Journal: bioRxiv

Article Title: Chromosomal instability and chromosome 17p loss drive convergent NDE1 synthetic lethality in metastatic cancer cells

doi: 10.64898/2026.02.10.704921

Figure Lengend Snippet: (A) IC50 curves of parental and metastatic cell line pairs treated with Nutlin, measured via cell titer glo, normalized internally to DMSO controls. (B) Clonogenic growth assays comparing sensitivity to NDE1 knockout in PC9 and RPE-hTERT cells after depletion of TP53 . (C) Violin plot of NDE1 gene effect across cell lines in DepMap, segmented by TP53 mutation status. (D) Western blot showing relative knockdown of NDEL1 across 4 selected shRNA constructs and an empty vector (EV) control. Numbers below the NDEL1 blot are relative protein quantifications normalized to EV control, as assessed by blot signal intensity in ImageJ. (E) Clonogenic growth assays measuring sensitivity to NDE1 knockout in PC9 cells after NDEL1 knockdown with 4 separate shRNAs from (D). (F) Clonogenic growth assays measuring sensitivity to NDE1 knockout in PC9 cells after PAFAH1B1 / LIS1 knockdown with 4 separate shRNAs. (G) Cell counting assay measuring rescue of NDE1 dependence in HT-29 cells after overexpression of NDEL1 and LIS1 .

Article Snippet: The NDEL1 and LIS1 open reading frames were separately shuttled from pcDNA3 Ndel1 (Addgene #12571) and pcDNA3 Lis1 (Addgene #12574) into N174-MCS (Addgene ##81061) using PCR amplification, restriction digest, and subsequent ligation.

Techniques: Knock-Out, Mutagenesis, Western Blot, Knockdown, shRNA, Construct, Plasmid Preparation, Control, Cell Counting, Over Expression

Journal: bioRxiv

Article Title: Chromosomal instability and chromosome 17p loss drive convergent NDE1 synthetic lethality in metastatic cancer cells

doi: 10.64898/2026.02.10.704921

Figure Lengend Snippet: (A) IC50 curves of parental and metastatic cell line pairs treated with Nutlin, measured via cell titer glo, normalized internally to DMSO controls. (B) Clonogenic growth assays comparing sensitivity to NDE1 knockout in PC9 and RPE-hTERT cells after depletion of TP53 . (C) Violin plot of NDE1 gene effect across cell lines in DepMap, segmented by TP53 mutation status. (D) Western blot showing relative knockdown of NDEL1 across 4 selected shRNA constructs and an empty vector (EV) control. Numbers below the NDEL1 blot are relative protein quantifications normalized to EV control, as assessed by blot signal intensity in ImageJ. (E) Clonogenic growth assays measuring sensitivity to NDE1 knockout in PC9 cells after NDEL1 knockdown with 4 separate shRNAs from (D). (F) Clonogenic growth assays measuring sensitivity to NDE1 knockout in PC9 cells after PAFAH1B1 / LIS1 knockdown with 4 separate shRNAs. (G) Cell counting assay measuring rescue of NDE1 dependence in HT-29 cells after overexpression of NDEL1 and LIS1 .

Article Snippet: The NDEL1 and LIS1 open reading frames were separately shuttled from pcDNA3 Ndel1 (Addgene #12571) and pcDNA3 Lis1 (Addgene #12574) into N174-MCS (Addgene ##81061) using PCR amplification, restriction digest, and subsequent ligation.

Techniques: Knock-Out, Mutagenesis, Western Blot, Knockdown, shRNA, Construct, Plasmid Preparation, Control, Cell Counting, Over Expression

Journal: NPJ Biofilms and Microbiomes

Article Title: TSP50 deficiency in neural stem cells aggravates colitis in mice by altering intestinal microbiome

doi: 10.1038/s41522-025-00737-3

Figure Lengend Snippet: a Scheme of FMT and AKK replantation protocol. b Body weight loss after DSS treatment ( n = 6). c , d The DAI scores and survival rates after DSS treatment ( n = 6). e Colon lengths and quantification after DSS treatment ( n = 6). f Representative HE staining and histopathological scores of colon tissues after DSS treatment ( n = 6). Scale bar: 50 μm. g ELISA analysis of serum TNF-α levels after DSS treatment ( n = 4). h ELISA analysis of serum IL-6 levels after DSS treatment ( TSP50 fl/fl , n = 3; TSP50 fl/fl Nestin Cre , n = 3; FMT- TSP50 fl/fl Nestin Cre , n = 4; AKK- TSP50 fl/fl Nestin Cre , n = 4). Values were expressed as means ± SEM. Two‑way ANOVA was used to analyze ( b , c ), one‑way ANOVA was used to analyze ( e , f , g , h ). ns (no significance), * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001.

Article Snippet: The sections were incubated with primary antibody: anti-MUC2 (1:1000; ab272692, Abcam, Cambridge, United Kingdom), anti- TSP50 (1:500; 12574-1-AP, Proteintech, Wuhan, China), anti- AChE (1:20; ab2803, Abcam), anti- NESTIN (1:200; 19483-1-AP, Proteintech) and corresponding secondary antibody.

Techniques: Staining, Enzyme-linked Immunosorbent Assay

Journal: NPJ Biofilms and Microbiomes

Article Title: TSP50 deficiency in neural stem cells aggravates colitis in mice by altering intestinal microbiome

doi: 10.1038/s41522-025-00737-3

Figure Lengend Snippet: a ELISA analysis of ACh levels in the colon after ACh supplementation ( TSP50 fl/fl , n = 6; TSP50 fl/fl Nestin Cre , n = 6; ACh- TSP50 fl/fl , n = 8; ACh- TSP50 fl/fl Nestin Cre , n = 8). b PCoA analysis of fecal microbiota using weighted UniFrac distances of beta diversity after ACh supplementation. c Histogram of phylum-level species composition after ACh supplementation. d Histogram of genus-level species composition after ACh supplementation. e Histogram of species difference comparison for the top 10 abundances at phylum-level ( n = 6). f Histogram of species difference comparison for the top 10 abundances at genus-level ( n = 6). g Heat map of the relative abundance of the dominant genus. h LEfSe analysis of differential microbiota in TSP50 fl/fl mice before and after ACh treatment. i LEfSe analysis of differential microbiota in TSP50 fl/fl Nestin Cre mice before and after ACh treatment. j GC-MS analysis of fecal SCFAs after ACh supplementation ( n = 5). k ELISA analysis of ACh levels in the colon after ABX treatment ( n = 6). l ELISA analysis of ACh levels in the colon after co-housing treatment ( n = 6). m ELISA analysis of ACh levels in the colon after FMT and AKK replantation ( n = 6). Values were expressed as means ± SEM. One‑way ANOVA was used to analyze ( a , j , k , l , m ), Kruskal-Wallis H test was used to analyze ( e , f ). ns (no significance), * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001.

Article Snippet: The sections were incubated with primary antibody: anti-MUC2 (1:1000; ab272692, Abcam, Cambridge, United Kingdom), anti- TSP50 (1:500; 12574-1-AP, Proteintech, Wuhan, China), anti- AChE (1:20; ab2803, Abcam), anti- NESTIN (1:200; 19483-1-AP, Proteintech) and corresponding secondary antibody.

Techniques: Enzyme-linked Immunosorbent Assay, Comparison, Gas Chromatography-Mass Spectrometry

Journal: NPJ Biofilms and Microbiomes

Article Title: TSP50 deficiency in neural stem cells aggravates colitis in mice by altering intestinal microbiome

doi: 10.1038/s41522-025-00737-3

Figure Lengend Snippet: a WB analysis and quantification of AChE protein levels in mouse brain and colon ( n = 3). b Co-IP analysis of proteins interacting with TSP50 in mouse brain and colon. c GST pull-down of AChE by GST-TSP50 using proteins purified in B21 bacteria, followed by WB analysis. d WB analysis and quantification of AChE protein levels in control and TSP50-overexpressing 293T cells after CHX treatment ( n = 4). e WB analysis and quantification of AChE protein levels after incubation with TSP50 protein at 20 mM Tris-HCL (pH7.6) for 1 h at 37 °C ( n = 4). (Ctr: No incubation; 1 h: Incubation for 1 h) f WB analysis and quantification of TSP50 and AChE protein levels in 293T cells with normal and overexpression TSP50 and different TSP50 mutants ( n = 3). g Representative IHC staining of TSP50 and AChE protein expression in CD patient tissues and quantification ( n = 19). Scale bar: 50 μm. h Pearson correlation analysis was performed between the relative levels of TSP50 and AChE protein in samples of CD patients. Values were expressed as means ± SEM. One‑way ANOVA was used to analyze ( a , d , f , g ), unpaired two-tailed Student’s t test was used to analyze ( e ). ns (no significance), * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001.

Article Snippet: The sections were incubated with primary antibody: anti-MUC2 (1:1000; ab272692, Abcam, Cambridge, United Kingdom), anti- TSP50 (1:500; 12574-1-AP, Proteintech, Wuhan, China), anti- AChE (1:20; ab2803, Abcam), anti- NESTIN (1:200; 19483-1-AP, Proteintech) and corresponding secondary antibody.

Techniques: Co-Immunoprecipitation Assay, Purification, Bacteria, Control, Incubation, Over Expression, Immunohistochemistry, Expressing, Two Tailed Test

Journal: NPJ Biofilms and Microbiomes

Article Title: TSP50 deficiency in neural stem cells aggravates colitis in mice by altering intestinal microbiome

doi: 10.1038/s41522-025-00737-3

Figure Lengend Snippet: a Scheme of NMS treatment protocol. b Body weight loss after DSS treatment ( TSP50 fl/fl , n = 8; TSP50 fl/fl Nestin Cre , n = 8; NMS- TSP50 fl/fl , n = 6; NMS- TSP50 fl/fl Nestin Cre , n = 6). c , d The DAI scores and survival rates after DSS treatment ( TSP50 fl/fl , n = 8; TSP50 fl/fl Nestin Cre , n = 8; NMS- TSP50 fl/fl , n = 6; NMS- TSP50 fl/fl Nestin Cre , n = 6). e Colon lengths and quantification after DSS treatment ( TSP50 fl/fl , n = 8; TSP50 fl/fl Nestin Cre , n = 8; NMS- TSP50 fl/fl , n = 6; NMS- TSP50 fl/fl Nestin Cre , n = 6). (T fl/fl : TSP50 fl/fl ; T fl/fl N Cre : TSP50 fl/fl Nestin Cre ; NMS-T fl/fl : NMS- TSP50 fl/fl ; NMS-T fl/fl N Cre : NMS- TSP50 fl/fl Nestin Cre ). f Representative HE staining and histopathological scores of colon tissues after DSS treatment ( n = 6). Scale bar: 50 μm. g ELISA analysis of serum TNF-α levels after DSS treatment ( TSP50 fl/fl , n = 6; TSP50 fl/fl Nestin Cre , n = 6; NMS- TSP50 fl/fl , n = 5; NMS- TSP50 fl/fl Nestin Cre , n = 5). h ELISA analysis of serum IL-6 levels after DSS treatment ( TSP50 fl/fl , n = 8; TSP50 fl/fl Nestin Cre , n = 8; NMS- TSP50 fl/fl , n = 6; NMS- TSP50 fl/fl Nestin Cre , n = 6). Values were expressed as means ± SEM. Two‑way ANOVA was used to analyze ( b , c ), one‑way ANOVA was used to analyze ( e , f , g , h ). ns (no significance), * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001.

Article Snippet: The sections were incubated with primary antibody: anti-MUC2 (1:1000; ab272692, Abcam, Cambridge, United Kingdom), anti- TSP50 (1:500; 12574-1-AP, Proteintech, Wuhan, China), anti- AChE (1:20; ab2803, Abcam), anti- NESTIN (1:200; 19483-1-AP, Proteintech) and corresponding secondary antibody.

Techniques: Staining, Enzyme-linked Immunosorbent Assay