Cellular Biochemistry

Rafat Siddiqui, PhD

Senior Investigator
Methodist Research Institute
Indiana University Health
1800 N. Capitol Avenue
P: 317.962.6941
F: 317.962.9369
Laboratory: 317.962.3178
Email: rsiddiqu@iuhealth.org

Current Projects
Recent Publications
Abbreviated Biography
Curriculum Vitae


The focus of the Cellular Biochemistry Laboratory is to investigate the cellular and molecular mechanisms through which nutrients affect human health. In particular, we are investigating how fatty acids influence the development and progression of cardiovascular diseases and cancer. Our cellular and animal models have shown that trans-fatty acids (found in hydrogenated oils) instigate molecular processes that induce atherosclerosis and sudden cardiac death, whereas omega-3 fatty acids (found in fish oil) provide protection against cardiovascular diseases.

We are also investigating the effects of dietary fatty acids on endothelial cell function and vascular remodeling as well as the synergistic properties of omega-3 fatty acids with other nutrients, particularly polyphenols (found in fruits and vegetables), for their beneficial cardio-protective and anti-cancer properties.

One other aspect of our research is to investigate processes that lead to muscle wasting (cachexia) in chronic diseases, particularly in cancer patients and to use nutritional compounds to prevent muscle wasting and improve the quality of life in cancer patients.

Current Projects

Cardiovascular Biology

Impact of Trans- and Omega-3 Fatty Acids on Vascular Modeling
Our long-range goal is to understand the mechanism(s) by which omega-3 polyunsaturated fatty acids (n-3 PUFAs) and Trans fatty acids (TFAs) modulate endothelial cell function that leads to vascular remodeling. Coronary artery disease is the leading cause of myocardial infarction, and for more than 12.4 million Americans the disease is clinically significant. Epidemiological studies, prospective randomized clinical trials, and laboratory investigations have reported a decrease in morbidity and mortality from heart disease in patients with diets supplemented with n-3 PUFAs. In contrast, partially hydrogenated fat, the major dietary source of TFAs, has been estimated to be responsible for 30,000 to 100,000 premature coronary deaths per year in the U.S. alone. We found from our 6-month survival studies, following coronary ligation and feeding rats a diet rich in either TFAs or n-3 PUFAs, that only 50% of the animals survived on a TFA diet, whereas 85% of the animals survived on an n-3 PUFA diet. n-3 PUFAs inhibit oxidative stress-mediated changes in endothelial cells that function to resist and/or inhibit pathological vascular remodeling and promote compensatory vascular remodeling. TFAs, on the other hand, promote oxidative stress-mediated changes in endothelial cells that stimulate pathological vascular remodeling and inhibit compensatory vascular remodeling. Our recent data indicate that TFAs promote inflammatory conditions that also contribute to an increased risk of cardiovascular diseases.

Modulation of Cellular Functions by Dietary Fatty Acids
Our long-range goal is to understand the mechanisms by which dietary fatty acids impact the development of inflammatory, cancer, and cardiovascular disease and to develop new therapies and dietary recommendations to improve outcomes. The rapid delivery of much needed calories was recognized as a treatment for critically ill patients as early as 1930 by Studley, who demonstrated a strong link between the presence of malnutrition and the development of postoperative mortality. This led to exploration of better ways to deliver adequate fuel calories to malnourished patients. It took another 30 years before Schuberth and Wretlind developed a nontoxic lipid emulsion prepared from soybean oil (SO) (Intralipid, Fresenius-Kabi, Bad Homburg, Germany) for delivering fuel to malnourished patients. Later Ivelip (Baxter, Maurepas, France), also based on SO, was developed. To decrease the high content of n-6 PUFAs in Intralipid, Lipofundin (B Braun, Melsungen, Germany) was introduced. Lipofundin is a mixture of soybean oil and coconut oil containing triglycerides of medium chain saturated fatty acids (MCTs). In the late 1990s, Baxter (Maurepas, France) introduced Clinoleic, an olive oil base emulsion for use in total parenteral nutrition (TPN). In Clinoleic, 80% of SO was replaced by olive oil (OO), which is rich in oleic acid (18:1), a long-chain n-9 monounsaturated fatty acid (MUFA). Omegaven (Fresenius-Kabi), an n-3 PUFA-enriched preparation was recently introduced. However, more recently, Lipiplus (also known as Lipidm), which contains mixtures of SO, CO, and FO and SMOFlipid, which contains SO, CO, OO, and FO were introduced by Fresenius-Kabi (Bad Homburg Germany). Although the newer products contained n-3 PUFAs, their ratios varied from product to product. These lipid products also contain significant amounts of saturated fatty acids, which have some harmful effects. Furthermore, recent data also suggest that instead of n-6/n-3 ratios, the total amount of n-3 PUFAs in lipid products are perhaps more important. Unquestionably, there is a knowledge gap concerning the optimum fatty acid mixture for modulating biological activities to make lipid infusion products more therapeutic and beneficial to patients. This research will help explain the role of different classes of fatty acids present in lipid emulsions and will help to better formulate lipid emulsions for treatment of critically ill patients.

Cellular Effects of Omega-3 Fatty Acids on Cardiac Function
The long-range goal of this research is to understand the mechanism by which omega-3 fatty acids provide beneficial protective effects for heart function. Epidemiological evidence from Greenland Eskimos and Japanese fisherman suggest that eating fish oil and marine animals can prevent coronary heart disease. Dietary studies from various laboratories have similarly indicated that regular fish oil intake affects several humoral and cellular factors involved in atherogenesis and may prevent atherosclerosis, arrhythmia, thrombosis, cardiac hypertrophy and sudden cardiac death. The beneficial effects of fish oil are attributed to their content of n-3 polyunsaturated fatty acids (also known as omega 3-fatty acids), particularly eicosapentaenoic acid (EPA, 20:5,n-3) and docosahexaenoic acid (DHA; 22:6 9,n-3). Dietary supplementation of DHA and EPA influences the fatty acid composition of plasma phospholipids that, in turn, may affect cardiac cell functions in vivo. Recent studies have demonstrated that long chain omega 3-fatty acids may exert beneficial effects by affecting a wide variety of cellular signaling mechanisms. Pathways involved in calcium homeostasis in the heart may be of particular importance. L-type calcium channels, the Na+-Ca2+ exchanger, and mobilization of calcium from intracellular stores are the most obvious key signaling pathways affecting the cardiovascular system; however, recent studies now suggest that other signaling pathways involving activation of phospholipases, synthesis of eicosanoids, regulation of receptor-associated enzymes and protein kinases also play very important roles in mediating the effects of n-3 PUFAs on cardiovascular health. This research is, therefore, focused on the molecular targets and signaling pathways that are regulated by n-3 PUFAs in relation to their cardioprotective effects.

Cancer Cell Biology

Characterization of Cellular and Molecular Processes for the Anti-cancer Effects of Omega-3 Fatty Acids
The long-term goal of this study is to elucidate the cellular and molecular mechanisms for the anticancer effects of n-3 PUFAs in cancer cells. DHA has a well-documented role in inhibiting or preventing cancer. Early epidemiological evidence strongly links fish oil [rich in DHA and eicosapentaenoic acid (EPA)] and the low incidence of several types of cancer, including breast cancer. In addition to strong epidemiological studies, dietary studies on many types of animals, including humans, and on numerous cultured cells have also substantiated DHA's role as an anticancer agent for breast cancer. For the past 15 years, our laboratory has investigated the relationship between DHA's alteration of membrane structure and its effects on cell signaling and apoptosis. DHA induces apoptosis in cancer cells through multiple mechanisms. We demonstrated that DHA induces cell cycle arrest in Jurkat cells via hypophosphorylation of pRb through p21-mediated inhibition of cdk2 kinase activity and stimulates protein phosphatase activity. These effects appear to be mediated through ceramide formation from activation of neutral sphingo-myelinase (N-SMYase) in both Jurkat leukemic and breast cancer cells. The effects were mediated through enhanced expression of p21. In addition, transport of DHA and other fatty acids to the nucleus and binding to nuclear receptors such as peroxisome proliferator-activated receptor (PPAR) and retinoid X receptors (RXRs) have been reported. DHA is a general ligand of PPARs, but binds more selectively to RXR transcription factors. RXRs form homo- or hetero-dimers with PPAR and other nuclear hormone receptor super-families that include receptors for steroids, thyroid hormones, retinoic acid, and vitamin D and are involved in the regulation of p21 expression. This recent research focuses on determining if DHA plays a role in attenuation of breast cancer growth through PPARg/RXR-mediated p21 expressionAntalis CJ, Uchida A, Buhman KK, Siddiqui RA. Migration of MDA-MB-231 breast cancer cells depends on the availability of exogenous lipids and cholesterol esterification. Clin Exp Metastasis. Dec 2011;28(8):733-741. Link

Recent Publications

  1. Siddiqui RA, Harvey KA, Xu Z, Natarajan SK, Davisson VJ. Characterization of lovastatin-docosahexaenoate anticancer properties against breast cancer cells. Bioorg Med Chem. 2014;22(6): 1899-908. Link
  2. Siddiqui RA, Harvey K. Omega-3 polyunsaturated fatty acids for treatment of nonalcoholic fatty liver disease: a possible case for personalized therapy. J Glycomics Lipidomics. 2014, 4:1. Link
  3. Harvey K, Xu Z, Walker C, Pavlina T, McGrath S, Zaloga G, Siddiqui RA. Parenteral lipid emulsions in guinea pigs differentially influence plasma and tissue levels offatty acids, squalene, cholesterol, and phytosterols. Lipids. 2014. Link
  4. Siddiqui RA, Harvey KA. Dietary interventions with n-3 fatty acids or probiotics targeting post-myocardial infarction depression. Br J Nutr. 2013;109(1):1-3 Link
  5. Siddiqui RA, Harvey K, Bammerlin E, Ikhlaque N. Docosahexaenoic acid: A potential modulator of brain tumors and metastasis. J Biomol Res Ther. 2013;2(3): 1000e119. Link
  6. Siddiqui RA. Targeting lung inflammation in cystic fibrosis. 2013. J Mol Genet Med 7: 2 (Editorial). Link
  7. Siddiqui RA, Harvey KA, Walker C, Altenburg J, Xu Z, Terry C, Camarillo I, Jones-Hall Y, Mariash C. Characterization of synergistic anti-cancer effects of docosahexaenoic acid and curcumin on DMBA-induced mammary tumorigenesis in mice. BMC cancer. 2013;13:418. Link
  8. Siddiqui RA, Harvey KA. Dietary interventions with n-3 fatty acids or probiotics targeting post-myocardial infarction depression. Br J Nutr. 2013;109(1):1-3. Link
  9. Xu Z, Harvey KA, Pavlina T, Dutot G, Hise M, Zaloga GP, Siddiqui RA. Steroidal compounds in commercial parenteral lipid emulsions. Nutrients. Aug 2012;4(8):904-921. Link
  10. Harvey KA, Walker CL, Xu Z, Whitley P, Siddiqui RA. Trans fatty acids: induction of a pro-inflammatory phenotype in endothelial cells. Lipids. Jul 2012;47(7):647-657. Link
  11. Vanhorn J, Altenburg JD, Harvey KA, Xu Z, Kovacs RJ, Siddiqui RA. Attenuation of niacin-induced prostaglandin D(2) generation by omega-3 fatty acids in THP-1 macrophages and Langerhans dendritic cells. J Inflamm Res. 2012;5:37-50. Link
  12. Siddiqui RA, Harvey KA, Xu Z, Bammerlin EM, Walker C, Altenburg JD. Docosahexaenoic acid: a natural powerful adjuvant that improves efficacy for anticancer treatment with no adverse effects. Biofactors. Nov-Dec 2011;37(6):399-412. Link
  13. Antalis CJ, Uchida A, Buhman KK, Siddiqui RA. Migration of MDA-MB-231 breast cancer cells depends on the availability of exogenous lipids and cholesterol esterification. Clin Exp Metastasis. Dec 2011;28(8):733-741. Link
  14. Altenburg JD, Harvey KA, McCray S, Xu Z, Siddiqui RA. A novel 2,6-diisopropylphenyl-docosahexaenoamide conjugate induces apoptosis in T cell acute lymphoblastic leukemia cell lines. Biochem Biophys Res Commun. Jul 29 2011;411(2):427-432. Link
  15. Altenburg JD, Bieberich AA, Terry C, Harvey KA, Vanhorn JF, Xu Z, Jo Davisson V, Siddiqui RA. A synergistic antiproliferation effect of curcumin and docosahexaenoic acid in SK-BR-3 breast cancer cells: unique signaling not explained by the effects of either compound alone. BMC Cancer. 2011;11:149. Link
  16. Xu Z, Harvey K, Pavlina T, Dutot G, Zaloga G, Siddiqui RA. An improved method for determining medium- and long-chain FAMEs using gas chromatography. Lipids. Feb 2010;45(2):199-208. Link
  17. Harvey KA, Xu Z, Whitley P, Davisson VJ, Siddiqui RA. Characterization of anticancer properties of 2,6-diisopropylphenol-docosahexaenoate and analogues in breast cancer cells. Bioorg Med Chem. Mar 1 2010;18(5):1866-1874. Link
  18. Harvey KA, Welch Z, Sliva D, Siddiqui RA. Role of Rho kinase in sphingosine 1-phosphate-mediated endothelial and smooth muscle cell migration and differentiation. Mol Cell Biochem. Sep 2010;342(1-2):7-19. Link
  19. Harvey KA, Walker CL, Xu Z, Whitley P, Pavlina TM, Hise M, Zaloga GP, Siddiqui RA. Oleic acid inhibits stearic acid-induced inhibition of cell growth and pro-inflammatory responses in human aortic endothelial cells. J Lipid Res. Dec 2010;51(12):3470-3480. Link
  20. Harvey KA, Walker CL, Pavlina TM, Xu Z, Zaloga GP, Siddiqui RA. Long-chain saturated fatty acids induce pro-inflammatory responses and impact endothelial cell growth. Clin Nutr. Aug 2010;29(4):492-500. Link
  21. Antalis CJ, Arnold T, Rasool T, Lee B, Buhman KK, Siddiqui RA. High ACAT1 expression in estrogen receptor negative basal-like breast cancer cells is associated with LDL-induced proliferation. Breast Cancer Res Treat. Aug 2010;122(3):661-670. Link
  22. Altenburg JD, Siddiqui RA. Docosahexaenoic acid downregulates interferon gamma-induced expression of CXCL16 in human aortic smooth muscle cells. Biochem Biophys Res Commun. Jan 1 2010;391(1):609-614. Link

Abbreviated Biography

Dr. Siddiqui earned his BSc and MSc degrees in Biochemistry from the University of Karachi, in Karachi, Pakistan. He was accepted as a candidate for PhD studies by the University of Oxford (UK), the University of Calgary (Canada), and the University of North Carolina (USA) but decided to accept a prestigious scholarship from the Australian National University in Canberra, Australia. While obtaining his PhD in Australia, he investigated the metabolic basis of cancer cachexia under the supervision of Professor John F. Williams, who is famous for his research on the pentose phosphate pathway. Dr. Siddiqui served as a postdoctoral fellow at Massey University in Palmerton North, New Zealand in the laboratory of Dr. Stuart McCutcheon (currently Vice Chancellor of Auckland University in New Zealand).

Dr. Siddiqui immigrated to America in 1989 at the invitation of Dr. John Exton and a Howard Hughes fellowship at Vanderbilt University Medical Center in Nashville. Dr. Siddiqui began his work as a researcher at Methodist Hospital in 1993 in the Bone Marrow Transplant Research Laboratory. He established his independent research laboratory in 1999 and is presently the Senior Investigator and Director of the Cellular Biochemistry Research Laboratory at the Methodist Research Institute. Dr. Siddiqui also has adjunct appointments in the Department of Biology, Indiana University-Purdue University and the Department of Medicine, Indiana University Medical School, Indianapolis.

Dr. Siddiqui's research interests are in the area of cancer, inflammation, and cardiovascular diseases. His research emphasis is on modulation of diseases by dietary fatty acids such as omega-3, omega-6, omega-9, and trans fatty acids. Dr. Siddiqui has received funding from the National Cancer Center (NIH), American Heart Association, Showalter Foundation, Abbott Pharmaceuticals, and Baxter Nutrition.

Dr. Siddiqui's Curriculum Vitae