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

Article Title: A Preclinical Study Combining the DNA Repair Inhibitor Dbait with Radiotherapy for the Treatment of Melanoma 1

doi: 10.1016/j.neo.2014.08.008

Figure Lengend Snippet: Effect of Dbait on H2AX phosphorylation. (A) SK28 and 501mel melanoma cells were transfected with an inactive control oligonucleotide or Dbait ± NU7026 (DNA-PK inhibitor). Immunofluorescence of γ-H2AX (red) and chromatin (DAPI; blue) was visualized. Dbait treatment led to non-localized pan-nuclear H2AX phosphorylation evidencing Dbait activity. This activity was dependent on DNA-PK activation. Bar, 50 μm. (B) SK28 melanoma cells were transfected with an inactive control oligonucleotide or Dbait. Immunofluorescence of γ-H2AX (red) and chromatin (DAPI; blue) was visualized immediately after irradiation and/or Dbait treatment. Irradiation alone resulted in localized γ-H2AX foci representing radio-induced DNA DSBs; Dbait treatment with or without irradiation led to non-localized pan-nuclear H2AX phosphorylation evidencing Dbait activity. Bar, 30 μm. (C) SK28 cells were transduced with lentiviruses that express either control, non-targeting shRNA, or shRNA targeting DNA-PKcs. After Dbait transfection, cells were immunostained with mouse monoclonal anti–DNA-PKcs or anti–γ-H2AX. Dbait activity was not detected in cells transduced with shRNA targeting DNA-PKcs. Bar, 50 μm.

Article Snippet: Subconfluent SK28 cells were transduced with lentiviruses that expressed either the control, non-targeting shRNA (shCTL; sc-108080; Santa Cruz Biotechnology, (Dallas, Texas, USA)), or shRNA targeting DNA-PKcs (shDNA-PK; sc-35200-V; Santa Cruz Biotechnology) at a multiplicity of infection of 3 using polybrene (5 μg/ml).

Techniques: Phospho-proteomics, Transfection, Control, Immunofluorescence, Activity Assay, Activation Assay, Irradiation, Transduction, shRNA

Journal: Journal of Translational Medicine

Article Title: CCDC137 knockdown suppresses bladder cancer progression by downregulating SCD

doi: 10.1186/s12967-025-07033-w

Figure Lengend Snippet: Exploration of potential downstream mechanism and upstream regulators of CCDC137. A Heatmap shows DEGs identified by RNA sequencing in T24-shCtrl and T24-shCCDC137-1 cells. B Bar plot displays GO and KEGG functional enrichment results of downregulated DEGs from RNA sequencing. C GSVA-Hallmark pathway enrichment analysis displayed differences between CCDC137 positive (CCDC137 +) and CCDC137 negative (CCDC137 −) cells based on single-cell sequencing data. D mRNA and protein expression of stearoyl-CoA desaturase (SCD) were detected by qRT-PCR and Western blot. E DecoupleR was used to analyze differences in transcription factor activity between CCDC137 + and CCDC137 − epithelial cells in single-cell sequencing data. F TF-Target Finder was employed to identify potential upstream transcription factors of CCDC137. * P < 0.05; ** P < 0.01; *** P < 0.001; **** P < 0.0001; ns, no statistical significance

Article Snippet: The shCCDC137 lentiviral particles and corresponding control lentiviral particles (shCtrl) were purchased from Genechem Co., Ltd (Shanghai, China).

Techniques: RNA Sequencing, Functional Assay, Sequencing, Expressing, Quantitative RT-PCR, Western Blot, Activity Assay

Journal: Journal of Translational Medicine

Article Title: CCDC137 knockdown suppresses bladder cancer progression by downregulating SCD

doi: 10.1186/s12967-025-07033-w

Figure Lengend Snippet: In vivo validation of CCDC137 regulating tumor growth. A Subcutaneous xenograft models were established in nude mice to validate the regulatory role of CCDC137 in tumor growth. B Tumor volume growth curves were plotted over 28 days after tumor cell inoculation. C Tumor weights of T24-shCtrl and T24-shCCDC137-1 groups were measured on day 28. D The Graphical Abstract described the key results in this study. * P < 0.05; ** P < 0.01; *** P < 0.001; **** P < 0.0001; ns, no statistical significance

Article Snippet: The shCCDC137 lentiviral particles and corresponding control lentiviral particles (shCtrl) were purchased from Genechem Co., Ltd (Shanghai, China).

Techniques: In Vivo, Biomarker Discovery

Journal: bioRxiv

Article Title: DECR1 is an androgen-repressed survival factor that regulates PUFA oxidation to protect prostate tumor cells from ferroptosis

doi: 10.1101/865626

Figure Lengend Snippet: (A) Schematic of DECR1 function in fatty acid (FA) β-oxidation. In order to translocate FAs into the mitochondria, CPT1 converts long-chain acyl-CoA species to their corresponding long-chain acylcarnitine species. This is followed by a dehydrogenation step mediated by acyl CoA dehydrogenase (ACAD) to generate trans-2-enoyl-CoA, the only intermediate that can be processed by downstream enzymes in the β-oxidation process. Many FAs have unsaturated bonds either on an odd-numbered carbon or in the cis-configuration, resulting in the generation of enoyl-CoA intermediates that cannot be directly processed via the downstream β-oxidation enzymes. These FAs require the activity of 3 auxiliary enzymes, ECI1, ECH1 and DECR1 in order to form trans-2-enoyl-CoA before undergoing β-oxidation. DECR1 catalyzes the conversion of either 2-trans,4-cis-dienoyl or 2-trans,4-trans-dienoyl-CoA to 3-trans-enoyl-CoA. A complete cycle of β-oxidation results in the release of the first two carbon units as acetyl-CoA, and a fatty-acyl-CoA minus two carbons. The acetyl-CoA enters the TCA cycle to produce energy (ATP). The shortened fatty-acyl-CoA is processed again starting with the ACADs to form trans-2-enoyl-CoA either directly or with the aid of the auxiliary enzymes depending on the presence of double bonds. This process continues until all carbons in the fatty acid chain are turned into acetyl-CoA. (B) DECR1 protein expression after 72 hours or 96 hours siRNA transfection. Densitometry quantification of relative DECR1 protein expression was normalized to the HSP90 internal control. (C) Linoleic acid level in LNCaP cells quantified in following 96 hours DECR1 knockdown using GC QQQ targeted metabolomics. (D) Relative quantities of the C10:2 acylcarnitine species in LNCaP cell conditioned medium (left) or cell lysates (right) (n=3). (E) Quantification of ATP levels in LNCaP cell lysates. LNCaP cells were transfected with DECR1 siRNAs for 48 hours and then starved in no-glucose medium and treated with the lipolysis inhibitor DEUP (100µM) in the presence (BSA-LA) or absence (BSA) of the PUFA linoleic acid for 48 hours before measuring ATP levels. ( F) Oxygen consumption rate (OCR) was assessed in LNCaP cells supplemented with the PUFA linoleic acid (LA) or (G) the saturated fatty acid palmitic acid (PA). Each data point represents an OCR measurement. ATP production, maximal mitochondrial respiration and mitochondrial spare capacity were assessed. (H) Extracellular acidification rate (ECAR) was assessed in LNCaP cells. Each data point represents an ECAR measurement. For experiments (F-H) LNCaP cells were transfected with DECR1 siRNAs for 72 hours, then starved in substrate limited medium for 24 hours; the assay was run in FAO assay medium. (I & J) Metabolites were quantified in LNCaP cells following 96 hours DECR1 knockdown using GC QQQ targeted metabolomics. Data in bar graphs are represented as the mean ± s.e.m (n=3). Statistical analysis was performed using two-tailed Student’s t -test: * p <0.05, ** p <0.01 and **** p <0.0001.

Article Snippet: LNCaP cells were transduced with the universal negative control shRNA lentiviral particles (shControl), DECR1 shRNA lentiviral particles (shDECR1) or hDECR1 (GFP-Puro) designed by GenTarget Inc. (San Diego, CA, USA) according to the manufacturer’s protocol.

Techniques: Activity Assay, Expressing, Transfection, Control, Knockdown, Two Tailed Test

Journal: bioRxiv

Article Title: DECR1 is an androgen-repressed survival factor that regulates PUFA oxidation to protect prostate tumor cells from ferroptosis

doi: 10.1101/865626

Figure Lengend Snippet: (A) Cell viability after DECR1 knockdown in non-malignant PNT1 prostate cells; hormone-responsive PCa cell lines (LNCaP and VCaP); castrate-resistant V16D and 22RV1 cell lines and enzalutamide-resistant MR94F cells cultured in full serum media. (B) Cell viability of stable DECR1-overexpressed LNCaP cells cultured in full serum media. Cell viability and cell death were measured using trypan blue exclusion following 96 hours DECR1 knockdown. Percentages are represented relative to the control siRNA; n = 3 independent experiments per cell line. (C) Clonogenic cell survival of LNCaP cells were assessed using colony formation assay. Stable DECR1-overexpressed cells or (D) stable DECR1 knockdown was achieved using two different short hairpin (sh) vectors and DECR1 expression was confirmed using western blot. Cells were cultured for 2 weeks, washed with PBS, fixed with paraformaldehyde and stained with 1% crystal violet for 30 minutes. Colonies with more than 50 cells were counted manually; data shown is representative of n = 2 independent experiments. (E) LNCaP and 22RV1 cell growth in 3D spheres. Spheroids were prepared using the hang drop assay following 48 hours DECR1 knockdown. Spheroid volumes were determined after five days of culturing the cells in 20 µl drops; at least 25 spheres per cell line were assessed using the ReViSP software, n = 3 independent experiments per cell line. (F) LNCaP, 22RV1 and MR49F cell migration and (G) 22RV1 cell invasion were assessed using transwell migration/invasion assay. Cells were transfected with DECR1 siRNA or control siRNA for 48 hours. Equal number of cells were transferred to the upper inserts in serum free medium; lower chambers were filled with medium containing 5% serum as a chemoattractant. Plates were incubated for a further 48 hours. Migrated/invaded cells on the lower face of the inserts were washed with PBS, fixed with paraformaldehyde, stained with 1% crystal violet for 30 minutes, and counted manually; data shown is representative of n = 3 independent experiments. (H) Violin plots of mKi67 and DECR1 mRNA expression in LNCaP tumors (n = 5 mice, shControl; n = 4 mice, shDECR1). (I) Representative KI67 IHC staining of LNCaP tumors. Scale bar, 100µm. Data in bar graphs are represented as the mean ± s.e.m. Statistical analysis was performed using one-way ANOVA, followed by Dunnett’s multiple comparisons test: * p <0.05, ** p <0.01, *** p <0.001 and **** p <0.0001.

Article Snippet: LNCaP cells were transduced with the universal negative control shRNA lentiviral particles (shControl), DECR1 shRNA lentiviral particles (shDECR1) or hDECR1 (GFP-Puro) designed by GenTarget Inc. (San Diego, CA, USA) according to the manufacturer’s protocol.

Techniques: Knockdown, Cell Culture, Control, Colony Assay, Expressing, Western Blot, Staining, Software, Migration, Invasion Assay, Transfection, Incubation, Immunohistochemistry

Journal: Cell Proliferation

Article Title: Linc RNA ‐p21 suppresses development of human prostate cancer through inhibition of PKM 2

doi: 10.1111/cpr.12395

Figure Lengend Snippet: Depletion of pyruvate kinase M2 (PKM2) reduces the tumorigenic capacity of cells with lowly expressed lincRNA‐p21. (A) LincRNA‐p21‐silenced LNCaP cells expressing shPKM2 or shCtrl were implanted into nude mice (n = 8) and tumours developed. The time point of 0 day represented 3 weeks after LNCaP cells injection. (B) LincRNA‐p21‐silenced DU145 cells expressing shPKM2 or shCtrl were implanted into nude mice (n = 8) and tumours developed. Immunoblotting was preformed to examine PKM2 expression (left). Tumour initiation were recorded (middle) and survival was analysed (right)

Article Snippet: ShlincRNA‐p21, shPKM2 and control shRNA (shCtrl) lentivirus particles were obtained from GenePharma.

Techniques: Expressing, Injection, Western Blot

Journal: Cell Proliferation

Article Title: Linc RNA ‐p21 suppresses development of human prostate cancer through inhibition of PKM 2

doi: 10.1111/cpr.12395

Figure Lengend Snippet: LincRNA‐p21 down‐regulates pyruvate kinase M2 (PKM2) to suppress aerobic glycolysis. (A) Relative glucose consumption, pyruvate concentration and lactate production were quantified in lincRNA‐p21 knockdown or control DU145 or LNCaP cells. (B) Relative glucose consumption, pyruvate concentration and lactate production were quantified in lincRNA‐p21‐silenced DU145 and LNCaP cells expressing shPKM2 or shCtrl. (C) DU145 cells with lowly expressed lincRNA‐p21 were treated with or without rapamycin, and then glucose consumption, pyruvate concentration and lactate production were examined. *P< .05; **P< .01; ***P< .001

Article Snippet: ShlincRNA‐p21, shPKM2 and control shRNA (shCtrl) lentivirus particles were obtained from GenePharma.

Techniques: Concentration Assay, Knockdown, Control, Expressing

Journal: Cell Proliferation

Article Title: Linc RNA ‐p21 suppresses development of human prostate cancer through inhibition of PKM 2

doi: 10.1111/cpr.12395

Figure Lengend Snippet: Pyruvate kinase M2 (PKM2) is critical for lincRNA‐p21 suppression of cell proliferation and colony formation of prostate cancer cells. (A) LincRNA‐p21‐silenced DU145 cells expressing shPKM2 or shCtrl were subjected to cell viability analysis at indicated time. (B and C) Cells described in (A) were subjected to colony formation assay. Representative images of cell colonies (B) and relative colony number were calculated (C). (D) LincRNA‐p21‐silenced LNCaP cells expressing shPKM2 or shCtrl were subjected to cell viability analysis at indicated time. (E and F) Cells described in (D) were subjected to colony formation assay. Representative images of cell colonies (E) and relative colony number were calculated (F). (G and H) DU145 cells with lowly expressed lincRNA‐p21 were treated with or without rapamycin (G) or 3‐Brpa (H) at different dosages for 48 hours, and cell viability was examined using CCK8 kit. *P< .05; **P< .01; ***P< .001

Article Snippet: ShlincRNA‐p21, shPKM2 and control shRNA (shCtrl) lentivirus particles were obtained from GenePharma.

Techniques: Expressing, Colony Assay

Journal: Molecular Metabolism

Article Title: Inhibition of mitochondrial fission and iNOS in the dorsal vagal complex protects from overeating and weight gain

doi: 10.1016/j.molmet.2020.101123

Figure Lengend Snippet: Knockdown of iNOS in the DVC protects from developing HFD-dependent insulin resistance and decreases body weight and food intake. ( A ) Experimental design and feeding study protocol. ( B ) Western blot analysis of the iNOS knockdown in the DVC. iNOS levels of n = 8 for shControl and n = 8 shiNOS are shown in the bar graph. A representative Western blot image is shown at the bottom. ( C ) Representative confocal image of iNOS labelling in animals expressing ShRNA for iNOS or the shControl in the NTS of the DVC. Bar = 20 μm ( D ) NO levels in the DVC of RC-fed rats compared with HFD-fed rats expressing the control virus and HFD-fed rats expressing shiNOS. Data are shown as mean ± SEM, with each single point highlighted of n = 9 RC rats and n = 6 HFD-fed rats expressing either shControl or shiNOS. ( E ) Acute feeding study: total food intake at 4 h, comparing animals treated with insulin or a vehicle in the DVC. Data are shown as mean ± SEM, with each single point highlighted of n = 10 rats for control vehicle, n = 7 for control insulin, n = 11 for shiNOS vehicle, n = 7 for shiNOS insulin. ( F ) Chronic cumulative food intake, from day 1 (see schematic in A). ( G ) Chronic data showing body weight increase from day 1. ( H ) White adipose tissue: epididymal, retroperitoneal, and visceral fat collected on the day of sacrifice. Data are shown as mean ± SEM, with each single point highlighted. Data from F to H are representative of n = 10 for shControl and n = 8 for shiNOS. ( I ) Western blot analysis of p-PERK levels in the DVC of animals expressing either ShiNOS or ShControl of n = 8 rats per group. A representative western blot image is shown at the bottom. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, ∗∗∗∗p < 0.0001.

Article Snippet: On day 0, a lentiviral system was used to deliver ShRNA to knockdown of iNOS (shiNOS) or a control scramble ShRNA (shControl; Santa Cruz Biotechnology, sc-29417-V and sc-108080, respectively), or on day 1, an adenoviral system was used to deliver either a constitutively active form of Drp1 (Drp1-S637A), a catalytically inactive form of Drp1 (Drp1-K38A), or a control of GFP expressed under CMV [ ] or GFAP promoters.

Techniques: Knockdown, Western Blot, Expressing, shRNA, Control, Virus

Journal: International journal of molecular sciences

Article Title: CD74 Promotes a Pro-Inflammatory Tumor Microenvironment by Inducing S100A8 and S100A9 Secretion in Pancreatic Cancer.

doi: 10.3390/ijms241612993

Figure Lengend Snippet: Figure 5. Reduced CD74 expression leads to reduced tumor growth and inflammatory conditions in orthotopic mouse models. (A) BALB/C nude mice were orthotopically injected with Capan-1 cells (3 × 106 cells). After two months, lentivirus particles carrying shControl or shCD74 were injected (2 × 106 particles). (B) Representative image of mice injected with control and shCD74 lentiviral particles, and image of tumors from the mice. The tumor weight was measured in grams. (C) Expressions of CD74, S100A8/A9, HIF-1α, and TRAF6, IL-6 in mice injected with control and shCD74 lentivirus were measured via RT-qPCR. (D) Representative images of immunofluorescence (IF) staining analyses of CD74-S100A8 and CD74-S100A9 double-stained tumors. (E) Representative images of IF staining analyses of HIF-1α, TNF-α, IL-6, and p-NFκB. * p < 0.05, ** p < 0.01, *** p < 0.0001. Scale bar = 20 µm.

Article Snippet: After eight weeks, the mice were divided into two groups of six and were injected with 2 × 106 shControl or shCD74-expressing lentiviral particles (OriGene, Rockville, MD, USA).

Techniques: Expressing, Injection, Control, Quantitative RT-PCR, Staining

Journal: Aging (Albany NY)

Article Title: GRSF1 suppresses cell senescence

doi: 10.18632/aging.101516

Figure Lengend Snippet: GRSF1 knockout or silencing elevates DNA damage, reduces DNA replication, and delays cell cycle progression. ( A ) Mitochondrial superoxide was assessed by fluorescent microscopy in shRNA-transfected WI-38 fibroblasts expressing normal (shCTRL) or reduced (shGRSF1) levels of GRSF1. The mitochondrial superoxide probe MitoSOX Red was employed to measure the relative production of superoxide, which was quantified as the average (avg.) fluorescence intensity ( left ); representative fluorescence images of the oxidized MitoSOX fluorescence signal (red) are shown ( right ). GRSF1 levels in infected WI-38 cells were assessed by Western blot analysis ( left ). ( B ) DNA double-strand breaks (DSBs) were monitored by measuring the phosphorylated histone H2A.X on serine 139 (γH2A.X) by using flow cytometry-based analysis at 4 and 8 days (D4 and D8) after IR (10 Gy). ( C ) WI-38 fibroblasts were infected with lentiviruses expressing shGRSF1 or shGRSF1; following ionizing irradiation (10 Gy) DNA damage was assessed by immunofluorescence to visualize 53BP1 foci ( right ); foci were counted in WI-38 fibroblasts expressing shCTRL or shGRSF1 that had been left untreated (-IR) or had been exposed to IR (+IR) ( Left ). ( D ) WI-38 fibroblasts that expressed constitutively shGRSF1 or shCTRL were synchronized at G1/S phase by double-thymidine block, released, and collected for analysis of cell cycle progression at the indicated time points by flow cytometry; the progression of cells through the division cycle was quantified (G2/M, G1/S). ( E ) WI-38 fibroblasts were infected with shGRSF1 or shCTRL lentiviruses and expanded for three weeks; the incorporation of [ 3 H]-thymidine was then quantified as a measure of cell proliferation. Data in ( B , C , E ) represent the means and S.D. from three independent experiments.

Article Snippet: To generate THP-1 cells expressing constitutively lower levels of GRSF1, cells were transduced with lentiviral particles expressing shGRSF1 or shCTRL (Origene) one week later they were treated with puromycin (0.5 μg/mL) to select for cells stably expressing integrated vectors.

Techniques: Knock-Out, Microscopy, shRNA, Transfection, Expressing, Fluorescence, Infection, Western Blot, Flow Cytometry, Irradiation, Immunofluorescence, Blocking Assay

Journal: Aging (Albany NY)

Article Title: GRSF1 suppresses cell senescence

doi: 10.18632/aging.101516

Figure Lengend Snippet: Silencing GRSF1 promotes senescence and IL6 production. ( A ) Three weeks after silencing GRSF1 by infection with shGRSF1- or shCTRL-expressing lentiviruses, SA-β-gal activity was assessed by light microscopy ( left ) and secreted IL6 was quantified by ELISA ( right ). (B) Pre-senescent WI-38 fibroblasts were transfected with siGRSF1 or siCTRL; SA-β-gal activity (micrographs) was assessed at day 8 (D8) and D15 after transfection. At D8, GRSF1 and GAPDH levels in WCL were assessed by Western blot analysis ( right ). (C,D) WI-38 cells transfected with siGRSF1 or siCTRL were irradiated (IR, 10 Gy) and subsequently cultured for 10 days; whereupon SA-β-gal activity was assessed ( C ); proteins in WCL prepared at D5 and D18 were assessed by Western blot analysis ( D , left ). RNA was extracted at D7 and D20, and IL6 mRNA levels were quantified by RT-qPCR analysis ( D , right ). ( E ) After transfection with siGRSF1 or siCTRL and irradiation, WI-38 cells were cultured in normal medium for 14 days and in serum-free condition for 24 h ( left ). CM was then collected, and the secreted IL6 was assayed by AlphaLISA ( right ). Data in ( D , E ) represent the means ±S.D. from three independent experiments.

Article Snippet: To generate THP-1 cells expressing constitutively lower levels of GRSF1, cells were transduced with lentiviral particles expressing shGRSF1 or shCTRL (Origene) one week later they were treated with puromycin (0.5 μg/mL) to select for cells stably expressing integrated vectors.

Techniques: Infection, Expressing, Activity Assay, Light Microscopy, Enzyme-linked Immunosorbent Assay, Transfection, Western Blot, Irradiation, Cell Culture, Quantitative RT-PCR

Journal: Aging (Albany NY)

Article Title: GRSF1 suppresses cell senescence

doi: 10.18632/aging.101516

Figure Lengend Snippet: Loss of GRSF1 increases the paracrine actions of IL6. ( A ) THP-1 monocytes expressing lentiviral shGRSF1 or shCTRL were maintained in normal culture medium (containing 10% FBS), and the amount of IL6 secreted into the CM was measured by ELISA. ( B ) Human monocyte THP-1 cells were infected with shGRSF1 or shCTRL lentiviruses to produce different steady-state levels of GRSF1 constitutively. The levels of IL6 secretion by these cells was measured by ELISA; treatments with LPS (50 ng/mL) for 24, 48, and 72 h were included as positive controls for IL6 production. ( C - E ) Schematic of the co-culture setup. Proliferating (PDL20-25) or senescent (PDL55-60) WI-38 fibroblasts were plated in the lower chamber, and THP-1 cells constitutively expressing different levels of GRSF1, as explained in ( A ), were plated in the upper chamber. The chambers were separated by a selectively permeable membrane with 0.4 µm-diameter pores ( C ). Lentiviral shRNA-expressing THP-1 cells were co-cultured with either proliferating or senescent WI-38 fibroblasts for 48 h, and the levels of IL6 mRNA in THP-1 cells ( D ) and WI-38 cells ( E ) were quantified by RT-qPCR analysis. Data in A , D , E represent the means ±S.D. from three independent experiments. ( F ) Model: we propose that loss of GRSF1 contributes to cellular senescence characterized by oxidative stress, DNA damage, growth suppression, and IL6 production.

Article Snippet: To generate THP-1 cells expressing constitutively lower levels of GRSF1, cells were transduced with lentiviral particles expressing shGRSF1 or shCTRL (Origene) one week later they were treated with puromycin (0.5 μg/mL) to select for cells stably expressing integrated vectors.

Techniques: Expressing, Enzyme-linked Immunosorbent Assay, Infection, Co-Culture Assay, Membrane, shRNA, Cell Culture, Quantitative RT-PCR