PRASHANT BOMMI

**** ***** ***. *** # ***, Evanston. IL 60201

773-***-**** : ac1tiu@r.postjobfree.com

EDUCATION

v University of Illinois at Chicago. Aug-2017

Ph.D in Oral Sciences, GPA: 3.5/4.0

v Murray State University, Murray, KY May-2004

MS. Molecular Genetics. GPA 4.0/4.0

v Marathawada Agril. University, MS, India. June-2002 MSc. GPA 7.9/10

v Mahatma Phule Agril. University. MS, India. June-2000 BSc. GPA 8.28/10.

PROFESSIONAL EXPERIENCE

Pre-Doc Fellow. Aug 2012 – Aug 2017

Oral Biology - College of Dentistry, University of Illinois at Chicago, Chicago, IL 801 S. Paulina Street. Chicago, IL 60612

o Damaged DNA Binding Protein-2 in as regulator of Hypoxia Response in Oral cancer (HNSCC) cells. DDB2 regulates hypoxia response genes (e.g. LOX and CAIX) by transcriptionally repressing the expression of hypoxia inducible factor, HIF1-alpha.

o Damaged DNA Binding Proteins (DDB1 and DDB2) in Epithelial and Mesenchymal Transition (EMT) of Oral HNSCC cells

Expression of DDB2 was significantly reduced in Oral SCC cell lines. DDB2 is required for stability of DDB1 and both DDB2 and DDB1 were expressed at very low levels. Re-expression or knockdown of DDB2 regulates expression of EMT inducing genes and DDB2 reverses EMT phenotype by inducing expression of epithelial makers (E-cadherin) and represses expression of mesenchymal markers (N-cadherin, Vimentin, and Fibronectin). Visiting Research Specialist Aug 2010 to July 2012 University of Illinois at Chicago

Oral Biology, College of Dentistry, University of Illinois at Chicago, Chicago, IL 801 S. Paulina Street. Chicago, IL 60612

o Damaged-DNA Binding Protein-2 (DDB2) and cellular senescence. DDB2, a Nucleotide excision repair (NER) protein, is shown to induce senescence via persistent accumulation of ROS after UV irradiation. It does so by repressing antioxidant genes by recruiting Cul4A and Suv39h and increasing trimethylation of H3K9. My research involved exploring other important targets of DDB2 in knockout mouse models. Research Assistant Jan 2005 to Aug 2010

NorthShore University HealthSystem – Research Institute A Teaching Affiliate of the University of Chicago - Pritzker School of Medicine Division of Molecular Oncology and Cancer Biology. Department of Medicine. 1001 University Place, Evanston. IL 60201.

o Oncogenic potential of Polycomb Protein BMI1.

BMI-1 is a c-Myc co-operating oncogene and belongs to polycomb group genes (PcG) repressive complex 1 (PRC1). Elevated levels of BMI1 are associated with many types of cancers including breast cancer. The major objective of this project is to study the oncogenic potential of BMI1 in human normal and breast carcinoma cells. I aided and prioritized in investigating the role of this gene in cell immortalization, regulation of tumor suppressor genes in normal mammary epithelial cells using modern in-vitro tools and techniques.

o Role of BMI1 in Aging and Stem Cells [Inducing Pluripotent stem cells (iPS)]. BMI1 is required for self renewal of stem cells and it increases the life span of fibroblast cells by downregulating p16 Ink4a gene transcript. Derivation of Induced Pluripotent stem cells (iPS) from somatic cells using BMI1 and a subset of transcription factors (Oct4, SOX2, and KLF4) is currently being studied. Retroviral transduction of transcription factors OCT4, SOX2, KLF4 and BMI1 and selecting colonies (iPS) over inactivated MEF cells. Analyzing colonies for their pluripotency markers using established human embryonic stem cell line H9. o A Cancer Model using combined overexpression of BMI1 and EZH2, and SUZ12. The aim of this project is to study oncogenic potential of polycomb Group. Using BMI1 in combination with other polycomb proteins Ezh2 and SUZ12 that belong to polycomb group proteins repressive complex 2 (PRC2), we are studying the aggressive characteristic mimicking cancer cell. Molecular characterization of a normal somatic cell after combined expression of BMI1, EZH2, and SUZ12 was exclusively studied with special attention to Senescence (Aging) in fibroblast cells.

o HDAC Inhibitors in Regulation of PcG Proteins and Cancer Therapy. Histone deacetylase inhibitors (HDACi) are emerging as novel and exciting class of potential anticancer drugs for the treatment of solid and hematological malignancies. Present research using HDACi have shown significant effect on regulation of Polycomb proteins and their effect on target genes. We are exclusively investigating the effects of HDACi on regulation of polycomb group of genes (PcG) in normal HMECs and cancer cell lines. This study will shed new light of information about chromatin modification after HDACi treatment and help us better understand the mechanism by which PcG expression is deregulated during cancer progression and metastasis which is imperative for cancer therapeutics. o Role of BMI1 in Retinal Pigment Epithelial cells (ARPE). Oxidative Injury to retinal cells contributes to pathogenesis of age related macular degeneration (AMD), which is a leading cause for blindness in patients over 60 years of age. RPE are specialized cells of eye tissue responsible for photoreceptor maintenance. Dysfunction of RPE cells causes several pathological events leading to AMD. A collaborative study highlights the protective role of BMI1 against Oxidative Stress and Senile Macular Degeneration. o Gene Regulation and Protein Stability studies of BMI1. A major study of factors responsible for BMI1 protein stability in human normal breast epithelial cells, fibroblast cells, and breast cancer cell lines. Detailed characterization and analysis of BMI1 protein domain and interacting molecules effecting BMI1 protein stability. The stability of BMI1 protein will have more pronounced role in regulation of tumor suppressor genes leading to uncontrolled proliferation of cells and causing Cancer. Research experience during Master’s degree Program School of Agriculture 2002-2004

Murray State University

Murray, KY 42240. USA

o Microsatellite Markers (SSR Markers) as a powerful genetic tool. Simple sequence repeat (SSR) markers provide a powerful genetic tool for distinguishing between different cultivars. My research was a part of Biodiesel project wherein it required a quick and veritable tool to segregate specific lots of Soybean. The objective of the study was to test the feasibility of using SSR markers to distinguish between four elite cultivars using only high-resolution agarose gel electrophoresis. I demonstrated a cheap and effective method of Soybean cultivar identification using only polymerase chain reaction (PCR) and gel electrophoresis. Department of Biological Sciences 2003-2004

Murray State University.

o Molecular taxonomy of Pine snakes of the Eastern United States using 16s rRNA sequence to determine the evolutionary relationships. Voluntary participation in this project comprised of molecular distinction of pine snakes by studying the sequence of 16s ribosomal RNA.

Graduate Research Assistant 2003-2004

Environmental Chemistry, Department of Biological Sciences Murray State University.

o PCB Congeners and Chlorinated Pesticide Concentrations in Amphibians. Polypchlorinated biphenyl congeners (PCBs) and chlorinated pesticides such as DDT, hexachlorobenzene and chlordane compounds are known for their widespread contamination, bioaccumulation and biomagnificaion in food chains and their long term toxic effects on wildlife and humans. Recent investigators have suggested that the global decline and morphological deformities are disturbing indicators of environmental degradation and possible human health hazard. The objective was to measure the organic contamination levels in normal and deformed amphibian populations of western Kentucky. Standard analytical procedures included Soxhlet extraction, Kuderna-Danish (K-D) concentration, silica gel column chromatography clean-up and gas chromatography with electron capture detector (GC-ECD) analysis. TECHNICAL EXPERTISE

Cell Biology

• Over 12 years of exclusive cell culture experience in human breast tissue derived normal and malignant cell lines, Oral keratinocytes and HNSCC along with Human Primary Skin and Lung derived fibroblast cells.

• Hands-on experience in culturing human embryonic stem cell line (H9).

• Expert in Retroviral transduction and plasmid DNA transfections.

• Cell viability assays (reagent based), FACS sorting, Senescence associated beta-Galactosidase assays (Aging) in majority of cell lines.

• Standard sterile culture methods, Cell growth and determination, Prevention of mycoplasma contamination.

• Mammalian cell culture including Soft agar assay, Matrigel assay, Invasion and Migration assay. Molecular Biology

• Nucleic acid extraction and purification (Mammalian, Plant, animal tissues, and bacterial).

• Isolation of total RNA, Real-time PCR, RT-PCR, and qPCR.

• Retroviral vector cloning for shRNA and cDNA, PCR mediated cloning (LM-PCR) and Sub-cloning.

• Reporter assays and other dye based (ROS) assays.

• Chromatin Immunoprecipitation (ChIP) and conventional immunoprecipitation.

• Primer designing and promoter analysis.

Biochemistry

• Preparation and analysis of protein extracts from cellular compartments

• Professional in SDS-PAGE gels and Western Blotting. Gas Chromatography (GC-ECD) Microscopy

• Confocal Microscopy (Nikon, UV-LSM Meta 710)

• Light, Fluorescent, and Digital Image processing and analysis. Computer and Software Use

• EpiChem3 UVP Bioanalyzer, Adobe Photoshop 6.0.

• BLAST searches for homology determination and comparative genomics.

• Microsoft Office applications and EndNote X8.

• GeneRunner and Primer Design and optimization Software including NCBI Primer-BLAST. Handling of animals.

• Experience in handling of experimental animal (Mice and Rats). LABORATORY MANAGER

Apart from full time research, I also performed duties as a laboratory manager at Northshore University Research Institute. My duties included but were not limited to –

• Ordering supplies and overseeing everyday functioning of the laboratory.

• Troubleshooting of Equipment whenever required and calling service to fix equipments.

• Receiving orders, stocking, and updating inventory for entire laboratory chemicals and plastic consumables.

• Maintaining safe laboratory practices and record keeping for radioactive materials. STUDENTS MENTORED

• Supervised and mentored over 22 students including, undergraduates (pre-medical and pre-dental), and international dentists since 2005 through 2017.

AWARDS AND SCHOLARSHIPS

• Awarded merit scholarship for maintaining highest CGPA during four years of undergraduate studies.

• Taraknath Das Foundation Scholarship of $3000 in August 2003.

• Graduate Research Assistantship Award. Department of Chemistry. Murray State University. Aug 2003 – May 2004. PRESENTATIONS

Poster

1. Bommi, P., and Bagchi, S.: High-Risk HPV Oncoprotein E6 Regulates Expression and Function of DDB2. Oral Presentation. 2017 IADR/ AADR/CADR General Session and Exhibition. San Francisco, Calif, USA. March 22-25, 2017 (Abstract ID - 2633663).

2. Bommi, P., and Bagchi, S.: DDB2 binds to and co-operates with the high-risk Human Papillomavirus (HPV) E6 oncoprotein to regulate tumorigenesis in HPV-associated Cancer. UIC, College of Dentistry, Annual Clinic and Research Day, 2016. (Second place prize)

3. Bommi, P., and Bagchi, S.: The role of DDB2 in Oral and Head and Neck Cancer (OHNC) Progression. UIC, Cancer Center – Cancer Research Forum, 2015.

4. Bommi, P., Li, Q., Taranum, A., and Bagchi, S. 2011. Title: DDB2 regulates p27/kip1 and Rb phosphorylation. Understanding the role of DDB2 in tumorigenesis. Center for Molecular Biology of Oral Diseases. University of Illinois at Chicago. 2011 Clinic and Research Day. (Third place prize.) 5. Bommi, P.V., Dimri, M., Sahasrabuddhe, A.A., Dimri, G, P. 2010. Title: The Polycomb Group Protein BMI1 is a target of HDAC Inhibitors. Spring 2010 Scientific Research Poster Reception at NorthShore University HealthSystem Research Institute, Evanston, IL.

6. Sainger, R.N., Bommi, P., Sahasrabuddhe A.A., and G. P. Dimri. 2008. Title: BMI1 cooperates with H-ras to transform human mammary epithelial cells via dysregulation of multiple growth regulatory pathways. 4th Annual Lewis Landsberg Day at Robert H. Lurie Medical Research Center of Northwestern University, Chicago IL. 7. Clint Metzger, Prashant Bommi, Beth Kobylarz and Loganathan B. 2004. Title: PCB Congeners and Chlorinated Pesticide Concentrations in Amphibians Collected From Western Kentucky. Sigma Xi Poster Competition at the Scholars Week held on April 19, 2004 at Murray State University, Murray, KY. LIST OF PUBLICATIONS

1) Bommi. P.V. Raychaudhuri, P. and S. Bagchi. DDB2 regulates epithelial to mesenchymal transition (EMT) and transcriptionally regulates HIF1a in Oral cancer. (manuscript under consideration with MCR). 2) Bommi, P.V, Raychauhuri, P. and S. Bagchi. DDB2 is required for nuclear localization and stabilization of DDB complex protein, DDB1. (manuscript under consideration with Intl. J. Cancer). 3) Roy N, Bommi PV, Bhat UG, Bhattacharjee S, Elangovan I, Li J, Patra KC, Kopanja D, Blunier A, Benya R, Bagchi S, Raychaudhuri P. (2013). DDB2 Suppresses Epithelial-to-Mesenchymal Transition in Colon Cancer. Cancer Res., 73; 3771. 4) Sahasrabuddhe AA., Dimri M, Bommi P.V., and G. P. Dimri. (2011). βTrCP regulates BMI1 protein turnover via ubiquitination and degradation. Cell Cycle. 10(8): 1322-30. 5) Yadav AK, Sahasrabuddhe, A., Dimri, M., Bommi. P., Sainger, R., and G.P. Dimri (2010). Deletion analysis of BMI1 Oncoprotein identifies its negative regulatory domain. Molecular Cancer. 22;9:158. 6) Bommi, P., Dimri, M., Sahasrabuddhe, A., Khandekar, J. D., and G.P. Dimri (2010). The polycomb group protein BMI1 is a transcriptional target of HDAC inhibitors. Cell Cycle. 9(13). 7) Coral Ho, Lee, S., Xu, C-R., Bommi, P., Huang, S-A., Cheung, S.T., Dimri, G., and Chen X. (2009). Bmi1 Functions as an Oncogene Independent of Ink4A/Arf Repression in Hepatic Carcinogenesis. Molecular Cancer Research. 7(12):1937- 45.

8) Dimri, M., Bommi, P., Sahasrabuddhe, A., Khandekar, J. D., and G.P. Dimri. (2009) Dietary omega-3 polyunsaturated fatty acids suppress expression of EZH2 in breast cancer cells. Carcinogenesis. 31(3):489-95. 9) Datta, S., Hoenerhoff, M. J., Bommi, P., Sainger, R., Guo, W.-J., Dimri, M., Band, H. Band, V., Green, J. E. and G. P. Dimri (2007). Bmi-1 cooperates with H-Ras to transform human mammary epithelial cells via dysregulation of multiple growth regulatory pathways. Cancer Research. 67:102**-*****. 10) Bommi, P. and D. L. Ferguson (2005). Soybean Cultivar Identification within a Selected Group Using Only an Agarose Gel System with Simple Sequence Repeat DNA Markers. Soy. Genetics. Vol 32. PATENTS

Bommi, Prashant. 2015. Miniature western blot membrane incubation system. US Patent 8961908, filed October 5, 2012 and issued February 24, 2015.

REFERENCES

1) Pradip Raychaudhuri, PhD.

Department of Biochemistry and Molecular Genetics

University of Illinois at Chicago,

900 S. Ashland Ave. M/C 669

Chicago, IL. 60607

Phone: 312-***-****

e-mail: ac1tiu@r.postjobfree.com

2) David L. Crowe, DDS, PhD.

Department of Oral Biology, College of Dentistry

University of Illinois at Chicago,

801 S. Paulina Street. Room 537-A

Chicago, IL. 60612

Phone: 312-***-****

e-mail: ac1tiu@r.postjobfree.com

3) Srilata Bagchi, PhD.

Department of Oral Biology, College of Dentistry

University of Illinois at Chicago,

801 S. Paulina Street. Room 537-A

Chicago, IL. 60612

Phone: 312-***-****

e-mail: ac1tiu@r.postjobfree.com

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