Histone deacetylase (HDAC) inhibitors - changes in gene expression

Histone acetyl transferases and histon deacetylases (HDAC) mediate the acetylation and deacetylation of histone proteins (1) which is an important regulator of gene expression (2).

Histones are proteins that play an important part in the regulation of transcription by helping to condense DNA into its compact form as chromosomes. The binding of histones to DNA is controlled by various enzymes present in the cell. When a certain gene in the DNA needs to be transcribed, histone acetyltransferases add an acetyl group to the histone proteins, releasing the restricted access to the DNA imposed by the histones. Transcription factors can bind to the DNA and activate gene transcription. When the gene no longer needs to be transcribed, histone deacetylases (HDACs) remove the acetyl group which enables histones to bind to the DNA.

Inhibitors of HDACs, such as the hydroxamic acid-based hybrid polar compound suberoylanilide hydroxamic acid (SAHA) (3), induce growth arrest, differentiation, and/or apoptosis of transformed cells in vitro (4, 5) and inhibit tumor growth in vivo (6-8), Especially tumor suppressor genes are often silenced in human cancer. This can occurr by transcriptional repression via deacetylation in promotor regions, mediated by histone deacetylases. HDAC inhibitors can block cancer cell growth by restoring expression of tumor suppressor genes (9).

Suberoylanilide hydroxamic acid (SAHA) is a well known HDAC inhibitor that interferes with the regulation of gene expression by decreasing the activity of histone deacetylases (10, 11).

The SAHA Capture Compound™ has the scaffold attached to the SAHA at the aromatic ring para to the hydroxamic acid moiety of SAHA, as the available crystal structures (pdb: e.g. 1ZZ1) (12) show this position to be ideal for the scaffold attachment. Indeed, similiar SAHA analogs inhibited HDAC activity up to the µM range (13). Therefore, SAHA Capture Compound™ enables an efficient complexity reduction of the proteome and allows discovering, isolating, and profiling members of functional histone deacetylases within a variety of biological samples.

The SAHA caproKit™ includes the SAHA Capture Compound, SAHA competitor, all buffers, positive control protein, and streptavidin magnetic beads.

Please note, that CCMS reagents (caproKits™) will perform best when used with the optimized equipment (caproBox™ and caproMag™).

For the most reproducible results it is recommended to standardize parameters such as UV wavelength, distance between sample and light source, temperature and incubation time. This can best be accomplished using a caproBox™ for cross-linking.

If you are using the proprietary CCMS technology for the first time, caprotec offers a convenient CCMS Starter Kit including a free choice of 3 independent caproKits™, Biotin Capping Kit, caproBox™, and caproMag™. Please feel free to contact us for any additional questions related to using caprotec products!

1) P.A. Marks, R.A. Rifkind, V.M. Richon, R. Breslow, T. Miller, W.K. Kelly, (2001) Histone deacetylases and cancer: causes and therapies; Nat Rev Cancer (1); 194-202.

2) M. Grunstein, (1997) Histone acetylation in chromatin structure and transcription; Nature (389); 349-352.

3) V.M. Richon, S. Emiliani, E. Verdin, Y. Webb, R. Breslow, et al., (1998) A class of hybrid polar inducers of transformed cell differentiation inhibits histone deacetylases; PNAS (95) 6; 3003-3007.

4) V.M. Richon, Y. Webb, R. Merger, T. Sheppard, B. Jursic, et al., (1996) Second generation hybrid polar compounds are potent inducers of transformed cell differentiation; PNAS (93) 12; 5705-5708.

5) P.N Munster, T. Troso-Sandoval, N. Rosen, R. Rifkind, P.A. Marks, V.M. Richon, (2001) The histone deacetylase inhibitor suberoylanilide hydroxamic acid induces differentiation of human breast cancer cells; Cancer Res (61); 8492-8497.

6) L. Qui, M.J. Kelso, C. Hansen, M.L. West, D.P. Fairlie, P.G. Parsons, (1999) Anti-tumor activity in vitro and in vivo of selective differentiating agents containing hydroxamate; Br J Cancer (80) 8; 1252-1258.

7) L.Z. He, T. Tolentino, P. Grayson, S. Zhong, R.P. Warrel Jr., et al., Histone deacetylase inhibitors induce remission in transgenic models of therapy-resistant acute promyelocytic leukemia; J Clin Invest (108) 9; 1321-1330.

8) L.M. Butler, D.B. Agus, H.I. Scher, B. Higgins, A. Rose, et al., (2000) Suberoylanilide hydroxamic acid, an inhibitor of histone deacetylsase, suppresses the growth of prostate cancer cells in vitro and in vivo; Cancer Res (60); 5165-5170.

9) T. Kumagai, N. Wakimoto, D. Yin, S. Gery, N. Kawamata, et al., (2007) Histone deacetylase inhibitor, suberoylanilide hydroxamic acid (Vorinostat, SAHA) profoundly inhibitis the growth of human pancreatic cancer cells; Int J Cancer (121) 3; 656-665.

10) A.V. Bieliauskas, S.V.W. Weerasinghe, M.K.H. Pflum, (2007) Structural requirements of HDAC inhibitors: SAHA analogs functionalized adjacent to the hydroxamic acid; Bioorg Med Chem Lett (17) 8; 2216-2219.

11) T.K. Nielson, C. Hildemann, A. Dickmanns, A. Schwienhorst, R. Ficner, (2005) Crystal structure of a bacterial class 2 histone deacetylase homologue; J Mol Biol (354); 107-120.

12) R. Breslow, P.A. Marks, R.A. Rifkind, B. Jursic, WO93/07148 (15. April 1993).