Thyroid and Breast Surgery, Northern Jiangsu People’s Hospital, Yangzhou, Jiangsu, China
| | - Xiao Huang
- Medical College of Yangzhou University, Yangzhou, Jiangsu, China
| | - Rong-Quan Gong
- Medical College of Yangzhou University, Yangzhou, Jiangsu, China
| | - De-Yuan Fu
- Department of Thyroid and Breast Surgery, Northern Jiangsu People’s Hospital, Yangzhou, Jiangsu, China
- *Correspondence: De-Yuan Fu,
| |
Collapse
|
4
|
Rab7 Investigation Insights into the Existence of White Spot Syndrome Virus in Crustaceans: An In Silico Approach. Adv Virol 2022; 2022:3887441. [PMID: 36313590 PMCID: PMC9613395 DOI: 10.1155/2022/3887441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022] Open
Abstract
In this study, previously published Rab7 sequences from National Center for Biotechnology Information (NCBI) have been investigated from chordates, mollusks, annelids, cnidarians, amphibians, priapulids, brachiopods, and arthropods including decapods and other groups. Among decapod crustacean isolates, amino acid variations were found in 13 locations. Penaeid shrimps had variations in positions 13 (I ⟶ J), 22 (T ⟶ A), 124 (G ⟶ X), and 149 (V ⟶ X) while interestingly the freshwater prawn and mitten crab both had amino acid substitutions in positions 87 (V ⟶ C) and 95 (T ⟶ S) along with the other disagreements in amino acid positions 178 (S ⟶ N), 201 (D ⟶ E), 181 (E ⟶ D), 182 (L ⟶ I), 183 (Y ⟶ G), 184 (N ⟶ H), and 198 (A ⟶ T). Among 100 isolates of Rab7 from organisms of various phyla, mutations were observed in several positions. These mutations caused variations in hydrophobicity and isoelectric point which impact the ligand-protein binding affinity. Some common mutations were found in the organisms of the same phylum and among different phyla. Homology modeling of Rab7 proteins from different organisms was done using SWISS-MODEL and validated further by developing Ramachandran plots. Protein-protein docking showed that active residues were there in the binding interfaces of Rab7 from organisms of seven different phyla and VP28 of WSSV. Similarities were observed in the Rab7-VP28 complexes in those selected organisms which differed from the Rab7-VP28 complex in the case of Penaeid shrimp. The findings of this study suggest that WSSV may exist in different marine organisms that have Rab7 protein and transmit to crustaceans like shrimps and crabs which are of commercial importance.
Collapse
|
5
|
Beyens A, Pottie L, Sips P, Callewaert B. Clinical and Molecular Delineation of Cutis Laxa Syndromes: Paradigms for Homeostasis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1348:273-309. [PMID: 34807425 DOI: 10.1007/978-3-030-80614-9_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Cutis laxa (CL) syndromes are a large and heterogeneous group of rare connective tissue disorders that share loose redundant skin as a hallmark clinical feature, which reflects dermal elastic fiber fragmentation. Both acquired and congenital-Mendelian- forms exist. Acquired forms are progressive and often preceded by inflammatory triggers in the skin, but may show systemic elastolysis. Mendelian forms are often pleiotropic in nature and classified upon systemic manifestations and mode of inheritance. Though impaired elastogenesis is a common denominator in all Mendelian forms of CL, the underlying gene defects are diverse and affect structural components of the elastic fiber or impair metabolic pathways interfering with cellular trafficking, proline synthesis, or mitochondrial functioning. In this chapter we provide a detailed overview of the clinical and molecular characteristics of the different cutis laxa types and review the latest insights on elastic fiber assembly and homeostasis from both human and animal studies.
Collapse
Affiliation(s)
- Aude Beyens
- Center for Medical Genetics Ghent, Department of Dermatology, Department of Biomolecular Medicine, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Lore Pottie
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Patrick Sips
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, Ghent University, Ghent, Belgium.
| |
Collapse
|
6
|
Lin W, Ren T, Li W, Liu M, He D, Liang S, Luo W, Zhang X. Novel 61-bp Indel of RIN2 Is Associated With Fat and Hatching Weight Traits in Chickens. Front Genet 2021; 12:672888. [PMID: 34276778 PMCID: PMC8280519 DOI: 10.3389/fgene.2021.672888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/09/2021] [Indexed: 11/28/2022] Open
Abstract
The Ras and Rab interactor 2 (RIN2) gene, which encodes RAS and Rab interacting protein 2, can interact with GTP-bound Rab5 and participate in early endocytosis. This study found a 61-bp insertion/deletion (indel) in the RIN2 intron region, and 3 genotypes II, ID, and DD were observed. Genotype analysis of mutation sites was performed on 665 individuals from F2 population and 8 chicken breeds. It was found that the indel existed in each breed and that yellow feathered chickens were mainly of the DD genotype. Correlation analysis of growth and carcass traits in the F2 population of Xinghua and White Recessive Rock chickens showed that the 61-bp indel was significantly correlated with abdominal fat weight, abdominal fat rate, fat width, and hatching weight (P < 0.05). RIN2 mRNA was expressed in all the tested tissues, and its expression in abdominal fat was higher than that in other tissues. In addition, the expression of the RIN2 mRNA in the abdominal fat of the DD genotype was significantly higher than that of the II genotype (P < 0.05). The transcriptional activity results showed that the luciferase activity of the pGL3-DD vector was significantly higher than that of the pGL3-II vector (P < 0.01). Moreover, the results indicate that the polymorphisms in transcription factor binding sites (TFBSs) of 61-bp indel may affect the transcriptional activity of RIN2, and thus alter fat traits in chicken. The results of this study showed that the 61-bp indel was closely related to abdominal fat-related and hatching weight traits of chickens, which may have reference value for molecular marker-assisted selection of chickens.
Collapse
Affiliation(s)
- Wujian Lin
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Tuanhui Ren
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Wangyu Li
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Manqing Liu
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Danlin He
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Shaodong Liang
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Wen Luo
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| |
Collapse
|
7
|
Wang XQ, Xu SW, Wang W, Piao SZ, Mao XL, Zhou XB, Wang Y, Wu WD, Ye LP, Li SW. Identification and Validation of a Novel DNA Damage and DNA Repair Related Genes Based Signature for Colon Cancer Prognosis. Front Genet 2021; 12:635863. [PMID: 33719345 PMCID: PMC7943631 DOI: 10.3389/fgene.2021.635863] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/01/2021] [Indexed: 12/14/2022] Open
Abstract
Backgrounds: Colorectal cancer (CRC) with high incidence, has the third highest mortality of tumors. DNA damage and repair influence a variety of tumors. However, the role of these genes in colon cancer prognosis has been less systematically investigated. Here, we aim to establish a corresponding prognostic signature providing new therapeutic opportunities for CRC. Method: After related genes were collected from GSEA, univariate Cox regression was performed to evaluate each gene's prognostic relevance through the TCGA-COAD dataset. Stepwise COX regression was used to establish a risk prediction model through the training sets randomly separated from the TCGA cohort and validated in the remaining testing sets and two GEO datasets (GSE17538 and GSE38832). A 12-DNA-damage-and-repair-related gene-based signature able to classify COAD patients into high and low-risk groups was developed. The predictive ability of the risk model or nomogram were evaluated by different bioinformatics- methods. Gene functional enrichment analysis was performed to analyze the co-expressed genes of the risk-based genes. Result: A 12-gene based prognostic signature established within 160 significant survival-related genes from DNA damage and repair related gene sets performed well with an AUC of ROC 0.80 for 5 years in the TCGA-CODA dataset. The signature includes CCNB3, ISY1, CDC25C, SMC1B, MC1R, LSP1P4, RIN2, TPM1, ELL3, POLG, CD36, and NEK4. Kaplan-Meier survival curves showed that the prognosis of the risk status owns more significant differences than T, M, N, and stage prognostic parameters. A nomogram was constructed by LASSO regression analysis with T, M, N, age, and risk as prognostic parameters. ROC curve, C-index, Calibration analysis, and Decision Curve Analysis showed the risk module and nomogram performed best in years 1, 3, and 5. KEGG, GO, and GSEA enrichment analyses suggest the risk involved in a variety of important biological processes and well-known cancer-related pathways. These differences may be the key factors affecting the final prognosis. Conclusion: The established gene signature for CRC prognosis provides a new molecular tool for clinical evaluation of prognosis, individualized diagnosis, and treatment. Therapies based on targeted DNA damage and repair mechanisms may formulate more sensitive and potential chemotherapy regimens, thereby expanding treatment options and potentially improving the clinical outcome of CRC patients.
Collapse
Affiliation(s)
- Xue-quan Wang
- Laboratory of Cellular and Molecular Radiation Oncology, Department of Radiation Oncology, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, China
| | - Shi-wen Xu
- Wenzhou Medical University, Wenzhou, China
| | - Wei Wang
- Wenzhou Medical University, Wenzhou, China
| | - Song-zhe Piao
- Department of Urology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Xin-li Mao
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, China
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Xian-bin Zhou
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, China
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Yi Wang
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, China
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Wei-dan Wu
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, China
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Li-ping Ye
- Wenzhou Medical University, Wenzhou, China
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Shao-wei Li
- Key Laboratory of Minimally Invasive Techniques & Rapid Rehabilitation of Digestive System Tumor of Zhejiang Province, Linhai, China
- Department of Gastroenterology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| |
Collapse
|
8
|
Beyens A, Boel A, Symoens S, Callewaert B. Cutis laxa: A comprehensive overview of clinical characteristics and pathophysiology. Clin Genet 2020; 99:53-66. [PMID: 33058140 DOI: 10.1111/cge.13865] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/17/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022]
Abstract
Cutis laxa (CL) syndromes comprise a rare group of multisystem disorders that share loose redundant skin folds as hallmark clinical feature. CL results from impaired elastic fiber assembly and homeostasis, and the known underlying gene defects affect different extracellular matrix proteins, intracellular trafficking, or cellular metabolism. Due to the underlying clinical and molecular heterogeneity, the diagnostic work-up of CL patients is often challenging. In this review, we provide a practical approach to the broad differential diagnosis of CL syndromes, provide an overview of the molecular pathogenesis of the different subtypes, and suggest general management guidelines.
Collapse
Affiliation(s)
- Aude Beyens
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Dermatology, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Annekatrien Boel
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sofie Symoens
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| |
Collapse
|
9
|
Harms FL, Parthasarathy P, Zorndt D, Alawi M, Fuchs S, Halliday BJ, McKeown C, Sampaio H, Radhakrishnan N, Radhakrishnan SK, Gorce M, Navet B, Ziegler A, Sachdev R, Robertson SP, Nampoothiri S, Kutsche K. Biallelic loss-of-function variants in TBC1D2B cause a neurodevelopmental disorder with seizures and gingival overgrowth. Hum Mutat 2020; 41:1645-1661. [PMID: 32623794 DOI: 10.1002/humu.24071] [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: 01/23/2020] [Revised: 06/08/2020] [Accepted: 06/30/2020] [Indexed: 12/15/2022]
Abstract
The family of Tre2-Bub2-Cdc16 (TBC)-domain containing GTPase activating proteins (RABGAPs) is not only known as key regulatorof RAB GTPase activity but also has GAP-independent functions. Rab GTPases are implicated in membrane trafficking pathways, such as vesicular trafficking. We report biallelic loss-of-function variants in TBC1D2B, encoding a member of the TBC/RABGAP family with yet unknown function, as the underlying cause of cognitive impairment, seizures, and/or gingival overgrowth in three individuals from unrelated families. TBC1D2B messenger RNA amount was drastically reduced, and the protein was absent in fibroblasts of two patients. In immunofluorescence analysis, ectopically expressed TBC1D2B colocalized with vesicles positive for RAB5, a small GTPase orchestrating early endocytic vesicle trafficking. In two independent TBC1D2B CRISPR/Cas9 knockout HeLa cell lines that serve as cellular model of TBC1D2B deficiency, epidermal growth factor internalization was significantly reduced compared with the parental HeLa cell line suggesting a role of TBC1D2B in early endocytosis. Serum deprivation of TBC1D2B-deficient HeLa cell lines caused a decrease in cell viability and an increase in apoptosis. Our data reveal that loss of TBC1D2B causes a neurodevelopmental disorder with gingival overgrowth, possibly by deficits in vesicle trafficking and/or cell survival.
Collapse
Affiliation(s)
- Frederike L Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Padmini Parthasarathy
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Dennis Zorndt
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sigrid Fuchs
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Benjamin J Halliday
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Colina McKeown
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Hugo Sampaio
- Department of Women and Children's Health, University of New South Wales, Randwick Campus, Randwick, NSW, Australia.,Sydney Children's Hospital, Randwick, NSW, Australia
| | - Natasha Radhakrishnan
- Department of Ophthalmology, Amrita Institute of Medical Sciences and Research Centre, Cochin, Kerala, India
| | - Suresh K Radhakrishnan
- Department of Neurology, Amrita Institute of Medical Sciences and Research Centre, Cochin, Kerala, India
| | - Magali Gorce
- Department of Metabolic Disease, Children University Hospital, Toulouse, France
| | - Benjamin Navet
- Department of Biochemistry and Genetics, University Hospital of Angers, Angers, France.,MitoLab, Institut MitoVasc, UMR CNRS6015, INSERM U1083, Angers, France
| | - Alban Ziegler
- Department of Biochemistry and Genetics, University Hospital of Angers, Angers, France.,MitoLab, Institut MitoVasc, UMR CNRS6015, INSERM U1083, Angers, France
| | - Rani Sachdev
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Stephen P Robertson
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Cochin, Kerala, India
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
10
|
Liu G, Shen J, Chen C, Jiao Y, Li Z, Tan H, Lin Y, Rong T. Genome-Wide Analysis of circular RNAs and validation of hsa_circ_0006719 as a potential novel diagnostic biomarker in congenital scoliosis patients. J Cell Mol Med 2020; 24:7015-7022. [PMID: 32394619 PMCID: PMC7299707 DOI: 10.1111/jcmm.15370] [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: 02/16/2020] [Revised: 03/31/2020] [Accepted: 04/22/2020] [Indexed: 01/01/2023] Open
Abstract
Congenital scoliosis (CS) is a form of spinal curvature resulting from anomalous development of vertebrae. Recent studies demonstrated that circRNAs could serve as potential biomarkers of disease diagnosis. Genome‐wide circRNAs expression in seven CS patients and three healthy controls was initially detected. Bioinformatics analysis was conducted to explore the potential pathological pathway of CS. Quantitative PCR (qPCR) was performed to validate the selected circRNAs in the replication cohort with 32 CS patients and 30 healthy controls. Logistic regression controlling for gender was conducted to compare the expression difference. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic value. Twenty‐two differentially expressed circRNAs were filtered from genome‐wide circRNA sequencing. Seven circRNAs were validated by qPCR. Only hsa_circ_0006719 was confirmed to have a higher expression level in the CS group than the healthy control group (P = 0.036). Receiver operating characteristic curve also suggested that hsa_circ_0006719 had significant diagnostic value for CS (AUC = 0.739, P = 0.001). We described the first study of circRNAs in CS and validated hsa_circ_0006719 as a potential novel diagnostic biomarker of CS.
Collapse
Affiliation(s)
- Gang Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Jianxiong Shen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Chong Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Department of Spine Surgery, Orthopedics Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yang Jiao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Zheng Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Haining Tan
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Youxi Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Tianhua Rong
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| |
Collapse
|
11
|
Kameli R, Ashrafi MR, Ehya F, Alizadeh H, Hosseinpour S, Garshasbi M, Tavasoli AR. Leukoencephalopathy in RIN2 syndrome: Novel mutation and expansion of clinical spectrum. Eur J Med Genet 2020; 63:103629. [DOI: 10.1016/j.ejmg.2019.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/21/2018] [Accepted: 02/10/2019] [Indexed: 02/02/2023]
|
12
|
Huang S, Wang Y. Golgi structure formation, function, and post-translational modifications in mammalian cells. F1000Res 2017; 6:2050. [PMID: 29225785 PMCID: PMC5710388 DOI: 10.12688/f1000research.11900.1] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/20/2017] [Indexed: 01/04/2023] Open
Abstract
The Golgi apparatus is a central membrane organelle for trafficking and post-translational modifications of proteins and lipids in cells. In mammalian cells, it is organized in the form of stacks of tightly aligned flattened cisternae, and dozens of stacks are often linked laterally into a ribbon-like structure located in the perinuclear region of the cell. Proper Golgi functionality requires an intact architecture, yet Golgi structure is dynamically regulated during the cell cycle and under disease conditions. In this review, we summarize our current understanding of the relationship between Golgi structure formation, function, and regulation, with focus on how post-translational modifications including phosphorylation and ubiquitination regulate Golgi structure and on how Golgi unstacking affects its functions, in particular, protein trafficking, glycosylation, and sorting in mammalian cells.
Collapse
Affiliation(s)
- Shijiao Huang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
13
|
Reinbolt RE, Sonis S, Timmers CD, Fernández-Martínez JL, Cernea A, de Andrés-Galiana EJ, Hashemi S, Miller K, Pilarski R, Lustberg MB. Genomic risk prediction of aromatase inhibitor-related arthralgia in patients with breast cancer using a novel machine-learning algorithm. Cancer Med 2017; 7:240-253. [PMID: 29168353 PMCID: PMC5773952 DOI: 10.1002/cam4.1256] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/05/2017] [Accepted: 10/13/2017] [Indexed: 02/06/2023] Open
Abstract
Many breast cancer (BC) patients treated with aromatase inhibitors (AIs) develop aromatase inhibitor‐related arthralgia (AIA). Candidate gene studies to identify AIA risk are limited in scope. We evaluated the potential of a novel analytic algorithm (NAA) to predict AIA using germline single nucleotide polymorphisms (SNP) data obtained before treatment initiation. Systematic chart review of 700 AI‐treated patients with stage I‐III BC identified asymptomatic patients (n = 39) and those with clinically significant AIA resulting in AI termination or therapy switch (n = 123). Germline DNA was obtained and SNP genotyping performed using the Affymetrix UK BioBank Axiom Array to yield 695,277 SNPs. SNP clusters that most closely defined AIA risk were discovered using an NAA that sequentially combined statistical filtering and a machine‐learning algorithm. NCBI PhenGenI and Ensemble databases defined gene attribution of the most discriminating SNPs. Phenotype, pathway, and ontologic analyses assessed functional and mechanistic validity. Demographics were similar in cases and controls. A cluster of 70 SNPs, correlating to 57 genes, was identified. This SNP group predicted AIA occurrence with a maximum accuracy of 75.93%. Strong associations with arthralgia, breast cancer, and estrogen phenotypes were seen in 19/57 genes (33%) and were functionally consistent. Using a NAA, we identified a 70 SNP cluster that predicted AIA risk with fair accuracy. Phenotype, functional, and pathway analysis of attributed genes was consistent with clinical phenotypes. This study is the first to link a specific SNP/gene cluster to AIA risk independent of candidate gene bias.
Collapse
Affiliation(s)
- Raquel E Reinbolt
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Stephen Sonis
- Primary Endpoint Solutions, Watertown, Massachusetts.,Brigham and Women's Hospital and the Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Cynthia D Timmers
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | | | - Ana Cernea
- Primary Endpoint Solutions, Watertown, Massachusetts.,University of Oviedo, Oviedo, Spain
| | | | - Sepehr Hashemi
- Primary Endpoint Solutions, Watertown, Massachusetts.,Harvard School of Dental Medicine, Boston, Massachusetts
| | - Karin Miller
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Robert Pilarski
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Maryam B Lustberg
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| |
Collapse
|
14
|
van Amen-Hellebrekers CJM, Jansen S, Stegmann APA, Stevens SJC, Pfundt R, de Vries BBA. Biallelicframeshift mutation in RIN2 in a patient with intellectual disability and cataract, without RIN2 syndrome. Am J Med Genet A 2017; 173:3238-3240. [PMID: 29048725 DOI: 10.1002/ajmg.a.38396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/22/2017] [Accepted: 07/18/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Claudia J M van Amen-Hellebrekers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sandra Jansen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| |
Collapse
|
15
|
Pavone P, Praticò AD, Rizzo R, Corsello G, Ruggieri M, Parano E, Falsaperla R. A clinical review on megalencephaly: A large brain as a possible sign of cerebral impairment. Medicine (Baltimore) 2017; 96:e6814. [PMID: 28658095 PMCID: PMC5500017 DOI: 10.1097/md.0000000000006814] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 02/23/2017] [Accepted: 02/27/2017] [Indexed: 11/26/2022] Open
Abstract
Megalencephaly and macrocephaly present with a head circumference measurement 2 standard deviations above the age-related mean. However, even if pathologic events resulting in both megalencephaly and macrocephaly may coexist, a distinction between these two entities is appropriate, as they represent clinical expression of different disorders with a different approach in clinical work-up, overall prognosis, and treatment. Megalencephaly defines an increased growth of cerebral structures related to dysfunctional anomalies during the various steps of brain development in the neuronal proliferation and/or migration phases or as a consequence of postnatal abnormal events. The disorders associated with megalencephaly are classically defined into 3 groups: idiopathic or benign, metabolic, and anatomic. In this article, we seek to underline the clinical aspect of megalencephaly, emphasizing the main disorders that manifest with this anomaly in an attempt to properly categorize these disorders within the megalencephaly group.
Collapse
Affiliation(s)
- Piero Pavone
- University-Hospital “Policlinico-Vittorio Emanuele”
| | - Andrea Domenico Praticò
- Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Renata Rizzo
- Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry
| | - Giovanni Corsello
- Department of Maternal and Child Health, University of Palermo, Palermo
| | - Martino Ruggieri
- Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry
| | - Enrico Parano
- National Research Council, Section of Catania, Catania, Italy
| | | |
Collapse
|
16
|
Hwang J, Kim YL, Kang S, Kim S, Kim SO, Lee JH, Han DH. Genetic analysis of hereditary gingival fibromatosis using whole exome sequencing and bioinformatics. Oral Dis 2016; 23:102-109. [DOI: 10.1111/odi.12583] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/14/2016] [Accepted: 08/30/2016] [Indexed: 12/22/2022]
Affiliation(s)
- J Hwang
- Department of IT Convergence and Engineering; Pohang University of Science and Technology; Pohang Korea
| | - Y-L Kim
- Department of Prosthodontics; College of Dentistry; Yonsei University; Seoul Korea
| | - S Kang
- Department of Prosthodontics; College of Dentistry; Yonsei University; Seoul Korea
| | - S Kim
- Department of Life Sciences; Pohang University of Science and Technology; Pohang Korea
| | - S-O Kim
- Department of Pediatric Dentistry; College of Dentistry; Yonsei University; Seoul Korea
| | - JH Lee
- Department of Prosthodontics; College of Dentistry; Yonsei University; Seoul Korea
| | - D-H Han
- Department of Prosthodontics; College of Dentistry; Yonsei University; Seoul Korea
| |
Collapse
|
17
|
Rosato S, Syx D, Ivanovski I, Pollazzon M, Santodirocco D, De Marco L, Beltrami M, Callewaert B, Garavelli L, Malfait F. RIN2 syndrome: Expanding the clinical phenotype. Am J Med Genet A 2016; 170:2408-15. [PMID: 27277385 DOI: 10.1002/ajmg.a.37789] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/22/2016] [Indexed: 01/12/2023]
Abstract
Biallelic defects in the RIN2 gene, encoding the Ras and Rab interactor 2 protein, are associated with a rare autosomal recessive connective tissue disorder, with only nine patients from four independent families reported to date. The condition was initially termed MACS syndrome (macrocephaly, alopecia, cutis laxa, and scoliosis), based on the clinical features of the first identified family; however, with the expansion of the clinical phenotype in additional families, it was subsequently coined RIN2 syndrome. Hallmark features of this condition include dysmorphic facial features with striking, progressive facial coarsening, sparse hair, normal to enlarged occipitofrontal circumference, soft redundant and/or hyperextensible skin, and scoliosis. Patients with RIN2 syndrome present phenotypic overlap with other conditions, including EDS (especially the dermatosparaxis and kyphoscoliosis subtypes). Here, we describe a 10th patient, the first patient of Caucasian origin and the oldest reported patient so far, who harbors the previously identified homozygous RIN2 mutation c.1878dupC (p. (Ile627Hisfs*7)). Besides the hallmark features, this patient also presents problems not previously associated with RIN2 syndrome, including cervical vertebral fusion, mild hearing loss, and colonic fibrosis. We provide an overview of the clinical findings in all reported patients with RIN2 mutations and summarize some of the possible pathogenic mechanisms that may underlie this condition. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Simonetta Rosato
- Clinical Genetics Unit, Department of Obstetrics and Pediatrics, Arcispedale Santa Maria Nuova-IRCCS, Reggio Emilia, Italy
| | - Delfien Syx
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Ivan Ivanovski
- Clinical Genetics Unit, Department of Obstetrics and Pediatrics, Arcispedale Santa Maria Nuova-IRCCS, Reggio Emilia, Italy.,Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Marzia Pollazzon
- Clinical Genetics Unit, Department of Obstetrics and Pediatrics, Arcispedale Santa Maria Nuova-IRCCS, Reggio Emilia, Italy
| | - Daniela Santodirocco
- Clinical Genetics Unit, Department of Obstetrics and Pediatrics, Arcispedale Santa Maria Nuova-IRCCS, Reggio Emilia, Italy
| | - Loredana De Marco
- Anatomic Pathology Unit, Arcispedale Santa Maria Nuova-IRCCS, Reggio Emilia, Italy
| | - Marina Beltrami
- Department of Internal Medicine, Arcispedale Santa Maria Nuova-IRCCS, Reggio Emilia, Italy
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Livia Garavelli
- Clinical Genetics Unit, Department of Obstetrics and Pediatrics, Arcispedale Santa Maria Nuova-IRCCS, Reggio Emilia, Italy
| | - Fransiska Malfait
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| |
Collapse
|
18
|
Vanakker O, Callewaert B, Malfait F, Coucke P. The Genetics of Soft Connective Tissue Disorders. Annu Rev Genomics Hum Genet 2015; 16:229-55. [DOI: 10.1146/annurev-genom-090314-050039] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Olivier Vanakker
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium;
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium;
| | - Fransiska Malfait
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium;
| | - Paul Coucke
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium;
| |
Collapse
|
19
|
Abstract
Increased amyloid beta (Aβ) production by sequential cleavage of the amyloid precursor protein (APP) by the β- and γ-secretases contributes to the etiological basis of Alzheimer's disease (AD). This process requires APP and the secretases to be in the same subcellular compartments, such as the endosomes. Since all membrane organelles in the endomembrane system are kinetically and functionally linked, any defects in the trafficking and sorting machinery would be expected to change the functional properties of the whole system. The Golgi is a primary organelle for protein trafficking, sorting and modifications, and Golgi defects have been reported in AD. Here we hypothesize that Golgi fragmentation in AD accelerates APP trafficking and Aβ production. Furthermore, Golgi defects may perturb the proper trafficking and processing of many essential neuronal proteins, resulting in compromised neuronal function. Therefore, molecular tools that can restore Golgi structure and function could prove useful as potential drugs for AD treatment.
Collapse
Affiliation(s)
- Gunjan Joshi
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | |
Collapse
|
20
|
Gardeitchik T, Mohamed M, Fischer B, Lammens M, Lefeber D, Lace B, Parker M, Kim KJ, Lim BC, Häberle J, Garavelli L, Jagadeesh S, Kariminejad A, Guerra D, Leão M, Keski-Filppula R, Brunner H, Nijtmans L, van den Heuvel B, Wevers R, Kornak U, Morava E. Clinical and biochemical features guiding the diagnostics in neurometabolic cutis laxa. Eur J Hum Genet 2014; 22:888-95. [PMID: 23963297 PMCID: PMC4060105 DOI: 10.1038/ejhg.2013.154] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 06/11/2013] [Accepted: 06/12/2013] [Indexed: 01/01/2023] Open
Abstract
Patients with cutis laxa (CL) have wrinkled, sagging skin with decreased elasticity. Skin symptoms are associated with variable systemic involvement. The most common, genetically highly heterogeneous form of autosomal recessive CL, ARCL2, is frequently associated with variable metabolic and neurological symptoms. Progeroid symptoms, dysmorphic features, hypotonia and psychomotor retardation are highly overlapping in the early phase of these disorders. This makes the genetic diagnosis often challenging. In search for discriminatory symptoms, we prospectively evaluated clinical, neurologic, metabolic and genetic features in our patient cohort referred for suspected ARCL. From a cohort of 26 children, we confirmed mutations in genes associated with ARCL in 16 children (14 probands), including 12 novel mutations. Abnormal glycosylation and gyration abnormalities were mostly, but not always associated with ATP6V0A2 mutations. Epilepsy was most common in ATP6V0A2 defects. Corpus callosum dysgenesis was associated with PYCR1 and ALDH18A1 mutations. Dystonic posturing was discriminatory for PYCR1 and ALDH18A1 defects. Metabolic markers of mitochondrial dysfunction were found in one patient with PYCR1 mutations. So far unreported white matter abnormalities were found associated with GORAB and RIN2 mutations. We describe a large cohort of CL patients with neurologic involvement. Migration defects and corpus callosum hypoplasia were not always diagnostic for a specific genetic defect in CL. All patients with ATP6V0A2 defects had abnormal glycosylation. To conclude, central nervous system and metabolic abnormalities were discriminatory in this genetically heterogeneous group, although not always diagnostic for a certain genetic defect in CL.
Collapse
Affiliation(s)
- Thatjana Gardeitchik
- Department of Pediatrics, Institute for Metabolic and Genetic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Miski Mohamed
- Department of Pediatrics, Institute for Metabolic and Genetic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Björn Fischer
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin, Berlin, Germany
| | - Martin Lammens
- Department of Pathology, Institute for Metabolic and Genetic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Dirk Lefeber
- Department of Neurology, Institute for Metabolic and Genetic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Baiba Lace
- Medical Genetics Clinic, Children's Clinical University Hospital, Riga, Latvia
| | - Michael Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Sheffield, UK
| | - Ki-Joong Kim
- Department of Pediatrics, Seoul National University Hospital, Seoul, South Korea
| | - Bing C Lim
- Department of Pediatrics, Seoul National University Hospital, Seoul, South Korea
| | - Johannes Häberle
- Department of Pediatrics, University Children's Hospital, Zürich, Switzerland
| | - Livia Garavelli
- Clinical Genetics Unit, Obstetric and Pediatric Department, Santa Maria Nuova Hospital IRCCS, Reggio Emilia, Italy
| | | | | | - Deanna Guerra
- Department of Biomedical Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Michel Leão
- Pediatric Neurology Unit and Neurogenetics Unit, Hospital S João, Porto, Portugal
| | | | - Han Brunner
- Department of Human Genetics, Institute for Metabolic and Genetic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Leo Nijtmans
- Department of Pediatrics, Institute for Metabolic and Genetic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Bert van den Heuvel
- Department of Pediatrics, Institute for Metabolic and Genetic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands
- Laboratory for Genetic Endocrine and Metabolic Diseases, Institute for Metabolic and Genetic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Ron Wevers
- Department of Pediatrics, Institute for Metabolic and Genetic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands
- Laboratory for Genetic Endocrine and Metabolic Diseases, Institute for Metabolic and Genetic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Uwe Kornak
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin, Berlin, Germany
- FG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Eva Morava
- Department of Pediatrics, Institute for Metabolic and Genetic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands
- Hayward Genetics Center, Tulane University Medical Center, New Orleans, LA, USA
| |
Collapse
|
21
|
Greally MT, Kalis NN, Agab W, Ardati K, Giurgea S, Kornak U, Van Maldergem L. Autosomal recessive cutis laxa type 2A (ARCL2A) mimicking Ehlers-Danlos syndrome by its dermatological manifestations: Report of three affected patients. Am J Med Genet A 2014; 164A:1245-53. [DOI: 10.1002/ajmg.a.36411] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 11/10/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Marie T. Greally
- National Centre for Medical Genetics; Our Lady's Children's Hospital, Crumlin; Dublin Ireland
- Bahrain Defence Forces Hospital; Department of Paediatric Cardiology; Riffa Kingdom of Bahrain
| | - Neale N. Kalis
- Bahrain Defence Forces Hospital; Department of Paediatric Cardiology; Riffa Kingdom of Bahrain
| | - Wahid Agab
- Bahrain Defence Forces Hospital; Department of Paediatric Cardiology; Riffa Kingdom of Bahrain
| | - Kasim Ardati
- Bahrain Specialist Hospital; Juffair Kingdom of Bahrain
| | - Sanda Giurgea
- Department of Neurology; CHU Tivoli; La Louvière Belgium
| | - Uwe Kornak
- Institute of Medical and Human Genetics; Charité-Universitaetsmedizin Berlin; Berlin Germany
| | | |
Collapse
|
22
|
Van Asbeck E, Wolthuis DF, Mohamed M, Wevers RA, Korenke CG, Gardeitchik T, Morava E. A novel phenotype associated with cutis laxa, abnormal fat distribution, cardiomyopathy and cataract. Am J Med Genet A 2014; 164A:1049-55. [DOI: 10.1002/ajmg.a.36392] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 11/07/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Ellyze Van Asbeck
- Department of Pediatrics; Radboud University Nijmegen Medical Center; Nijmegen Gelderland Netherlands
- Hayward Genetics Center and Department of Pediatrics; Tulane University Medical School; New Orleans Louisiana
| | - David F.G.J. Wolthuis
- Department of Pediatrics; Radboud University Nijmegen Medical Center; Nijmegen Gelderland Netherlands
- Hayward Genetics Center and Department of Pediatrics; Tulane University Medical School; New Orleans Louisiana
| | - Miski Mohamed
- Department of Pediatrics; Radboud University Nijmegen Medical Center; Nijmegen Gelderland Netherlands
| | - Ron A. Wevers
- Laboratory of Genetic, Endocrine and Metabolic Disease; Radboud University Nijmegen Medical Center; Nijmegen Gelderland Netherlands
| | | | - Thatjana Gardeitchik
- Department of Pediatrics; Radboud University Nijmegen Medical Center; Nijmegen Gelderland Netherlands
| | - Eva Morava
- Department of Pediatrics; Radboud University Nijmegen Medical Center; Nijmegen Gelderland Netherlands
- Hayward Genetics Center and Department of Pediatrics; Tulane University Medical School; New Orleans Louisiana
| |
Collapse
|
23
|
|
24
|
Aslanger AD, Altunoglu U, Aslanger E, Satkın BN, Uyguner ZO, Kayserili H. Newly described clinical features in two siblings with MACS syndrome and a novel mutation in RIN2. Am J Med Genet A 2013; 164A:484-9. [DOI: 10.1002/ajmg.a.36277] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 09/09/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Ayca D. Aslanger
- Medical Genetics Unit; Kocaeli Derince Research and Education Hospital; Kocaeli Turkey
| | - Umut Altunoglu
- Medical Genetics Department; Istanbul Medical Faculty; Istanbul University; Istanbul Turkey
| | - Emre Aslanger
- Cardiology Unit; Kocaeli Gölcük State Hospital; Kocaeli Turkey
| | - Bilge N. Satkın
- Medical Genetics Department; Istanbul Medical Faculty; Istanbul University; Istanbul Turkey
| | - Zehra Oya Uyguner
- Medical Genetics Department; Istanbul Medical Faculty; Istanbul University; Istanbul Turkey
| | - Hülya Kayserili
- Medical Genetics Department; Istanbul Medical Faculty; Istanbul University; Istanbul Turkey
| |
Collapse
|
25
|
Bexiga MG, Simpson JC. Human diseases associated with form and function of the Golgi complex. Int J Mol Sci 2013; 14:18670-81. [PMID: 24025425 PMCID: PMC3794802 DOI: 10.3390/ijms140918670] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 08/09/2013] [Accepted: 09/03/2013] [Indexed: 11/16/2022] Open
Abstract
The Golgi complex lies at the heart of the secretory pathway and is responsible for modifying proteins and lipids, as well as sorting newly synthesized molecules to their correct destination. As a consequence of these important roles, any changes in its proteome can negatively affect its function and in turn lead to disease. Recently, a number of proteins have been identified, which when either depleted or mutated, result in diseases that affect various organ systems. Here we describe how these proteins have been linked to the Golgi complex, and specifically how they affect either the morphology, membrane traffic or glycosylation ability of this organelle.
Collapse
Affiliation(s)
| | - Jeremy C. Simpson
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +353-1-716-2345; Fax: +353-1-716-1153
| |
Collapse
|
26
|
Urban Z, Davis EC. Cutis laxa: intersection of elastic fiber biogenesis, TGFβ signaling, the secretory pathway and metabolism. Matrix Biol 2013; 33:16-22. [PMID: 23954411 DOI: 10.1016/j.matbio.2013.07.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 07/08/2013] [Accepted: 07/09/2013] [Indexed: 12/11/2022]
Abstract
Cutis laxa (CL), a disease characterized by redundant and inelastic skin, displays extensive locus heterogeneity. Together with geroderma osteodysplasticum and arterial tortuosity syndrome, which show phenotypic overlap with CL, eleven CL-related genes have been identified to date, which encode proteins within 3 groups. Elastin, fibulin-4, fibulin-5 and latent transforming growth factor-β-binding protein 4 are secreted proteins which form elastic fibers and are involved in the sequestration and subsequent activation of transforming growth factor-β (TGFβ). Proteins within the second group, localized to the secretory pathway, perform transport and membrane trafficking functions necessary for the modification and secretion of elastic fiber components. Key proteins include a subunit of the vacuolar-type proton pump, which ensures the efficient secretion of tropoelastin, the precursor or elastin. A copper transporter is required for the activity of lysyl oxidases, which crosslink collagen and elastin. A Rab6-interacting goglin recruits kinesin motors to Golgi-vesicles facilitating the transport from the Golgi to the plasma membrane. The Rab and Ras interactor 2 regulates the activity of Rab5, a small guanosine triphosphatase essential for the endocytosis of various cell surface receptors, including integrins. Proteins of the third group related to CL perform metabolic functions within the mitochondria, inhibiting the accumulation of reactive oxygen species. Two of these proteins catalyze subsequent steps in the conversion of glutamate to proline. The third transports dehydroascorbate into mitochondria. Recent studies on CL-related proteins highlight the intricate connections among membrane trafficking, metabolism, extracellular matrix assembly, and TGFβ signaling.
Collapse
Affiliation(s)
- Zsolt Urban
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, United States.
| | - Elaine C Davis
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7 Canada
| |
Collapse
|
27
|
Abstract
Intracellular membrane trafficking requires the complex interplay of several classes of trafficking proteins. Rab proteins, the largest subfamily of the Ras superfamily of small G-proteins, are central regulators of all aspects of intracellular trafficking processes including vesicle budding and uncoating, motility, tethering and fusion. In the present paper, we discuss the discovery, evolution and characterization of the Rab GTPase family. We examine their basic functional roles, their important structural features and the regulatory proteins which mediate Rab function. We speculate on outstanding issues in the field, such as the mechanisms of Rab membrane association and the co-ordinated interplay between distinct Rab proteins. Finally, we summarize the data implicating Rab proteins in an ever increasing number of diseases.
Collapse
|
28
|
The Complexity of Elastic Fiber Biogenesis: The Paradigm of Cutis Laxa. J Invest Dermatol 2012; 132 Suppl 3:E12-4. [DOI: 10.1038/skinbio.2012.4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
29
|
Uitto J, Li Q, Urban Z. The complexity of elastic fibre biogenesis in the skin--a perspective to the clinical heterogeneity of cutis laxa. Exp Dermatol 2012; 22:88-92. [PMID: 23088642 DOI: 10.1111/exd.12025] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2012] [Indexed: 11/28/2022]
Abstract
Elastic fibres are critical connective tissue components providing elasticity and resilience to skin and other tissues. These fibres are composed of elastin and a number of elastin-associated microfibrillar proteins that assemble in a complex fibre network in a multi-step process. Multiple cellular processes, including mitochondrial function, specific molecules in the secretory pathways and temporally and spatially ordered production of elastic fibre components, are required for the biogenesis of functional elastic fibres. Abnormalities in these processes can lead to loss of functional elastic fibres manifesting phenotypically as a skin disease. The paradigm of elastic fibre diseases affecting the skin is cutis laxa, a clinically and genetically heterogeneous group of disorders characterized by loose and sagging skin, frequently associated with extracutaneous manifestations in the lungs and the arterial blood vessels. The complexity of cutis laxa is emphasized by the fact that as many as 10 distinct genes can harbour mutations in this and related disorders. Understanding of the pathomechanistic pathways involved in perturbed elastic fibre assembly in cutis laxa provides information potentially helpful for the development of molecular strategies towards treatment of these, currently intractable, diseases.
Collapse
Affiliation(s)
- Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Jefferson Medical College, Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | | | | |
Collapse
|
30
|
Abstract
Endothelial cell adhesion to the extracellular matrix regulates migration and outgrowth of blood vessels during angiogenesis. Cell adhesion is mediated by integrins, which transduce signals from the extracellular environment into the cell and, in turn, are regulated by intracellular signaling molecules. In a paper recently published in Cell Research, Sandri et al. show that RIN2 connects three GTPases, R-Ras, Rab5 and Rac1, to promote endothelial cell adhesion through the regulation of integrin internalization and Rac1 activation.
Collapse
|
31
|
Sarig O, Nahum S, Rapaport D, Ishida-Yamamoto A, Fuchs-Telem D, Qiaoli L, Cohen-Katsenelson K, Spiegel R, Nousbeck J, Israeli S, Borochowitz ZU, Padalon-Brauch G, Uitto J, Horowitz M, Shalev S, Sprecher E. Short stature, onychodysplasia, facial dysmorphism, and hypotrichosis syndrome is caused by a POC1A mutation. Am J Hum Genet 2012; 91:337-42. [PMID: 22840363 DOI: 10.1016/j.ajhg.2012.06.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 05/24/2012] [Accepted: 06/05/2012] [Indexed: 11/26/2022] Open
Abstract
Disproportionate short stature refers to a heterogeneous group of hereditary disorders that are classified according to their mode of inheritance, clinical skeletal and nonskeletal manifestations, and radiological characteristics. In the present study, we report on an autosomal-recessive osteocutaneous disorder that we termed SOFT (short stature, onychodysplasia, facial dysmorphism, and hypotrichosis) syndrome. We employed homozygosity mapping to locate the disease-causing mutation to region 3p21.1-3p21.31. Using whole-exome-sequencing analysis complemented with Sanger direct sequencing of poorly covered regions, we identified a homozygous point mutation (c.512T>C [p.Leu171Pro]) in POC1A (centriolar protein homolog A). This mutation was found to cosegregate with the disease phenotype in two families. The p.Leu171Pro substitution affects a highly conserved amino acid residue and is predicted to interfere with protein function. Poc1, a POC1A ortholog, was previously found to have a role in centrosome stability in unicellular organisms. Accordingly, although centrosome structure was preserved, the number of centrosomes and their distribution were abnormal in affected cells. In addition, the Golgi apparatus presented a dispersed morphology, cholera-toxin trafficking from the plasma membrane to the Golgi was aberrant, and large vesicles accumulated in the cytosol. Collectively, our data underscore the importance of POC1A for proper bone, hair, and nail formation and highlight the importance of normal centrosomes in Golgi assembly and trafficking from the plasma membrane to the Golgi apparatus.
Collapse
|
32
|
Mohamed M, Kouwenberg D, Gardeitchik T, Kornak U, Wevers RA, Morava E. Metabolic cutis laxa syndromes. J Inherit Metab Dis 2011; 34:907-16. [PMID: 21431621 PMCID: PMC3137780 DOI: 10.1007/s10545-011-9305-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 02/11/2011] [Accepted: 02/17/2011] [Indexed: 01/09/2023]
Abstract
Cutis laxa is a rare skin disorder characterized by wrinkled, redundant, inelastic and sagging skin due to defective synthesis of elastic fibers and other proteins of the extracellular matrix. Wrinkled, inelastic skin occurs in many cases as an acquired condition. Syndromic forms of cutis laxa, however, are caused by diverse genetic defects, mostly coding for structural extracellular matrix proteins. Surprisingly a number of metabolic disorders have been also found to be associated with inherited cutis laxa. Menkes disease was the first metabolic disease reported with old-looking, wrinkled skin. Cutis laxa has recently been found in patients with abnormal glycosylation. The discovery of the COG7 defect in patients with wrinkled, inelastic skin was the first genetic link with the Congenital Disorders of Glycosylation (CDG). Since then several inborn errors of metabolism with cutis laxa have been described with variable severity. These include P5CS, ATP6V0A2-CDG and PYCR1 defects. In spite of the evolving number of cutis laxa-related diseases a large part of the cases remain genetically unsolved. In metabolic cutis laxa syndromes the clinical and laboratory features might partially overlap, however there are some distinct, discriminative features. In this review on metabolic diseases causing cutis laxa we offer a practical approach for the differential diagnosis of metabolic cutis laxa syndromes.
Collapse
Affiliation(s)
- Miski Mohamed
- Institute for Genetic and Metabolic Disease, Radboud University Medical Centre Nijmegen, P.O Box 9101, 6500 HB Nijmegen, The Netherlands
- Department of Pediatrics, Radboud University Medical Centre Nijmegen, P.O Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Dorus Kouwenberg
- Institute for Genetic and Metabolic Disease, Radboud University Medical Centre Nijmegen, P.O Box 9101, 6500 HB Nijmegen, The Netherlands
- Department of Pediatrics, Radboud University Medical Centre Nijmegen, P.O Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Thatjana Gardeitchik
- Institute for Genetic and Metabolic Disease, Radboud University Medical Centre Nijmegen, P.O Box 9101, 6500 HB Nijmegen, The Netherlands
- Department of Pediatrics, Radboud University Medical Centre Nijmegen, P.O Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Uwe Kornak
- Max Planck Institute for Molecular genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ron A. Wevers
- Laboratory of Genetic, Endocrine and Metabolic Diseases, Radboud University Medical Centre Nijmegen, Nijmegen, The Netherlands
| | - Eva Morava
- Institute for Genetic and Metabolic Disease, Radboud University Medical Centre Nijmegen, P.O Box 9101, 6500 HB Nijmegen, The Netherlands
- Department of Pediatrics, Radboud University Medical Centre Nijmegen, P.O Box 9101, 6500 HB Nijmegen, The Netherlands
| |
Collapse
|
33
|
Agola JO, Jim PA, Ward HH, Basuray S, Wandinger-Ness A. Rab GTPases as regulators of endocytosis, targets of disease and therapeutic opportunities. Clin Genet 2011; 80:305-18. [PMID: 21651512 PMCID: PMC3187864 DOI: 10.1111/j.1399-0004.2011.01724.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Rab GTPases are well-recognized targets in human disease, although are underexplored therapeutically. Elucidation of how mutant or dysregulated Rab GTPases and accessory proteins contribute to organ specific and systemic disease remains an area of intensive study and an essential foundation for effective drug targeting. Mutation of Rab GTPases or associated regulatory proteins causes numerous human genetic diseases. Cancer, neurodegeneration and diabetes represent examples of acquired human diseases resulting from the up- or downregulation or aberrant function of Rab GTPases. The broad range of physiologic processes and organ systems affected by altered Rab GTPase activity is based on pivotal roles in responding to cell signaling and metabolic demand through the coordinated regulation of membrane trafficking. The Rab-regulated processes of cargo sorting, cytoskeletal translocation of vesicles and appropriate fusion with the target membranes control cell metabolism, viability, growth and differentiation. In this review, we focus on Rab GTPase roles in endocytosis to illustrate normal function and the consequences of dysregulation resulting in human disease. Selected examples are designed to illustrate how defects in Rab GTPase cascades alter endocytic trafficking that underlie neurologic, lipid storage, and metabolic bone disorders as well as cancer. Perspectives on potential therapeutic modulation of GTPase activity through small molecule interventions are provided.
Collapse
Affiliation(s)
- J O Agola
- Department of Pathology Cancer Center, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
| | | | | | | | | |
Collapse
|
34
|
Rohrbach M, Vandersteen A, Yiş U, Serdaroglu G, Ataman E, Chopra M, Garcia S, Jones K, Kariminejad A, Kraenzlin M, Marcelis C, Baumgartner M, Giunta C. Phenotypic variability of the kyphoscoliotic type of Ehlers-Danlos syndrome (EDS VIA): clinical, molecular and biochemical delineation. Orphanet J Rare Dis 2011; 6:46. [PMID: 21699693 PMCID: PMC3135503 DOI: 10.1186/1750-1172-6-46] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 06/23/2011] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The kyphoscoliotic type of Ehlers-Danlos syndrome (EDS VIA) (OMIM 225400) is a rare inheritable connective tissue disorder characterized by a deficiency of collagen lysyl hydroxylase 1 (LH1; EC 1.14.11.4) due to mutations in PLOD1. Biochemically this results in underhydroxylation of collagen lysyl residues and, hence, an abnormal pattern of lysyl pyridinoline (LP) and hydroxylysyl pyridinoline (HP) crosslinks excreted in the urine. Clinically the disorder is characterized by hypotonia and kyphoscoliosis at birth, joint hypermobility, and skin hyperelasticity and fragility. Severe hypotonia usually leads to delay in gross motor development, whereas cognitive development is reported to be normal. METHODS We describe the clinical, biochemical and molecular characterisation, as well as electron microscopy findings of skin, in 15 patients newly diagnosed with this rare type of Ehlers-Danlos syndrome. RESULTS Age at diagnosis ranged from 5 months to 27 years, with only 1/3 of the patients been diagnosed correctly in the first year of life. A similar disease frequency was found in females and males, however a broad disease severity spectrum (intra- and interfamilial), independent of molecular background or biochemical phenotype, was observed. Kyphoscoliosis, one of the main clinical features was not present at birth in 4 patients. Importantly we also noted the occurrence of vascular rupture antenatally and postnatally, as well as developmental delay in 5 patients. CONCLUSION In view of these findings we propose that EDS VIA is a highly variable clinical entity, presenting with a broad clinical spectrum, which may also be associated with cognitive delay and an increased risk for vascular events. Genotype/phenotype association studies and additional molecular investigations in more extended EDS VIA populations will be necessary to further elucidate the cause of the variability of the disease severity.
Collapse
Affiliation(s)
- Marianne Rohrbach
- Division of Metabolism, University Children's Hospital and Children's Research Centre, Zurich, Switzerland.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Albrecht B, de Brouwer AP, Lefeber DJ, Cremer K, Hausser I, Rossen N, Wortmann SB, Wevers RA, Kornak U, Morava E. MACS syndrome: A combined collagen and elastin disorder due to abnormal Golgi trafficking. Am J Med Genet A 2011; 152A:2916-8. [PMID: 20954239 DOI: 10.1002/ajmg.a.33712] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Beate Albrecht
- Department of Human Genetics, University of Essen, Essen, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Abstract
Classic Ehlers-Danlos syndrome is a heritable connective tissue disorder characterized by skin hyperextensibility, fragile and soft skin, delayed wound healing with formation of atrophic scars, easy bruising, and generalized joint hypermobility. It comprises Ehlers-Danlos syndrome type I and Ehlers-Danlos syndrome type II, but it is now apparent that these form a continuum of clinical findings and differ only in phenotypic severity. It is currently estimated that approximately 50% of patients with a clinical diagnosis of classic Ehlers-Danlos syndrome harbor mutations in the COL5A1 and the COL5A2 gene, encoding the α1 and the α2-chain of type V collagen, respectively. However, because no prospective molecular studies of COL5A1 and COL5A2 have been performed in a clinically well-defined patient group, this number may underestimate the real proportion of patients with classic Ehlers-Danlos syndrome harboring a mutation in one of these genes. In the majority of patients with molecularly characterized classic Ehlers-Danlos syndrome, the disease is caused by a mutation leading to a nonfunctional COL5A1 allele and resulting in haploinsufficiency of type V collagen. A smaller proportion of patients harbor a structural mutation in COL5A1 or COL5A2, causing the production of a functionally defective type V collagen protein. Most mutations identified so far result in a reduced amount of type V collagen in the connective tissues available for collagen fibrillogenesis. Inter- and intrafamilial phenotypic variability is observed, but no genotype-phenotype correlations have been observed. No treatment for the underlying defect is presently available for Ehlers-Danlos syndrome. However, a series of preventive guidelines are applicable.
Collapse
|