Journal: Odontology

Article Title: miR-708-3p targetedly regulates LSD1 to promote osteoblast differentiation of hPDLSCs in periodontitis

doi: 10.1007/s10266-024-00963-9

Figure Lengend Snippet: All antibodies in this study

Article Snippet: LSD1 , Bioss , rabbit , bs-3821R.

Techniques:

Journal: ACS Chemical Biology

Article Title: Substrate- and Cofactor-independent Inhibition of Histone Demethylase KDM4C

doi: 10.1021/cb500374f

Figure Lengend Snippet: Peptide Sequences Targeting KDM1A, -B, and KDM4A–C Identified from Phage Display, As Well As the Apparent EC 50 Values of the Peptide-Phages

Article Snippet: KDM1A was purchased from BPSBioscience (Cat. No. 50097); KDM1B cloning, expression, and purification.

Techniques: Sequencing

Journal: Cell death discovery

Article Title: UM171 cooperates with PIM1 inhibitors to restrict HSC expansion markers and suppress leukemia progression.

doi: 10.1038/s41420-022-01244-6

Figure Lengend Snippet: Fig. 3 UM171 binds to PIM1 and activates its phosphorylation. A Q-RT-PCR analysis of HEL cells treated with UM171 (6 μM) for expression of the PIM1. B Q-RT-PCR analysis of HEL cells treated with UM171 (6 μM) for expression of the PIM2, and PIM3 genes. C Western blot of HEL cells treated with the indicated concentration of UM171 compound. GAPDH was used as a loading control. D Molecular docking of the compound UM171 and PIM1 (PDB:5O12). The phosphorylation site of PIM1 kinase was shown as insert. E The molecular binding energy between PIM1 and UM171 as well as pan-PIM inhibitors LGH447, TP3654, SGI1776 ad AZ1208. F Binding of PIM1 to UM171 in pull-down experiment using affinity ES6B beads. G Q-RT-PCR analysis of HEL cells treated with UM171 (6 uM), LGH447(5 μM), and UM171 + LGH447 for 24 hours for expression of PIM1. H Western blot of HEL cells treated with UM171 and DMSO for expression of LSD1.

Article Snippet: The antibodies used were as follow: Polyclonal rabbit PIM1 (ab54503), FLI1 Cell Death Discovery (2022) 8:448 (ab133485) and ERK (ab184699) were purchased from Abcam (UK); the GAPDH (AB-P-R001) antibody was obtained from Goodhere Biotech (CN); c-KIT (18696-1-AP), LSD1 (20813-1-AP) and P21CIP1 (10355-1-AP) were obtained from Protein Technology (CN); p-ERK (9101 S), stat3 (4904), p-stat3 (9145), goat anti-mouse IgG (H+ L) DyLight (TM) 680 (5470 s) and goat anti-rabbit IgG (H+ L) DyLight (TM) 680 (5151 s) antibodies were obtained from Cell Signaling Technology (US).

Techniques: Phospho-proteomics, Reverse Transcription Polymerase Chain Reaction, Expressing, Western Blot, Concentration Assay, Control, Binding Assay

Journal: Neuron

Article Title: Recapitulation and reversal of schizophrenia-related phenotypes in Setd1a -deficient mice

doi: 10.1016/j.neuron.2019.09.014

Figure Lengend Snippet: (A) Neurod6 locus. ChIP-Seq of LSD1 (grey), Setd1a (black), Mef2 (dark blue), H3K27ac (green), H3K4me3 (light blue) is shown. Grey, black and dark blue boxes below Lsd1, Setd1a and Mef2 tracks respectively represent significant peaks that passed all quality checks (see methods).

Article Snippet: We transfected 5ng of pRL Renilla vector, 50 ng of 3X Mef2-Luciferase vector (Addgene #32967), 75 ng of Mef2c CDS (Addgene #32515) and/or Setd1a CDS (Origene #MR215352), Lsd1 CDS (Origene #MR210741), pcDNA3.1 vector.

Techniques: ChIP-sequencing

Journal: Neuron

Article Title: Recapitulation and reversal of schizophrenia-related phenotypes in Setd1a -deficient mice

doi: 10.1016/j.neuron.2019.09.014

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: We transfected 5ng of pRL Renilla vector, 50 ng of 3X Mef2-Luciferase vector (Addgene #32967), 75 ng of Mef2c CDS (Addgene #32515) and/or Setd1a CDS (Origene #MR215352), Lsd1 CDS (Origene #MR210741), pcDNA3.1 vector.

Techniques: Recombinant, Luciferase, Plasmid Preparation, Software

Journal: Clinical Epigenetics

Article Title: LSD1 dual function in mediating epigenetic corruption of the vitamin D signaling in prostate cancer

doi: 10.1186/s13148-017-0382-y

Figure Lengend Snippet: LSD1 expression in prostate tissues is increased in advanced prostate tumors. Western blot and immunohistochemistry (IHC) staining were used to measure protein levels of LSD1 and VDR in wild-type (WT) and TRAMP mice. CWR22 xenograft mice were used to investigate the role of LSD1 and VDR in PCa growth kinetics. a Western blotting image showing the expression of LSD1 and VDR protein levels in wild-type and TRAMP prostate lysates. WT wild-type mouse, T tumor/TRAMP mouse, CR castration-recurrent tumor from TRAMP mouse. b LSD1 ( left ) and VDR ( right ) protein quantification of LSD1, or VDR, normalized to GAPDH. Data from wild-type samples were compared with the data from tumor samples using Student’s t test. p values are indicated in the plot. c LSD1 and VDR IHC staining in age-matched prostate samples of 25-week-old TRAMP and WT mice. Staining shows a strong nuclear localization, in brown , in both WT and TRAMP tumors, with a stronger signal in tumor. Labels in the image indicate protein (LSD1, VDR), magnification (× 10, × 20), and tissue type (WT, tumor (T)). d Kaplan-Meier plots showing time to recurrence for CWR22 xenografts, measured as time necessary for the tumor to reach 1000 mm 3 in volume. The X -axis indicates weeks of the experiment where time 0 is the time of testosterone pellet removal. The Y -axis indicates the percentage of mice with tumor that did not reach 1000 mm 3 . The black lines indicate mice with low LSD1/VDR levels, and the red lines indicate mice with high LSD1/VDR levels measured via IHC. Log-rank p value and median time to recurrence are indicated in the figure

Article Snippet: RNA was quantified using ThermoScientific NanoDrop 8000, and 1 μg of RNA was reverse-transcribed into cDNA using the SuperScript First Strand Synthesis kit (Invitrogen, 11904-018). qRT-PCR-TaqMan primers for Lsd1, E2f1, Cdkn1a, Cyp24a1, and S100g were ordered from Applied Biosystems (Mm01181042_m1 Mm00432936_m1, Mm00432448_m1, Mm00407244_m1, and Mm00486654_m1, respectively). qRT-PCR universal MasterMix (Roche) was used.

Techniques: Expressing, Western Blot, Immunohistochemistry, Staining

Journal: Clinical Epigenetics

Article Title: LSD1 dual function in mediating epigenetic corruption of the vitamin D signaling in prostate cancer

doi: 10.1186/s13148-017-0382-y

Figure Lengend Snippet: a Immunoprecipitation (IP) and western blotting (WB) data showing that LSD1 and VDR belong to the same transcriptional complex. IP was performed from nuclear lysate in samples treated with vehicle control or 1,25-D 3 using the same LSD1 antibody described for IHC and WB. In post-IP, the samples were probed for LSD1 and VDR. The same double band visible in Fig. was also detected in this sample. b , c Effect of LSD1 knockdown and 1,25-D 3 treatment on gene expression of VDR target genes. Every graph compares the effect of vitamin D in control (CTR) cells and LSD1 knockdown (siLSD1) cells. Each bar is the mean of at least three biological replicates with SEM, showing the fold changes of treated (+ D3) vs. vehicle-treated (− Veh) samples. The columns indicate, from left to right , siCTR + Veh, siCTR + 1,25-D 3 , siLSD1 + Veh, and siLSD1 + 1,25-D 3 . Transcript levels were measured for b E2f1 and Cdkn1a and c Cyp24a1 and S100g. Statistical significance was evaluated with one-way ANOVA and Tukey post hoc correction (*** p < 0.001, ** p < 0.01, * p < 0.05)

Article Snippet: RNA was quantified using ThermoScientific NanoDrop 8000, and 1 μg of RNA was reverse-transcribed into cDNA using the SuperScript First Strand Synthesis kit (Invitrogen, 11904-018). qRT-PCR-TaqMan primers for Lsd1, E2f1, Cdkn1a, Cyp24a1, and S100g were ordered from Applied Biosystems (Mm01181042_m1 Mm00432936_m1, Mm00432448_m1, Mm00407244_m1, and Mm00486654_m1, respectively). qRT-PCR universal MasterMix (Roche) was used.

Techniques: Immunoprecipitation, Western Blot, Control, Knockdown, Gene Expression

Journal: Clinical Epigenetics

Article Title: LSD1 dual function in mediating epigenetic corruption of the vitamin D signaling in prostate cancer

doi: 10.1186/s13148-017-0382-y

Figure Lengend Snippet: Viability of a BC1A and b C4-2 cells as measured via cell count upon LSD1 knockdown and 1,25-D 3 treatment. Each bar represents the mean of at least three biological replicates, and the Y -axis indicates the percentage of viable cells compared to the control. From left to right , in both graphs, the columns indicate shCTR + Veh, shCTR + 100 nM 1,25-D 3 , shLSD1 + Veh, and shLSD1 + 100 nM 1,25-D 3 . Statistical significance was evaluated with one-way ANOVA and Tukey post hoc correction (*** p < 0.001, ** p < 0.01, * p < 0.05)

Article Snippet: RNA was quantified using ThermoScientific NanoDrop 8000, and 1 μg of RNA was reverse-transcribed into cDNA using the SuperScript First Strand Synthesis kit (Invitrogen, 11904-018). qRT-PCR-TaqMan primers for Lsd1, E2f1, Cdkn1a, Cyp24a1, and S100g were ordered from Applied Biosystems (Mm01181042_m1 Mm00432936_m1, Mm00432448_m1, Mm00407244_m1, and Mm00486654_m1, respectively). qRT-PCR universal MasterMix (Roche) was used.

Techniques: Cell Counting, Knockdown, Control

Journal: Clinical Epigenetics

Article Title: LSD1 dual function in mediating epigenetic corruption of the vitamin D signaling in prostate cancer

doi: 10.1186/s13148-017-0382-y

Figure Lengend Snippet: Visual representation of the methylation changes observed using the Qiagen methylation arrays. A linear model was built to identify differentially methylated regions and the 95% confidence intervals calculated and plotted ( blue lines ); green dots show the genes whose methylation significantly differs between the selected conditions. Each quadrant reflects the results listed in Additional file : Table S1. a Contribution of vitamin D at basal conditions. b Contribution of LSD1 at basal conditions. c Contribution of vitamin D in knockdown conditions (shLSD1). d Contribution of LSD1 in the presence of vitamin D

Article Snippet: RNA was quantified using ThermoScientific NanoDrop 8000, and 1 μg of RNA was reverse-transcribed into cDNA using the SuperScript First Strand Synthesis kit (Invitrogen, 11904-018). qRT-PCR-TaqMan primers for Lsd1, E2f1, Cdkn1a, Cyp24a1, and S100g were ordered from Applied Biosystems (Mm01181042_m1 Mm00432936_m1, Mm00432448_m1, Mm00407244_m1, and Mm00486654_m1, respectively). qRT-PCR universal MasterMix (Roche) was used.

Techniques: Methylation, Knockdown

Journal: Clinical Epigenetics

Article Title: LSD1 dual function in mediating epigenetic corruption of the vitamin D signaling in prostate cancer

doi: 10.1186/s13148-017-0382-y

Figure Lengend Snippet: Graphical overview of the alterations in the LSD1/DNMT1/VDR signature. The Regulome Explorer was used to identify genes correlating with LSD1/DNMT1 status, followed by functional enrichment analysis and survival analysis on two independent TCGA datasets. a Circos plot showing the genes correlating with LSD1 and DNMT1 status. b List of the genes in the LSD1/DNMT1/VDR signature. c Functional enrichment analysis of the genes in the LSD1/DNMT1/VDR signature indicating pathway name and origin, p value, and FDR-corrected q value. d , e Kaplan-Meier plot indicating progression-free survival in patients with primary tumor ( d ) or overall survival in patients with recurrent metastatic tumor ( e ). The red lines indicate patients with altered LSD1/DNMT1/VDR signature ( z score > ± 2), and the blue lines indicate patients whose signature is not altered ( z score between − 2 and + 2). Statistical significance was calculated via log-rank test with a threshold of p < 0.05

Article Snippet: RNA was quantified using ThermoScientific NanoDrop 8000, and 1 μg of RNA was reverse-transcribed into cDNA using the SuperScript First Strand Synthesis kit (Invitrogen, 11904-018). qRT-PCR-TaqMan primers for Lsd1, E2f1, Cdkn1a, Cyp24a1, and S100g were ordered from Applied Biosystems (Mm01181042_m1 Mm00432936_m1, Mm00432448_m1, Mm00407244_m1, and Mm00486654_m1, respectively). qRT-PCR universal MasterMix (Roche) was used.

Techniques: Functional Assay

Journal: Clinical Epigenetics

Article Title: LSD1 dual function in mediating epigenetic corruption of the vitamin D signaling in prostate cancer

doi: 10.1186/s13148-017-0382-y

Figure Lengend Snippet: Graphical representation of the model for VDR/LSD1/DNMT1 activity in a loci where LSD1 acts as coactivators vs. b loci where LSD1 acts as a corepressor. me methyl residue, PTM post-translational modification, VDR-BP VDR binding partner (i.e., RXR), KDMs non-LSD1 lysine demethylases, H3 histone 3, K9Ac acetylated lysine position 9, K9me3 trimethylated lysine position 9, K4me2 dimethylated lysine position 4, pPol-II phosphorylated RNA polymerase II

Article Snippet: RNA was quantified using ThermoScientific NanoDrop 8000, and 1 μg of RNA was reverse-transcribed into cDNA using the SuperScript First Strand Synthesis kit (Invitrogen, 11904-018). qRT-PCR-TaqMan primers for Lsd1, E2f1, Cdkn1a, Cyp24a1, and S100g were ordered from Applied Biosystems (Mm01181042_m1 Mm00432936_m1, Mm00432448_m1, Mm00407244_m1, and Mm00486654_m1, respectively). qRT-PCR universal MasterMix (Roche) was used.

Techniques: Activity Assay, Residue, Modification, Binding Assay

Journal: The Journal of Biological Chemistry

Article Title: Lysine demethylase KDM1A promotes cell growth via FKBP8–BCL2 axis in hepatocellular carcinoma

doi: 10.1016/j.jbc.2022.102374

Figure Lengend Snippet: Cytoplasmic KDM1A promotes HCC cell growth . A and B , left panel , same number of HLF control or KDM1A-KD cells were seeded. Cell proliferation over 5 days was measured with CCK-8. Fold of growth was normalized to that in control cells. Right panel shows Western blot (WB) for indicated cells. Error bars denote standard deviation of six biological replicates. p Value was calculated by one-way ANOVA followed by pair-wise comparison as indicated. C , 500 HLF control or KDM1A-KD cells were seeded in 6-well plate. About 14 days later, cell colonies were stained with crystal violet . D and E , HLF control cells ( D ) or cells expressing Myc-KDM1A ( E ) were fractionated into cytoplasm (Cyto) and nucleus (Nuc). Shown are the WB results with indicated antibodies. F , GFP-KDM1A were expressed in HLF cells with lentivirus. Shown are photos taken with fluorescent microscopy. The scale bar represents 20 μm. G and H , left panel , same number of HLF KDM1A-KD and rescue cells were seeded. Cell proliferation over 5 days was measured with CCK-8. Fold of growth was normalized to that in control cells. Right panel shows WB for indicated cells. (Ctrl for control, KD for KDM1A-KD, WT for KDM1A-WT rescue, AA for K114A/R115A rescue, AA-DN for K114A/R115A–A539E/K661A rescue). Error bars denote standard deviation of six biological replicates. p Value was calculated by one-way ANOVA. CCK-8, Cell Counting Kit-8; HCC, hepatocellular carcinoma; KD, knockdown; KDM1A, lysine demethylase 1A.

Article Snippet: Coexpression with KDM1A-WT but not inactive mutant decreased FKBP8 methylation ( E ).Consistently, treatment with KDM1A selective inhibitor ORY1001 (TargetMol; catalog no.: T6922) increased FKBP8 methylation ( F ).

Techniques: Control, CCK-8 Assay, Western Blot, Standard Deviation, Comparison, Staining, Expressing, Microscopy, Cell Counting, Knockdown

Journal: The Journal of Biological Chemistry

Article Title: Lysine demethylase KDM1A promotes cell growth via FKBP8–BCL2 axis in hepatocellular carcinoma

doi: 10.1016/j.jbc.2022.102374

Figure Lengend Snippet: KDM1A–K117 is acetylated by KAT8. A , FLAG-KDM1A was cotransfected with HA-tagged acetyltransferases into 293T cells. KDM1A acetylation was analyzed with IP–WB. B , FLAG-KDM1A was cotransfected with increasing HA-KAT8 into 293T cells. KDM1A acetylation was analyzed with IP–WB. C , FLAG-KDM1A was cotransfected with HA-KAT8-WT or inactive -K274A (DN) into 293T cells. KDM1A acetylation was analyzed with IP–WB. D , FLAG-KDM1A fragments were cotransfected with HA-KAT8 into 293T cells. FLAG-KDM1A acetylation was analyzed with IP–WB. E , FLAG-KDM1A-WT or -K117R was cotransfected with KAT8 into 293T cells. KDM1A acetylation was analyzed with IP–WB. F , FLAG-KDM1A-WT or -K117R was cotransfected with KAT8 into 293T cells. Cells were then treated with 3.3 μM TSA and/or 20 mM NIM for 4 h before collection. KDM1A acetylation was analyzed with IP–WB. HA, hemagglutinin; IP, immunoprecipitation; K117, lysine 117; KAT8, lysine acetyltransferase 8; KDM1A, lysine demethylase 1A; NIM, nicotinamide; TSA, trichostatin A; WB, Western blot.

Article Snippet: Coexpression with KDM1A-WT but not inactive mutant decreased FKBP8 methylation ( E ).Consistently, treatment with KDM1A selective inhibitor ORY1001 (TargetMol; catalog no.: T6922) increased FKBP8 methylation ( F ).

Techniques: Immunoprecipitation, Western Blot

Journal: The Journal of Biological Chemistry

Article Title: Lysine demethylase KDM1A promotes cell growth via FKBP8–BCL2 axis in hepatocellular carcinoma

doi: 10.1016/j.jbc.2022.102374

Figure Lengend Snippet: K117 acetylation promotes cytoplasmic localization and protein stability of KDM1A. A and B , KDM1A-WT or mutants were rescue expressed in HLF KDM1A-KD cells. A , shown is the result of immunofluorescence with myc-tag antibody. The scale bar represents 20 μm. B , cells were fractionated into cytoplasmic and nuclear fractions. Fractions were analyzed with WB. C , KDM1A-WT or mutants were expressed in HLF cells, whereas endogenous KDM1A was knocked down with doxycycline-inducible shRNA. Cells were analyzed with WB. D , 0.2 μg Myc-KDM1A-WT or mutants were transiently cotransfected with 0.05 μg GFP into 293T cells in 3.5 cm dish. Cells were analyzed with WB with GFP and actin as loading control. E , KAT8 was knocked down in HLF cells with lentivirus-expressed shRNA. Cells were analyzed with WB. F and G , 0.4 μg Myc-KDM1A-WT or 0.2 μg -K117Q, -K114A/R115A was transfected into 293T cells in 3.5 cm dish. About 24 h later, cells were split equally into three or four dishes as indicated. The next day, cells were treated with 25 μg/ml Chx for indicated time and analyzed with WB. H , 0.4 μg KDM1A-WT or 0.2 μg KDM1A-K114A/K115A were transfected into control or JADE2-KD 293T cells in 3.5 cm dish. About 24 h later, cells were split equally into three dishes as indicated. The next day, cells were then treated with 25 μg/ml Chx for indicated time and analyzed with WB. Chx, cycloheximide; JADE2, Jade family PHD finger 2; K117, lysine 117; KD, knockdown; KDM1A, lysine demethylase 1A; WB, Western blot.

Article Snippet: Coexpression with KDM1A-WT but not inactive mutant decreased FKBP8 methylation ( E ).Consistently, treatment with KDM1A selective inhibitor ORY1001 (TargetMol; catalog no.: T6922) increased FKBP8 methylation ( F ).

Techniques: Immunofluorescence, shRNA, Control, Transfection, Knockdown, Western Blot

Journal: The Journal of Biological Chemistry

Article Title: Lysine demethylase KDM1A promotes cell growth via FKBP8–BCL2 axis in hepatocellular carcinoma

doi: 10.1016/j.jbc.2022.102374

Figure Lengend Snippet: KDM1A–FKBP8–BCL2 axis increases cellular resistance to sorafenib. A , 293T cells were transfected with GST-FKBP8, Myc-SMYD3, Myc-KDM1A, and HA-KAT8. Cells were analyzed with GST-pulldown (PD) and WB. B and C , KDM1A-WT or KDM1A–K117R was rescue expressed in HLF KDM1A-KD cells. Cells were analyzed with WB ( B ). In ( C ), cells were treated with 5 μM sorafenib for 80 h. Cell proliferation was measured with CCK-8. Fold of cell proliferation was normalized to that of control cells. Error bars denote standard deviation of six biological replicates. p Value was calculated with one-way ANOVA followed by pair-wise comparison as indicated. D , WB analysis for sorafenib-resistant HLF cell. E , KDM1A was knocked down in sorafenib-resistant HLF cells. Cells were treated with 5 μM sorafenib for 4 days. Cell proliferation was measured with CCK-8. Fold of cell proliferation was normalized to that of control. Error bars denote standard deviation of six biological replicates. p Value was calculated with one-way ANOVA followed by pair-wise comparison as indicated. F , primary HCC cell culture 1 was treated with 10 μM GSK2879552 (GSK) or 10 μM ORY1001 (ORY) for 5 days. Cells were analyzed with WB. G , primary HCC cell culture 1 was infected with lentivirus expressing KAT8-shRNA. After selection with puromycin for 5 days, cell lysates were analyzed with WB. H , primary HCC cell culture 1 was treated with 5 μM sorafenib and/or 10 μM ORY1001. Cell proliferation was measured with CCK-8. Fold of cell proliferation was normalized to that of control. Error bars denote standard deviation of six biological replicates. p Value was calculated with one-way ANOVA followed by pair-wise comparison as indicated. BCL2, B-cell lymphoma-2; CCK-8, Cell Counting Kit-8; FKBP8, FKBP prolyl isomerase 8; GST, glutathione- S -transferase; HA, hemagglutinin; HCC, hepatocellular carcinoma; KAT8, lysine acetyltransferase 8; KDM1A, lysine demethylase 1A; SMYD3, SET and MYND domain–containing 3; WB, Western blot.

Article Snippet: Coexpression with KDM1A-WT but not inactive mutant decreased FKBP8 methylation ( E ).Consistently, treatment with KDM1A selective inhibitor ORY1001 (TargetMol; catalog no.: T6922) increased FKBP8 methylation ( F ).

Techniques: Transfection, CCK-8 Assay, Control, Standard Deviation, Comparison, Cell Culture, Infection, Expressing, shRNA, Selection, Cell Counting, Western Blot