Journal: bioRxiv

Article Title: PCSK9 Exhibits Novel Nuclear Localization in LSEC and Its Targeting with Bioinspired Nanoparticles Reduces Colorectal Liver Metastasis

doi: 10.64898/2026.05.26.727886

Figure Lengend Snippet: A) LSEC cell culture activation with differentiated metastatic colorectal tumor cells and colorectal CSC conditioned media. B) Immunofluorescent staining of PCSK9 (red), tubulin (green) and DAPI (blue) in human LSEC cell cultures in basal conditions and activation with differentiated metastatic colorectal tumor cells SW620 and colorectal CSC-like from SW620 conditioned media. C) DAPI (blue), CD31(green) and PCSK9 (red) staining on liver tissue samples from colorectal cancer patients with liver metastases. The areas highlighted in the images in the upper row are shown enlarged in the lower row.

Article Snippet: The human metastatic colorectal adenocarcinoma cell line SW620 and the murine metastatic colorectal adenocarcinoma cell line CT26 were acquired from the American Type Culture Collection (ATCC).

Techniques: Cell Culture, Activation Assay, Staining

Journal: Nature Communications

Article Title: DKC1 promotes colorectal cancer progression and therapy resistance by dysregulating sphingolipid biosynthesis

doi: 10.1038/s41467-026-72800-2

Figure Lengend Snippet: a DAVID analysis showing deregulated biological processes in DKC1 knockdown vs control SW620 cells; bars represent -log 10 ( P -value) and frequency polygon represents the number of genes. Pathways with FDR ≤ 0.05 are highlighted in red. b Cell proliferation using shSCRM, sh DKC1 −2, and sh DKC1 −3 SW620 cells at indicated time points. c Representative images for foci formation assay using the same cells as in ( b ). Scale bar represents 1 mm (top). The bar plot depicts the data quantification (bottom). d Representative images for tumor sphere formation assay using the same cells as in ( b ); Scale bar represents 400μm. e Expression of cancer stemness markers using tumorspheres same as in ( d ). f Expression of genes involved in G2/M phase of the cell cycle using the same cells as in ( b ). g Immunoblot showing relative expression of apoptosis markers using the same cells as in ( b ). h Mean tumor volume for the same cells as in ( b ), xenografted in NOD/SCID mice ( N = 6). i Same as ( h ), except the representative image of tumors (top) and bar graph depicting percentage reduction in tumor volume (bottom). j Immunostaining for DKC1 and Ki67 using CRC tumors excised from xenografted mice (scale bar = 50 μm) (left) and box plots depicting data quantification blindly done from 5 random histological fields (right). k Same as ( h ), except doxycycline-inducible cells xenografted in athymic nude mice ( N = 5). l Same as ( i ), except for doxycycline-inducible cells. m Same as ( j ), except for doxycycline-inducible cells. Quantification was blindly done from 15 and 10 random histological fields for DKC1 and Ki67, respectively. For panels, ( a ) Fisher exact test was used; ( b , h and k ) Two-way ANOVA, Dunnett’s multiple comparisons test was used; ( c – f , i , j , and l ) Unpaired Student’s two-tailed t test was used. m One-way ANOVA, Tukey’s multiple comparisons was used. For panels, ( j , m ) data presented as box-and-whisker plots indicating median (middle line), 25th and 75th percentile (box), minimum and maximum values (whiskers). Data shown in the panels ( 2b – g ) are from one representative experiment out of three independent replicates with similar results, each experiment includes 3 biological replicates per group ( n = 3, except 2 d , where the mean area of spheres is calculated for n = 33). Data expressed as mean ± SEM. Figure 2k was created in BioRender. KUNDU, S. (2026) https://BioRender.com/ydueu0j . Source data are provided as a Source Data file.

Article Snippet: Colo320HSR cells were maintained in RPMI1640 media, whereas WiDr and SW620 cells were maintained in MEM and Leibovitz’s L-15 medium, respectively, supplemented with 10% FBS and 0.5% Penicillin/Streptomycin and grown in culture conditions as per ATCC recommendations.

Techniques: Knockdown, Control, Tube Formation Assay, Expressing, Western Blot, Immunostaining, Two Tailed Test, Whisker Assay

Journal: Nature Communications

Article Title: DKC1 promotes colorectal cancer progression and therapy resistance by dysregulating sphingolipid biosynthesis

doi: 10.1038/s41467-026-72800-2

Figure Lengend Snippet: a Heatmap depicting DKC1 expression in CRC patients across CMS categories and its association with WNT target genes; data derived and reanalyzed from TCGA-COADREAD. The color bar indicates z-score values. b Relative expression of DKC1 in CRC patient samples ( N = 76) categorized based on CMS classification; data retrieved from the Clinical Proteomic Tumor Analysis Consortium (CPTAC). c Box and whiskers plot showing Dkc1 expression in murine colon tissue ( n = 3) based on Apc alteration status ( GSE65461 ) across different time points of Apc floxing. d Bar plot showing DKC1 transcript upon siRNA-mediated silencing of CTNNB1 (β-catenin) in SW620, WiDr, and Colo320HSR cell lines. e Same as in ( d ), except protein expression. CD44 was used as a positive control. f Immunoblots showing subcellular DKC1 expression upon WNT signaling stimulation across three independent CRC patient-derived organoids (PDOs). Lamin A was immunoblotted separately as a nuclear loading control, and α-tubulin was used as a cytosolic loading control, respectively. p-β-Catenin (Ser675) was used as a positive control for assessing active WNT signaling. g Schema depicting the chromosomal location of β-Catenin Binding Motif (CBM 1 to 4) at the DKC1 promoter (top). ChIP-qPCR data showing enrichment of β-catenin on DKC1 promoter using SW620 cells ( P < 0.0001); LGR5 and ANKARD5 were used as positive controls, and CD70 was used as a negative control (bottom). h Schema representing the proposed canonical WNT signaling-driven DKC1 oncogenicity and the positive feedback loop. For panels, ( b ) One-way ANOVA, Dunnett’s multiple comparisons test was used; c One-way ANOVA, Sidak’s multiple comparisons test was used; ( d , g ) Unpaired Student’s two-tailed t test was applied. For panels, ( b , c ), data are presented as box-and-whisker plots indicating median (middle line), 25th and 75th percentile (box) and minimum and maximum values (whiskers). Data shown in the panels ( 3d–g ) are from one representative experiment out of three independent replicates with similar results, each experiment includes 3 biological replicates per group. Data expressed as mean ± SEM. Figure 3h was created in BioRender. KUNDU, S. (2026) https://BioRender.com/h9o2vi8 . Source data are provided as a Source Data file.

Article Snippet: Colo320HSR cells were maintained in RPMI1640 media, whereas WiDr and SW620 cells were maintained in MEM and Leibovitz’s L-15 medium, respectively, supplemented with 10% FBS and 0.5% Penicillin/Streptomycin and grown in culture conditions as per ATCC recommendations.

Techniques: Expressing, Derivative Assay, Positive Control, Western Blot, Control, Binding Assay, ChIP-qPCR, Negative Control, Two Tailed Test, Whisker Assay

Journal: Nature Communications

Article Title: DKC1 promotes colorectal cancer progression and therapy resistance by dysregulating sphingolipid biosynthesis

doi: 10.1038/s41467-026-72800-2

Figure Lengend Snippet: a Gene Set Enrichment Analysis (GSEA) for lipid metabolic process using RNA-seq data of DKC1 knockdown and control SW620 cells. b Volcano plot depicting various lipid species showing more than or less than 1.5-fold up or down-regulated levels upon DKC1 knockdown in SW620 cells (lipid species with FDR ≤ 0.05 have been highlighted; dashed horizontal line represents P-value of 0.05). c Variable importance of projection (VIP) score plot shows important features (VIP score > 1.7), for the same as in ( b ). d Same as in ( b ), except for tumor tissues of DKC1 -high (P1, P6, P7, P8, and P9) and DKC1 -low (P2, P3, P4, P5) CRC patient specimens (lipid species with FDR ≤ 0.05 have been highlighted; dashed horizontal line represents P-value of 0.05). e Variable importance of projection (VIP) score plot shows important features (VIP score > 1.5); C23 and C24 Ceramide species were upregulated in DKC1 -high tumors (marked in red). f Lipid ontology network (LION) analysis using DKC1- high and DKC1 -low CRC specimens; significantly upregulated sphingolipids and ceramides related ontologies, and downregulated sphingomyelin related ontologies are highlighted. g Concentration of Cer(d18:1/24:0) and Cer(d18:2/23:0) using DKC1-high ( n = 5) and -low ( n = 4) tumor specimens and receiver operating characteristic (ROC) curve applying univariate analysis. h Immunoblot depicting DKC1 expression in chemoresistant CRC patients’ tumors (T100 – T104) and the corresponding adjacent normal (N100 – N104). β-actin was used as a loading control (top). Box plot representing C24 Ceramide levels in the serum of CRC patients and healthy volunteers (bottom). For panels, ( b , d ) Unpaired two-sample Student’s t test and Benjamini-Hochberg (BH) procedure for FDR correction was used; ( g , h ) Unpaired Student’s two-tailed t test was applied. For panel h, data are presented as box-and-whisker plots indicating median (middle line), 25th and 75th percentile (box) and minimum and maximum values (whiskers). Data shown in the panel 4 h is from one representative experiment out of three independent replicates with similar results; each experiment includes 3 biological replicates per group. Data expressed as mean ± SEM. Source data are provided as a Source Data file.

Article Snippet: Colo320HSR cells were maintained in RPMI1640 media, whereas WiDr and SW620 cells were maintained in MEM and Leibovitz’s L-15 medium, respectively, supplemented with 10% FBS and 0.5% Penicillin/Streptomycin and grown in culture conditions as per ATCC recommendations.

Techniques: RNA Sequencing, Knockdown, Control, Concentration Assay, Western Blot, Expressing, Two Tailed Test, Whisker Assay

Journal: Nature Communications

Article Title: DKC1 promotes colorectal cancer progression and therapy resistance by dysregulating sphingolipid biosynthesis

doi: 10.1038/s41467-026-72800-2

Figure Lengend Snippet: a Heatmap depicting DKC1 and SGPP2 levels in Indian CRC specimens ( N = 49). b Immunohistochemical staining of DKC1 and SGPP2 in CRC specimens ( N = 75); scale bar is 100 μm (whole section), and inset 40 μm (inset). c Contingency analysis for the same as in ( b ). d Bar plot showing quantification of DKC1 and SGPP2, as in ( b ). e Immunofluorescence staining for SGPP2 in tumor ( N = 6) and adjacent normal ( N = 5) tissues of Indian CRC patients. Scale bar represents 5 μm. f Same as ( e ), except bar plot depicting quantification. g Transcript (bottom) and protein (top) levels of SGPP2 upon DKC1 knockdown in SW620 cells. h Immunoprecipitation for DKC1 showing interaction with SOX2 using SW620 cells. i ChIP-PCR data for SOX2 binding on SGPP2 promoter using shSCRM and sh DKC1 SW620 cells. j Relative cell proliferation using SGPP2 knockdown SW620 cells at the indicated time points. k Same as ( j ), except representative images for foci formation assay (top) and data quantification (bottom). Scale bar represents 0.5 mm. l Same as ( j ), except using stable isogenic SW620 cells; control shSCRM and sh DKC1 stably transfected with vector backbone (EV), and sh DKC1 with ectopic expression of SGPP2 . m Same as ( k ), except using cells as in ( l ). n Bar plot showing S1P levels using same cells as in ( i ). o Transcript expression of CD44 using the same cells as in ( j ). p Same as ( o ), except CTNNB1 expression in the same cells as in ( l ). q Same as ( o ), except using DKC1 -silenced; SGPP2- rescued SW620 cells versus control. r Same as ( p ), except immunoblot for protein levels in nuclear and cytoplasmic fractionations. Lamin A was immunoblotted separately as a nuclear loading control. For panels, ( c ) Two-tailed Fisher’s exact test for contingency analysis was used; ( d ) Two-sided Chi square test for comparison of frequencies was used for both panels; ( f ) Paired two-tailed t test was used; ( g , i , m , n , and q ) Unpaired Student’s two-tailed t test was used; ( j , l ) Two-way ANOVA, Dunnett’s multiple comparisons test was used; ( k , o , and p ) One-way ANOVA, Dunnett’s multiple comparisons test was used. Data shown in the panels ( 5a , f – r ) are from one representative experiment out of three independent replicates with similar results; each experiment includes 3 biological replicates per group. Data expressed as mean ± SEM. Source data are provided as a Source Data file.

Article Snippet: Colo320HSR cells were maintained in RPMI1640 media, whereas WiDr and SW620 cells were maintained in MEM and Leibovitz’s L-15 medium, respectively, supplemented with 10% FBS and 0.5% Penicillin/Streptomycin and grown in culture conditions as per ATCC recommendations.

Techniques: Immunohistochemical staining, Staining, Immunofluorescence, Knockdown, Immunoprecipitation, Binding Assay, Tube Formation Assay, Control, Stable Transfection, Transfection, Plasmid Preparation, Expressing, Western Blot, Two Tailed Test, Comparison