Journal: International Journal of Hematology-Oncology and Stem Cell Research

Article Title: Thalidomide is more efficient than sodium butyrate in enhancing GATA-1 and EKLF gene expression in erythroid progenitors derived from HSCs with β-globin gene mutation

doi:

Figure Lengend Snippet: EKLF gene expression during erythroid differentiation in the presence of drugs. On the 6th day of differentiation, cells were divided into four different groups. The studied groups were as follows: non-treated cells at day 6 as baseline control group; group treated with 100 μM thalidomide; sodium butyrate 100 μM; and 0.1% dimethylsolfoxide (DMSO) at days 9 and 12 of erythroid differentiation. Results are expressed with relative to non-treated control group/ as Mean ± SD (n = 3).* p<0.05 vs. control group.

Article Snippet: Drugs and Erythroid Growth factors In the present study, recombinant human erythropoietin (rhEPO, R&D systems, Minneapolis, MN, USA), interleukin–3 (IL-3, Stem Cell Technologies and Vancouver, BC, Canada), thalidomide (Tocris Bioscience, Missouri, USA) and sodium butyrate (Sigma, Saint Louis, MO, USA) were used in order to induce gene expression and erythroid differentiation.

Techniques: Gene Expression, Control

Journal: bioRxiv

Article Title: A Cryptic Interfacial Pocket Uncovered in Full CRL4 CRBN –IKZF3 Ubiquitylation Complex Enhances IMiD Efficacy

doi: 10.1101/2025.06.08.658527

Figure Lengend Snippet: ( A ) Diagram comparing the formation and geometry of the native transthiolation intermediate for IMiD-induced IKZF3 ubiquitylation and its more stable mimic. The mimic was generated through the Michael addition reaction between the activity-based probe (ABP) and the UbcH5a catalytic cysteine. ( B ) Synthetic scheme of the IKZF3–Ub ABP. The IKZF3 ZF2–ZF3 K166C was conjugated to the C-terminal G75 of the donor Ub through a BmDPA handle. ( C ) Electrospray ionization-mass spectrometry (ESI-MS) spectra and deconvoluted MS spectra of Ub–BmDPA with the calculated (Calc.) and observed (Obs.) molecular weight shown. ( D ) SDS–PAGE analysis of the size-exclusion chromatography (SEC)-purified nucleophilic substitution reaction between Ub–BmDPA and IKZF3 ZF2–ZF3 K166C construct. Pooled fractions containing IKZF3–Ub ABP for structural study are indicated by the red rectangle. ( E ) SDS–PAGE analysis of chemically-trapped ubiquitylation assembly formation in the presence of eight individual IMiD molecules. Fractions pooled for cryo-EM analysis were indicated by colored rectangles. ( F ) Size-exclusion chromatograms of ubiquitylation assemblies containing eight individual IMiD molecules. The complex containing pomalidomide or mezigdomide was purified by a Superdex 200 Increase (SD200I) column (Cytiva, GE Healthcare). The complex containing thalidomide, lenalidomide, iberdomide, golcadomide, cemsidomide, or avadomide was purified by a Superose 6 Increase (SP6I) column (Cytiva, GE Healthcare).

Article Snippet: Thalidomide (Cat# S1193), avadomide (CC-122, Cat# S7892), iberdomide (CC-220, Cat# S8760), mezigdomide (CC-92480, Cat# S8975), golcadomide (CC-99282, Cat# E1212), and cemsidomide (CFT7455, Cat# E1184) were purchased from Selleck.

Techniques: Generated, Activity Assay, Mass Spectrometry, Molecular Weight, SDS Page, Size-exclusion Chromatography, Purification, Construct, Cryo-EM Sample Prep

Journal: bioRxiv

Article Title: A Cryptic Interfacial Pocket Uncovered in Full CRL4 CRBN –IKZF3 Ubiquitylation Complex Enhances IMiD Efficacy

doi: 10.1101/2025.06.08.658527

Figure Lengend Snippet: ( A ) The thalidomide complex. ( B ) The lenalidomide complex. ( C ) The pomalidomide complex. ( D ) The avadomide complex. ( E ) The iberdomide complex. ( F ) The mezigdomide complex. ( G ) The golcadomide complex. ( H ) The cemsidomide complex.

Article Snippet: Thalidomide (Cat# S1193), avadomide (CC-122, Cat# S7892), iberdomide (CC-220, Cat# S8760), mezigdomide (CC-92480, Cat# S8975), golcadomide (CC-99282, Cat# E1212), and cemsidomide (CFT7455, Cat# E1184) were purchased from Selleck.

Techniques:

Journal: bioRxiv

Article Title: A Cryptic Interfacial Pocket Uncovered in Full CRL4 CRBN –IKZF3 Ubiquitylation Complex Enhances IMiD Efficacy

doi: 10.1101/2025.06.08.658527

Figure Lengend Snippet: ( A ) Substrate binding region in which eight individual IMiD molecules bind to the CRBN TBD pocket and IKZF3 ZF2 degron. ( B ) Representative interfaces within the ubiquitylation assembly. The structures of complexes containing thalidomide or mezigdomide are exhibited as examples.

Article Snippet: Thalidomide (Cat# S1193), avadomide (CC-122, Cat# S7892), iberdomide (CC-220, Cat# S8760), mezigdomide (CC-92480, Cat# S8975), golcadomide (CC-99282, Cat# E1212), and cemsidomide (CFT7455, Cat# E1184) were purchased from Selleck.

Techniques: Binding Assay

Journal: Developmental dynamics : an official publication of the American Association of Anatomists

Article Title: Misregulation of gene expression in the redox-sensitive NF-kappab-dependent limb outgrowth pathway by thalidomide.

doi: 10.1002/dvdy.10150

Figure Lengend Snippet: Fig. 1. Mercury orange (HgO) -stained rat (gestation day [GD] 13) and rabbit (GD 12) limbs treated with 300 and 70 mg thalidomide/kg per day, respectively. Black arrows denote the region of the progress zone (PZ); and white arrows denote the area of the apical ectodermal ridge (AER). Rat thalidomide-treated limb buds did not show any relevant decrease in HgO staining compared with control rat limb buds, suggest- ing little or no oxidative stress. In thalidomide-treated rabbit limb buds, there is a clear decrease in HgO fluorescence in the PZ but not the overlying AER compared with control rabbit limb buds, indicating a de- pletion of PZ glutathione and regional oxidative stress.

Article Snippet: Thalidomide was purchased from Toronto Research Chemicals (Toronto, Ontario, Canada).

Techniques: Staining, Control

Journal: Developmental dynamics : an official publication of the American Association of Anatomists

Article Title: Misregulation of gene expression in the redox-sensitive NF-kappab-dependent limb outgrowth pathway by thalidomide.

doi: 10.1002/dvdy.10150

Figure Lengend Snippet: Fig. 2. pNF-B-d2EGFP–transfected rat and rabbit limb bud cells show a decrease in GFP fluorescence with thalidomide treatment but are rescued by redox modulating agents, N-acetylcysteine (NAC) and -phe- nyl-N-t-butylnitrone (PBN). Diamide, an oxidant and known inhibitor NF- B/DNA binding, acted as a positive control. Data are represented as percentage of control GFP expression: hatched bars denote transfected rat limb bud cells, and open bars denote transfected rabbit limb bud cells. Asterisks (*) denote a statistically significant (0.05) difference from control GFP expression. Crosses (†) represent a statistically significant (0.05) difference between transfected cells treated with thalidomide (THAL) and thalidomide NAC or PBN. TPA, tetradecanoylphorbol acetate.

Article Snippet: Thalidomide was purchased from Toronto Research Chemicals (Toronto, Ontario, Canada).

Techniques: Transfection, Binding Assay, Positive Control, Control, Expressing

Journal: Developmental dynamics : an official publication of the American Association of Anatomists

Article Title: Misregulation of gene expression in the redox-sensitive NF-kappab-dependent limb outgrowth pathway by thalidomide.

doi: 10.1002/dvdy.10150

Figure Lengend Snippet: Fig. 3. In situ hybridization of control and thalidomide-treated rat embryos for Fgf-10, Twist, and Fgf-8 expression in the gestation day (GD) 11.5 rat limb bud. Thalidomide treatment had no effect on the expression of Fgf-10, Twist, and Fgf-8 compared with control. Arrows denote the limb and regions where Fgf-10, Twist, and Fgf-8 expression normally occurs.

Article Snippet: Thalidomide was purchased from Toronto Research Chemicals (Toronto, Ontario, Canada).

Techniques: In Situ Hybridization, Control, Expressing

Journal: Developmental dynamics : an official publication of the American Association of Anatomists

Article Title: Misregulation of gene expression in the redox-sensitive NF-kappab-dependent limb outgrowth pathway by thalidomide.

doi: 10.1002/dvdy.10150

Figure Lengend Snippet: Fig. 4. In situ hybridization of control and thalidomide-treated rat embryos for Fgf-10, Twist, and Fgf-8 expression in the gestation day (GD) 13 rat limb bud. Thalidomide treatment had no effect on the expres- sion of Fgf-10, Twist, and Fgf-8 compared with control. Arrows denote regions where Twist expression normally occurs.

Article Snippet: Thalidomide was purchased from Toronto Research Chemicals (Toronto, Ontario, Canada).

Techniques: In Situ Hybridization, Control, Expressing

Journal: Developmental dynamics : an official publication of the American Association of Anatomists

Article Title: Misregulation of gene expression in the redox-sensitive NF-kappab-dependent limb outgrowth pathway by thalidomide.

doi: 10.1002/dvdy.10150

Figure Lengend Snippet: Fig. 5. In situ hybridization of control, thalidomide-treated, and tha- lidomide -phenyl-N-t-butylnitrone (PBN) rabbit embryos for Fgf-10 expression in the gestation day (GD) 10–12 rabbit limb bud. Thalidomide greatly reduced the expression of Fgf-10 at each stage of limb develop- ment. However, gene expression was not affected in embryos that re- ceived both thalidomide and the free radical trapping agent, PBN. Loss of normal limb morphology is evident in GD 12 embryos treated with tha- lidomide where the outer most portion of the limb is not uniformly devel- oped. Arrows denote regions where Fgf-10 expression normally occurs.

Article Snippet: Thalidomide was purchased from Toronto Research Chemicals (Toronto, Ontario, Canada).

Techniques: In Situ Hybridization, Control, Expressing, Gene Expression

Journal: Developmental dynamics : an official publication of the American Association of Anatomists

Article Title: Misregulation of gene expression in the redox-sensitive NF-kappab-dependent limb outgrowth pathway by thalidomide.

doi: 10.1002/dvdy.10150

Figure Lengend Snippet: Fig. 6. In situ hybridization of control, thalidomide-treated, and - phenyl-N-t-butylnitrone (PBN) rabbit embryos for Twist expression in the gestation day (GD) 10–12 rabbit limb bud. Thalidomide greatly reduced the expression of Twist at each stage of limb development. However, gene expression was not affected in embryos that received both thalid- omide and PBN. Loss of normal limb morphology is evident in GD 12 embryos treated with thalidomide where limb bud paddles have failed to develop normally and Twist expression is absent. Arrows denote regions where Twist expression normally occurs.

Article Snippet: Thalidomide was purchased from Toronto Research Chemicals (Toronto, Ontario, Canada).

Techniques: In Situ Hybridization, Control, Expressing, Gene Expression

Journal: Developmental dynamics : an official publication of the American Association of Anatomists

Article Title: Misregulation of gene expression in the redox-sensitive NF-kappab-dependent limb outgrowth pathway by thalidomide.

doi: 10.1002/dvdy.10150

Figure Lengend Snippet: Fig. 7. In situ hybridization of control, thalidomide-treated, and - phenyl-N-t-butylnitrone (PBN) rabbit embryos for Fgf-8 expression in the gestation day (GD) 10–12 rabbit limb bud. Thalidomide greatly reduced the expression of Fgf-8 at each stage of limb development. However, gene expression was not affected in embryos that received both thalid- omide and PBN. Loss of Fgf-8 expression is most notable in the region of the zone of polarizing activity. Arrows denote regions where Fgf-8 ex- pression normally occurs.

Article Snippet: Thalidomide was purchased from Toronto Research Chemicals (Toronto, Ontario, Canada).

Techniques: In Situ Hybridization, Control, Expressing, Gene Expression, Activity Assay

Journal: Frontiers in Physiology

Article Title: MicroRNA-18a-5p regulates hepatic lipid accumulation in response to high-fat diet

doi: 10.3389/fphys.2025.1661428

Figure Lengend Snippet: HFD affects miR-18a-5p expression and activates the UPR ER pathway in the liver of rats. (A) qRT-PCR analysis of miR-18a-5p in serum and liver samples of N and HFD rats (B) qRT-PCR analysis of Srebp1c, Perk and Eif2α in liver samples of N and HFD rats (C) WB images and densitometry of SREBP1c, nSREBP1c, P-PERK (Thr980), P-eiF2α(Ser51) and ATF4 in liver samples of N and HFD rats. Histograms show the results of densiometric analysis of immunoblots. The protein level was normalized to that of B-ACTIN and/or to the total forms for phosphorylated proteins. Representative blots are shown. N: rats receiving a standard diet for 5 weeks; HFD: rats fed on a high-fat diet for 5 weeks. Values are the means ± SEM of six different rats (n = 6). Values with different symbols are significantly different: *P < 0.05 vs. N.

Article Snippet: Membranes were probed with the following antibodies: SREBP1c (1:1,000 dilution, Santa Cruz Biotechnology, sc-366, RRID:AB_2194229), p-PERK(Thr980) (1:1,000 dilution, Cell Signaling, Cat# 3179, RRID:AB_2095853), PERK (1:1,000 dilution, Cell Signaling, Cat# 3192, RRID:AB_2095847), p-eIF2α(Ser51) (1:1,000 dilution, Cell Signaling, Cat# 3398, RRID:AB_2096481), eiF2α (1:1,000 dilution, Cell Signaling, Cat#2103, RRID:AB_836874), ATF4 (1:1,000 dilution, Abclonal, Cat. A18687, RRID:AB_2862422), LC3B (1:1,000 dilution, Santa Cruz Biotechnology, sc-376404, RRID:AB_11150489), ATG5 (1:1,000 dilution, Novus Biologicals, NB110-53818, RRID:AB_828587), ATG16L1 (1:1,000 dilution, Novus Biologicals, NB110-82384, RRID:AB_1144849), ATG9A (1:1,000 dilution, Novus Biologicals, NB110-56893, RRID:AB_837629), Beclin-1 (1:1,000 dilution, Cell Signaling, Cat#3738, RRID:AB_490837), p62 (1:1,000 dilution, Cell Signaling, Cat#5114, RRID:AB_10624872), Caspase-3 (1:1,000 dilution, Cell Signaling, Cat#9662, RRID:AB_331439), Bcl-2 (1:1,000 dilution, Santa Cruz Biotechnology, sc-7382, RRID:AB_626736), B-ACTIN (1:1,000 dilution, Bioss Antibodies, bs-0061R, RRID:AB_10855480).

Techniques: Expressing, Quantitative RT-PCR, Western Blot

Journal: Frontiers in Physiology

Article Title: MicroRNA-18a-5p regulates hepatic lipid accumulation in response to high-fat diet

doi: 10.3389/fphys.2025.1661428

Figure Lengend Snippet: FAs mixture affects miR-18a-5p expression and activates the UPR ER pathway in HepG2 cells. (A) ORO staining of TG accumulation in HepG2 cells treated with or without FAs. Original magnification: 40x. Scale bar = 100 μm (B) Oil Red O quantification in HepG2 cells treated with or without FAs (C) MTT assay to measure cell viability in HepG2 cells treated with or without FAs (D) qRT-PCR analysis of miR-18a-5p in cell culture medium and HepG2 cells treated with or without FAs (E) WB images and densitometry of SREBP1c, P-PERK (Thr980) and P-eiF2α (Ser51) in HepG2 cells treated with or without FAs. Histograms show the results of densiometric analysis of immunoblots. The protein level was normalized to that of B-ACTIN and/or to the total forms for phosphorylated proteins. Representative blots are shown. Ctrl: HepG2 cells treated with 1% BSA-free fatty acids for 24 h; FAs: HepG2 cells treated with oleate and palmitate (1.5 mM final concentration, 2:1 M ratio) for 24 h. Values are the means ± SEM of three independent experiments (n = 3). Values with different symbols are significantly different: *p < 0.05 vs. Ctrl.

Article Snippet: Membranes were probed with the following antibodies: SREBP1c (1:1,000 dilution, Santa Cruz Biotechnology, sc-366, RRID:AB_2194229), p-PERK(Thr980) (1:1,000 dilution, Cell Signaling, Cat# 3179, RRID:AB_2095853), PERK (1:1,000 dilution, Cell Signaling, Cat# 3192, RRID:AB_2095847), p-eIF2α(Ser51) (1:1,000 dilution, Cell Signaling, Cat# 3398, RRID:AB_2096481), eiF2α (1:1,000 dilution, Cell Signaling, Cat#2103, RRID:AB_836874), ATF4 (1:1,000 dilution, Abclonal, Cat. A18687, RRID:AB_2862422), LC3B (1:1,000 dilution, Santa Cruz Biotechnology, sc-376404, RRID:AB_11150489), ATG5 (1:1,000 dilution, Novus Biologicals, NB110-53818, RRID:AB_828587), ATG16L1 (1:1,000 dilution, Novus Biologicals, NB110-82384, RRID:AB_1144849), ATG9A (1:1,000 dilution, Novus Biologicals, NB110-56893, RRID:AB_837629), Beclin-1 (1:1,000 dilution, Cell Signaling, Cat#3738, RRID:AB_490837), p62 (1:1,000 dilution, Cell Signaling, Cat#5114, RRID:AB_10624872), Caspase-3 (1:1,000 dilution, Cell Signaling, Cat#9662, RRID:AB_331439), Bcl-2 (1:1,000 dilution, Santa Cruz Biotechnology, sc-7382, RRID:AB_626736), B-ACTIN (1:1,000 dilution, Bioss Antibodies, bs-0061R, RRID:AB_10855480).

Techniques: Expressing, Staining, MTT Assay, Quantitative RT-PCR, Cell Culture, Western Blot, Concentration Assay

Journal: Frontiers in Physiology

Article Title: MicroRNA-18a-5p regulates hepatic lipid accumulation in response to high-fat diet

doi: 10.3389/fphys.2025.1661428

Figure Lengend Snippet: miR-18a-5p Overexpression reduces fat accumulation and ER Stress in HepG2 cells. (A) ORO staining of triglycerides accumulation in HepG2 cells transfected with or without miR-18a-5p. Original magnification: 40x. Scale bar = 100 μm (B) ORO quantification in HepG2 cells transfected with or without miR-18a-5p (C) qRT-PCR analysis of Srebp1c, Perk, and Eif2α in HepG2 cells transfected with or without miR-18a-5p (D) WB images and densitometry of SREBP1c, P-PERK (Thr980), and P-eiF2α (Ser51) in HepG2 cells transfected with or without miR-18a-5p. Histograms show the results of densiometric analysis of immunoblots. The protein level was normalized to that of B-ACTIN and/or to the total forms for phosphorylated proteins. Representative blots are shown. Crtl: HepG2 cells treated with 1% BSA-free fatty acids for 24 h; Ctrl + miRNA NC: HepG2 cells transfected with miRNA mimic Negative Control for 36 h; Ctrl + miR-18a-5p: HepG2 cells transfected with miR-18a-5p for 36 h; FAs: HepG2 cells treated with oleate and palmitate (1.5 mM final concentration, 2:1 M ratio) for 24 h; FAs+ miRNA NC: HepG2 cells transfected with miRNA mimic Negative Control for 36 h; FAs + miR-18a-5p: HepG2 cells transfected with miR-18a-5p for 36 h and subsequently treated with oleate and palmitate (1.5 mM final concentration, 2:1 M ratio) for 24 h. Values are the means ± SEM of three independent experiments (n = 3). Values with different symbols are significantly different: *P < 0.05 vs. Crtl; $P < 0.05 vs. FAs and Ctrl + miR-18a-5p.

Article Snippet: Membranes were probed with the following antibodies: SREBP1c (1:1,000 dilution, Santa Cruz Biotechnology, sc-366, RRID:AB_2194229), p-PERK(Thr980) (1:1,000 dilution, Cell Signaling, Cat# 3179, RRID:AB_2095853), PERK (1:1,000 dilution, Cell Signaling, Cat# 3192, RRID:AB_2095847), p-eIF2α(Ser51) (1:1,000 dilution, Cell Signaling, Cat# 3398, RRID:AB_2096481), eiF2α (1:1,000 dilution, Cell Signaling, Cat#2103, RRID:AB_836874), ATF4 (1:1,000 dilution, Abclonal, Cat. A18687, RRID:AB_2862422), LC3B (1:1,000 dilution, Santa Cruz Biotechnology, sc-376404, RRID:AB_11150489), ATG5 (1:1,000 dilution, Novus Biologicals, NB110-53818, RRID:AB_828587), ATG16L1 (1:1,000 dilution, Novus Biologicals, NB110-82384, RRID:AB_1144849), ATG9A (1:1,000 dilution, Novus Biologicals, NB110-56893, RRID:AB_837629), Beclin-1 (1:1,000 dilution, Cell Signaling, Cat#3738, RRID:AB_490837), p62 (1:1,000 dilution, Cell Signaling, Cat#5114, RRID:AB_10624872), Caspase-3 (1:1,000 dilution, Cell Signaling, Cat#9662, RRID:AB_331439), Bcl-2 (1:1,000 dilution, Santa Cruz Biotechnology, sc-7382, RRID:AB_626736), B-ACTIN (1:1,000 dilution, Bioss Antibodies, bs-0061R, RRID:AB_10855480).

Techniques: Over Expression, Staining, Transfection, Quantitative RT-PCR, Western Blot, Negative Control, Concentration Assay