Search of miRNAs critical for medulloblastoma      formation using MiRaGE method○Y-h. Taguchi(Dept. Phys., Chuo Univ.)    ...
Experiments microRNA vs tumor      Computer oriented prediction              (uncertain)  Target genes     genom          ...
3
miRNA target gene list                          Gene8                          Gene7                          Gene6       ...
MaterialsP6=6 days after birth, normal but growingP6P30=30 days after birth, normal and notP30growingMB=a few month after ...
mRNA/miRNA expression byArray: AgilentatP6, P30 and MB    log(xg[mRNA/miRNA:MB or P6])                  vs       log(xg[mR...
t te s t fo r m iRNA e x p re s s io n             log(xg[miRNA:P6/MB]) vs                log(miRNA:xg[P30])              ...
t test for miRNA target genes (MiRaGE method)log(xg[mRNA:P6/MB]) – log(xg[mRNA:P30])in target genes of considered miRNA   ...
P30         P6/MBGether the information of miRNA targets   Compare the expressions of targets   for each miRNAs  Calculate...
MiRaGE   miRNA   Targets         Dow n        P-value        FDR   miR-a              54            3            0.5      ...
selected bymiRNA miRNA expression / MiRaGE                                          miRNA   P30< MB   1 mmu-miR-25        ...
selected by                                        miRNA   P30> MBmiRNA miRNA expression / MiRaGE                         ...
selected bymiRNA miRNA expression / MiRaGE                                           miRNA   P30< P6   1 mmu-miR-106b     ...
selected bymiRNA miRNA expression / MiRaGE       miRNA   P30> P6m m u-m iR-29c        1.00   1.00     target gene P30< P6m...
MiRaGE method + miRNA expressionsuccessfully pick up biologically importantmiRNAs. Further (wet) experiments whichsupress ...
Significance of reciprocal relationship between miRNA and its target genes.〈 log 1 0 P〉                          t.test of...
Significance of reciprocal relationshipbetween miRNA and its target genes.〈 log 1 0 P〉                          t.test of ...
MiRaGE method + miRNA expression satisfyreciprocal relationship very well. In ourknowledge, this is for the first time to ...
Discussion:What causes successful achievement?Point 1:Usage of “good” maicroarryAffymetric ☓Agilent ○Point 2:Negative set ...
let-7a transfection (Taguchi & Yasuda, 2010)As for Points:Although we donot know thereason, off-target genestargeted byoth...
Conclusion:MiRaGE (MiRNA Ranking by Gene Expression)method is very simple, but1) can successfully pickup biologically impo...
Acknowledgements: We thank Drs. Tetsuo Nodaand Katsuyuki Yaginuma for    providing reagents.These works were supported by ...
Related Talk:Tomorrow(38)/SIG-BIO 15:30 - 15:45Gene expression regulation duringdifferentiation from murine ES cells due t...
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Search of miRNAs critical for medulloblastoma formation using MiRaGE method

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Search of miRNAs critical for medulloblastoma formation using MiRaGE method

  1. 1. Search of miRNAs critical for medulloblastoma formation using MiRaGE method○Y-h. Taguchi(Dept. Phys., Chuo Univ.) Jun Yasuda(Tohoku Univ.) Present address: Cancer Research Inst. Ariake, Tokyo
  2. 2. Experiments microRNA vs tumor Computer oriented prediction (uncertain) Target genes genom e microRNA mRN A microRNA mRNA 2
  3. 3. 3
  4. 4. miRNA target gene list Gene8 Gene7 Gene6 Gene5 Gene4 Gene3 Gene2 Gene1(計算機による予測)simple seed match miRNA1 ○ × ○ ○ ○ ○ × × miRNA2 ○ × ○ ○ × × ○ ○ miRNA3 × ○ ○ × ○ ○ × × 予 miRNA4 ○ ○ ○ × ○ ○ × × 測 VS miRNA1 gene1 Murine Medulloblastoma(MB) (Dr. Tetsuo Noda’ group gene2 (The JFCR-Cancer Institute)). gene3 4
  5. 5. MaterialsP6=6 days after birth, normal but growingP6P30=30 days after birth, normal and notP30growingMB=a few month after birth, malignantMBneoplasm30% of the Ptc1 +/- mice suffers from MB. 5
  6. 6. mRNA/miRNA expression byArray: AgilentatP6, P30 and MB log(xg[mRNA/miRNA:MB or P6]) vs log(xg[mRNA/miRNA:P30]) xg: mRNA/miRNA expressionTarget gene list: simple seed match 6
  7. 7. t te s t fo r m iRNA e x p re s s io n log(xg[miRNA:P6/MB]) vs log(miRNA:xg[P30]) of considered miRNA(*) (*) each miRNA is measured by multiple probe 7
  8. 8. t test for miRNA target genes (MiRaGE method)log(xg[mRNA:P6/MB]) – log(xg[mRNA:P30])in target genes of considered miRNA VSlog(xg[mRNA:P6/MB]) – log(xg[mRNA:P30]) in target genes of any of other miRNA 8
  9. 9. P30 P6/MBGether the information of miRNA targets Compare the expressions of targets for each miRNAs Calculate False Discovery Rate Generate ranking 9
  10. 10. MiRaGE miRNA Targets Dow n P-value FDR miR-a 54 3 0.5 0.4 miR-b 120 54 0.0001 0.005 miR-c 36 1 0.5 0.7 ... ... ... ... ... miR-X 60 18 0.001 0.007 Reject miR-a & c because the FDR > 0.05Filtrate with miRNA expression profiles Ranking 10
  11. 11. selected bymiRNA miRNA expression / MiRaGE miRNA   P30< MB 1 mmu-miR-25 1 1 target gene P30> MB 2 m m u-m iR-466i-5p 1 1 3 mmu-miR-92a 0.75 1 4 mmu-miR-19a 1 0.69 miR-17~92 cluster family 5 mmu-miR-19b 1 0.69 members are ranked in top 5 6 m m u-m iR-3082-5p 1 0.56 by combination of MiRaGE 7 m m u-m iR-130a 1 0.5 methods and miRNA 8 m m u-m iR-130b 1 0.5 expression profiling. 9 m m u-m iR-15b 1 0.5 10 m m u-m iR-2861 1 0.5 11 m m u-m iR-3096-5p 1 0.5 12 m m u-m iR-32 0.5 1 13 m m u-m iR-322 1 0.5 14 m m u-m iR-721 1 0.5 15 m m u-m iR-149* 0.5 0.88 16 m m u-m iR-3081* 1 0.38 17 m m u-m iR-574-5p 1 0.31 18 m m u-m iR-669n 0.5 0.81 suggested contribution 11 19 m m u-m iR-1187 1 0.25 to cancer formation
  12. 12. selected by miRNA   P30> MBmiRNA miRNA expression / MiRaGE target gene P30< MBmmu-miR-100 1 1mmu-miR-126-3p 1 1mmu-miR-29c 1 1 Some of the neuron-mmu-miR-376a 1 1 specific miRNAs and miRNAmmu-miR-451 1 1 tumor-suppressivemmu-miR-99b 1 1 miRNAs seem to contributemmu-miR-136* 1 0.9375 to the gene expressionmmu-miR-299* 0.75 1 profiles of P30.mmu-miR-26a 1 0.5mmu-miR-26b 1 0.5mmu-miR-29a 0.5 1mmu-miR-7a-1* 1 0.5mmu-miR-3107 1 0.4375mmu-miR-340-5p 1 0.3125mmu-miR-369-5p 1 0.3125mmu-let-7a 1 0.25mmu-let-7e 1 0.25 tumor-suppressive miRNAsmmu-let-7g 1 0.25 neuron-specific miRNAs 12mmu-let-7i 1 0.25
  13. 13. selected bymiRNA miRNA expression / MiRaGE miRNA   P30< P6 1 mmu-miR-106b 1.00 1.00 target gene P30> P6 2 m m u-m iR-130a 1.00 1.00 3 m m u-m iR-130b 1.00 1.00 4 m m u-m iR-15b 1.00 1.00 miR-17~92, mir-106b-25 , 5 mmu-miR-17 1.00 1.00 mir-106a-363 6 mmu-miR-20a 1.00 1.00 cluster family members are ranked in top 5 by combination of 7 mmu-miR-20b 1.00 1.00 MiRaGE methods and miRNA 8 m m u-m iR-301b 1.00 1.00 expression profiling. 9 m m u-m iR-322 1.00 1.00 10 m m u-m iR-721 1.00 1.00 11 mmu-miR-93 1.00 1.00 12 m m u-m iR-542-3p 1.00 0.94 13 m m u-m iR-3081* 1.00 0.88 14 m m u-m iR-335-3p 1.00 0.88 15 m m u-m iR-199a-5p 1.00 0.81 16 m m u-m iR-199b* 1.00 0.81 17 mmu-miR-19a 1.00 0.81 13 18 mmu-miR-1 9 b 1.00 0.81
  14. 14. selected bymiRNA miRNA expression / MiRaGE miRNA   P30> P6m m u-m iR-29c 1.00 1.00 target gene P30< P6mmu-miR-376a 1.00 1.00m m u-m iR-451 1.00 1.00 Some of the neuron-mmu-let-7b 1.00 0.94 specific miRNAs and miRNAmmu-let-7e 1.00 0.94 tumor-suppressivemmu-let-7g 1.00 0.94 miRNAs seem to contributemmu-let-7i 1.00 0.94 to the gene expressionm m u-m iR-98 1.00 0.94 profiles of P30.m m u-m iR-126-3p 0.75 1.00m m u-m iR-299* 0.75 1.00m m u-m iR-29a 0.75 1.00mmu-let-7a 0.75 0.94m m u-m iR-3070b-3p 1.00 0.69m m u-m iR-138 1.00 0.63m m u-m iR-3107 1.00 0.56m m u-m iR-181a-1* 0.50 1.00 tumor-suppressive miRNAsmmu-let-7d 0.50 0.94 neuron-specific miRNAs 14m m u-m iR-1937b 0.25 1.00
  15. 15. MiRaGE method + miRNA expressionsuccessfully pick up biologically importantmiRNAs. Further (wet) experiments whichsupress miRNA expression with tiny LNA isnow planed.If it is successful, our method can find miRNAswhich control tumor formation. 15
  16. 16. Significance of reciprocal relationship between miRNA and its target genes.〈 log 1 0 P〉 t.test of P-values between top n miRNAs and others: P30 → MB P(mRNA:down|miRNA:up) P=0.05 P(mRNA:up|miRNA:down) P(miRNA:down|mRNA:up) P(miRNA:up|mRNA:down) 16 n
  17. 17. Significance of reciprocal relationshipbetween miRNA and its target genes.〈 log 1 0 P〉 t.test of P-values between P=0.05 top n miRNAs and others: P30 → P6 P(mRNA:down|miRNA:up) P(mRNA:up|miRNA:down) P(miRNA:down|mRNA:up) P(miRNA:up|mRNA:down) 17 n
  18. 18. MiRaGE method + miRNA expression satisfyreciprocal relationship very well. In ourknowledge, this is for the first time to do this forsuch a large number of miRNAs 18
  19. 19. Discussion:What causes successful achievement?Point 1:Usage of “good” maicroarryAffymetric ☓Agilent ○Point 2:Negative set = genes not targeted byconsidered miRNA but done by other miRNAs 19
  20. 20. let-7a transfection (Taguchi & Yasuda, 2010)As for Points:Although we donot know thereason, off-target genestargeted byother miRNAsare moreexpressive. off target target 20
  21. 21. Conclusion:MiRaGE (MiRNA Ranking by Gene Expression)method is very simple, but1) can successfully pickup biologically importantgenesand2) can detect reciprocal relationship betweenmiRNAs and their target genes (mRNA). 21
  22. 22. Acknowledgements: We thank Drs. Tetsuo Nodaand Katsuyuki Yaginuma for providing reagents.These works were supported by KAKENHI (23300357) . 22
  23. 23. Related Talk:Tomorrow(38)/SIG-BIO 15:30 - 15:45Gene expression regulation duringdifferentiation from murine ES cells due tomicroRNA○Masato Yoshizawa,Y-h. Taguchi(Chuo Univ.) 23

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