Journal: PLoS ONE

Article Title: Cdx1 and c-Myc Foster the Initiation of Transdifferentiation of the Normal Esophageal Squamous Epithelium toward Barrett's Esophagus

doi: 10.1371/journal.pone.0003534

Figure Lengend Snippet: Affymetrix analysis of the Myc Pathway

Article Snippet: The following Taqman assays (PE Applied Biosystems) used were: TFF1 (Hs00170216_m1), TFF2 (Hs00193719_m1), TFF3 (Hs00173625_m1), Muc2 (Hs00159374_m1), Muc5AC (Hs01365601_m1), Muc13 (Hs00217230_m1), CD164 (Hs00174789_m1), ODC1 (Hs00159739_m1), CA2 (Hs00163869_m1).

Techniques:

Journal: Infection and Immunity

Article Title: Polyamines and hypusination are important for Clostridioides difficile toxin B (TcdB)-mediated activation of group 3 innate lymphocytes (ILC3s)

doi: 10.1128/iai.00236-23

Figure Lengend Snippet: mRNA levels upregulated in MNK-3 cells by TcdB treatment (at least twofold with an adjusted P -value < 0.05)

Article Snippet: Primer–probe sets used were Hprt (IDT, Mm.PT.39a.22214828), Il22 (IDT, Mm.PT.58.44024580.g), Odc1 (ThermoFisher, Mm02019269_g1), and Srm (ThermoFisher, Mm00726089_m1). cDNA was semi-quantitated using the delta C T method with Hprt as an internal control for all samples.

Techniques:

Journal: Infection and Immunity

Article Title: Polyamines and hypusination are important for Clostridioides difficile toxin B (TcdB)-mediated activation of group 3 innate lymphocytes (ILC3s)

doi: 10.1128/iai.00236-23

Figure Lengend Snippet: TcdB upregulates the polyamine biosynthesis pathway in ILC3s. (A) MNK-3 cells were treated with TcdB1 for 4 h or left untreated and analyzed by NanoString nCounter analysis using a mouse metabolism panel with 748 genes and 20 internal reference genes. Shown is a volcano plot with Odc1 and other notable genes marked. mRNA levels were compared between untreated control and TcdB1-activated cells. Genes on the right are upregulated by TcdB1, and those on the left are downregulated by TcdB1. Analysis was performed with n = 4 for each group. (B) MNK-3 cells were treated with TcdB1 or a catalytic mutant (TcdB1 D270N) for 4 h or left untreated (NT). Il22, Odc1, and Srm mRNA levels were semi-quantitated by real-time RT-PCR with normalization to Hprt levels. Each point represents one well; bar indicates mean, n = 6. Data are representative of three independent experiments. (C) MNK-3 cells were treated with TcdB1 for 6 h or left untreated (NT), and cell lysates were analyzed by Western blotting to examine ODC and β-actin levels. Each point represents one well; line indicates mean, n = 4. Data are representative of three independent experiments. **P < 0.01; ***P < 0.001; ****P < 0.0001. Differences that were not significant (P > 0.05) are marked as ns.

Article Snippet: Primer–probe sets used were Hprt (IDT, Mm.PT.39a.22214828), Il22 (IDT, Mm.PT.58.44024580.g), Odc1 (ThermoFisher, Mm02019269_g1), and Srm (ThermoFisher, Mm00726089_m1). cDNA was semi-quantitated using the delta C T method with Hprt as an internal control for all samples.

Techniques: Control, Mutagenesis, Quantitative RT-PCR, Western Blot

Journal: Nature Communications

Article Title: Polyamine metabolism impacts T cell dysfunction in the oral mucosa of people living with HIV

doi: 10.1038/s41467-023-36163-2

Figure Lengend Snippet: HTOC CD4 + T cells were TCR activated and infected with HIV. ARI (Efavirenz; 50 nM), DFMO (ODC-1 inhibitor I; 2.5 mM), POB (ODC-1 inhibitor II; 100 μM), Control shRNA lentiviral particles-A with polybrene (2 μg/ml), and ODC1 shRNA lentiviral particles with polybrene (2 μg/ml) were added as indicated, 36 h post-infection. A Fluorometric polyamine estimation in cell lysates on day 6 post- infection. n = 3 independent experiments; Mean values +/− SD; ** P < 0.003; **** P < 0.0001; Two-tailed; Welch’s t test. B Statistical analysis of EIF5A expression (MFI), and C Statistical analysis of hypusinated EIF5A expression (MFI) from three experiments. Flow cytometric overlays are provided in Supplementary Fig. . D Contour plots showing FOXP3 and CD25 (T regs ) expression in CD4 cells (above) and PD-1 and IFN-γ (T regDys ) in FOXP3 + cells (below). E Contour plots showing ROR-γt and CCR6 expression (Th17) in CD4 cells. Quantification of T reg , T regDys , Th17 ( F ), and T regDys /Th17 ratios ( G ) based on the data from D and E . Data are representative of four ( n = 4) independent experiments and are presented as mean values +/− SEM. **** P < 0.0001; *** P = 0.0001; ** P < 0.005; * P < 0.02; Two-tailed; Unpaired t test in A – C and F – G . Circles within box plots represent each replicate.

Article Snippet: Indicated ODC-1 inhibitors and control and ODC-shRNA lentiviral particles were purchased from Santa Cruz Biotechnology.

Techniques: Infection, Control, shRNA, Two Tailed Test, Expressing

Journal: Neoplasia (New York, N.Y.)

Article Title: High-dose DFMO alters protein translation in neuroblastoma

doi: 10.1016/j.neo.2025.101215

Figure Lengend Snippet: ODC1 and MYCN co-occurring amplification. (A) Neuroblastoma cell lines with distinct genomic profiles are shown: NBLS cells have neither MYCN nor ODC1 amplification, IMR5 has MYCN amplification (and ALK amplification, not shown), and KCN has both MYCN and ODC1 amplification; data represents Log R ratio output from lllumina Bead-Chip SNP arrays. (B) Fluorescence in situ hybridization (FISH) results for a primary neuroblastoma sample using probes for MYCN (2p24.3, red), ODC1 (2p25.1, aqua) and 2p centromere (CEN2, green) showing 4 CEN2 signals and amplification of both MYCN and ODC1 . Images courtesy of CHOP Division of Genomic Diagnostics (DGD).

Article Snippet: Primers: MTTP assay #Hs04877005_cn, ODC1 assay #Hs02651018_cn, and MYCN assay #Hs00201049_cn (Applied Biosystems), chosen for similar amplicon size (80-100 bps) for matched amplification efficiency.

Techniques: Amplification, Fluorescence, In Situ Hybridization

Journal: Neoplasia (New York, N.Y.)

Article Title: High-dose DFMO alters protein translation in neuroblastoma

doi: 10.1016/j.neo.2025.101215

Figure Lengend Snippet: DFMO-mediated translation effects. (A) Phospho-4EBP1 is not altered by DFMO (5 uM) but is reduced by the mTOR1/2 inhibitor, MLN0128 (100 μ M). (B) More sensitive IEF immunoblot confirms incomplete hypusination in most cell lines at higher DFMO exposures. (C) Dose response to DFMO for IMR5 and SK-N-BE2C cells (cells with higher proportion of non-hypusinated eIF5A in (B)). Cell line genomic status: M , MYC amplification; N , MYCN amplification; O , ODC1 amplification.

Article Snippet: Primers: MTTP assay #Hs04877005_cn, ODC1 assay #Hs02651018_cn, and MYCN assay #Hs00201049_cn (Applied Biosystems), chosen for similar amplicon size (80-100 bps) for matched amplification efficiency.

Techniques: Western Blot, Amplification

Journal: Neoplasia (New York, N.Y.)

Article Title: High-dose DFMO alters protein translation in neuroblastoma

doi: 10.1016/j.neo.2025.101215

Figure Lengend Snippet: Puromycin incorporation by DFMO exposure in vitro. Puromycin incorporation was assessed across neuroblastoma cell lines of distinct MYCN and ODC1 gene status, as denoted. Densitometry was used to define relative change from vehicle control lanes; replicates are shown in line graph form with the immunoblots corresponding to the data from the circle-marked line. Cell line genomic status: M , MYC amplification; N , MYCN amplification; O , ODC1 amplification.

Article Snippet: Primers: MTTP assay #Hs04877005_cn, ODC1 assay #Hs02651018_cn, and MYCN assay #Hs00201049_cn (Applied Biosystems), chosen for similar amplicon size (80-100 bps) for matched amplification efficiency.

Techniques: In Vitro, Control, Western Blot, Amplification

Journal: Neoplasia (New York, N.Y.)

Article Title: High-dose DFMO alters protein translation in neuroblastoma

doi: 10.1016/j.neo.2025.101215

Figure Lengend Snippet: Impact of AMXT-1501 and DFMO on puromycin incorporation. Puromycin incorporation was assessed across neuroblastoma cell lines of distinct MYCN and ODC1 gene status, as denoted, treated with both DFMO and AMXT-1501. Densitometry was used to define relative change from vehicle control lanes; replicates are shown in line graphs with the immunoblots corresponding to the data from the cirlce-marked line. Cell line genomic status: M , MYC amplification; N , MYCN amplification; O , ODC1 amplification.

Article Snippet: Primers: MTTP assay #Hs04877005_cn, ODC1 assay #Hs02651018_cn, and MYCN assay #Hs00201049_cn (Applied Biosystems), chosen for similar amplicon size (80-100 bps) for matched amplification efficiency.

Techniques: Control, Western Blot, Amplification

Journal: Neoplasia (New York, N.Y.)

Article Title: High-dose DFMO alters protein translation in neuroblastoma

doi: 10.1016/j.neo.2025.101215

Figure Lengend Snippet: Colony Formation Assay across a range of DFMO exposures. Colony formation was assessed across neuroblastoma cell lines of distinct MYCN and ODC1 gene status, as denoted, treated with DFMO across a range of concentrations. Data represents replicate wells with representative well-images shown above. Cell line genomic status: M , MYC amplification; N , MYCN amplification; O , ODC1 amplification; *= p < 0.05, **= p < 0.01, ***= p < 0.001.

Article Snippet: Primers: MTTP assay #Hs04877005_cn, ODC1 assay #Hs02651018_cn, and MYCN assay #Hs00201049_cn (Applied Biosystems), chosen for similar amplicon size (80-100 bps) for matched amplification efficiency.

Techniques: Colony Assay, Amplification

Journal: Neoplasia (New York, N.Y.)

Article Title: High-dose DFMO alters protein translation in neuroblastoma

doi: 10.1016/j.neo.2025.101215

Figure Lengend Snippet: ODC protein in response to DFMO exposure. (A, B) Treatment with DFMO leads to increased ODC protein levels by immunoblot across cell lines. (C) Dose response of IMR5 and CHLA136 cells to DFMO: ODC is increased at baseline in the ODC1- amplified cell line without significant increase in response to DFMO; shown as immunoblot and by densitometry relative to control lanes. Cell line genomic status: M , MYC amplification; N , MYCN amplification; O , ODC1 amplification.

Article Snippet: Primers: MTTP assay #Hs04877005_cn, ODC1 assay #Hs02651018_cn, and MYCN assay #Hs00201049_cn (Applied Biosystems), chosen for similar amplicon size (80-100 bps) for matched amplification efficiency.

Techniques: Western Blot, Amplification, Control