Aging & Human Core Duplicons Lab

Within next 10 years, every fourth person will be 65 or older in Europe, Japan and USA. By 2050, Turkey will face the same problem of aging populations with the rest of the world. Since old age is the main risk factor for developing cancer, neurodegenerative (Alzheimers) and metabolic diseases, our lab focuses on determining the molecular mechanisms that prolong health during aging. In order to model the process of aging and longevity in human, we are using the human primary cells as a pioneering model system. This is because it is known that the mechanism of human aging and longevity lies within the life history of cells and their interactions with the environment. We define this, depending on the cells intrinsic factors, life history of cells and the environment, as a cellular context. Since the aging is the accumulative interactions of these factors in time and space, we call this as context dependent cellular aging. Recently, we have discovered that human specific SPATA31 CNV genes are important factor for cellular senescence in human primary cells and human lifespan. Our preliminary data suggest a involvement of SPATA31 CNV genes with cellular context due to association of genomic instability. Our primary targets will be to use, test and modify human primary cell cultures including stem cells in order to translate them and to initiate clinical trials. These efforts aim to develop novel strategies to treat human specific age-related pathologies and thereby improving human health during aging and lifespan.

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• Work Experience
• Assistant Professor, Feb. 2020 - Present
  Department of Molecular Biology and Genetics, Bahcesehir University, Istanbul, Turkey
• Associated Project Leader, September 2018 - September 2022
  Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Biology, Ploen, Germany
• Project Leader, August 2013 - September 2018
  Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Biology, Ploen, Germany
• Research Assistant Prof. (MBG-Bridge), April 2010 - September 2013
  Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
  
• Visiting Scientist, January 2011 - February 2012
  SIAF,Swiss Institute of Allergy and Asthma Research, Davos, Switzerland 
• Education
• Postdoctoral Fellow, September 2006 - December 2009
  Eichler Lab, Department of Genome Sciences, U. Washington, Seattle, WA, United States
  
• Ph.D., Department of Cell Genetics, February 2006
  Institute of Genetics, University of Cologne, Cologne, Germany
  
• M.Sc., Biological Sciences, September 2001
  Middle East Technical University, Ankara, Turkey
  
• B. Sc., Department of Biology, 1995-1998
  Abant Izzet Baysal University, Bolu, Turkey
  
• B. Sc., Department of Biology, 1994-1995
  Hacettepe University, Ankara, Turkey
  

1. Xie C., Bekpen C., Kunzel S, Keshavarz M, Krebs-Wheaton R, Skrabar N, Ullrich KK, Zhang W., Tautz D.*, (2020) Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines
   PLOS Computational Biology November 12, 2020 Full Text (HTML) | PDF
2. Xie C., Bekpen C., Kunzel S, Keshavarz M, Krebs-Wheaton R, Skrabar N, Ullrich KK, Tautz D.*, (2019) A de novo evolved gene in the house mouse regulates female pregnancy cycles.
   Elife Aug 22;8 [Epub ahead of print] Full Text (HTML) | PDF
3. Bekpen C., Xie C. and Tautz D.*, (2018) Dealing with the adaptive immune system during de novo evolution of genes from intergenic sequences,
   BMC Evolutionary Biology 18:121 Full Text (HTML) | PDF
4. *Bekpen C., Xie C., Nebel A and Tautz D.*, (2018) Involvement of SPATA31copy number variable genes in human lifespan
   Aging (Albany NY) Apr; 10(4) 674-688 Full Text (HTML) | PDF
   * Corresponding authors
5. *Bekpen C., Kunzel S., Xie C., Eaaswarkhanth M., Lin YL., Gokcumen O., Akdis CA and Tautz D.*, (2017) Segmental duplications and evolutionary acquisition of UV damage response in the SPATA31 gene family of primates and humans
   BMC Genomics March 6 Full Text (HTML) | PDF
   * Corresponding authors
6. *Bekpen C., Baker C., Herbert M., Sahin HB., Johnson M., Celik A., Mullikin J., Eichler EE. (2017) Functional characterization of morpheus gene family.
   biorxiv-preprint March 12 Full Text (HTML) | PDF
   * Corresponding author
7. Alkan C., Kavak P., Somel M., Gökçümen O.,Ugurlu S., Dal E., Bilge BK, Gungor T., Sahinalp CS., Ozören N.* Bekpen C.*(2014) Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa
   BMC Genomics November 7 Full Text (HTML) | PDF
   * Corresponding author
8. Zaleska A, Eiwegger T, Soyer O, van de Veen W, Rhyner C, Soyka MB, Bekpen C, Demiröz D, Treis A, Sollner S, Palomares O, Kwok WW, Rose H, Senti G, Kundig TM, Ozoren N, Jutel M, Akdis CA, Crameri R, Akdis M.(2014) Immune regulation by intralymphatic immunotherapy with modular allergen translocation MAT vaccine
   Allergy, Sep;69(9):1162-70.
9. *Bekpen C., Tastekin I., Siswara P., Akdis AC., *Eichler EE. (2012) Primate segmental duplication creates novel promoters for the LRRc37 gene family within the 17q21.31 inversion polymorphism region
   Genome Research, Apr 11. Full Text (HTML) | PDF
   * Corresponding author
10. Sin BA., Akdis M., Zumkehr J., Bezzine S., Bekpen C., Lambeau G., Akdis CA., (2011) T Cell and Antibody Responses to Phospholipase A2 from Different Species Show Distinct Cross-Reactivity Patterns.
    Allergy, Dec. 66(12):1513 Full Text (HTML) | PDF
11. Bekpen C., Marques-Bonet T, Alkan C, Antonacci F, Leogrande MB, Ventura M, Kidd JM, Siswara P, Howard JC, Eichler EE. (2009) Death and resurrection of the human IRGM gene.
    PLoS Genet. Mar;5(3):e1000403. Full Text (HTML) | PDF
    *Highlighted as news from;
    - Science "A Curious Case of Genetic Resurrection"
    - Nature "The resurrection of a disease-linked gene"
    - NewScientist "First 'resurrected' gene found in humans" 
12. Bekpen C., Hunn JP, Rohde C, Parvanova I, Guethlein L, Dunn DM, Glowalla E, Leptin M, Howard JC. (2005) The interferon-inducible p47 (IRG) GTPases in vertebrates: loss of the cell autonomous resistance mechanism in the human lineage.
    Genome Biology, 6(11):R92. Full Text (HTML) | PDF
    Editors' Choice: Highlights of the recent literature, Science, Vol: 310, Number 5752, Issue of 25 Nov. 2005.
    
13. Leonhardt RM, Keusekotten K, Bekpen C., Knittler MR., (2005) Critical role for the tapasin-docking site of TAP2 in the functional integrity of the MHC class I-peptide-loading complex.
    J Immunol. Oct 15;175(8):5104-14. Full Text (HTML) | PDF

1. Bekpen C.*, and Tautz D. Involvement of SPATA31 copy number variable genes in human lifespan Jena Aging Meeting, 2018 Jena / Germany Oral Presentation
2. Bekpen C.*, Xie C., Nebel A. and Tautz D. Involvement of SPATA31 copy number variable genes in human lifespan Annual Meeting of the German Foundation for Aging Research (DGfA), 2017 Cologne / Germany Oral Presentation
3. Bekpen C.*, Xie C., Nebel A. and Tautz D. Copy number variation of SPATA31 antagonistically correlates with germline and somatic mutation rates and shorter life span in humans Gordon Research Conference, Molecular Mechanisms of Evolution, 2017 Boston / USA Oral/Poster Presentation
4. Bekpen C.*, Tautz D. Birth of a new gene: the problem of self-tolerance versus autoimmune reaction Annual Meeting of the German Zoological Society (DZG), 2016 Kiel / Germany Oral/Poster Presentation
   
5. Bekpen C.*, Tautz D. Birth of a new gene: the problem of self-tolerance versus autoimmune reaction SMBE 2016 / Australia
   
6. Bekpen C.*, Tautz D. Evolutionary and functional characterization of SPATA31 gene family SMBE 2015 / Austria
   
7. Bekpen C.*, Tautz D. Evolutionary and functional characterization of Human Core Duplicons SMBE 2014 / Puerto Rico
   
8. Giannuzzi G.*, Bekpen C.*, Siswara P., Ventura M., Eichler EE. Evolution of LRRC37 primate gene family from a functional perspective 14th Human Genome Meeting 2010 Montpellier/ France *These two authors contributed equally to this work
9. Bekpen C.,Comparative genomics analysis and dynamic structure of segmentally duplicated gene families.International Symposium on Health Informatics and Bioinformatics, (HIBIT), 2008 Ankara / Turkey Invited Speaker
   
10. Bekpen C.,The interferon-inducible p47 (IRG) GTPases in vertebrates: loss of the cell-autonomous resistance mechanism in the human lineage.International Symposium on Health Informatics and Bioinformatics, (HIBIT), 2005 Antalya / Turkey Oral Presentation
11. Bekpen C.,J. Hunn, I. Parvanova, E. Glowalla, L. Guethlein, J. C. Howard, Systematics and evolution of the p47 resistance GTPases; Gain and loss of immune function. ENII-EMBO Workshop on Mechanisms of Immunity, 2005 Ile des Embiez/France Oral Presentation
    
12. Bekpen C.,J. Hunn, S. Martens, I. Parvanova, S. Weisshaar, and J. Howard, Mediators of cell-autonomous immunity: the p47 GTPases. 34th Annual Meeting of the German Society of Immunology, Immunobiology, Volume 208, Number 1-3, 2003 Berlin/Germany
    

1. Bekpen C., and *Tautz D. (2019)
   Human core duplicon gene families: game changers or game players?,
   Briefings in Functional Genomics, 16 Sept 2019, Online First, Full Text (HTML) | PDF
   * Corresponding author
   
2. Bekpen C., Ramnik X. and Eichler E.E. (2010)
   Human IRGM gene "To be or not to be",
   Seminars in Immunopathology,25 August 2010, Online First, Full Text (HTML) | PDF
   * Corresponding author

1. Bekpen C. (2006)
   Evolutionary and functional studies of p47 GTPases involved in cell autonomous immunity.
   Ph.D. thesis, Institute for Genetics, University of Cologne, Cologne, Germany | PDF

1. SPATA31 Gene Family Copy Numbers as a Human Example of Antagonistic Pleiotropy
   FIGHT AGING | April 20th, 2018 | 
   

1. NTV Bugün-Yarın Pogramı
   NTV.com | Video Streaming |
   
2. Türklere özel bir genom bulunamad
   Hurriyet.com | Ocak 21, 2012 |
   
3. Somona karşı sağlık hizmeti
   Hurriyet.com | 13 Ocak 2012 |
   
4. Türklerin gen haritası çıkarıldı
   Ensonhaber..com | 21.01.2012 |
   

1. x, y, z (31 Ocak 2013)
   NTV.com | 04.02.2013 | Video |
   

1. A Curious Case of Genetic Resurrection
   Science.com | 6 MAR 2009 |
2. The resurrection of a disease-linked gene
   Nature.com | 5 MAR 2009 |
3. First 'resurrected' gene found in humans
   Newscientist.com | 6 MAR 2009 |
4. Resurrection In Evolution: IRGM Gene's Death And Rebirth
   Science20.com | 4 MAR 2009 |
5. A dead gene comes back to life in humans
   SMedicalexpress.com | 6 MAR 2009 |

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