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Naseem Ahmed, Ph.D.

Office (Week days): Postdoctoral Research Scientist, Department of Oncology, Montefiore Medical Center, The Teaching Hospital for Albert Einstein College of Medicine, Hofheimer 413, 111, East 210th Street, Bronx, NY 10467. Tel.: 718-920-6583 FAX: 718-882-4464. Office (Weekends): Professor of Pharmacology, New York Medical Career Training Center, New York State University, 36-09 Main Street, 5th floor, Flushing, New York 11354 Tel.: 718-460-1717, 718-4604096 FAX: 718-539-9655. E-mail addresses: [email protected] / [email protected] / [email protected]


1999: 1988: 1980: Ph.D. Biological Sciences, University of Wales, United Kingdom M.Phil. Biochemistry, University of Karachi, Pakistan M.Sc. Biochemistry, University of Karachi, Pakistan. The courses studied were as follows: Endocrinology, Enzymology, Biophysics, Molecular Genetics, Techniques in Biochemistry, Biochemistry of Natural Products. 1978: Advance Intermediary Metabolism, Biostatistics, Comparative Biochemistry, Contemporary Biochemistry, Molecular Biophysics,

B.Sc. Biochemistry, Microbiology and Chemistry, University of Karachi, Pakistan

Professional Experience:

Research Expertise and Experience:

Postdoctoral Research Scientist August 2007­ June 2009: Working as a Postdoctoral Research Fellow in Dr. John Mariadason's Oncology research laboratory at Montefiore Medical Center, the university hospital for the Albert Einstein College of Medicine. The primary focus of my work is to determine the mechanisms of action of chemotherapeutic agents used in the treatment of colon cancer, with the ultimate goal of identifying biomarkers which can predict likelihood of response of individual patients to specific chemotherapeutic agents. Specifically, I have been investigating the mechanisms by which HDAC inhibitors induce apoptosis in colon cancer cells and

identifying genomic biomarkers predictive of response to these agents. Recently tissue microarrays were developed to analyze large number of human colon cancer biopsy sections, xenografts and mouse tissues from mouse model of colon cancer. Research Associate October 2006­ June 2007: Worked as a Research Associate in the laboratory of Dr. Mary E Fabry, Professor of Medicine and Ronald Nagel, Professor of Medicine, Albert Einstein College of Medicine, Bronx, New York. Work involved research on acute chest syndrome (ACS) which is a common cause of death in sickle cell disease. Postdoctoral Research Fellow May 2006­October 2006: Volunteer/ Postdoctoral Research Fellow, Montefiore Medical Center, Bronx, New York. Since May 2006-Oct. 2006: Worked as a volunteer on two colon cancer-related projects in the laboratory of Dr. John Mariadason. 1. Determination of the molecular mechanisms by which HADC-inhibitors induce apoptosis and differentiation in colon cancer cell lines in vitro. HDAC inhibitors are a novel class of chemotherapeutic agents presently undergoing phase I and II clinical trial to determine efficacy in a variety of hematopoietic and solid tumors. Previous studies in the laboratory have identified colon cancer cell lines sensitive and resistant to HDAC inhibitor-induced apoptosis and cell differentiation. The goal of this study is to understand the molecular basis for this differential sensitivity. 2. Application of a Systems Biology approach for predicting response of human colon tumors to chemotherapeutic agents. The overall goal of this ongoing study is to determine whether a combination of gene expression profiling, methylation profiling and Comparative Genome Hybridization (CGH) can identify molecular patterns predict likelihood of colon tumors undergoing relapse and response to chemotherapy. Harvard Fellow of Pediatric Medicine and Developmental Immunology 2000-2005: Research Fellow, Department of Pediatrics, Laboratory of Developmental Immunology, Harvard Medical School (HMS) & Massachusetts General Hospital (MGH), Boston, MA. The overall goal of my studies as a post-doctoral fellow in the laboratory of Dr. Thilo Stehle at HMS and MGH was to study the interactions between viruses and receptors, in order to describe mechanisms of viral attachment to target cells and to provide a basis for vaccine and drug design. 1. Structural analysis of the receptor of measles virus Signaling lymphocytic activation molecule (SLAM). The goal of this project was develop a foundation for the development of improved therapies against measles virus, by determining the crystal structure of SLAM. A virus that results in a rash, cough, runny nose, fever, and eye irritation, and can lead to ear infection, pneumonia, seizures, brain damage, and death causes measles. Despite available vaccines, measles is still a major cause of death worldwide, and also a continued cause of serious health problems in the United States and other developed countries. This is evidenced by the recent, massive outbreak of measles in Italy in the year 2002. Measles virus infects human cells by binding to a molecule on the cellular surface known as SLAM. I succeeded in expressing and purifying the SLAM protein, and I was actively engaged in crystallizing and determining its structure, when my PI Dr. Stehle, accepted a position in his native Germany. 2. Determination of the crystal structure of the Lymphotrophic Papovavirus (LPV) protein. LPV is an important member of the family of polyoma viruses, which is double stranded DNA virus, plays a critical role in the development of human warts, cervical cancer and tumors in certain animals. The mechanism by the LPV virus binds to its cell surface receptor is not clearly understood. I successfully expressed, purified and crystallized the LPV protein.

Doctoral Research Student 1995-1999: Doctoral Research Student, North East Wales Institute (NEWI), University of Wales, Department of Biochemistry & Biotechnology. I completed my PhD in the laboratory of Dr. Glenn Morris at the University of Wales. The main objective of my thesis was to identify new potential immunogenic regions within the dystrophin protein by analyzing turn predicted regions, four flexible hinge regions and computer predicted regions of high hydrophilicity and antigenicity indices. I then synthesized and purified peptides of these regions to produce monoclonal antibodies. Dystrophin was chosen as a disease related model protein for the study. The region specific peptide antibodies were produced to avoid long and time consuming epitope mapping procedure. The approach can be applied to other proteins where antigenic determinants are still a mystery. Dystrophin is a protein, which is absent in patients with early childhood Duchenne muscular dystrophy (DMD), and defectively or abnormally expressed in middle and old age group Becker muscular dystrophy (BMD) patients. BMD is rare X-linked genetic disease which can develop in any adult of age forty or over without any family history and cause death within next few years. There is presently no treatment available for these severe muscle-wasting diseases. I produced 13 monoclonal antibodies against flexible hinges, WW domain, and ZZ domain regions of dystrophin during this research project were first reported monoclonal antibodies against these regions. These antibodies are presently being evaluated for better understanding of protein, diagnosis of the disease and also in gene therapy studies for monitoring re-expression of the dystrophin protein. Please check list of monoclonal antibodies for muscular dystrophy research from CIND supported by MDA, USA, ( Consultant Clinical Biochemist and Pathology Laboratory Director 1988-1995: Clinical Biochemist and Pathology Laboratory Director, POLYCLINIC Dr. Saifullah Jan, SA. This is a privately owned Poly Clinic. The patient's volume was more than hundred patients a day. I established this lab in 1988 and was a Director of the lab until 1995. Clinical research projects conducted during this time were as follows. 1994: Participated in " Blood Lipid Level Survey NIDDM patients" The population of various nationalities in the S.A. The project was sponsored by a pharmaceutical firm Parke-Davis. The instrument I used was Cholestech L.D.X. Lipid Analyzer from Cholestech Corporation, Hayward, USA. 1992-1993: Participated in "Cholesterol Level Survey" of the population in SA. This study included Cholesterol level Check-up of normal, hypertensive and, diabetic hypertensive persons. Male and female of various age groups and different nationalities were considered for the study. The project was sponsored by a pharmaceutical firm Merck, Sharp and Dome (MSD). Biochemist (Medical Technologist) 1984-1988: Biochemist (Medical Technologist), Department of Nephro-Urology, Jinnah Postgraduate Medical Center (JPMC), Karachi (Pakistan). In these two positions I was responsible for performing clinical biochemistry, hematology, and serology tests for the diagnosis of heath related problems. I was also responsible for the teaching and training of postgraduate medical research students and junior laboratory staff. While working as a Biochemist in the Department of Nephro-Urology at JPMC I also undertook the following two research projects related to chronic renal failure and nephrotic syndrome: 1) Serum lipids, their subfractions and hemoglobin A1 in patients with chronic renal failure (CRF). This project was undertaken in fulfillment for the requirements of degree of Master of Philosophy in Biochemistry. The goal of this project was to compare levels of lipids and lipid subfractions in CRF

patients and in healthy control subjects. In addition, urea derived carbamylated hemoglobin was determined in CRF patients and compared with the severity of the disease. 2) Serum proteins and lipid levels in patients with nephrotic syndrome (NS). NS is kidney disorder that can occur at any age but is more prevalent in children than in adults. This condition is marked by proteinurea and hypoproteinemia; edema, especially around the eyes, feet, and hands; and high cholesterol. Disease results in damage to the kidney's glomeruli, which gradually lose their ability to filter waste and excess water from the blood, and ultimately patients undergo CRF. The goal of this project was to find abnormalities in lipids and their subfractions in NS patients and to compare levels with the severity of the disease.

Work Experience:

Assistant Manager (Quality Control) 1983-1984: Assistant Manager (Quality Control), S.J & G Fazul Ellahi Ltd., Pharmaceutical Firm Manufacturer of Continental Pharma, Belgium. In this position I was responsible for the testing of raw materials (chemicals), analysis of deionized water for ingestible, analysis of medications including tablets, parenteral medicines and syrups. All tests were performed according to the protocols developed from United States Pharmacopoeia.

Teaching Experience:

New York Medical Career Training Center, New York State University Professor of Pharmacology May 2007­ Present: Part time Pharmacology Professor in New York Medical Career Training Center, Flushing, New York. I have been teaching an ongoing eight week course (one hundred and thirty hours) in Pharmacology. Biochemistry related course. Only few selected titles of the Pharmacology / Biochemistry related teaching course is as follows. History of Pharmacy, Medical abbreviations, Basic anatomy and physiology, Endocrine system and hormones, Alkaloids, Biopharmaceutics, Pharmacodynamics, Medical Complementary Alternative Medicine, Nutrition included Lipids, proteins, Carbohydrates, Vitamins and Minerals, Retail and Hospital Pharmacy, Pharmacy Calculations, Drug Doses, Sources of medicines, Vaccines and basic concepts of vaccine development, Antineoplastic agents, Biotechnology and Genetic Engineering. Globe Institute of Technology Adjunct Faculty Professor of Medical Management January 2008-May 2008: Adjunct Faculty Professor in the Department of Business at Globe Institute of Technology. Taught courses included Pharmacy Operation, Medical Laboratory and Medical Office Management. Each course runs for fifteen weeks. Average student strength is up to 26 per class. Selected titles of the Pharmacology / Biochemistry related teaching courses are as follows. History of Pharmacy, Medical abbreviations and terminology, Basic anatomy and physiology, Endocrine system and hormones, Natural Products, Biopharmaceutics, Pharmacodynamics, Medical Complementary Alternative Medicine, Aseptic Techniques /Sterile Products Preparation, Drug Absorption, Distribution, Metabolism and Excretion, Nutrition, Antineoplastic Agents, Biotechnology and Genetic Engineering, Introduction to Laboratory Medicine included Handling of Biological specimens, Clinical Chemistry/ Microbiology and Immunology/ Hematology / Serology/ Blood Bank/ Urinalysis/ Cytology/ Histopathology.

Harvard University Fellow of Developmental Immunology and Pediatric Medicine May 2000-June 2005: Worked as fellow of pediatric medicine and developmental immunology at Harvard Medical School and Massachusetts General Hospital. Teaching junior postdoctoral researchers, medical school undergraduate and summer students was a part of the fellowship program. The teaching was included design small projects that students can complete during the limited time they spend in research during their medical education. North East Wales Institute of Higher Education, University of Wales, United Kingdom Teaching Assistant June 1995-May 1998: Engaged in part time teaching in the Department of chemistry in North East Wales Institute of Higher Education during Ph.D. studies. The responsibilities were included performing and demonstrating B.Sc. Part III (Honors) organic chemistry practical to part time undergraduate (four years bachelor degree program) students. July 1995-May 1999: Served as a Tutor and taught Biochemistry, Biology, Chemistry and Pre-university student brush up students for General Biology, Hunan Biology (included Physiology and Biochemistry) and Chemistry. Registration No. 66220, Personal Tutors (Dept. T), Cheadle House, Mary Street, Cheadle, Cheshire SK8 1YA, United Kingdom. 1982-1983: Appointed as a Lecturer in Chemistry at Sadiq Memorial College, North Nazimabad, Karachi. I taught theory and supervised practical classes. Pathology Laboratory Director June 1988-March 1995: Worked as Director of Dr. Saifullah Jan's Polyclic's Pathology Laboratory recognized and registered by ministry of health. Job responsibilities were teaching and training laboratory persons and provide awareness of advancement of laboratory protocols. Conducted several clinical research programs for patient's awareness of health related issues and advantages of medical laboratory tests with disease related specificity. Furthermore, conducted clinical trials for pharmaceutical companies. Created health checkup tests profiles considering patient's health related complains. Clinical Biochemist and Nephro-Urology Laboratory Manager June 1984-March 1988: Worked as Medical Technologist (Clinical Biochemist) and Master of Philosophy research student in the Clinical Laboratory. I was engaged in teaching and training students were pursuing for postgraduate medical education at Jinnah Postgraduate Medical Center, Pakistan. The laboratory of Department of Nephro-Urology of 1250-beds Hospital is well equipped and place of learning for Medical undergraduate and postgraduate, Pharmacology, Biochemistry, Pathology, Nephrology and Urology students. I was engaged in weekly presentations and during clinical teaching sessions and solving problems created in laboratory diagnostic tests related issues. I also provided guidance to students were writing M.D., M.Phil. and Ph.D. thesis.

Teaching Certifications:

June 2007-May 2008: Provisional Pharmacology teaching license, New York State University. June 2008-May 2012: Full Pharmacology teaching license, New York State University.

NHA Examiner:

Examiner of NHA licensing for allied healthcare professionals at New York Medical Career Training Center since 2008. The licenses are valid to practice in all states in the United States.

Memberships of Professional Organizations

American Association for the Advancement of Science (2007-2009), American Society of hematology (2007-2008), Life Member of Pakistan pharmacological society (1993), Association for Research in Vision and Ophthalmology, (2004-2005), The Association of Clinical Biochemists (1998-1999), Muscular Dystrophy Group of Great Britain and Northern Ireland (1998), Institute of Biomedical Sciences (1994) and Pakistan Society of Biochemists (1990).

Computer Skills and Experience:

I have knowledge on Microsoft Word, Excel, Power point, Outlook and Internet. I prepare power point material for most of my classroom instructions.


Original Articles:

1 Gene expression profiling of primary and metastatic colon cancers identifies a reduced proliferative rate in metastatic tumors. Ganepola AP, Chang D, Mazziota M, Weeresinghe D, Corner GA, Ashbahian J, Parish CJ, Tebbutt N, Murone C, Ahmed N, Augenlicht LH, Librera N, Korst R, Mariadason JM. (Manuscript in preparation). Byun DS, Wilson AJ, Ahmed N, Nasser S, Scherer S, Augenlicht LH, Mariadason JM. Reduced intestinal ALP expression in HDAC3-villin transgenic mice. Manuscript in preparation. Wilson AJ, Corner GA, Ahmed N, Byun DS, Nasser S, Arango D, Houston MA, Jhawer M, Smartt HJ, Murray L, Nicholas C, Heerdt BG, Augenlicht LH, and Mariadason, JM. A coordinated Sp1/Sp3-mediated transcriptional response involving immediate-early gene induction drives HDACi-induced apoptosis in colon cancer cells. Manuscript in preparation. Proteomic changes during intestinal cell maturation in vivo. Chang J, Chance MR, Nicholas C, Ahmed N, Guilmeau S, Flandez M, Wang D, Byun DS, Nasser S, Albanese JM, Tanaka K, Corner GA, Heerdt BG, Wilson AJ, Augenlicht LH, and Mariadason JM. (2008) J Proteomics. 71(5):530-546. Pereboev, AV, Ahmed, N, Nguyen thi Man, Morris, GE. (2001) Epitopes in the interacting regions of Bdystroglycan (PPxY motif) and dystrophin (WW domain). Biochimica et Biophysica Acta 1527: 54-60. Ahmed N, Nguyen thi Man, Morris, GE. (1998) Flexible hinges in dystrophin. Biochem Soc. Trans 1998; 26, S310. Ahmed, N and Jahangeer, S. (1996) The relation between the degree of renal functional impairment and haemoglobin A1 in nondiabetic patients with chronic renal failure. Pakistan J Pharmacol; 13:1-12. Ahmed, N, Jahangeer S, Naqvi SAJ. (1994) Lipid abnormalities in patients with chronic renal failure. Pakistan J Pharmacol; 1135-44. Ahmed, N, Jahangeer S, Naqvi, SAJ. (1994) The relation between the serum lipids and haemoglobin A1 in patients with chronic renal failure. Pakistan J. Pharmacol.; 11:9-19 Ahmed, N, Jahangeer S, Naqvi, SAJ, Shaikh, MA. (1991) High-density lipoprotein cholesterol in normal subjects and patients with nephrotic syndrome. Kar. Univ. J. Sc.; 19: 171-175. Ahmed, N, Jahangeer S, Naqvi SAJ. (1990) The relation between the Hemoglobin A1 and fasting serum glucose in nondiabetic patients with chronic renal failure. Pakistan J. Pharmacol; 7:11-18. Ahmed, N, Jahangeer S, Naqvi SAJ, Shaikh MA. (1990) Serum protein and lipid levels in the nephrotic syndrome. Pakistan J. Biochem; 23: 77-86. Ahmed, N and Jahangeer S. (1987) Free amino acids in blood, muscle, liver, kidney, heart and brain of varanus bengalensis. Kar. Univ. J. Sc.; 15: 63-69.

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Poster Presentations/ Abstacts:







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Wilson, AJ, Ahmed, N, Corner G, Nasser, S, Byun, DS, Scherer, S, Jhawer, M, Smartt, HJ, Murray, LB, Nicholas, C, Houston, M, Heerdt, B, Arango, D, Augenlicht, LH, Mariadason, JM. (2008) A coordinated Sp1/Sp3-mediated transcriptional response involving immediate-early gene induction drives HDACiinduced apoptosis in colon cancer cells. Abs. Young Investigator Research Symposium. Byun, DS, Wilson, AJ, Ahmed, N, Nasser, S, Scherer, S, Augenlicht, LH, Mariadason, JM. (2008) Reduced intestinal ALP expression in HDAC3-villin transgenic mice. Abs. AACR Annual Meeting, San Diego, CA. Mariadason, JM, Nasser, S, Byun, DS, Arango, D, Jhawer, M, Ahmed, N, Smartt, HJ, Murray, LB, Countney Nicholas, Georgia A. Corner, Andrew J. Wilson and Leonard A. Augenlicht (2007). Molecular determinants of colon cancer cells to histone deacetylase (HDAC) inhibitors. Abs. 2479. AACR Annual Meeting, Los Angeles, CA. An A13 repeat within the 3'UTR of EGFR is frequently mutated in MSI colon cancers and is associated with increased EGFR expression. (2007) Ziqiang Yuan, Joongho Shin, Andrew Wilson, Sanjay Goel, YiHe Ling, Naseem Ahmed, Higinio Dopeso, Minaxi Jhawer, Shannon Nasser, Cristina Montagna, Kenneth Fordyce, Leonard H. Augenlicht, Lauri Aaltonen, Diego Arango Thomas K. Weber, and John M. Mariadason. Abs. Society of Surgical Oncology. Fabry, ME, Ahmed, N, Suzuka, SM, Nagel, RL, Sellers R. and Klings, ES. (2007) A transgenic mouse model for adult acute chest syndrome. Submitted at the Thirty Fifth Anniversary of the National Sickle Cell Disease Program. The National Heart, Lung and Blood Institute, National Institute of Heath and The Sickle Cell Disease Association of America, INC. Ahmed N and Stehle T. (2001) Crystallization of the coat protein from lymphotrophic papovirus. Presented at the Seventh Annual Harvard Structural Biology Retreat, American Academy of Arts and Sciences, Norton's Woods, 136 Irving Street, Cambridge, MA. Ahmed, N, Nguyen thi Man, Morris, GE. (1998) Flexible hinges in dystrophin. Biochem Soc Trans 1998; 26, S310. Nguyen thi Man, Manilal, S, Pereboev, A, Young, P, Ahmed, N, Fitzgerald, TA, Wilkinson, F, and Morris GE. (1998) Monoclonal antibody studies of the diagnosis and pathogenesis of muscular dystrophies and other neuromuscular diseases. Muscle and Nerve, IX International Congress on Neuromuscular diseases. Abstract. P2th-08. Morris GE, Pereboev A, Ahmed, N and Nguyen thi Man. (1997) Structural studies of dystrophin and utrophin using monoclonal antibodies. The Federation of American Societies for Experimental Biology Journal. Abstract. 11(9): A2085.

Scientific Techniques

· · · · · · · · · · Cell and Molecular Biology and Pharmacology Cell culture RNA and protein extraction from human and mouse tissue and cell lines (Trizol, RNeasy) Gel Electrophoresis of DNA and RNA Q-PCR (Sybr Green) Enzyme assays (Alkaline phosphatase) Western blot Probe preparation for Affymetrix and Nimblegen micro array analysis PCR FACS analysis (PI staining and cell cycle analysis) Immunohistochemistry (paraffin embedded and frozen sections)

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Archival RNA extraction from archival formalin-fixed tissue Tissue Array Mouse handling, coding, genotyping and sacrifice Mouse injection for Brdu incorporation Crystallography Bacterial expression of Lymphotrophic Papovavirus (LPV) protein, His-Tag and FPLC purification and enzyme cleavage of His-Tag. Initial crystallization of LPV protein by Hampton Research crystal growth solutions. Further crystals growth and optimization was performed by freshly prepared solutions and growth measurements were recorded on regular basis. Prepare constructs for bacterial and yeast expression of SLAM. Yeast expression and purification of SLAM by affinity column (Ni) chromatography and Fast protein liquid chromatography (FPLC) column. Mammalian CHO cells protein expression, affinity column (Protein A) and FPLC column purification. Protein crystallization trials setup by Hampton Research and Wizard solutions. Peptide Synthesis, Antibody production, Purification and Characterization Fmoc peptide synthesis of dystrophin molecule. Desalting and HPLC column purification of peptides. Peptide freeze-drying, conjugation with BSA and KLH for immunization. Chemical coupling of peptides confirmation on SDS-PAGE. Use of conjugated synthetic peptides to produce monoclonal antibodies. Immunization of mice with conjugated peptides. Antibody screening (ELISA, Western Blot and immunohistochemistry) and characterization of monoclonal antibodies. Epitope Mapping of monoclonal antibodies by phage displayed peptide library. Determination of epitopes of monoclonal antibodies. Studies of peptide attachment to ELISA plates using mouse polyclonal sera and monoclonal antibodies. Determination of Ig subtypes of monoclonal antibodies.

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Translational Medicine/ Pharmacology Research Techniques · Mouse basic and advanced level surgery trainings included survival surgery from Einstein College of Medicine. · Mouse handing, coding and performance of dug deliveries.


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