Can Küçük Laboratory

Functional Genomics of Cancer and Rare Diseases

 

Kucuk Research Lab Picture can.kucuk@deu.edu.tr, cankucuk.ibgizmir@gmail.com
Room Nmb. 2031
Members
Hongling Yuan, M.D. (Specialist)
Burcu Akman (Ph.D. student)
Esra Baytak (MSc student)
Deniz Kurşun (MSc student)

RESEARCH INTERESTS

Our current research mainly focuses on the identification and characterization of novel mutations and epigenetic alterations of tumor suppressor genes or oncogenes in cancers and aberrant genes in rare diseases. Our interest mainly resides in hematological malignancies with a particular focus on common lymphomas (e.g. follicular lymphoma) and leukemias (e.g. acute myeloid leukemia) which are neoplastic diseases having a high degree of genetic heterogeneity.

Can Küçük Şekil

We frequently use next generation sequencing (NGS) based technologies to generate a candidate list of aberrant genes using panels of lymphoma patient samples. We then validate mutations by applying Sanger sequencing that is identified through whole exome sequencing (WES) and/or RNA-sequencing. Moreover, our studies focus on genome-wide methylation changes in gene promoter regions of cancer samples. Altogether, we characterize these aberrations using a combination of genetic, epigenetic and molecular biology assays. In general, our studies follow a wholistic approach which involves the cooperation of a variety interrelated biomedical disciplines such as pathology, functional genomics, and computational bio-informatics. Our eventual goal is to identify and characterize genetic and epigenetic abnormalities in every cancer patient to translate the discoveries as personalized medicine.

Lab members

Küçük lab is currently seeking highly-motivated graduate students. If interested, please contact Dr. Küçük by email: cankucuk.ibgizmir@gmail.com

Can Küçük’s CV
04/15 – present Assistant Professor of Medical Biology, Izmir International Biomedicine and Genome Institute, Izmir, Turkey.
11/14 – 03/15 Tübitak 2232 grantee, Dokuz Eylul University Izmir Biomedicine and Genome Center, Izmir, Turkey.
10/13 – 10/14 Postdoctoral Research Fellow, Department of Pathology, City of Hope Medical Center, Duarte, CA, USA.
10/12 – 09/13 Postdoctoral Research Associate, Department of Pathology and Microbiology, University of Nebraska Medical Center (UNMC), Omaha, NE, USA.
12/06 – 10/12 Ph.D. in Cancer Biology and Oncology, Cancer Research Graduate Program (CRGP), University of Nebraska Medical Center (UNMC), Omaha, NE, USA.
09/05 – 12/06 Graduate Research Assistant* in Development, Cell and Neurobiology, Lousiana State University Health Sciences Center (LSUHSC), New Orleans, LA, USA.
09/01 – 07/05 B.Sc. in Molecular Biology and Genetics, Middle East Technical University (METU), Ankara, Turkey.
*: Transferred to a new Ph.D. program due to Hurricane Kathrina.
AWARDS AND RECOGNITION

• Turkish Academy of Sciences (TÜBA)-The Young Scientists Award Programme (GEBIP), Turkey, 2017.
• XV. National Medical Biology and Genetic Congress, Young Investigator 1st Ranking Award, Turkey, 2017.
• Science Academy – Young Scientist Award (BAGEP),Turkey, 2015.
• TÜBİTAK – BİDEB 2232 Reintegration Grant, Turkey, 2014.
• American Society of Hematology (ASH) – Abstract Achievement Award, USA, 2013.
• UNMC – Graduate Studies Assistantship (Competetive renewal at 2010), USA, 2009.
• TÜBİTAK – Basic Sciences B Scholarship, Turkey, 2002.
PUBLICATIONS
Full list and citations: Google Scholar: Can Kucuk

  1. Wan Y, He D, Ye Y, Zhang W, Zhao S, Long Y, Chen M, Küçük C. “Primary cardiac diffuse large B-cell lymphoma with concurrent high MYC and BCL2 expression in an immunocompetent Chinese elderly woman.” Cardiovasc Pathol. 2017 Nov 1;31:54-6.
  2. Baytak E, Gong Q, Akman B, Yuan H, Chan W.C., Küçük C#“Whole transcriptome analysis reveals dysregulated oncogenic lncRNAs in natural killer/T-cell lymphoma and establishes MIR155HG as a target of PRDM1.” Tumour Biol. 2017 39(5) p.1010428317701648.
  3. Hu X, Baytak E, Li J, Akman B, Okay K, Hu G, Scuto A, Zhang W#, Küçük C#. “The relationship of REL proto-oncogene to pathobiology and chemoresistance in follicular and transformed follicular lymphoma.” Leuk Res. 2017 Mar;54:30-38.
  4. Küçük C, Chan WC. “Selective expression of KIR2DL4 for improved diagnosis and as a potential therapeutic target in natural killer/T cell lymphomas: Beyond the Abstract”, OncToday.com, 2016 Oct 3; 23985.
  5. Küçük C#, Hu X, Gong Q, Jiang B, Cornish A, Gaulard P, McKeithan T, Chan WC#. “Diagnostic and Biological Significance of KIR Expression Profile Determined by RNA-Seq in Natural Killer/T-Cell Lymphoma.” Am. J Pathol. 2016 Jun 30;186(6):1435-41.
  6. Gao LM, Zhao S, Liu WP, Zhang WY, Li GD, Küçük C, Hu XZ, Chan WC, Tang Y, Ding WS, Yan JQ, Yao WQ, Wang JC. “Clinicopathologic Characterization of Aggressive Natural Killer Cell Leukemia Involving Different Tissue Sites.”Am J Surg Pathol. 2016 Jun 1;40(6):836-46.
  7. Xiaozhou Hu, Wing C.Chan, Can Küçük#. “Generation of a genetically engineered aggressive NK-cell leukemia cell line with stable IL2 expression”. Acta Medica International 2015 July-Dec;2(2):78-84.
  8. Can Küçük#, Xiaozhou Hu, Timothy McKeithan, and Wing C. Chan. “Lack of Evidence that HACE1 Is Not a Tumor Suppressor Gene in NKTCL: To the Editor-in-Chief.” Am. J Pathol. 2015. 185, no. 4: 1167-1168.
  9. C Küçük*, X Hu*, B Jiang, D Klinkebiel, H Geng, A Bouska, J Iqbal, P Gaulard, TW. McKeithan, and WC. Chan. “Global promoter methylation analysis reveals novel candidate tumor suppressor genes in natural killer cell lymphoma.” Clin. Cancer Res. 21(7):1699- 711 2015.
  10. C Küçük*, B Jiang*, X Hu, W Zhang, JK.C. Chan, W Xiao, N Lack, C Alkan, JC. Williams, KN. Avery, P Kavak, A Scuto, E Sen, P Gaulard,L Staudt, J Iqbal, W Zhang, A Cornish, Q Gong, Q Yang, H Sun, F d’Amore, S Leppä, W Liu , K Fu, L de Leval,T McKeithan , WC. Chan. “Activating mutations of STAT5B and STAT3 in lymphomas derived from γδ-T or NK cells.” Nat Commun. 2015 Jan 14; 6:6025.
  11. A Bouska, T W McKeithan, KE Deffenbacher, C Lachel, GW Wright, J Iqbal, LM Smith, W Zhang, C Kucuk , A Rinaldi, F Bertoni, J Fitzgibbon, K Fu, DD Weisenburger, TC Greiner,BJ Dave, RD Gascoyne, A Rosenwald, E Campo, LM Rimsza, J Delabie, ES Jaffe, RM Braziel, J Connors, LM Staudt, and WC Chan. “Genome-wide copy number analyses reveal genomic abnormalities involved in transformation of follicular lymphoma.” Blood 2014 Mar 13;123(11):1681-90.
  12. AM. Perry, RA. Warnke, Q Hu, P Gaulard, C Copie- Bergman, S Alkan, HY Wang, JX. Cheng, CM. Bacon, J Delabie, E Ranheim, C Kucuk, X Hu, DD. Weisenburger, ES. Jaffe, WC. Chan. “Indolent T-cell lymphoproliferative disease of the gastrointestinal tract.” Blood 2013 Nov 21;122(22):3599-606.
  13. Liu C, Iqbal J, Teruya-Feldstein J, Shen Y, Dabrowska MJ, Dybkaer K, Lim MS, Piva R, Barreca A, Pellegrino E, Spaccarotella E, Lachel CM, Kucuk C , Jiang CS,Hu X, Bhagvati S, Greiner TC, Weisenburger DD, Aoun P, Perkins SL, McKeithan TW, Inghirami G, Chan WC. “MicroRNA expression profiling identifies molecular signatures associated with anaplastic large cell lymphoma.” Blood 2013 Sep 19;122(12):2083-92.
  14. Küçük C*, Hu X*, Iqbal J, Gaulard P, Klinkebiel D ,Cornish A, Dave BJ, Chan WC. “HACE1 is a Tumor Suppressor Gene Candidate in Natural Killer Cell Neoplasms.” Am. J Pathol. 182(1):49-55.2013.
  15. RA Cairns*, J Iqbal*, F Lemonnier*, C Kucuk, L de Leval, JP Jais, M Parrens, A Martin, L Xerri, P Brousset, LC Chan, WC Chan, P Gaulard, and Tak W Mak. “IDH2 mutations are frequent in angioimmunoblastic T-cell lymphoma.” Blood 2012 Feb 23; 119(8):1901-3.
  16. Küçük C, Iqbal J, Hu X, Gaulard P, De Leval L, Srivastava G, Au WY, McKeithan TW, Chan WC. “PRDM1 is a Tumor Suppressor Gene in Natural Killer Cell Malignancies.” Proc Natl Acad Sci U S A. 2011 Dec 13;108 (50):20119-24. Epub 2011 Dec 5.
  17. Iqbal J, Weisenburger DD, Chowdhury A, Tsai MY, Srivastava G, Greiner TC, Kucuk C , Deffenbacher K, Vose J, Smith L, Au WY, Nakamura S, Seto M, Delabie J, Berger F, Loong F, Ko YH, Sng I, Liu X, Loughran TP, Armitage J, Chan WC. “NK-cell lymphoma shares strikingly similar molecular features with a distinct subset of T-cell lymphoma and is highly sensitivity to a novel aurora kinase A inhibitor in vitro.” Leukemia 2011 Feb 1;25(2):348-58.
  18. Martha E.Bickford, Arkadiusk Slusarczyk,Emil K.Dilger,Thomas E. Krahe, Can Kucuk, and William Guido. “Synaptic Development of the Mouse Dorsal Geniculate Nucleus.” J. Comp Neurol. 2010 Mar 1; 518 (5):622-35.
  19. Javeed Iqbal, Dennis Weisenburger, Timothy C Greiner, Julie M Vose, Timothy McKeithan, Can Kucuk, Huimin Geng, Karen Deffenbacher, Lynette Smith, Karen Dybkaer, Shigeo Nakamura, Masao Seto, Jan Delabie, Francoise Berger, Florence Loong, Wing Y Au, Young- Hyeh Ko, Ivy Sng, James Olen Armitage, and Wing C Chan. ‘Molecular signatures to improve diagnosis in peripheral T-cell lymphoma and prognostication in angioimmunoblastic T-cell lymphoma.’ Blood 2010 Feb 4;115(5):1026-1036.
  20. Javeed Iqbal*, Can Kucuk*, Ronald J. deLeeuw, Gopesh Srivastava, Wayne Tam, Huimin Geng, David Klinkebiel, Judith K. Christman, Kavita Patel, Kajia Cao, Lijun Shen, Karen Dybkaer, Ivy F.L. Tsui, Hesham Ali, Norio Shimizu, Wing Yan Au, Wan L. Lam and Wing C. Chan. ‘Genomic analyses reveal global functional alterations that promote tumor growth and novel tumor suppressor genes in natural killer-cell malignancies.’ Leukemia 2009 June; 23, 1139-1151.
  21. Javeed Iqbal, Shantaram Joshi, Kavita N Patel, Sofi I Javed, Can Kucuk, Afeera Aabida, Francesco d’Amore, Kai Fu. ‘Clinical implication of genome-wide profiling in diffuse large B-cell lymphoma and other subtypes of B-cell lymphoma.’ IJC 2007 Apr-Jun; 44(2):72-86.
    *: Equal contribution. #: Corresponding author.

 

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