De novo mutations in mitochondrial DNA of iPSCs produce immunogenic neoepitopes in mice and humans

[1]  D. van der Kooy,et al.  Cell competition during reprogramming gives rise to dominant clones , 2019, Science.

[2]  Mark M. Davis,et al.  Hypoimmunogenic derivatives of induced pluripotent stem cells evade immune rejection in fully immunocompetent allogeneic recipients , 2019, Nature Biotechnology.

[3]  Bjoern Peters,et al.  The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design , 2017, Front. Immunol..

[4]  Cathy H. Wu,et al.  UniProt: the universal protein knowledgebase , 2016, Nucleic Acids Research.

[5]  Xinjian Wang,et al.  Age-Related Accumulation of Somatic Mitochondrial DNA Mutations in Adult-Derived Human iPSCs. , 2016, Cell stem cell.

[6]  Daniel R. Zerbino,et al.  Ensembl 2016 , 2015, Nucleic Acids Res..

[7]  D. Clegg,et al.  Humanized Mice Reveal Differential Immunogenicity of Cells Derived from Autologous Induced Pluripotent Stem Cells. , 2015, Cell stem cell.

[8]  M. Kay,et al.  Novel codon-optimized mini-intronic plasmid for efficient, inexpensive, and xeno-free induction of pluripotency , 2015, Scientific Reports.

[9]  Irving L. Weissman,et al.  SCNT-derived ESCs with mismatched mitochondria trigger an immune response in allogeneic hosts. , 2015, Cell stem cell.

[10]  K. Shokat,et al.  A sharp T-cell antigen receptor signaling threshold for T-cell proliferation , 2014, Proceedings of the National Academy of Sciences.

[11]  Daniel T. Montoro,et al.  Transplanted Terminally Differentiated Induced Pluripotent Stem Cells Are Accepted By Immune Mechanisms Similar To Self-Tolerance , 2014, Nature Communications.

[12]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[13]  Y. Hoki,et al.  Induced Pluripotent Stem Cell Generation-Associated Point Mutations Arise during the Initial Stages of the Conversion of These Cells , 2014, Stem cell reports.

[14]  N. Rodrigues,et al.  Lack of immune response to differentiated cells derived from syngeneic induced pluripotent stem cells. , 2013, Cell stem cell.

[15]  Y. Hoki,et al.  Negligible immunogenicity of terminally differentiated cells derived from induced pluripotent or embryonic stem cells , 2013, Nature.

[16]  Philip E. Bourne,et al.  Immune epitope database analysis resource , 2012, Nucleic Acids Res..

[17]  Christopher A. Miller,et al.  Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells. , 2012, Cell stem cell.

[18]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[19]  George M. Church,et al.  Elevated Coding Mutation Rate During the Reprogramming of Human Somatic Cells into Induced Pluripotent Stem Cells , 2012, Stem cells.

[20]  Christopher A. Miller,et al.  VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. , 2012, Genome research.

[21]  Ira M. Hall,et al.  Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming. , 2011, Cell stem cell.

[22]  Tim R. Mercer,et al.  The Human Mitochondrial Transcriptome , 2011, Cell.

[23]  Yang Xu,et al.  Immunogenicity of induced pluripotent stem cells , 2011, Nature.

[24]  Julie V. Harness,et al.  Dynamic changes in the copy number of pluripotency and cell proliferation genes in human ESCs and iPSCs during reprogramming and time in culture. , 2011, Cell stem cell.

[25]  H. Hakonarson,et al.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.

[26]  D. Dressman,et al.  Heteroplasmic mitochondrial DNA mutations in normal and tumor cells , 2010, Nature.

[27]  A. Connolly,et al.  Effects of cell number on teratoma formation by human embryonic stem cells , 2009, Cell cycle.

[28]  D. Sachs,et al.  Cytoplasmic Inheritance of Transplantation Antigens in Animals Produced by Nuclear Transfer , 2009, Transplantation.

[29]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[30]  D. Turnbull,et al.  Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA , 1999, Nature Genetics.

[31]  T. Zastawny,et al.  Comparison of oxidative base damage in mitochondrial and nuclear DNA. , 1998, Free radical biology & medicine.

[32]  B. Van Houten,et al.  Mitochondrial DNA damage is more extensive and persists longer than nuclear DNA damage in human cells following oxidative stress. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[33]  H. Yonekawa,et al.  Maternally transmitted histocompatibility antigen of mice: A hydrophobic peptide of a mitochondrially encoded protein , 1990, Cell.

[34]  W. Brown,et al.  Rapid evolution of animal mitochondrial DNA. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Cathy H. Wu,et al.  UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..