Specificity, Diversity, and Self-tolerance

1

• Specificity, Diversity, and Self-tolerance
• of T-Cell Receptors by Thymic Selection
• Andrej Kosmrlj
  Abhishek Jha
• Mehran Kardar
• Eric Huseby
  Arup K. Chakraborty

2
T Cells orchestrate adaptive immunity,
via Receptors that recognize short peptides from
pathogen proteins
T Cell
TCR
pMHC
Antigen Presenting Cell
3
T Cells Receptors (TCRs) must be
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.
pMHC
4
What is the shortest peptide length that ensures
self-tolerance?
Number of distinct human peptides
n 5.3
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?
5
T Cells are designed in the Thymus where 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).
6
Model for TCR selection in the Thymus
conserved variable

TCR L

Miyazawa-Jernigan
pMHC J
peptide
MHC
Surviving T cells E gt EP for at least one
peptide, EltEN for all peptides

E
?
--
7
Diversity
The selection process biases the composition of
amino-acids in mature TCRs Negative selection
leads to a slight preference for weak amino-acids.
8
Frequency of TCR amino-acids from known TCR-pMHC
crystal structures
(Thermophiles used for ordering, Shakhnovich et
al., PLOS, 2007)
(MJ used for ordering)
Frequency in TCR/Frequency in proteome
9
Specificity

• 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 peptides 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

10

• Specificity to antigen peptide
• Single peptide mutations dont matter
  cross-reactive T-cells
• Many peptides mutations destroy reactivity
  specific T-cells

11
Numerical results for hot-spots mirror the
experimental situation
frequency
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
12
Frustration during negative selection constrains
TCR sequences
One peptide
T C R
Ep lt E lt EN
selected

13
Frustration during negative selection constrains
TCR sequences
One peptide
T C R
selected

14
Frustration during negative selection constrains
TCR sequences
One peptide
T C R
selected

Many peptides
T C R
E gt EN
negatively selected

Optimizing interactions with one peptide can lead
to bad interactions with another
FRUSTRATION. Positive selection does not involve
frustration.
15

• Specificity, Diversity, and Self-tolerance
• of T-Cell Receptors by Thymic Selection
• Andrej Kosmrlj
  Abhishek Jha
• Mehran Kardar
• Eric Huseby
  Arup K. Chakraborty

16
Frustration during negative selection constrains
TCR sequences
17
Frustration during negative selection constrains
TCR sequences
Solution
Prob. that a TCR is selected
negative selection lead to choice of TCR amino
acids which minimize interactions with other
amino acids in En peptides.
18
COMPUTATIONAL RESULTS


Frequency in TCR/Frequency in proteome
strong
weak
Robust to variations in potential
19
AMINO ACID FREQUENCIES FROM TCR-PMHC CRYSTAL
STRUCTURES (Thermophiles used for ordering,
Shakhnovich et al., PLOS, 2007)
Frequency in TCR/Frequency in proteome


20
Distribution of single site contact energies for
selected T cell-antigenic peptide interactions
Increased number of moderate interactions
Decreased number of strong interactions
strong
weak
Selection with many peptides TCR sequences
contain amino acids that interact with Ag peptide
amino acids moderately
21
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

22
How much Free Energy of Binding is due to each
amino acid for specific versus degenerate TCRs?
B3K 506 TCR C57BL/6 derived MHC peptide specific
YAe62.8 TCR IAb-SP derived MHC peptide
degenerate
23
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
24
ADAPTIVE IMMUNITY IN HEALTH AND DISEASE
Mis-regulation leads to autoimmune diseases
Flexible system to combat diverse pathogens
Multiple Sclerosis
Diabetes
The challenge develop principles that govern
the emergence of an immune response or
autoimmunity and design rules for therapies The
problem underlying mechanisms characterized by
cooperative dynamic processes involving many
components and a spectrum of length/time scales
25
T CELLS RECOGNIZE SHORT PEPTIDES DERIVED FROM
PATHOGENS PROTEINS
26
Extraordinary Sensitivity of T cells for Antigen
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?
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)
27
INFLUENCE OF PARAMETERS IN MODEL
Parameters Ec, EN, Ep
Positive selection limiting These are the TCRs
that are not positively selected (MHC
restriction) one or many types of peptides lead
to similar consequences
28
Ec-EN is small (conserved TCR-MHC interactions
are very strong)
Small gap
Ec
Ep
EN
Large gap
Ec
Ep
EN
Negative selection very easy For many types of
peptides almost all T cells are negatively
selected.
29
An approach at the intersection of disciplines
Theory/computation
Experiments
statistical physics genetics
biochemistry imaging
chemical kinetics
30
THYMIC SELECTION THRESHOLDS
Palmer lab, Nature (2006)
weakest
strongest
Sharp boundary separates positive and negative
selectors MOLECULAR MECHANISM (w/A.Weiss lab.)
31
A MEMBRANE-PROXIMAL SIGNALING MODULE IMPLICATED

(with Jayajit Das, Ashok
Prasad Jeroen Roose, Art Weiss_at_UCSF)
A positive feedback loop results in digital
signaling and a sharp threshold Cell, PNAS,
in review (2008)
32
SHORT PEPTIDES ARE SUFFICIENT TO RENDER T CELLS
SELF-TOLERANT AND REACTIVE TO FOREIGN
33
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
34
SHORT PEPTIDES ARE SUFFICIENT TO RENDER T CELLS
SELF-TOLERANT AND REACTIVE TO FOREIGN
n5.3
Condition for plateau
Total of unique peptides of size, n
Total size of human proteins
35
ACKNOWLEDGMENTS
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.
Funding NIH
Immune Response Consortium
36
Is there an optimal peptide length?
Most TCR negatively selected
37
(No Transcript)
38
IMPORTANCE OF PEPTIDE IN ALLO REACTIVITY DEPENDS
UPON THE ALLO MHC

Modest change
Bigger change
39
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.