Blood expression profiles for tuberous sclerosis complex 2, neurofibromatosis type 1, and Down's syndrome

Blood gene expression profiling has been applied to a variety of hematological malignancies, autoimmune disorders, and infectious diseases. This study applies this approach to genetic diseases without obvious blood phenotypes. Three genetic diseases including tuberous sclerosis complex 2, neurofibromatosis type 1, and Down's syndrome were compared with a group of healthy controls. RNA from whole blood was surveyed using Affymetrix U133A arrays. Each disease was associated with a unique gene expression pattern in blood that can be accurately distinguished by a classifier. Genes on chromosome 21 were overexpressed in Down's syndrome, and genes controlling cell cycle and proliferation were associated with tuberous sclerosis complex type 2 or neurofibromatosis type 1. A subset of genes involved in cardiac development or remodeling were overexpressed in patients with Down's syndrome and congenital heart defects. These findings suggest that blood gene expression profiling on a broader basis might be useful for genetic disease screening/diagnosis and might help elucidate mechanisms and pathways that lead to genotype-phenotype differences.     

Ⅱ型神经纤维瘤病分子遗传分析指导临床个体化诊疗的研究

目的 建立临床适用的Ⅱ型神经纤维瘤病(NF2)的分子遗传分析方法,对NF2患者及其后代进行分子遗传诊断,以指导NF2家族的遗传咨询及个体化病情监测、随访及临床干预.方法 以天津医科大学总医院神经外科自2009年1月至2010年1月收治的10例NF2患者为研究对象,收集患者的肿瘤组织标本,原代培养并鉴定术中获取的许旺细胞瘤组织.抽提原代培养的肿瘤性许旺细胞及患者血液的基因组DNA(2例NF2患者已有后代且同意接受基因测序,同时对其后代的血液进行基因组DNA提取),对2例NF2患者亲子二代血液及患者的肿瘤性许旺细胞基因组DNA进行NF2基因测序.制定不同的临床干预及随访计划,结合亲子二代分子遗传检测结果,对NF2家族制定后代的长期随访计划.结果 初步建立NF2许旺细胞瘤组织标本与基因组DNA库.基因测序结果显示肿瘤性许旺细胞与患者血液提取的NF2基因突变位点相同.第一组母女存在完全相同的基因突变位点,第二组母子基因突变位点不完全一致,二组检测到的突变位点均位于靠近外显子的调控区.结论 NF2许旺细胞瘤组织标本及基因组DNA库可以为该病分子遗传研究提供组织及基因组DNA资源.分子遗传分析可以指导临床工作,提前预计后代罹患风险,为高风险人群制定个体化的随访计划.个体化的临床干预可以提高患者的生活质量,延长生存期.

Abstract：

Objective To establish a molecular genetic analysis method applicable clinically for genetic diagnosis of patients with neurofibromatosis type Ⅱ (NF2) and their offsprings, and further guide the genetic counseling of NF2 family, condition monitoring, follow-up as well as clinical intervention of the patients. Methods Ten patients with NF2, admitted to our hospital from January 2009 to January 2010, were chosen;tumorigenic Schwann cells in Schwannoma were isolated and purified for primary culture. Genomic DNA was extracted from tumorigenic Schwann cells and from the blood of 2 patients and their offsprings who agreed to accept gene sequencing;the NF2 gene was sequenced (El-15 and El7 exons and adjacent introns). According to the implication of NF2 gene sequencing, genetic counseling was given to the NF2 family, and the potential NF2 patients in offsprings were followed up in a long-term. Results Schwannoma tissue and genomic DNA bank were established initially. Totallysame NF2 gene mutations were detected in genomic DNA extracted both from tumorigenic Schwann cells and blood cells in the same patient. By comparing the genotypes between the patients and the offsprings,consistent NF2 gene mutations were found between a female patient and her daughter aged 3, but not completely consistent gene mutations between another female patient and her son aged 15. All of the mutations in NF2 gene were located in the control region near the exons. Based on the patient's clinical manifestations and symptoms, reasonable plans for clinical interventions and follow-up were developed.Conclusion Schwannoma tissue and genomic DNA bank could supply the bio-resource for genetic molecular testing and treatment studies. Molecular genetic analysis would apply in clinical practice guidance, NF2 risk prediction, and follow-up plan for high-risk NF2 individuals. Early diagnosis and treatment, condition monitoring and long term follow-up and personalized clinical intervention are needed to improve the quality of life and prolong the survival.     

The future of genomic profiling of neurological diseases using blood

Sequencing of the human genome and new microarray technology make it possible to assess all genes on a single chip or array. Recent studies show different patterns of gene expression related to different tissues and diseases, and these patterns of gene expression are beginning to be used for diagnosis and treatment decisions in various types of lymphoid and solid malignancies. Because of obvious problems obtaining brain tissue, progress in genomics of neurological diseases has been slow. To address this, we demonstrated that different types of acute injury in rodent brain produced different patterns of gene expression in peripheral blood. These animal studies have now been extended to human studies. Two groups have shown that there are specific genomic profiles in the blood of patients after ischemic stroke that are highly sensitive and specific for predicting stroke. Other recent studies demonstrate specific genomic profiles in the blood of patients with Down syndrome, neurofibromatosis, tuberous sclerosis, Huntington disease, multiple sclerosis, Tourette syndrome, and others. In addition, data demonstrate specific profiles of gene expression in the blood related to different drugs, toxins, and infections. Although all of these studies are still preliminary basic scientific endeavors, they suggest that this approach will have clinical applications to neurological diseases in humans.     

Complex Genetic Disease: Can Genetic Strategies in Alzheimer's Disease and New Genetic Mechanisms Be Applied to Epilepsy?

Summary: Strategies used in molecular genetics have changed modern neurology. The gene or genes responsible for several major neurologic diseases have now been identified using "reverse" or positional genetics. Unexpected new genetic mechanisms have been discovered in human neurologic diseases, including (a) identical mutations of the prion protein gene in Creutzfeldt-Jakob disease and fatal familial insomnia with the phenotypic expression directed by an accompanying polymorphism; (b) stable duplications of chromosome 17 in Charcot-Marie-Tooth disease (type 1 A) that involve many genes, only one of which appears to cause neuropathy; and (c) highly variable, dynamic mutations in myotonic dystrophy, fragile X syndrome, and Kennedy's syndrome that modulate variable expressivity in multiple tissues. There is growing recognition that neurologic diseases are often complex genetic diseases with multifactorial rather than simple modes of inheritance. For example, genetic association/linkage strategies have interacted with biochemistry and immunopathology studies to produce new insights into the disease mechanism of late-onset Alzheimer's disease. The role of apolipoprotein E in late-onset Alzheimer's disease is an example of how new analytical techniques of genetic disease can be applied to dissect multiple genes. Similar research strategies are suggested for the study of epilepsy as a complex disease.     

Molecular Therapies for Tuberous Sclerosis and Neurofibromatosis

Neurofibromatosis type 1 (NF1) and tuberous sclerosis complex (TSC) are autosomal-dominant genetic disorders that result from dysregulation of the PI3K/AKT/mammalian target of rapamycin (mTOR) pathway. NF1 is caused by mutations in the NF1 gene on chromosome 17q11.2. Its protein product, neurofibromin, functions as a tumor suppressor and ultimately produces constitutive upregulation of mTOR. TSC is caused by mutations in either the TSC1 (chromosome 9q34) or TSC2 (chromosome 16p.13.3) genes. Their protein products, hamartin and tuberin, respectively, form a dimer that acts via the GAP protein Rheb (Ras homolog enhanced in brain) to directly inhibit mTOR, again resulting in upregulation. Specific inhibitors of mTOR are in clinical use, including sirolimus, everolimus, temsirolimus, and deforolimus. Everolimus has been shown to reduce the volume and appearance of subependymal giant cell astrocytomas (SEGA), facial angiofibromas, and renal angiomyolipomas associated with TSC, with a recent FDA approval for SEGA not suitable for surgical resection. This article reviews the use of mTOR inhibitors in these diseases, which have the potential to be a disease-modifying therapy in these and other conditions.     

Optimizing human post-mortem brain tissue gene expression profiling in Parkinson's disease and other neurodegenerative disorders: from target "fishing" to translational breakthroughs

Insights on the etiopathogenesis of common neurodegenerative disorders such as Parkinson's disease (PD) and Alzheimer's disease (AD) have been largely based on the discovery of gene mutations in genetically determined forms. Although these discoveries have been helpful in elucidating the basic molecular pathogenesis of familial forms, they represent a small fraction of cases, leaving the large majority classified as idiopathic. In the postgenomic era, brain tissue gene expression profiling has allowed relative quantitative assessment of thousands of genes simultaneously from one tissue sample, providing clues for novel candidate genes and processes implicated in neurodegenerative disorders. Some remain critical of "fishing expedition" science, but gene expression profiling is a discovery-based procedure well suited for the study of largely idiopathic and multifactorial diseases. However, the technology is still under development, and many methodological and biological aspects contribute to the heterogeneous results obtained from gene expression profiling. In this Review, we discuss the advantages and limitations of this technology in simple terms and identify the key variables that influence/limit gene expression profiling-derived translational breakthroughs in neurodegenerative diseases.     

Quantitation of T-cell receptor V beta chain expression on lymphocytes from blood, brain, and spinal fluid in patients with multiple sclerosis and other neurological diseases.

Multiple sclerosis (MS) is an inflammatory, demyelinating disease of the central nervous system in which large numbers of T cells enter the brain and cerebrospinal fluid (CSF). To determine whether these cells represent restricted populations, we studied expression of T-cell receptor V beta chains on paired samples from the central nervous system and blood of patients with MS or other neurological diseases (OND) using a quantitative polymerase chain reaction. The distribution of V beta chain expression in blood was skewed, with a significant preponderance of message from V beta genes 1 through 8 (p = 0.0001). Such skewing was not present in samples from the CSF and brain. Patterns of V beta gene expression were different among paired samples from spinal fluid and blood and were relatively heterogeneous. Blood and CSF samples from a patient with acute meningitis were studied on two separate occasions. The patterns of V beta expression changed over 72 hours in both the blood and the CSF. With one exception, no oligoclonal populations of T cells were observed nor were there disease-specific patterns of V beta gene expression in the blood or CSF. Samples from 2 MS brains and 1 OND brain expressed patterns of V beta genes that were different and less heterogeneous than those in paired blood. In addition, expression of V beta 12 was remarkably increased in the 2 MS brains, suggesting a selective recruitment or expansion of T cells expressing this gene. These data demonstrate that populations of T cells from blood, spinal fluid, and brain differ from one another and can fluctuate during periods of acute inflammation.(ABSTRACT TRUNCATED AT 250 WORDS)     

Differential gene expression in nerve biopsies of inflammatory neuropathies

DNA microarray analysis is a powerful tool for simultaneous analysis and comparison of gene products expressed in normal and diseased tissues. We used this technique to identify differentially expressed genes (DEGs) in nerve biopsy samples of chronic inflammatory demyelinating polyneuropathy (CIDP) and vasculitic neuropathy (VAS) patients. We found novel previously uncharacterized genes of relevance to CIDP or VAS pathogenesis. Of particular interest in CIDP were tachykinin precursor 1, which may be involved in pain mediation, stearoyl-co-enzyme A (CoA) desaturase, which may be a marker for remyelination, HLA-DQB1, CD69, an early T-cell activation gene, MSR1, a macrophage scavenger receptor, and PDZ and LIM domain 5 (PDLIM5), a factor regulating nuclear factor (NF)-kappa B activity. Genes upregulated in VAS included IGLJ3, IGHG3, IGKC, and IGL, which all function in B-cell selection or antigen recognition of B cells. Other upregulated genes included chemokines, such as CXCL9 and CCR2, as well as CPA3, a mast cell carboxypeptidase. Allograft inflammatory factor-1 (AIF-1), a modulator of immune response was upregulated both in CIDP and VAS. Microarray-based analysis of human sural nerve biopsies showed distinct gene expression patterns in CIDP and VAS. DEGs might provide clues to the pathogenesis of the diseases and be potential targets for therapeutics.     

Blood genomic responses differ after stroke, seizures, hypoglycemia, and hypoxia: blood genomic fingerprints of disease.

Using microarray technology, we investigated whether the gene expression profile in white blood cells could be used as a fingerprint of different disease states. Adult rats were subjected to ischemic strokes, hemorrhagic strokes, sham surgeries, kainate-induced seizures, hypoxia, or insulin-induced hypoglycemia, and compared with controls. The white blood cell RNA expression patterns were assessed 24 hours later using oligonucleotide microarrays. Results showed that many genes were upregulated or downregulated at least twofold in white blood cells after each experimental condition. Blood genomic response patterns were different for each condition. These results demonstrate the potential of blood gene expression profiling for diagnostic, mechanistic, and therapeutic assessment of a wide variety of disease states.     

Tumor suppressor mutations and growth factor signaling in the pathogenesis of NF1-associated peripheral nerve sheath tumors: II. The role of dysregulated growth factor signaling

Patients with neurofibromatosis type 1 (NF1), one of the most common genetic disease affecting the nervous system, develop multiple neurofibromas that can transform into aggressive sarcomas known as malignant peripheral nerve sheath tumors (MPNSTs). Studies of human tumors and newly developed transgenic mouse models indicate that Schwann cells are the primary neoplastic cell type in neurofibromas and MPNSTs and that development of these peripheral nerve sheath tumors involves mutations of multiple tumor suppressor genes. However, it is widely held that tumor suppressor mutations alone are not sufficient to induce peripheral nerve sheath tumor formation and that dysregulated growth factor signaling cooperates with these mutations to promote neurofibroma and MPNST tumorigenesis. In Part I of this review, we discussed findings demonstrating that a loss of NF1 tumor suppressor gene function in neoplastic Schwann cells is a key early step in neurofibroma formation and that progression from neurofibroma to MPNST is associated with abnormalities of additional tumor suppressor genes, including p53, INK4A, andp27(kip1). In Part II of this review, we consider evidence that dysregulated signaling by specific growth factors and growth factor receptors promotes the proliferation, migration, and survival of neoplastic Schwann cells in neurofibromas and MPNSTs.     

Gene expression profiling in developing human hippocampus

The gene expression profile of developing human hippocampus is of particular interest and importance to neurobiologists devoted to development of the human brain and related diseases. To gain further molecular insight into the developmental and functional characteristics, we analyzed the expression profile of active genes in developing human hippocampus. Expressed sequence tags (ESTs) were selected by sequencing randomly selected clones from an original 3'-directed cDNA library of 150-day human fetal hippocampus, and a digital expression profile of 946 known genes that could be divided into 16 categories was generated. We also used for comparison 14 other expression profiles of related human neural cells/tissues, including human adult hippocampus. To yield more confidence regarding differential expression, a method was applied to attach normalized expression data to genes with a low false-positive rate (<0.05). Finally, hierarchical cluster analysis was used to exhibit related gene expression patterns. Our results are in accordance with anatomical and physiological observations made during the developmental process of the human hippocampus. Furthermore, some novel findings appeared to be unique to our results. The abundant expression of genes for cell surface components and disease-related genes drew our attention. Twenty-four genes are significantly different from adult, and 13 genes might be developing hippocampus-specific candidate genes, including wnt2b and some Alzheimer's disease-related genes. Our results could provide useful information on the ontogeny, development, and function of cells in the human hippocampus at the molecular level and underscore the utility of large-scale, parallel gene expression analyses in the study of complex biological phenomena.