Human Molecular Genetics Research Articles

Genetic Inheritance and Its Contribution to Tinnitus.

Tinnitus is the abnormal perception of sound that affects more than 15% of adult population around the globe. Severe tinnitus is considered a complex disorder that arises as result of the interaction of genetic and environmental factors, and it is associated with several comorbidities such as hearing loss, anxiety, and insomnia. We begin this review with an introduction to human molecular genetics and the role of genetic variation on the inheritance. There are some genetic reports on tinnitus heritability including concordance studies in twins and adoptees or aggregation in families providing some evidence for familial aggregation in patients with severe tinnitus and high concordance in monozygotic twins with bilateral tinnitus. So, sex differences in familial aggregation and heritability of bilateral tinnitus suggest a potential sexual dimorphism in tinnitus inheritance.Molecular genetic studies have been demonstrated to be a useful tool to understand the role of genetic variation in rare diseases and complex disorders. The reported associations in common variants in neurotrophic factors such as GDNF, BDNF, or potassium channels genes were underpowered, and the lack of replication questions these findings. Although candidate gene approaches have failed in replicating these genetic associations, the development of high throughput sequencing technology and the selection of extreme phenotypes are strategies that will allow the clinicians and researchers to combine genetic information with clinical data to implement a personalized diagnosis and therapy in patients with tinnitus.

Creation of Cultures Containing Mutations Linked with Cardiovascular Diseases using Transfection and Genome Editing.

In this review article, we analyzed the literature on the creation of cultures containing mutations associated with cardiovascular diseases (CVD) using transfection, transduction and editing of the human genome. We described different methods of transfection, transduction and editing of the human genome, used in the literature. We reviewed the researches in which the creation of сell cultures containing mutations was described. According to the literature, system CRISPR/Cas9 proved to be the most preferred method for editing the genome. We found rather promising and interesting a practically undeveloped direction of mitochondria transfection using a gene gun. Such a gun can direct a genetically-engineered construct containing human DNA mutations to the mitochondria using heavy metal particles. However, in human molecular genetics, the transfection method using a gene gun is unfairly forgotten and is almost never used. Ethical problems arising from editing the human genome were also discussed in our review. We came to a conclusion that it is impossible to stop scientific and technical progress. It is important that the editing of the genome takes place under the strict control of society and does not bear dangerous consequences for humanity. To achieve this, the constant interaction of science with society, culture and business is necessary. The most promising methods for the creation of cell cultures containing mutations linked with cardiovascular diseases, were system CRISPR/Cas9 and the gene gun.

A Proposed Roadmap for Parkinson's Disease Proof of Concept Clinical Trials Investigating Compounds Targeting Alpha-Synuclein.

The convergence of human molecular genetics and Lewy pathology of Parkinson’s disease (PD) have led to a robust, clinical-stage pipeline of alpha-synuclein (α-syn)-targeted therapies that have the potential to slow or stop the progression of PD and other synucleinopathies. To facilitate the development of these and earlier stage investigational molecules, the Michael J. Fox Foundation for Parkinson’s Research convened a group of leaders in the field of PD research from academia and industry, the Alpha-Synuclein Clinical Path Working Group. This group set out to develop recommendations on preclinical and clinical research that can de-risk the development of α-syn targeting therapies. This consensus white paper provides a translational framework, from the selection of animal models and associated end-points to decision-driving biomarkers as well as considerations for the design of clinical proof-of-concept studies. It also identifies current gaps in our biomarker toolkit and the status of the discovery and validation of α-syn-associated biomarkers that could help fill these gaps. Further, it highlights the importance of the emerging digital technology to supplement the capture and monitoring of clinical outcomes. Although the development of disease-modifying therapies targeting α-syn face profound challenges, we remain optimistic that meaningful strides will be made soon toward the identification and approval of disease-modifying therapeutics targeting α-syn.

2016 Banbury Meeting On Clinical Applications of Advances In Psychiatric Genetics: Background And Rationale

In December 2016, in partnership with the US-based National Society of Genetic Counselors, ISPG co-supported a Banbury meeting on the topic of Clinical Applications of Advances in Psychiatric Genetics. The purpose of this presentation is to provide the background and rationale for the meeting as a frame and context for the contributions of the subsequent presenters, each of whom will present on one major theme of the meeting.Broadly, the foundation for the meeting was the recognition that genomic advances at the molecular level in psychiatry will not make a difference to human health if we cannot find effective strategies to translate these findings into clinical practice that are both effective and extensively adopted. Therefore, as co-chairs for the meeting, Francis McMahon and I brought representatives with relevant expertise from psychiatry, human molecular genetics, clinical genetics, and genetic counseling together with representatives of relevant professional societies. We challenged participants to consider the foundational question "How do we translate our ever-increasing understanding of the genetics of psychiatric disorders into interventions that improve outcomes for patients and their families?"As well as tackling issues around the application of genetic testing (including testing to predict risk, as well as diagnostic testing, and pharmacogenomic testing) in the context of psychiatric disorders, we also asked participants to consider the broader issue of the application of genetic counselling in the context of psychiatric disorders. Genetic counselling can be applied in the context of psychiatric illness even in the absence of genetic testing, and under these circumstances has been shown to result in important improvements in patient outcomes (like empowerment and self-esteem). Therefore, we also discussed barriers and opportunities to the application of genetic counselling in psychiatry.This presentation will focus on presenting the assumptions that we articulated and the questions that we wrestled with during the course of this meeting in an effort to push progress in helping people with psychiatric disorders and their families with the knowledge we are generating from molecular psychiatric genetics studies. This presentation will frame those that follow.

Association of matrix metalloproteinase 2 and matrix metalloproteinase 9 gene polymorphism in aggressive and nonaggressive odontogenic lesions: A pilot study.

Context:The exact factors that determine the biological behavior of odontogenic lesions have not been thoroughly established yet. The influence of the matrix metalloproteinases (MMPs) on the clinical behavior of these lesions was recently brought to light.Aims:We did a pioneer study to investigate the association of MMP9 (rs3918242 [−1562 C/T] and rs17576) and MMP2 (rs243865 [−1306 C/T] and rs865094) gene polymorphisms and aggressiveness of ameloblastomas, keratocystic odontogenic tumors (KCOT) and dentigerous cysts (DC).Settings and Design:A case–control study conducted in the Department of Oral Pathology and Microbiology, Government Dental College, Trivandrum and Human Molecular Genetics Laboratory, Rajiv Gandhi Institute of Biotechnology and Poojappura, Trivandrum, Kerala.Subjects and Methods:DNA from the blood samples of histopathologically proven ameloblastoma (n = 15), KCOT (n = 11) and DC (n = 13) patients were extracted using standard protocols. Primers were designed based on the functionality and relevance for polymerase chain reaction (PCR). PCR products were analyzed by PCR-restriction fragment length polymorphism and sequencing.Statistical Analysis Used:Chi-square analysis was done to assess the association of gene polymorphisms among the cases and controls.Results:Ameloblastomas showed a higher frequency of mutant allele (T = 0.43; P = 0.05) of MMP9 rs3918242 (−1562C/T) compared to the control population. All the cases showed a statistically significant difference in the distribution of genotype (P = 0.046) and allele (P = 0.03; odds ratio [OR] = 2.06 [1.08–3.95]) frequency of MMP2 rs2438659 (−1306C/T). KCOT samples also showed a significant association in distribution of both genotype (P = 0.01) and allele (P = 0.01 with an OR at 3.42 [1.31–8.92]) frequency, on comparison with control population.Conclusions:MMP2 rs243865 polymorphism has a plausible role in increasing the aggressiveness of ameloblastomas and KCOT compared to that of the control population. Furthermore, MMP9 rs3918242 polymorphism may contribute to the aggressive behavior of ameloblastomas.

A day in the life of a Science Communicator

Alison Halliday is a freelance science communicator, specializing in research topics across the life sciences, medicine and health. After completing an undergraduate degree in Biochemistry and Genetics at Sheffield University, Alison was awarded a PhD in Human Molecular Genetics at the University of Newcastle, when she won first prize in the MRC's Max Perutz science writing competition. She carried out 5 years as a Senior Postdoctoral Research Fellow at UCL, investigating the genes involved in a childhood obesity syndrome. Moving into science communications, Alison spent 10 years at Cancer Research UK engaging the public about the charity's work before moving into freelance work. Peter Wotherspoon (Training & Careers Intern, Biochemical Society) spoke with her about her work.

Abstract 618: Identification of Novel Disease Genes for Metabolic Syndrome

Factors that underlie the association of diverse traits of the metabolic syndrome have remained largely unknown. The strong heritable nature of this condition provides an exceptional avenue for discovery of the disease mechanisms by using modern techniques of human molecular genetics. Strikingly, efforts by genome-wide association studies to identify common variants that show association with two or more traits have largely failed. Growing evidence indicates excess of rare genetic variants through recent exponential population growth, raising the possibility for their causal role in common diseases. With the advent of high throughput sequencing the power for identification of functional rare variants has dramatically increased. By biasing for extreme phenotypes and utilizing traditional method of segregation analysis we have discovered a number of disease genes for metabolic syndrome and coronary artery disease. A major benefit of this strategy is that true causal relationships has been established between rare variations in a gene, its cognate pathways and the disease of interest. These, in turn, have provided fundamental new insight into pathogenesis of poorly understood diseases such as plaque erosion, and logical starting points for identifying new targets and pathways for therapeutic intervention. By dissecting cognate pathways, we have identified novel targets, including Dyrk1B kinase, a novel incretin and components of Wnt signaling pathway to treat CAD, diabetes and hyperlipidemia and have implemented those succesfuly in animal models.

The functional genomics laboratory: functional validation of genetic variants

Currently, one of the main challenges in human molecular genetics is the interpretation of rare genetic variants of unknown clinical significance. A conclusive diagnosis is of importance for the patient to obtain certainty about the cause of the disease, for the clinician to be able to provide optimal care to the patient and to predict the disease course, and for the clinical geneticist for genetic counseling of the patient and family members. Conclusive evidence for pathogenicity of genetic variants is therefore crucial. This review gives an introduction to the problem of the interpretation of genetic variants of unknown clinical significance in view of the recent advances in genetic screening, and gives an overview of the possibilities for functional tests that can be performed to answer questions about the function of genes and the functional consequences of genetic variants (“functional genomics”) in the field of inborn errors of metabolism (IEM), including several examples of functional genomics studies of mitochondrial disorders and several other IEM.

Human Molecular Genetics Has Not Yet Contributed to Measurable Public Health Advances.

For more than half a century, we have lived in a world dominated by the idea that the gene is the central and primary agent in biology, an era some have called the "Genetic Age." Each decade since the discovery of the double-helical structure of DNA in 1953 has seen scientific advances in genetics, discoveries that have led to at least 17 Nobel Prizes. Although the time span occupied by the Genetic Age has also been a time of great public health advances, no advance in human molecular genetics can be shown to have had any measurable effect on any public health parameter of importance. It is hard to think of another field of biomedical research in which such massive public fund investments have had less public health impact to date than human molecular genetics. The only arena in which precision medicine, with its reliance on human genomic information, is likely to be helpful, is selected inherited diseases. To measurably alter the health of the population, the focus of biomedical research should be on the molecular, cellular, clinical, and population effects of the external agents and exposures that drive the incidence of most health conditions.

Human molecular genetics and its impact on Dentistry

Human molecular genetics and its impact on Dentistry

Multiplexed and Sensitive DNA Methylation Testing Using Methylation-Sensitive Restriction Enzymes "MSRE-qPCR".

DNA methylation is a chemically stable key-player in epigenetics. In the vertebrate genome the 5-methyl cytosine (5mC) has been found almost exclusively in the CpG dinucleotide context. CpG dinucleotides are enriched in CpG islands very frequently located within or close to gene promoters. Analyses of DNA methylation changes in human diagnostics have been conducted classically using methylation-sensitive restriction enzymes (MSRE). Since the discovery of bisulfite conversion-based sequencing and PCR assays, MSRE-based PCR assays have been less frequently used, although especially in the field of cancer epigenetics MSRE-based genome-wide discovery and targeted screening applications have been and are still performed successfully. Even though epigenome-wide discovery of altered DNA methylation patterns has found its way into various fields of human disease and molecular genetics research, the validation of findings upon discovery is still a bottleneck. Usually several multiples of 10 up to 100 candidate biomarkers from discovery have to be confirmed or are of interest for further work. In particular, bisulfite PCR assays are often limited in the number of candidates which can be analyzed, due to their low multiplexing capability, especially, if only small amounts of DNA are available from for example clinical specimens. In clinical research and diagnostics a similar situation arises for the analyses of cell-free DNA (cfDNA) in body fluids or circulating tumor cells (CTCs). Although tissue- or disease- (e.g., cancer) specific DNA methylation patterns can be deduced very efficiently in a genome-wide manner if around 100ng of DNA are available, confirming these candidates and selecting target-sequences for studying methylation changes in liquid biopsies using cfDNA or CTCs remains a big challenge. Along these lines we have developed MSRE-qPCR and introduce here method details, which have been found very suitable for the efficient confirmation and testing of DNA methylation in a quantitative multiplexed manner (e.g., 48-96 plex) from ng amounts of DNA. The method is applicable in a standard qPCR setting as well for nanoliter scaled high-throughput qPCR, enabling detection of <10 copies of targets, thus suitable to pick up 0.1-1% of specific methylated DNA in an unmethylated background.

Elena Matsa: Lighting Fires for Heart Disease.

Elena Matsa attended the University of Nottingham for her BSc (Hons) degree in Biochemistry and Genetics. She then earned her MSc at Imperial College, London, in Human Molecular Genetics before returning to the University of Nottingham for her PhD in Stem Cell Biology. After a 2-year postdoctoral fellowship in Nottingham, she moved onto Stanford University as a postdoctoral research fellow. Elena currently works as an Instructor for the Joseph Wu lab and teaches courses on Bioengineering, and Progenitor Cell Biology at Stanford, where she encourages her students to keep the fire in their belly burning. Elena Matsa Yes, most of my time is spent in the lab, and I am currently working on two main projects, both dealing with precision medicine.1 One project2,3 tries to figure out new treatments for people who are born with heart disease and have a mutation that causes the disease. This project is especially exciting since it’s what I’ve been working on since my postdoctoral fellowship in the UK under my mentor Chris Denning. Right now, at Stanford, we have progressed to using nanomaterials to deliver the new treatment to the heart. The other project4 relates to how our genetic makeup affects our response to medications. Some people are fine, but others may experience side effects when taking a drug, which can lead to heart complications. Fourteen percent of people who take antidiabetic medications have heart …

DNA damage-induced immune response: Micronuclei provide key platform.

DNA damage-induced activation of the cytoplasmic DNA sensor cGAS influences the outcome of infections, autoinflammation, and cancer. Recent studies by Harding et al. (2017. Nature. http://dx.doi.org/10.1038/nature23470), Mackenzie et al. (2017. Nature. http://dx.doi.org/10.1038/nature23449), and Bartsch et al. (2017. Human Molecular Genetics. https://doi.org/10.1093/hmg/ddx283) demonstrate a role for micronuclei formation in DNA damage-induced immune activation.

Expression of Contactin 4 Is Associated With Malignant Behavior in Pheochromocytomas and Paragangliomas.

Pheochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine, usually benign, tumors. Currently, the only reliable criterion of malignancy is the presence of metastases. The aim of this study was to identify genes associated with malignancy in PPGLs. Transcriptomic profiling was performed on 40 benign and 11 malignant PPGLs. Genes showing a significantly different expression between benign and malignant PPGLs with a ratio ≥4 were confirmed and tested in an independent series by quantitative real-time polymerase chain reaction (qRT-PCR). Immunohistochemistry was performed for the validated genes on 109 benign and 32 malignant PPGLs. Functional assays were performed with hPheo1 cells. This study was conducted at the Department of Pathology of the Erasmus MC University Medical Center Rotterdam Human Molecular Genetics laboratory of the de Duve Institute, University of Louvain. PPGL samples from 179 patients, diagnosed between 1972 and 2015, were included. Associations between gene expression and malignancy were tested using supervised clustering approaches. Ten differentially expressed genes were selected based on messenger RNA (mRNA) expression array data. Contactin 4 (CNTN4) was overexpressed in malignant vs benign tumors [4.62-fold; false discovery rate (FDR), 0.001]. Overexpression at the mRNA level was confirmed using qRT-PCR (2.90-fold, P = 0.02; validation set: 4.26-fold, P = 0.005). Consistent findings were obtained in The Cancer Genome Atlas cohort (2.7-fold; FDR, 0.02). CNTN4 protein was more frequently expressed in malignant than in benign PPGLs by immunohistochemistry (58% vs 17%; P = 0.002). Survival after 7 days of culture under starvation conditions was significantly enhanced in hPheo1 cells transfected with CNTN4 complementary DNA. CNTN4 expression is consistently associated with malignant behavior in PPGLs.

Some pioneers of European human genetics.

Some of the pioneers of human genetics across Europe are described, based on a series of 100 recorded interviews made by the author. These interviews, and the memories of earlier workers in the field recalled by interviewees, provide a vivid picture, albeit incomplete, of the early years of human and medical genetics. From small beginnings in the immediate post-World War 2 years, human genetics grew rapidly across many European countries, a powerful factor being the development of human cytogenetics, stimulated by concerns over the risks of radiation exposure. Medical applications soon followed, with the recognition of human chromosome abnormalities, the need for genetic counselling, the possibility of prenatal diagnosis and later, the applications of human molecular genetics. The evolution of the field has been strongly influenced by the characters and interests of the relatively small number of founding workers in different European countries, as well as by wider social, medical and scientific factors in the individual countries.European Journal of Human Genetics advance online publication, 10 May 2017; doi:10.1038/ejhg.2017.47.

Optimization and validation of analysis method based on 27-plex SNP panel for ancestry inference.

Anthropology generally divides the individuals into the East Asian Mongolia race, European Caucasian race and African Nigro race. The 27-plex single nucleotide polymorphism (SNP) panel for ancestry information has been established to differentiate samples from East Asian, European, African and admixture populations of East Asian and European origin by genotyping and ancestry inference. To infer ancestry for unknown individuals, we established an optimized analysis pipeline based on the likelihood ratio, ancestry component and individual ancestry assignment. Four samples from East Asian, European, African and admixture populations of East Asian and European origin were tested using the optimized analysis pipeline. Cross validation within basic referential database and validation of 1 010 test samples were both used to evaluate the inference process. The results showed that accuracy of the method was higher than 99% in East Asia, Europe, Africa and admixture populations. The inference method can characterize the ancestry information of DNA donors, and has important practical application values in the field of human molecular and forensic genetics.

Recorded interviews with human and medical geneticists

A series of 100 recorded interviews with human and medical geneticists has been carried out and some general results are reported here. Twenty countries across the world are represented, mostly European, with a particular emphasis on the United Kingdom. A priority was given to older workers, many of whom were key founders of human genetics in their own countries and areas of work, and over 20 of whom are now no longer living. The interviews also give valuable information on the previous generation of workers, as teachers and mentors of the interviewees, thus extending the coverage of human genetics back to the 1930s or even earlier. A number of prominent themes emerge from the interview series; notably the beginnings of human cytogenetics from the late 1950s, the development of medical genetics research and its clinical applications in the 1960s and 1970s, and more recently the beginnings and rapid growth of human molecular genetics. The interviews provide vivid personal portraits of those involved, and also show the effects of social and political issues, notably those arising from World War 2 and its aftermath, which affected not only the individuals involved but also broader developments in human genetics, such as research related to risks of irradiation. While this series has made a start in the oral history of this important field, extension and further development of the work is urgently needed to give a fuller picture of how human genetics has developed.

MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics.

Traditional Sanger sequencing as well as Next-Generation Sequencing have been used for the identification of disease causing mutations in human molecular research. The majority of currently available tools are developed for research and explorative purposes and often do not provide a complete, efficient, one-stop solution. As the focus of currently developed tools is mainly on NGS data analysis, no integrative solution for the analysis of Sanger data is provided and consequently a one-stop solution to analyze reads from both sequencing platforms is not available. We have therefore developed a new pipeline called MutAid to analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. It performs format conversion, base calling, quality trimming, filtering, read mapping, variant calling, variant annotation and analysis of Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as insertions and deletions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms including Sanger, Illumina, 454 and Ion Torrent. Furthermore, for NGS data analysis, five read mappers including BWA, TMAP, Bowtie, Bowtie2 and GSNAP and four variant callers including GATK-HaplotypeCaller, SAMTOOLS, Freebayes and VarScan2 pipelines are supported. MutAid is freely available at https://sourceforge.net/projects/mutaid.

MRNA and microRNA transcriptomics analyses in a murine model of dystrophin loss and therapeutic restoration.

Duchenne muscular dystrophy (DMD) is a pediatric, X-linked, progressive muscle-wasting disorder caused by loss of function mutations affecting the gene encoding the dystrophin protein. While the primary genetic insult in DMD is well described, many details of the molecular and cellular pathologies that follow dystrophin loss are incompletely understood. To investigate gene expression in dystrophic muscle we have applied mRNA and microRNA (miRNA) microarray technology to the mdx mouse model of DMD. This study was designed to generate a complete description of gene expression changes associated with dystrophic pathology and the response to an experimental therapy which restores dystrophin protein function. These datasets have enabled (1) the determination of gene expression changes associated with dystrophic pathology, (2) identification of differentially expressed genes that are restored towards wild-type levels after therapeutic dystrophin rescue, (3) investigation of the correlation between mRNA and protein expression (determined by parallel mass spectrometry proteomics analysis), and (4) prediction of pathology associated miRNA-target interactions. Here we describe in detail how the data were generated including the basic analysis as contained in the manuscript published in Human Molecular Genetics with PMID 26385637. The data have been deposited in the Gene Expression Omnibus (GEO) with the accession number GSE64420.

Genome-wide expression analysis comparing hypertrophic changes in normal and dysferlinopathy mice.

Because myostatin normally limits skeletal muscle growth, there are extensive efforts to develop myostatin inhibitors for clinical use. One potential concern is that in muscle degenerative diseases, inducing hypertrophy may increase stress on dystrophic fibers. Our study shows that blocking this pathway in dysferlin deficient mice results in early improvement in histopathology but ultimately accelerates muscle degeneration. Hence, benefits of this approach should be weighed against these potential detrimental effects. Here, we present detailed experimental methods and analysis for the gene expression profiling described in our recently published study in Human Molecular Genetics (Lee et al., 2015). Our data sets have been deposited in the Gene Expression Omnibus (GEO) database (GSE62945) and are available at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62945. Our data provide a resource for exploring molecular mechanisms that are related to hypertrophy-induced, accelerated muscular degeneration in dysferlinopathy.