Investigating genomic mechanisms of transcription, metabolism, and disease progression

Publications & Datasets

2024

Meyer MB, Lee SM, Towne JM, Cichanski SR, Kaufmann M, Jones G, Pike JW. In vivo contribution of Cyp24a1 promoter vitamin D response elements. Endocrinology. 2024 Oct 4:bqae134. doi: 10.1210/endocr/bqae134. Epub ahead of print. PMID: 39363152. [PubMed]

Meyer MB, Lee SM, Cichanski SR, Cobice DF, Pike JW. Spatial detection and consequences of nonrenal calcitriol production as assessed by targeted mass spectrometry imaging. JCI Insight. 2024 Jun 25;9(15):e181763. doi: 10.1172/jci.insight.181763. PMID: 38916957. [PubMed]

Meyer MB, Benkusky NA, Lee SM, Pike JW. Regulation of renal vitamin D metabolism. Feldman and Pike’s Vitamin D. 2024 Jan. p. 139-154. doi:10.1016/B978-0-323-91386-7.00002-7

Pike JW, Lee SM, Benkusky NA, Meyer MB. Genome-wide perspectives on vitamin D receptor actions. Feldman and Pike’s Vitamin D. 2024 Jan. p. 213-228. doi:10.1016/B978-0-323-91386-7.00005-2

2023

Verlinden L, Stedfanie D, Iris J, Meyer MB, Pike JW, Geert C, Annemieke V. Neuropilin 2 in osteoblasts regulates trabecular bone mass in male mice. Front Endocrinol (Lausanne). 2023 July 31; 14;1213361. doi: 10.3389/fendo.2023.1223021 [PubMed]

Pike JW, Lee SM, Meyer MB. Molecular insights into mineralotropic hormone inter-regulation. Front Endocrinol (Lausanne). 2023 Jun 27;14:1213361. doi: 10.3389/fendo.2023.1213361. PMID: 37441497; PMCID: PMC10334211. [PubMed]

Oda Y, Wong CT, Oh DH, Meyer MB, Pike JW, Bikle DD. Vitamin D Receptor Cross-talk with p63 Signaling Promotes Epidermal Cell Fate. J Steroid Biochem Mol Biol. 2023 Jun 15:106352. doi: 10.1016/j.jsbmb.2023.106352. Epub ahead of print. PMID: 37330071. [PubMed]

Lee SM, Meyer MB, Benkusky NA, Pike JW. Genome-wide analyses of gene expression profile identify key genes and pathways involved in skeletal response to phosphate and 1,25-dihydroxyvitamin D3 in vivo. J Steroid Biochem Mol Biol. 2023 May 27;232:106335. doi: 10.1016/j.jsbmb.2023.106335. Epub ahead of print. PMID: 37245694. [PubMed]

Yoon SH, Meyer MB, Arevalo Rivas C, Tekguc M, Zhang C, Wang JS, Castro Andrade CD, Strauss KE, Sato T, Benkusky N, Lee SM, Berdeaux R, Foretz M, Sundberg TB, Xavier RJ, Adelmann CH, Brooks DJ, Anselmo A, Sadreyev RI, Rosales IA, Fisher DE, Gupta N, Morizane R, Greka A, Pike JW, Mannstadt M, Wein MN. A parathyroid hormone/salt-inducible kinase signaling axis controls renal vitamin D activation and organismal calcium homeostasis. J Clin Invest. 2023 Mar 2:e163627. doi: 10.1172/JCI163627. Epub ahead of print. PMID: 36862513. [PubMed]

Meyer MB, Pike JW. Genomic mechanisms controlling renal vitamin D metabolism. J Steroid Biochem Mol Biol. 2023 Jan 16;228:106252. doi: 10.1016/j.jsbmb.2023.106252. PMID: 36657729. [PubMed]

Meyer MB, Bernal-Mizrachi C, Bikle DD, Biyani M, Campbell MJ, Chaudhari SN, Christakos S, Ingles SA, Knuth MM, Lee SM, Lisse TS, Liu ES, Piec I, Plum LA, Rao SD, Reynolds CJ, Thacher TD, White JH, Cantorna MT. Highlights from the 24th workshop on vitamin D in Austin, September 2022. J Steroid Biochem Mol Biol. 2023 Jan 10;228:106247. doi: 10.1016/j.jsbmb.2023.106247. PMID: 36639037. [PubMed]

2022

Meyer MB, Benkusky NA, Lee SM, Yoon SH, Mannstadt M, Wein MN, Pike JW. Rapid genomic changes by mineralotropic hormones and kinase SIK inhibition drive coordinated renal Cyp27b1 and Cyp24a1 expression via CREB modules. J Biol Chem. 2022 Sep 29:102559. doi: 10.1016/j.jbc.2022.102559. PMID: 36183832. [PubMed] GEO Data Accession Link: GSE206777

2021

MacLeod RS, Meyer MB, Xiong J, Cawley KM, Liu Y, Onal M, Benkusky NA, Thostenson JD, Pike JW, O’Brien CA. Deletion of a putative promoter-proximal Tnfsf11 regulatory region in mice does not alter bone mass or Tnfsf11 expression in vivo. PLoS One. 2021 May 10;16(5):e0250974. doi: 10.1371/journal.pone.0250974. [PubMed]

Pike JW, Meyer MB. New Approaches to Assess Mechanisms of Action of Selective Vitamin D Analogues. Int J Mol Sci. 2021 Nov 16;22(22):12352. doi: 10.3390/ijms222212352. PMID: 34830234; PMCID: PMC8619157. [PubMed]

2020

Pike JW, Lee SM, Benkusky NA, Meyer MB. Genomic Mechanisms Governing Mineral Homeostasis and the Regulation and Maintenance of Vitamin D Metabolism. JBMR Plus. 2020 Nov 12. doi:10.1002/jbm4.10433 [PubMed]

Oda Y, Nguyen T, Hata A, Meyer MB, Pike JW, Bikle DD. Deletion of Mediator 1 suppresses TGFβ signaling leading to changes in epidermal lineages and regeneration. PLoS One. 2020 Aug 28;15(8):e0238076. doi: 10.1371/journal.pone.0238076 [PubMed]

Pike JW, Meyer MB. The unsettled science of non renal calcitriol production and its clinical relevance. J Clin Invest. 2020 Sep 1;130(9):4519-4521. doi: 10.1172/JCI141334 [PubMed]

Meyer MB, Pike JW. Mechanistic homeostasis of vitamin D metabolism in the kidney through reciprocal modulation of Cyp27b1 and Cyp24a1 expression. J Steroid Biochem Mol Biol. 2020 Feb;196:105500. doi: 10.1016/j.jsbmb.2019.105500 [PubMed]

2019

Lee SM, Carlson AH, Onal M, Benkusky NA, Meyer MB, Pike JW. A control region near the fibroblast growth factor 23 gene mediates response to phosphate, 1,25(OH)2Dand LPS in vivo. Endocrinology, 2019 Dec 1;160(12):2877-2891. doi: 10.1210/en.2019-00622 [PubMed]

Meyer MB, Lee SM, Carlson AH, Benkusky NA, Kaufmann M, Jones G, Pike JW. A chromatin-based mechanism controls differential regulation of the cytochrome P450 gene Cyp24a1 in renal and non-renal tissues. J Biol Chem. 2019 Sep 27;294(39):14467-14481. doi: 10.1074/jbc.RA119.010173. [PubMed] GEO Data Accession Links: Mouse GSE133025 and Human GSE129585

Meyer MB, Benkusky NA, Kaufmann M, Lee SM, Redfield RR, Jones G, Pike JW. Targeted genomic deletions identify diverse enhancer functions and generate a kidney-specific, endocrine-deficient Cyp27b1 pseudo-null mouse. J Biol Chem. 2019 Jun 14;294(24):9518-9535. doi: 10.1074/jbc.RA119.008760 [PubMed] GEO Data Accession Links: Mouse GSE133025 and Human GSE129585

Helzer KT, Szatkowski Ozers M, Meyer MB, Benkusky NA, Solodin N, Reese RM, Warren CL, Pike JW, Alarid ET. The Phosphorylated Estrogen Receptor α (ER) Cistrome Identifies a Subset of Active Enhancers Enriched for Direct ER-DNA Binding and the Transcription Factor GRHL2. Mol Cell Biol. 2019 Jan 16;39(3). doi: 10.1128/MCB.00417-18 [PubMed]

2018

Onal M, Carlson AH, Thostenson JD, Meyer MB, Lee SM, Pike JW. A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene. JBMR Plus. 2018 Jan;2(1):32-47. doi: 10.1002/jbm4.10023 [PubMed]

2017

Meyer MB, Benkusky NA, Kaufmann M, Lee SM, Onal M, Jones G, Pike JW. A kidney-specific genetic control module in mice governs endrocrine regulation of the cytochrome P450 gene Cyp27b1 essential for vitamin D3 activation. 2017 June 14. pii: jbc.M117.806901. doi: 10.1074/jbc.M117.806901. [PubMed] GEO Data Accession Link: GSE133025

Lee SM, Meyer MB, Benkusky NA, O’Brien CA, Pike JW. The impact of VDR expression and regulation in vivo. J Steroid Biochem Mol Biol. 2017 Jun 9. pii: S0960-0760(17)30153-X. doi: 10.1016/j.jsbmb.2017.06.002. [PubMed]

Pike JW, Meyer MB, Lee SM, Onal M, Benkusky NA. The vitamin D receptor: contemporary genomic approaches reveal new basic and translational insights. J Clin Invest. 2017 Apr 3;127(4):1146-1154. doi: 10.1172/JCI88887. [PubMed]

Ryynänen J, Kriebitzsch C, Meyer MB, Janssens I, Pike JW, Verlinden L, Verstuyf A. Class 3 semaphorins are transcriptionally regulated by 1,25(OH)2D3 in osteoblasts. J Steroid Biochem Mol Biol. 2017 Feb 9. pii: S0960-0760(17)30039-0. doi: 10.1016/j.jsbmb.2017.02.005. [PubMed]

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2014-2016

2016

Meyer MB, Benkusky NA, Sen B, Rubin J, Pike JW. Epigenetic Plasticity Drives Adipogenic and Osteogenic Differentiation of Marrow-Derived Mesenchymal Stem Cells. J Biol Chem. 2016 July 11  doi:10.1074/jbc.M116.736538 [PubMed] [JBC link] GEO Data Accession Link: GSE79815
To display the ChIP-seq overlaid data track HUBs in the UCSC genome browser, Go to UCSC Genome Browser (mm9), Search Public Hubs for GSE79815, Click “connect”, then on the next screen enter your genomic region of interest and hit “Go”

Pike JW, Meyer MB, Benkusky NA, Lee SM, St John H, Carlson A, Onal M, Shamsuzzaman S. Genomic Determinants of Vitamin D-Regulated Gene Expression. Vitam Horm. 2016;100:21-44. [PubMed]

2015

Lee SM, Riley EM, Meyer MB, Benkusky NA, Plum LA, DeLuca HF, Pike JW. 1,25-Dihydroxyvitamin D3 Controls a Cohort of Vitamin D Receptor Target Genes in the Proximal Intestine that is Enriched for Calcium Regulating Components. J Biol Chem 2015 Jun 3 doi: jbc.M115.665794. [PubMed] GEO Data Accession Link: GSE69180

Meyer MB, Benkusky NA, Pike JW.  Selective Distal Enhancer Control of the Mmp13 Gene Identified through CRISPR Genomic Deletions. J Biol Chem. 2015 Apr 24;290(17):11093-107. [PubMed] [JBC link] Primer table PDF or Excel

Pike JW, Meyer MB, St John HC, Benkusky NA. Epigenetic histone modifications and master regulators as determinants of context dependent nuclear receptor activity in bone cells. Bone. 2015 Mar 27. pii: S8756-3282(15)00090-3. [PubMed]

Meyer MB, Benkusky NA, Pike JW. Profiling histone modifications by chromatin immunoprecipitation coupled to deep sequencing in skeletal cells. Methods Mol Biol. 2015;1226:61-70. [PubMed]

2014

St John HC, Meyer MB, Benkusky NA, Carlson AH, Prideaux M, Bonewald LF, Pike JW. The parathyroid hormone-regulated transcriptome in osteocytes: Parallel actions with 1,25-dihydroxyvitamin D3 to oppose gene expression changes during differentiation and to promote mature cell function. Bone 2014 Nov 22;72C:81-91. [PubMed] GEO Data Accession Link: GSE62981

Meyer MB, Benkusky NA, Lee CH, Pike JW.  Genomic Determinants of Gene Regulation by 1,25-Dihydroxyvitamin D3 During Osteoblast-Lineage Cell Differentiation.  J Biol Chem. 2014 Jul 11;289(28):19539-54. [PubMed] GEO Data Accession Link: GSE51515

St John HC, Bishop KA, Meyer MB, Benkusky NA, Leng N, Kendziorski C, Bonewald LF, Pike JW.  The Osteoblast to Osteocyte Transition: Epigenetic Changes and Response to the Vitamin D3 Hormone.  Mol Endocrinol. 2014 Jul;28(7):1150-65.[PubMed] GEO Data Accession Link: GSE54784

Meyer MB, Benkusky NA, Pike JW. The RUNX2 Cistrome in Osteoblasts: Characterization, Downregulation Following Differentiation and Relationship to Gene Expression. J Biol Chem. 2014 Jun 6;289(23):16016-31. [PubMed] GEO Data Accession Link: GSE41955

Pike JW, Lee SM, Meyer MB. Regulation of gene expression by 1,25-dihydroxyvitamin D3 in bone cells: exploiting new approaches and defining new mechanisms. Bonekey Rep. 2014 Jan 8;3:482. Review. [PubMed]

Wang L, Zhao Z, Meyer MB, Saha S, Yu M, Guo A, Wisinski KB, Huang W, Cai W, Pike JW, Yuan M, Ahlquist P, Xu W. CARM1 Methylates Chromatin Remodeling Factor BAF155 to Enhance Tumor Progression and Metastasis. Cancer Cell. 2014 Jan 13;25(1):21-36. [PubMed]

2010-2013

2013

Meyer MB, Benkusky NA, Pike JW. 1,25-Dihydroxyvitamin D3 induced histone profiles guide discovery of VDR action sites. J Steroid Biochem Mol Biol. 2013 Sep 13. pii: S0960-0760(13)00165-9. [PubMed]

Pike JW, Meyer MB. Fundamentals of vitamin D hormone-regulated gene expression. J Steroid Biochem Mol Biol. 2013 Nov 12. pii: S0960-0760(13)00234-3. [PubMed]

2012

Styner M, Meyer MB, Galior K, Case N, Xie Z, Sen B, Thompson WR, Pike JW, Rubin J. Mechanical Strain Downregulates C/EBPβ in MSC and Decreases Endoplasmic Reticulum Stress. PLoS One. 2012;7(12):e51613. doi: 10.1371/journal.pone.0051613. [PubMed]

Eelen G, Verlinden L, Meyer MB, Gijsbers R, Pike JW, Bouillon R, Verstuyf A. 1,25-Dihydroxyvitamin D(3) and the aging-related Forkhead Box O and Sestrin proteins in osteoblasts. J Steroid Biochem Mol Biol. 2012 Sep 16. doi:pii: S0960-0760(12)00167-7. 10.1016/j.jsbmb.2012.09.011. [PubMed]

Meyer MB, Pike JW. Corepressors (NCoR and SMRT) as well as Coactivators are Recruited to Positively Regulated 1α,25-Dihydroxyvitamin D3-Responsive Genes. J Steroid Biochem Mol Biol. 2012 Aug 25. doi:pii: S0960-0760(12)00149-5. 10.1016/j.jsbmb.2012.08.006. [PubMed] GEO Data Accession Link: GSE39277

Pike JW, Meyer MB. The vitamin D receptor: new paradigms for the regulation of gene expression by 1,25-dihydroxyvitamin D3. Rheum Dis Clin North Am. 2012 Feb;38(1):13-27. [PubMed]

Lieben L, Masuyama R, Torrekens S, Van Looveren R, Schrooten J, Baatsen P, Lafage-Proust MH, Dresselaers T, Feng JQ, Bonewald LF, Meyer MB, Pike JW, Bouillon R, Carmeliet G. Normocalcemia is maintained in mice under conditions of calcium malabsorption by vitamin D-induced inhibition of bone mineralization. J Clin Invest. 2012 May 1;122(5):1803-15. [PubMed]

Pike JW, Meyer MB. Regulation of mouse Cyp24a1 expression via promoter-proximal and downstream-distal enhancers highlights new concepts of 1,25-dihydroxyvitamin D(3) action. Arch Biochem Biophys. 2012 Jul 1;523(1):2-8.[PubMed]

Meyer MB, Goetsch PD, Pike JW. VDR/RXR and TCF4/β-Catenin Cistromes in Colonic Cells of Colorectal Tumor Origin: Impact on c-FOS and c-MYC Gene Expression. Mol Endocrinol. 2012 Jan;26(1):37-51. [PubMed] GEO Data Accession Link: GSE31939

2011

Kriebitzsch C, Verlinden L, Eelen G, van Schoor NM, Swart K, Lips P, Meyer MB, Pike JW, Boonen S, Carlberg C, Vitvitsky V, Bouillon R, Banerjee R, Verstuyf A. 1,25-dihydroxyvitamin D(3) influences cellular homocysteine levels in murine pre-osteoblastic MC3T3-E1 cells by direct regulation of cystathionine β-synthase. J Bone Miner Res. 2011 Dec;26(12):2991-3000. [PubMed]

Pike JW, Meyer MB, Bishop KA. Regulation of target gene expression by the vitamin D receptor – an update on mechanisms.Rev Endocr Metab Disord. 2012 Mar;13(1):45-55.[PubMed]

Bishop KA, Coy HM, Nerenz RD, Meyer MB, Pike JW. Mouse Rankl expression is regulated in T cells by c-Fos through a cluster of distal regulatory enhancers designated the T cell control region. J Biol Chem. 2011 Jun 10;286(23):20880-91. [PubMed]

Martowicz ML, Meyer MB, Pike JW. The mouse Rankl gene locus is defined by a broad pattern of histone acetylation and regulated through distinct distal enhancers. J Cell Biochem. 2011 Aug;112(8):2030-45. [PubMed]

2010

Pike JW, Meyer MB. The vitamin D receptor: new paradigms for the regulation of gene expression by 1,25-dihydroxyvitamin D(3). Endocrinol Metab Clin North Am. 2010 Jun;39(2):255-69. Review. [PubMed]

Ajibade DV, Dhawan P, Fechner AJ, Meyer MB, Pike JW, Christakos S. Evidence for a Role of Prolactin in Calcium Homeostasis: Regulation of Intestinal Transient Receptor Potential Vanilloid Type 6, Intestinal Calcium Absorption, and the 25-Hydroxyvitamin D3 1{alpha} Hydroxylase Gene by Prolactin. Endocrinology. 2010 May 12. [PubMed]

Meyer MB, Goetsch PD, Pike JW. A downstream intergenic cluster of regulatory enhancers contributes to the induction of CYP24A1 expression by 1alpha,25-dihydroxyvitamin D3. J Biol Chem. 2010 Mar 17. [PubMed]

Pike JW, Meyer MB, Martowicz ML, Bishop KA, Lee SM, Nerenz RD, Goetsch PD. Emerging regulatory paradigms for control of gene expression by 1,25-dihydroxyvitamin D3. J Steroid Biochem Mol Biol. 2010 Mar 7. [PubMed]

Meyer MB, Goetsch PD, Pike JW. Genome-wide analysis of the VDR/RXR cistrome in osteoblast cells provides new mechanistic insight into the actions of the vitamin D hormone. J Steroid Biochem Mol Biol. 2010 Feb 18. [PubMed]

Zella LA, Meyer MB, Nerenz RD, Lee SM, Martowicz ML, Pike JW. Multifunctional enhancers regulate mouse and human vitamin D receptor gene transcription. Mol Endocrinol. 2010 Jan;24(1):128-47. [PubMed]

2006-2009

2009

Bishop KA, Meyer MB, Pike JW. A novel distal enhancer mediates cytokine induction of mouse RANKL gene expression. Mol Endocrinol. 2009 Dec;23(12):2095-110. [PubMed]

Zella LA, Meyer MB, Nerenz RD, Pike JW.  The enhanced hypercalcemic response to 20-epi-1,25-dihydroxyvitamin D3results from a selective and prolonged induction of intestinal calcium-regulating genes. Endocrinology. 2009 Aug;150(8):3448-56. [PubMed]

2007

Pike JW, Zella LA, Meyer MB, Fretz JA, Kim S. Molecular actions of 1,25-dihydroxyvitamin D3 on genes involved in calcium homeostasis. J Bone Miner Res. 2007 Dec;22 Suppl 2:V16-9. Review. [PubMed]

Meyer MB, Zella LA, Nerenz RD, Pike JW. Characterizing early events associated with the activation of target genes by 1,25-dihydroxyvitamin D3 in mouse kidney and intestine in vivo. J Biol Chem. 2007 Aug 3;282(31):22344-52. [PubMed]

Pike JW, Meyer MB, Watanuki M, Kim S, Zella LA, Fretz JA, Yamazaki M, Shevde NK. Perspectives on mechanisms of gene regulation by 1,25-dihydroxyvitamin D3 and its receptor. J Steroid Biochem Mol Biol. 2007 Mar;103(3-5):389-95. [PubMed]

Kim S, Yamazaki M, Zella LA, Meyer MB, Fretz JA, Shevde NK, Pike JW. Multiple enhancer regions located at significant distances upstream of the transcriptional start site mediate RANKL gene expression in response to 1,25-dihydroxyvitamin D3. J Steroid Biochem Mol Biol. 2007 Mar;103(3-5):430-4. [PubMed]

2006

Meyer MB, Watanuki M, Kim S, Shevde NK, Pike JW. The human transient receptor potential vanilloid type 6 distal promoter contains multiple vitamin D receptor binding sites that mediate activation by 1,25-dihydroxyvitamin D3 in intestinal cells. Mol Endocrinol. 2006 Jun;20(6):1447-61. [PubMed]