Cited by 80

Higher-Density Culture in Human Embryonic Stem Cells Results in DNA Damage and Genome Instability

Jacobs, Kurt, Zambelli, Filippo, Mertzanidou, Afroditi, Smolders, Ilse, Geens, Mieke, Nguyen, Ha Thi, Barbé, Lise, Sermon, Karen +1 more·2016·Stem Cell Reports

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.stemcr.2016.01.015

Cites

2 of 2 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Such genetic changes appear to occur at any time during passage and may be associated with culture conditions such as medium acidification, frequent single cell dissociation, or repeated use of Rho kinase inhibitors.

    “Such changes appear to occur at any time during passage (International Stem Cell Initiative, 2011) and may be associated with culture conditions - such as medium acidification - as a consequence of suboptimal culturing and passaging (e.g., frequent single cell dissociation) or the repeated use of Rho kinase inhibitors (Assou et al., 2018; Jacobs et al., 2016).”

    From Guidance document on Good cell and tissue culture practice 2.0 (GCCP 2.0) (2021) · cites this paper as Jacobs et al., 2016

    The Results section reports that medium acidification caused by lactate accumulation was a key factor in DNA damage in high-density hESC cultures; the Discussion links suboptimal culture conditions to genomic instability. The paper does not establish frequent single-cell dissociation or repeated Rho kinase inhibitor use as causes. The claim about changes occurring at any time during passage is cited to a different source, not Jacobs et al. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 32

  1. Amps K. Andrews P.W. Anyfantis G. Armstrong L. Avery S. Baharvand H. Baker J. Baker D. Munoz M.B. Beil S. Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage Nat. Biotechnol. 29 2011 1132 1144 22119741 PMC3454460
  2. Avery S. Hirst A.J. Baker D. Lim C.Y. Alagaratnam S. Skotheim R.I. Lothe R.A. Pera M.F. Colman A. Robson P. BCL-XL mediates the strong selective advantage of a 20q11.21 amplification commonly found in human embryonic stem cell cultures Stem Cell Rep. 1 2013 379 386 PMC3841249 24286026
  3. Bárta T. Vinarský V. Holubcová Z. Dolezalová D. Verner J. Pospísilová S. Dvorák P. Hampl A. Human embryonic stem cells are capable of executing G1/S checkpoint activation Stem Cells 28 2010 1143 1152 20518019
  4. Becker K.A. Ghule P.N. Therrien J.A. Lian J.B. Stein J.L. van Wijnen A.J. Stein G.S. Self-renewal of human embryonic stem cells is supported by a shortened G1 cell cycle phase J. Cell. Physiol. 209 2006 883 893 16972248
  5. Ben-Nun I.F. Benvenisty N. Human embryonic stem cells as a cellular model for human disorders Mol. Cell. Endocrinol. 252 2006 154 159 16690205
  6. Burrell R.A. McClelland S.E. Endesfelder D. Groth P. Weller M.-C. Shaikh N. Domingo E. Kanu N. Dewhurst S.M. Gronroos E. Replication stress links structural and numerical cancer chromosomal instability Nature 494 2013 492 496 23446422 PMC4636055
  7. Chen X. Chen A. Woo T.L. Choo A.B.H. Reuveny S. Oh S.K.W. Investigations into the metabolism of two-dimensional colony and suspended microcarrier cultures of human embryonic stem cells in serum-free media Stem Cells Dev. 19 2010 1781 1792 20380517
  8. De Boeck M. Lombaert N. De Backer S. Finsy R. Lison D. Kirsch-Volders M. In vitro genotoxic effects of different combinations of cobalt and metallic carbide particles Mutagenesis 18 2003 177 186 12621074
  9. Dekel-Naftali M. Aviram-Goldring A. Litmanovitch T. Shamash J. Reznik-Wolf H. Laevsky I. Amit M. Itskovitz-Eldor J. Yung Y. Hourvitz A. Screening of human pluripotent stem cells using CGH and FISH reveals low-grade mosaic aneuploidy and a recurrent amplification of chromosome 1q Eur. J. Hum. Genet. 20 2012 1248 1255 22713809 PMC3499752
  10. Fazeli A. Liew C.G. Matin M.M. Elliott S. Jeanmeure L.F.C. Wright P.C. Moore H. Andrews P.W. Altered patterns of differentiation in karyotypically abnormal human embryonic stem cells Int. J. Dev. Biol. 55 2011 175 180 21671221
  11. Fraga A.M. Souza de Araújo É.S. Stabellini R. Vergani N. Pereira L.V. A survey of parameters involved in the establishment of new lines of human embryonic stem cells Stem Cell Rev. 7 2011 775 781 21416256
  12. Gopalakrishna-Pillai S. Iverson L.E. Astrocytes derived from trisomic human embryonic stem cells express markers of astrocytic cancer cells and premalignant stem-like progenitors BMC Med. Genomics 3 2010 12 20423517 PMC2873256
  13. Herszfeld D. Wolvetang E. Langton-Bunker E. Chung T.-L. Filipczyk A.A. Houssami S. Jamshidi P. Koh K. Laslett A.L. Michalska A. CD30 is a survival factor and a biomarker for transformed human pluripotent stem cells Nat. Biotechnol. 24 2006 351 357 16501577
  14. Lim H. Han J. Woo D. Kim S. Kim S. Biochemical and morphological effects of hypoxic environment on human embryonic stem cells in long-term culture and differentiating embryoid bodies Mol. Cells 31 2011 123 132 21347709 PMC3932683
  15. Lund R.J. Närvä E. Lahesmaa R. Genetic and epigenetic stability of human pluripotent stem cells Nat. Rev. Genet. 13 2012 732 744 22965355
  16. Mateizel I. De Temmerman N. Ullmann U. Cauffman G. Sermon K. Van de Velde H. De Rycke M. Degreef E. Devroey P. Liebaers I. Van Steirteghem A. Derivation of human embryonic stem cell lines from embryos obtained after IVF and after PGD for monogenic disorders Hum. Reprod. 21 2006 503 511 16284066
  17. Mateizel I. De Becker A. Van de Velde H. De Rycke M. Van Steirteghem A. Cornelissen R. Van der Elst J. Liebaers I. Van Riet I. Sermon K. Efficient differentiation of human embryonic stem cells into a homogeneous population of osteoprogenitor-like cells Reprod. Biomed. Online 16 2008 741 753 18492382
  18. Mateizel I. Spits C. De Rycke M. Liebaers I. Sermon K. Derivation, culture, and characterization of VUB hESC lines In Vitro Cell. Dev. Biol. Anim. 46 2010 300 308 20224973
  19. Mertzanidou A. Spits C. Nguyen H.T. Van de Velde H. Sermon K. Evolution of aneuploidy up to day 4 of human preimplantation development Hum. Reprod. 28 2013 1716 1724 23526301
  20. Nguyen H.T. Geens M. Spits C. Genetic and epigenetic instability in human pluripotent stem cells Hum. Reprod. Update 19 2013 187 205 23223511
  21. Nguyen H.T. Geens M. Mertzanidou A. Jacobs K. Heirman C. Breckpot K. Spits C. Gain of 20q11.21 in human embryonic stem cells improves cell survival by increased expression of Bcl-xL Mol. Hum. Reprod. 20 2014 168 177 24217388
  22. Olive P.L. Banáth J.P. Induction and rejoining of radiation-induced DNA single-strand breaks: “tail moment” as a function of position in the cell cycle Mutat. Res. 294 1993 275 283 7692267
  23. Rodin S. Antonsson L. Niaudet C. Simonson O.E. Salmela E. Hansson E.M. Domogatskaya A. Xiao Z. Damdimopoulou P. Sheikhi M. Clonal culturing of human embryonic stem cells on laminin-521/E-cadherin matrix in defined and xeno-free environment Nat. Commun. 5 2014 3195 24463987
  24. Sokolov M. Neumann R. Lessons learned about human stem cell responses to ionizing radiation exposures: a long road still ahead of us Int. J. Mol. Sci. 14 2013 15695 15723 23899786 PMC3759881
  25. Spits C. Mateizel I. Geens M. Mertzanidou A. Staessen C. Vandeskelde Y. Van der Elst J. Liebaers I. Sermon K. Recurrent chromosomal abnormalities in human embryonic stem cells Nat. Biotechnol. 26 2008 1361 1363 19029912
  26. Tabar V. Studer L. Pluripotent stem cells in regenerative medicine: challenges and recent progress Nat. Rev. Genet. 15 2014 82 92 24434846 PMC4539940
  27. Van Hemelrijck A. Sarre S. Smolders I. Michotte Y. Determination of amino acids associated with cerebral ischaemia in rat brain microdialysates using narrowbore liquid chromatography and fluorescence detection J. Neurosci. Methods 144 2005 63 71 15848240
  28. Werbowetski-Ogilvie T.E. Bossé M. Stewart M. Schnerch A. Ramos-Mejia V. Rouleau A. Wynder T. Smith M.-J. Dingwall S. Carter T. Characterization of human embryonic stem cells with features of neoplastic progression Nat. Biotechnol. 27 2009 91 97 19122652
  29. Wojewódzka M. Buraczewska I. Kruszewski M. A modified neutral comet assay: elimination of lysis at high temperature and validation of the assay with anti-single-stranded DNA antibody Mutat. Res. 518 2002 9 20 12063063
  30. Yang S. Lin G. Tan Y. Zhou D. Deng L. Cheng D. Luo S. Liu T. Zhou X. Sun Z. Tumor progression of culture-adapted human embryonic stem cells during long-term culture Genes Chromosomes Cancer 47 2008 665 679 18470900
  31. Yeo D. Kiparissides A. Cha J.M. Aguilar-Gallardo C. Polak J.M. Tsiridis E. Pistikopoulos E.N. Mantalaris A. Improving embryonic stem cell expansion through the combination of perfusion and Bioprocess model design PLoS One 8 2013 e81728 24339957 PMC3858261
  32. Yuan J. Narayanan L. Rockwell S. Glazer M.P. Diminished DNA repair and elevated mutagenesis in mammalian cells exposed to hypoxia and low pH Cancer Res. 60 2000 4372 4376 10969780

Cited by

Sorted by citations

Authors
Jacobs, K., Zambelli, F., Mertzanidou, A., Smolders, I., Geens, M., Nguyen, H. T., Barbé, L., Sermon, K., & Spits, C.
Venue
Stem Cell Reports
Publisher
Elsevier BV
Published
2016-03
Volume
6
Issue
3
Pages
330-341
ISSN
2213-6711
Cited by
80
References
2
Language
en
Funders
  • Scientific Research Flanders
  • Methusalem
  • Vrije Universiteit Brussel
  • Leerstoel Mireille Aerens

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review