Chibo Hong, PhD
Research interests: Genetic and epigenetic profiling of gliomas; intratumoral heterogeneity and treatment-associated malignant progression of gliomas
Other interests: Loves nature and sports; enjoys reading with her kids
Email: chibo.hong@ucsf.edu
We use novel quantitative imaging methods to guide biopsies to biologically distinct regions of brain tumors for targeted exome and transcriptome analysis. Our goal is to identify naturally evolving and treatment-induced mutations that drive malignant transformation (MT) of low grade glioma (LGG) to high grade glioma (HGG). We incorporate MRI-guided tumor biopsies and treatment data with longitudinal genomics to allow the reconstruction of tumor evolution in the context of the human tumor in vivo. We use cutting-edge technology, the Next Generation Sequencing (NGS), to discover patterns and interdependencies of genetic mutations, epigenetic alternations and gene expression. Our goal is to understand the full evolutionary history of human brain tumors, from the first mutation and epimutation through clonal selection and tumor recurrence.
Our exome and RNA-seq data suggests that evolution of mutations differs dramatically in temozolomide (TMZ) treated and non-treated patients, and this commonly used chemotherapeutic agent itself may induce transformation-promoting driver mutations that converge on common signaling pathways. We will interrogate the genetic underpinnings of MT in TMZ-treated and untreated patients with two complementary approaches. Through collaboration, we will be exploring the application of immune therapies to target tumor specific mutations and tumors that emerge as hypermutated following chemotherapy.
1990: MD, Zhejiang University
2001: PhD, University of California, Berkeley
2001-2004: Postdoctoral Fellow, Costello Lab, UCSF
2004: The American Brain Tumor Association Research Fellowship
2004: American Association for Cancer Research-AFLAC Awards
2007: Gordon Research Conferences: Cancer Genetics and Epigenetics Travel Award
Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors
Zardo, G; Tiirikainen, M; Hong, C; Misra, A; Feuerstein, BG; Volik, S; Collins, CC; Lamborn, KR; Bollen, A; Pinkel, D; Albertson, D and Costello, JF
Nat Genet. 2002 Nov;32(3):453-8.
Epigenome scans and cancer genome sequencing converge on WNK2, a kinase-independent suppressor of cell growth
Hong C, Moorefield KS, Jun P, Aldape KD, Kharbanda S, Phillips HS, Costello JF.
Proc Natl Acad Sci USA. 2007 Jun 26;104(26):10974-9. Epub 2007 Jun 19.
DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape
Xie M, Hong C, Zhang B, Lowdon RF, Xing X, Li D, Zhou X, Lee HJ, Maire CL, Ligon KL, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A, O'Geen H, Farnham PJ, Madden PA, Mungall AJ, Tam A, Kamoh B, Cho S, Moore R, Hirst M, Marra MA, Costello JF, Wang T.
Nat Genet. 2013 Jul;45(7):836-41. doi: 10.1038/ng.2649. Epub 2013 May 26.
Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma
Johnson BE, Mazor T, Hong C, Barnes M, Aihara K, McLean CY, Fouse SD, Yamamoto S, Ueda H, Tatsuno K, Asthana S, Jalbert LE, Nelson SJ, Bollen AW, Gustafson WC, Charron E, Weiss WA, Smirnov IV, Song JS, Olshen AB, Cha S, Zhao Y, Moore RA, Mungall AJ, Jones SJ, Hirst M, Marra MA, Saito N, Aburatani H, Mukasa A, Berger MS, Chang SM, Taylor BS, Costello JF
Science. 2014 Jan 10;343(6167):189-193. doi: 10.1126/science.1239947. Epub 2013 Dec 12.
Intermediate DNA methylation is a conserved signature of genome regulation
Elliott G, Hong C, Xing X, Zhou X, Li D, Coarfa C, Bell RJ, Maire CL, Ligon KL, Sigaroudinia M, Gascard P, Tlsty TD, Harris RA, Schalkwyk LC, Bilenky M, Mill J, Farnham PJ, Kellis M, Marra MA, Milosavljevic A, Hirst M, Stormo GD, Wang T, Costello JF.
Nat Commun. 2015 Feb 18;6:6363. doi: 10.1038/ncomms7363.
DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors
Mazor T, Pankov A, Johnson BE, Hong C, Hamilton EG, Bell RJ, Smirnov IV, Reis GF, Phillips JJ, Barnes MJ, Idbaih A, Alentorn A, Kloezeman JJ, Lamfers ML, Bollen AW, Taylor BS, Molinaro AM, Olshen AB, Chang SM, Song JS,Costello JF.
Cancer Cell. 2015 Sep 14;28(3):307-17.