22145 Immunological Bioinformatics Course Programme January 2021

COURSE PLAN FOR 2021

EXAM

The pdf with the exam will be uploaded here on Friday January 22nd, 13 - 15hs

Guidelines

• The exam will be made available at the wiki at 13.00hs. Upload a pdf with your answers no later than 15.00hs on DTU inside written exam assignment.
• You must connect at Zoom 5 minutes before the exam, and have the camera turned ON during the whole exam. Failing to meet this requirement will invalidate the exam.
• This is an individual exam. Remember sharing or copying answers is not allowed and will be severely punished according to DTU rules and code-of-honor.

Information for Course Participants

Course Format

• NEWS! Due to new restrictions on Covid19 this course will be completely conducted online and all classes will be recorded and uploaded
• Due to group work on some classes, it will be mandatory that you are connected and work online on the allocated time for those
• This will be needed for the entire first day, the question and answer sessions, and the final exam
• Classes will be a mixture of lectures, group work and individual exercises
• Most of the group work will consist of computer exercises, where students are required to use their laptops
• General Question and Answer will be live and uploaded after the session
• Specif Question and Answers for exercise-lectures will be held on Piazza, where you need to create an user
• 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 Resources

• Official course website
• Official course description
• ZOOM link for live classes(registration with DTU mail needed)
• Piazza link for Q&A on exercises
• 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

• [CB] Carolina Barra
• [PM] Paolo Marcatili
• [MN] Morten Nielsen
• [BR] Birkir Reynisson
• [HP] Helle Rus Povlsen
• [MV] Milena Vujovic
• [AM] Alessandro Montemurro

General Daily Schedule

• 09.00 - 12.00 Lectures
• 12.00 - 13.00 Lunch
• 13.00 - 13.30 Live sessions Q&A
• 13.30 - 17.00 Exercises

Location

• NOTE: This edition of the course will be completely online

Profiles of Invited Speakers for Mini Symposium

• 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: PhD, Adjunkt Professor Sunil Kumar Saini, Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark
• Biomedical Industry perspective: upon confirmation.
• Bioinformatics Industry perspective: PhD, Head of Bioinformatics Monika Sekelja, Vaccibody A/S

2021 Course Schedule Overview

Teaching Day 1-8

	Monday Jan. 4th	Tuesday Jan. 5th	Wednesday Jan. 6th	Thursday Jan. 7th	Friday Jan. 8th	Monday Jan. 11th	Tuesday Jan. 12th	Wednesday Jan. 13th
Topic	Introduction and Basic Immunology	T-Cell Epitopes	Antigen Processing and Presentation, HLA Clustering, and Vaccine Design	Protein Structure of B-/T-Cell Receptors and B-Cell Epitopes	Immunopeptidomics, T-Cell Repertoires and the IEDB	Antibody Humanization and T-Cell Interaction Models	De-Immunization and Chimeric Antigen Receptor (CAR) Immunotherapy	Mini-symposium on Immunoinformatics by Invited Speakers
09.00 - 09.30	Course Introduction Live on Zoom Recording: MP4 [CB]	Lecture: Prediction of MHC peptide binding Part 1 [MN]. Session materials: Slides [PDF]. Recording: [MP4], Logo handout: [PDF], Answer Logo handout Logo handout Recording [MP4].	Lecture: MHC motif deconvolution - Identifying sequence motifs in large scale ligand data sets [MN]. Session materials: Slides [PDF]. Recording: [MP4].	Lecture: TCR and BCR structure. Recording: Antibody Modelling [PM] Solution	Lecture: Immunopeptidomics Live on Zoom Recording: MP4 [CB]	Lecture: Antibody Humanization Video [PM]	Lecture: Protein Drug Deimmunization Live on Zoom pdf mp4 [BR]	Talk 1: Cancer immunotherapy in the clinic. Marco Donia Live! video
09.30 - 10.15	Micro project group work Live on Zoom [CB]	Lecture: Prediction of MHC peptide binding part 2 [MN]. Session materials: Slides [PDF]. Recording: [MP4]. NN handout [PDF]. NN handout Recording [MP4].	Lecture: What defines a T cell epitope? Is there any thing beyond MHC binding? [MN] Session materials: Slides [PDF]. Recording: [MP4].	Exercise: Antibody Structure Prediction and Analysis Recording: Exercise [PM]	Exercise files: Peptides Alleles_list Answers: AnswersLive on Zoom [CB]	Exercise: Antibody Humanization [PM]	Exercise: Protein Drug Deimmunization [BR]	Talk 2: SARS-CoV-2 full genome profiling for T cell immunity and immunodominance in COVID-19 infection. Sunil Kumar Saini Live! video
10.15 - 10.30	Break	Break	Break	Break	Break	Break	Break	Break
10.30 - 11.15	Micro project group work Live on Zoom [CB]	Lecture: Prediction of MHC peptide binding part 3 [MN]. Session materials: Slides [PDF]. Recording: [MP4].	Lecture: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN]. Session materials: Slides [PDF]. Recording: [MP4].	Lecture: Linear B-cell epitope prediction. Recording: [1] [PM]	Lecture: T-Cell Receptor Repertoires Live on Zoom Slides Recording: [[MP4] [MV]	Lecture: Single cell technologies for T-cell epitopes Single Cell and NetTCR Project videoLive on Zoom [HP]	Lecture: Humanization and deimmunization for cancer T cell therapy molecules video [PM]	Talk 3: The utilization of bioinformatics to guide drug design. Monika Sekelja Live! video
11.15 - 12.00	Micro project group work Live on Zoom [CB]	Lecture: Performance measures [MN]. Recording: [MP4].	Lecture: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN] cont.	Lecture: Conformational B-cell epitope prediction. Recording: [2][PM]	Lecture: The Immune Epitope Database & Tools Live on Zoom PDF mp4 [BR]	Lecture: Modelling TCRpMHC interactions videoLive on Zoom [AM]	Lecture: Humanization and deimmunization for cancer T cell therapy molecules [PM]	Talk 4: TBC Live!
12.00 - 13.00	Lunch Break	Lunch Break	Lunch Break	Lunch Break	Lunch Break	Lunch Break	Lunch Break	Lunch Break
13.00 - 13.30	Live: Q&A Session [CB]	Live: Quiz: MHC binding. Q&A Session [MN]. Recordings: R1 [MP4]. R2 [MP4]. R3 [MP4].	Live: Exercise recap [MN]. Quiz: MHC processing, epitope discovery and vaccine design. Q&A Session [MN]. Recordings: R1 [MP4].	Live: Exercise recap [MN] Recordings: R1 [MP4].	Live: Exercise recap Recordings: [MP4] [PM]	Live: Exercise recap video [CB] and [BR]	Live: Exercise recap video [HP]	Live: Exercise recap [PM]
13.30 - 17.00	Micro project group work Live on Zoom Presentations_part1 Presentations_part2 [CB]	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: B cell epitope predictions [PM]	Exercise: T-Cell Receptor Repertoires [MV] Suggested answers Exercise: IEDB [BR]	Exercise: Single cell technologies for T-cell epitopes [HP]	Exercise: CAR T-cell humanisation and de-immunisation [PM]	Live on Zoom Introduction to project and exam [CB]
Learning Resources	Required Paper: Peptide Presentation to T Cells: Solving the Immunogenic Puzzle Video: Tumour immunology and immunotherapy Video: Decoding cancer immunology: Hunting hidden tumours Optional Video: Back to Basics	Required Book: Immuno. Bioinfo. Ch. 3 Book: Immuno. Bioinfo. Ch. 4 Paper: Modeling the adaptive immune system: predictions and simulations Paper: Immunoinformatics: Predicting Peptide–MHC Binding Optional Paper: NNAlign_MA; MHC Peptidome Deconvolution for Accurate MHC Binding Motif Characterization and Improved T-cell Epitope Predictions Paper: Improved Prediction of MHC II Antigen Presentation through Integration and Motif Deconvolution of Mass Spectrometry MHC Eluted Ligand Data	Required Book: Immuno. Bioinfo. Ch. 13 Book: Immuno. Bioinfo. Ch. 14 Paper: T Cell Epitope Predictions Optional Paper: Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach 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	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	Rstudio: Get it Quick guide Getting started Required 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 Paper: The immune epitope database (IEDB) 3.0. Optional None	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 13th - Wednesday January 20nd - Project Work

Please note the following (***time has been updated***):

• The deadline for uploading the final project Poster presentation (i.e. not a report) to DTU inside will be Wednesday January 20nd at 11.59AM
• 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 2021

• Groups will be preset based on educational diversity

• The groups list for 2021

Exam Schedule

• General exam format will consist on 2 parts (course learning objectives):

 Oral presentation of the poster project ~10 minutes for all group presentation + 5 minutes for questions (15 minutes total) 
  Date: January 21st 2021 (specific times per group to be announced)

 Written exam ~20 questions 2hs, all conducted online on DTU Inside
  Date: January 22st 2021

• Individual grades will be given after the finalization of the course