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Medicine in the light of evolution Yong Edward Zhang Computational & Evolutionary Genomics Group Key Laboratory of Zoological Systematics and Evolution Institute of Zoology, CAS http://zhanglab.ioz.ac.cn Peking University 2013/11/26 Preface First, we must insist that evolution is much more than just a topic in biology – it is the foundation of the entire discipline. Biology without evolution is like physics without gravity. Carroll, S, et al (2005) In 1973, Dobzhansky penned a short commentary titled “ Nothing in biology makes sense except in the light of evolution. ” ……Given the central position of evolutionary thought in biology, it is sadly ironic that evolutionary perspectives outside the sciences have often been neglected, misunderstood, or purposefully misrepresented. Ayala, F, et al (2012) Outline 1. Basic concepts of molecular evolution 2. Evolutionary theory of human disease 3. Application of evolutionary strategy in medicine 1. Basic concepts of molecular evolution 1.1 Speciation and tree 1.2 Ortholog and paralog 1.3 Mutation 1.4 Polymorphism and divergence 1.5 Selection 1.1 Speciation and tree Darwin, C. (1837) From tree of life to web of life Adapted from Eugene V. Koonin (2009) Nucleic Acids Res. Is it time to redefine evolutionary biology? 1.2 Ortholog and paralog Gene duplication a Hemoglobin b Hemoglobin Speciation Mouse a Hb Rat a Hb Paralogs Mouse b Hb Rat b Hb Orthologs By David Pollock Detection of orthologs We can perform BLAST all-against-all search and pull out one-to-one best hits. A more convinient way is to download Ensembl pre-computed annotation. http://www.ensembl.org Detection of orthologs (continued) http://genome.ucsc.edu Orthologs may not be functionally more similar between each other “It is widely assumed that orthologs share similar functions, whereas paralogs are expected to diverge more from each other. But does this assumption hold up on further examination? We present evidence that orthologs and paralogs are not so different in either their evolutionary rates or their mechanisms of divergence.“ Studer, R. et al. (2009) Trends in Genet. 1.3 Mutation: single nucleotide polymorphism (SNP) From Wikipedia Types of SNP Purines: Transitions A G Transversions Pyrimidines: C T David Pollock (2011) SNP in coding regions Cys Arg Lys UGU/AGA/AAG Silent Nonsense Missense UGU/CGA/AAG Cys Arg Lys UGU/GGA/AAG Cys Gly Lys Cys STOP Lys First position: 4% of all changes silent Second position: no changes silent Third position: 70% of all changes silent (wobble position) David Pollock (2011) Indels …TGTACAAAG… Insertion Deletion …TGTAAAAG… …TGTTACAAAG… Adapted from David Pollock (2011) Indels may increase the local substitution rate Tian, D. et al (2008) Nature Structural variation Sharp, A., Cheng, Z. & Eichler, E.E. (2006) Annu. Rev. Genomics Hum. Genet. 1.4 Polymorphism and divergence Innan, H & Kondrashov, F (2010) Nature Rev. Genet. Population genetics and molecular evolution is intrinsically interconnected. Conventionally, the key question for evolutionary biologists is to infer the evolutionary history of DNAs and the underlying evolutionary forces. 1.5 Positive or adaptive Selection From Wikipedia Negative or purifying selection In natural selection, negative selection or purifying selection is the selective removal of alleles that are deleterious. From Wikipedia Ka/Ks The Ka/Ks ratio (or ω, dN/dS), is the ratio of the number of non-synonymous substitutions per nonsynonymous site (Ka) to the number of synonymous substitutions per synonymous site (Ks). Ka/Ks > 1, positive selection Ka/Ks = 1, neutral evolution Ka/Ks < 1, negative selection http://abacus.gene.ucl.ac.uk/software/paml.html Outline 1. Basic concepts of molecular evolution 2. Evolutionary theory of human disease 3. Application of evolutionary strategy in medicine Evolutionary root of human disease Evolutionary root of human disease (continued) Adaptive landscape Sewall Wright Evolutionary root of human disease (continued) Randolph M. Nesse & Stephen C. Stearns (2008) Genetic basis for Mendelian diseases and common diseases is different Bernard J. Crespi (2011) Mismatch theory suggests common disease allele may follow the ancestral susceptibility (AS) model or the thrifty model Anna Di Rienzo (2006) Cardiovascular disease may be a representative case following AS model. Mitochondria is subject to a shift of selection Douglas C. Wallace (2005) Mitochondria is subject to a shift of selection (continued) Raj S Bhopal & Snorri B Rafnsson (2009) Genes underlying Coronary Heart Disease are often subject to recent adaptive selection Keyue Ding & Iftikhar J. Kullo (2009) Outline 1. Basic concepts of molecular evolution 2. Evolutionary theory of human disease 3. Application of evolutionary strategy in medicine 3. Application of evolutionary strategy in medicine 3.1 Conservation guided practice 3.2 Evolution guided practice 3.3 Opportunities with next generation sequencing (NGS) 3.1 Conservation guided practice The central dogma of Evo devo Hedgehog is important for the cuticle development Tool kit gene classification Hox Hedgehog Hedgehog as a demo case of biomedicine study Conservation as a proxy of disease gene 3.2 Evolution guided practice Paradigm shift: deal with lineage-specific trait, for example, human brain Complexity of human brain Johnson, M. et al. (2009) Neuron Expansion of human brain Rakic, P. et al. (2009) Nature Rev. Neurosci. Regulatory changes drives brain expansion “Their macromolecules are so alike that regulatory mutations may account for their biological differences.” King, M. et al. (1975) Science “Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution.” Haygood, R., et al. (2007) Nature Genet. Torgerson, D., et al. (2009) PLoS Genet. Accelerated evolution of brain genes in human Dorus, S., et al. (2004) Cell Brain genes are generally constrained “We suggest that such abundant and complex transcription may increase gene–gene interactions and constrain CDS evolution.” Wang, H., et al. (2007) PLoS Bio. Protein-level evolution appears generally irrelevant with brain evolution. Is it true? How about new gene origination? Brain preferentially recruited new genes in human lineage relative to other organ/tissues Zhang, Y. E., Landback, P., Vibranovski, M. D.& Long, M. (2011) PLoS Biology This excess is mainly contributed by fetal brain Developing neocortex contributes to most excess New genes upregulated in developing neocortex is highly enriched with primate-specific transcription factors New gene origination parallels the morphological evolution of brain Conclusion: the uniqueness of human brain is at least partially contributed by new gene origination Broad impact Human-specific genes are indeed involved in brain development Charrier, C. et al.(2012) Cell 3.3 Opportunities with next generation sequencing (NGS) “We have learned nothing from the genome” Venter, C. HGP is dead. Long live HGP! Rapidly decreased cost enabled by next generation sequencing (NGS) techniques Our journey is to the ocean of stars. Things previously impossible become possible 1. GWAS-like disease allele hunting 2. Searching for loci underlying population differentiation 3. Cancer evolution 4. Meta-genomics 1. Disease allele hunting Ng, S. et al. (2009) Nature Genet. 2. Searching for loci underlying population differentiation Yi, X., et al. (2010) Science MacLnnis, M., et al. (2011) High Alt. Med. & Biol. PCSK9 as a demo case 3. Search cancer-causing mutations by phylogenetic reconstruction Tao, Y et al. (2011) PNAS On timing of cancer progress “A quantitative analysis of the timing of the genetic evolution of pancreatic cancer was performed, indicating at least a decade between the occurrence of the initiating mutation and the birth of the parental, non-metastatic founder cell.” Yachida, S. et al. (2010) Nature 4. Meta-genomics Coghlan, M.L. et al. (2012) PLoS Genet. 4. Meta-genomics (continued) Qin, J. et al. (2012) Nature It is time to play, Many thanks. Any question is welcome! Email: [email protected]