Kadir C. Akdemir, Ph.D.
Department of Neurosurgery, Division of Surgery
About Dr. Kadir C. Akdemir
Kadir Akdemir, Ph.D. is an Assistant Professor of the Department of Neurosurgery at MD Anderson. Raised in Turkey, he studied computer science and genetics at Yeditepe University in Istanbul. He obtained a PhD from the University of Texas Health Science Center at Houston for his work on p53 protein’s functions during human embryonic stem cell differentiation. He then completed his post-doctoral training with Dr. Andrew Futreal at MD Anderson’s Genomic Medicine department on cancer genomics and three-dimensional chromatin organization. His work on the integration of the three-dimensional chromatin organization with cancer genomic datasets provided unique insights into the mechanisms and consequences of somatic alterations observed in human tumors (Akdemir et al. Nature Genetics - PMID: 3302066; Akdemir et. al. Nature Genetics - PMID: 32024999). He has an extensive research program focused on genomic alterations observed in human central nervous system tumors.
Dr. Akdemir has been part of the several international genomic efforts such as the International Cancer Genome Consortia’s pan-cancer whole-genome analyses initiative and NIH’s 4Dnucleome comprehensive chromatin profiling initiative. He holds multiple foundation grants. He is collaborating with the world-renowned brain cancer researchers by being a part of the MD Anderson’s SPORE in Brain Cancer Program, GBM Moonshot program and the Break Through Cancer’s GBM program.
His lab has developed a large set of techniques to study mechanisms and patterns of chromatin folding and somatic rearrangements that occur in cancer genomes during neoplastic transformation.
Present Title & Affiliation
Primary Appointment
Assistant Professor, Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX
Research Interests
Central Nervous System Tumors
Rare Tumors
Cancer Genomics
Chromatin Organization
Epigenetics
Education & Training
Degree-Granting Education
| 2008 | Yeditepe University, Istanbul, TUR, BS, Computer Engineering |
| 2007 | Yeditepe University, Istanbul, TUR, BS, Genetics and Bioengineering |
Postgraduate Training
| 2013-2017 | Research Fellowship, MD Anderson Cancer Center, Houston, TX |
Professional Memberships
Selected Publications
Peer-Reviewed Articles
- Inoue A, Robinson FS, Minelli R, Tomihara H, Rizi BS, Rose JL, Kodama T, Srinivasan S, Harris AL, Zuniga AM, Mullinax RA, Ma X, Seth S, Daniele JR, Peoples MD, Loponte S, Akdemir KC, Khor TO, Feng N, Roszik J, Sobieski MM, Brunell D, Stephan C, Giuliani V, Deem AK, Shingu T, Deribe YL, Menter DG, Heffernan TP, Viale A, Bristow CA, Kopetz S, Draetta GF, Genovese G, Carugo A. Sequential administration of XPO1 and ATR inhibitors enhances therapeutic response in TP53-mutated colorectal cancer. Gastroenterology 161(1):196-210, 2021. e-Pub 2021. PMID: 33745946.
- Akdemir KC, Le VT, Kim JM, Killcoyne S, King DA, Lin YP, Tian Y, Inoue A, Amin SB, Robinson FS, Nimmakayalu M, Herrera RE, Lynn EJ, Chan K, Seth S, Klimczak LJ, Gerstung M, Gordenin DA, O'Brien J, Li L, Deribe YL, Verhaak RG, Campbell PJ, Fitzgerald R, Morrison AJ, Dixon JR, Andrew Futreal P. Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure. Nat Genet 52(11):1178-1188, 2020. e-Pub 2020. PMID: 33020667.
- Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L, PCAWG Consortium. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun 11(1):4748, 2020. e-Pub 2020. PMID: 32958763.
- Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N, PCAWG Tumour Subtypes and Clinical Translation, Boutros PC, PCAWG Consortium. Sex differences in oncogenic mutational processes. Nat Commun 11(1):4330, 2020. e-Pub 2020. PMID: 32859912.
- Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PAW, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine K, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH, PCAWG Structural Variation Working Group, Campbell PJ, Tubio JMC, PCAWG Consortium. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet 52(3):306-319, 2020. e-Pub 2020. PMID: 32024998.
- Yuan Y, Ju YS, Kim Y, Li J, Wang Y, Yoon CJ, Yang Y, Martincorena I, Creighton CJ, Weinstein JN, Xu Y, Han L, Kim HL, Nakagawa H, Park K, Campbell PJ, Liang H, PCAWG Consortium. Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat Genet 52(3):342-352, 2020. e-Pub 2020. PMID: 32024997.
- Akdemir KC, Le VT, Chandran S, Li Y, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA, PCAWG Structural Variation Working Group, PCAWG Consortium. Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nat Genet 52(3):294-305, 2020. e-Pub 2020. PMID: 32024999.
- Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS, PCAWG Structural Variation Working Group, Park PJ, PCAWG Consortium. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat Genet 52(3):331-341, 2020. e-Pub 2020. PMID: 32025003.
- ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature 578(7793):82-93, 2020. e-Pub 2020. PMID: 32025007.
- Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M, PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Campbell PJ, PCAWG Consortium. Patterns of somatic structural variation in human cancer genomes. Nature 578(7793):112-121, 2020. e-Pub 2020. PMID: 32025012.
- Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M, PCAWG-Structural Variation Working Group, Brors B, Rippe K, Jones DTW, Feuerbach L, PCAWG Consortium. Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun 11(1):733, 2020. e-Pub 2020. PMID: 32024817.
- Genovese G, Carugo A, Tepper J, Robinson FS, Li L, Svelto M, Nezi L, Corti D, Minelli R, Pettazzoni P, Gutschner T, Wu CC, Seth S, Akdemir KC, Leo E, Amin S, Molin MD, Ying H, Kwong LN, Colla S, Takahashi K, Ghosh P, Giuliani V, Muller F, Dey P, Jiang S, Garvey J, Liu CG, Zhang J, Heffernan TP, Toniatti C, Fleming JB, Goggins MG, Wood LD, Sgambato A, Agaimy A, Maitra A, Roberts CW, Wang H, Viale A, DePinho RA, Draetta GF, Chin L. Synthetic vulnerabilities of mesenchymal subpopulations in pancreatic cancer. Nature 542(7641):362-366, 2017. e-Pub 2017. PMID: 28178232.
- Akdemir KC, Chin L. HiCPlotter integrates genomic data with interaction matrices. Genome Biol 16(1):198, 2015. e-Pub 2015. PMID: 26392354.
Other Articles
- Cancer Genome Atlas Network Genomic Classification of Cutaneous Melanoma. Cell 161(7):1681-96, 2015. PMID: 26091043.
Grant & Contract Support
| Title: | Brain SPORE DRP Award |
| Funding Source: | NIH/NCI |
| Role: | Principal Investigator |
| Title: | SPORE in Brain Cancer, Biostatistics and Bioinformatics Core |
| Funding Source: | NIH/NCI |
| Role: | Co-Program Leader |
| Title: | Investigating the effects of structural variants on 3D genome organization and gene regulation in cancer genomes |
| Funding Source: | NIH/NCI |
| Role: | Sub-Principal Investigator |
| Title: | Oncogene and tumor suppressor-induced common fragile sites: a new paradigm for understanding genome instability in cancer |
| Funding Source: | The San Diego Biomedical Research Institute/NIH |
| Role: | Sub-Principal Investigator |
| Title: | Informative clinical trial platform of longitudinal sampling to accelerate development of therapeutics for glioblastoma |
| Funding Source: | Commonwealth Cancer Consortium (dba Break Through Cancer) |
| Role: | Project Leader |
| Title: | Breakthrough Cancer Data Science Hub |
| Funding Source: | Commonwealth Cancer Consortium (dba Break Through Cancer) |
| Role: | Project Leader |
| Title: | Identifying and visualizing complex chromosomal rearrangements at the molecular level in malignant brain tumors |
| Funding Source: | NIH/NCI |
| Role: | Principal Investigator |
| Title: | Leveraging Chromatin Folding Patterns in Chordoma Genomes to Develop Predictive and Prognostic Biomarkers |
| Funding Source: | UT MD Anderson Cancer Center- Institutional Research Grant |
| Role: | Principal Investigator |
| Title: | Epigenetic modulation of chromatin to enhance cancer immunotherapy response in hypermutated gliomas |
| Funding Source: | Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation |
| Role: | Principal Investigator |
| Title: | Multifaceted Genomic Analyses of Spine and Skull Chordomas to Develop Predictive and Prognostic Biomarkers |
| Funding Source: | Chordoma Foundation |
| Role: | Principal Investigator |
| Title: | Uncovering the structural organization of extrachromosomal DNA and its relevance to the onset of glioblastoma |
| Funding Source: | Gulf Coast Consortia (Subcontract with UT Medical Branch, Galveston) |
| Role: | Co-Principal Investigator |
| Title: | Investigating the Effects of Whole-Genome Doubling on Chordoma Recurrence and Genome Organization |
| Funding Source: | Chordoma Foundation |
| Role: | Principal Investigator |
| Title: | Single cell RNA-seq on anatomically guided biopsies to dissect regional intratumoral heterogeneity in clival chordomas |
| Funding Source: | Nico Corporation |
| Role: | Principal Investigator |
Patient Reviews
CV information above last modified June 21, 2024