Lysine deacetylase inhibitors have low selectivity in cells and exhibit predominantly off‐target effects
Lysine deacetylases (KDACs or HDACs) are metal‐dependent enzymes that regulate lysine acetylation, a post‐translational modification that is present on thousands of human proteins, essential for many cellular processes, and often misregulated in diseases. The selective inhibition of KDACs would allo...
Saved in:
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2025-01-01
|
| Series: | FEBS Open Bio |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/2211-5463.13896 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841556996882432000 |
|---|---|
| author | Kiara E. Bornes Marcus A. Moody Thomas M. Huckaba Megan C. Benz Emily C. McConnell Maryam Foroozesh Van H. Barnes Bridgette M. Collins‐Burow Matthew E. Burow Terry J. Watt Tasha B. Toro |
| author_facet | Kiara E. Bornes Marcus A. Moody Thomas M. Huckaba Megan C. Benz Emily C. McConnell Maryam Foroozesh Van H. Barnes Bridgette M. Collins‐Burow Matthew E. Burow Terry J. Watt Tasha B. Toro |
| author_sort | Kiara E. Bornes |
| collection | DOAJ |
| description | Lysine deacetylases (KDACs or HDACs) are metal‐dependent enzymes that regulate lysine acetylation, a post‐translational modification that is present on thousands of human proteins, essential for many cellular processes, and often misregulated in diseases. The selective inhibition of KDACs would allow for understanding of the biological roles of individual KDACs and therapeutic targeting of individual enzymes. Recent studies have suggested that purportedly specific KDAC inhibitors have significant off‐target binding, but the biological consequences of off‐target binding were not evaluated. We compared the effects of treatment with two of the reportedly most KDAC‐selective inhibitors, Tubastatin A and PCI‐34051, in HT1080 cells in which the endogenous KDAC6 or KDAC8 gene has been mutated to inactivate enzyme catalysis while retaining enzyme expression. Genetic inactivation results in much stronger deacetylation defects on known targets compared to inhibitor treatment. Gene expression analysis revealed that both inhibitors have extensive and extensively overlapping off‐target effects in cells, even at low inhibitor doses. Furthermore, Tubastatin A treatment led to increased histone acetylation, while inactivation of KDAC6 or KDAC8 did not. Genetic inactivation of KDAC6, but not KDAC8, impaired tumor formation in a xenograft model system, in contrast to previous reports with KDAC inhibitors suggesting the reverse. We conclude that the majority of observed biological effects of treatment with KDAC inhibitors are due to off‐target effects rather than the intended KDAC inhibition. Developing a truly specific KDAC6 inhibitor could be a promising therapeutic avenue, but it is imperative to develop new inhibitors that selectively mimic genetic inactivation of individual KDACs. |
| format | Article |
| id | doaj-art-2b0a8d5f4aa142abbad2c69f8adc7808 |
| institution | Kabale University |
| issn | 2211-5463 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | FEBS Open Bio |
| spelling | doaj-art-2b0a8d5f4aa142abbad2c69f8adc78082025-01-07T02:27:34ZengWileyFEBS Open Bio2211-54632025-01-011519410710.1002/2211-5463.13896Lysine deacetylase inhibitors have low selectivity in cells and exhibit predominantly off‐target effectsKiara E. Bornes0Marcus A. Moody1Thomas M. Huckaba2Megan C. Benz3Emily C. McConnell4Maryam Foroozesh5Van H. Barnes6Bridgette M. Collins‐Burow7Matthew E. Burow8Terry J. Watt9Tasha B. Toro10Department of Chemistry Xavier University of Louisiana New Orleans LA USATulane University School of Medicine New Orleans LA USADepartment of Biology Xavier University of Louisiana New Orleans LA USATulane University School of Medicine New Orleans LA USATulane University School of Medicine New Orleans LA USADepartment of Chemistry Xavier University of Louisiana New Orleans LA USATulane University School of Medicine New Orleans LA USATulane University School of Medicine New Orleans LA USATulane University School of Medicine New Orleans LA USADepartment of Chemistry Xavier University of Louisiana New Orleans LA USADepartment of Chemistry Xavier University of Louisiana New Orleans LA USALysine deacetylases (KDACs or HDACs) are metal‐dependent enzymes that regulate lysine acetylation, a post‐translational modification that is present on thousands of human proteins, essential for many cellular processes, and often misregulated in diseases. The selective inhibition of KDACs would allow for understanding of the biological roles of individual KDACs and therapeutic targeting of individual enzymes. Recent studies have suggested that purportedly specific KDAC inhibitors have significant off‐target binding, but the biological consequences of off‐target binding were not evaluated. We compared the effects of treatment with two of the reportedly most KDAC‐selective inhibitors, Tubastatin A and PCI‐34051, in HT1080 cells in which the endogenous KDAC6 or KDAC8 gene has been mutated to inactivate enzyme catalysis while retaining enzyme expression. Genetic inactivation results in much stronger deacetylation defects on known targets compared to inhibitor treatment. Gene expression analysis revealed that both inhibitors have extensive and extensively overlapping off‐target effects in cells, even at low inhibitor doses. Furthermore, Tubastatin A treatment led to increased histone acetylation, while inactivation of KDAC6 or KDAC8 did not. Genetic inactivation of KDAC6, but not KDAC8, impaired tumor formation in a xenograft model system, in contrast to previous reports with KDAC inhibitors suggesting the reverse. We conclude that the majority of observed biological effects of treatment with KDAC inhibitors are due to off‐target effects rather than the intended KDAC inhibition. Developing a truly specific KDAC6 inhibitor could be a promising therapeutic avenue, but it is imperative to develop new inhibitors that selectively mimic genetic inactivation of individual KDACs.https://doi.org/10.1002/2211-5463.13896HDAC6HDAC8HDACiimmunofluorescenceRNA‐seq |
| spellingShingle | Kiara E. Bornes Marcus A. Moody Thomas M. Huckaba Megan C. Benz Emily C. McConnell Maryam Foroozesh Van H. Barnes Bridgette M. Collins‐Burow Matthew E. Burow Terry J. Watt Tasha B. Toro Lysine deacetylase inhibitors have low selectivity in cells and exhibit predominantly off‐target effects FEBS Open Bio HDAC6 HDAC8 HDACi immunofluorescence RNA‐seq |
| title | Lysine deacetylase inhibitors have low selectivity in cells and exhibit predominantly off‐target effects |
| title_full | Lysine deacetylase inhibitors have low selectivity in cells and exhibit predominantly off‐target effects |
| title_fullStr | Lysine deacetylase inhibitors have low selectivity in cells and exhibit predominantly off‐target effects |
| title_full_unstemmed | Lysine deacetylase inhibitors have low selectivity in cells and exhibit predominantly off‐target effects |
| title_short | Lysine deacetylase inhibitors have low selectivity in cells and exhibit predominantly off‐target effects |
| title_sort | lysine deacetylase inhibitors have low selectivity in cells and exhibit predominantly off target effects |
| topic | HDAC6 HDAC8 HDACi immunofluorescence RNA‐seq |
| url | https://doi.org/10.1002/2211-5463.13896 |
| work_keys_str_mv | AT kiaraebornes lysinedeacetylaseinhibitorshavelowselectivityincellsandexhibitpredominantlyofftargeteffects AT marcusamoody lysinedeacetylaseinhibitorshavelowselectivityincellsandexhibitpredominantlyofftargeteffects AT thomasmhuckaba lysinedeacetylaseinhibitorshavelowselectivityincellsandexhibitpredominantlyofftargeteffects AT megancbenz lysinedeacetylaseinhibitorshavelowselectivityincellsandexhibitpredominantlyofftargeteffects AT emilycmcconnell lysinedeacetylaseinhibitorshavelowselectivityincellsandexhibitpredominantlyofftargeteffects AT maryamforoozesh lysinedeacetylaseinhibitorshavelowselectivityincellsandexhibitpredominantlyofftargeteffects AT vanhbarnes lysinedeacetylaseinhibitorshavelowselectivityincellsandexhibitpredominantlyofftargeteffects AT bridgettemcollinsburow lysinedeacetylaseinhibitorshavelowselectivityincellsandexhibitpredominantlyofftargeteffects AT mattheweburow lysinedeacetylaseinhibitorshavelowselectivityincellsandexhibitpredominantlyofftargeteffects AT terryjwatt lysinedeacetylaseinhibitorshavelowselectivityincellsandexhibitpredominantlyofftargeteffects AT tashabtoro lysinedeacetylaseinhibitorshavelowselectivityincellsandexhibitpredominantlyofftargeteffects |