MOLECULAR GENETICS OF THE HLA AND CYTOKINE SYSTEMS 
David D. Chaplin, M.D., Ph.D., Associate Investigator 
During the past year investigations in this labora- 
tory have focused on two principal areas: 1) analy- 
sis of the structure of the human major histocom- 
patibility complex (MHC) and 2) characterization of 
the interleukin-1 (IL-1) family of molecules. 
I. Structure of the Human MHC. 
A. General characteristics. The MHC (in humans 
designated the HLA complex) is one of the best 
characterized genetic regions in higher vertebrates. 
It spans 3-4 x 10^ bp of DNA and contains at least 
20 functional genes. The complex is of interest not 
only because of the pivotal role of its gene products 
in many immunological reactions but also because 
it is one of the largest and best characterized mam- 
malian gene clusters. Although in general its gene 
products display related functions, selected genes 
or subsets of genes show discrete regulation, both in 
terms of the developmental and tissue-specific con- 
trol of their expression and of the inter- and intra- 
cellular mediators that modulate their expression. 
The organization of the cluster has been gener- 
ally conserved in all vertebrates studied to date. 
The complex can be divided into three regions that 
encode distinct classes of molecules. The class I 
and II genes encode structurally related polymor- 
phic cell surface glycoproteins that are required for 
antigen presentation and lymphocyte-mediated kill- 
ing of virally infected cells. Primary structural analy- 
ses indicate that the class I and class II genes have 
evolved by duplication of a common ancestral gene 
sequence and comprise two limbs of the immuno- 
globulin supergene family. The class III region, 
characterized in detail by this laboratory, encodes 
apparently unrelated molecules with diverse func- 
tions, including activation of the blood comple- 
ment system, biosynthesis of adrenal steroid hor- 
mones, and regulation of nonspecific inflammatory 
reactions. Additional genes with unknown func- 
tions have recently been identified within this por- 
tion of the MHC. 
B. Polymorphism and linkage disequilibrium. 
Most of the genes within the MHC show a high de- 
gree of polymorphism. Certain alleles are found to 
be present with marked linkage disequilibrium. In 
Caucasians, ~30% of all HLA haplotypes are found 
as linkage disequilibrium groups (or extended hap- 
lotypes). These extended haplotypes are particu- 
larly important because they have been shown to 
be associated at high frequency with a large num- 
ber of human disease states. 
C. Physical characterization of the HLA complex. 
Analyses of the evolution, genetics, and disease as- 
sociations of the MHC remain hampered by the cur- 
rent incomplete knowledge of the structure and 
composition of the full complex. Although the 
human MHC has been extensively studied, only ap- 
proximately half of the complex has been analyzed 
at the molecular level. The remaining half has been 
mapped only at low resolution, using long-range 
restriction fragment analysis. 
To obtain the physical substrate to analyze the 
MHC at high resolution, Dr. Chaplin's laboratory is 
isolating genomic clones spanning the entire com- 
plex. Because of the large size of the MHC, empha- 
sis is being placed on yeast artificial chromosome 
(\AC) vectors for isolation of very large molecular 
clones. The feasibility of this cloning effort has 
been demonstrated. Twelve \AC clones containing 
HLA sequences have been isolated. They average 
—270 kb in length and together represent more 
than half of the predicted structure of the MHC. In- 
dividual clones establish for the first time physical 
linkages of certain loci. For example, one \AC of 
210 kb contains both the class I HLA-B and -C loci 
and establishes that they are separated by —100 kb. 
Another clone links the class II HLA-DQa, -DQP, 
-DRa, and -DR(3 loci. Future studies will focus first 
on completion of the \AC map and on high-resolu- 
tion analysis of the structure of each Y\C clone. 
Subsequently this mapping data will be applied to 
a comparison of the structures of different MHC ex- 
tended haplotypes and to a search for unrecog- 
nized genes within the newly cloned regions. 
II. Characterization of Mouse IL-1. 
Molecular and cell biological analyses first identi- 
fied two forms of IL-1 in humans. Although the 
genes encoding these two forms (IL-la and IL-1 (3) 
share only —65% nucleotide sequence identity, the 
protein products they encode show identical recep- 
tor binding affinities and indistinguishable biologi- 
cal activities. Both molecules are synthesized as 
—31 kDa intracellular promolecules and are found 
extracellularly as carboxyl-terminal 17 kDa pro- 
cessed fragments. Neither promolecule contains a 
Continued 
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