Cursul de Medicina Moleculara 2015 contine elemente din : Materialele prezentate sunt exclusiv destinate procesului de invatamant

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1 Cursul de Medicina Moleculara 2015 contine elemente din : Materialele prezentate sunt exclusiv destinate procesului de invatamant

2 Cellules souches Cellules souches adultes- cellules souches hématopoïétiques Multipotence, totipotence, médecine régénérative Transplantation Cellules souches embryonnaires: renouvellement et différenciation Clonage, transfert du noyau de cellule somatique Cellules pluripotentes induites (ips)

3 Lodish et al. Molecular Cell Biology 2000, Freeman Press * Alberts et al., Molecular Biology of the Cell, 2002, Garland Science

4 Embryonic Stem Cells: Totipotent Cells Les cellules ES - les cellules sont totipotentes et peuvent évoluer vers tous les types de cellules et de tissus lorsqu elles sont injectées dans des blastocystes - en culture, elles se différencient via des corps embryonnaires dans de nombreux types de tissus mais de façon désordonnée - expression de nombreux gènes impliqués dans la totipotence * Les cellules ES se renouvellent dans un milieu avec du Leukemia Inhibitory Factor (LIF) En absence du LIF, les cellules ES se différencient

5 Embryonic Stem Cells Mouse ES renew in Leukemia Inhibitory Factor medium Renewal requires: Nanog (homeodomein protein, Tir Na Nog:= land of ever young) Oct 4 (POU transcription factor) Sox2 and FoxD3 are Oct4 partners Nanog allows mouse ES cells to renew without LIF Nanog is a 305 amino acid protein that binds to DNA promoter at the consensus sequence C/GG/AC/GCG/CATTANG/C

6 Constantinescu SN J Cell Mol Med 2000 *

7 * Lodish et al. Molecular Cell Biology 2000, Freeman Press

8 * ES cells induce teratomas when injected in adult mice

9 Constantinescu SN J Cell Mol Med 2000 *

10 Embryon humain au stade blastocytaire

11 Inner Cell Mass HuES cell line

12 15 human ES cell lines, NIH * Culture on mitotically inactivated MEFs FGF, LIF, human plasma Initially 150 h doubling time After extended passages: trisomy, chromosome 12 additions to chromosome 2

13 Ethical problem: destruction and use of human embryos

14 Major Question in Biology Is Terminal Differentiation Reversible?

15 Socolovsky et al., Proc. Natl. Acad. Sci. USA 1998, 95, 6574

16 Phenotype Function Alberts et al., Molecular Biology of the Cell, 2002, Garland Science

17 In the 1950s, no one knew if all cells in the body had the same genes," says John. "The hypothesis was that as cells grew they lost the genes they didn't need." His finding proved that cells all carry the same genes, with other factors telling the cell which to use. The biologist John Haldane dubbed John's achievement "cloning", borrowing a term from plant biology, and a new field was born. A female Xenopus frog the first sexually mature adult vertebrate produced by nuclear transplantation which Gurdon created in the 1950s. Photograph: J B Gurdon

18 Les noyaux de cellules spécialisées (complètement différenciées comme cellules kératinisées de peaux de grenouilles) conservent le potentiel d induire la formation de tous types cellulaires et de diriger le développement d un organisme chez les amphibiens. Adult frogs derived from the nuclei of single somatic cells. GURDON JB. Dev Biol Apr;4:

19 Ian Wilmut s cloning of Dolly Kara Rogers, Encyclopedia Britannica, Biography of Sir Ian Wilmut

20 Isolation of adult cells: mammary gland cells from a six-year-old ewe. Use of these cells as nucleus donors for transfer into non-fertilized egg cells= somatic cell nuclear transfer (SCNT). Wilmut and his team constructed 277 embryos containing adult cell nuclei that were implanted into 13 surrogate mothers, only one of which became pregnant. This pregnancy was carried to term successfully. The Finn Dorset lamb, born on July 5, 1996, was Dolly. Many embryos died following implantation, immediately following birth or were born with birth defects. Kara Rogers, Encyclopedia Britannica, Biography of Sir Ian Wilmut

21 3% of transferred nuclei result in viable clones Sheep, cow, rabbit, mouse, cat, pig, goat clones The Finn Dorset lamb, born on July 5, 1996, was Dolly Dolly, the Sheep, died on February 14, 2003 (7 years) Nature March 3, 2003

22 T and B cell nuclei from peripheral node- 1,000 transplanted oocytes, 41 blastocysts, 2 ES cell lines Hochedlinger and Jaenisch Nature 2002, 415, 1035

23 Production of a heavy chain B Van den Eynde and P. Coulie

24 Production of a light chain B Van den Eynde and P. Coulie

25 Induction des cellules souches pluripotentes d un embryon de souris et de cultures de fibroblastes adultes par des facteurs définis

26 "The Nobel Prize in Physiology or Medicine 2012". Nobelprize.org. 21 Oct

27 Adult differentiated cells: tranduction with retroviruses (lenti) coding for 4 genes: Klf4+Sox2+Myc+Oct4 results in reprogramming from a differentiated to a pluripotent cell= induced pluripotent cells ips which resemble functionally the ES cells. Like ES cells, ips cells must pass three tests: 1) Formation of embryoid bodies in vitro with chaotic differentiation to all cell types. 2) Injection to adult mice (congenic for ips or immunodeficient for human ips cells) results in teratoma formation in vivo. 3) Introduction of mouse ips cells in blastocysts leads to the presence in the born mouse of ips descendants in all tissues.

28 Constantinescu SN J Cell Mol Med 2000 *

29 * ips cells induce teratomas when injected in adult mice Les cellules souches pluripotentes induites provoquent des tératomas lorsqu elles sont injectées chez la souris adulte

30 * Lodish et al. Molecular Cell Biology 2000, Freeman Press

31 Klf4+Sox2+Myc+Oct4= ips or ES-like

32 Brambrink et al.

33 4 facteurs sont nécessaires pour la reprogrammation Oct4, Sox2, KIF4, c-myc La reprogrammation avec des lenti- (retro-) virus requiert une intégration dans le génome qui peut être oncogénique. On a créé des souris transgéniques exprimant GFP en fusion avec des gènes normalement exprimés par des cellules ES. Certaines souris génétiquement modifiées ont été davantage modifiées pour également exprimer de façon transgénique un, deux ou trois des quatre facteurs de reprogrammation. Un criblage des bibliothèques de petites molécules a été effectué sur des cellules appartenant à ces souris afin d identifier de petites molécules capables de remplacer le facteur manquant.

34 4 Factors are necessary for reprogramming: Oct4, Sox2, KIF4, c-myc Reprogramming using lenti- (retro-) virus requires genome integration and can be oncogenic. Knock-in mice have been created where GFP is fused in frame with one of the genes normally expressed only in ES cells but not in other cell types. Such mice have been engineered to express one, or two or three of the four factors required for reprogramming. Screening of a small molecule library can identify molecules that induce endogenous expression of one of the factors required for reprogramming, in the presence of the the other three, leading to GFP induction in cells that are reprogrammed.

35 L expression de la GFP (Green Flourescence Protein) traduit l induction de Nanog et de Oct4 qui sont spécifiques pour les cellules ES Brambrink et al.

36 Jaenisch and Young *

37 Genome

38 Universal Genetic Code TTT phe F TCT ser S TAT tyr Y TGT cys C TTC phe F TCC ser S TAC tyr Y TGC cys C TTA leu L TCA ser S TAA OCH * TGA OPA * TTG leu L TCG ser S TAG AMB * TGG trp W CTT leu L CCT pro P CAT his H CGT arg R CTC leu L CCC pro P CAC his H CGC arg R CTA leu L CCA pro P CAA gln Q CGA arg R CTG leu L CCG pro P CAG gln Q CGG arg R ATT ile I ACT thr T AAT asn N AGT ser S ATC ile I ACC thr T AAC asn N AGC ser S ATA ile I ACA thr T AAA lys K AGA arg R ATG met M ACG thr T AAG lys K AGG arg R GTT val V GCT ala A GAT asp D GGT gly G GTC val V GCC ala A GAC asp D GGC gly G GTA val V GCA ala A GAA glu E GGA gly G GTG val V GCG ala A GAG glu E GGG gly G DNA Strider Program

39 Plasmids-4 Kb Cosmids-40 Kb BAC, YAC Kb Bacterial genome-2mb E. Coli F plasmid- BAC allows stable cloning of up to 1 million bp Lander et al., Nature 2001, 409, 877

40 Lander et al., Nature 2001, 409, 877

41 Lander et al., Nature 2001, 409, 877

42 Mardis et al. SANGER SEQUENCING

43 Lander et al., Nature 2001, 409, 877 -Human genome = 30,000 genes, 3x10 9 bp -Hundreds of genes acquired by horizontal transfer from bacteria -Dozens of genes acquired from transposons -50% of the genome is derived from transposable elements of which DNA and LTR transposons are inactive

44 -SNP= Single Nucleotide Polymorphism -Two human genomes compared will differ at 2.5 million places corresponding to a frequency of 1 per 1300 nucleotide pairs -Rate of nucleotide change/genome 5 nt/ 1000 are changed in 1 million years due to the acuracy of replication -Human and chimpanzee chromosomes are separated by 5 million years of evolution- very similar: human and mouse chromosomes separated by 100 million years of evolution are much more different Lander et al., Nature 2001, 409, 877

45 -3 million transposable elements remain in the human genome -Presently these elements are responsible for new mutations, like for 2/1000 mutations -Hypothesis: 170 million years ago : critical speciation events leading to mammalian radiation for a common ancestor may have involved a burst in transposition activity

46 Types of Interspersed Sequences: 4 Classes of Transposons Lander et. al., Nature 2001, 409, 877

47 LINE: Long Interspersed Nuclear Sequence -LINE1 and Alu (SINE) constitute 60% of all interspersed repeat seqs -LINE1 and Alu are vertically transmitted -Genomes of the worm, fly, and mustard weed have many more types of recent active transposons of which LINE and SINE elements are 5-6% Lander et. al., Nature 2001, 409, 877

48 LINES (LINE1) -LINES (LINE1 is still active!) are most ancient, 6 kb in length, -encode 2 orfs and have a polymerase II promoter, -move to the nucleus a complex of proteins -the RNA endonuclease makes a ss nick -the reverse transcriptase uses the nicked RNA to prime RT from the 3 end- imperfect with unfinished 5 ends -new insertions are flanked by 7-20 bp target site -LINES target AT rich gene-poor regions due to the endo- nuclease preferred cleavage site TTTT/A Long interspersed nuclear elements- can insert into the gene for Factor VIII and produce hemophilia

49 Nature Mar 10;332(6160): Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Kazazian HH Jr1, Wong C, Youssoufian H, Scott AF, Phillips DG, Antonarakis SE. Author information Abstract... We now report insertions of L1 elements into exon 14 of the factor VIII gene in two of 240 unrelated patients with haemophilia A. Both of these insertions (3.8 and 2.3 kilobases respectively) contain 3' portions of the L1 sequence, including the poly (A) tract, and create target site duplications of at least 12 and 13 nucleotides of the factor VIII gene. In addition, their 3'-trailer sequences following orf-2 are nearly identical to the consensus sequence of L1 cdnas (ref. 6). These results indicate that certain L1 sequences in man can be dispersed, presumably by an RNA intermediate, and cause disease by insertional mutation.

50

51 SINE= Short Interspersed Nuclear Sequence -SINES are short bp and use LINES to function as they are non-autonomous. -Promoter regions are shared with trna sequences or with the 7SL RNA of the signal recognition particle The Alu repeat is a SINE which accumulates in GC-rich DNA via a yet to be understood mechanism!

52 SINE= Short Interspersed Nuclear Sequence -Why are Alu elements accumulating in GC rich regions? -Higher loss in AT-rich regions -Negative selection for Alu elements in AT-rich regions -Positive selection for GC rich regions -Rapid transcription of SINE elements into RNA can only occur near genes in opened chromatin; SINE RNA can appear in massive amounts, inhibit PKR (protein kinase R), stimulating translation. -Stress induced SINE transcription which leads to massive increases in protein translation- mechanism of evolution? -Y chromosome has lower levels of somatic genes transcribed and shows lower than expected numbers of Alu elements; the reverse is true for chromosome 19 Lander et al., Nature 2001, 409, 877

53 SINE= Short Interspersed Nuclear Sequence Human Alu seqs (1 million) and mouse B1 (400,000) evolved from the 7SL RNA which encodes the SRP RNA Alu restriction site = ag/ct

54 Methionine (Met)- rich p54 binds hydrophobic signal sequences RNA component Lodish et al., Molecular Cell Biology, 2000, Freeman Press

55 LTR and DNA Transposons -LTR transposons are flanked by LTRs and contain gag, pol coding for RT and RNAse-H; transposition occurs via the RT in a cytoplasmic virus-like structure, primed by a trna as opposed to chromosomal priming for SINES. They generated extracellular retroviruses by acquiring an envelope protein -DNA transposons resemble bacterial transposons having terminal Inverted repeats and using cut and paste mechanisms- they are short lived elements

56 Repetitive Elements in the Human Genome -The human genome contains much longer intron sequences -Only 5% of the 28% that is transcribed into RNA actually codes for proteins -Repetitive elements: 45% the transposons; 3% repeats of CA type* and 5% recent duplications CA repeats: simple form of repeats of the dinucleootide seq CA (short tandem repeat polymorphisms (STRP's) Microsatellites, also known as simple sequence repeats (SSRs) or short tandem repeats (STRs), are repeating sequences of 2-5 base pairs of DNA Lander et al., Nature 2001, 409, 877

57 CONSERVATION -Homologs of human genes can be found in nematode worms, fruit fly, yeasts and bacteria -Hundreds of bacterial genes were transferred horizontally to humans -Gene sequences are more conserved than genome structures -Number of genes: 6,000 for yeast Saccharomyces cerevisiae; 18,000 for the nematode C. elegans; 13,000 for Drosophila melanogaster; 30,000 for humans -There is no machinery dedicated to evolution except mistakes: substitutions, deletions, inversions, translocations, transposons -A total of 3 billion years of evolution Lander et al., Nature 2001, 409, 877

58 CONSERVATION HUMAN-CHIMPANZEE Chimpanzee and human chromosomes are almost identical except for human chromosome 2 99% of Alu repeats are in the same place in the human and chimpanzee genomes The 1% repeats that differ contain human-specific Alu, still active which can induce genetic diseases. Lander et al., Nature 2001, 409, 877

59 coding genome sequen non-coding genome sequen

60 Human Genome: 3 Mb (3x10 9 bp) 30,000 genes 48% repetitive sequences, silent transposon sequences >95% non-coding sequences Eukaryote gene structure: cis cis // cis cis cis TATA exons + introns // cis cis enhancer/ silencer promoter ( pb) enhancer/ silencer 60

61 Altered kinetics and levels of expression of coding regions Mutated non-coding regions Impaired expression of coding regions

62

63 Genomics Informed Medicine FIRST GENOME SEQUECING: SANGER METHOD, 1.5 BILLION US $ NGS approaches Massive Parallel Sequencing - a very dynamic fieldchoice of test: Whole Exome Sequencing WES- only coding regions explored, 700 /sample. Whole Genome Sequencing WGS-entire genome explored, approx 10,000 /sample. RNA-seq- determines sequence and levels of gene expression, 800 /sample. Chip-seq- determines DNA sequences bound to proteins, 700 /sample

64 Guessing The Future...