22145 Immunological Bioinformatics Course Programme January 2020

Information for Course Participants

Course Format

• Classes will be a mixture of lectures and group work
• Most of the group work will consist of computer exercises, students are required to bring their own laptop
• All learning resources will be available through DTU inside or this site
• Expected time usage: 1 ECTS point equals approx. 28 hours, this translates to an expected time usage of ~10 hours/day for a 5 ECTS 3-week course

Course Ressources

• Official course website
• Official course description
• IMPORTANT: Please note, that the below course programme can be subject to changes or updates. Make sure to reload the page, to get the newest version of the programme.

Course Teachers

• [LEJ] Leon Eyrich Jessen
• [PM] Paolo Marcatili
• [MN] Morten Nielsen
• [BR] Birkir Reynisson
• [HP] Helle Rus Povlsen

General Daily Schedule

• 09.00 - 12.00 Lectures
• 12.00 - 13.00 Lunch
• 13.00 - 17.00 Exercises

Location

• Building and room: Building 208, room 062 (Down the stairs, through the glass doors on your left)
• Should you be new to DTU, a map of DTU Lyngby Campus is available here

Profiles of Invited Speakers for Seminar on Cancer Immunotherapy

• Clinical perspective: MD, PhD, Clinical Associate Professor Marco Donia, Center for Cancer Immune Therapy (CCIT) and Unit for Experimental Cancer Treatment (EFEK), Herlev-Gentofte Hospital and University of Copenhagen
• Molecular Biology perspective: MSc, PhD, Professor Sine Reker Hadrup, Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark
• Bioinformatics perspective: MSc, PhD, Associate Professor Lars Rønn Olsen, Section for Bioinformatics, Department of Health Technology, Technical University of Denmark
• Biomedical Industry perspective: MSc, PhD, Bioinformatics Specialist Christian Garde, Evaxion Biotech A/S

2020 Course Schedule Overview

Teaching Day 1-8

	Monday Jan. 6th	Tuesday Jan. 7th	Wednesday Jan. 8th	Thursday Jan. 9th	Friday Jan. 10th	Monday Jan. 13th	Tuesday Jan. 14th	Wednesday Jan. 15th
Topic	Introduction and Basic Immunology	B-/T-Cell Receptor Genetics, Repertoires and the IEDB	Protein Structure of B-/T-Cell Receptors and B-Cell Epitopes	T-Cell Epitopes	Antigen Processing and Presentation, HLA Clustering, and Vaccine Design	Antibody Humanization and T-Cell Interaction Models	De-Immunization and Chimeric Antigen Receptor (CAR) Immunotherapy	Mini-symposium on Cancer Immunotherapy by Invited Speakers
09.00 - 09.30	Course Introduction [LEJ]	Exercise: T-Cell Receptor Repertoires [LEJ]	Exercise recap [BR]	Exercise recap [PM]	Exercise recap [MN]	Exercise recap [MN]	Exercise recap [LEJ]	Talk 1+2 NB! Meeting room 1, in B101, 1st floor
09.30 - 10.15	Micro project group work [LEJ]	Exercise: T-Cell Receptor Repertoires [LEJ]	Lecture: TCR and BCR structure [PM]	Lecture: Prediction of MHC peptide binding using PSSMs and ANNs [MN]. Session materials: Slides [PDF], Logo handout, Answer Logo handout. NN handout.	Lecture: GibbsClustering. Identifying multiple sequence motifs in large scale peptide data sets] Slides [MN	Lecture: Antibody Humanization [PM]	Lecture: Protein Drug Deimmunization [BR]	Talk 1+2 NB! Meeting room 1, in B101, 1st floor
10.15 - 10.30	Break	Break	Break	Break	Break	Break	Break	Break
10.30 - 11.15	Micro project group work [LEJ]	Exercise: T-Cell Receptor Repertoires [LEJ]	Exercise: Antibody Structure Prediction and Analysis [PM]	Lecture: Rational epitope discovery using immunoinformatics [MN]	Lecture: Supertypes and functional clustering of MHC molecules [MN]	Exercise: Antibody Humanization [PM]	Exercise:_Protein_drug_de-immunization, Ipython notebook with solution to exercise, not mandatory [BR]	Talk 3+4 NB! Meeting room 1, in B101, 1st floor
11.15 - 12.00	Micro project group work [LEJ]	Exercise recap and B-/T-Cell Receptor Genetics and Repertoires wrap up [LEJ] Suggested answers	Lecture: Linear and Conformational B-cell epitope prediction [PM]	Lecture: MHC class II binding and Performance measures [MN]	Lecture: What defines a T cel epitope? Is there any thing beyond MHC binding?, and Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN]	Lecture: Single cell technologies for T-cell epitopes presentation1 presentation2 [HP]	Lecture: Humanization and deimmunization for cancer T cell therapy molecules [PM]	Talk 3+4 NB! Meeting room 1, in B101, 1st floor
12.00 - 13.00	Lunch Break	Lunch Break	Lunch Break	Lunch Break	Lunch Break	Lunch Break	Lunch Break	Lunch Break
13.00 - 17.00	Micro project group work [LEJ]	Exercise: The Immune Epitope Database [BR]	Exercise: B cell epitope predictions [PM]	Exercise:Prediction of MHC:peptide binding using PSSM and ANN Answers: Prediction of MHC:peptide binding using PSSM and ANN	Exercise: Development of vaccines against HCV [MN] Answers	Exercise: Single cell technologies for T-cell epitopes [LEJ], Lecture: Modelling TCRpMHC interactions [LEJ]	Exercise: CAR T-cell humanisation and de-immunisation [PM]	Introduction to project work and exam [LEJ]
Learning Resources	Required Video: Tumour immunology and immunotherapy Video: Decoding cancer immunology: Hunting hidden tumours Optional None	Required Paper: The immune epitope database (IEDB) 3.0. Video: Immunology wars: A billion antibodies Video: Antibody (BCR) and TCR Diversity Video: Antibody Somatic (VDJ) Recombination I Video: Antibody Somatic (VDJ) Recombination II Book: Kuby Ch. 7: The Organization and Expression of Lymphocyte Receptor Genes Optional None	Mini Quiz Pymol license Required None Optional Paper: BepiPred 2.0 Paper: B-cell epitope prediction Video: Simplified B-cell walkthrough (Nice and easy understandable explanation of B-cells) Resource: PDB 101: Introduction to PDB Data	Required Book: Immuno. Bioinfo. Ch. 3 Book: Immuno. Bioinfo. Ch. 4 Paper: Modeling the adaptive immune system: predictions and simulations Paper: Major histocompatibility complex class I binding predictions as a tool in epitope discovery Paper: MHC Class II epitope predictive algorithms	Required Book: Immuno. Bioinfo. Ch. 13 Book: Immuno. Bioinfo. Ch. 14 Paper: Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach Optional Paper: A Quantitative Analysis of the Variables Affecting the Repertoire of T Cell Specificities Recognized after Vaccinia Virus Infection Paper: Identification and HLA-tetramer-validation of human CD4+ and CD8+ T cell responses against HCMV proteins IE1 and IE2	Required Paper: NetTCR: sequence-based prediction of TCR binding to peptide-MHC complexes using convolutional neural networks Paper: T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide–MHC complexes Paper: TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes Paper: Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring Tech report: A New Way of Exploring Immunity – Linking Highly Multiplexed Antigen Recognition to Immune Repertoire and Phenotype Optional None	Required None Optional Paper: Design and engineering of deimmunized biotherapeutics

Project Period and Exam

Project

Wednesday January 15th - Wednesday January 22nd - Project Work

Please note the following:

• The deadline for uploading the final project presentation (i.e. not a report) to DTU inside will be Wednesday January 22nd at 23.59
• It is a prerequisite for the exam to complete this assignment and as such, failure to meet the deadline will result in a failed exam
• Furthermore and very important - Each group member is responsible for all aspects of the group work and subsequent presentation

Groups and Projects 2020

Each group will consist of 4-5 students

Click here to see 2020 group list

Exam Schedule

• General exam format will be ~10-12 minutes of project presentation followed by 2-3 minutes questions, so 15 min in total and then a ~10 minute individual exam in the project and general course learning objectives
• Individual grades will be given after all group members have completed the oral exam
• In the same room as the teaching, i.e. building 208, room 062
• Conducted by Morten Nielsen and Leon Eyrich Jessen

Random draw:

set.seed(498401)
sample(1:10)
[1]  5  8  9  6  2  4  1  3 10  7

Thursday January 23rd

• 09:00 - 10:00 Group 5
• 10:00 - 11:00 Group 8
• 11:00 - 12:00 Group 9
• Lunch
• 13:00 - 14:00 Group 6
• 14:00 - 15:00 Group 2
• 15:00 - 16:00 Group 4

Friday January 24th

• 09:00 - 10:00 Group 1
• 10:00 - 11:00 Group 3
• 11:00 - 12:00 Group 10
• Lunch
• 13:00 - 14:00 Group 7