Benjamin Kidder (ff2646)

4100 John R St
HWCRC Room 624
Detroit, MI 48201 

http://benjaminkidderlab.com/

• Stem cell and Cancer Epigenetics
• Transcriptional Networks
• Reprogramming and Transdifferentiation
• Genome Stability 

One of the research goals of Dr. Benjamin Kidder's lab is to understand how stem cells pattern the epigenetic landscape in a way that facilitates distinct expression programs throughout development. Humans develop from a single fertilized egg into a complex organism with many cell types, each with its own distinct gene expression and epigenetic profile. These complex cellular states, when perturbed, can lead to diseases such as cancer. Our lab uses experimental, genomics, and computational biology tools to study the epigenetic regulation of stem cell and cancer function, genome stability, and reprogramming/transdifferentiation. We are particularly interested in understanding how epigenetic landscapes are regulated in cancer vs. normal cells, the role for heterochromatin in regulating genome stability, and how histone modifying enzymes contribute to the diverse cellular repertoire that exists in mammals. 

Allison V Mitchell, Ling Wu, C James Block, Mu Zhang, Justin Hackett, Douglas B Craig, Wei Chen, Yongzhong Zhao, Bin Zhang, Yongjun Dang, Xiaohong Zhang, Shengping Zhang, Chuangui Wang, Heather Gibson, Lori A Pile, Benjamin Kidder, Larry Matherly, Zhe Yang, Yali Dou, Guojun Wu. FOXQ1 recruits the MLL complex to activate transcription of EMT and promote breast cancer metastasis. Nature Communications 2022;13:6548. 

He R, Xhabija B, Gopi LK, Kurup JT, Xu Z, Liu Z, Kidder BL. H3K4 demethylase KDM5B regulates cancer cell identity and epigenetic plasticity. Oncogene. 2022;41:2958-72.

Gopi LK, Kidder BL. Integrative pan cancer analysis reveals epigenomic variation in cancer type and cell specific chromatin domains. Nature Communications. 2021;12:1419. 

Kurup JT, Kidder BL. H4K20me3 methyltransferase SUV420H2 shapes the chromatin landscape of pluripotent embryonic stem cells. Development. 2020;147:188516. 

KDM5B is a master regulator of the H3K4-methylome in stem cells, development and cancer. Xhabija B, Kidder BL. Semin Cancer Biol. 2019;57:79-85.

Contribution of H3K4 demethylase KDM5B to nucleosome organization in embryonic stem cells revealed by micrococcal nuclease sequencing. Kurup JT, Campeanu IJ, Kidder BL. Epigenetics Chromatin. 2019;12:20.

Kurup JT, Kidder BL. Identification of H4K20me3 and H3K4me3-associated RNAs using CARIP-Seq expands the transcriptional and epigenetic networks of embryonic stem cells. J Biol Chem. 2018 Aug 16. pii: jbc.RA118.004974. [Epub ahead of print].

He R, Kidder BL. Culture of haploid blastocysts in FGF4 favors the derivation of epiblast stem cells with a primed epigenetic and transcriptional landscape. Sci Rep. 2018;8:10775.

Xu J, Kidder BL. H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells. BMC Genomics. 2018;19:514.

Kidder BL. CARIP-Seq and ChIP-Seq: Methods to Identify Chromatin-Associated RNAs and Protein-DNA Interactions in Embryonic Stem Cells. J Vis Exp. 2018;29889205.

Xu J, Kidder BL. KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation. Biol Open. 2018;7:bio031245.

Vizcardo R, Klemen ND, Islam SMR, Gurusamy D, Tamaoki N, Yamada D, Koseki H, Kidder BL, Yu Z, Jia L, Henning AN, Good ML, Bosch-Marce M, Maeda T, Liu C, Abdullaev Z, Pack S, Palmer DC, Stroncek DF, Ito F, Flomerfelt FA, Kruhlak MJ, Restifo NP. Generation of Tumor Antigen-Specific iPSC-Derived Thymic Emigrants Using a 3D Thymic Culture System. Cell Rep. 2018;22:3175-90.

B.A. in Chemistry and Biology (2001): Saint Olaf College, Northfield, MN
Ph.D. in Molecular, Cellular, Developmental Biology and Genetics (2007): University of Minnesota, Minneapolis, MN
Postdoctoral Fellow: EMD/Merck Serono Research Institute, Rockland, MA
Principal Investigator: EMD/Merck Serono Research Institute, Rockland, MA
Research Fellow in Epigenome Biology: National Heart, Lung and Blood Institute (NHLBI, NIH), Bethesda, MD 

CB7210 Fundamentals of Cancer Biology 2018
CB7220 Molecular Biology of Cancer Development
CB7300 Biomarkers in Cancer
CB7300 Epigenomics and Transcriptomics
CB7460 Mechanisms of Neoplasia: Alterations to Cellular Signaling

Associate Professor
Basic Science

Karmanos Cancer Institute
4100 John R. Rd
Mailcode: HW06AO
Detroit, MI 48201

Education
(2002-2007)  Ph.D. Molecular, Cellular, Developmental Biology and Genetics (MCDB&G), University of Minnesota, Minneapolis, MN
(1997-2001)  B.A. Chemistry and Biology, Saint Olaf College, Northfield, MN

Postgraduate Training
(2012-2015)  Research Fellow, National Heart, Lung and Blood Institute, (NHLBI, NIH), Bethesda, MD
(2011-2012)  IRTA-Fellow, National Heart, Lung and Blood Institute (NHLBI, NIH), Bethesda, MD
(2007-2009)  Postdoctoral Fellow, EMD/Merck Serono Research Institute, Rockland, MA

Faculty Appointments
(2024 - Present) Associate Professor, Department of Oncology, Wayne State University School of Medicine, Detroit, MI
(2015 - 2024) Assistant Professor, Department of Oncology, Wayne State University School of Medicine, Detroit, MI

Hospital or Other Professional Appointments
(2015-Present)  Scientific Member, Tumor Biology and Microenviornment Program, Karmanos Cancer Institute, Detroit, MI
(2009-2011)  Principal Investigator, EMD/Merck Serono Research Institute, Rockland, MA

(2013-2014)  American Society for Microbiology (ASM)
(2010-2012)  International Society for Stem Cell Research (ISSCR)
(2008-2009)  Society for the Study of Reproduction (SSR)
(2008-2010)  American Society for Reproductive Medicine (ASRM)

(2024) College Teaching Award, Wayne State University School of Medicine, Detroit, MI
(2016) NHLBI Career Transition Award (K22), National Heart, Lung and Blood Institute, NIH, Bethesda, MD
(2015) NIH Fellows Award for Research Excellence (FARE) Winner, National Heart, Lung and Blood Institute, NIH, Bethesda, MD
(2014) Genome Engineering Technology Award, NHLBI, NIH, National Heart, Lung and Blood Institue
(2013) Performance Award, NHLBI, NIH, National Heart, Lung and Blood Institute, NIH, Bethesda, MD
(2010) EMD/Merck Serono Research Institute On-The-Spot Award, EMD/Merck Serono Research Institute, Rockland, MA
(2010) EMD/Merck Millipore Tech Expo Poster Award, EMD/Merck Millipore, Billerica, MA
(2004-2005) NIH NIGMS Biotechnology Training Grant, University of Minnesota, Minneapolis, MN
(2002) Award for Excellence, NIDCR, NIH, National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD
(2001-2002) Postbaccalaureate pre-IRTA Fellow at the NIH
(2001-2002) National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD
(1998-2000) Finstad Grant Recipient/Entrepreneurs Club, St. Olaf College, Northfield, MN

CB 7210: Fundamentals of Cancer Biology
CB 7460: Mechanisms of Neoplasia - Alterations to Cellular Signaling
CB 7700: Recent Developments in Cancer Biology 

Stem cell Epigenetics
Transcriptional Networks
Reprogramming and Transdifferentiation
Genome Stability

1.Kidder BL, Hu G, Zhao K. KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation. GENOME BIOLOGY 2014 Feb 4;15(2):R32 (Epub).

2.Kidder BL, Zhao K. Efficient library preparation for next-generation sequencing analysis of genome-wide epigenetic and transcriptional landscapes in embryonic stem cells. METHODS IN MOLECULAR BIOLOGY. 2014;1150:3-20. doi: 10.1007/978-1-4939-0512-6_1.PMID:24743988

3. Kidder BL, Hu G, Yu Z, Liu C, Zhao K. Extended self-renewal and accelerated reprogramming in the absence of Kdm5b. MOLECULAR AND CELLULAR BIOLOGY 2013 Dec;33(24):4793-810. PMID: 24100015

4. Kidder BL, Palmer S. HDAC1 regulates pluripotency and lineage specific transcriptional networks in embryonic and trophoblast stem cells. NUCLEIC ACIDS RESEARCH 2012 Apr;40(7):2925-39. PMID: 22156375

5. Kidder BL, Hu G, Zhao K. ChIP-Seq: technical considerations for obtaining high quality data. NATURE IMMUNOLOGY 2011 Sep 20;12(10):918-22. PMID: 21934668

6. Kidder BL, Palmer S. Examination of transcriptional networks reveals an important role for TCFAP2C, SMARCA4, and EOMES in trophoblast stem cell maintenance. GENOME RESEARCH 2010 Apr;20(4):458-72. PMID: 20176728

7. Kidder BL, Palmer S, Knott JG.  SWI/SNF-Brg1 regulates self-renewal and occupies core pluripotency-related genes in embryonic stem cells. STEM CELLS 2009 FEB; 27(2):317-28. PMID: 19056910

8. Kidder BL, Yang J, Palmer S. Stat3 and c-Myc genome-wide promoter occupancy in embryonic stem cells. PLOS ONE. 2008;3(12):e3932 PMID: 19079543

9. Kidder BL, Oseth L, Miller SC, Hirsch B, Verfaillie C, Coucouvanis E. Embryonic stem cells contribute to mouse chimeras in the absence of detetable cell fusion. CLONING STEM CELLS 10 (2): 231-248 JUN 2008. PMID: 18338954

10.Ulloa-Montoya F*, Kidder BL*, Pauwelyn K, Chase L, Luttun A, Crabbe A, Geraerts M, Sharov AA, Piao Y, Ko MS, Hu WS, Verfaillie CM. Comparative transcriptome analysis of embryonic and adult stem cells with extended and limited differentiation capacity. GENOME BIOLOGY 8 (8): R163 2007.PMID: 17683608

 * authors contributed equally

Benjamin L. Kidder, PhD