1) Department of Ophthalmology and Visual Science, Yale University School of ... A subtractive cDNA library was developed for the purpose of identifying ... in the ciliary body, complement component C4; α2 macroglobulin; selenoprotein-P; ...
J. Biochem. 118, 921-931 (1995)
Isolation and Characterization of Cell-Specific cDNA Clones from a Subtractive Library of the Ocular Ciliary Body of a Single Normal Human Donor: Transcription and Synthesis of Plasma Proteins1 Julio
Escribano,2
Department
of
CT
USA
06520,
Received
Javier
Ophthalmology
for publication,
A subtractive
of
significant
homologies
significant
genes
ciliary
body,
protein other confirmed
or
proteins, [35S]methionine of synthesis
the
Key
in
the
humor
mechanisms of
yet
secretory
vessels, ed
smooth
adrenergic
bilayer,
the
ciliary by
gap
(3), (4-6). epithelia
This
work
and
The
differences
barrier, (7).
The
tissues
of
was
supported
whereas
aqueous
the
the
segment
research
by
blood
forming
the (NPE) to
each
marked to
grant
and ƒÀ
and
layer
humor
anterior by
(IOP)
in comparison
NPE
carrier
establishes
PE
layer
fluid
nourishes of
from
the the
a
forms
a the
eye
and
National
Institutes of Health EY-04873. Additional support was from a Vision Core Grant EY-00785, and Research to Prevent Blindness, Inc. J. E. was a recipient of a postdoctoral fellowship from the Ministerio de Education 2 Present
y Ciencia of Spain. address: Section de
Regional, Spain. To whom
3
- 2742, Fax: mail.yale.edu
Universidad
de
correspondence +1-203-785-7694,
Vol. 118, No. 5, 1995
Biotecnologia
Castilla-La should
be e-mail:
, Instituto de Desarrollo Mancha, 02071 Albacete,
addressed: miguel
group
of
biologically
expression
cells
this
to
two
the
apolipo these and factor)
(pigmented,
that
nonpig
human
metabolically
are work
in
and
Antibodies epithelium-derived
that the in aqueous
number revealed
plasma
labeled
with
ciliary body is an organ humor. These results imported
should affecting
be the
from
outside
very
useful
ciliary
body,
of for or
C4, ƒ¿2
macroglobulin,
ocular
ciliary
exhibits immunosuppresive and antioxidant properties (8, 9). The rate of secretion and drainage of aqueous humor determines the level of IOP, which in mammalians follows a circadian rhythm influenced by a light-dark cycle (10). Previous studies have documented that elevated IOP is a high risk factor in developing primary open-angle glau coma, a severe eye disease that can lead to blindness. Very little is known about the cellular and molecular biology of the ciliary body and aqueous humor secretion. Recently, our laboratory applied several immunoscreening strategies to isolate and characterize genes highly express ed in the ocular ciliary epithelium from directional expres sion cDNA libraries (6, 11). These studies suggest that the ocular ciliary epithelium exhibits many functions other than secretory. Specifically, the high levels of expression of genes coding for anti-oxidative, and detoxification enzymes suggest an additional functional role in protecting the anterior segment of the eye from oxidative stress (6, 9). We sought to identify biologically significant genes, conferring selective phenotype to the different cell types of the ciliary body, by characterizing a subtractive cDNA library from the ciliary body of a normal human single donor. The construction of highly representative cDNA libraries is critical to determine the tissue-specific func tions. In the case of the ciliary body, which is comprised of distinct cell types, the specificity of expression might be
regulates
exhibit
receptors, the
A
evidence
abnormalities
component
subunit ƒ¿
neurotransmitter
ocular
a large
pressure.
coupled
cells
genes.
humor in
of
genes regulating
databases
transcriptional
are
aqueous
innervat
and
Na+,K+-ATPase
Furthermore,
in
sequence
epithelial
suggesting present
in
for
protein
hybridization. pigment
ciliary
of a bilayer
cells
NPE
and
reported
nonpigmented
polarized 2).
Haven,
cell-specific
selenoprotein-P;
provide
explants, proteins
containing
epithelial
physiological
blood-aqueous
avascular 1
are
including
proteins leaky
The
(1,
(CB)
postsynaptically
(PE),
cells,
and cells,
isoforms
tight
fibers.
junctions
biochemical PE
cells
pigmented
epithelial
other
the
muscle
St., New
library.
pressure
stroma
have
and ƒ¿2-macroglobulin
complement
is comprised
a
and
known
in
genes
body
CB
DNA
acid
to
We
intraocular
D,
ciliary
The
Cedar
responsible
macroglobulin;
proteins
of
intraocular
cells,
330
identifying
tissue
Partial
Northern protein
library
subtractive
the
unknown.
by
C4
candidate
regulation
and
epithelial
and
by
eye,
C4; ƒ¿2
of
a
nucleic
known
cells.
cDNA
apolipoprotein
secretion
of
not
plasma
selenoprotein-P,
mammalian
aqueous
the
words:
body,
In
that
potential
involved
of Medicine,
purpose
independently
processes of plasma
subtractive
identifying
School
body,
expression
ciliary secretion
notion
The
90
component
and the
eye.
least
the
pressure.
previously
endothelial
in
challenge
at
cell-restricted
vascular
for
searches
component
complement
University
ciliary
further demonstrated (i.e., tyrosinase-related
their
mented),
to were
complement
D, were proteins
Yale
intraocular
homology
that
Coca-Prados3
developed ocular
and
and
Science,
was
human
secretion
clones
Miguel
1, 1995
the
humor
and
Visual
library
within
cDNA
and
June
cDNA
expressed aqueous
Ortego,
Tel:
+1-203-785
coca-prados@quick
921
922
J. Escribano
determined type.
by
By
from
the
clones
genes
selecting
body
this
enriching
subtractive an
directional
a high
the
GenBank/EMBL
level
of
to
endocrine,
immune
encoded
the
proteins
(i.e.,
globulin)
was
also
processes
explants
plasma ciliary of
by
C4
labeled
in
are to
ized
genes
synthesized the protein
these
AND
Directional
cDNA
phagemid this work. the
ciliary
bodies
primary
bone,
and
cancer.
of
2
that within composition
The
of
sense
the
obtained
by
the
cDNA
eyes
enucleation. of
and
La
column
chromatography,
400-bp
were
and
titer
the
of
and
library
amplified
and
contained
the
the DNA
phagemid
procedures
(12),
cDNA
poly(A)+ ODM-2,
RNA using a human previously characterized
lower
in
than
cDNA
[as
body phage
protocol ed with
(Stratagene). VCS-M13
ity and
NH4-acetate
and
and
cells XR and
of infections significant
was
in
were ciliary
at 10:1
following
infected body
incubated
sense
tics,
NY).
and
the
found.
1:2
4h
12•~106 and
at 37•Ž.
(helper: were
cell)
detected
a pre-hybridization
and
multiplic also yield
step
specific
resulted
fied
this
step,
of
was EcoRI
in a considerable
Diagnos
extracted the in
to
of
ssDNA
block
and
Mole
carried the
pBluescript T3
by
presence
was
of
by
PCR
48-bp
the
169-bp
out, multi
phagemid T7
reduction
promoters. in
multicloning
pBluescript using
T3/T7
were
generated
multicloning used
(Enzo
the
loss
of
clones.
For
- and
polymerase,
in
the
Xhol
RNA
Region
by
with biotinylated
hybridization
flanked
10M
inserts
vitro
kit
step
of
DNA
digested
precipitated
1
amplifica
phenol-chloro
ethanol.
T3
480
consisted 63•Ž for
volume
purified,
sequences
are
by
in
at
Cycler
After
of 0.1
was
Multicloning
polylinker)
which
non-recombinant
pfu from the 12•~107 R408
in the
the
performed
This
and ethanol.
5 min.
labeling
RNA
1.5 cycle
amplification
Thermal
of
RNA
and
polymerization
purified,
presence
Biotinylated
(or
1mM
(T7),
by
synthesize
we
12•~107
were
the
BioProbe
of
ssDNA,
and
cold
were to
subtractive
was compar ssDNA, and
Other
kb
of
cules-Before
cloning
primers. PCR of 0.25mM
denaturation
extracted
volume
(ss)
the
initial
for
modified and T7
polymerase,
presence
was
manufacturer's
Routinely
3
in
ENZO
4•Ž,
phenol-chloroform, NH4-acetate
human
using
at
templates
RNA(+)
line, of
using
primer
DNA
72•Ž
in the
0.3-1.6
as
the
(ssDNA) the
cells
phage R408 in rescuing
with library
for
differences
from
XL1-Blue
The helper its efficiency was
DNA
cooled
from used
using
Single-Stranded
SK(-)] in
and
difference
phage
no
precipitated
from
libraries
phagemid
library
R408
significant
helper
to
pBluescript
cDNA
helper
XL1-Blue ă-Uni-Zap
cDNA
Libraries
single-stranded
rescued
no
and
1.5•~1010
constructed
PCR
stan
phagemid
Cetus, Norwalk, CT). The process at 94•Ž for 1 min, annealing at at
double by
in
followed
Elmer
the cDNA cells,
The
volumes
63•Ž
was
polymerization
ranging
epithelial cell The proportion
amplified
DNA
at
This
a Perkin
form
an
excising
isolated
DNA
with
first
inserts
reverse
annealing
min.
on
Blocking of
DNA-Antisense
ciliary
ciliary (12).
1.5
tion
were
AmpTaq 1mM
inserts ODM-2
the ODM-2 and SOLR
then
cDNA
for
the
Stratagene.
was
70•Ž
dsDNA-Bio
by from phage
of
cycles,
1 min,
for
and
unamplified
contained
40
min,
was
recombinants
was
for
for
72•Ž
1%.
Conversion
was
estimated
MgCl2
of
the
dsDNA
from
DNA helper
and
and
from
accomplished
DNA
(T3),
by than
size
5U
(Perkin Elmer of denaturation
cloning
insert
mix, primer
The as
polymerase
2 min,
from
(5•Œ-GTAATACGACTCACTATAGGGCG-3•Œ) reactions were carried out in 300ƒÊl
performed
bigger Xhol
for
RNA
recommendations
kit
manufacturer's fractionated
average
library
both
synthesized
and
library
A
of
DNA
50•Ž
pBluescript SK(-) were amplified by T3 (5•Œ-GCAATTAACCCTCACTAAAGGGAA-3•Œ)
forward
cells.
phagemid
amplification
was
stranded
at 94•Ž
24h
at
phagemid ExAssist
following
mM
National
synthesis
inserts
million
pfu/ml.
non-recombinants
were
to size
an
One
amplified
second
the
This
XL1-Blue
synthesized
DNA
ssDNA
electrotransformation
AmpliTaq
was
DNA
the
(5•Œ-GCAATTAACCCTC
Biotinylated
PCR
(ds) by
ssDNA
primer
sug
was evaluated and the dsDNA synthes
coli
CT)
RNA
library.
nucleotide
and breast
within
EcoRI
The
donor liver
was
a cDNA
cDNAs the
phage.
pfu/ml.
death
strands using
into
in
through
CA) according cDNAs were
XR
4•~106
of
(NDRI)
second
subcloned
of ă-Uni-Zap
1-kb,
cause
RNA,
Jolla, The
female
metastasis
obtained
poly(A)+
(Stratagene, recommendations.
was
XR
were used in RNA from
a 34-year-old
Interchange
First
8ƒÊg
of
death
were
Vectors-Two
after
and
of
tinylated
enzymes,
previously
obtained
using
Wilton,
eliminated
Double-Stranded
ssDNA,
T3
pBluescript SK(-) library using the
in ă-Uni-ZAP
La Jolla, CA) from poly(A)+
secondary
Research
Phagemid
constructed
eyes
cause whose
Disease
from
in
libraries
the
a modified
was
above, with
as
contami
restriction as
units
synthesized
Preparation
of ciliary
METHODS
vectors (Stratagene, One was constructed
whose
sites
Libraries
cDNA
into
Escherichia
was
dard
directional
from
(Perkin-Elmer, 4 min.
humor.
MATERIALS
vitro
Xhol
as described titer obtained
electrocompetent
template,
and ƒ¿2-macro
propose
ssDNA
colony-forming
purified with the
in
preparation and
purified,
(dsDNA)
MgCl2-phenol,
ACTAAAGGGAA-3•Œ)
of
from
We
of
was
DNA
EcoRI with
15). of
titer
phagemid
phagemid
with
extraction
dsDNA
immunoprecipitation
vitro.
- The
of
of
ssDNA
gested (14, Conversion
in
neuro
some
(ii)
ssDNA
Double-stranded
digestion
phagemid, compared
immunodetected of
extracted
proteins reported here body aaaaad they contribute
aqueous
also
proteins
(i)
of shar
registered
group
synthesis
demonstrated
round
secretory,
component
labeled
two
multifunctional
(i.e. were
a
body,
genes
genes
A prominent
complement
[35S]methionine
one
conferring
novo
in the
by:
The
(13).
nation be
of
many
known
which
De
cDNA
between
obtained.
described
will
ciliary
After
identified
epithelium
proteins
humor.
ssDNA
and
ocular
XR.
to
privilege).
plasma
aqueous
we
homology
of we
strategy
Uni-ZAP
ciliary
excess
characterization
the
databases,
properties
in
from
hybridization,
ing
cell
genes),
clones.
hybridization in ă
a certain
(driver)
the
library
libraries
subtractive
an
library
describe
efficient
to
(housekeeping
cell-specific
we
cDNA
following
unique
with
cDNA
report
be
genes
(target)
another
and
might
common
ciliary
from
In
which
subtracting
et al.
flanked restriction
fragment by
the site
SK(-) primers.
with T3
of
was
ampli
Two
fragments
after
the
digestion
XhoI.
The
largest
promoter
at the
fragment plasmid
3•Œ-end.
at The
the
of
the
fragment
5•Œ-end, smallest
121
of
and
the
fragment
J.
Biochem.
a
Subtracted
was
Human
flanked
at
Ciliary
the
5•Œ-end
Pre-hybridization by
mixing
ments
and
50mM
Subtractive
pre-hybridization under mineral
ssDNA
(250ƒÊg) subtracted
(Vector ssDNA
by
agar
E.
plates
mented
XhoI
and
amplification
ciliary
but
body
the
with
onto supple
library
body
were
probe
gel
DNA blots
of
expected
library,
generated
from
the
1%
at
Bevervely,
For
immunoprecipitation,
X-100;
for
washing
and
from
deoxycholate;
from
cipitates
with
body
the
inserts,
ODM-2
cDNA
on
4-8
0.01M
Tris
was
Culture
also
collected
microconcentrator
1%
with ice,
or
0.1%
detected
total
10
min
were
three
(Phar in
1%
SDS).
with
1
at
pre
times
1•~
sodium
Immunopre volume
2-ƒÀ-mercaptoethanol, and
the
for
pH=7.8;
95•Ž
and
A-Sepharose
washed
X-100; at
with
complexes
Tris-HCl
denatured
C4
1:100
was
protein
and
Triton
component diluted
medium
Immune
(0.01M
SDS-PAGE,
for
sodium
fluoride).
Incubation
ice.
on
containing
10%
were
1%
SDS
were
culture
incubation
buffer
buffer
0.1%
microcon
processes.
min
were
NaCl;
complement
either
4h
90
mCi/ml,
processes
MA).
ciliary
after
macia)
in
mCi/mmol;
of 0.5
proteins
a
old),
Essential (50
(0.15M
antisera
then
years
suspended
Ciliary
radiolabeled
with
(86
phenyl-sulphonyl
(Amicon,
cipitated
37•Ž.
using
processes
Minimal
buffer
Triton
containing
and
donor saline,
at a concentration
1mM
from
using
to
ciliary
a human
48h
concentrated
extract
Axioskop
taken
[35S]methionine
RIPA
pH=7.8;
PCR
to hybridize ciliary
for in
by
clones
the
Science)
incubated
37•Ž
transferred was then
subtracted
from
electro
obtained
cDNA
Specific
generated
the
and
with
Life
incubated
with
with Fluo
Immunoprecipitation-Prior
methionine-free
(MEM)
deoxycholate;
then
a Zeiss were
[35S]methionine,
from
and
homogenized
and antibody.
with
phosphate-buffered
serum-free
and
from
digestion
agarose
pair
and with
and ƒ¿2-macroglobulin insert
inserts
ciliary
Labeling
with
medium
performed Photographs
microdissected
- HC1
selected
after
in 0.8%
library.
probe
not
and
The
1:400; second
(Kodak).
labeling
washed
and D
(100 ƒÊg/ml),
duplicate Each
film
Amersham
from
mixture. electrotransform
Screening-The
radiolabeled
cDNA
radiolabeled
Vectrex-Avidin
isolated
run in filters.
from
the
of
cells,
separated
were
with
ODM-2
Blot was
TMAX-400
Medium
iso-propyl-b-thio-galactopyrano described (16).
clone
phoresis. Gels into nitrocellulose
the
the
continued hybridization, separated
ampicillin
Southern
hybridized
to
5-bromo-4-chloro-3-indolyl-ƒÀ-D-galacto
subtracted and
added
were
excess
XLl-Blue
(X-gal), and as previously
Differential
EcoRI
were
was
microscope.
were
(10-30ƒÊ
Bethesda) anti-rabbit
microscopy
Metabolic
Specific
RNA
NIH,
fluorescent
NaCl,
of
sense
to the hybridization used directly to
containing
with
pyranoside side (IPTG),
Purification
library
an
coli
40%
500mM
Becerra,
metabolic
hybrids
adding
Labs.) was
electrocompetent
and
Patricia
rescence
frag of
Dr.
a rhodamine-conjugated
3•~106
presence
=7.2,
T7.
10ƒÊl,
to
and hybridization at 52•Ž. After
RNA
unbound
the
and
cDNA
ssDNA/biotinylated
each
pH
mixture, for 26h
oil
of
digested
of biotynilated
ODM-2
3•Œ-end by
a volume
overnight.
Hybridization
the
923
(equivalent
in
52•Ž
at the in
multicloning
HEPES, at
microliters
from
LB
of
SK(-),
incubated
ssDNA-Ten
and out
ssDNA
1ƒÊg
pBluescript
then
g)
of
with
formamide,
XhoI,
carried
0.5-0.8ƒÊg
of
by
was
transformants)
Body cDNA Library
of
SDS
fractionated
by
fluorography
by
at
-70•Ž
days.
library. DNA
Sequencing-Double-stranded
[pBluescript
SK(-)],
sequenced using
using the
cent
the
dideoxy
Sequenase
RNA
gel
described (RNA)
the
ODM-2
was
method
(18),
size-fractionated
naturing
1%
agarose-formaldehyde
Nytran
filters
(Schleicher
with
prepared
of
probes,
or
rat
humor
sulfate
ferred
or
and
line
as
de to
NH).
The
conditions
previously
or
de
Filters
were
gels
as
from
previously
(19).
antibodies
at
anti-rat
selenoprotein-P F. 1:300; (21)
Burk
(20) and
Kristina
anti-rat (provided 1:200;
with
Vol. 118, No. 5, 1995
rat
ciliary
Sections the
bodies
were
following
(provided E. Hill,
generously PEDF
by (22)
incubated
generously
by
Dr.
Ruth
Halaban, generously
RNA
nating
dsDNA
the
EcoRl
and
XhoI
MgCl2
(Fig.
2,
as
previously
5)
DNA
Drs.
produced colonies on
then
number
with
Yale by
lane
4)
was units containing in
appoximately when compared results, to
mants
after
cDNA
library.
and shown
synthesized
these
with
separated
we 143,000
dsDNA
from
first with
within
the
the
2, lane
3).
presence
dsDNA
represented estimated of
in by
XL1-Blue
(Fig.
2,
with
transformants, synthesis
was
of
(Fig.
2,
(15).
in
vitro,
the
ssDNA
calculating cells
the
selected
on
Double-stranded lane
a 20-fold increase with ssDNA (Fig. started
intro
digested
(Fig. in
line
contami
from
ampicillin.
vitro
we
then
phenol
(+)
cell
material
2),
pBluescript
of transformants
plates
ssDNA
cut
dsDNA
mole
epithelial
ssDNA
2, lane
to by
sense
at eliminating
The (Fig.
two
vectors
with
antisense aimed
purified
of colony-forming agar
library a ciliary
of
of
XR
from used
was accomplished ssDNA (target)
endonucleases,
preparation
equivalent
(brown
of
region was
LB
(driver)
library
ssDNA
used
cDNA
(pBluescript).
from
titer
body
procedure
excised
1, we
in ă-Uni-ZAP
cDNA library. the purification a two-step
Library
in Fig.
library. This (-) circular
ciliary
cDNA
outlined
constructed
duced
sec
Human
Body-As
subtracted antisense a
phagemid
Univer
protein
of
The
(12).
were
a
(ODM-2) During
designat
Vanderbilt
(provided
cules
lane
trans
concentrations:
tyrosinase-related
and
and
semithin
and
described
first
Raymond
bovine
sodium
described
libraries
multicloning
aque body
on
probed
visualized
rat
ciliary
electrophoresed polyacrylamide
and
or
rat
Immunofluorescence-Cryostat
(0.5ƒÊm)
University)
human
cDNA
a Subtracted
Ciliary
biotinylated
transferred
washing
human
were
(SDS)-10%
specific
locus)
and
conducted
and
antibodies
Indirect
sity)
cell
on
Keene,
(0.5 ƒÊg/lane),
to nitrocellulose.
sera
as
plasma
(60 ƒÊg/lane)
dodecyl
tions
the
of
Ocular
prepare hybridizing
electrophoresis
Schuell,
was
as
isothiocyanate
gels,
(60 ƒÊg/lane),
extracts
ed
and
guanidinium
&
probes
completed
the
Blotting-Total
body
by
per
(12).
Human ous
the
hybridization,
designated
scribed
by
(Protein)
Construction
method Six
was
ciliary
RESULTS
were
Biochemical).
electrophoresis
from
DNA
inserts,
termination
(U.S.
(17). and Western
(20 ƒÊg/lane)
labeling
cDNA chain
system
polyacrylamide
previously Northern
plasmid
containing
ssDNA
6)
from
ssDNA
in transformant 2, lane 4). Based antisense
or
3•~106
from
the
(-) transfor
ciliary
body
924 J
Fig. 1. Scheme describing the subtractive hybridization strat egy. Antisense phagemid single-stranded (ss) DNA molecules were excised from a human ciliary body cDNA library and purified from contaminating double-stranded (ds) DNA with MgCl2-phenol. The ssDNA molecules [pBluescript SK(-)] were comprised of cDNA clones with inserts (common and specific), and without inserts (nonre combinants). The multicloning sequences (MCS) present in all the antisense ssDNA molecules were first blocked in a pre-hybridization step with complementary MCS, then hybridized with biotinylated
. Escribano
et al.
sense RNA prepared from the ODM-2 cDNA library. Hybrids (ssDNA/biotinylated RNA) were separated from ssDNA (specific clones) with an excess of Vectrex-Avidin D. Unbound material was purified and used directly to electrotransform electrocompetent E. coli X-Blue cells as described (16). Color selection of recombinants transformant colonies (white) from nonrecombinants (blue) was carried out on LB agar ampicillin plates in the presence of X-gal and IPTG. Specific clones were further characterized by differential Southern blot screening and Northern blot analysis.
J. Biochem.
Subtracted
The
ssDNA
region in
Human
(or
with
DNA
polylinker)
"MATERIALS
this
Ciliary
containing of
AND
of
ing
T3
and
EcoRI
molecule.
The
subtractive
adding
will
the
ciliary
then
competent on
LB
blue)
directly
and
Preliminary
estimated
of
to be
that
the
of
After
one
round
Southern METHODS." readily
signal
with Figure
to
3
shows
the
in
exposure
ential
expression by
DNA
in to
be by
a
low
of
Clones-Table
Human I lists
after
sequencing. from
the
differential
that
ODM-2
of
analysis
whereas required
showed
further
We 5•Œ and
sequenced 3•Œ ends
between of
each
cDNA
blot
(clone
#71),
and
AND
the
copies
subtracted
Southern
selenoprotein-P
than
#42), ƒ¿2
clones
Fig.
2.
body
in
with
vivo
EcoRI
differ
Purification
ciliary
Ciliary
Body
cDNA
clones
analysis 100-150
clone
and
DNA
basepairs (a total
of
R408
with
XhoI
100mM
303
phage
and
separated
of the
ssDNA
number
of to
dsDNA
positions
of
indicated
with
(lane
(lane
from to
induced indicated 3-kb
on
fragment
these
ssDNA. lanes
marker
and
con
markers 7.
and
On
the
R408
(arrow
conversion,
a 20-fold
XLl-Blue
with
extracted
conditions,
Enzymatic
Ladder 1 and
excised
is linearized
5).
coli
a human was
digestion
3),
6) originated
(E. by
to
(lane
(lane
(lane
transformants
are
subjected
Under
from
ssDNA
(pBluescript)
ssDNA
dsDNA
DNA
XR.
2),
4).
DNA
that
a
Uni-ZAP
endonucleases
double-stranded
vitro,
1kb
helper
(ss)
in ă
restriction
heads)
the
library
MgCl2-phenol
taminated
character
of single-stranded
cDNA
and
compared
identified
(clone
(72%)
some
type
Subtracted the
C4
hybridization
of
were
their
differential
library,
Clones
analysis
on
(higher
initial
55). This differential some clones were
number
proteins.
based
similarity
component #16),
plasma
2,700
with
subtracted
detected. this
from
such
and that
(clone
for was
we
significant
high
sequencing.
Characterization cDNA
the
42,
complement
work,
biologically
clones
sequence
this
heter
to
"MATERIALS
than of
in
were
large
seventy-two
stronger
results
clones #31, signal suggested
the
by
inserts
probe
identified
these
clones
the
since
1,940
hundred
in
a much
these
1%.
characterized
body
represented
longer
Six
of
nucleotide
GenBank/EMBL
to
blot (Fig. 4). of cDNA clones coded
nucleotide with
in
of few
(29%). subtract
registered
Due
clones expression
genes
additional
from
1kb).
of 127 result
sug a
of which
described
give
enriched
others
ized
as
ciliary
from
selectively
and
hybridization,
found the
(see inserts hybridization
(white).
the
Northern group
extensive
inserts
functional
identification
macroglobulin
hybridization,
obtained,
cDNA
any
were
I. Out once,
known
deposited
The
genes
in Table more than
to
genes
clones
EMBL).
known
176
cDNA
registered and
independent
(average
only
cDNA
occurred, in
of
examined
properties repeated
homology
The
subtracted
with
determined
or
large
90%),
result
than
90
(EST)
databases.
homology
have
without
(16).
estimated
clones less
subtractive
analysis,
28%
clones
the with
were
hybridization
was
studied
After
were
and
ed
The or
colonies
molecules
were
color
been blot
probe.
of
by
have
of we
all
(GenBank
related 21 were
total
genes by A small
(white
described
preliminary
subtractive
library
colonies
selected
clones
a
ogeneity an
grown
Subtracted
nonrecombinant
cDNA
transformant were
the
This
nonrecombinant
proportion
unsubtracted
their clones,
relatively
subtracted
color
transformant (white)
(blue).
of
with
colonies
by
of
to
bound
electro
and
previously
the
recombinants
during
enrichment
high
by
in
of
homologous
searched
exhibiting
sequences
unbound
The
selected
as
of
library RNA
from
(Stratagene) and
72%
cDNA
Labs.).
by
RNA
to electrotransform
IPTG,
nonrecombinants
gested
grouped identified ing
42% were
databases
since
out
sequences,
Characterization total
carried
separated
specific
ampicillin
X-gal
Clones-A
be
was
cells
with
with
the
clones
flank
biotinylated
biotinylated
D (Vector
used
XL1-Blue plates
in
sequenced
large
pBluescript
then
ODM-2 The
putative
of Vectrex-Avidin was
lost,
circular
(+)
epithelial
ssDNA
containing
ssDNA
any
of sense
mixture.
complementary
excess
been
sequences
was
excess
human
ssDNA,
a
Approximately
clones If
introduced,
have
to
clones).
described
pre-hybridized.
not
hybridization
prehybridization
to
multicloning (as
multicloning
anneal
925
Furthermore,
a 10-30-fold
from
was
would
containing
entire
SK(-)
were
clones
RNA
ssDNA
the
step
specific
biotinylated
the
pBluescript
METHODS")
prehybridization
number
Body cDNA Library
in
increase
colonies)
in when
(Gibco/BRL) left phage
of the
of gel
DNA
the are
arrows.
Fig. 3. Differential Southern blot analysis of eight subtracted cDNA clones. Inserts from eight cDNA clones were isolated and resolved by gel electrophoresis in 0.8% agarose gels in duplicated (panels A and B). After transferring DNA in gels into nitrocellulose filters, they were hybridized with two radio labeled probes, as described in "MATERIALS AND METHODS" (panels in B). Clone #55 shows a strong differential hybridization with the C. B. probe but not with the ODM-2 probe. Clones #31 and #42 (arrows in panel B) show low differential hybridization, and clone #41 (arrow head) does not show differential hybrid ization. Vol. 118, No. 5, 1995
926 TABLE I. Identification of subtracted human ciliary body library.
J. Escribano cDNA
clones
from
et al.
a
J. Biochem.
Subtracted
Rep.,
Human
number
of times
apolipoprotein blot
D
analysis,
restricted the they
were
(clone
C4,
and
cell
was
(Fig.
precursor agreed were
these by
5A).
The
detected
an
extracts, protein-P and 62
kDa.
lower
cell
humor,
humor
180
and
and
molecular
ciliary
weight
kDa,
generously (25) detected
in serum,
ciliary
body
The
and
as
Northern
muscle for
not
#82,
opposed
and
not
a
bands of 57 was detect and
to seleno
three samples apolipoprotein Univ. expected
in aqueous
actin
epithelial
Vol. 118, No. 5, 1995
this
clone
specific blot
#211,
subtractive
analysis
##136,
on
and
#223
homology
neurotrophic
epithelium
the is
cell
a marker
cells.
The
line.
This for
cross
probed
with
and
cDNA
clone
synthase, D
Oviedo, size, 26
humor
and
clones
was
few
additional
(Fig.
4).
Clone
is expected,
smooth
muscle
reaction,
seen
since cells in Fig.
RNA
from
is
abundant
the
following
to
a gene
ODM-2 in
an
glandin tissue
radiolabeled
recently
named
pigment
epithelium-derived
homology the
with
Rab
We
were
certain
with
their
case
in
homology
(28);
for the
this cell
only
detected
DNA
molecules
the
human
processing and
a group
corresponding
component
tissue
the may
of clones to
the
present that URF1-4
hybridi hybridization This
clone
carboxypeptidase enzyme
and
RNA.
escape
genes:
of
(27),
subtractive
molecules. of
D2 prosta
detected in #233 showed
(GGTase-II)
RNA
restrict line (Fig.
of
catalytic
during
group
also cell
synthesis
in the
that
prominent to
the
for
pigment factor
were NPE
clone were line. Clone
of
evidence
retinal
to prostaglandin
the
transferase
complementary two
neuropeptide
proteins
in
subunit
geranylgeranyl
present
zation,
cells
the ƒÀ
in
PEDF to the
homology
involved
Transcripts but not
the
#211
as coding
from
showed
Clone
identified
derived
#136
corresponded
cells.
factor
enzyme
D2. RNA,
cells
these
(PEDF) (22, 26). Transcripts for ed to the ciliary body as opposed 4).
(Fig.
to smooth muscle actin, and tran to the ciliary body (likely ciliary to
were
with
which
showed
Seleno
in serum,
of
to ƒÀ-actin
transcripts
homology restricted
smooth
levels
cells
Rab geranylgeranyl transferase ƒÀ subunit, clone #223; and CPE= carboxypeptidase E, clone #294. ƒÀ-actin was used as control. C. B. = human ciliary body; ODM-2=human cell line. Arrows to the left of each probe indicate the position and size (in kb) of specific transcript. Arrowhead with probe SM actin, denotes cross reaction with ƒÀ-actin.
4,
body
5B).
two band
C. Lopez-Otin, band of the
ODM-2
probes: URF-4, clone #3; C4= Complement component C4, clone #42; ƒ¿ƒ¿ 2-M=ƒ¿2-macroglobulin, clone #16; SM actin=smooth muscle actin, clone #82; PEDF=pigment epithelium-derived factor, clone # 211; Se-P=selenoprotein P, clone #71; Apo D=apolipoprotein D, clone #158; PD2S=prostaglandin D2 synthase, clone #136; GGT=
the
5D).
by
#82 showed scripts were
ciliary
(corresponding in the purified
of
immuno
in
(Fig.
but
body and
antibodies.
also
serum
(ƒ¿, ƒÀ
and
analysis of subtracted ciliary body tissue and ODM-2 cells. Blots containing amounts of RNA from intact human ciliary
C4 antibodies these proteins
same
(24)
body,
low
of selecting
including
muscle)
in very
(Fig.
efficiency
demonstrated clones,
by
kDa
band
by Dr. a major
ciliary humor size
(Sigma)
of
to
private investiga three subunits
of C4 in in aqueous
line
in using
antibodies
molecular
protein-P) was immunodetected 5C). Finally, antibodies against (provided Spain)
by
antibodies (20) immunodetected The higher molecular weight
ed in aqueous the
band
aqueous
or
Fig. 4. Northern blot clones in ciliary body approximately equivalent body
among
analysis,
detected with (23). None of
antibodies
expected
subtractive
proteins
blot
(pro), subunits
ODM-2
that
enriched
plasma
Western
expected
in the
ƒ¿ 2-Macroglobulin
in
indicating
5%). of
provided recognized
subunits studies
were
detected
the
antibodies
generously (Sigma)
and three with previous
4),
highly
groups
verified
not
during
available
recognized
(Fig.
was
, and ƒÁ), and the precursor extracts, and only the three serum
line
Northern
clones
were
(approximately
commercially
purified proteins tors. C4 antibodies
four
they
enriched
of
By
these
in particular,
clones
humor
either
body
927
determined.
respectively. for
efficiently
identification
aqueous
N. D., not
#158),
epithelial
subtracted The
repeated;
ciliary
ciliary
hybridization. the
Body cDNA Library
transcripts
to the
NPE
Ciliary
was
#294, E
the with
(CPE),
in neuroendocrine
encoded subunits
mitochondrial of
NADH
a
928
J . Escribano
dehydrogenases, URF-A6L (ATPase 6), cytochrome b, and cytochrome c oxidases I, II, and III. URF-4, alone, was found to represent 5-8% of the entire subtracted library, and by Northern blot it was found to be very abundant in
the ciliary body when compared to the NPE cell line (Fig. 4, clone #3). One possible explanation for the less effective hybridiza tion between some of the common clones in both libraries
Fig.
5.
Western
blot
noprecipitation plasma D)
proteins.
or
rat
humor,
tionation
by and
nent
C4
Human and
ciliary
of
subunits
of
Arrow ing
in
and
(panel
the
tein-D
(panel culture - Sepharose.
A)
of
molecular
protein
markers
and ƒ¿2-macroglobulin
medium
were
Immune
(panel
is B).
immunoprecipitated complexes
were
indicated Ciliary
with resolved
in processes
complement by
SDS-PAGE
kDa.
Immunoprecipitation were
metabolically
component and
C4
antibodies
of labeled
(panel
A)
Arrows
a
compo
in
A,
and ƒÁ
component main
band Arrow
in
related
position On
the
left
protein.
of
each
blot
component
proteins
or ƒ¿2-macroglobulin
indi kDa),
of apolipopro
complement and
C, (57
a possible
kDa).
C4.
correspond
selenoprotein-P
labeled
indicate
(pro), ƒ¿, ƒÀ,
indicate
[35S]methionine
frac into
A); ƒ¿2-macro
complement
of
(26-32
[35S]methionine with
D).
B indicates
D,
were
(panel B); selenoprotein C); and apolipoprotein-D
arrowhead in
and
serum,
complement
precursor
position
Arrows
position
body
to ƒ¿2-macroglobulin.
cates
B,
from
transferred
against
(panel
positions
A,
C)
SDS-PAGE,
antibodies
antibodies
immu labeled
(panels
(panel
blotted
and
metabolically
proteins
aqueous
filter
analysis
of
globulin antibodies P antibodies (panel
the
et al.
secreted
(panel
B),
C4 into
and
the
protein
A
autoradiography.
Fig.
6.
Differential
labeling
selenoprotein-P, related
protein,
bodies
on
tion
of
and
and
rat
indirect
bovine (A-D)
sections
or
were
with
antibodies (A
sinase-related (C
antibodies
and
F).
B,
pigmented
(21)
D,
ciliary
PEDF
dilution)
and
photographs
tyro (1:200
or
(1:300 F
are
of A,
respectively.
mented
B),
D),
(22)
(20)
and
protein
dilution)
E,
by
immunofluorescence
dilution)
and
bovine
labeled
(1:300
contrast
sec ciliary
selenoprotein-P
(E
anti
frozen
and Rat
F)
PEDF
semithin
processes. (E
of
tyrosinase
NPE,
phase C,
and
nonpig
epithelium;
ciliary
PE,
epithelium;
ve,
vascular
endothelium;
bm,
basal
plasma
membrane.
Magnifica
tion•~600.
J.
Biochem.
Subtracted
could
be
Human
the
presence
synthesized
in
of
- F,
the
coded
and
indirect
rat
bovine
and
-
in
pigmented rat ciliary
ciliary processes
labeled
with
either
macroglobulin
or
subtracted
cell-specific
phenotype.
further
we
methionine.
Fig.
[35S]methionine complement
ly
a
proceses
labeled
in
proteins
secreted
of
[35S]methionine
identical
pattern
of
immunodetected serum, and
B).
These is
and
show
an
results organ
proteins with those present
were
(data the
not
and
medium
(Fig.
5,
complement component immunoprecipitated
labeled
secreted
and
proteins
mobilities Western
ciliary
body
blot (Fig.
demonstrate and
identical
molecular
from
A
ciliary plasma with
this
work,
a human
ciliary
generated summarized
in
body phagemid in Fig.
Vol. 118, No. 5, 1995
and
a single
related
compounds
cDNA
library human
from donor
ciliary
pBluescript, following the 1. Previous studies demonstrated
the
On
was
tein-P,
strategy that
the
epithelial
(20).
plasma,
The
in the
eye?
differ
Our
prelimi in
the
between proteins
in
aque
targeting; (24).
arachidonic
C4
it may
cells
as
roles
gene
by
actively
partici as
that
has
selenopro
extracellular in the
in
expression
glycoprotein an
(Dr.
responses, (23, 31).
suggested
selenium-rich
sub heme
properties
important
component
been
Apolipo
acid)
These
suggests
im
hydrophobic esters, or
biologically
of this
root
of ƒ¿2-macroglobulin
(or
functions
the
the
differences
peptides
30),
it has
expression
through
immunodetected
inflammation and kidney
extracellular, in
of the
different cholesteryl
play
plasma from
synthesized
small
an the
pigmented that
translocated eye
by into
modifications
foreign
cells
the
clearance;
Complement
hand,
of
communication).
proteins
other an
be
properties
in immune-mediated shown in intestinal
originally idant
are
to
Whether
indicate
proteins
inhibition;
humor.
com
are synthe contribute
cells
that
(25,
certain
chamber
plasma
of
least,
anterior
serum and plasma body (see Fig. 5).
personal these
the
of the
and transport cholesterol,
is that
outside results
the
nonpigmented
outside
processing
D binds including
pate been
normal
from ciliary
protein stances,
suggest
at
space
indicate
ciliary
ciliary body are directly by the ciliary epithelial
could
synthesized
of
humor.
studies
mobility
Lopez-Otin,
that
posttranslational
proteinase
aqueous
subtractive of
Do the
multifunctional
port;
the
ocular
those
include:
DISCUSSION In
29).
observations
The
a
explants
complement
chamber
undergo
plasma proteins ous humor or
those
mass
(7,
body
see
5, panels the
iris
electrophoretic
in
of
of the
novo C and
of these findings time assumption
aqueous
Recent humor
de
component
are synthesized based on
paracellular
anterior
the
analysis
that secretion
the
nary
with as
into
ent
the
aqueous
blood
ciliary
ciliary with
in
proteins
selonoprotein-P) and they could
the
and
plasma
in
into
from
P,
Furthermore,
in the chamber
redirected
known.
cDNA
these
suggested
of
not
proteins
separate the
is
four
(complement
indicates
humor However,
be
(i.e.,
se
which
relevance the long
composition
are
ciliary
subtractive dbEST data
on
complement
D, body
route
were
the
expressed
body and
demonstrated
can
their
evidence for
apolipoprotein the ciliary
through
cells)
300
(i.e., ƒ¿2-macroglobulin,
or they
stroma
of
it
on
in
proteins
body.
aqueous liver).
I).
clones
selenoprotein
of
of
Table
based
attention
serum
proteins synthesized into the posterior
alternative
im
in
here,
plasma secreted
with respec
from
ciliary
secretion
protein
cells,
over
present
was
C4, within
the
pattern
carried
shown)
culture
synthesis
appararent in serum.
the
the
proteins
ponent sized
com
B). Both antibodies
further of
only
We
I
search
homology
identified
ciliary GenBank
our
to
D).
proteins eye (i.e.,
plasma
im
and autoradiogra
focused
Ninety by
(see
expressed of
selection
date for
Table
the
being
in vitro. The since it challenges
plasma of the presented
to
for
character
sequenced.
genes
in of
activity
and
processes important
medium,
human
we homology
color
databases
the human entered in
ƒ¿ 2-macroglobulin
[35S]
were
to
derived
conventional
humor,
culture
antibodies
we
synthesis
ciliary
with
work
by
useful estimated
partially
identified
sequencing
from been
within
a
were
as
transcriptional
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clones
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occurs
processes
48h
proteins,
electrophoretic
by
aqueous
body
for
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apolipoprotein
component
ciliary
eye
extract
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component
from
the
classified
identified
are An
registered
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with
were
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partial
this
at
with
within
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together,
proteins immunoprecipitated C4 and ƒ¿2-macroglobulin
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bases.
and
vectors (28).
isolated
clones
been
identity.
tags have
in to
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vitro
the
not
proteins
complement
B,
B);
ciliary
consistent
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synthesized
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total
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identified
labeled
labeled component
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with
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Taken
to
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plement component C4 munocomplexes resolved In
hown).
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cells
bovine
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determine
from
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of
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clones
of
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ciliary
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cDNA profile
epithelium
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membrane
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results
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labeled
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subtracted
using
obtained
cDNA libraries out subtractive
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specific In Fig.
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nonpigmented
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sections of paraffin
shown).
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processes analysis
on
RNA
subtracted
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basolateral
of
cellular
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independent
related
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structures
identify
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in to
proteins
[selenoprotein-P (clone bodies
secondary
Distribution attempted
several
Body cDNA
vitro.
Cell-Specific Genes-We of
Ciliary
human
found antiox ciliary
930
J. Escribano
body,
and
that
its
the
detection
ciliary
antioxidant
in aqueous
body
humor
is a major
defense
in the
site
supports
of
anterior
the
idea
detoxification
segment
of
IOP.
and
the
eye
The
clones
(6,
highly
expressed
9). The
largest
group
enzymes
This
may
ciliary
reflect
body
division, the
ciliary
very
coding
little
cells.
no
in
activity
cell
and
that
the
than
cell
at
occurs
all
in
vivo. gene
identified E,
candidate
enzyme
was
a
and
We
thank
would
and
with opens
for
hormones
being
nonpigmented The
ciliary
homology
contraction
and
during C.
con
hormones. neuropeptides
This
receptors
human
in
contraction ocular
synthase, which
the of
(32), ciliary
ciliary
have
in the
3.
of PGD2 there
and
is
4.
of
all
identified
ocular
tissues,
restricted the
by
case
with
in
to
a few
ciliary
with
the ƒÀ
Northern examples
body
clone
of
with
found
within
which the
analysis
we
tissue
#223
subunit
blot
that
the
exhibited
catalytic
product
transferase were found
other
they
eye.
and
compared
lens
when
cornea, not
iris,
retina,
to
and
other
(27). the
ocular
retinal
the
6.
Rab
Transcripts ciliary body
tissues,
pigment
such
epithelium
7.
as
(data
8.
few
cell
specificity
cases,
using
acterized.
In
obtained
of
subtracted
antibodies
which
general,
with
the
these
clones were
pattern
specific
was
studied
in
extensively
of
Coca-Prados,
immunostaining cell labeling
tyrosinase-related suggests
protein,
that
these
cell-types
within
conclusion
that
The
strategy
potential
genes
precise
onset
primary
that
correlated
are
regulate
body. cDNA
genes
to
used
in
work or
mechanisms
ciliary
humor
secretion.
Stone,
R. A.
Thus,
and St.
by
a or
donor
RNA
(driver)
genes
patient, affecting
hence from
ciliary
The
the
a ciliary be
of
possible
summary,
we
generate a subtracted body of a single normal responsible
for
applied human human
regulating
subtractive cDNA donor aqueous
library patient. humor
in
the
Kumar,
N.
gap
M.
junction
epithelium.
J. M.,
Curr.
K(+)
the
nonpig
in
aqueous
184-194
(1989)
The
Glaucomas Vol.
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149,
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The
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Hernando,
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J. W.,
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659-669
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Res.
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2,
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Streilein,
S-trans
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epithelium.
la,
Cousins,
intestinal activity
Vol.
Academic
J. W.,
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153,
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711-718 Ocular
H.,
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3rd
ed.
in
Press,
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S. W.
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Im
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aqueous
The York
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to
the
J.
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1080-1086
Martin-Alonso,
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Rowland,
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12.
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(1993)
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13.
Hong,
Potter,
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cellular
114,
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forms
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284-291
D. E.,
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T. J.,
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Circadian
Curr.
M.
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Eye
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antisera Invest.
N.,
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protein
in the
Sambrook, Cloning:
14.
Gosh,
from
Res.
1,
raised
Isolation
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Ophthalmol. S.,
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Vis. J. W.,
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958-981
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Res.
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ssDNA
normal
a glaucoma
candidate
6)
to search
prevalent
and
Burk
antibodies.
Intercellular
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J.
Martin-Alonso,
of cDNA
applied
the
R.
discus
Louis
malian
11.
during
most
subtracting of
support
(1978)
epithelium:
and
Expression
distinct
To understand this molecular mechanisms
secretion
ssDNA of
the
unknown. into the
humor
library
be
induced
glaucoma
(Fig. in
and
could
Becerra;
providing
pigmented
N., M.
pressure
Cloning
expressed.
underlining
largely is needed
library
identify
this
We
stimulating
a
cell-specificity. with PEDF,
processed
processes
assistance.
the
P.
for
S.,
reveals
mented
munol. 9.
was
well
selenoprotein-P being
differentially
repressed
complementary cDNA
are
ciliary are
aqueous
ciliary body
the they
indicates obtained
and
proteins
open-angle
glaucoma, investigation
that pattern
Drs.
cellular
Hernando,
peroxidase
pattern of The distinct
technical for
Ophthalmol.
ocular
immunosuppressive
a
char
labeling
antibodies
the
S.,
and
munoreactive
shown). The
pharmacol
113-122
P.,
Eye
(85%)
of
and
retinaldehyde
was
homology
in
to
potential
body.
excellent
E.
Ghosh,
in
11,
Coca-Prados,
were
Such
component
(GGTase-II) exclusively
and
physiology,
Swaroop
Halaban
Invest.
Ghosh,
ferase
geranylgeranyl for clone #223
the
with
R.
Raviola,
M.,
Res.
Co.,
the 5.
clones
along
Expression
intraocular
resulting
expression
and
Coca-Prados,
M. B.,
the
A.
and
G.
- ATPase
synthesis
(33),
muscle
compared
work,
epithelium.
Eye
35).
not
Raviola,
(1992)
theory muscle
activation
muscle
smooth
(34,
we
the
to prosta
supports the in smooth
Upon
this
ciliary 2.
in
showed
is involved
body.
sphincter
hypotension
Although
strongly involved
is
human
the
enzyme
#136
Dr.
biological
ciliary
for
thank
Lopez-Otin;
gene
clone
the
differentially a framework
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