ipsc genomic instability and impact on product safety Prof Peter Andrews, University of Sheffield, UK

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1 ipsc genomic instability and impact on product safety Prof Peter Andrews, University of Sheffield, UK

2 PSC genomic instability and impact on product safety Peter W Andrews

3 variability PSC genomic instability and impact on product safety Peter W Andrews

4 The Pluripotent Stem Cell Problem Self Renewal Differentiation Death Fate Determination

5 The Pluripotent Stem Cell Problem Selection Self Renewal Differentiation Death Fate Determination

Normal and Culture Adapted H7 Human ES Cells Cells ( x 1-5 ) 5 4 3 2 1 Day 4 Day 6

6 Normal and Culture Adapted H7 Human ES Cells Cells ( x 1-5 ) Day 4 Day 6 Days after Seeding H7 Normal H7 Adapted 1 5 Cells Seeded H7 S6 - der(6)t(6;17)(q27q1)

7 Distribution of cytogentic abnormalities from literature ISCI - Nature Biotechnology (211) 29:

8 Non-Random Mutation or Selection? Rate of Take over of Abnormal Cells that Appear Spontaneously Mixing Exp S = 2. Olariu et al 21. Stem Cell Research 4: 5-56.

9 Driver Gene in Chr2 Minimal Amplicon is BCL2L1 Chr2 HM13 ID1 BCL2L1 TPX2 Expressed gene But other amplicons much larger (more genes)! Avery, Hirst, et al. 213 Stem Cell Reports. 1:

10 Genetic Variants What are the Issues? Mutation Detection What is mutation rate? << Can it be reduced? Types of mutation? Selection Source of selective advantage? Survival; differentiation; proliferation? Can it be reduced? Consequences What is sensitivity? Can it be improved? ISCI 217 Stem Cell Reports 9: 1 4. Differentiation? Function? Engraftment Cancer?

11 Sensitvity of G-Band Karyotype Each row represents a level of mosaicism. The columns have upper (ul) and lower (ll) limits on the expected number of abnormal cells Number of Metaphases Scored ll ul ll ul ll ul ll ul ll ul ll ul ll ul ll ul ll ul ll ul ll ul ll ul

PCR and FISH Mixing of normal and trisomic cells (17q) Copy Number 3.5 3. 2.5 2. 1.

12 PCR and FISH Mixing of normal and trisomic cells (17q) Copy Number qpcr % Abnormal cells 8 1 % abnormal cells as detected by FISH FISH % abnormal cells 1

13 ROCK inhibitor Minimises the Selective Advantage of Chr 2q Variants (Y-27632)

14 Assessing the Consequences of Variants Isogenic sets of clonal lines with and without common variants Ø Gains of chr 1, 12, 17, 2 Ø Losses from chr 1, 18, 22 Ø Point mutations p53 Chromosome 2 2q ,, 31,25, 31,5, 31,75, 32,, 32,25, 32,5, 32,75, 33,, DEFB115 BCL2L1 TTLL9 DEFB123 REM1 TPX2 MYLK2 XKR7 TM9SF4 ASXL1 DNMT3B NCRM1 Shef5 ESI35 H1 HES3

15 ES Cells in Culture & EC Cells in Tumours Are they subject to similar selective pressures? Human EC cells in testicular Teratocarcinomas commonly gain 17q, 12p chromosomes Self Renewal Selection Differentiation Death

16 Pluripotent Stem Cells Can Form Teratomas Teratomas contain differentiated derivatives of all three germ layers Damjanov and Andrews 216 A Histopathology Atlas Int. J. Dev. Biol. 6:

17 Pluripotent Stem Cells Can Form Teratocarcinomas Undifferentiated Stem Cells Yolk Sac extraembryonic endoderm Damjanov and Andrews 216 A Histopathology Atlas Int. J. Dev. Biol. 6:

18 No Correlation between Aneuploidy and Persistence of Primitive Cells 12 1 Tig18 4f3 TIG18-4f3 DF T.H DF T.4 ips(imr9)-4 IMR9-4 Shef3 H14 ipsc RM3.5 TeratoScore Analysis % Expression Undifferentiated Markers Xenograft tumors with persisting stem cells or yolk sac elements - Diploid Karyotype 2 Tissues Teratomas Nissim Benvenisty and Yishai Avior The International Stem Cell Initiative 218 Assessment of established techniques to determine developmental and malignant potential of human pluripotent stem cells. Nature Communications, in press

19 Tumours from ES Cells Teratoma - benign? Teratocarcinoma - malignant Secondary Cancer

20 Addressing the Issues Freezing & thawing ISCI Genetic Group, Steering Committee Martin Pera (Chair) Peter Andrews Nissim Benvenisty Kevin Eggan Tenneille Ludwig Yoji Sato Derivation Expansion Differentiation Transplantation Mutation & Selection Variants of Origin Acquired Variants

21 Sheffield Duncan Baker Ivana Barbaric Jonathan Draper Paul Gokhale Jason Halliwell Neil Harrison Adam Hirst Oliver Thompson Acknowledgements Collaborators Stuart Avery AStar Barbara Knowles AStar Martin Pera Jackson laboratory Nissim Benvenisty - Israel Paul Robson AStar Glyn Stacey NIBSC/UKSCB Horizon 22

The Pathology of Germ Cell Tumours of the Ovary

The Pathology of Germ Cell Tumours of the Ovary Professor Mike Wells University of Sheffield Amman, Jordan November 2013 Professor Francisco Paco Nogales I. Primitive germ cell tumors A. Dysgerminoma