The Observed T cell receptor Space database enables paired-chain repertoire mining, coherence analysis and language modelling
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: May 21, 2024
T
cell
activation
is
governed
through
receptors
(TCRs),
heterodimers
of
two
sequence-variable
chains
(often
an
alpha
[
α
]
and
beta
β
chain)
that
recognise
linear
antigen
fragments
presented
on
the
surfaces.
Early
sequencing
technologies
limited
study
immune
repertoire
TCRs
to
unpaired
transcripts,
leading
extensive
analysis
-chain
data
alone
as
its
greater
sequence
diversity
suggested
it
should
dominate
recognition.
Over
time,
structural
has
revealed
both
contribute
binding
most
antigens
highthroughput
single-cell
handling
have
been
increasingly
applied
obtain
samples
complete
TCR
variable
region
sequences
from
repertoires.
Despite
this,
there
currently
no
repository
dedicated
curation
publicly
available
paired
data.
We
addressed
this
gap
by
creating
Observed
receptor
Space
(OTS)
database,
a
source
consistently
processed
annotated,
full-length,
paired-chain
50
studies
at
least
75
individuals.
Currently,
OTS
contains
5.35M
redundant
(1.63M
nonredundant)
predominantly
human
and,
based
recent
availability
trends,
will
grow
rapidly.
perform
initial
OTS,
identification
pairing
biases,
public
TCRs,
distinct
chain
coherence
patterns
relative
antibodies.
also
harness
build
language
model,
providing
embedding
representations
method
for
residue
in-filling
conditional
partner
chain.
be
updated
maintained
central
community
resource
freely
downloadable
web
application
https://opig.stats.ox.ac.uk/webapps/ots
.
Language: Английский
The Observed T Cell Receptor Space database enables paired-chain repertoire mining, coherence analysis, and language modeling
Cell Reports,
Journal Year:
2024,
Volume and Issue:
43(9), P. 114704 - 114704
Published: Aug. 29, 2024
T
cell
activation
is
governed
through
receptors
(TCRs),
heterodimers
of
two
sequence-variable
chains
(often
an
α
and
β
chain)
that
synergistically
recognize
antigen
fragments
presented
on
surfaces.
Despite
this,
there
only
exist
repositories
dedicated
to
collecting
single-chain,
not
paired-chain,
TCR
sequence
data.
We
addressed
this
gap
by
creating
the
Observed
Space
(OTS)
database,
a
source
consistently
processed
annotated,
full-length,
paired-chain
sequences.
Currently,
OTS
contains
5.35
million
redundant
(1.63
non-redundant),
predominantly
human
sequences
from
across
50
studies
at
least
75
individuals.
Using
OTS,
we
identify
pairing
biases,
public
TCRs,
distinct
chain
coherence
patterns
relative
antibodies.
also
release
language
model,
providing
paired
embedding
representations
method
for
residue
in-filling
conditional
partner
chain.
will
be
updated
as
central
community
resource
freely
downloadable
available
web
application.
Language: Английский
Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning
Cell Systems,
Journal Year:
2024,
Volume and Issue:
15(12), P. 1168 - 1189
Published: Dec. 1, 2024
Language: Английский
Quantifying conformational changes in the TCR:pMHC-I binding interface
Frontiers in Immunology,
Journal Year:
2024,
Volume and Issue:
15
Published: Dec. 2, 2024
T
cells
form
one
of
the
key
pillars
adaptive
immunity.
Using
their
surface
bound
cell
antigen
receptors
(TCRs),
these
screen
millions
antigens
presented
by
major
histocompatibility
complex
(MHC)
or
MHC-like
molecules.
In
other
protein
families,
dynamics
protein-protein
interactions
have
important
implications
for
function.
Case
studies
TCR:class
I
peptide-MHCs
(pMHC-Is)
structures
reported
mixed
results
on
whether
binding
interfaces
undergo
conformational
change
during
engagement
and
no
robust
statistical
quantification
has
been
done
to
generalise
results.
Thus,
it
remains
an
open
question
movement
occurs
in
interface
that
enables
recognition
activation
cells.
Language: Английский