1
|
Lv S, Wang Q, Zhang X, Ning F, Liu W, Cui M, Xu Y. Mechanisms of multi-omics and network pharmacology to explain traditional chinese medicine for vascular cognitive impairment: A narrative review. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 123:155231. [PMID: 38007992 DOI: 10.1016/j.phymed.2023.155231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/07/2023] [Accepted: 11/18/2023] [Indexed: 11/28/2023]
Abstract
BACKGROUND The term "vascular cognitive impairment" (VCI) describes various cognitive conditions that include vascular elements. It increases the risk of morbidity and mortality in the elderly population and is the most common cognitive impairment associated with cerebrovascular disease. Understanding the etiology of VCI may aid in identifying approaches to target its possible therapy for the condition. Treatment of VCI has focused on vascular risk factors. There are no authorized conventional therapies available right now. The medications used to treat VCI are solely approved for symptomatic relief and are not intended to prevent or slow the development of VCI. PURPOSE The function of Chinese medicine in treating VCI has not yet been thoroughly examined. This review evaluates the preclinical and limited clinical evidence to comprehend the "multi-component, multi-target, multi-pathway" mechanism of Traditional Chinese medicine (TCM). It investigates the various multi-omics approaches in the search for the pathological mechanisms of VCI, as well as the new research strategies, in the hopes of supplying supportive evidence for the clinical treatment of VCI. METHODS This review used the Preferred Reporting Items for Preferred reporting items for systematic reviews and meta-analyses (PRISMA) statements. Using integrated bioinformatics and network pharmacology approaches, a thorough evaluation and analysis of 25 preclinical studies published up to July 1, 2023, were conducted to shed light on the mechanisms of TCM for vascular cognitive impairment. The studies for the systematic review were located using the following databases: PubMed, Web of Science, Scopus, Cochrane, and ScienceDirect. RESULTS We discovered that the multi-omics analysis approach would hasten the discovery of the role of TCM in the treatment of VCI. It will explore components, compounds, targets, and pathways, slowing the progression of VCI from the perspective of inhibiting oxidative stress, stifling neuroinflammation, increasing cerebral blood flow, and inhibiting iron deposition by a variety of molecular mechanisms, which have significant implications for the treatment of VCI. CONCLUSION TCM is a valuable tool for developing dementia therapies, and further research is needed to determine how TCM components may affect the operation of the neurovascular unit. There are still some limitations, although several research have offered invaluable resources for searching for possible anti-dementia medicines and treatments. To gain new insights into the molecular mechanisms that precisely modulate the key molecules at different levels during pharmacological interventions-a prerequisite for comprehending the mechanism of action and determining the potential therapeutic value of the drugs-further research should employ more standardized experimental methods as well as more sophisticated science and technology. Given the results of this review, we advocate integrating chemical and biological component analysis approaches in future research on VCI to provide a more full and objective assessment of the standard of TCM. With the help of bioinformatics, a multi-omics analysis approach will hasten the discovery of the role of TCM in the treatment of VCI, which has significant implications for the treatment of VCI.
Collapse
Affiliation(s)
- Shi Lv
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian 271000, China
| | - Qian Wang
- Department of Central Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian 271000, China
| | - Xinlei Zhang
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian 271000, China
| | - Fangli Ning
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian 271000, China
| | - Wenxin Liu
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian 271000, China
| | - Mengmeng Cui
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian 271000, China
| | - Yuzhen Xu
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian 271000, China.
| |
Collapse
|
2
|
Kim HR, Jeon JW, Lee EJ, Ham YR, Na KR, Lee KW, Park KH, Kim SY, Choi DE. Confirming Genetic Abnormalities of Hypokalemic Periodic Paralysis Using Next-Generation Sequencing: A Case Report and Literature Review. Electrolyte Blood Press 2021; 19:10-14. [PMID: 34290819 PMCID: PMC8267070 DOI: 10.5049/ebp.2021.19.1.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 11/05/2022] Open
Abstract
Hypokalemic periodic paralysis (hypoPP) is a disorder characterized by episodic, short-lived, and hypo-reflexive skeletal muscle weakness. HypoPP is a rare disease caused by genetic mutations related to expression of sodium or calcium ion channels. Most mutations are associated with autosomal dominant inheritance, but some are found in patients with no relevant family history. A 28-year-old man who visited the emergency room for paralytic attack was assessed in this study. He exhibited motor weakness in four limbs. There was no previous medical history or family history. The initial electrocardiogram showed a flat T wave and QT prolongation. His blood test was delayed, and sudden hypotension and bradycardia were observed. The blood test showed severe hypokalemia. After correcting hypokalemia, his muscle paralysis recovered without any neurological deficits. The patient's thyroid function and long exercise test results were normal. However, because of the history of high carbohydrate diet and exercise, hypoPP was suspected. Hence, next-generation sequencing (NGS) was performed, and a mutation of Arg669His was noted in the SCN4A gene. Although hypoPP is a rare disease, it can be suspected in patients with hypokalemic paralysis, and iden tification of this condition is important for preventing further attacks and improving patient outcomes. Diagnosing hypoPP through targeted NGS is a cost-effective and useful method.
Collapse
Affiliation(s)
- Hae Ri Kim
- Department of Internal Medicine, Division of Nephrology, Chungnam National University Sejong Hospital, Sejong, Republic of Korea
| | - Jae Wan Jeon
- Department of Internal Medicine, Division of Nephrology, Chungnam National University Sejong Hospital, Sejong, Republic of Korea
| | - Eu Jin Lee
- Department of Internal Medicine, Division of Nephrology, Chungnam National University Hospital, Daejeon, Republic of Korea
| | - Young Rok Ham
- Department of Internal Medicine, Division of Nephrology, Chungnam National University Hospital, Daejeon, Republic of Korea
| | - Ki Ryang Na
- Department of Internal Medicine, Division of Nephrology, Chungnam National University Hospital, Daejeon, Republic of Korea
| | - Kang Wook Lee
- Department of Internal Medicine, Division of Nephrology, Chungnam National University Hospital, Daejeon, Republic of Korea
| | - Kee Hong Park
- Department of Neurology, Seoul Medical Center, Seoul, Republic of Korea
| | - Seon Young Kim
- Department of Laboratory Medicine, Chungnam National University Hospital, Daejeon, Republic of Korea
| | - Dae Eun Choi
- Department of Internal Medicine, Division of Nephrology, Chungnam National University Hospital, Daejeon, Republic of Korea
| |
Collapse
|
3
|
Vrablik M, Tichý L, Freiberger T, Blaha V, Satny M, Hubacek JA. Genetics of Familial Hypercholesterolemia: New Insights. Front Genet 2020; 11:574474. [PMID: 33133164 PMCID: PMC7575810 DOI: 10.3389/fgene.2020.574474] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
Familial hypercholesterolemia (FH) is one of the most common monogenic diseases, leading to an increased risk of premature atherosclerosis and its cardiovascular complications due to its effect on plasma cholesterol levels. Variants of three genes (LDL-R, APOB and PCSK9) are the major causes of FH, but in some probands, the FH phenotype is associated with variants of other genes. Alternatively, the typical clinical picture of FH can result from the accumulation of common cholesterol-increasing alleles (polygenic FH). Although the Czech Republic is one of the most successful countries with respect to FH detection, approximately 80% of FH patients remain undiagnosed. The opportunities for international collaboration and experience sharing within international programs (e.g., EAS FHSC, ScreenPro FH, etc.) will improve the detection of FH patients in the future and enable even more accessible and accurate genetic diagnostics.
Collapse
Affiliation(s)
- Michal Vrablik
- 3rd Department of Internal Medicine, 1st Faculty of Medicine, Charles University, Prague, Czechia
| | - Lukas Tichý
- Centre of Molecular Biology and Gene Therapy, University Hospital, Brno, Czechia
| | - Tomas Freiberger
- Centre for Cardiovascular Surgery and Transplantation, Brno, and Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Vladimir Blaha
- Internal Gerontometabolic Department, Charles University and University Hospital Hradec Kralove, Hradec Kralove, Czechia
| | - Martin Satny
- 3rd Department of Internal Medicine, 1st Faculty of Medicine, Charles University, Prague, Czechia
| | - Jaroslav A Hubacek
- 3rd Department of Internal Medicine, 1st Faculty of Medicine, Charles University, Prague, Czechia.,Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia
| |
Collapse
|
4
|
A Customized Next-Generation Sequencing-Based Panel to Identify Novel Genetic Variants in Dementing Disorders: A Pilot Study. Neural Plast 2020. [PMID: 32908482 DOI: 10.1155/2020/8078103.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Purpose The advancements in the next-generation sequencing (NGS) techniques have allowed for rapid, efficient, and cost-time-effective genetic variant detection. However, in both clinical practice and research setting, sequencing is still often limited to the use of gene panels clinically targeted on the genes underlying the disease of interest. Methods We performed a neurogenetic study through an ad hoc NGS-based custom sequencing gene panel in order to screen 16 genes in 8 patients with different types of degenerative cognitive disorders (Alzheimer's disease, mild cognitive impairment, frontotemporal dementia, and dementia associated with Parkinson's disease). The study protocol was based on previous evidence showing a high sensitivity and specificity of the technique even when the panel is limited to some hotspot exons. Results We found variants of the TREM2 and APP genes in three patients; these have been previously identified as pathogenic or likely pathogenic and, therefore, considered "disease causing." In the remaining subjects, the pathogenicity was evaluated according to the guidelines of the American College of Medical Genetics (ACMG). In one patient, the p.R205W variant in the CHMP2B gene was found to be likely pathogenic of the disease. A variant in the CSF1R and SERPINI1 genes found in two patients was classified as benign, whereas the other two (in the GRN and APP genes) were classified as likely pathogenic according to the ACMG. Conclusions Notwithstanding the preliminary value of this study, some rare genetic variants with a probable disease association were detected. Although future application of NGS-based sensors and further replication of these experimental data are needed, this approach seems to offer promising translational perspectives in the diagnosis and management of a wide range of neurodegenerative disorders.
Collapse
|
5
|
Dron JS, Wang J, McIntyre AD, Iacocca MA, Robinson JF, Ban MR, Cao H, Hegele RA. Six years' experience with LipidSeq: clinical and research learnings from a hybrid, targeted sequencing panel for dyslipidemias. BMC Med Genomics 2020; 13:23. [PMID: 32041611 PMCID: PMC7011550 DOI: 10.1186/s12920-020-0669-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 01/23/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In 2013, our laboratory designed a targeted sequencing panel, "LipidSeq", to study the genetic determinants of dyslipidemia and metabolic disorders. Over the last 6 years, we have analyzed 3262 patient samples obtained from our own Lipid Genetics Clinic and international colleagues. Here, we highlight our findings and discuss research benefits and clinical implications of our panel. METHODS LipidSeq targets 69 genes and 185 single-nucleotide polymorphisms (SNPs) either causally related or associated with dyslipidemia and metabolic disorders. This design allows us to simultaneously evaluate monogenic-caused by rare single-nucleotide variants (SNVs) or copy-number variants (CNVs)-and polygenic forms of dyslipidemia. Polygenic determinants were assessed using three polygenic scores, one each for low-density lipoprotein cholesterol, triglyceride, and high-density lipoprotein cholesterol. RESULTS Among 3262 patient samples evaluated, the majority had hypertriglyceridemia (40.1%) and familial hypercholesterolemia (28.3%). Across all samples, we identified 24,931 unique SNVs, including 2205 rare variants predicted disruptive to protein function, and 77 unique CNVs. Considering our own 1466 clinic patients, LipidSeq results have helped in diagnosis and improving treatment options. CONCLUSIONS Our LipidSeq design based on ontology of lipid disorders has enabled robust detection of variants underlying monogenic and polygenic dyslipidemias. In more than 50 publications related to LipidSeq, we have described novel variants, the polygenic nature of many dyslipidemias-some previously thought to be primarily monogenic-and have uncovered novel mechanisms of disease. We further demonstrate several tangible clinical benefits of its use.
Collapse
Affiliation(s)
- Jacqueline S. Dron
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London, ON N6A 5B7 Canada
| | - Jian Wang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
| | - Adam D. McIntyre
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
| | - Michael A. Iacocca
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London, ON N6A 5B7 Canada
- Department of Biomedical Data Science, Stanford School of Medicine, Stanford University, 450 Serra Mall, Stanford, CA 94305 USA
| | - John F. Robinson
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
| | - Matthew R. Ban
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
| | - Henian Cao
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
| | - Robert A. Hegele
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London, ON N6A 5B7 Canada
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond St, London, ON N6A 5B7 Canada
| |
Collapse
|
6
|
Lanza G, Calì F, Vinci M, Cosentino FII, Tripodi M, Spada RS, Cantone M, Bella R, Mattina T, Ferri R. A Customized Next-Generation Sequencing-Based Panel to Identify Novel Genetic Variants in Dementing Disorders: A Pilot Study. Neural Plast 2020; 2020:8078103. [PMID: 32908482 PMCID: PMC7450320 DOI: 10.1155/2020/8078103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 06/13/2020] [Accepted: 07/13/2020] [Indexed: 02/07/2023] Open
Abstract
PURPOSE The advancements in the next-generation sequencing (NGS) techniques have allowed for rapid, efficient, and cost-time-effective genetic variant detection. However, in both clinical practice and research setting, sequencing is still often limited to the use of gene panels clinically targeted on the genes underlying the disease of interest. METHODS We performed a neurogenetic study through an ad hoc NGS-based custom sequencing gene panel in order to screen 16 genes in 8 patients with different types of degenerative cognitive disorders (Alzheimer's disease, mild cognitive impairment, frontotemporal dementia, and dementia associated with Parkinson's disease). The study protocol was based on previous evidence showing a high sensitivity and specificity of the technique even when the panel is limited to some hotspot exons. RESULTS We found variants of the TREM2 and APP genes in three patients; these have been previously identified as pathogenic or likely pathogenic and, therefore, considered "disease causing." In the remaining subjects, the pathogenicity was evaluated according to the guidelines of the American College of Medical Genetics (ACMG). In one patient, the p.R205W variant in the CHMP2B gene was found to be likely pathogenic of the disease. A variant in the CSF1R and SERPINI1 genes found in two patients was classified as benign, whereas the other two (in the GRN and APP genes) were classified as likely pathogenic according to the ACMG. CONCLUSIONS Notwithstanding the preliminary value of this study, some rare genetic variants with a probable disease association were detected. Although future application of NGS-based sensors and further replication of these experimental data are needed, this approach seems to offer promising translational perspectives in the diagnosis and management of a wide range of neurodegenerative disorders.
Collapse
Affiliation(s)
- Giuseppe Lanza
- 1Department of Surgery and Medical-Surgical Specialties, University of Catania, Catania, Italy
- 2Oasi Research Institute–IRCCS, Troina, Italy
| | | | | | | | | | | | - Mariagiovanna Cantone
- 3Department of Neurology, Sant'Elia Hospital, ASP Caltanissetta, Caltanissetta, Italy
| | - Rita Bella
- 4Department of Medical and Surgical Sciences and Advanced Technologies, University of Catania, Catania, Italy
| | - Teresa Mattina
- 5Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | | |
Collapse
|
7
|
|
8
|
Dilliott AA, Farhan SMK, Ghani M, Sato C, Liang E, Zhang M, McIntyre AD, Cao H, Racacho L, Robinson JF, Strong MJ, Masellis M, Bulman DE, Rogaeva E, Lang A, Tartaglia C, Finger E, Zinman L, Turnbull J, Freedman M, Swartz R, Black SE, Hegele RA. Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease. J Vis Exp 2018. [PMID: 29683450 PMCID: PMC5933375 DOI: 10.3791/57266] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) is quickly revolutionizing how research into the genetic determinants of constitutional disease is performed. The technique is highly efficient with millions of sequencing reads being produced in a short time span and at relatively low cost. Specifically, targeted NGS is able to focus investigations to genomic regions of particular interest based on the disease of study. Not only does this further reduce costs and increase the speed of the process, but it lessens the computational burden that often accompanies NGS. Although targeted NGS is restricted to certain regions of the genome, preventing identification of potential novel loci of interest, it can be an excellent technique when faced with a phenotypically and genetically heterogeneous disease, for which there are previously known genetic associations. Because of the complex nature of the sequencing technique, it is important to closely adhere to protocols and methodologies in order to achieve sequencing reads of high coverage and quality. Further, once sequencing reads are obtained, a sophisticated bioinformatics workflow is utilized to accurately map reads to a reference genome, to call variants, and to ensure the variants pass quality metrics. Variants must also be annotated and curated based on their clinical significance, which can be standardized by applying the American College of Medical Genetics and Genomics Pathogenicity Guidelines. The methods presented herein will display the steps involved in generating and analyzing NGS data from a targeted sequencing panel, using the ONDRISeq neurodegenerative disease panel as a model, to identify variants that may be of clinical significance.
Collapse
Affiliation(s)
- Allison A Dilliott
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University; Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University
| | - Sali M K Farhan
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Harvard Medical School, Massachusetts General Hospital, Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard
| | - Mahdi Ghani
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto
| | - Christine Sato
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto
| | - Eric Liang
- School of Medicine, Faculty of Health Sciences, Queen's University
| | - Ming Zhang
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto
| | - Adam D McIntyre
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University
| | - Henian Cao
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University
| | - Lemuel Racacho
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa; CHEO Research Institute, Faculty of Medicine, University of Ottawa
| | - John F Robinson
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University
| | - Michael J Strong
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University; Department of Clinical Neurological Sciences, Western University
| | - Mario Masellis
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto; Division of Neurology, Department of Medicine, University of Toronto
| | - Dennis E Bulman
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa; CHEO Research Institute, Faculty of Medicine, University of Ottawa
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto
| | - Anthony Lang
- Division of Neurology, Department of Medicine, University of Toronto; Morton and Gloria Shulman Movement Disorders Centre, Toronto Western Hospital
| | - Carmela Tartaglia
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto; Division of Neurology, Department of Medicine, University of Toronto
| | - Elizabeth Finger
- Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University; Parkwood Institute, St. Joseph's Health Care
| | - Lorne Zinman
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto
| | - John Turnbull
- Department of Medicine, Division of Neurology, McMaster University
| | - Morris Freedman
- Division of Neurology, Department of Medicine, University of Toronto; Division of Neurology, Department of Medicine, Baycrest Health Sciences
| | - Rick Swartz
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto
| | - Sandra E Black
- Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto; Canadian Partnership for Stroke Recovery Sunnybrook Site, Sunnybrook Health Science Centre, University of Toronto
| | - Robert A Hegele
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University; Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University;
| |
Collapse
|
9
|
Farhan SMK, Nixon KCJ, Everest M, Edwards TN, Long S, Segal D, Knip MJ, Arts HH, Chakrabarti R, Wang J, Robinson JF, Lee D, Mirsattari SM, Rupar CA, Siu VM, Poulter MO, Hegele RA, Kramer JM. Identification of a novel synaptic protein, TMTC3, involved in periventricular nodular heterotopia with intellectual disability and epilepsy. Hum Mol Genet 2018; 26:4278-4289. [PMID: 28973161 PMCID: PMC5886076 DOI: 10.1093/hmg/ddx316] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/08/2017] [Indexed: 12/30/2022] Open
Abstract
Defects in neuronal migration cause brain malformations, which are associated with intellectual disability (ID) and epilepsy. Using exome sequencing, we identified compound heterozygous variants (p.Arg71His and p. Leu729ThrfsTer6) in TMTC3, encoding transmembrane and tetratricopeptide repeat containing 3, in four siblings with nocturnal seizures and ID. Three of the four siblings have periventricular nodular heterotopia (PVNH), a common brain malformation caused by failure of neurons to migrate from the ventricular zone to the cortex. Expression analysis using patient-derived cells confirmed reduced TMTC3 transcript levels and loss of the TMTC3 protein compared to parental and control cells. As TMTC3 function is currently unexplored in the brain, we gathered support for a neurobiological role for TMTC3 by generating flies with post-mitotic neuron-specific knockdown of the highly conserved Drosophila melanogaster TMTC3 ortholog, CG4050/tmtc3. Neuron-specific knockdown of tmtc3 in flies resulted in increased susceptibility to induced seizures. Importantly, this phenotype was rescued by neuron-specific expression of human TMTC3, suggesting a role for TMTC3 in seizure biology. In addition, we observed co-localization of TMTC3 in the rat brain with vesicular GABA transporter (VGAT), a presynaptic marker for inhibitory synapses. TMTC3 is localized at VGAT positive pre-synaptic terminals and boutons in the rat hypothalamus and piriform cortex, suggesting a role for TMTC3 in the regulation of GABAergic inhibitory synapses. TMTC3 did not co-localize with Vglut2, a presynaptic marker for excitatory neurons. Our data identified TMTC3 as a synaptic protein that is involved in PVNH with ID and epilepsy, in addition to its previously described association with cobblestone lissencephaly.
Collapse
Affiliation(s)
- Sali M K Farhan
- Molecular Medicine Research Group, Robarts Research Institute, London, ON, Canada, N6A 5B7.,Department of Biochemistry
| | - Kevin C J Nixon
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Michelle Everest
- Molecular Medicine Research Group, Robarts Research Institute, London, ON, Canada, N6A 5B7.,Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Tara N Edwards
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Shirley Long
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Dmitri Segal
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Maria J Knip
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Heleen H Arts
- Molecular Medicine Research Group, Robarts Research Institute, London, ON, Canada, N6A 5B7.,Division of Genetics and Development, Children's Health Research Institute, London, ON, Canada, N6A 5W9.,Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre Nijmegen, The Netherlands
| | - Rana Chakrabarti
- Division of Genetics and Development, Children's Health Research Institute, London, ON, Canada, N6A 5W9.,Department of Pediatrics
| | - Jian Wang
- Molecular Medicine Research Group, Robarts Research Institute, London, ON, Canada, N6A 5B7
| | - John F Robinson
- Molecular Medicine Research Group, Robarts Research Institute, London, ON, Canada, N6A 5B7
| | | | - Seyed M Mirsattari
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1.,Departments of Clinical Neurological Sciences, Medical Biophysics, Medical Imaging and Psychology
| | - C Anthony Rupar
- Department of Biochemistry.,Division of Genetics and Development, Children's Health Research Institute, London, ON, Canada, N6A 5W9.,Department of Pediatrics.,Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Victoria M Siu
- Department of Biochemistry.,Division of Genetics and Development, Children's Health Research Institute, London, ON, Canada, N6A 5W9.,Department of Pediatrics
| | | | - Michael O Poulter
- Molecular Medicine Research Group, Robarts Research Institute, London, ON, Canada, N6A 5B7.,Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Robert A Hegele
- Molecular Medicine Research Group, Robarts Research Institute, London, ON, Canada, N6A 5B7.,Department of Biochemistry
| | - Jamie M Kramer
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1.,Division of Genetics and Development, Children's Health Research Institute, London, ON, Canada, N6A 5W9.,Department of Biology, Faculty of Science, Western University, London, ON, Canada, N6A 5B7
| |
Collapse
|
10
|
Iacocca MA, Hegele RA. Recent advances in genetic testing for familial hypercholesterolemia. Expert Rev Mol Diagn 2017; 17:641-651. [DOI: 10.1080/14737159.2017.1332997] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Michael A. Iacocca
- Departments of Medicine and Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Robert A. Hegele
- Departments of Medicine and Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| |
Collapse
|
11
|
Farhan SMK, Dilliott AA, Ghani M, Sato C, Liang E, Zhang M, McIntyre AD, Cao H, Racacho L, Robinson JF, Strong MJ, Masellis M, St George-Hyslop P, Bulman DE, Rogaeva E, Hegele RA. The ONDRISeq panel: custom-designed next-generation sequencing of genes related to neurodegeneration. NPJ Genom Med 2016; 1:16032. [PMID: 29263818 PMCID: PMC5685311 DOI: 10.1038/npjgenmed.2016.32] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 08/01/2016] [Accepted: 08/05/2016] [Indexed: 12/13/2022] Open
Abstract
The Ontario Neurodegenerative Disease Research Initiative (ONDRI) is a multimodal, multi-year, prospective observational cohort study to characterise five diseases: (1) Alzheimer's disease (AD) or amnestic single or multidomain mild cognitive impairment (aMCI) (AD/MCI); (2) amyotrophic lateral sclerosis (ALS); (3) frontotemporal dementia (FTD); (4) Parkinson's disease (PD); and (5) vascular cognitive impairment (VCI). The ONDRI Genomics subgroup is investigating the genetic basis of neurodegeneration. We have developed a custom next-generation-sequencing-based panel, ONDRISeq that targets 80 genes known to be associated with neurodegeneration. We processed DNA collected from 216 individuals diagnosed with one of the five diseases, on ONDRISeq. All runs were executed on a MiSeq instrument and subjected to rigorous quality control assessments. We also independently validated a subset of the variant calls using NeuroX (a genome-wide array for neurodegenerative disorders), TaqMan allelic discrimination assay, or Sanger sequencing. ONDRISeq consistently generated high-quality genotyping calls and on average, 92% of targeted bases are covered by at least 30 reads. We also observed 100% concordance for the variants identified via ONDRISeq and validated by other genomic technologies. We were successful in detecting known as well as novel rare variants in 72.2% of cases although not all variants are disease-causing. Using ONDRISeq, we also found that the APOE E4 allele had a frequency of 0.167 in these samples. Our optimised workflow highlights next-generation sequencing as a robust tool in elucidating the genetic basis of neurodegenerative diseases by screening multiple candidate genes simultaneously.
Collapse
Affiliation(s)
- Sali M K Farhan
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Allison A Dilliott
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Mahdi Ghani
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Christine Sato
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Eric Liang
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Ming Zhang
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Adam D McIntyre
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Henian Cao
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Lemuel Racacho
- Department of Microbiology and Immunology, Faculty of Medicine, Department of Biochemistry, University of Ottawa, Ottawa, ON, Canada.,Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - John F Robinson
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Michael J Strong
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Department of Clinical Neurological Sciences, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Mario Masellis
- Department of Medicine (Neurology), Sunnybrook Health Sciences Centre, LC Campbell Cognitive Neurology Research Unit, Hurvitz Brain Science Research Program, Sunnybrook Research Institute, University of Toronto, Toronto, ON, Canada
| | - Peter St George-Hyslop
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada.,Department of Clinical Neurosciences, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Dennis E Bulman
- Department of Microbiology and Immunology, Faculty of Medicine, Department of Biochemistry, University of Ottawa, Ottawa, ON, Canada.,Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Robert A Hegele
- Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | | |
Collapse
|
12
|
Abstract
PURPOSE OF REVIEW Plasma lipids, namely cholesterol and triglyceride, and lipoproteins, such as low-density lipoprotein (LDL) and high-density lipoprotein, serve numerous physiological roles. Perturbed levels of these traits underlie monogenic dyslipidemias, a diverse group of multisystem disorders. We are on the verge of having a relatively complete picture of the human dyslipidemias and their components. RECENT FINDINGS Recent advances in genetics of plasma lipids and lipoproteins include the following: (1) expanding the range of genes causing monogenic dyslipidemias, particularly elevated LDL cholesterol; (2) appreciating the role of polygenic effects in such traits as familial hypercholesterolemia and combined hyperlipidemia; (3) accumulating a list of common variants that determine plasma lipids and lipoproteins; (4) applying exome sequencing to identify collections of rare variants determining plasma lipids and lipoproteins that via Mendelian randomization have also implicated gene products such as NPC1L1, APOC3, LDLR, APOA5, and ANGPTL4 as causal for atherosclerotic cardiovascular disease; and (5) using naturally occurring genetic variation to identify new drug targets, including inhibitors of apolipoprotein (apo) C-III, apo(a), ANGPTL3, and ANGPTL4. SUMMARY Here, we compile this disparate range of data linking human genetic variation to plasma lipids and lipoproteins, providing a "one stop shop" for the interested reader.
Collapse
Affiliation(s)
- Jacqueline S. Dron
- Departments of Medicine and Biochemistry, and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 4288A - 1151 Richmond Street North, London, ON N6A 5B7 Canada
| | - Robert A. Hegele
- Departments of Medicine and Biochemistry, and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, 4288A - 1151 Richmond Street North, London, ON N6A 5B7 Canada
| |
Collapse
|
13
|
Upadhyay RK. Emerging risk biomarkers in cardiovascular diseases and disorders. J Lipids 2015; 2015:971453. [PMID: 25949827 PMCID: PMC4407625 DOI: 10.1155/2015/971453] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 12/16/2022] Open
Abstract
Present review article highlights various cardiovascular risk prediction biomarkers by incorporating both traditional risk factors to be used as diagnostic markers and recent technologically generated diagnostic and therapeutic markers. This paper explains traditional biomarkers such as lipid profile, glucose, and hormone level and physiological biomarkers based on measurement of levels of important biomolecules such as serum ferritin, triglyceride to HDLp (high density lipoproteins) ratio, lipophorin-cholesterol ratio, lipid-lipophorin ratio, LDL cholesterol level, HDLp and apolipoprotein levels, lipophorins and LTPs ratio, sphingolipids, Omega-3 Index, and ST2 level. In addition, immunohistochemical, oxidative stress, inflammatory, anatomical, imaging, genetic, and therapeutic biomarkers have been explained in detail with their investigational specifications. Many of these biomarkers, alone or in combination, can play important role in prediction of risks, its types, and status of morbidity. As emerging risks are found to be affiliated with minor and microlevel factors and its diagnosis at an earlier stage could find CVD, hence, there is an urgent need of new more authentic, appropriate, and reliable diagnostic and therapeutic markers to confirm disease well in time to start the clinical aid to the patients. Present review aims to discuss new emerging biomarkers that could facilitate more authentic and fast diagnosis of CVDs, HF (heart failures), and various lipid abnormalities and disorders in the future.
Collapse
Affiliation(s)
- Ravi Kant Upadhyay
- Department of Zoology, DDU Gorakhpur University, Gorakhpur 273009, India
| |
Collapse
|
14
|
Bamimore MA, Zaid A, Banerjee Y, Al-Sarraf A, Abifadel M, Seidah NG, Al-Waili K, Al-Rasadi K, Awan Z. Familial hypercholesterolemia mutations in the Middle Eastern and North African region: A need for a national registry. J Clin Lipidol 2015; 9:187-94. [DOI: 10.1016/j.jacl.2014.11.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 11/15/2014] [Accepted: 11/23/2014] [Indexed: 01/01/2023]
|
15
|
Farhan SMK, Robinson JF, McIntyre AD, Marrosu MG, Ticca AF, Loddo S, Carboni N, Brancati F, Hegele RA. A novel LIPE nonsense mutation found using exome sequencing in siblings with late-onset familial partial lipodystrophy. Can J Cardiol 2014; 30:1649-54. [PMID: 25475467 DOI: 10.1016/j.cjca.2014.09.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 09/11/2014] [Accepted: 09/11/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Familial lipodystrophies are rare inherited disorders associated with redistribution of body fat and development of dyslipidemia, insulin resistance, and diabetes. We previously reported 2 siblings with unusual late-onset familial partial lipodystrophy in whom heretofore known causative genes had been excluded. We hypothesized they had a mutation in a novel lipodystrophy gene. METHODS Our approach centred on whole exome sequencing of the patients' DNA, together with genetic linkage analysis and a bioinformatic prioritization analysis. All candidate variants were assessed in silico and available family members were genotyped to assess segregation of mutations. RESULTS Our prioritization algorithm led us to a novel homozygous nonsense variant, namely p.Ala507fsTer563 in the hormone sensitive lipase gene encoding, an enzyme that is differentially expressed in adipocytes and steroidogenic tissues. Pathogenicity of the mutation was supported in bioinformatic analyses and variant cosegregation within the family. CONCLUSIONS We have identified a novel nonsense mutation in hormone sensitive lipase gene, which likely explains the lipodystrophy phenotype observed in these patients.
Collapse
Affiliation(s)
- Sali M K Farhan
- Departments of Medicine and Biochemistry, Western University, London, Ontario, Canada; Robarts Research, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - John F Robinson
- Robarts Research, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Adam D McIntyre
- Robarts Research, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Maria G Marrosu
- Department of Public Health, Clinical and Molecular Medicine, University of Cagliari, Cagliari, Italy
| | - Anna F Ticca
- Department of Public Health, Clinical and Molecular Medicine, University of Cagliari, Cagliari, Italy
| | - Sara Loddo
- IRCCS Casa Sollievo della Sofferenza, Istituto Mendel, San Giovanni Rotondo, Italy
| | - Nicola Carboni
- Division of Neurology, Hospital San Francesco of Nuoro, Nuoro, Italy
| | - Francesco Brancati
- Department of Medical, Oral and Biotechnological Sciences, Gabriele D'Annunzio University of Chieti-Pescara, Italy
| | - Robert A Hegele
- Departments of Medicine and Biochemistry, Western University, London, Ontario, Canada; Robarts Research, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.
| |
Collapse
|