My research program focuses on understanding the cellular and molecular mechanisms contributing to obesity, insulin resistance and the Metabolic Syndrome. Contributory to the pathophysiology of these diseases are the many roles of adipose tissue, lipid metabolism, and the regulation of lipid droplet formation and trafficking. Obesity is a very important factor in the devlopment of diabetes. At present, the only treatment for morbid obesity proven to be consistently effective over the long term is bariatric surgery. Interestingly, the Type 2 Diabetes that is frequently a comorbidity in these patients, is resolved after surgery, frequently before weight loss occurs. The reasons for this are not known. We use powerful mass spectrometry-based lipidomics and proteomics techniques to profile human adipose and muscle biopsies acquired before and after dramatic weight loss. The relative expression changes of select lipids and proteins gleaned from these analyses are correlated with various clinical parameters and validated in model cell culture systems. The methodologies and approaches we use in cell culture are varied, but include stable isotopic labeling, live cell imaging, fluorescent protein and siRNA expression along with traditional biochemistry. The long term aim of our studies is to design cell permeable peptide and/or lipid mimetics of candidate markers identified through metabolic profiling that could be used in the restoration of desired metabolic phenotypes.


The following timeline graph is generated from all co-authored publications.

Featured publications are shown below:

  1. Fecal metagenomics and metabolomics reveal gut microbial changes after bariatric surgery. Yu D, Shu XO, Howard EF, Long J, English WJ, Flynn CR (2020) Surg Obes Relat Dis 16(11): 1772-1782
    › Primary publication · 32747219 (PubMed) · PMC9057387 (PubMed Central)
  2. Pro-inflammatory HDL in women with obesity and nonalcoholic steatohepatitis. Sarkar S, Tsuchida Y, Diab R, Xu C, Yermalitsky V, Davies SS, Ikizler TA, Hung AM, Kon V, Flynn CR (2020) Obes Res Clin Pract 14(4): 333-338
    › Primary publication · 32595023 (PubMed) · PMC7507596 (PubMed Central)
  3. Collision Cross Section Conformational Analyses of Bile Acids via Ion Mobility-Mass Spectrometry. Poland JC, Leaptrot KL, Sherrod SD, Flynn CR, McLean JA (2020) J Am Soc Mass Spectrom
    › Primary publication · 32525305 (PubMed) · PMC8059067 (PubMed Central)
  4. Symmetrically substituted dichlorophenes inhibit -acyl-phosphatidylethanolamine phospholipase D. Aggarwal G, Zarrow JE, Mashhadi Z, Flynn CR, Vinson P, Weaver CD, Davies SS (2020) J Biol Chem 295(21): 7289-7300
    › Primary publication · 32284327 (PubMed) · PMC7247316 (PubMed Central)
  5. Roux-en-Y gastric bypass surgery improves hepatic glucose metabolism and reduces plasma kisspeptin levels in morbidly obese patients with type 2 diabetes. Flynn CR, Albaugh VL, Tamboli RA, Gregory JM, Bosompem A, Sidani RM, Winnick JJ (2020) Am J Physiol Gastrointest Liver Physiol 318(2): G370-G374
    › Primary publication · 31709832 (PubMed) · PMC7052573 (PubMed Central)
  6. Utilizing Untargeted Ion Mobility-Mass Spectrometry To Profile Changes in the Gut Metabolome Following Biliary Diversion Surgery. Poland JC, Schrimpe-Rutledge AC, Sherrod SD, Flynn CR, McLean JA (2019) Anal Chem 91(22): 14417-14423
    › Primary publication · 31573190 (PubMed) · PMC7076733 (PubMed Central)
  7. Two-week administration of engineered Escherichia coli establishes persistent resistance to diet-induced obesity even without antibiotic pre-treatment. Dosoky NS, Chen Z, Guo Y, McMillan C, Flynn CR, Davies SS (2019) Appl Microbiol Biotechnol 103(16): 6711-6723
    › Primary publication · 31203417 (PubMed) · PMC7066869 (PubMed Central)
  8. Metabolic Effects of Bile Acids: Potential Role in Bariatric Surgery. Flynn CR, Albaugh VL, Abumrad NN (2019) Cell Mol Gastroenterol Hepatol 8(2): 235-246
    › Primary publication · 31075353 (PubMed) · PMC6664228 (PubMed Central)
  9. GLP-1: Molecular mechanisms and outcomes of a complex signaling system. Smith NK, Hackett TA, Galli A, Flynn CR (2019) Neurochem Int : 94-105
    › Primary publication · 31002893 (PubMed) · PMC7081944 (PubMed Central)
  10. Systemic bile acids induce insulin resistance in a TGR5-independent manner. Syring KE, Cyphert TJ, Beck TC, Flynn CR, Mignemi NA, McGuinness OP (2019) Am J Physiol Endocrinol Metab 316(5): E782-E793
    › Primary publication · 30779633 (PubMed) · PMC6732652 (PubMed Central)
  11. Treating Nonalcoholic Fatty Liver Disease From the Outside In? Flynn CR (2019) Cell Mol Gastroenterol Hepatol 7(3): 682-683
    › Primary publication · 30677403 (PubMed) · PMC6477184 (PubMed Central)
  12. Role of Bile Acids and GLP-1 in Mediating the Metabolic Improvements of Bariatric Surgery. Albaugh VL, Banan B, Antoun J, Xiong Y, Guo Y, Ping J, Alikhan M, Clements BA, Abumrad NN, Flynn CR (2019) Gastroenterology 156(4): 1041-1051.e4
    › Primary publication · 30445014 (PubMed) · PMC6409186 (PubMed Central)
  13. In vitro safety pharmacology evaluation of 2-hydroxybenzylamine acetate. Fuller JC, Pitchford LM, Morrison RD, Daniels JS, Flynn CR, Abumrad NN, Oates JA, Boutaud O, Rathmacher JA (2018) Food Chem Toxicol : 541-548
    › Primary publication · 30253245 (PubMed) · PMC6220894 (PubMed Central)
  14. Bile diversion, a bariatric surgery, and bile acid signaling reduce central cocaine reward. Reddy IA, Smith NK, Erreger K, Ghose D, Saunders C, Foster DJ, Turner B, Poe A, Albaugh VL, McGuinness O, Hackett TA, Grueter BA, Abumrad NN, Flynn CR, Galli A (2018) PLoS Biol 16(7): e2006682
    › Primary publication · 30048457 (PubMed) · PMC6061973 (PubMed Central)
  15. Regulation of Insulin Receptor Pathway and Glucose Metabolism by CD36 Signaling. Samovski D, Dhule P, Pietka T, Jacome-Sosa M, Penrose E, Son NH, Flynn CR, Shoghi KI, Hyrc KL, Goldberg IJ, Gamazon ER, Abumrad NA (2018) Diabetes 67(7): 1272-1284
    › Primary publication · 29748289 (PubMed) · PMC6014550 (PubMed Central)
  16. CD36 Modulates Fasting and Preabsorptive Hormone and Bile Acid Levels. Shibao CA, Celedonio JE, Tamboli R, Sidani R, Love-Gregory L, Pietka T, Xiong Y, Wei Y, Abumrad NN, Abumrad NA, Flynn CR (2018) J Clin Endocrinol Metab 103(5): 1856-1866
    › Primary publication · 29546316 (PubMed) · PMC6446573 (PubMed Central)
  17. Limiting Injury During Saphenous Vein Graft Preparation For Coronary Arterial Bypass Prevents Metabolic Decompensation. Cheung-Flynn J, Song J, Voskresensky I, Wise ES, Liu Y, Xiong Y, Eagle SS, Brophy CM, Flynn CR (2017) Sci Rep 7(1): 14179
    › Primary publication · 29079734 (PubMed) · PMC5660200 (PubMed Central)
  18. Sirt3 Impairment and SOD2 Hyperacetylation in Vascular Oxidative Stress and Hypertension. Dikalova AE, Itani HA, Nazarewicz RR, McMaster WG, Flynn CR, Uzhachenko R, Fessel JP, Gamboa JL, Harrison DG, Dikalov SI (2017) Circ Res 121(5): 564-574
    › Primary publication · 28684630 (PubMed) · PMC5562527 (PubMed Central)
  19. Bile acids and bariatric surgery. Albaugh VL, Banan B, Ajouz H, Abumrad NN, Flynn CR (2017) Mol Aspects Med : 75-89
    › Primary publication · 28390813 (PubMed) · PMC5603298 (PubMed Central)
  20. Non-alcoholic fatty liver disease phosphoproteomics: A functional piece of the precision puzzle. Wattacheril J, Rose KL, Hill S, Lanciault C, Murray CR, Washington K, Williams B, English W, Spann M, Clements R, Abumrad N, Flynn CR (2017) Hepatol Res 47(13): 1469-1483
    › Primary publication · 28258704 (PubMed) · PMC5583035 (PubMed Central)
  21. Comprehensive evaluation of extracellular small RNA isolation methods from serum in high throughput sequencing. Guo Y, Vickers K, Xiong Y, Zhao S, Sheng Q, Zhang P, Zhou W, Flynn CR (2017) BMC Genomics 18(1): 50
    › Primary publication · 28061744 (PubMed) · PMC5219650 (PubMed Central)
  22. Recent advances in metabolic and bariatric surgery. Albaugh VL, Flynn CR, Tamboli RA, Abumrad NN (2016) F1000Res
    › Primary publication · 27239296 (PubMed) · PMC4879937 (PubMed Central)
  23. A micro-RNA expression signature for human NAFLD progression. Guo Y, Xiong Y, Sheng Q, Zhao S, Wattacheril J, Flynn CR (2016) J Gastroenterol 51(10): 1022-30
    › Primary publication · 26874844 (PubMed) · PMC4983265 (PubMed Central)
  24. Lipoprotein Profiles in Class III Obese Caucasian and African American Women with Nonalcoholic Fatty Liver Disease. Garcia AE, Kasim N, Tamboli RA, Gonzalez RS, Antoun J, Eckert EA, Marks-Shulman PA, Dunn J, Wattacheril J, Wallen T, Abumrad NN, Flynn CR (2015) PLoS One 10(11): e0142676
    › Primary publication · 26599819 (PubMed) · PMC4657895 (PubMed Central)
  25. Bile diversion to the distal small intestine has comparable metabolic benefits to bariatric surgery. Flynn CR, Albaugh VL, Cai S, Cheung-Flynn J, Williams PE, Brucker RM, Bordenstein SR, Guo Y, Wasserman DH, Abumrad NN (2015) Nat Commun : 7715
    › Primary publication · 26197299 (PubMed) · PMC4518285 (PubMed Central)
  26. Early Increases in Bile Acids Post Roux-en-Y Gastric Bypass Are Driven by Insulin-Sensitizing, Secondary Bile Acids. Albaugh VL, Flynn CR, Cai S, Xiao Y, Tamboli RA, Abumrad NN (2015) J Clin Endocrinol Metab 100(9): E1225-33
    › Primary publication · 26196952 (PubMed) · PMC4570157 (PubMed Central)
  27. Hepatic TLR4 signaling in obese NAFLD. Sharifnia T, Antoun J, Verriere TG, Suarez G, Wattacheril J, Wilson KT, Peek RM, Abumrad NN, Flynn CR (2015) Am J Physiol Gastrointest Liver Physiol 309(4): G270-8
    › Primary publication · 26113297 (PubMed) · PMC4537925 (PubMed Central)
  28. A post-developmental genetic screen for zebrafish models of inherited liver disease. Kim SH, Wu SY, Baek JI, Choi SY, Su Y, Flynn CR, Gamse JT, Ess KC, Hardiman G, Lipschutz JH, Abumrad NN, Rockey DC (2015) PLoS One 10(5): e0125980
    › Primary publication · 25950913 (PubMed) · PMC4423964 (PubMed Central)
  29. Statistical strategies for microRNAseq batch effect reduction. Guo Y, Zhao S, Su PF, Li CI, Ye F, Flynn CR, Shyr Y (2014) Transl Cancer Res 3(3): 260-265
    › Primary publication · 25258704 (PubMed) · PMC4171948 (PubMed Central)
  30. SIRT3 deacetylates ATP synthase F1 complex proteins in response to nutrient- and exercise-induced stress. Vassilopoulos A, Pennington JD, Andresson T, Rees DM, Bosley AD, Fearnley IM, Ham A, Flynn CR, Hill S, Rose KL, Kim HS, Deng CX, Walker JE, Gius D (2014) Antioxid Redox Signal 21(4): 551-64
    › Primary publication · 24252090 (PubMed) · PMC4085980 (PubMed Central)
  31. Hyperoxia synergizes with mutant bone morphogenic protein receptor 2 to cause metabolic stress, oxidant injury, and pulmonary hypertension. Fessel JP, Flynn CR, Robinson LJ, Penner NL, Gladson S, Kang CJ, Wasserman DH, Hemnes AR, West JD (2013) Am J Respir Cell Mol Biol 49(5): 778-87
    › Primary publication · 23742019 (PubMed) · PMC3931097 (PubMed Central)
  32. Effects of proximal gut bypass on glucose tolerance and insulin sensitivity in humans. Breitman I, Isbell JM, Saliba J, Jabbour K, Flynn CR, Marks-Shulman PA, Laferrère B, Abumrad NN, Tamboli RA (2013) Diabetes Care 36(4): e57
    › Primary publication · 23520381 (PubMed) · PMC3609508 (PubMed Central)
  33. Differential intrahepatic phospholipid zonation in simple steatosis and nonalcoholic steatohepatitis. Wattacheril J, Seeley EH, Angel P, Chen H, Bowen BP, Lanciault C, Caprioli RM, Abumrad N, Flynn CR (2013) PLoS One 8(2): e57165
    › Primary publication · 23451176 (PubMed) · PMC3581520 (PubMed Central)
  34. Sirt3-mediated deacetylation of evolutionarily conserved lysine 122 regulates MnSOD activity in response to stress. Tao R, Coleman MC, Pennington JD, Ozden O, Park SH, Jiang H, Kim HS, Flynn CR, Hill S, Hayes McDonald W, Olivier AK, Spitz DR, Gius D (2010) Mol Cell 40(6): 893-904
    › Primary publication · 21172655 (PubMed) · PMC3266626 (PubMed Central)
  35. A novel cell permeant peptide inhibitor of MAPKAP kinase II inhibits intimal hyperplasia in a human saphenous vein organ culture model. Lopes LB, Brophy CM, Flynn CR, Yi Z, Bowen BP, Smoke C, Seal B, Panitch A, Komalavilas P (2010) J Vasc Surg 52(6): 1596-607
    › Primary publication · 20864298 (PubMed) · PMC3005888 (PubMed Central)
  36. Characterization of the Human Adipocyte Proteome and Reproducibility of Protein Abundance by One-Dimensional Gel Electrophoresis and HPLC-ESI-MS/MS. Xie X, Yi Z, Bowen B, Wolf C, Flynn CR, Sinha S, Mandarino LJ, Meyer C (2010) J Proteome Res 9(9): 4521-34
    › Primary publication · 20812759 (PubMed) · PMC2935302 (PubMed Central)
  37. Proteomics analysis of human skeletal muscle reveals novel abnormalities in obesity and type 2 diabetes. Hwang H, Bowen BP, Lefort N, Flynn CR, De Filippis EA, Roberts C, Smoke CC, Meyer C, Højlund K, Yi Z, Mandarino LJ (2010) Diabetes 59(1): 33-42
    › Primary publication · 19833877 (PubMed) · PMC2797941 (PubMed Central)
  38. In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS. Højlund K, Bowen BP, Hwang H, Flynn CR, Madireddy L, Geetha T, Langlais P, Meyer C, Mandarino LJ, Yi Z (2009) J Proteome Res 8(11): 4954-65
    › Primary publication · 19764811 (PubMed) · PMC2783959 (PubMed Central)
  39. The small heat shock protein, HSPB6, in muscle function and disease. Dreiza CM, Komalavilas P, Furnish EJ, Flynn CR, Sheller MR, Smoke CC, Lopes LB, Brophy CM (2010) Cell Stress Chaperones 15(1): 1-11
    › Primary publication · 19568960 (PubMed) · PMC2866971 (PubMed Central)
  40. Proteome profile of functional mitochondria from human skeletal muscle using one-dimensional gel electrophoresis and HPLC-ESI-MS/MS. Lefort N, Yi Z, Bowen B, Glancy B, De Filippis EA, Mapes R, Hwang H, Flynn CR, Willis WT, Civitarese A, Højlund K, Mandarino LJ (2009) J Proteomics 72(6): 1046-60
    › Primary publication · 19567276 (PubMed) · PMC2774790 (PubMed Central)
  41. Inhibition of HSP27 phosphorylation by a cell-permeant MAPKAP Kinase 2 inhibitor. Lopes LB, Flynn C, Komalavilas P, Panitch A, Brophy CM, Seal BL (2009) Biochem Biophys Res Commun 382(3): 535-9
    › Primary publication · 19289101 (PubMed) · PMC2745729 (PubMed Central)