Publication
Dr. Yuan-Xiang Pan
Dr. Hong Chen
Selected Publications
2023
Xu, G.; Pan, Y.-X.; Mei, W.; Chen, H. Single-Cell RNA Sequencing (scRNA-seq) Identifies L1CAM as a Key Mediator between Epithelial Tuft Cell and Innate Lymphoid Cell in the Colon of Hnrnp I Knockout Mice. Biomedicines 2023, 11, 2734. https://doi.org/10.3390/biomedicines11102734
Xu, G.B.; Cai, M.; Kadayifci, F.Z.; Dong, J.; Zheng, S.; Mei, W.; Zhao, W.; Pan, Y.X.; Chen, H. Increasing dietary nutrient levels modulates colon immune adaptation and alleviates inflammation in the epithelial heterogeneous nuclear ribonucleoprotein I (Hnrnp I) knockout mice. J Nutr Biochem 2023, 119, 109406, doi:10.1016/j.jnutbio.2023.109406.
Han, X.; Zhou, Q.; Gao, Z.; Bianca Xu, G.; Chen, H.; Chitrakar, B.; Sun, Y.; Zhao, W.; Lin, X.; Zhou, K.; et al. Characterization of procyanidin extracts from hawthorn (Crataegus pinnatifida) in human colorectal adenocarcinoma cell line Caco-2, simulated Digestion, and fermentation identified unique and novel prebiotic properties. Food Res Int 2023, 165, 112393, doi:10.1016/j.foodres.2022.112393.
Pramana, A., Liang, S., Xu, G., Vazquez, E., Pan, Y. X., & Chen, H. (2023). Dysbiosis of Gut Microbiota Increases Colon Cancer Risks in a Novel Mouse Model of Colitis. Journal of Biological Chemistry, 299(3), S44.
Xu, G., Liang, S., Zheng, V., Garcia, G. V., Pan, Y. X., & Chen, H. (2023). Serotonin-secreting enteroendocrine cells are key mediators in the colon to cellular stresses via ATF4-ATF3 mediated stress-responsive signaling. Journal of Biological Chemistry, 299(3), S791-S792.
Liang, S., Pramana, A., Xu, G., Zeng, Y., Pan, Y. X., & Chen, H. (2023). Regenerating Islet Derived 3 (Reg3) Gene Expression Mediated by STAT3 is an Indicator of Colonic Dysplasia in a Mouse Model of NF-κB-dependent Colitis. Journal of Biological Chemistry, 299(3), S802.
2022
Moody, L; Xu, G.B; Pan, Y-X and Chen, H.Genome-wide cross-cancer analysis illustrates the critical role of bimodal miRNA in patient survival and drug responses to PI3K inhibitors. PLOS Computational Biology. 2022 May 31. doi:10.1371/journal.pcbi.1010109.
Han X, Zhou Q, Gao Z, Lin X, Zhou K, Cheng X, Chitrakar B, Chen H, Zhao W. In vitro digestion and fecal fermentation behaviors of polysaccharides from Ziziphus Jujuba cv. Pozao and its interaction with human gut microbiota. Food Res Int. 2022 Dec;162(Pt A):112022. doi: 10.1016/j.foodres.2022.112022. Epub 2022 Oct 6. PMID: 36461244.
Han X, Zhao W, Zhou Q, Chen H, Yuan J, Xiaofu Z, Zhang Z. Procyanidins from hawthorn (Crataegus pinnatifida) alleviate lipid metabolism disorder via inhibiting insulin resistance and oxidative stress, normalizing the gut microbiota structure and intestinal barrier, and further suppressing hepatic inflammation and lipid accumulation. Food Funct. 2022 Jul 18;13(14):7901-7917. doi: 10.1039/d2fo00836j. PMID: 35781311.
2021
Roubus, S; D'Souza, D; Hernández-Saavedra, D; Xu, G.B; Collao, N; Emmons, R; Larkin, J; Lloyd, J; Vanhie, J; Pan, Y-X; Chen, H and De Lisio, M. Weight loss with exercise improves muscle architecture and progenitor cell populations compared to weight loss alone in mice with preneoplastic colorectal lesions. Applied Physiology, Nutrition and Metabolism. 2021 Feb 12. doi: 10.1139/apnm-2020-0956. Epub ahead of print. PMID: 33577399.
Cai, M; Zhang, J; Chen, H and Pan, Y-X. A maternal low-protein diet during gestation induces hepatic autophagy-related gene expression in a sex-specific manner in Sprague-Dawley rats. British Journal of Nutrition. 2021 Sep 13. doi:10.1017/S0007114521003639. PMCID: PMC9346618
2020
Wang, H., Xu, G.B., Chen, H. and Pan, Y-X. Maternal High Fat Diet Activates Hepatic Interleukin 4 in Rat Male Offspring Accompanied by Increased Eosinophil Infiltration. Am J Physiol Gastrointest Liver Physiol. 2020 Oct 28. doi: 10.1152/ajpgi.00153.2019.
Moody, L., Chen, H. and Pan, Y-X. Considerations for feature selection using gene pairs and applications in large-scale dataset integration, novel oncogene discovery, and interpretable cancer screening. BMC Med Genomics 13 (Suppl 10), 148 (2020). doi: 10.1186/s12920-020-00778-x.
Moody, L., Crowder, S.L., Fruge, A.D. et al. Epigenetic stratification of head and neck cancer survivors reveals differences in lycopene levels, alcohol consumption, and methylation of immune regulatory genes. Clin Epigenet 12, 138 (2020). doi: 10.1186/s13148-020-00930-5
Tiffany Y Yang, Jennie C Gardner, Zijun Gao, Yuan-Xiang Pan and Nu-Chu Liang. Role of Glucocorticoid Signaling in Exercise-Associated Changes in High-Fat Diet Preference in Rats. American Journal of Physiology-Regulatory, Integrative and Comparative Physiology. doi: 10.1152/ajpregu.00288.2019
H Wang, GB Xu, D Hernández-Saavedra, H Chen, YX Pan. A Low Protein Diet during Gestation and Lactation Increases Hepatic Lipid Accumulation through Autophagy and Histone Decetylase. American Journal of Physiology-Endocrinology and Metabolism. doi: 10.1152/ajpendo.00263.2019
2019
Fatma Zehra Kadayifci, Sage Haggard, Sookyoung Jeon, Katie Ranard, Dandan Tao, Yuan-Xiang Pan. Early-life Programming of Type 2 Diabetes Mellitus: Understanding the Association between Epigenetics/Genetics and Environmental Factors. doi: 10.2174/1389202920666191009110724
Lei Ma, Guanying Bianca Xu, Xinyu Tang, Cheng Zhang, Wen Zhao, Jie Wang and Hong Chen. Anti-cancer potential of polysaccharide extracted from hawthorn (Crataegus.) on human colon cancer cell line HCT116 via cell cycle arrest and apoptosis. doi: 10.1016/j.jff.2019.103677
Laura Moody, Justin Shao, Hong Chen, Yuan-Xiang Pan. Maternal Low-Fat Diet Programs the Hepatic Epigenome despite Exposure to an Obesogenic Postnatal Diet. Nutrients. doi: https://doi.org/10.3390/nu11092075
Laura Moody, Svyatoslav Dvoretskiy, Ruopeng An, Suparna Mantha, Yuan-Xiang Pan. The Efficacy of miR-20a as a Diagnostic and Prognostic Biomarker for Colorectal Cancer: A Systematic Review and Meta-Analysis. Cancers. doi: https://doi.org/10.3390/cancers11081111
Laura Moody, Diego Hernández-Saavedra, Daniel G Kougias, Hong Chen, Janice M Juraska, Yuan-Xiang Pan. Tissue-specific changes in Srebf1 and Srebf2 expression and DNA methylation with perinatal phthalate exposure, Environmental Epigenetics. doi: https://doi.org/10.1093/eep/dvz009
Diego Hernández-Saavedra, Laura Moody, Guanying Bianca Xu, Hong Chen, Yuan-Xiang Pan, Epigenetic Regulation of Metabolism and Inflammation by Calorie Restriction, Advances in Nutrition. doi: https://doi.org/10.1093/advances/nmy129
Emmons R, Ngu M, Xu GB, Hernández-Saavedra D, Chen H and De Lisio M. Effects of Obesity and Exercise on Bone Marrow Progenitor Cells following Radiation. Medicine & Science in Sports & Exercise. JAN 2019; doi: 10.1249/MSS.0000000000001894
Batistel, F.; Alharthi, A.S.; Yambao, R.R.C.; Elolimy, A.A.; Pan, Y.X.; Parys, C.; Loor, J.J. Methionine supply during late-gestation triggers offspring sex-specific divergent changes in metabolic and epigenetic signatures in bovine placenta. J Nutr2019.
2018
Moody, L.; Kougias, D.; Jung, P.M.; Digan, I.; Hong, A.; Gorski, A.; Chen, H.; Juraska, J.; Pan, Y.X. Perinatal phthalate and high-fat diet exposure induce sex-specific changes in adipocyte size and DNA methylation. J Nutr Biochem 2018, 65, 15-25.
Kadayifci, F.Z.; Zheng, S.; Pan, Y.X. Molecular mechanisms underlying the link between diet and DNA methylation. Int J Mol Sci 2018, 19.
Moody L, Xu GB, Chen H and Pan YX. Epigenetic regulation of carnitine palmitoyltransferase 1 (Cpt1a) by high fat diet. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 2018 Dec 31; doi: 10.1016/j.bbagrm.2018.12.009
Xu GB, Emmons R, Hernández-Saavedra D, Kriska A, Pan YX, Chen H and De Lisio M. Effects of Obesity and Exercise on Colon Cancer Induction and Hematopoiesis in Mice. Am J Physiol Endocrinol Metab. 2018 Dec 4; doi: 10.1152/ajpendo.00237.2018
Wise, L.M.; Hernandez-Saavedra, D.; Boas, S.M.; Pan, Y.X.; Juraska, J.M. Perinatal high-fat diet and bisphenol a: Effects on behavior and gene expression in the medial prefrontal cortex. Dev Neurosci 2018, 1-16.
Moody L, Mantha S, Chen H and Pan YX. Computational Methods to Identify Bimodal Gene Expression and Facilitate Personalized Treatment in Cancer Patients. Journal of Biomedical Informatics: X. doi: 10.1016/j.yjbinx.2018.100001
Batistel, F.; Pan, Y.X.; Parys, C.; Loor, J.J. 162 Methionine Supply during Late-Gestation Triggers Sex-Specific Divergent Trajectories of Metabolism and Epigenetic Systems in Bovine Placenta.Journal of Animal Science. 2018. doi: 10.1093/jas/sky073.159
Zhang X, Xu GB, Zhou D, Pan YX. High-fat diet modifies expression of hepatic cellular senescence gene p16(INK4a) through chromatin modifications in adult male rats. Genes Nutr. 2018 Mar 14;13:6. doi: 10.1186/s12263-018-0595-5.
Kougias DG, Cortes LR, Moody L, Rhoads S, Pan YX, Juraska JM. Effects of Perinatal Exposure to Phthalates and a High-Fat Diet on Maternal Behavior and Pup Development and Social Play. Endocrinology. 2018 Feb 1;159(2):1088-1105. doi: 10.1210/en.2017-03047.
2017
Hernández-Saavedra D, Strakovsky RS, Ostrosky-Wegman P, Pan YX. Epigenetic Regulation of Centromere Chromatin Stability by Dietary and Environmental Factors. Adv Nutr. 2017 Nov 15;8(6):889-904. doi: 10.3945/an.117.016402. Print 2017 Nov.
Moody L, He H, Pan YX, Chen H. Methods and novel technology for microRNA quantification in colorectal cancer screening. Clin Epigenetics. 2017 Oct 24;9:119. doi: 10.1186/s13148-017-0420-9. eCollection 2017.
Moody L, Chen H, Pan YX. Postnatal diet remodels hepatic DNA methylation in metabolic pathways established by a maternal high-fat diet. Epigenomics. 2017 Nov;9(11):1387-1402. doi: 10.2217/epi-2017-0066. Epub 2017 Sep 8.
Moody L, Chen H, Pan YX. 2017. Early-Life Nutritional Programming of Cognition-The Fundamental Role of Epigenetic Mechanisms in Mediating the Relation between Early-Life Environment and Learning and Memory Process. Adv Nutr. 2017 Mar 15;8(2):337-350. doi: 10.3945/an.116.014209.
2016
Patel S, Peretz J, Pan YX, Helferich WG, Flaws JA.Genistein exposure inhibits growth and alters steroidogenesis in adult mouse antral follicles. Toxicol Appl Pharmacol. 2016 Feb 15;293:53-62. doi: 10.1016/j.taap.2015.12.026.
2015
Zhang Y, Wang H, Zhou D, Moody L, Lezmi S, Chen H, Pan YX. 2015. A High Fat Diet Caused Widespread Epigenomic Differences on Hepatic Methylome in Rat. Physiol Genomics. 2015 Jul 21:physiolgenomics.00110.2014. doi:10.1152/physiolgenomics.00110.2014. [Epub ahead of print] PMID: 2619940
Wang H, Wilson GJ, Zhou D, Lezmi S, Chen X, Layman DK, Pan YX. 2015 Induction of autophagy through the activating transcription factor 4 (ATF4)-dependent amino acid response pathway in maternal skeletal muscle may function as the molecular memory in response to gestational protein restriction to alert offspring to maternal nutrition. Br J Nutr. 2015 Jul 22:1-14. [Epub ahead of print] PMID: 26198178
Strakovsky RS, Lezmi S, Shkoda I, Flaws JA, Helferich WG, Pan. 2015. In utero growth restriction and catch-up adipogenesis after developmental di (2-ethylhexyl) phthalate exposure cause glucose intolerance in adult male rats following a high-fat dietary challenge. J Nutr Biochem. 2015 Jun 20. pii: S0955-2863(15)00145-X. doi: 10.1016/j.jnutbio.2015.05.012. [Epub ahead of print]
PMID: 26188368
Strakovsky RS, Wang H, Engeseth NJ, Flaws JA, Helferich WG, Pan YX, Lezmi S. 2015. Developmental bisphenol A (BPA) exposure leads to sex-specific modification of hepatic gene expression and epigenome at birth that may exacerbate high-fat diet-induced hepatic steatosis. Toxicol Appl Pharmacol. 2015 Apr 15;284(2):101-12. doi: 10.1016/j.taap.2015.02.021. Epub 2015 Mar 5. PMID: 25748669
2014
Strakovsky, R. S., S. Lezmi, J. A. Flaws, S. Schantz, Y-X Pan and W. G. Helferich. 2014. Genistein exposure during the early postnatal period favors the development of obesity in female, but not male rats. Toxicol Sci. 2014 Jan 24. [Epub ahead of print], PMID: 24361872.
Strakovsky, R. S., X. Zhang, D. Zhou, and Y-X Pan. 2014. The Regulation of Hepatic Pon1 by a Maternal High-Fat Diet is Gender-specific and May Occur Through Promoter Histone Modifications in Neonatal Rats. J Nutr Biochem. 25(2):170-6.
Zhou D, Lezmi S, Wang H, Davis J, Banz W, Chen H. Fat accumulation in the liver of obese rats is alleviated by soy protein isolate through β-catenin signaling. Obesity (Silver Spring). 2014 Jan;22(1):151-8. doi: 10.1002/oby.20421.Epub 2013 Jun 13. PubMed PMID: 23512909; PubMed Central PMCID: PMC3690171.
2013
Zhang Y, Li Q, Chen H. DNA methylation and histone modifications of Wnt genes by genistein during colon cancer development. Carcinogenesis. 2013 Aug;34(8):1756-63. doi: 10.1093/carcin/bgt129. Epub 2013 Apr 18. PubMed PMID:23598468; PubMed Central PMCID: PMC3731807
Zhang Y, Li Q, Zhou D, Chen H. Genistein, a soya isoflavone, prevents azoxymethane-induced up-regulation of WNT/β-catenin signalling and reduces colon pre-neoplasia in rats. Br J Nutr. 2013 Jan 14;109(1):33-42. doi: 10.1017/S0007114512000876. Epub 2012 Apr 3. PubMed PMID: 22716201
2012
Zhou, D. R. S. Strakovsky, X. Zhang, and Y-X. Pan. 2012. The Skeletal Muscle Wnt Pathway May Modulate Insulin Resistance and Muscle Development In A Diet-Induced Obese Rat Model. Obesity (Silver Spring). 2012 Aug;20(8):1577-84.
Li Q, Chen H. Silencing of Wnt5a during colon cancer metastasis involves histone modifications. Epigenetics. 2012 Jun 1;7(6):551-8. Epub 2012 Jun 1. PubMed PMID: 22522911; PubMed Central PMCID: PMC3398984.
Wang H, Li Q, Chen H. Genistein affects histone modifications on Dickkopf-related protein 1 (DKK1) gene in SW480 human colon cancer cell line. PLoS One. 2012;7(7):e40955. doi: 10.1371/journal.pone.0040955. Epub 2012 Jul 18. PubMed PMID: 22815877; PubMed Central PMCID: PMC3399800
Zheng, S.*, Li, Q.*, Zhang, Y., Balluff Z., Y-X. Pan. 2012. Histone Deacetylase 3 (HDAC3) Participates in the Transcriptional Repression of the p16INK4a Gene in Mammary Gland of the Female Rat Offspring Exposed to an Early-Life High-Fat Diet. Epigenetics. 2012 Feb;7(2):183-90.
Strakovsky R. and Y-X. Pan. 2012. A Decrease In Dkk1, A Wnt Inhibitor, Contributes to Placental Lipid Accumulation In An Obesity-Prone Rat Model. Biol Reprod. 2012 Mar 22;86(3):81.
Zhang, X., Zhou, D., R. S. Strakovsky, Zhang YK, and Y-X. Pan. 2012. Hepatic Cellular Senescence Pathway Genes Are Induced Through Histone Modifications In A Diet-Induced Obese Rat Model. Am J Physiol Gastrointest Liver Physiol. 2011 Dec 22. [Epub ahead ofprint] PubMed PMID: 22194422.
Zheng, S., K. Yang, M. Rollet, and Y-X. Pan. 2012. A Gestational Low Protein Diet Represses p21WAF1/Cip1 Expression in Mammary Gland of Offspring Rats through Promoter Histone Modifications. Br J Nutr. 2011 Dec 9:1-10.
2011
Zhang Y, Chen H. Genistein attenuates WNT signaling by up-regulating sFRP2 in a human colon cancer cell line. Exp Biol Med (Maywood). 2011 Jun 1;236(6):714-22.Epub 2011 May 13. PubMed PMID: 21571909.
Strakovsky, R. and Y-X. Pan. 2011. In Utero Oxidative Stress Epigenetically Programs Antioxidant (AOX) Defense Capacity and Adulthood Diseases. Antioxidants & Redox Signaling. Accepted (ahead of print. doi:10.1089/ars.2011.4372)
Zhang Y, Chen H. Genistein, an epigenome modifier during cancer prevention. Epigenetics. 2011 Jul;6(7):888-91. Epub 2011 Jul 1. Review. PubMed PMID: 21610327.
Zhou D, Zhang Y, Pan YX, Chen H. Dickkopf homolog 1, a Wnt signaling antagonist, is transcriptionally up-regulated via an ATF4-independent and MAPK/ERK-dependent pathway following amino acid deprivation. Biochim Biophys Acta. 2011 Jul;1809(7):306-15. Epub 2011 Jun 13. PubMed PMID: 21683813; PubMed Central PMCID: PMC3199130.
Li Q, Chen H. Epigenetic modifications of metastasis suppressor genes in colon cancer metastasis. Epigenetics. 2011 Jul;6(7):849-52. Review. PubMed PMID: 21758003.
Zhou D and Y-X. Pan. 2011. Gestational Low Protein Diet Selectively Induces the Amino Acid Response Pathway Target Genes in the Liver of Offspring Rats through Transcription Factor Binding and Histone Modifications. Biochim Biophys Acta-Gene Regulatory Mechanism. Oct;1809(10):549-56. Epub 2011 Jul 18.
Zheng, S., M. Rollet, and Y-X. Pan. 2011. Protein restriction during gestation alters histone modifications at the glucose transporter 4 (GLUT4) promoter region and induces GLUT4 expression in skeletal muscle of female rat offspring. J Nutr Biochem. Nov 11. [Epub ahead of print] PMID: 22079207.
Zhou D, Zhang Y, Y-X. Pan, and Chen H. 2011. Dickkopf homolog 1, a Wnt Signaling antagonist, is transcriptionally up-regulated via an ATF4-independent and MAPK/ERK-dependent pathway following amino acid deprivation. Biochim Biophys Acta-Gene Regulatory Mechanism. Jul;1809(7):306-15. Epub 2011 Jun 13.
Zhang, XY, Strakovsky, R. D. Zhou, and Y-X. Pan. 2011. A Maternal High Fat Diet Represses the Expression of Antioxidant Defense Genes and Induces the Cellular Senescence Pathway in the Liver of Male Offspring Rats. J. Nutr. Jul;141(7):1254-9
Zhang Y, Chen H. Genistein attenuates WNT signaling by up-regulating sFRP2 in a human colon cancer cell line. Exp Biol Med (Maywood). 2011 Jun 1;236(6):714-22.Epub 2011 May 13. PubMed PMID: 21571909.
Strakovsky, R. Zhang, XY, D. Zhou, and Y-X. Pan. 2011. Gestational High Fat Diet Programs Hepatic Phosphoenolpyruvate Carboxykinase (Pck) Expression and Histone Modification in Neonatal Offspring Rats. J Physiol. Jun 1;589(Pt 11):2707-17.
Zheng, S., M. Rollet and Y-X. Pan. 2011. Maternal Protein Restriction during Pregnancy Induces CCAAT/enhancer-binding protein (C/EBPβ) Expression through the Regulation of Histone Modification at Its Promoter Region in Female Offspring Rat Skeletal Muscle. Epigenetics, Feb 30; 6(2):161-70.
Li Q, Chen H. Transcriptional silencing of N-Myc downstream-regulated gene 1(NDRG1) in metastatic colon cancer cell line SW620. Clin Exp Metastasis. 2011Feb;28(2):127-35. Epub 2010 Dec 24. PubMed PMID: 21184144.
2010
Strakovsky, R., D. Zhou and Y-X. Pan. 2010. A Low Protein Diet During Gestation in Rats Activates The Placental Mammalian Amino Acid Response Pathway And Programs The Growth Capacity Of Offspring. J. Nutr.140(12):2116-20
Haafiz, A., Y-X. Pan, D.A. Novak. 2010. Placental amino acid transport system A: an assessment of SNAT1 and SNAT2 expression in F1 and F2 placentas in a rat model of gestational protein restriction. Adv Clin Exp Med, 19 (5), 1-10
Zheng, S. and Y-X. Pan. 2010. Histone modifications, not DNA methylation, cause transcriptional repression of p16 (CDKN2A) in the mammary glands of offspring of protein-restricted rats. J Nutr Biochem, 22(6):567-73.
Gong, L. Y-X. Pan, H. Chen. 2010. Gestational low protein diet in the rat mediates Igf2 gene expression in male offspring via altered hepatic DNA methylation. Epigenetics. 5(7): 619-26
Wang Z, Chen H. Genistein increases gene expression by demethylation of WNT5a promoter in colon cancer cell line SW1116. Anticancer Res. 2010. Nov;30(11):4537-45. PubMed PMID: 21115903.
Gong L, Pan YX, Chen H. Gestational low protein diet in the rat mediates Igf2gene expression in male offspring via altered hepatic DNA methylation.Epigenetics. 2010 Oct 1;5(7):619-26. Epub 2010 Oct 1. PubMed PMID: 20671425.
2009
Wang Z, Chen H. Amino acid limitation induces down-regulation of WNT5a at transcriptional level. Biochem Biophys Res Commun. 2009 Jan 23;378(4):789-94.Epub 2008 Dec 6. PubMed PMID: 19063862.
2006
Chen, H. and M.S. Kilberg. (2006) Alignment of the transcription start site coincides with increased transcriptional activity from the human asparagine synthetase gene following amino acid deprivation of HepG2 cells. J. Nutr. 136(10):2463-2467.
2005
Chen, H., Y.X. Pan, E.A. Wong, and K.E. Webb, Jr. (2005) Dietary protein level and stage of development affect expression of an intestinal peptide transporter (cPepT1) in chickens. J. Nutr. 135(2):193-198.
2004
Chen, H., Y-X. Pan, E.E. Dudenhausen, and M.S. Kilberg. (2004) Amino acid deprivation induces the transcription rate of the human asparagine synthetase gene through a timed program of expression and promoter binding of nutrient-responsive basic region/leucine zipper transcription factors as well as localized histone acetylation. J. Biol. Chem. 279(49):50829-50839.