Biology subjects

Kocabas, F.

Publications and source records attributed to Kocabas, F..

3 recordsLinked to original sources

bioRxiv2020

Development of Small Molecule MEIS Inhibitors that modulate HSC activity

Meis1, which belongs to TALE-type class of homeobox gene family, appeared as one of the key regulators of hematopoietic stem cell (HSC) self-renewal and a potential therapeutical target. However, small molecule inhibitors of MEIS1 remained unknown. This led us to develop inhibitors of MEIS1 that could modulate HSC activity. To this end, we have established a library of relevant homeobox family inhibitors and developed a high-throughput in silico screening strategy against homeodomain of MEIS proteins using the AutoDock Vina and PaDEL-ADV platform. We have screened over a million druggable small molecules in silico and selected putative MEIS inhibitors (MEISi) with no predicted cytotoxicity or cardiotoxicity. This was followed by in vitro validation of putative MEIS inhibitors using MEIS dependent luciferase reporter assays and analysis in the ex vivo HSC assays. We have shown that small molecules named MEISi-1 and MEISi-2 significantly inhibit MEIS-luciferase reporters in vitro and induce murine (LSKCD34low cells) and human (CD34+, CD133+, and ALDHhi cells) HSC self-renewal ex vivo. In addition, inhibition of MEIS proteins results in downregulation of Meis1 and MEIS1 target gene expression including Hif-1, Hif-2 and HSC quiescence modulators. MEIS inhibitors are effective in vivo as evident by induced HSC content in the murine bone marrow and downregulation of expression of MEIS target genes. These studies warrant identification of first-in-class MEIS inhibitors as potential pharmaceuticals to be utilized in modulation of HSC activity and bone marrow transplantation studies.

molecular biology↗

bioRxiv2020

Development of Gene Editing Strategies for Human β-Globin (HBB) Gene Mutations

Recent developments in gene editing technology have enabled scientists to modify DNA sequence by using engineered endonucleases. These gene editing tools are promising candidates for clinical applications, especially for treatment of inherited disorders like sickle cell disease (SCD). SCD is caused by a point mutation in human {beta}-globin gene (HBB). Clinical strategies have demonstrated substantial success, however there is not any permanent cure for SCD available. CRISPR/Cas9 platform uses a single endonuclease and a single guide RNA (gRNA) to induce sequence-specific DNA double strand break (DSB). When this accompanies a repair template, it allows repairing the mutated gene. In this study, it was aimed to target HBB gene via CRISPR/Cas9 genome editing tool to introduce nucleotide alterations for efficient genome editing and correction of point mutations causing SCD in human cell line, by Homology Directed Repair (HDR). We have achieved to induce target specific nucleotide changes on HBB gene in the locus of mutation causing SCD. The effect of on-target activity of bone fide standard gRNA and newly developed longer gRNA were examined. It is observed that longer gRNA has higher affinity to target DNA while having the same performance for targeting and Cas9 induced DSBs. HDR mechanism was triggered by co-delivery of donor DNA repair templates in circular plasmid form. In conclusion, we have suggested methodological pipeline for efficient targeting with higher affinity to target DNA and generating desired modifications on HBB gene. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/908319v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@18f810org.highwire.dtl.DTLVardef@1461dfcorg.highwire.dtl.DTLVardef@5a9546org.highwire.dtl.DTLVardef@fe5815_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG HighlightsO_LIHBB gene were targeted by spCas9 in close proximity to the SCD mutation C_LIO_LILong gRNA, which is designed to target SCD mutation, is sickle cell disease specific and exhibits indistinguishable level of cleavage activity on target locus. C_LIO_LIFunctional HBB HDR repair templates with 1 Kb and 2 Kb size were generated to cover all known mutations in the HBB gene. C_LIO_LIReplacement of PAM sequence in HDR template with HindIII recognition sequence allowed a quick assessment of the HDR efficiency. C_LIO_LIHDR template: Cas9-GFP vector 2:1 ratio yielded the highest HDR events/GFP+ cells. C_LI

molecular biology↗

bioRxiv2018

c-Myc inhibition is critical for HSC expansion and Rad51 expression

c-Myc plays a major role in the maintenance of glycolytic metabolism and hematopoietic stem cell (HSC) quiescence. Targeting modulators of HSC quiescence and metabolism could lead to HSC cell cycle entry with concomitant expansion. Here we show that c-Myc inhibitor 10074-G5 treatment leads to 2-fold increase in murine LSKCD34low HSC compartment post 7 days. In addition, c-Myc inhibition increases CD34+ and CD133+ human HSC number. c-Myc inhibition leads to downregulation of glycolytic and cyclin-dependent kinase inhibitor (CDKI) gene expression ex vivo and in vivo. In addition, c-Myc inhibition upregulates major HDR modulator Rad51 expression in hematopoietic cells. Besides, c-Myc inhibition does not alter proliferation kinetics of endothelial cells, fibroblasts or adipose derived mesenchymal stem cells, however; it limits bone marrow derived mesenchymal stem cell proliferation. We further demonstrate that a cocktail of c-Myc inhibitor 10074-G5 along with tauroursodeoxycholic acid (TUDCA) and i-NOS inhibitor L-NIL provides a robust HSC maintenance and expansion ex vivo as evident by induction of all stem cell antigens analyzed. Intriguingly, the cocktail of c-Myc inhibitor 10074-G5, TUDCA and L-NIL improves HDR related gene expression. These findings provide tools to improve ex vivo HSC maintenance and expansion, autologous HSC transplantation and gene editing through modulation of HSC glycolytic and HDR pathways.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC=\"FIGDIR/small/403584_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (65K):\norg.highwire.dtl.DTLVardef@a34597org.highwire.dtl.DTLVardef@12dcc37org.highwire.dtl.DTLVardef@1ba68edorg.highwire.dtl.DTLVardef@13edbfd_HPS_FORMAT_FIGEXP M_FIG Graphical abstract\n\nC_FIG HighlightsO_LIc-Myc inhibition induces ex vivo murine and human hematopoietic stem and progenitor cell proliferation and in vivo murine HSC pool\nC_LIO_LIc-Myc inhibition downregulates CDKIs and glycolytic gene expression in hematopoietic cells\nC_LIO_LIc-Myc inhibition do not cause apparent changes to endothelial cells, fibroblasts, or AD-MSCs but it limits BM-MSC proliferation\nC_LIO_LIc-Myc inhibition along with TUDCA and L-NIL improves HSC maintenance and expansion as evident by induction of all HSC surface antigens analyzed\nC_LIO_LIc-Myc inhibition alone upregulates major HDR modulator Rad51 expression in hematopoietic cells\nC_LIO_LICocktail of c-Myc inhibitor 10074-G5, TUDCA and L-NIL improves HDR and S-phase related gene expression\nC_LI

cell biology↗