Large confetti LF MU 2020 New Trends in Clinical Genetics: Genomic Medicine Petr Hořín Institute of Medical Genetics MUNI Institute of Experimental Biology MUNI Institute of Medical Genetics, Faculty of Veterinary Medicine Ceitec University of Veterinary and Pharmaceutical Sciences Brno [USEMAP] Large confetti Genomic medicine: prediction Green et al. 2011 Top of your professional career [USEMAP] Large confetti Precision medicine [USEMAP] Large confetti Terminology: confusion of languages Brueghel Ø Genetics Ø Genomics Systematic and complex (holistic) analysis of the genome [USEMAP] Large confetti Corn_1.jpg Corn_2.jpg Slide courtesy of Prof. Jamie McLeod, UK Lexington Corn_Maze_3.jpg Corn_maze_2.jpg Holistic approaches [USEMAP] Large confetti Reminder: the GENOME Ø> 1m DNA Ø24 chromosomes, mtDNA Ø> 3,100,000,000 bp Ø20,000–25,000 protein coding genes (< 2% of the genome) Ø> 5 MG SNPs Ø„Junk“ DNA: RNA, repeats, ?? [USEMAP] Large confetti Holism and genomics: Genome is more than the sum of its genes • 1atgtgcccgc cgcgcggcct cctccttgtg gccatcctgg tcctcctaaa ccacctggac 61 cacctcagtt tggccaggaa cctccccaca gccacaccag gcccaggaat gttccagtgc 121 ctcaaccact cccaaaacct gctgaggacc gtcagcaaca cgcttcagaa ggccaggcaa 181 accctagaat tctactcctg cacttctgaa gagatcgatc atgaggatat cacaaaagac 241 aagagcagca ccgtggcggc ctgcctcccc ctggaactcg ccccgaacga gagttgcctg 301 gcttccagag agatctcttt cataactaat gggagttgcc tgacccccgg aaaggcctct 361 tctatgatga cgctgtgcct tagcagcatc tatgaggact tgaagatgta ccaggtggag 421 ttcaaggcca tgaatgccaa gctgttgata gatcctcaga ggcagatctt tctggatgag 481 aacatgctga cagccattga caagctgatg caggccctga acttcaacag tgagactgtg 541 ccacaaaagc cctcccttga aggactggat ttttataaaa ctaaagtcaa gctctgcatc 601 cttcttcatg ccttcagaat ccgcgcagtg accatcaaca ggatgatggg ctatctgaat 661 gcttcctaa flask_animation2 flames [USEMAP] Large confetti Postgenomic era Full genome sequences determined (human genome 2001) http://www.ncbi.nlm.nih.gov/Genomes/ Annotation of genomes [USEMAP] Large confetti Genomic medicine - from theory to practice: financial aspects [USEMAP] Large confetti Genomic medicine - from theory to practice: technical advances Miniaturization and automation Chips and arrays [USEMAP] Large confetti Genomic medicine: clinical practice [USEMAP] Large confetti Genomic medicine: clinical practice [USEMAP] Large confetti An example: Clinical Genome and Exome Sequencing (CGES) [USEMAP] Large confetti Examples of practical applications [USEMAP] Large confetti Recommendations for health care providers [USEMAP] Large confetti Genomic medicine: Role of MDs in the process üUnderstanding of principles üMedical interpretation of data [USEMAP] Large confetti Another example: genomic medicine and complex disease üMendelian (OMIM) 3000 loci ü Complex 900-1000 loci Inherited diseases [USEMAP] Large confetti Why complex disease? Genomes in disease ü0.6% chromosome abnormalities ü8% Mendelian diseases, ü90% Multifactorial disease, ü1.4% other than genetic problem [USEMAP] Large confetti Simple is not always simple üThe same mutation in different genomes üThe same genome in different environments üThe same genome throughout ontogenesis üThe same genome with different microbiomes [USEMAP] Large confetti Really complex situations: different genomes in different environments ü üHow to decipher complex traits: molecular dissection üInterpretation of data and practical applications [USEMAP] Large confetti Deciphering complex traits: the omics Holistic approaches allow addressing complex issues, e.g. Mechanisms (pathogenesis) of disease [USEMAP] Large confetti Precision medicine [USEMAP] Large confetti •Disease Reaction of an organism to pathogenic insults Affected by the nature of the insults, environmental factors, current condition of the organism and its genetic make-up [USEMAP] Large confetti Resolution of complex traits Complex traits Simple traits Structural, effector, signaling, regulatory proteins and pathways and their genes [USEMAP] Large confetti Inheritance of complex traits ØSmall additive effects of individual polymorphisms, mostly SNPs, composing the complex phenotype ØGene-gene interactions identified by analysis of composed genotypes ØGenes/genotypes with major effects can be used as markers [USEMAP] Large confetti Reminder: individual variability of the human genome Single nucleotide polymorphisms (SNPs): 10 M throughout the genome cgcgcggcctcctccttgtggccatcctggtcctcctaaaccacctggac cgcgcggcctcctccttgtggtcatcctggtcctcctaaaccacctggac Insertions/deletions (indels) cgcgcggcctcctccttgtggccatcctggtcctcctaaaccacctggac cgcgcggcctcctccttgtgg-------ctggtcctcctaaaccacctggac [USEMAP] Large confetti Single nucleotide polymorphisms (SNP chips) http://www.humgen.nl/SNP_databases.html [USEMAP] Large confetti Central dogma of molecular biology DNA Protein TranslationN RNA Specific phenotype Transkripce Transcription, reverse transcription ? ? ? ? Decomposition of complex traits [USEMAP] Large confetti A tool: Genome-wide association studies (GWAS) [USEMAP] Large confetti Principles of GWAS üGenotyping of markers (SNPs) spanning the entire genome üSNP chip: up to 1 Mb üStatistical comparison of allele/genotype frequencies in groups with extreme phenotypes üIdentification of SNPs with major contribution to the phenotype studied [USEMAP] Large confetti ng [USEMAP] Large confetti Molecular dissection of complex traits Phenotypes cDNA microarrays 2 1 3 4 5 GWAS Candidate genes Candidate genes Gene pathways (custom arrays) Mechanisms of disease [USEMAP] Large confetti Immunoselekce Disease: fine mapping [USEMAP] Large confetti Pathway analysis (regulatory, signaling, metabolic pathways) http://www.polygenicpathways.co.uk/ [USEMAP] Large confetti http://www.polygenicpathways.co.uk/ Example of a really complex disease: Genes associated with atherosclerosis/hypercholesterolemia and Alzheimer's disease Family Gene Cholesterol and lipoprotein-related A2M, ABCA1, APOA1, APOA4, APOC1, APOC2, APOC3, APOE, CD36, CETP, HMGCR, LDLR, LIPA, LRP1, LRP6, LPA, LPL, OLR1, SREBF1 Cytokines CCL2, CCR2, IL1B, IL1RN, IL6,IL18, TGFB1, TNF Oxidative stress ALDH2, GSTM1, GSTT1, HFE, MPO, NOS3, PON1, PON2 Nuclear receptor and related CYP19A1, ESR1, PPARA Proteases ACE, CST3, MMP1, MMP3, SERPINE1 Miscellaneous BCHE, CBS, CD14, CRP, GNB3, HLA-A2, HTR6, ICAM1, MEF2A, MTHFR, PTGS2, TLR4 [USEMAP] Large confetti How to prioritize? [USEMAP] Large confetti An example: genetic susceptibility to infections Ramsay FEBS Lett 2012 [USEMAP] Large confetti [USEMAP] Large confetti Genetic resistance and tolerance as defined by Doeschl/Wilson & Kyriazakis (2012) •*Resistance: ability to reduce pathogen replication in the host •vs. •*Tolerance: ability to maintain homeostasis in the presence of replicating pathogen • • • non-genetic factors, selection • • • * Difficult to uncoupling them • Different genes may be involved Susceptibility Tolerance, carrier status, shedding Resistance [USEMAP] Large confetti Infectious disease as a result of host-pathogen interactions „The infection must be seen in the context of the countermeasures produced by the parasite, and judged as a dynamic interaction of host and parasite rather than the clearance of an inert antigen by the host immune response“ Riffkin et al., 1996 [USEMAP] Large confetti Infectious disease as a result of host-pathogen interactions üDisease as a defense reaction of the host üOften unique host/pathogen combinations üIndividual variability in using different immunological mechanisms against the same pathogen üSymptomatologies determined mostly by the pathogens or by the host [USEMAP] Large confetti Scylla and Charybdis of immune responses: genetic variation •The dilemma: •too high/too low immune responses? Protective immunity Resistance to infection Autoimmunity Inflammation [USEMAP] Large confetti Genetic susceptibility to disease as a complex trait Baker, Antonovics 2012 [USEMAP] Large confetti Immunity-related (IR) genes: the immunogenome üGenes involved in host immune reactions ü Immunome: products of IR genes ü Despite the same biological importance, IR genes underlie many different functions in all branches of immunity [USEMAP] Large confetti •Immunogenome and immunome 5% of the mammalian genome (~1,000 human genes) are protein coding genes related to immune mechanisms Ortutay et al. Immunogenetics 2007 [USEMAP] Large confetti Immunity-related (IR) genes and disease üImmune functions as simple and/or complex traits (Mendelian vs. complex inheritance) üImmune functions in mechanisms of infectious diseases [USEMAP] Large confetti Genetic resistance/susceptibility to infections ü Genes affecting health (interactions with environmental factors) ü Their polymorphisms are not causative for diseases, but they influence reactions of the host to environmental pathogens ü Pathogens as a driving force of evolution: IR genes/immunogenome have been shaped by evolutionary interactions with pathogens, ü In practical terms, resistance/susceptibility are usually relative to a population average [USEMAP] Large confetti Genetic resistance/susceptibility to infections: modes of inheritance Casanova, Abel EMBO J 2007 [USEMAP] Large confetti Mendelian inheritance ØMajor effects ØExpected to result from low-frequency variants ØLess knowledge than for complex traits Picard et al Curr Opin Immunol 2006 [USEMAP] Large confetti GWAS and infections in humans De Bakker, Telenti Nature Genet 2010 [USEMAP] Large confetti Genetic resistance/susceptibility to infections: untranslated genome üMost GWAS hits observed in (protein) non-coding regions üMany SNPs found in regulatory regions of protein coding genes üEffects on expression and consequently on diseases, including infections [USEMAP] Large confetti Genetic resistance/susceptibility to infections: untranslated genome [USEMAP] Large confetti Mechanisms of immunity-related diseases studied with genomic tools ü Infections ü Allergies ü Autoimmunity ü Complex immunopathologies ü [USEMAP] Large confetti Examples of genetic susceptibility to infections üNorovirus, rotavirus (FUT2) üAIDS (CCR5) üMalaria (Duffy) üCOVID 19 (AB0, IFN type 1) [USEMAP] Large confetti [USEMAP] Large confetti Individual variation in antibody responses [USEMAP] Large confetti Genetics of vaccination üIndividual variation in post-vaccination IRs ü üPharmacogenomics [USEMAP] Large confetti Normal (Gaussian) distribution gauss_kurve [USEMAP] Large confetti [USEMAP] Large confetti Genetics of vaccination [USEMAP] Large confetti • •Genetic susceptibility to disease •as a complex trait [USEMAP] Large confetti ØClinical: definition of genes and alleles responsible for individual susceptibility to infection: > 200 PIDs ØEpidemiological: definition of genes and alleles responsible individual susceptibility to infection, GWAS ØEvolutionary: study of genes selected by previous infections: evolution/speciation, signatures of selection (interspecies/within species), population diversity Genetics of infectious disease in humans (Quintana-Murci et al. Nature Immunology 8, 2007: 1165-1171 [USEMAP] Large confetti Evolutionary aspects http://ancients-bg.com/wp-content/uploads/2016/04/0021.jpg üMigrations and sympatry of hominoid populations, sharing different infections üLower overall genome diversity and mostly lower IR gene in Neanderthals üHigher MHC gene diversity üArchaic Neanderthal haplotypes TLR6-TLR1-TLR10 üSusceptibility to COVID 19, ethnic differences [USEMAP] Large confetti Ethical issues: how to cope with information generated by genomic techniques Examples üMendelian diseases: e.g. carrier tests, PGD üComplex diseases e.g. interpretation of GWAS, DTC ü Only people understanding principles can cope with this problem [USEMAP] Large confetti Practical applications Minimum variant for you üTo know, when and where to refer a patient for a genetic consultation üTo know how to interpret clinical geneticist’s reports üTo know when not to refer a patient for a genetic consultation [USEMAP]