Focusing diagnostics and therapeutics on those most likely to benefit is a key to successful intervention at both the public health and clinical levels. The translational goal of the Spivack laboratory is to identify individuals at particularly high risk for lung malignancy, and selected non-malignant lung diseases, upon whom to focus smoking/toxin exposure cessation (primary prevention), chemoprevention (secondary prevention), and early disease detection efforts (disease screening, tertiary prevention).
The laboratory is currently exploring individual Gene x Environment signatures as susceptibility markers by exploring quantitative gene (mRNA) expression phenotypes, and the DNA sequence, methylation, microRNA, and other epigenetic features potentially underlying these expression phenotypes, in vitro and in human populations. This is performed in the setting of defined tobacco, diet, and other exposures. There are both mechanistic and translational components to the studies.
Mechanistically, the role of epigenetic variation in promoter regions in the 5' and 3' regulatory regions of carcinogenesis and oxidant pathway genes is being explored in vitro, using human genomic DNA reporter constructs, and native gene regulation models. High resolution technologies include the realtime quantitation of native mRNA and microRNA by the laboratory's RNA-specific strategy (patented); the tagged-bisulfite genomic sequencing strategy to determine single base resolution CpG methylation status (tBGS, patented); evaluation of functional consequences of DNA methylation detail, using a novel patch reporter construct, not previously reported (patent pending); and an experimental strategy for assaying microRNA binding to mRNA, for determining the role of miRNA in candidate gene regulation, not previously reported (patent pending).
Whole (epi)genome approaches to identify molecular events unique to lung cancer are being completed, which will represent one of the initial cross-platform 'omics level discovery examinations of lung tissues. The execution of each individual discovery platform involves expert local collaborators and cores in (epi)genetics and genomics, and the "integromics" is critically reliant on Einstein strengths in informatics and biostatistical analyses.
Translationally, lung carcinogenesis biomarkers are being established by pairing laser capture microdissected lung and several unique, non-invasively collected surrogate specimens developed in the laboratory, such as mRNA expression signatures from brush-exfoliated buccal mucosa cells, and DNA methylation and microRNA-PCR from exhaled breath condensate, representing first reports for a new airway biomarker class. These airway-derived specimens continue to accrue from a sampling (currently n>950) of a population assembled in a lung cancer case-control context. The specimens are being studied for quantitative gene expression, and its regulatory underpinnings, in carcinogenesis pathways, by both the RNA-specific RT-PCR approaches, and by the tBGS DNA methylation sequencing, and related approaches, with a view toward non-invasive assays.
These expression, genetic, and epigenetic data at the genome-wide and locus-specific levels are linked to precise measurements of tobacco, diet, and other exposures, as well as downstream molecular events, as an approach to putting a metric to gene-environment interaction for risk stratification for diagnostic and disease screening purposes .
Other translational projects include: (i) Discovery and testing of plant-derived chemopreventive mixture and individual candidate compounds for antimutagen, antioxidant and other activity; (ii) MTb diagnostics by novel non-invasive means.
The overall aim is to develop informative non-invasive risk profiling, preventive, and early disease detection strategies for the lung in human populations.
Work is funded by ongoing NIH and Foundation support.
- lung nodule evaluation
- lung cancer diagnostics
- interstitial lung disease
- environmental lung disease
- general pulmonary medicine
Selected Recent Publications/Manuscripts, as of December, 2012:
Ghombar S, Shi M, Tang W, Suh Y, Spivack SD. A micronome-wide survey of lung cancer using microRNA-seq coupled to transcriptome expression assays. [in prep].
Mullapudi N, Han W, Suzuki M, Wang T, Fazarri M, Spivack SD. A methylome survey of human lung cancer coupled to genome-wide expression [in prep].
Shi M, Han W, Spivack SD. Affirmation of microRNA:mRNA binding by affinity pull-down. [submitted].
Lin J, Marquardt G, Mullapudi N, Wang, T, Han W, Shi W, Zhu C, Keller S, Zhu C, Locker J, Spivack SD. Lung cancer transcriptomes refined with laser capture microdissection. [submitted].
Han W, Shi M, Spivack SD. Site-specific methylated reporter constructs for functional analysis of DNA methylation [submitted].
Alberg AJ, Brock MV, Ford JG, Samet JM, Spivack, SD. Epidemiology of lung cancer. In Evidence-based Practice Guidelines. Diagnosis and Management of Lung Cancer (ACCP position statement). CHEST. [in press].
Tan XT, Marquardt G, Shi M, Han W, Spivack SD. High throughput library screening identifies phytochemical inducers of phase II mutagen/oxidant metabolism enzymes GSTP1 and NQO1 in human lung cells. Am J Resp Cell Molec Biol, 46(3): 365-71, 2012.
Englert NA, Turesky RJ, Han W, Bessette EE, Spivack SD, Caggana M, Spink DC, Spink BC. Genetic and epigenetic regulation of AHR gene expression in MCF-7 breast cancer cells: role of the proximal promoter GC-rich region. (epubl, Biochemical Pharmacology), 2012.
Brock GJ, Moschos S, Spivack SD, Hurteau GJ. The 3' prime paradigm of the miR-200 family and other microRNAs. Epigenetics (6:3, 1-5), 2011.
Tan XT, Shi M, Minna JD, Han W, Spivack SD. Candidate phytopreventive agent modulation of phase II metabolism enzymes GSTP1 and NQO1 in human bronchial cells. J Nutrition, 140(8): 1404-10, 2010.
Bessette EE, Spivack SD, Goodenough AK, Wang T, Pinto S, Kadlubar FF, Turesky RJ. Identification of Carcinogen DNA Adduct in Human Saliva by Linear Quadropole Ion Trap/Multistage Tandem Mass Spectrometry. Chem Res Toxicol. 2010 May 5. [Epub ahead of print].
Tan, XT, Wang T, Xiong S, Kumar SV, Han W, Spivack SD. Smoking-related gene expression in laser capture microdissected human lung. Clin Cancer Res, 15(24): 7562-70, 2009.
Han W, Tang T, Reilly AA, Keller S, Spivack SD. Gene promoter methylation analyses from exhaled breath, with differences in smokers and lung cancer cases. Resp Res, 10:86 epubl, 2009.
Tan X-L, Moslehi R, Han W, Spivack SD. Haplotype tagging single nucleotide polymorphisms in the glutathione S-transferase P1 gene promoter and susceptibility to lung cancer. Cancer Detection Prev,32:403-415, 2009.
Tan X-L, Spivack SD. Dietary chemoprevention strategies for induction of phase II metabolism: a review. Lung Cancer,65(2):129-37, 2009.
Hurteau GJ, Carlson AJ, Spivack, SD, Brock GJ. Restoration of E-Cadherin expression by over-expression of the microRNA hsa-miR-200c via reduced expression of the transcription factor TCF8. Cancer Res. 67:7972-76, 2007.
Hurteau, GJ, Spivack SD, Brock G. Parallel identification of miRNA and target mRNA by combined informatics and qRT-PCR approaches: application to has-miR-200c. Cell Cycle 5(17):1951-56, 2006.
Han W, Cauchi S, Herman JG, Spivack SD. Methylation mapping of DNA by tag-modified bisulfite genomic DNA sequencing. Analytic Biochem. 355: 50-61, 2006.
Cauchi S, Han W, Kumar SV, Spivack SD. Haplotype-environment interactions regulating the human GSTP1 promoter Cancer Res. 66(12): 6439-6448, 2006.
Kumar SV, Hurteau GJ, Spivack SD. Validity of mRNA expression analyses of human saliva. Clin. Cancer Res. 12: 5033-39, 2006.
Han W, Pentecost BT, Pietropaolo RL, Fasco MJ, Spivack SD. ERá increases basal and cigarette smoke-induced expression of CYP1A1 and CYP1B1, but not GSTP1 in normal human bronchial epithelial cells. Molec. Carcinogenesis, 44(3):202-211, 2005.
Spivack SD, Hurteau GJ, Jain R, Kumar SV, Aldous KM, Gierthy JF, Kaminsky LS. Gene-environment interaction signatures by quantitative mRNA profiling in exfoliated buccal mucosal cells. Cancer Res, 64:6805-6813, 2004.
Spivack SD, Hurteau GJ, Fasco MJ, Kaminsky LS. Phase I and II carcinogen metabolism gene expression in human lung tissue and tumors. Clinical Cancer Research, 9:6002-6011, 2003.
Han W, Pentecost BT, Spivack SD. Functional evaluation of novel SNPs and haplotypes in the promoter region of CYP1B1 and CYP1A1 genes. Molec. Carcinogenesis 37:158-69, 2003.
Fasco MJ*, Hurteau, GJ, SpivackSD. Gender-dependent expression of alpha and beta estrogen receptors in human nontumor and tumor lung tissue. Molecular Cellular Endocrin, 188(1-2):125-40. 2002.
Hurteau GJ, Spivack SD. mRNA-Specific RT-PCR from human tissue extracts. Analytic Biochemistry 307:304-15. 2002.
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