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The Journal of Immunology, 1999, 162: 2581-2588.
Copyright © 1999 by The American Association of Immunologists

Genome-Wide Linkage Analysis of Chronic Relapsing Experimental Autoimmune Encephalomyelitis in the Rat Identifies a Major Susceptibility Locus on Chromosome 91

Ingrid Dahlman2,*, Lena Jacobsson{ddagger}, Anna Glaser{ddagger}, Johnny C. Lorentzen{dagger}, Magnus Andersson*, Holger Luthman{ddagger} and Tomas Olsson*

* Neuroimmunology Unit and {dagger} Rheumatology Unit, Department of Medicine, Karolinska Hospital, Stockholm, Sweden; and {ddagger} Rolf Luft Center for Diabetes Research, Department of Molecular Medicine, Karolinska Hospital, Stockholm, Sweden


    Abstract
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
The immunization of inbred Dark Agouti (DA) rats with an emulsion containing homogenized spinal cord and CFA induces chronic relapsing experimental autoimmune encephalomyelitis (EAE), a disease with many similarities to multiple sclerosis. We report here the first genome-wide search for quantitative trait loci regulating EAE in the rat using this model. We identified one quantitative trait locus on chromosome 9, Eae4, in a [DA(RT1av1) x BN(RT1n)]F2 intercross showing linkage to disease susceptibility and expression of mRNA for the proinflammatory cytokine IFN-{gamma} in the spinal cord. Eae4 had a larger influence on disease incidence among rats that were homozygous for the RT1av1 MHC haplotype (RT1av1 rats) compared with RT1n/av1 rats, suggesting an interaction between Eae4 and the MHC. Homozygosity for the DA allele at markers in Eae4 and in the MHC was sufficient for EAE. Thus, Eae4 is a major genetic factor determining susceptibility to EAE in this cross of DA rats. In addition, there was support for linkage to phenotypes of EAE on chromosomes 1, 2, 5, 7, 8, 12, and 15. The chromosome 12 region has been shown previously to predispose DA rats to arthritis, and the chromosome 2 region is syntenic to Eae3 in mice. We conclude that Eae4 and probably the other identified genome regions harbor genes regulating susceptibility to neuroinflammatory disease. The identification and functional characterization of these genes may disclose critical events in the pathogenesis of multiple sclerosis; understanding these events could be essential for the development of new therapies against the disease.


    Introduction
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Multiple sclerosis (MS)3 is a chronic inflammatory disease of the central nervous system (CNS) causing neurological defects. The etiology of MS is unknown, but epidemiological studies have shown that both genetic and environmental factors influence disease susceptibility 1 . The identification and functional characterization of such genes and environmental factors will lead to a better understanding of the etiology and pathogenesis of MS, which is essential for the development of new therapies against the disease.

The first evidence of a genetic influence on susceptibility to MS was the demonstration of an association between the disease and certain HLA haplotypes 2, 3 . The familial aggregation of MS has later been shown to be genetically determined 4, 5 . Furthermore, the inheritance pattern (e.g., the drop in concordance rate for MS between monozygotic (~25%) and dizygotic twins (~2%) 6, 7) suggests that MS is a complex disease that is influenced by several genes 8 and probably by environmental factors. A number of genes with a putative influence on the inflammatory process in MS have been tested for association with or linkage to MS. The TCR {alpha} 9, 10 and ß chains 11, 12, 13, 14, 15 , myelin basic protein 16 , and Ig heavy chain loci 17, 18, 19 have shown association or linkage to MS in some studies, but these results have not been confirmed in other studies 20, 21, 22, 23, 24, 25, 26 . Furthermore, a number of chromosome regions that may harbor MS-predisposing genes have been identified in four genome scans of MS families 27, 28, 29, 30 , but none of these fulfill the criteria for genome-wide significant linkage 31 . This may be due to genetic heterogeneity (e.g., different genes predispose individuals to disease in different families) and/or to a low impact on disease susceptibility of MS-regulating genes. As a consequence, very large family materials will be required to detect linkage 32 , and such materials may be difficult to collect.

An alternative to human genetic studies is to define the quantitative trait loci (QTLs) regulating the proper experimental models of the disease, which may lead either to the identification of genes predisposing to MS or to the definition of disease pathways. Immunizing certain inbred rat and mouse strains with CNS Ags induces experimental autoimmune encephalomyelitis (EAE), an inflammatory disease of the CNS resembling MS. A few QTLs influencing EAE susceptibility have been identified in the mouse 33, 34, 35 . The human syntenic chromosome region to one of these QTLs has some impact on MS in a Finnish MS population 36 . However, it is likely that other animal models for MS will reveal additional genes of interest.

Most EAE models are monophasic with sparse or no demyelination 37 . A more MS-like relapsing/remitting demyelinating disease can be induced in Dark Agouti (DA) rats by immunization with homogenized whole spinal cord and adjuvant 38 . In this DA rat model, there is prolonged inflammatory activity and expression of proinflammatory cytokines such as IFN-{gamma} in the CNS 39 . We have demonstrated previously that the incidence of severe EAE in DA rats is almost 100% after immunization with spinal cord, whereas Brown Norway (BN) rats are resistant to EAE induction; this difference is controlled by both MHC and non-MHC genes 40 .

We report here the first genome-wide search for non-MHC QTLs showing linkage to EAE in the rat. A new MHC-dependent QTL with major influence on EAE was identified in this F2 intercross between DA(RT1av1) and BN(RT1n) rats.


    Materials and Methods
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Animal breeding

DA rats were originally obtained from Zentralinstitut für Versuchstierzucht (Hannover, Germany); BN rats were provided by Prof. Hedrich (Medizinische Hochschule, Hannover, Germany). An F2 intercross, originating from DA females and BN males, was bred at the Biomedical Center in Uppsala, Sweden. All rats were bred and kept under specific pathogen-free conditions. They were free from pathogens as determined by a health monitoring program for rats at the National Veterinary Institute in Uppsala.

Induction and clinical assessment of EAE

Groups of ~50 F2 rats at a time were immunized and clinically evaluated in Uppsala or at the Karolinska Institute in Stockholm. Rats were between 11 and 17 wk old at the start of the experiment.

The rats were anesthetized with ether and injected s.c. at the dorsal base of the tail with 200 µl of emulsion containing homogenized DA rat spinal cord mixed 1/1 (w/v) with IFA (Difco, Detroit, MI) complemented with 20 mg/ml of Mycobacterium tuberculosis, strain 37 RA (Difco) (CFA) 38 . Rats were examined daily for signs of EAE and weighed every fourth day from day 7 postimmunization until sacrifice at day 30 postimmunization. Clinical scoring was as follows: 0 = no illness, 1 = flaccid tail, 2 = moderate paraparesis (i.e., unsteady walk), 3 = severe paraparesis (i.e., lying down), and 4 = tetraparesis or moribund. An index of maximum weight loss was calculated as follows: (weight at immunization - lowest weight after immunization)/weight at immunization.

Immunohistochemistry

To obtain a phenotype measuring the degree of inflammation in the spinal cord, infiltrating cells were analyzed as described previously 38 . Briefly, ~15 mm of the lumbar spinal cord was snap-frozen in liquid nitrogen. Cryostat sections were melted onto microscopic slides and exposed to appropriate dilutions of the following mAbs to rat cell surface Ags: OX39 = anti-IL-2R 41 (Seralab, Cramley-Down, U.K.); OX6 = anti-MHC class II 42 . OX6 was purified from the culture supernatants of hybridomas 43 . The avidin-biotin peroxidase method was used for staining (ABC Vectastain Elite kit, Vector Laboratories, Burlingame, CA). Omission of the primary Ab served as a negative control. Sections of peripheral lymphoid tissue served as positive controls. The spinal cord sections from different rats were assessed without access to other phenotype or genotype data for individual rats. The number of OX39-stained cells on whole sections was counted using x20 magnification. The areas of the sections were measured by image analysis, and the number of stained cells/100 mm2 was calculated 44 . OX6-stained infiltrates were semiquantitatively scored as follows: 0 = no cellular infiltrates (i.e., no staining), 1 = a few perivascular infiltrates, 2 = perivascular infiltrates and moderate staining of the parenchyma, and 3 = perivascular infiltrates and massive staining of the parenchyma.

In situ hybridization for detection of IFN-{gamma} mRNA

IFN-{gamma} mRNA expression in the spinal cord was assessed with in situ hybridization in spinal cord sections from the first 174 immunized rats of the total 352 rats. In situ hybridization was performed essentially as described previously 45 . Briefly, cryostat sections of lumbar spinal cords were thaw-mounted onto ProbeOn slides (Fisher, Pittsburgh, PA). A mixture of four different labeled synthetic oligonucleotide probes was used to detect IFN-{gamma} mRNA. A sense probe with a nucleotide sequence for exon 4 of IFN-{gamma} was used as a control. [{alpha}-35S]Deoxyadenosine 5'-{alpha}-thiotriphosphate (New England Nuclear, Boston, MA) and terminal deoxynucleotidyl transferase (Amersham, Little Chalfont, U.K.) were used for the labeling of oligonucleotides. After emulsion autoradiography, cells expressing numerous grains over their cytoplasm were counted as reported previously 45 , and numbers of positive cells/100 mm2 were calculated 44 .

Genome scan and statistical analysis

Genomic DNA from the F2 animals were prepared from tail tips according to a standard protocol 46 . Genotypes were determined by amplification of polymorphic DNA fragments containing simple sequence length polymorphisms (SSLPs) by PCR essentially as described previously 47 , except that the primers were end-labeled with [{gamma}-33P]ATP. Primers were obtained from Research Genetics (Huntsville, AL) or from Genset (Paris, France). Some primers were a kind gift of Dr. Howard J. Jacobs (Whitehead Institute for Biomedical Research, Cambridge, MA). The PCR products were size-fractionated on 6% polyacrylamide gels and visualized by autoradiography. All genotypes were scored manually and double-checked.

The MHC haplotypes of individual rats were determined with an SSLP in the TNF-{alpha} gene 48 .

RT1n/av1 (n = 180) and RT1av1 (n = 91) rats were analyzed as separate groups to eliminate any MHC influence on EAE susceptibility. The RT1n rats (n = 81) were not analyzed further, because only five of these rats developed EAE. A genome-wide scan was performed on 45 RT1n/av1 rats that were selected to include the 23 rats with the highest cumulative score and 22 rats with no clinical signs of EAE. Both groups had a similar distribution with regard to sex and age at immunization. They were also distributed equally between different immunization sessions. These rats were genotyped with 228 SSLPs (Map Version 2.0 MGH/MIT/March 1997, http://www.genome.wi.mit.edu/rat/public/mar97/index.html). The genotype at each marker was determined as DA homozygous (D/D), heterozygous (D/B), or BN homozygous (B/B). A few genotypes were excluded because the genotype was difficult to determine or no band had been amplified. However, the median number of genotypes determined for each marker was 45.

Marker mapping was performed with the MAPMAKER computer package 49 . Approximately 77% of the genome laid within a distance of 10 cM from an SSLP (Table IGo).


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Table I. Chromosomal distribution of 228 SSLPs in 45 (DA x BN) F2 rats

 
The Pearson {chi}2 test statistic with 2 degrees of freedom (df) was used to determine whether there was a significant difference (p <= 0.05) in genotype distribution at individual markers among the 45 rats between rats with a positive clinical score and rats with no clinical signs of EAE. For such markers, the genotypes at nearby markers were also determined. The remaining 135 RT1n/av1 rats were also genotyped in these genome regions. The median number of genotypes determined for each marker was 178. Next, all 180 RT1n/av1 rats were analyzed using the Kruskal-Wallis test to determine whether the different genotypes at individual markers differed with regard to 1) clinical phenotypes: (a) maximum score and (b) score at different days; and 2) histopathological phenotypes in the CNS: (a) degree of MHC class II-positive infiltrates, (b) number of IL-2R-expressing cells, and (c) number of IFN-{gamma} mRNA-expressing cells. Finally, in those regions in which there was support for an influence on any of the studied phenotypes (p <= 0.01) when analyzing all RT1n/av1 rats, the 91 RT1av1 rats were genotyped. In this group, the median number of genotypes determined for each marker was 90.

To estimate the relative influence on the risk of developing the disease associated with an allele at a QTL, an odds ratio was calculated as follows: (affected with the allele x unaffected without the allele)/(affected without the allele x unaffected with the allele) 50 .

Kendall’s coefficient, {tau}, was applied for a nonparametric analysis of correlation.


    Results
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Phenotype distribution

As reported previously, DA rats are highly susceptible to protracted/relapsing EAE, whereas BN rats are resistant 40 . In the F2 intercross reported here, 136 of the 352 rats (39%) showed some degree of clinical signs of EAE (Fig. 1GoA). A total of 81 rats (23%) displayed severe disease with paraparesis. The onset of disease was from day 10 postimmunization. Most rats had recovered completely by day 20, and only 25 rats showed signs of neurological defects for >7 days in total (Fig. 1GoB), some of which developed a relapsing disease course. Six rats died or were sacrificed because of severe tetraparesis during the experiment. Maximum disease score was positively correlated with weight loss ({tau} = 0.5835). Sex, body weight, or age at immunization did not have a significant influence on the incidence of EAE (data not shown).



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FIGURE 1. Distribution of clinical score and histopathological phenotypes in the F2 generation. (DA x BN)F2 rats (n = 352) were immunized with spinal cord in CFA. All rats were sacrificed at day 30 postimmunization. The number of rats was plotted against the maximum clinical score (A), number of days with positive clinical score (B), degree of MHC class II infiltration in the spinal cord as described in Materials and Methods. (C), number of IL-2R-expressing cells in the spinal cord/100 mm2 (D), and number of IFN-{gamma} mRNA-expressing cells in spinal cord/100 mm2 (E).

 
We subsequently assessed how the clinical disease was related to the histopathological phenotypes. Maximum disease score was positively correlated with the degree of MHC class II-positive infiltration ({tau} = 0.3583) as well as with the number of IL-2R-expressing cells ({tau} = 0.2165) and IFN-{gamma} mRNA-expressing cells ({tau} = 0.1568) in the spinal cord. IFN-{gamma} mRNA expression showed a stronger correlation with EAE score late after immunization (e.g., {tau} = 0.2872 with score on day 24 postimmunization). Fig. 1Go, C–E shows the distribution of the histopathological phenotypes in the F2 generation.

Genetic regulation of EAE phenotypes

MHC had a significant influence on maximum score, due to an influence on the incidence of EAE but not on disease severity (i.e., maximum score among affected rats) (Table IIGo). The RT1av1 MHC haplotype was EAE-predisposing (Table IIIGo). Genes within the MHC also controlled the degree of MHC class II-positive infiltration and the number of IL-2R- and IFN-{gamma} mRNA-expressing cells in the spinal cord (Table IIGo).


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Table II. MHC influence of EAE phenotypes1

 

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Table III. MHC influence on the incidence of EAE

 
The non-MHC genetic regulation of EAE differed between the RT1av1 and the RT1n/av1 rats, respectively (Table IVGo). Although there was support for an influence on all measured phenotypes for some genome regions, others seemed to influence only one phenotype.


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Table IV. Linkage analysis of EAE phenotypes

 
Due to multiple tests of the null hypothesis in a genome-wide linkage study, random deviations exceeding the nominal p value of 0.05 are expected to occur frequently 31 . A nominal p value of 5.2 x 10-5 is therefore necessary for a genome-wide significance of 5%. We have further increased this threshold to p = 5.2 x 10-6 due to the analysis of multiple phenotypes and the separate analysis of RT1n/av1 and RT1av1 rats, for a total of ten different analyses. This is a conservative threshold, because it assumes that the different phenotypes and groups are independent. In one region on rat chromosome 9, the observed p value was 4.6 x 10-6 for linkage to maximum score (Table IVGo). This QTL was designated Eae4. Eae4 had a larger influence on EAE susceptibility among the RT1av1 rats than among the RT1n/av1 rats. The odds ratio for Eae4 was 15.4 in the former group compared with 1.8 in the latter, assuming a recessive DA predisposing influence on EAE (Table VGo). The observed frequency of EAE affected rats among RT1av1 rats homozygous for DA alleles at the marker D9Mgh5 was slightly higher than expected if Eae4 and the MHC had an additive effect on EAE susceptibility (calculation not shown).


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Table V. Interaction between Eae4 and MHC

 
Next, we analyzed the influence of Eae4 on EAE in more detail among the RT1av1 rats. The linkage of this locus to maximum disease score was due to an influence on the incidence but not the severity of EAE (Table VIGo). Eae4 also influenced the incidence of EAE late after immunization. This influence was compatible with a recessively acting EAE-permissive DA allele. Finally, Eae4 showed linkage to the number of IFN-{gamma} mRNA-expressing cells in the spinal cord (Fig. 2Go).


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Table VI. Eae4 among RT1av1 rats, linkage to EAE phenotypes

 


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FIGURE 2. Influence of Eae4 on IFN-{gamma} expression. (DA x BN)F2 rats were immunized with spinal cord in CFA and sacrificed at day 30 postimmunization. The rats with at least one D allele with the marker in the TNF-{alpha} gene in the MHC class III region (n = 115), were grouped according to genotype at the marker D9Rat46 on chromosome 9. Columns show the mean number of IFN-{gamma}-expressing cells in the spinal cord/100 mm2. Bars show the SE. *, p = 8 x 10-4.

 
No other chromosomal regions fulfilled the stringent criteria for significant linkage. However, in regions on chromosomes 2, 7, and 8, there was support for linkage to maximum score (Table IVGo). On chromosome 2, at the marker D2Mgh11, the BN allele was EAE predisposing. On chromosome 7, at the marker D7Mgh9, there was support for linkage to maximum score and degree of inflammation in the spinal cord. The regions on chromosomes 2 and 7 only showed evidence of linkage to EAE phenotypes among the RT1n/av1 rats. In addition, in a region on chromosome 8, there was support for linkage to maximum score among both the RT1av1 and RT1n/av1 rats (p = 5.8 x 10-3). At the marker D8Mit7, heterozygosity predisposed to EAE.

In other chromosomal regions, there was support for linkage to the degree of inflammation in the spinal cord. Notably, on chromosome 12, the marker MDH2 was linked to number of IL-2R-expressing cells among both the RT1av1 and RT1n/av1 rats (p = 3.0 x 10-4). Rats with DA alleles at this marker had a higher number of IL-2R-expressing cells in the spinal cord. Furthermore, on chromosomes 8 and 15, there was support for linkage to the number of IL-2R-expressing cells. Finally, regions on chromosomes 1, 5, and 12 showed suggestive linkage to the degree of MHC class II expression in the spinal cord.


    Discussion
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Here, we report a new QTL outside the MHC controlling susceptibility to relapsing EAE and a number of additional chromosomal regions with support for linkage to EAE phenotypes in the rat. The influence of these regions on EAE is MHC haplotype-dependent.

Eae4 on chromosome 9 had a major influence on the incidence of EAE among the RT1av1 rats. This QTL also showed support for linkage to the incidence of EAE late after immunization, which suggests that Eae4 promotes the chronic disease course of EAE in DA rats. This possibility is supported by two additional observations. First, the influence of Eae4 on the incidence of EAE late after immunization was compatible with recessively acting genes, and the inheritance pattern of the protracted relapsing disease course of EAE in the DA rat has been shown in a previous study to be compatible with recessively acting DA alleles 40 . Second, rats homozygous for the DA allele at markers in this region had a higher number of IFN-{gamma} mRNA-expressing cells in the spinal cord late after immunization; IFN-{gamma} expression has been shown previously to correlate with clinical signs of EAE 39, 45, 51 .

In view of the strong impact of Eae4 on disease, it is important to identify the disease susceptibility gene or genes within this QTL and to define the pathogenic mechanisms. The demonstrated influence of Eae4 on IFN-{gamma} mRNA expression may be pathogenic in EAE. The most direct evidence of IFN-{gamma}-mediated pathogenic mechanisms in neuroinflammation is the observation that transgenic IFN-{gamma} expression in the CNS causes MS-like inflammatory lesions 52, 53 . Although IFN-{gamma} has a potential pathogenic influence in EAE, other studies suggest that IFN-{gamma} may just be a disease marker 54 . We are now breeding Eae4 congenic strains that will enable detailed studies of the pathogenic mechanisms regulated by this QTL. Possible candidate genes located in the region of Eae4 on chromosome 9 are also analyzed for influence on EAE.

Eae4 had a larger influence on EAE among the RT1av1 rats than among the RT1n/av1 rats. A similar difference between individuals homozygous vs heterozygous for an MHC haplotype has been shown in insulin-dependent diabetes 55 . At present, we do not know the cause of this dose-dependent influence of EAE, but it will be analyzed further by studying the influence on EAE of Eae4 congenic rats that carry different MHC haplotypes.

The region on chromosome 2 with support for an influence on the clinical signs of EAE in the present study is located in a region syntenic with Eae3, a QTL in the mouse controlling susceptibility to EAE 33, 56 . This influence on EAE in two species is a strong argument in favor of the importance of the chromosome 2 region in EAE. In this case, the BN allele was EAE-permissive, which shows that relatively disease-resistant strains also carry disease-predisposing genes. This finding may not be surprising with regard to BN rats, considering the strong protective effect of the RT1n MHC haplotype expressed by this strain.

In addition, a region on chromosome 12 showed suggestive linkage to IL-2R expression in the spinal cord. This region colocalizes with a QTL controlling arthritis in DA rats 57 , which suggests that this region harbors one or more genes regulating different organ-specific inflammatory diseases.

It is notable that no region showed genome-wide significant linkage to EAE phenotypes among the RT1n/av1 rats. This could be due to the fact that the genome scan covered <100% of the genome or, more likely, to the fact that the genetic regulation of EAE is complex and involves MHC/non-MHC interactions.

We conclude that the complex genetic regulation of EAE seen in this study may mimic the situation in MS and illustrates the difficulties in human studies to find genes regulating disease. Despite this complexity, our results show that animal studies provide a practical method to dissect the genetic control of neuroinflammatory disease. For this purpose, it will be important to identify and functionally characterize the genes within Eae4 and in the regions on chromosomes 2, 7, 8, and 12 showing linkage to EAE phenotypes, because this may unravel disease pathways of importance in MS.


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Table 4A. Continued

 

    Footnotes
 
1 This investigation was supported in part by grants from the Swedish Medical Research Council, the Swedish Society for Neurologically Disabled, the Swedish Foundation for Strategic Research, the Swedish Diabetes Association, the Arbetsmarknadens Forsakrings Aktiebolag Foundation, and the following foundations: Novo Nordisk, Petrus och Augusta Hedlund, Ulf Widengrens Minne, and Tore Nilsson. Back

2 Address correspondence and reprint requests to Dr. Ingrid Dahlman, Unit of Neuroimmunology, CMM L8:04, Karolinska Hospital, 171 76 Stockholm, Sweden. E-mail: Back

3 Abbreviations used in this paper: MS, multiple sclerosis; CNS, central nervous system; QTL, quantitative trait locus; DA, Dark Agouti; BN, Brown Norway; EAE, experimental autoimmune encephalomyelitis; SSLP, simple sequence length polymorphism; df, degree(s) of freedom. Back

Received for publication May 21, 1998. Accepted for publication November 16, 1998.


    References
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 

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