Core C: Genomics and Analytical Chemistry (Archived)


The overall goals of the SRP are to use ‘omic’ technologies and modern analytical methods to develop biological markers for application in human studies and site remediation to allow better detection and remediation of Superfund priority chemicals and emerging contaminants in the environment; and to better evaluate the risk they pose to human health.  Core C is set up specifically for the purposes of providing the laboratory infrastructure and expertise for Projects 1-6 to achieve these goals.  To meet many of the Aims of Projects 1- 4 and ensure their success, investigators require access, know-how and technical support to apply cutting-edge technologies such as functional genomics, transcriptomics, proteomics, genetics and epigenetics. Project 3 is an epidemiological study that requires effective handling and management of biological samples so that these technologies can be applied.  To accomplish these goals, detailed collection and storage protocols have been designed and the Core will provide facilities for the genetic and proteomic studies that will be conducted in Projects 1-4.  Projects 3 and 5 will also require sophisticated mass spectrometry analyses that will be provided by the QB3/Chemistry Mass Spectrometry Facility.  The Core will also provide support for high-throughput analysis of toxic metabolites for Project 6 through the Berkeley Screening Center.  The specific aims of Core C are to: 1) process, maintain and store biological samples and cell lines; 2) provide facilities and methodologies for gene expression and epigenetic studies; 3) provide analytical support for proteomic studies, for the identification of proteins and organic and inorganic compounds through our QB3/Chemistry Mass Spectrometry Facility, and toxicity screening support; 4) provide facilities and methodologies to analyze genetic polymorphisms; and, 5) provide sequencing capabilities at our QB3 DNA sequencing facility. The Core will provide expertise and analytical support in all required areas that, along with the computational biology skills of Core D, will allow for the successful completion of Projects 1-6 of the Berkeley SRP.

This is relevant because it provides a centralized source of specialized facilities and equipment, services, well-tested collection and storage protocols, and expert technical support using the latest “-omics” technologies and analytical instruments for Berkeley Superfund Research Program project investigators.  These services will greatly enhance the success of Projects 1-6 investigators to achieve their overall goals.

Core Leadership

Martyn T. Smith, PhD

Professor of Toxicology

Environmental Health Sciences,
School of Public Health
University of California, Berkeley

Daniel K. Nomura, PhD


Department of Nutritional Science and Toxicology, College of Natural Resources
University of California, Berkeley

Core Update


We developed and used an innovative chemoproteomic strategy termed isotopic tandem orthogonal proteolysis-enabled activity-based protein profiling (isoTOP-ABPP) to characterize the toxicological mechanisms of the widely used herbicides acetochlor and glyphosate.  We showed that both chemicals inhibit thiolases involved in fatty acid oxidation in vivo in mouse liver, leading disruption of lipid metabolism and development of hepatic steatosis.  Two manuscripts are in press at ACS Chemical Biology and Cell Chemical Biology.


Over the past year, we have been developing and applying an innovative chemoproteomic strategy termed isotopic tandem orthogonal proteolysis-enabled activity-based protein profiling (isoTOP-ABPP) to map proteome-wide targets of various environmental chemicals to better understand their toxicological mechanisms.  IsoTOP-ABPP uses reactivity-based chemical probes to map proteome-wide reactive, functional, and ligandable hotspots directly in complex proteomes.  When used in a competitive manner, small-molecules can be competed against binding of reactivity-based probes to ligandable hotspots to identify targets and off-targets of environmental chemicals.  We have used isoTOP-ABPP to recently characterize the toxicological mechanisms of the widely used herbicides acetochlor and glyphosate.  We show that both chemicals, acetochlor in its parent form and glyphosate through its metabolism to glyoxylate, inhibit the catalytic cysteines of several thiolases involved in fatty acid oxidation in vivo in mouse liver.  We show that inhibition of these targets leads to a diversion of fatty acids away from degradation and towards other lipid pathways, including triglycerides leading to hepatic steatosis.  These studies have been accepted to ACS Chemical Biology and Cell Chemical Biology, and will be published in the very near future.

Core Update Archive

Core News

In 2016, Core Leader Dan Nomura served as a study section member for an NIH Scientific Review Group, Special Emphasis Panel ZRG1 BSTU 50.  Nomura was a 2016 invited speaker and delivered his presentation, “Mapping Metabolic Drivers of Cancer using Chemoproteomic and Metabolomic Platforms”, at these venues:

  • Gilead Medicinal Chemistry Seminar Series, Foster City, CA.
  • Gordon Conference on Bioorganic Chemistry, New Hampshire.
  • AACR National Meeting, New Orleans, Louisiana.
  • University of Pavia, Italy.
  • Medical University of Graz, Graz, Austria.
  • Keystone Science Lecture Speaker at National Institutes for Environmental Health Sciences, Research Triangle Park, North Carolina.
News Archive

Selected Publications


Counihan JL, Ford B, Nomura DK (2016) Mapping proteome-wide interactions of reactive chemicals using chemoproteomic platforms. Curr Opin Chem Biol. Feb;30:68-76. PMCID: PMC4731263. [PDF]


Medina-Cleghorn D, Bateman LA, Ford B, Heslin A, Fisher KJ, Dalvie ED, Nomura DK (2015) Mapping proteome-wide targets of environmental chemicals using reactivity-based chemoproteomic platforms. Chemistry and Biology. Oct 22;22(10):1394-1405. PMCID: PMC4621755. [PDF]


Morris PJ, Medina-Cleghorn D, Heslin A, King SM, Orr J, Mulvihill MM, Krauss RM, Nomura DK (2014) Organophosphorus Flame Retardants Inhibit Specific Liver Carboxylesterases and Cause Serum Hypertriglyceridemia. ACS Chem Biol. May 16;9(5):1097-103. PMICD: PMC4027947. [PDF]

Bassig BA, Zhang L, Cawthon RM, Smith MT, Yin S, Li G, et al. (2014) Alterations in leukocyte telomere length in workers occupationally exposed to benzene. Environ Mol Mutagen. 55(8):673-8. PMCID: PMC4360990. [PDF]

Daniels SI, Sille FC, Goldbaum A, Yee B, Key EF, Zhang L, et al. (2014) Improving power to detect changes in blood miRNA expression by accounting for sources of variability in experimental designs. Cancer Epidemiol Biomarkers Prev. 23(12):2658-66. PMCID: PMC4256675.

Thomas R, Hubbard AE, McHale CM, Zhang L, Rappaport SM, Lan Q, et al. (2014) Characterization of changes in gene expression and biochemical pathways at low levels of benzene exposure. PLoS One. 9(5):e91828. PMCID: PMC4006721. [PDF]

McHale CM, Zhang L, Lan Q, Vermeulen R, Li G, Hubbard AE, et al. (2011) Global gene expression profiling of a population exposed to a range of benzene levels. Environ Health Perspect. 119(5):628-34. PMCID: PMC3094412. [PDF]

Medina-Cleghorn D, Heslin A, Morris PJ, Mulvihill MM, Nomura DK (2014) Multidimensional profiling platforms reveal metabolic dysregulation caused by organophosphorus pesticides. ACS Chemical Biology 9, 423-432. PMCID: PMC4042408. [PDF]

Medina-Cleghorn D, Nomura DK (2014) Exploring metabolic pathways and regulation through functional chemoproteomic and metabolomic platforms. Chemistry & Biology 21, 1171-1184. PMCID: PMC4171689. [PDF]

Zhou J, He Z, Yang Y, Deng Y, Tringe SG, Alvarez-Cohen L (2014) High-throughput metagenomic technologies for complex microbial community analysis. mBio. Jan 27;6(1):e02288-14. PMCID: PMC4324309. [PDF]


Zhang L, Bassig BA, Mora JL, Vermeulen R, Ge Y, Curry JD, Hu W, Shen M, Qiu C, Ji Z, Reiss B, McHale CM, Liu S, Guo W, Purdue MP, Yue F, Li L, Smith MT, Huang H, Tang X, Rothman N, Lan Q (2013) Alterations in serum immunoglobulin levels in workers occupationally exposed to trichloroethylene. Carcinogenesis. Jan16. [Epub ahead of print]. PMID: 23276795. (PMC Journal- In Progress). [PDF]

Thomas R, McHale CM, Lan Q, Hubbard AE, Zhang L, Vermeulen R, et al. Global gene expression response of a population exposed to benzene: a pilot study exploring the use of RNA-sequencing technology. Environ Mol Mutagen. 2013;54(7):566-73. PMCID: PMC4353497. [PDF]


Zhang L, Lan Q, Ji Z, Li G, Shen M, Vermeulen R, et al. (2012) Leukemia-related chromosomal loss detected in hematopoietic progenitor cells of benzene-exposed workers. Leukemia. 26(12):2494-8. PMCID: PMC3472034. [PDF]


Smith MT, Zhang L, McHale CM, Skibola CF, Rappaport SM (2011) Benzene, the exposome and future investigations of leukemia etiology. Chem Biol Interact. Jun 30;192(1-2):155-9. PMID: 21333640. [PDF]


Lightfoot TJ, Roman E, Smith MT, Skibola CF (2010) Acute lymphoblastic leukaemia in children – is there a role for MTHFR? Br J Haematol. Feb 8; PMID: 20148884. [PDF]

Vlaanderen J, Moore LE, Smith MT, Lan Q, Zhang L, Skibola CF, Rothman N, Vermeulen R (2010) Application of OMICS technologies in occupational and environmental health research; current status and projections. Occup Environ Med. Feb; 67(2):136-43. PMID: 19933307. [PDF]

Lightfoot TJ, Johnston WT, Painter D, Simpson J, Roman E, Skibola CF, Smith MT, Allan JM, Taylor GM (2010) Genetic variation in the folate metabolic pathway and risk of childhood leukemia. Blood. Jan 25; PMID: 20101025. [PDF]


McHale CM, Zhang L, Lan Q, Li G, Hubbard AE, Forrest MS, Vermeulen R, Chen J, Shen M, Rappaport SM, Yin S, Smith MT, Rothman N (2009) Changes in the peripheral blood transcriptome associated with occupational benzene exposure identified by cross-comparison on two microarray platforms. Genomics. Apr; 93(4):343-9. PMID: 19162166. PMCID: PMC2693268. [PDF]

Scelo G, Metayer C, Zhang L, Wiemels JL, Aldrich MC, Selvin S, Month S, Smith MT, Buffler PA (2009) Household exposure to paint and petroleum solvents, chromosomal translocations, and the risk of childhood leukemia. Environ Health Perspect. Jan; 117(1):133-9. PMID: 19165400. [PDF]


Wiemels JL, Hofmann J, Kang M, Selzer R, Green R, Zhou M, Zhong S, Zhang L, Smith MT, Marsit C, Loh M, Buffler P, Yeh RF (2008) Chromosome 12p deletions in TEL-AML1 childhood acute lymphoblastic leukemia are associated with retrotransposon elements and occur postnatally. Cancer Res. Dec 1; 68(23):9935-44. PMID: 19047175. PMCID: PMC2597307. [PDF]

Hegedus CM, Skibola CF, Warner M, Skibola DR, Alexander D, Lim S, Dangleben NL, Zhang L, Clark M, Pfeiffer RM, Steinmaus C, Smith AH, Smith MT, Moore LE (2008) Decreased urinary beta-defensin-1 expression as a biomarker of response to arsenic. Toxicol Sci. Nov; 106(1):74-82. PMID: 18511430. PMCID: PMC2563143. [PDF]


Paynter RA, Skibola DR, Skibola CF, Buffler PA, Wiemels JL, Smith MT (2006) Accuracy of multiplexed Illumina platform-based single-nucleotide polymorphism genotyping compared between genomic and whole genome amplified DNA collected from multiple sources.Cancer Epidemiol Biomarkers Prev. Dec; 15(12):2533-6. PMID: 17164381. [PDF]

Aldrich MC, Zhang L, Wiemels JL, Ma X, Loh ML, Metayer C, Selvin S, Feusner J, Smith MT, Buffler PA (2006) Cytogenetics of Hispanic and White children with acute lymphoblastic leukemia in California. Cancer Epidemiol Biomarkers Prev. Mar; 15(3):578-81. PMID: 16537719. [PDF]

Birkner MD, Hubbard AE, van der Laan MJ, Skibola CF, Hegedus CM, Smith MT (2006) Issues of processing and multiple testing of SELDI-TOF MS proteomic data. Stat Appl Genet Mol Biol. 5:Article11. PMID: 16646865. [PDF]


Hegedus CM, Gunn L, Skibola CF, Zhang L, Shiao R, Fu S, Dalmasso EA, Metayer C, Dahl GV, Buffler PA, Smith MT (2005) Proteomic analysis of childhood leukemia. Leukemia. Oct; 19(10):1713-8. PMID: 16136170. [PDF]

Smith MT, McHale CM, Wiemels JL, Zhang L, Wiencke JK, Zheng S, Gunn L, Skibola CF, Ma X, Buffler PA (2005) Molecular biomarkers for the study of childhood leukemia. Toxicol Appl Pharmacol. Aug 7; 206(2):237-45. PMID: 15967214. [PDF]

Forrest MS, Lan Q, Hubbard AE, Zhang L, Vermeulen R, Zhao X, Li G, Wu YY, Shen M, Yin S, Chanock SJ, Rothman N, Smith MT (2005) Discovery of novel biomarkers by microarray analysis of peripheral blood mononuclear cell gene expression in benzene-exposed workers.Environ Health Perspect. Jun; 113(6):801-7. PMID: 15929907. PMCID: PMC1257610. [PDF]

Moore LE, Pfeiffer R, Warner M, Clark M, Skibola C, Steinmous C, Alguacil J, Rothman N, Smith MT, Smith AH (2005) Identification of biomarkers of arsenic exposure and metabolism in urine using SELDI technology. J Biochem Mol Toxicol. 19(3):176. PMID: 15977200. [PDF]