Human blood genomics: distinct profiles for gender, age and neurofibromatosis type 1

doi:10.1016/j.molbrainres.2003.10.014

Molecular Brain Research

Volume 132, Issue 2, 20 December 2004, Pages 155-167

https://doi.org/10.1016/j.molbrainres.2003.10.014 Get rights and content

Abstract

Application of gene expression profiling to human diseases will be limited by availability of tissue samples. It was postulated that germline genetic defects affect blood cells to produce unique expression patterns. This hypothesis was addressed by using a test neurological disease-neurofibromatosis type 1 (NF1), an autosomal dominant genetic disease caused by mutations of the NF1 gene at chromosome 17q11.2. Oligonucleotide arrays were used to survey the blood gene expression pattern of 12 NF1 patients compared to 96 controls. A group of genes related to tissue remodeling, bone development and tumor suppression were down-regulated in NF1 blood samples. In addition, there were blood genomic patterns for gender and age: Y chromosome genes showing higher expression in males, indicating a gene-dosage effect; and genes related to lymphocyte functions showing higher expression in children. The results suggest that genetic mutations can be manifested at the transcriptional level in peripheral blood cells and blood gene expression profiling may be useful for studying phenotypic differences of human genetic diseases and possibly providing diagnostic and prognostic markers.

Introduction

Gene expression profiling using microarray technology has the potential to be a powerful tool in diagnosis and classification of cancers [1], [8], [11], [35]. However, its application to the study of other human diseases may be limited by difficulties in obtaining routine tissue samples from patients. This stimulated us to determine if blood—the most readily available tissue in the human body—can be used for expression profiling of some human diseases. This notion was supported by our previous findings that acute injury models in rats including stroke, cerebral hemorrhage, seizures, hypoglycemia and hypoxia produced a unique gene expression profile in lymphocytes [27]. However, it was unclear whether this could be applied to human diseases.

Leukemias associated with a specific chromosome translocation or a trisomy produced unique expression patterns that were distinct from other types of leukemia [2], [31]. Hereditary breast cancers due to mutations of two separate genes (BRCA1 and BRCA2) exhibit distinct gene expression profiles that differ from the profiles of sporadic breast cancers [9]. These findings raised the possibility that chromosome abnormalities or individual gene mutations might result in characteristic gene expression profiles in a variety of diseases in addition to cancer.

We postulated that mutations of genes, that were passed through the germline and that were expressed in blood cells, would produce downstream transcriptional changes in the blood cells. If so, gene expression profiling of peripheral blood might provide diagnostic and prognostic markers and could provide insights into how the genetic mutations produce end-organ phenotypes.

To address this hypothesis, Affymetrix human U95A arrays were used to survey the gene expression patterns from 108 human blood samples. First, male and female samples were compared to determine if the difference in sex chromosomal composition affected the transcriptional pattern in peripheral blood cells. Then samples from different age groups were compared to determine if development or aging affected blood genomic expression patterns. Finally, neurofibromatosis type 1 (NF1), an autosomal dominant disease caused by the mutation of NF1 gene on chromosome 17q11.2, was used as a test case to determine whether a single gene defect can cause a characteristic gene expression pattern in blood. The results are consistent with the suggestion that genetic defects including chromosomal abnormalities and single gene mutations can be manifested at the transcriptional level in peripheral blood cells. This suggests that blood genomic expression profiling can be used to supplement end-organ tissue genomic studies.

Section snippets

Blood sample collection and processing

After an informed consent was obtained, a peripheral venous blood sample was drawn during 2001–2002 either at the University of Cincinnati Medical Center, Cincinnati Children's Hospital Medical Center or the Cincinnati Veteran Affairs Medical Center. The 108 subjects in this study included healthy people and patients with miscellaneous diagnoses including NF1, epilepsy, bipolar affective disorders, schizophrenia, idiopathic Parkinson's disease, progressive supranuclear palsy, acute migraine

Blood genomic expression pattern for gender

To test whether sex chromosome differences produced differences in blood genomic expression profiles, 26 female blood samples were compared to 26 male blood samples. These samples were randomly selected from 51 female blood samples and 57 male blood samples. There was no bias toward a particular disease when selecting samples and there were no significant age differences between the female and male groups. Using the parametric t-test, 24 genes were differentially expressed in whole blood in

Discussion

Genetic mutations passed through the germline are present in every cell in the body. In the current study, we demonstrate that the NF1 gene mutation or the presence of the Y chromosome can cause specific gene expression patterns in peripheral blood cells even though no obvious phenotypes are observed in the blood. This finding suggests that peripheral blood can be used to study functional genomics and phenotypes of genetic diseases and blood genomic expression profiling holds promise for

Acknowledgements

This study was supported by ES 08822/ES/NIEHS (B.J.A.); by NS28167, AG19561, NS38084, NS42774, NS43252, and an American Heart Association Bugher Award (F.R.S.); Veterans Affairs Medical Research Service and NARSAD Essel Investigator Award (N.W.R.); and by The Neuroscience Institute (T.N.I.), University of Cincinnati (M.P., A.D., F.R.S.).

References (35)

E.O. Berglund et al.
Ataxia and abnormal cerebellar microorganization in mice with ablated contactin gene expression
Neuron
(1999)
R.M. Cawthon et al.
A major segment of the neurofibromatosis type 1 gene: cDNA sequence, genomic structure, and point mutations
Cell
(1990)
T. Kato
Molecular genetics of bipolar disorder
Neurosci. Res
(2001)
E. Maestrini et al.
Identifying autism susceptibility genes
Neuron
(2000)
K. Mirnics et al.
Molecular characterization of schizophrenia viewed by microarray analysis of gene expression in prefrontal cortex
Neuron
(2000)
S. Mundlos et al.
Mutations involving the transcription factor CBFA1 cause cleidocranial dysplasia
Cell
(1997)
H. Sirotkin et al.
Identification of a new human catenin gene family member (ARVCF) from the region deleted in velo-cardio-facial syndrome
Genomics
(1997)
K. Tsutsumi et al.
Functional expression and genomic structure of human chondroitin 6-sulfotransferase
FEBS Lett
(1998)
E.J. Yeoh et al.
Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling
Cancer Cell
(2002)
A.A. Alizadeh et al.
Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling (see comments)
Nature
(2000)

S.A. Armstrong et al.

MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia

Nat. Genet

(2002)

P. Das et al.

Haploinsufficiency of PAX9 is associated with autosomal dominant hypodontia

Hum. Genet

(2002)

M.B. Eisen et al.

Cluster analysis and display of genome-wide expression patterns

Proc. Natl. Acad. Sci. USA

(1998)

E. Gaozza et al.

AATYK: a novel tyrosine kinase induced during growth arrest and apoptosis of myeloid cells

Oncogene

(1997)

T.R. Golub et al.

Molecular classification of cancer: class discovery and class prediction by gene expression monitoring

Science

(1999)

I. Hedenfalk et al.

Gene-expression profiles in hereditary breast cancer

New Engl. J. Med

(2001)

J. Khan et al.

Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks

Nat. Med

(2001)

Cited by (39)

Genome-wide RNA profiling of long-lasting stem cell-like memory CD8 T cells induced by Yellow Fever vaccination in humans
2015, Genomics Data
Citation Excerpt :
The highest weights in the second principal component were assigned to probes corresponding to genes located on the sex chromosomes (Table 3), several of which have been previously shown to be strongly associated with gender [5–7].
The live-attenuated Yellow Fever (YF) vaccine YF-17D induces a broad and polyfunctional CD8 T cell response in humans. Recently, we identified a population of stem cell-like memory CD8 T cells induced by YF-17D that persists at stable frequency for at least 25 years after vaccination. The YF-17D is thus a model system of human CD8 T cell biology that furthermore allows to track and study long-lasting and antigen-specific human memory CD8 T cells. Here, we describe in detail the sample characteristics and preparation of a microarray dataset acquired for genome-wide gene expression profiling of long-lasting YF-specific stem cell-like memory CD8 T cells, compared to the reference CD8 T cell differentiation subsets from total CD8 T cells. We also describe the quality controls, annotations and exploratory analyses of the dataset. The microarray data is available from the Gene Expression Omnibus (GEO) public repository with accession number GSE65804.
Expression profiling in peripheral blood reveals signature for penetrance in DYT1 dystonia
2010, Neurobiology of Disease
Citation Excerpt :
In several neurological disorders, i.e. Huntington's disease or Parkinson's disease, alteration of gene expression in blood cells (Borovecki et al., 2005) or muscle tissue (Luthi-Carter et al., 2002) correlates with changes in gene expression in the brain. Furthermore, the observed expression changes in blood cells reflect changes relevant for disease pathology, although they do not cause a specific phenotype in blood cells (Borovecki et al., 2005; Scherzer et al., 2007; Tang et al., 2004). This motivated us to look for molecular functions and pathways affected in patients suffering from DYT1 dystonia due to a GAG deletion in the TOR1A gene.
DYT1 dystonia is an autosomal-dominantly inherited movement disorder, which is usually caused by a GAG deletion in the TOR1A gene. Due to the reduced penetrance of ∼ 30–40%, the determination of the mutation in a subject is of limited use with regard to actual manifestation of symptoms.
In the present study, we used Affymetrix oligonucleotide microarrays to analyze global gene expression in blood samples of 15 manifesting and 15 non-manifesting mutation carriers in order to identify a susceptibility profile beyond the GAG deletion which is associated with the manifestation of symptoms in DYT1 dystonia.
We identified a genetic signature which distinguished between asymptomatic mutation carriers and symptomatic DYT1 patients with 86.7% sensitivity and 100% specificity. This genetic signature could correctly predict the disease state in an independent test set with a sensitivity of 87.5% and a specificity of 85.7%.
Conclusively, this genetic signature might provide a possibility to distinguish DYT1 patients from asymptomatic mutation carriers.
Gene expression changes in children with autism
2008, Genomics
The objective of this study was to identify gene expression differences in blood differences in children with autism (AU) and autism spectrum disorder (ASD) compared to general population controls. Transcriptional profiles were compared with age- and gender-matched, typically developing children from the general population (GP). The AU group was subdivided based on a history of developmental regression (A–R) or a history of early onset (A–E without regression). Total RNA from blood was processed on human Affymetrix microarrays. Thirty-five children with AU (17 with early onset autism and 18 with autism with regression) and 14 ASD children (who did not meet criteria for AU) were compared to 12 GP children. Unpaired t tests (corrected for multiple comparisons with a false discovery rate of 0.05) detected a number of genes that were regulated more than 1.5-fold for AU versus GP (n = 55 genes), for A–E versus GP (n = 140 genes), for A–R versus GP (n = 20 genes), and for A–R versus A–E (n = 494 genes). No genes were significantly regulated for ASD versus GP. There were 11 genes shared between the comparisons of all autism subgroups to GP (AU, A–E, and A–R versus GP) and these genes were all expressed in natural killer cells and many belonged to the KEGG natural killer cytotoxicity pathway (p = 0.02). A subset of these genes (n = 7) was tested with qRT-PCR and all genes were found to be differentially expressed (p < 0.05). We conclude that the gene expression data support emerging evidence for abnormalities in peripheral blood leukocytes in autism that could represent a genetic and/or environmental predisposition to the disorder.
Transcriptional profiling of Alzheimer blood mononuclear cells by microarray
2007, Neurobiology of Aging
Citation Excerpt :
This conundrum may be circumvented by analysis of AD peripheral tissues in light of mounting evidence of systemic derangements in key cellular functions in affected individuals, including alterations in APP metabolism, antioxidant defenses, acute phase reactants and post-translational protein modifications [13,50,63]. In this regard, expression profiling of fresh blood mononuclear cells (BMC) may offer advantages in deciphering aberrant patterns of gene regulation in AD because (a) these cells are readily procured by simple venipuncture, (b) the CNS communicates with the immune system through multiple molecular, hormonal and neurotransmitter mechanisms [19], (c) abnormal APP expression, altered levels of antioxidant enzymes, oxidative damage to DNA, RNA and protein, deregulated cytokine secretion and augmented rates of apoptosis are features shared by AD brain and lymphocytes [1,31,36,40,50] and (d) BMC have been previously employed in the diagnosis and prognosis of other neurological diseases [28,53,57]. The concept of BMC as a “window” into the CNS has been proposed by Percy et al. in their comprehensive review of the peripheral manifestations of AD [44].
We evaluated pathomechanisms and systemic manifestations of Alzheimer disease (AD), an aging-related dementing neurodegenerative disorder, by expression profiling. Blood mononuclear cell (BMC) transcriptomes of sporadic AD subjects and aged-matched normal elderly controls (NEC) were compared using the human NIA microarray.
Relative to the NEC samples, the Alzheimer BMC exhibited a significant decline in the expression of genes concerned with cytoskeletal maintenance, cellular trafficking, cellular stress response, redox homeostasis, transcription and DNA repair. We observed decreased expression of several genes which may impact amyloid-beta production and the processing of the microtubule-associated protein tau. The microarray results were validated by quantitative real time PCR and revealed gender differences in the levels of altered gene expression.
Our findings attest to the systemic nature of gene dys-regulation in sporadic AD, implicate disruption of cytoskeletal integrity, DNA repair mechanisms and cellular defenses in this condition, and suggest novel pathways of β-amyloid deposition in this disease. BMC are highly accessible and may reflect molecular events germane to the neuropathophysiology of AD.
Expression of reactive oxygen species–related transcripts in egyptian children with autism
2017, Biomarker Insights
Plasma proteomics biomarkers in Alzheimer’s disease: Latest advances and challenges
2016, Methods in Molecular Biology

View all citing articles on Scopus

^☆: Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.molbrainres.2003.10.014.

View full text

Research reportHuman blood genomics: distinct profiles for gender, age and neurofibromatosis type 1☆

Abstract

Introduction

Section snippets

Blood sample collection and processing

Blood genomic expression pattern for gender

Discussion

Acknowledgements

Neuron

Cell

Neurosci. Res

Neuron

Neuron

Cell

Genomics

FEBS Lett

Cancer Cell

Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling (see comments)

Nature

MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia

Nat. Genet

Haploinsufficiency of PAX9 is associated with autosomal dominant hypodontia

Hum. Genet

Cluster analysis and display of genome-wide expression patterns

Proc. Natl. Acad. Sci. USA

AATYK: a novel tyrosine kinase induced during growth arrest and apoptosis of myeloid cells

Oncogene

Molecular classification of cancer: class discovery and class prediction by gene expression monitoring

Science

Gene-expression profiles in hereditary breast cancer

New Engl. J. Med

Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks

Nat. Med

Research report
Human blood genomics: distinct profiles for gender, age and neurofibromatosis type 1☆