Specificity, Diversity, and Self-tolerance of T-Cell Receptors by Thymic Selection
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Transcript of Specificity, Diversity, and Self-tolerance of T-Cell Receptors by Thymic Selection
Specificity, Diversity, and Self-tolerance
of T-Cell Receptors by Thymic Selection
Andrej Kosmrlj Abhishek Jha
Mehran Kardar
Eric Huseby Arup K. Chakraborty
Antigen Presenting Cell
T Cell
T Cells orchestrate adaptive immunity, via
Receptors that recognize short peptides from pathogen proteins
TCR
pMHC
Self-tolerant, i.e. weakly binding to endogenous pMHC, to avoid autoimmune diseases, e.g.
Multiple sclerosis, diabetes, …
Diverse, to recognize an evolving landscape of pathogens.
Specific/degenerate, to lock on specific pathogen, and tolerate its mutants.
T Cells Receptors (TCRs) must be:
pMHC
n*= 5.3
What is the shortest peptide length that ensures self-tolerance?
Nu
mb
er o
f d
isti
nct
hu
man
pep
tid
es
Length of peptide, n
In principle all human peptides can be recognized from sequences of length 5-6.What is the physical mechanism that enables recognition of self-peptides?
T Cells are designed in the Thymuswhere a diverse repertoire of thymocytes is culled by encounters with self pMHC.
Positive selection TCR must bind sufficiently strongly to at least one self pMHC (implicated in MHC restriction, and sensitivity).
Negative selection TCR must not bind any self pMHC too strongly (deleting autoimmune TCR).
( )∑=
=
=10
1
,N
iii JLUE
TCR {L}
pMHC {J}
conserved variable
Miyazawa-Jernigan
Surviving T cells: E > EP for at least one peptide, E<EN for all peptides
Model for TCR selection in the Thymus
MHC peptide
E
+
--
✓
Diversity
The selection process biases the composition of amino-acids in mature TCRs:Negative selection leads to a slight preference for weak amino-acids.
STRONG WEAK
Frequency of TCR amino-acids
from known TCR-pMHC crystal structures
Fre
qu
ency
in T
CR
/Fre
qu
ency
in p
rote
ome
(MJ used for ordering)(Thermophiles used for ordering, Shakhnovich et al., PLOS, 2007)
Eric S. Huseby et al, Cell (2005); Nature Immunol. (2007),
compared the T cells of normal mice, with mice genetically engineered to present only one type of peptide in their thymus.
T cells selected in the thymus are challenged with an antigenic peptide, and reactive T cells identified.
Does a reactive T cell remain reactive upon mutating the peptide’s amino acids?
If mutations to an amino acid destroy reactivity with at least half the T cells,
the amino-acid is labeled a “hot spot”.
• Main results:
– Single peptide selection: few hot spots – cross-reactive T cells
– Many peptide selection: many hot spots – specific T cells
Specificity
• Specificity to antigen peptide:– Single peptide: mutations don’t matter – cross-reactive T-cells– Many peptides: mutations destroy reactivity – specific T-cells
† Hot-spots are defined as locations along the sequence, where mutations of a peptide amino acid destroy reactivity with more than half the reactive T cells
freq
uenc
y
Numerical results for hot-spots† mirror the experimental situation
Frustration during negative selection constrains TCR sequences
T C R
One peptide
Ep < E < EN
selected
Frustration during negative selection constrains TCR sequences
pii iN EjlUE >>∑ ),(T C R
One peptide
selected
Frustration during negative selection constrains TCR sequences
pii iN EjlUE >>∑ ),(T C R
One peptide
selected
E > ENnegatively selected
Many peptides
Optimizing interactions with one peptide can lead to “bad” interactions with another – FRUSTRATION.
Positive selection does not involve frustration.
T C R
Specificity, Diversity, and Self-tolerance
of T-Cell Receptors by Thymic Selection
Andrej Kosmrlj Abhishek Jha
Mehran Kardar
Eric Huseby Arup K. Chakraborty
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Frustration during negative selection constrains TCR sequences
Frustration during negative selection constrains TCR sequences
Solution:
negative selection lead to choice of TCR amino acids which minimize interactions with other amino acids in En peptides.
Prob. that a TCR is selected
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exp)(
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20
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strong weak
COMPUTATIONAL RESULTSF
req
uen
cy i
n T
CR
/Fre
qu
ency
in
pro
teo
me
Robust to variations in potential
AMINO ACID FREQUENCIES FROM TCR-PMHC CRYSTAL STRUCTURES
(Thermophiles used for ordering, Shakhnovich et al., PLOS, 2007)
Fre
qu
ency
in
TC
R/F
req
uen
cy i
n p
rote
om
e
STRONG WEAK
Distribution of single site contact energies for selected T cell-antigenic peptide interactions
Increased number of moderate interactions
Decreased number of strong interactions
Selection with many peptides: TCR sequences contain amino acids that interact with Ag peptide amino acids moderately
strong weak
Modest interactions lead to specificity:
Weak multivalent interactions stabilize the interface, making each interaction important for recognition
Selection against one peptide – only few important sites
T C R
B3K 506 TCRC57BL/6 derived
MHC + peptide specific
YAe62.8 TCRIAb-SP derived
MHC + peptide degenerate
How much Free Energy of Binding is due to each amino acid for specific versus degenerate TCRs?
P-1EP-1E P8KP5KP3KP2Q
IAb + 3K KDΔΔG
Mutation μM kcal/molWT 7 0.0P-1 A 26 0.7P2 A 278 2.2P3 A > 550 > 2.6P5 A > 550 > 2.6P8 A 92 1.5
IAb + 3K KDΔΔG
Mutation μM kcal/molWT 8 0.0P-1 A 9 0.0P2 A 56 1.1P3 A 62 1.2P5 A > 550 > 2.5P8 A 7 -0.1
TCR sequences are specific, but diverse
One type of sequences are selected – ones with a predominance of weak amino acids
+
+
-
+
+
-+
+
++
+
-
TCR sequences are cross-reactive (degerate)
Several antigenic peptides composed of sufficient number of strong amino acids can interact productively with a given TCR
+
+
+
-
ADAPTIVE IMMUNITY IN HEALTH AND DISEASEFlexible system to combat
diverse pathogens
Mis-regulation leads to autoimmune diseases
Multiple Sclerosis
The challenge: develop principlesprinciples that govern the emergence of an immune response or autoimmunity and design design rulesrules for therapies
The problem: underlying mechanisms characterized by cooperative dynamic cooperative dynamic processesprocesses involving many componentsmany components and a spectrum of length/time scalesspectrum of length/time scales
Diabetes
dendriticcells
cytokines
chemokines
B7
B7 CD28+
CTLA4 -
TCRpMHC
B7
B7 CD28+
CTLA4 -
TCRpMHC
tissue
T CELLS RECOGNIZE SHORT PEPTIDES DERIVED FROM PATHOGEN’S PROTEINS
mixture of self (En) and antigenic (Ag/agonist)
As few as 3 Ag molecules in a sea of 30,000 En can activate a T cell (Nature, 2002)
How does this exquisite sensory apparatus work without frequent “noise”-induced autoimmune responses?
Extraordinary Sensitivity of T cells for Antigen
T cell sensitivity to Ag pMHC is predicated upon degenerate weak interactions with En pMHC. With Mark Davis’ lab. (Nature Imm., 2004; Nature, 2005; PNAS, 2007; unpublished)
INFLUENCE OF PARAMETERS IN MODEL
Parameters: Ec, EN, Ep
Ec-EN is large (conserved TCR-MHC interactions are very weak)
Ec Ep EN
Small gap
EcEp EN
Large gap
Positive selection limiting; These are the TCRs that are not positively selected (MHC restriction); one or many types of
peptides lead to similar consequences
Ec-EN is small (conserved TCR-MHC interactions are very strong)
Ec EpEN
Small gap
EcEp EN
Large gap
Negative selection very easy; For many types of peptides almost all T cells are negatively selected.
Theory/computation Experiments
statistical physics genetics biochemistry imaging
Life Sciences
Physical Sciences
Engineering sciences
chemical kinetics
An approach at the intersection of disciplines
THYMIC SELECTION THRESHOLDS
Sharp boundary separates positive and negative selectors MOLECULAR MECHANISM (w/A.Weiss’ lab.)
strongest weakest
Palmer lab, Nature (2006)
A MEMBRANE-PROXIMAL SIGNALING MODULE IMPLICATED (with Jayajit Das, Ashok
Prasad; Jeroen Roose, Art Weiss@UCSF)
A positive feedback loop results in digital signaling and a sharp threshold Cell, PNAS, in review (2008)
SHORT PEPTIDES ARE SUFFICIENT TO RENDER T CELLS SELF-TOLERANT AND REACTIVE TO FOREIGN
SHORT PEPTIDES ARE SUFFICIENT TO RENDER T CELLS SELF-TOLERANT AND REACTIVE TO FOREIGN
Longer peptides (length = n) will enable sampling of more distinct peptides ~ 20n
SHORT PEPTIDES ARE SUFFICIENT TO RENDER T CELLS SELF-TOLERANT AND REACTIVE TO FOREIGN
5 10 15 20 25101
102
103
104
105
106
107
108
# Unique peptides of length
n
Length of peptide, n
Condition for plateau:
20ln
ln ; 20
NnNn ==
Total # of unique peptides of size, nTotal size of human proteins
n=5.3
Group members:J. Das, A. Prasad, M. Artomov,
C. Govern, H. Zheng, A. Jha, J. Locasale, K. Fowler,M. Wolfson, A. Prabhakar, M. Yang, F. Liang, A. Kosmrlj.
Collaborators: M. Davis, A. Shaw, P. Allen, A. Weiss, J. Roose, H. Ploegh M. Dustin, M. Kardar, A Perelson, J. Chen, U. von Andrian, H. Eisen, V. Kuchroo, E. Palmer, E. Huseby.
ACKNOWLEDGMENTS
Immune Response Consortium
Funding: NIH
Is there an optimal peptide length?
0 5 10 15 20 250.00
0.01
0.02
0.03
0.04
0.05Constant Negative Selection Threshold ΔE=ΔE E
Neg−E
Neg=0.4
Length of Peptide n
Fraction of Reactive T Cells
Most TCR negatively selected
IMPORTANCE OF PEPTIDE IN ALLO REACTIVITY DEPENDS UPON THE ALLO MHC
Modest change Bigger change
Theoretical models and experimental tests (Nature Imm. (2004); Nature (2005); PNAS (2007); unpublished)
T cell sensitivity to Ag pMHC is predicated upon degenerate weak interactions with En pMHC that are tuned in the thymus.