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Zhang H, Wei Q, Tsushima H, Puviindran V, Tang YJ, Pathmanapan S, Poon R, Ramu E, Al-Jazrawe M, Wunder J, Alman BA. Intracellular cholesterol biosynthesis in enchondroma and chondrosarcoma. JCI Insight 2019; 5:127232. [PMID: 31039139 DOI: 10.1172/jci.insight.127232] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Enchondroma and chondrosarcoma are the most common benign and malignant cartilaginous neoplasms. Mutations in isocitrate dehydrogenase 1 and 2 (IDH1/2) are present in the majority of these tumors. We performed RNA-seq analysis on chondrocytes from Col2a1Cre;Idh1LSL/+ animals and found that genes implied in cholesterol synthesis pathway were significantly upregulated in the mutant chondrocytes. We examined the phenotypic effect of inhibiting intracellular cholesterol biosynthesis on enchondroma formation by conditionally deleting SCAP (sterol regulatory element-binding protein cleavage-activating protein), a protein activating intracellular cholesterol synthesis, in IDH1 mutant mice. We found fewer enchondromas in animals lacking SCAP. Furthermore, in chondrosarcomas, pharmacological inhibition of intracellular cholesterol synthesis significantly reduced chondrosarcoma cell viability in vitro and suppressed tumor growth in vivo. Taken together, these data suggest that intracellular cholesterol synthesis is a potential therapeutic target for enchondromas and chondrosarcomas.
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Affiliation(s)
- Hongyuan Zhang
- Department of Cell Biology and.,Department of Orthopeadic Surgery, Duke University, Durham, North Carolina, USA
| | - Qingxia Wei
- Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | | | - Vijitha Puviindran
- Department of Orthopeadic Surgery, Duke University, Durham, North Carolina, USA
| | - Yuning J Tang
- Department of Cell Biology and.,Department of Orthopeadic Surgery, Duke University, Durham, North Carolina, USA
| | - Sinthu Pathmanapan
- Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Raymond Poon
- Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Eyal Ramu
- Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mushriq Al-Jazrawe
- Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jay Wunder
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Benjamin A Alman
- Department of Cell Biology and.,Department of Orthopeadic Surgery, Duke University, Durham, North Carolina, USA
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Pallan PS, Marquez VE, Egli M. The conformationally constrained N-methanocarba-dT analogue adopts an unexpected C4'-exo sugar pucker in the structure of a DNA hairpin. Biochemistry 2012; 51:2639-41. [PMID: 22409313 DOI: 10.1021/bi300215k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Incorporation of a bicyclo[3.1.0]hexane scaffold into the nucleoside sugar was devised to lock the embedded cyclopentane ring in conformations that mimic the furanose North and South sugar puckers. To analyze the effects of North-methanocarba-2'-deoxythymidine (N-MCdT) on the B-form DNA, we crystallized d(CGCGAA[mcTmcT]CGCG) with two N-MCdTs. Instead of a duplex, the 12mer forms a tetraloop hairpin, whereby loop N-MCdTs adopt the C4'-exo pucker (NE; P = 50°). Thus, the bicyclic framework does not limit the pucker to the anticipated C2'-exo range (NNW; P = -18°).
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Affiliation(s)
- Pradeep S Pallan
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States
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Kim T, Barchi JJ, Marquez VE, Shapiro BA. Understanding the effects of carbocyclic sugars constrained to north and south conformations on RNA nanodesign. J Mol Graph Model 2011; 29:624-34. [PMID: 21159533 PMCID: PMC3040123 DOI: 10.1016/j.jmgm.2010.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 11/05/2010] [Accepted: 11/10/2010] [Indexed: 11/28/2022]
Abstract
Relatively new types of the modified nucleotides, namely carbocyclic sugars that are constrained to north or south (C2' or C3' exo) conformations, can be used for RNA nanoparticle design to control their structures and stability by rigidifying nucleotides and altering the helical properties of RNA duplexes. Two RNA structures, an RNA dodecamer and an HIV kissing loop complex where several nucleotides were replaced with north or south constrained sugars, were studied by molecular dynamics (MD) simulations. The substituted south constrained nucleotides in the dodecamer widened the major groove and narrowed and deepened the minor groove thus inducing local conformational changes that resemble a B-form DNA helix. In the HIV kissing loop complex, north and south constrained nucleotides were substituted into flanking bases and stems. The modified HIV kissing loop complex showed a lower RMSD value than the normal kissing loop complex. The overall twist angle was also changed and its standard deviation was reduced. In addition, the modified RNA dodecamer and HIV kissing loop complex were characterized by principal component analysis (PCA) and steered molecular dynamics (SMD). PCA results showed that the constrained sugars stabilized the overall motions. The results of the SMD simulations indicated that as the backbone δ angles were increased by elongation, more force was applied to the modified RNA due to the constrained sugar analogues.
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Affiliation(s)
- Taejin Kim
- Center for Cancer Research Nanobiology Program (CCRNP), National Cancer Institute at Frederick, Frederick, MD, USA
| | - Joseph J. Barchi
- Laboratory of Medicinal Chemistry, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Victor E. Marquez
- Laboratory of Medicinal Chemistry, National Cancer Institute at Frederick, Frederick, MD, USA
| | - Bruce A. Shapiro
- Center for Cancer Research Nanobiology Program (CCRNP), National Cancer Institute at Frederick, Frederick, MD, USA
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Maderia M, Shenoy S, Van QN, Marquez VE, Barchi JJ. Biophysical studies of DNA modified with conformationally constrained nucleotides: comparison of 2'-exo (north) and 3'-exo (south) 'locked' templates. Nucleic Acids Res 2007; 35:1978-91. [PMID: 17341464 PMCID: PMC1895885 DOI: 10.1093/nar/gkm025] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The biophysical properties of oligodeoxyribonucleotides (ODNs) selectively modified with conformationally ‘locked’ bicyclo[3.1.0]hexane pseudosugars (Maier,M.A., Choi,Y., Gaus,H., Barchi,J.J. Jr, Marquez,V.E., Manoharan,M. (2004) Synthesis and characterization of oligonucleotides containing conformationally constrained bicyclo[3.1.0]hexane pseudosugar analogs Nucleic Acids Res., 32, 3642–3650) have been studied by various techniques. Six separate synthetic ODNs based on the Dickerson Drew dodecamer sequence (CGCGAAT*T*CGCG) were examined where each one (or both) of the thymidines (T*) were substituted with a bicyclic pseudosugar locked in either a North (2′-exo) or South (3′-exo) ring pucker. Circular dichroism spectroscopy, differential scanning calorimetry and 1H NMR spectroscopy were used to examine the duplex stability and conformational properties of the ODNs. Replacement of one or both thymidines with North-locked sugars (RNA-like) into the dodecamer did not greatly affect duplex formation or melt temperatures but distinct differences in thermodynamic parameters were observed. In contrast, incorporation of South-locked sugar derivatives that were predicted to stabilize this standard B-DNA, had the unexpected effect of causing a conformational equilibrium between different duplex forms at specific strand and salt concentrations. Our data and those of others suggest that although DNA can tolerate modifications with RNA-like (North) nucleotides, a more complicated spectrum of changes emerges with modifications restricted to South (DNA-like) puckers.
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Affiliation(s)
- Melissa Maderia
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Shilpa Shenoy
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Que N. Van
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Victor E. Marquez
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
| | - Joseph J. Barchi
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702 USA, Molecular Targets Development Program and Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Frederick, MD 21702 USA
- *To whom correspondence should be addressed. +1 301 846 5905+1 301 846 6033
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