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Computational Systems Biology of Cancer:

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Presentation on theme: "Computational Systems Biology of Cancer:"— Presentation transcript:

1 Computational Systems Biology of Cancer:

2 Professor of Computer Science, Mathematics and Cell Biology
Bud Mishra Professor of Computer Science, Mathematics and Cell Biology Courant Institute, NYU School of Medicine, Tata Institute of Fundamental Research, and Mt. Sinai School of Medicine


4 War on Cancer “Reports that say that something hasn't happened are always interesting to me, because as we know, there are known knowns; there are things we know we know. We also know there are known unknowns; that is to say we know there are some things we do not know. But there are also unknown unknowns – the ones we don't know we don't know.” US Secretary of Defense, Mr. Donald Rumsfeld, Quoted completely out of context.

5 Introduction: Cancer and Genomics:
What we know & what we do not “Cancer is a disease of the genome.”

6 Outline Genomics Genome Modification & Repair
Segmental Duplications Models

7 Genomics Genome: Hereditary information of an organism is encoded in its DNA and enclosed in a cell (unless it is a virus). All the information contained in the DNA of a single organism is its genome. DNA molecule can be thought of as a very long sequence of nucleotides or bases: S = {A, T, C, G}

8 Complementarity DNA is a double-stranded polymer and should be thought of as a pair of sequences over S. However, there is a relation of complementarity between the two sequences: A , T, C , G

9 DNA Structure. The four nitrogenous bases of DNA are arranged along the sugar- phosphate backbone in a particular order (the DNA sequence), encoding all genetic instructions for an organism. Adenine (A) pairs with thymine (T), while cytosine (C) pairs with guanine (G). The two DNA strands are held together by weak bonds between the bases.

10 Structure and Components
Complementary base pairs (A-T and C-G) Cytosine and thymine are smaller (lighter) molecules, called pyrimidines Guanine and adenine are bigger (bulkier) molecules, called purines. Adenine and thymine allow only for double hydrogen bonding, while cytosine and guanine allow for triple hydrogen bonding.

11 Inert & Rigid Thus the chemical (hydrogen bonding) and the mechanical (purine to pyrimidine) constraints on the pairing lead to the complementarity and makes the double stranded DNA both chemically inert and mechanically quite rigid and stable.

12 The Central Dogma The central dogma(due to Francis Crick in 1958) states that these information flows are all unidirectional: “The central dogma states that once `information' has passed into protein it cannot get out again.” DNA RNA Protein Transcription Translation

13 The Central Dogma “…The transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein, may be possible, but transfer from protein to protein, or from protein to nucleic acid is impossible. Information means here the precise determination of sequence, either of bases in the nucleic acid or of amino acid residues in the protein.” DNA RNA Protein Transcription Translation

14 The New Synthesis DNA RNA Protein Genome Evolution Selection
Part-lists, Annotation, Ontologies Transcription Translation Genotype Phenotype

15 Cancer Initiation and Progression
Mutations, Translocations, Amplifications, Deletions Epigenomics (Hyper & Hypo-Methylation) Alternate Splicing Cancer Initiation and Progression Proliferation, Motility, Immortality, Metastasis, Signaling

16 Multi-step Nature of Cancer:
Cancer is a stepwise process, typically requiring accumulation of mutations in a number of genes. ~6-7 independent mutations typically occur over several decades: Conversion of proto-oncogenes to oncogenes Inactivation of tumor suppressor gene

17 Amplifications & Deletions
Mutation in a TSG Epigenomics Conversion of a Proto-Oncogene Deletion of a TSG Deletion of a TSG

18 P53 Gene (TSG)

19 The Cancer Genome Atlas
Obtain a comprehensive description of the genetic basis of human cancer. Identify and characterize all the sites of genomic alteration associated at significant frequency with all major types of cancers.

20 The Cancer Genome Atlas
Increase the effectiveness of research to understand tumor initiation and progression, susceptibility to carcinogensis, development of cancer therapeutics, approaches for early detection of tumors & the design of clinical trials.

21 Specific Goals Identify all genomic alterations significantly associated with all major cancer types. Such knowledge will propel work by thousands of investigators in cancer biology, epidemiology, diagnostics and therapeutics.

22 To Achieve this goal … Create large collection of appropriate, clinically annotated samples from all major types of cancer; and Characterize each sample in terms of: All regions of genomic loss or amplification, All mutations in the coding regions of all human genes, All chromosomal rearrangements, All regions of aberrant methylation, and Complete gene expression profile, as well as other appropriate technologies.

23 Biomedical Rationale Cancer is a heterogeneous collection of heterogeneous diseases. For example, prostate cancer can be an indolent disease remaining dormant throughout life or an aggressive disease leading to death. However, we have no clear understanding of why such tumors differ.

24 Biomedical Rationale Cancer is fundamentally a disease of genomic alteration. Cancer cells typically carry many genomic alterations that confer on tumors their distinctive abilities (such as the capacity to proliferate and metastasize, ignoring the normal signals that block cellular growth and migration) and liabilities (such as unique dependence on certain cellular pathways, which potentially render them sensitive to certain treatments that spare normal cells).

25 History 1960s The genetic basis of cancer was clear from cytogenetic studies that showed consistent translocations associated with specific cancers (notably the so-called Philadelphia chromosome in chronic myelogenous leukemia). 1970s Recognize specific cancer-causing mutations through recombinant DNA revolution of the 1970s. The identification of the first vertebrate and human oncogenes and the first tumor suppressor genes, These discoveries have elucidated the cellular pathways governing processes such as cell-cycle progression, cell-death control, signal transduction, cell migration, protein translation, protein degradation and transcription. For no human cancer do we have a comprehensive understanding of the events required.

26 Scientific Foundation for a Human Cancer Genome Project
Gene resequencing. Specific gene classes (such as kinases and phosphatases) in particular cancer types. Epigenetic changes. Loss of function of tumor suppressor genes by epigenetic modification of the genome — such as DNA methylation and histone modification. Genomic loss and amplification. Consistent association with genomic loss or amplification in many specific regions, indicating that these regions harbor key cancer associated genes Chromosome rearrangements. Activate kinase pathways through fusion proteins or inactivating differentiation programs through gene disruption. Hematological malignancies: a single stereotypical translocation in some diseases (such as CML) and as many as 20 important translocations in others (such as AML). Adult solid tumors have not been as well characterized, in part owing to technical hurdles.

27 Human Genome Structure

28 EBD J.B.S. Haldane (1932): Susumu Ohno (1970):
“A redundant duplicate of a gene may acquire divergent mutations and eventually emerge as a new gene.” Susumu Ohno (1970): “Natural selection merely modified, while redundancy created.”

29 Evolution by Duplication
Genome Evolution Non-random distribution in Genomic data Short words frequency Protein family size Long range orrelation Motifs in cellular etworks Leu3 LEU1 BAT1 ILV2 UMP UDP UTP CTP Regulatory motifs Metabolic pathways Interaction clusters Functional modules Living cells Organism ?

30 Human Condition

31 Mer-scape… Overlapping words of different sizes are analyzed for their frequencies along the whole human genome Red: 24-mers, Green: 21-mers Blue:18 mers Gray:15 mers To the very left is a ubiquitous human transposon Alu. The high frequency is indicative of its repetitive nature. To the very right is the beginning of a gene. The low frequency is indicative of its uniqueness in the whole genome.

32 Doublet Repeats Serendipitous discovery of a new uncataloged class of short duplicate sequences; doublet repeats. almost always < 100 bp (Top) . The distance between the two loci of a doublet is plotted versus the chromosomal position of the first locus. (Bottom) : Distribution of doublets (black) and segmental duplications (red) across human chromosome 2

33 Segmental Duplications
3.5% ~ 5% of the human genome is found to contain segmental duplications, with length > 5 or 1kb, identity > 90%. These duplications are estimated to have emerged about 40Mya under neutral assumption. The duplications are mostly interspersed (non-tandem), and happen both inter- and intra-chromosomally. Human From [Bailey, et al. 2002]

34 The Model f - - f ++ f + - f - - f ++ f + -
Mutation accumulation in the duplicated sequences f - - f ++ f + - insertion deletion or mutation Duplication by recombination between repeats Duplication by recombination between other repeats or other mechanisms

35 The Mathematical Model
α 1-α-2β 1-α-2γ 1-α-β/2-γ γ β/2 h0 h1 h1++ h1-- h0+- h0-- h0++ f - - f ++ f + - Time after duplication 0 ≤ d < ε ε ≤ d < 2ε (k-1)ε ≤ d < kε h1: proportion of duplications by repeat recombination; h1++: proportion of duplications by recombination of the specific repeat; h1- - : proportion of duplications by recombination of other repeats; h0: proportion of duplications by other repeat-unrelated mechanism; h0++: proportion of h0 with common specific repeat in the flanking regions; h0+-: proportion of h0 with no common specific repeat in the flanking regions; h0- -: proportion of h0 with no specific repeat in the flanking regions; α: mutation rate in duplicated sequences; β: insertion rate of the specific repeat; γ: mutation rate in the specific repeat; d: divergence level of duplications; ε: divergence interval of duplications.

36 h1Alu ≈ 0.76; h1++Alu ≈ 0.3; h1L1 ≈ 0.76; h1++ L1 ≈ 0.35.
Model Fitting Diversity: f - - f ++ f + - Alu L1 The model parameters (αAlu, βAlu, γAlu, αL1, βL1, γL1) are estimated from the reported mutation and insertion rates in the literature. The relative strengths of the alternative hypotheses can be estimated by model fitting to the real data. h1Alu ≈ 0.76; h1++Alu ≈ 0.3; h1L1 ≈ 0.76; h1++ L1 ≈ 0.35.

37 Polya’s Urn Random drawn Duplication Put back

38 Repetitive Random Eccentric GOD
Genome Organizing Devices (GOD) Polya’s Urn Model: F’s: functions deciding probability distributions F1 (decide an initial position) F2 (decide selected length) F3 (decide copy number) k copies F4 (decide insertion positions)

39 DNA polymerase stuttering (replication slippage)
Deletion: Insertion (duplication): normal replication DNA polymerase normal replication polymerase pausing and dissociation polymerase pausing and dissociation 3’ realignment and polymerase reloading 3’ realignment and polymerase reloading

40 Transposons ~ causes: deletions and duplications
Transposon actions in genomic DNA: Donor DNA Duplication: transposon DNA intermediates Target DNA Transposase cuts in target DNA Deletion: transposon IS IS Transposon looping out Transposon inserted Transposon deleted DNA is repaired-resulting in a duplication of the transposon and target site

41 DNA mismatch repair mechanism ~ prevents duplications and deletions
Mismatch recognition on daughter strand MSH6 MSH2 Degradation of the mismatched daughter strand in the a-loop MSH6 MSH2 PMS2 MLH1 MSH2 MSH6 MLH1 PMS2 Exo DNA a-loop formation by translocation through the proteins Refilling the gap by DNA polymerase Corrected daughter strand DNA polymerase

42 Graph Model Graph description A. Deletion: With probability p0
G = {V, E}, G is a directed multi-graph; V  {Vi, all n-mer’s, i = 1…4n}, ; E  { (Vi , Vj ), when Vi represents the n-mer immdiately upstream of the n-mer represented by Vj in the genomic sequence}; ki = incoming (or outgoing) degree of node i (Vi) = copy number of the n-mer represented by Vi; During the graph evolution, at each iteration, one of the following happens: deletion (with probability p0), duplication (with probability p1) or substitution (with probability q). p0 + p1 + q = 1. For an arbitrary node Vi , the probabilities of one of the above events happens is as follows: B. Duplication:With probability p1 C. Substitution: With probability q

43 Model Fitting Real distribution from genome analysis
Expected distribution from random sequences Model fitting results Model fitting results: Initial condition.

44 Model Fitted Parameter
The substitution rate, q, increases with the sizes of mer’s. The ratio between duplication and deletion rate, p1/p0, increases with sizes of mer’s. The substitution rate, q, tends to decrease when the genome sizes are larger. Especially, q is much smaller in eukaryotic genomes than in prokaryotic genomes. Mer size 6 mer 7 mer 8 mer 9 mer q p1/p0 M. genitalium 0.0176 1.1 0.0436 0.1587 1.5 0.3222 M. pneumoniae 0.0319 0.1151 0.2309 0.4363 P. abyssi 0.0269 0.0672 1.2 0.1778 1.4 0.3897 P. horikoshii 0.0234 0.0443 0.1390 1.3 0.3456 P. furiosus 0.0213 0.0384 0.1119 0.3114 H. pylori 0.0180 0.0320 0.0925 0.2262 H. influenzae 0.0202 0.0366 0.1364 0.2802 S. tokodaii S. subtilis 0.0187 0.0326 0.1139 0.2585 E. coli K12 0.0207 0.0334 0.0698 0.2389 S. cerevisiae 0.0113 0.0459 0.1311 C.elegans -- 0.0076 0.0115 0.0275 Two independent parameters are fitted. And there are some trends: The value of q gets bigger with the size of mer. The value of p1/p0 also seems to get bigger with the size of mer. The value of q seems to go smaller when genome size increases. Q: Do the parameters have any biological meanings? A: Yes, refer to supplementary slides – under the assumption of power—law distribution of the lengths of duplication and deletion events, the parameter can be predictive for length and frequency of duplication and deletion events in a specific genome.

45 J.B.S. Haldane “If I were compelled to give my own appreciation of the evolutionary process…, I should say this: In the first place it is very beautiful. In that beauty, there is an element of tragedy…In an evolutionary line rising from simplicity to complexity, then often falling back to an apparently primitive condition before its end, we perceive an artistic unity … “To me at least the beauty of evolution is far more striking than its purpose.” J.B.S. Haldane, The Causes of Evolution

46 Human Cancer Genome

47 Cancer Normal epithelial mucosa Neoplastic polyp

48 A Challenge “At present, description of a recently diagnosed tumor in terms of its underlying genetic lesions remains a distant prospect. Nonetheless, we look ahead 10 or 20 years to the time when the diagnosis of all somatically acquired lesions present in a tumor cell genome will become a routine procedure.” Douglas Hanahan and Robert Weinberg Cell, Vol. 100, 57-70, 7 Jan 2000

49 Karyotyping

50 CGH: Comparative Genomic Hybridization.
Equal amounts of biotin-labeled tumor DNA and digoxigenin-labeled normal reference DNA are hybridized to normal metaphase chromosomes The tumor DNA is visualized with fluorescein and the normal DNA with rhodamine The signal intensities of the different fluorochromes are quantitated along the single chromosomes The over-and underrepresented DNA segments are quantified by computation of tumor/normal ratio images and average ratio profiles Amplification Deletion

51 CGH: Comparative Genomic Hybridization.

52 Microarray Analysis of Cancer Genome
Normal DNA Normal LCR Tumor DNA Tumor LCR Label Hybridize Representations are reproducible samplings of DNA populations in which the resulting DNA has a new format and reduced complexity. We array probes derived from low complexity representations of the normal genome We measure differences in gene copy number between samples ratiometrically Since representations have a lower nucleotide complexity than total genomic DNA, we obtain a stronger specific hybridization signal relative to non-specific and noise

53 Copy Number Fluctuation

54 Measuring gene copy number differences between complex genomes
Hybridize to 500,000 features microarray Genomic DNA patient samples Statsitical Analysis Compare the genomes of diseased and normal samples Error Control: The use of representations augmenting microarrays Representations reproducibly sample the genome thereby reducing its complexity. This increases the signal-to-noise ratio and improves sensitivity Statistical Modeling the sources of Noise Bayesian Analysis

55 Nattering Nabobs of Negativism
Some scientists are concerned about the cost and the possibility that a project of this scale could take money away from smaller ones… Craig Venter, who led a private project to determine the human DNA blueprint in competition with the human genome project, said it would make more sense to look at specific families of genes known to be involved in cancer. Lee Hood, president of the Institute for Systems Biology, has called the premise of the Cancer Genome Project “naïve,” suggesting that signal-to-noise issues its researchers are likely to encounter will be “absolutely enormous.”

56 Challenges ArrayCGH data is noisy!
Better computational biology algorithms Better statistical modeling…In some technologies, the noise is systematic (e.g., affy SNP-chips) Better bio-technologies (GRIN: Genomics, Robotics, Informatics, Nanotechnology) No efficient technology for epigenomics, translocations or de novo mutations. Algorithms for multi-locus association studies Systems view of cancer by integrating data from multiple sources: Genomic, Epigenomic, Transcriptomic, Metabolomic & Proteomic. Regulatory, Metabolic and Signaling pathways

57 Mishra’s Mystical 3M’s Rapid and accurate solutions
Bioinformatic, statistical, systems, and computational approaches. Approaches that are scalable, agnostic to technologies, and widely applicable Promises, challenges and obstacles— Measure Mine Model

58 Discussions Q&A…

59 Answer to Cancer “If I know the answer I'll tell you the answer, and if I don't, I'll just respond, cleverly.” US Secretary of Defense, Mr. Donald Rumsfeld.

60 To be continued… Break…

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