Aaron Diaz PhD

Aaron Diaz, PhDAssistant Professor in Residence of Neurological Surgery

Principal Investigator, Brain Tumor Research Center

 

 

 

The Diaz Lab is interested in developing targeted therapeutics for the treatment of glioma. We apply molecular and computational approaches to elucidate targets and pathways mediating cancer progression. We integrate the rapidly growing wealth of biomedical Big Data, with high-throughput genetic and epigenetic assays, to study tumor growth and response to treatment.

To date, some of the most effective cancer therapies have been those that hone in on molecular defects associated with specific driver genes. However, in highly diverse tumors, such as gliomas, clinical trials of promising targeted therapeutics often produce mixed results. This is at least partially due to intra-tumor regional heterogeneity in response to treatment. To address this pressing challenge, we combine high-throughput single-cell and functional assays with state-of-the-art machine-learning algorithms. These methods produce quantitative models of tumor heterogeneity, and micro-environment interaction. The long-term goal of these studies is to help to guide the design of clinical trials with targeted agents, and improve the management of gliomas through precision therapies.

Education, Training, and Previous Positions

1993-1997: BS, New York University, Mathematics
1997-2003: MS, Cornell University, Computer Science
1997-2003: PhD, Cornell University, Applied Mathematics
2002-2003: Intern, Sandia National Laboratory
2003-2010: Assistant Professor, Dept. of Mathematics, Santa Clara University
2010-2014: Postdoctoral Fellow, Inst. for Human Genetics, UCSF
2014-present: Assistant Professor, Dept. of Epidemiology & Biostatistics, UCSF
2015-present: Assistant Professor, Dept. of Neurological Surgery, UCSF

Professional Memberships and Associations

Society of Neuro-Oncology
IEEE

Selected Honors and Awards

2010: BCATS Plenary Talk Award
2008: Santa Clara University Dean's Award
2003: Santa Clara University Technology Innovation Award
1997: Cornell University Sage Fellowship
1997: Institute for Advanced Study Research Fellowship
1996: Carnegie Mellon University Research Fellowship
1993: New York University Tuition Scholarship

Selected Recent Publications

Müller S, Agnihotri S, Shoger KE, Myers MI, Smith N, Chaparala S, Villanueva CR, Chattopadhyay A, Lee AV, Butterfield LH, Diaz A, Okada H, Pollack IF, Kohanbash G. Peptide vaccine immunotherapy biomarkers and response patterns in pediatric gliomas. JCI Insight. 2018 Apr 5;3(7). pii: 98791.

Bulut-Karslioglu A, Macrae TA, Oses-Prieto JA, Covarrubias S, Percharde M, Ku G, Diaz A, McManus MT, Burlingame AL, Ramalho-Santos M. The Transcriptionally Permissive Chromatin State of Embryonic Stem Cells Is Acutely Tuned to Translational Output. Cell Stem Cell. 2018 Mar 1;22(3):369-383.

Müller S, Kohanbash G, Liu SJ, Alvarado B, Carrera D, Bhaduri A, Watchmaker PB, Yagnik G, Di Lullo E, Malatesta M, Amankulor NM, Kriegstein AR, Lim DA, Aghi M, Okada H, Diaz A. Single-cell profiling of human gliomas reveals macrophage ontogeny as a basis for regional differences in macrophage activation in the tumor microenvironment. Genome Biol. 2017 Dec 20;18(1):234.

Bartlett TE, Müller S, Diaz A. Single-cell Co-expression Subnetwork Analysis. Sci Rep. 2017 Nov 8;7(1):15066.

Müller S, Diaz A. Single-Cell mRNA Sequencing in Cancer Research: Integrating the Genomic Fingerprint. Front Genet. 2017 May 31;8:73.

Müller S, Liu SJ, Di Lullo E, Malatesta M, Pollen AA, Nowakowski TJ, Kohanbash G, Aghi M, Kriegstein AR, Lim DA, Diaz A. Single-cell sequencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas. Mol Syst Biol. 2016 Nov 25;12(11):889. doi: 10.15252/msb.20166969. PubMed PMID: 27888226; PubMed Central PMCID: PMC5147052.

Diaz A, Liu SJ, Sandoval C, Pollen A, Nowakowski TJ, Lim DA, Kriegstein A. SCell: integrated analysis of single-cell RNA-seq data. Bioinformatics. 2016 Jul 15;32(14):2219-20. doi: 10.1093/bioinformatics/btw201. Epub 2016 Apr 19. PubMed PMID: 27153637; PubMed Central PMCID: PMC4937196.

Liu SJ, Nowakowski TJ, Pollen AA, Lui JH, Horlbeck MA, Attenello FJ, He D, Weissman JS, Kriegstein AR, Diaz AA, Lim DA. Single-cell analysis of long non-coding RNAs in the developing human neocortex. Genome Biol. 2016 Apr 14;17:67.

Suzawa M, Miranda DA, Ramos KA, Ang KK, Faivre EJ, Wilson CG, Caboni L, Arkin MR, Kim YS, Fletterick RJ, Diaz A, Schneekloth JS, Ingraham HA. A gene-expression screen identifies a non-toxic sumoylation inhibitor that mimics SUMO-less human LRH-1 in liver. Elife. 2015 Dec 11;4. pii: e09003.

Pollen AA, Nowakowski TJ, Chen J, Retallack H, Sandoval-Espinosa C, Nicholas CR, Shuga J, Liu SJ, Oldham MC, Diaz A, Lim DA, Leyrat AA, West JA, Kriegstein AR. Molecular identity of human outer radial glia during cortical development. Cell. 2015 Sep 24;163(1):55-67.

Diaz AA, Qin H, Ramalho-Santos M, Song JS. HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis. Nucleic Acids Res. 2015 Feb 18;43(3):e16.

Qin H*, Diaz A*, Blouin L, Lebbink RJ, Patena W, Tanbun P, LeProust EM, McManus MT, Song JS, Ramalho-Santos M. Systematic identification of barriers to human iPSC generation. Cell 2014;158(2):449-461.

Nagarajan RP, Zhang B, Bell RJ, Johnson BE, Olshen AB, Sundaram V, Li D, Graham AE, Diaz A, Fouse SD, Smirnov I, Song J, Paris PL, Wang T, Costello JF. Recurrent epimutations activate gene body promoters in primary glioblastoma. Genome Res 2014;24(5):761-774.

Ramos AD, Diaz A, Nellore A, Delgado RN, Park KY, Gonzales-Roybal G, Oldham MC, Song JS, Lim DA. Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. Cell Stem Cell 2013;12(5):616-28.

Nellore A, Bobkov K, Howe E, Pankov A, Diaz A, Song JS. NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data. Front Genet 2013;3:320.

Diaz A, Nellore A, Song JS. CHANCE: comprehensive software for quality control and validation of ChIP-seq data. Genome Biol 2012;13(10):R98.

Diaz A, Park K, Lim DA, Song JS. Normalization, bias correction, and peak calling for ChIP-seq. Stat Appl Genet Mol Biol 2012;11(3):Article 9.

Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS, Reiter JF. Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal. PLoS Genet 2012;8(3):e1002576.