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chronic myeloid leukemia cell line k562 (ATCC)

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ATCC chronic myeloid leukemia cell line k562
Chronic Myeloid Leukemia Cell Line K562, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 11088 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/chronic+myeloid+leukemia/K-562/pm42888846-174-10-36
Average 99 stars, based on 11088 article reviews

chronic myeloid leukemia cell line k562 - by Bioz Stars, 2026-11

99/100 stars

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In Vitro:

Article Title: Mechanochemical Solvent-Free Synthesis and Biological Profiling of Novel 2-Hydrazone-Bridged Benzothiazoles as Potent Anticancer Agents
Article Snippet: .. In Vitro Antiproliferative Activity Tumor cell lines of human origin: acute myeloid leukemia (HL-60), chronic myeloid leukemia (K-562), non-Hodgkin′s lymphoma (Z-138), pancreatic adenocarcinoma (CAPAN1), colon cancer (HCT-116), human brain glioblastoma (LN-229) and non-small cell lung cancer cells (NCI-H460) were obtained from American Type Culture (ATCC, Manassas, VA, USA), except for the acute lymphoblastic leukemia cell line (DND-41) which was provided by the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ Leibniz-Institut, Germany). ..

Activity Assay:

Article Title: Engineering of biocompatible Zn-MOFs for efficient delivery of curcumin and amplified anticancer potential against Leukemia cells
Article Snippet: Metal-organic frameworks (MOFs) are used as effective drug delivery vehicles owing to their higher structural integrity, low toxicity, biodegradability, and flexible surface functionalities.. Zn-MOFs provide a variety of options for drug delivery systems such as zinc ions act as attachment sites, providing cavities among organic ligands, serving as carriers, and they self-assemble via ligand into adaptable structures.. However, a lack of knowledge of their biocompatibility at the organic and cellular levels limits their widespread use in biomedical applications.

MTT Assay:

Article Title: Development and characterization of palmitoyl-modified arginine containing curcumin-loaded niosomal vesicles for improved antioxidant and anticancer activities
Article Snippet: The objective of this study was to enhance the anticancer potential of curcumin (CR)-loaded niosomal formulation against human myeloid leukemia cell lines and its antioxidant activity by the incorporation of amphiphilic palmitoyl-modified arginine (PL-ARG) serving as a positively charged amphiphile.. PL-ARG was synthesized by using palmitoyl chloride (PL) and l-arginine (ARG) followed by characterization through ESI–MS, 1H-NMR, and FT-IR.. The proportion of niosomal constituents including Tween 80/20 and cholesterol was optimized using experimental design to achieve small size vesicle with enhanced encapsulation of CR, and the optimized proportion was then used for the development of niosomal formulation functionalized with synthesized PL-ARG (PL-ARG-CR-NSMs).

other:

Article Title: Evaluating Bis-Phenacyl Bromide-Based Bis-Heterocyclic Templates as Anticancer Prototypes and Potential PARP1 Inhibitors.
Article Snippet: Poly(ADP-ribose) polymerase 1 (PARP1) plays a pivotal role in DNA damage repair and represents a promising antineoplastic target.. Novel bis-heterocyclic derivatives based on a bis-phenacyl bromide scaffold were synthesized and assessed for their antineoplastic potential against eight malignant cell lines, and PARP1 inhibitory activity.. These derivatives exhibited selective cytotoxicity toward MCF7 and PC-3 cancer cell lines, while showing limited or no toxicity to other malignant cell lines.

Image Search Results

Results from K562/luc (expressing shNEG, Firefly luciferase, and GFP) alone (mono) or mixed with human primary bone marrow mesenchymal stem cells (with hMSC) were subcutaneously injected in mice to form xenografts. (A) Scheme demonstrating the experimental setup; samples were collected 21 days after subcutaneous injection of cells in mice. (B) Weight of xenografts formed by K562/luc mono or a mix with hMSCs in mice (n=5 in each variant), and the two-tailed, nonparametric Mann-Whitney test was used to check the difference significance; the exact significance ( P ) values are presented in the plot. (C-H) Short-read sequencing RNA analysis results of samples from cells isolated from xenografts mono and with hMSC treated for the last 14 days with vehicle (shNEG) by the fluorescence-activated cell sorting (FACS) with BD Aria. (C) Representative scatterplots (n=3) with the gating strategy used for the FACS-sorting of live xenograft cells (negative for Viability dye-eFluor780 staining), expressing GFP (GFP+) and stained positive with the antibody against human CD45 with BV421 fluorophore (hCD45+). (D-G) Results of differential expression analysis of the variant shNEG versus mono by DeSeq2 of RNA sequenced from FACS-sorted cells. Presented are the results from cells isolated from three different xenografts for each variant. (D) Principal component analysis. (E) Number of genes with fold change absolute value ≥ 50% and p-value corrected for multiple testing using the Benjamini-Hochberg P adj. ≤ 0.05, that are upregulated (UP) or downregulated (DOWN) in cells from xenograft (Xgraft) shNEG versus mono. (F) Expression level (counts corrected for the sample sequencing depth) in each xenograft (n=3) of the top 150 genes (each row) with the most significant (P adj. ) fold change in expression level. (G) The top of Gene Ontology Biological Processes (GOBP) terms from the Gene Set Enrichment Analysis (GSEA) of the DeSeq2 results, with the highest positive (left) and negative (right) normalized enrichment score (NES), P adj. ≤ 0.05 (FDR) and number of genes in the sample annotated per term (size) > 20. The running enrichment score is presented by a grey line for each of the ranked genes marked with a vertical black line. (H) The Reactome terms identified by the GSEA of the UP or DOWN genes in the variant shNEG versus mono, with NES ≥ 1.5 (absolute value), p value ≤ 0.05, and size > 30.

Journal: bioRxiv

Article Title: TIAR-dependent coordination of alternative splicing and lipid peroxidation is required for CML cell resistance to imatinib in the bone marrow stroma

doi: 10.64898/2026.05.29.728710

Figure Lengend Snippet: Results from K562/luc (expressing shNEG, Firefly luciferase, and GFP) alone (mono) or mixed with human primary bone marrow mesenchymal stem cells (with hMSC) were subcutaneously injected in mice to form xenografts. (A) Scheme demonstrating the experimental setup; samples were collected 21 days after subcutaneous injection of cells in mice. (B) Weight of xenografts formed by K562/luc mono or a mix with hMSCs in mice (n=5 in each variant), and the two-tailed, nonparametric Mann-Whitney test was used to check the difference significance; the exact significance ( P ) values are presented in the plot. (C-H) Short-read sequencing RNA analysis results of samples from cells isolated from xenografts mono and with hMSC treated for the last 14 days with vehicle (shNEG) by the fluorescence-activated cell sorting (FACS) with BD Aria. (C) Representative scatterplots (n=3) with the gating strategy used for the FACS-sorting of live xenograft cells (negative for Viability dye-eFluor780 staining), expressing GFP (GFP+) and stained positive with the antibody against human CD45 with BV421 fluorophore (hCD45+). (D-G) Results of differential expression analysis of the variant shNEG versus mono by DeSeq2 of RNA sequenced from FACS-sorted cells. Presented are the results from cells isolated from three different xenografts for each variant. (D) Principal component analysis. (E) Number of genes with fold change absolute value ≥ 50% and p-value corrected for multiple testing using the Benjamini-Hochberg P adj. ≤ 0.05, that are upregulated (UP) or downregulated (DOWN) in cells from xenograft (Xgraft) shNEG versus mono. (F) Expression level (counts corrected for the sample sequencing depth) in each xenograft (n=3) of the top 150 genes (each row) with the most significant (P adj. ) fold change in expression level. (G) The top of Gene Ontology Biological Processes (GOBP) terms from the Gene Set Enrichment Analysis (GSEA) of the DeSeq2 results, with the highest positive (left) and negative (right) normalized enrichment score (NES), P adj. ≤ 0.05 (FDR) and number of genes in the sample annotated per term (size) > 20. The running enrichment score is presented by a grey line for each of the ranked genes marked with a vertical black line. (H) The Reactome terms identified by the GSEA of the UP or DOWN genes in the variant shNEG versus mono, with NES ≥ 1.5 (absolute value), p value ≤ 0.05, and size > 30.

Article Snippet: Human chronic myeloid leukemia cell line K562 (#CCL-243) and bone marrow stroma fibroblast cell line HS-5 (#CRL-11882) were obtained from American Type Culture Collection (USA); human chronic myeloid leukemia cell line LAMA-84 (#ACC 168) was from DSMZ.

Techniques: Expressing, Luciferase, Injection, Variant Assay, Two Tailed Test, MANN-WHITNEY, Sequencing, Isolation, Fluorescence, FACS, Staining, Quantitative Proteomics

(A) Scheme explaining experimental steps of xenograft formation by K562/luc (expressing shNEG, Firefly luciferase, and GFP) mixed with human primary bone marrow mesenchymal stem cells (hMSC) subcutaneously injected in mice 7 days before initiation of treatment with IM for the following 14 days, when the GFP and human CD45 positive cells were FACS-sorted from xenografts for RNA isolation and sequencing. (B) Number of intersecting genes (compared groups indicated by black dot) that at the RNA level are upregulated (UP; log2 value of fold change ≥ 0.6) or downregulated (DOWN; log2 value of fold change ≤ -0.6) in shNEG cells xenografts imatinib versus vehicle treated and in CD34 positive cells from bone marrow biopsies of a patient with CML (data deposited at GEO under accession number GSE310243; from ) obtained after 6 months of imatinib therapy (combined samples SRR36072325 and SRR36072321) versus obtained at the diagnosis (combined SRR36072320 and SRR36072324). (B-D) Yellow shadow marks a group of genes that are UP or DOWN upon imatinib treatment in shNEG and CML cells (shNEG&CML), selected for subsequent analysis in (C) and (D). (C) Reactome terms identified by the GSEA analysis of the UP or DOWN genes in shNEG&CML with normalized enrichment score ≥ 1.5 (absolute value), p value ≤ 0.05, and number of genes in the sample annotated per term (size) ≥ 15. (C-D) The Reactome leading-edge genes identified by GSEA, annotated to terms marked with a brown triangle in (C) were selected to compare their expression level in single-cell RNA-seq data in (D) from bone marrow biopsies of healthy donors and CML patients with different responses to imatinib therapy. (D) Analysis of data at the Single-cell atlas of diagnostic Chronic Myeloid Leukemia bone marrow (scdbm) for CD34+ cells subtype . Data and detailed description of patient classification available: http://scdbm.ddnetbio.com ; A – responded to IM within 12 months; B – IM treatment failed within 18 months; C – resistant to IM and other TKI-s.

Journal: bioRxiv

Article Title: TIAR-dependent coordination of alternative splicing and lipid peroxidation is required for CML cell resistance to imatinib in the bone marrow stroma

doi: 10.64898/2026.05.29.728710

Figure Lengend Snippet: (A) Scheme explaining experimental steps of xenograft formation by K562/luc (expressing shNEG, Firefly luciferase, and GFP) mixed with human primary bone marrow mesenchymal stem cells (hMSC) subcutaneously injected in mice 7 days before initiation of treatment with IM for the following 14 days, when the GFP and human CD45 positive cells were FACS-sorted from xenografts for RNA isolation and sequencing. (B) Number of intersecting genes (compared groups indicated by black dot) that at the RNA level are upregulated (UP; log2 value of fold change ≥ 0.6) or downregulated (DOWN; log2 value of fold change ≤ -0.6) in shNEG cells xenografts imatinib versus vehicle treated and in CD34 positive cells from bone marrow biopsies of a patient with CML (data deposited at GEO under accession number GSE310243; from ) obtained after 6 months of imatinib therapy (combined samples SRR36072325 and SRR36072321) versus obtained at the diagnosis (combined SRR36072320 and SRR36072324). (B-D) Yellow shadow marks a group of genes that are UP or DOWN upon imatinib treatment in shNEG and CML cells (shNEG&CML), selected for subsequent analysis in (C) and (D). (C) Reactome terms identified by the GSEA analysis of the UP or DOWN genes in shNEG&CML with normalized enrichment score ≥ 1.5 (absolute value), p value ≤ 0.05, and number of genes in the sample annotated per term (size) ≥ 15. (C-D) The Reactome leading-edge genes identified by GSEA, annotated to terms marked with a brown triangle in (C) were selected to compare their expression level in single-cell RNA-seq data in (D) from bone marrow biopsies of healthy donors and CML patients with different responses to imatinib therapy. (D) Analysis of data at the Single-cell atlas of diagnostic Chronic Myeloid Leukemia bone marrow (scdbm) for CD34+ cells subtype . Data and detailed description of patient classification available: http://scdbm.ddnetbio.com ; A – responded to IM within 12 months; B – IM treatment failed within 18 months; C – resistant to IM and other TKI-s.

Techniques: Expressing, Luciferase, Injection, Isolation, Sequencing, Biomarker Discovery, Single Cell, RNA Sequencing, Diagnostic Assay

(A) Colony formation by K562 cells expressing shRNA non-targeting (shNEG) or targeting mRNA of TIAL1 (shTIAR), TIA1 (shTIA-1), or FMR1 (shFMRP) that were collected from ex vivo hypoxic (1.5% O2) co-culture with HS-5 bone marrow stromal fibroblasts and treated with 1 μM imatinib (IM) or 50nM Talazoparib (BMN) added in two doses following the experimental scheme (left panel). Number of colonies in each of the 3 technical replicates from 3-4 independent biological experiments presented as % change relative to the untreated cells (dashed black line) set as 100 %. Student’s two-tailed t-test was used to compare two samples marked by the black line; #### or **** - p<0.0001, ns - p > 0.05. (B) Scheme explaining the experimental setup based on the subcutaneous implantation in mice of 3D printed scaffolds (photo taken with a Samsung mobile phone camera) seeded with human cells differentiated into osteoblasts and K562/luc cells with shNEG, shTIAR or shTIA-1, followed by IM treatment for 14 days. (C) Bioluminescence signal monitored in mice after 2 weeks of IM or vehicle treatment (timeline explained in (B) ) following luciferin injection, collected in the Burker’s Xtreme In-Vivo chamber for 30 sec, and overlaid on the mouse X-ray image. Scale presents the signal intensity of the color coding. (D) Sum of the signal intensity (P) collected per second (s) and area (mm 2 ) for each mouse analyzed (single dot) is presented. (E) Scheme explaining experimental steps of xenograft formation by K562/luc (expressing shNEG or shTIAR, Firefly luciferase, and GFP) mixed with human primary bone marrow mesenchymal stem cells (hMSC) subcutaneously injected in mice 7 days before initiation of treatment with IM for the following 14 days. (F) Weight of each xenograft isolated from mice (single dot) formed by K562/luc cells with shNEG or shTIAR (as in (E) ) presented as fold change of the weight mean value of xenografts from mice treated with vehicle; mean value indicated with the black line. The nonparametric two-tailed Mann-Whitney test was used for comparisons indicated by black lines underneath the exact significance ( P ) values are presented in the plot. (A,D,F) Two-way Anova was used to compare shTIAR upon IM versus other variants; @ - P < 0.002.

Journal: bioRxiv

Article Title: TIAR-dependent coordination of alternative splicing and lipid peroxidation is required for CML cell resistance to imatinib in the bone marrow stroma

doi: 10.64898/2026.05.29.728710

Figure Lengend Snippet: (A) Colony formation by K562 cells expressing shRNA non-targeting (shNEG) or targeting mRNA of TIAL1 (shTIAR), TIA1 (shTIA-1), or FMR1 (shFMRP) that were collected from ex vivo hypoxic (1.5% O2) co-culture with HS-5 bone marrow stromal fibroblasts and treated with 1 μM imatinib (IM) or 50nM Talazoparib (BMN) added in two doses following the experimental scheme (left panel). Number of colonies in each of the 3 technical replicates from 3-4 independent biological experiments presented as % change relative to the untreated cells (dashed black line) set as 100 %. Student’s two-tailed t-test was used to compare two samples marked by the black line; #### or **** - p<0.0001, ns - p > 0.05. (B) Scheme explaining the experimental setup based on the subcutaneous implantation in mice of 3D printed scaffolds (photo taken with a Samsung mobile phone camera) seeded with human cells differentiated into osteoblasts and K562/luc cells with shNEG, shTIAR or shTIA-1, followed by IM treatment for 14 days. (C) Bioluminescence signal monitored in mice after 2 weeks of IM or vehicle treatment (timeline explained in (B) ) following luciferin injection, collected in the Burker’s Xtreme In-Vivo chamber for 30 sec, and overlaid on the mouse X-ray image. Scale presents the signal intensity of the color coding. (D) Sum of the signal intensity (P) collected per second (s) and area (mm 2 ) for each mouse analyzed (single dot) is presented. (E) Scheme explaining experimental steps of xenograft formation by K562/luc (expressing shNEG or shTIAR, Firefly luciferase, and GFP) mixed with human primary bone marrow mesenchymal stem cells (hMSC) subcutaneously injected in mice 7 days before initiation of treatment with IM for the following 14 days. (F) Weight of each xenograft isolated from mice (single dot) formed by K562/luc cells with shNEG or shTIAR (as in (E) ) presented as fold change of the weight mean value of xenografts from mice treated with vehicle; mean value indicated with the black line. The nonparametric two-tailed Mann-Whitney test was used for comparisons indicated by black lines underneath the exact significance ( P ) values are presented in the plot. (A,D,F) Two-way Anova was used to compare shTIAR upon IM versus other variants; @ - P < 0.002.

Techniques: Expressing, shRNA, Ex Vivo, Co-Culture Assay, Two Tailed Test, Injection, In Vivo, Luciferase, Isolation, MANN-WHITNEY

(A) Comparison of gene expression in K562/luc cells with shNEG or shTIAR, FACS-sorted from xenografts (Xgraft), with level upon 2 weeks of IM versus vehicle (C) treatment changed with log2 value of fold change (Log2FC) ≥ 0.6 (UP) or ≤ -0.6 (DOWN); reversed regulation in shTIAR cells in purple. (B) Gene Ontology Molecular Function terms identified by the GSEA of genes that upon IM vs C in Xgraft of shNEG are reversely regulated in shTIAR (shaded in purple). In grey circles - UP (Log2FC > 0.6) n = 1993, brown circles DOWN (Log2FC < -0.6) n = 1756. Selected terms with NESabs ≥ 1.45, p-value ≤ 0.05, and the number of genes in the sample annotated per term (size) ≥ 10; n -number of genes. (C) Proportion of alternative splicing events (AS) changed upon shTIAR versus shNEG in cells from xenografts treated with vehicle (C) or imatinib (IM) for 2 weeks. Significant events from rMATS analysis requiring at least 20 reads/event, absolute change in PSI (Percent Spliced In) > 0.1 with FDR ≤ 0.05; total number in 3 experiments (n) above the bar. (D) Comparison of intron retention (RI; left panel) and cassette exon (CE; right panel) AS with significant PSI changed in shTIAR versus shNEG in cells from Xgraft or CO treated with IM. (E) Change in expression level of genes in Xgraft IM versus vehicle-treated for a subset of genes with significant changes shTIAR vs shNEG in RI (left panel) or SE (right panel) in cells from Xgraft and CO treated with IM; Log2FC ≤ -0.6 in brown, ≥ 0.6 in grey. (F) Difference in PSI value of CE, RI, and mutually exclusive exons (MXE) AS in: moro – shTIAR versus shNEG xenograft cells from mice treated with IM (Xgraft_IM); yellow – CD34 + enriched cells from bone marrow biopsies of a CML patient collected at 6-month IM therapy versus diagnosis GSE310243 (see in ). Included only with PSI > 0.1 and with FDR ≤ 0.05. (G) Expression level of genes with changes in AS (selected in (E) and (F) ) analyzed at the scdbm for the CD34 + cells subtype. Patient classification in .

Journal: bioRxiv

Article Title: TIAR-dependent coordination of alternative splicing and lipid peroxidation is required for CML cell resistance to imatinib in the bone marrow stroma

doi: 10.64898/2026.05.29.728710

Figure Lengend Snippet: (A) Comparison of gene expression in K562/luc cells with shNEG or shTIAR, FACS-sorted from xenografts (Xgraft), with level upon 2 weeks of IM versus vehicle (C) treatment changed with log2 value of fold change (Log2FC) ≥ 0.6 (UP) or ≤ -0.6 (DOWN); reversed regulation in shTIAR cells in purple. (B) Gene Ontology Molecular Function terms identified by the GSEA of genes that upon IM vs C in Xgraft of shNEG are reversely regulated in shTIAR (shaded in purple). In grey circles - UP (Log2FC > 0.6) n = 1993, brown circles DOWN (Log2FC < -0.6) n = 1756. Selected terms with NESabs ≥ 1.45, p-value ≤ 0.05, and the number of genes in the sample annotated per term (size) ≥ 10; n -number of genes. (C) Proportion of alternative splicing events (AS) changed upon shTIAR versus shNEG in cells from xenografts treated with vehicle (C) or imatinib (IM) for 2 weeks. Significant events from rMATS analysis requiring at least 20 reads/event, absolute change in PSI (Percent Spliced In) > 0.1 with FDR ≤ 0.05; total number in 3 experiments (n) above the bar. (D) Comparison of intron retention (RI; left panel) and cassette exon (CE; right panel) AS with significant PSI changed in shTIAR versus shNEG in cells from Xgraft or CO treated with IM. (E) Change in expression level of genes in Xgraft IM versus vehicle-treated for a subset of genes with significant changes shTIAR vs shNEG in RI (left panel) or SE (right panel) in cells from Xgraft and CO treated with IM; Log2FC ≤ -0.6 in brown, ≥ 0.6 in grey. (F) Difference in PSI value of CE, RI, and mutually exclusive exons (MXE) AS in: moro – shTIAR versus shNEG xenograft cells from mice treated with IM (Xgraft_IM); yellow – CD34 + enriched cells from bone marrow biopsies of a CML patient collected at 6-month IM therapy versus diagnosis GSE310243 (see in ). Included only with PSI > 0.1 and with FDR ≤ 0.05. (G) Expression level of genes with changes in AS (selected in (E) and (F) ) analyzed at the scdbm for the CD34 + cells subtype. Patient classification in .

Techniques: Comparison, Gene Expression, Alternative Splicing, Expressing, Biomarker Discovery

(A) Scheme explaining experimental setup to determine proteomic changes using the quantitative BONCAT (QuaNCAT). K562 cells expressing shNEG or shTIAR growing in co-culture with HS-5 cells under hypoxia (1.5% O2) for 1.5 days were treated with imatinib (IM) for 18h before the bioorthogonal noncanonical amino acid tagging (BONCAT) of nascent proteins synthesized in cells for 4h. (B) Upper panel - number of genes and nascent proteins showing increased (UP; log₂ fold change [Log₂FC] ≥ 0.6) or decreased (DOWN; Log₂FC ≤ −0.6) abundance in IM-treated shTIAR cells compared with shNEG cells, with a significance threshold of p ≤ 0.05. In total, 2186 nascent proteins were quantified in the BONCAT experiment. Lower panel - scatter plot showing intensity-based absolute quantification (iBAQ), used as an estimate of relative protein molar abundance, plotted against Log₂FC values for BONCAT-identified proteins in shTIAR versus shNEG cells. Purple dots indicate hits with significant changes at both the protein and mRNA levels. Dashed vertical lines mark the Log₂FC thresholds of −0.6 and 0.6. (C) Functional annotation Gene Ontology Molecular Function enrichment analysis of UP (brown) or DOWN (purple) proteins with ClueGO/CytoScape, displaying proteins annotated with the term; only one side enriched terms with FDR < 0.05. (D) Lower panel - number of proteins that upon shTIAR are UP and DOWN regulated, for which mRNA was detected in the RNA immunoprecipitated (IP) in TIAR protein complexes (RIP), enriched in samples obtained with anti-TIAR antibody versus the same isotype non-binding antibody (ISO) (n=3647). Upper panel - example Image of Western blotting analysis of IP, with a sample of cell lysate used for IP loaded for reference (input). (E) Changes in the mRNA level, determined by real-time PCR and quantified using the ddCT method, expressed as log2 of change between IM-treated versus untreated cells, detected in samples from whole cells (upper panel) and anti-TIAR RIP (lower panel). Mean of 3 independent experiments with ± range is presented. Student’s t-test two-way was used to compare the difference between IM to C; * p ≤ 0.05, ** p≤0.005. (F) Number of genes identified in anti-TIAR RIP that show significant changes in intron retention (RI) or cassette exon alternative splicing (CE) in shTIAR versus shNEG alternative splicing analysis of RNA from IM-treated cells. Number of genes in the intersection provided above the bar; comparisons indicated by the black dot. (G) Sashimi plot (middle panel) demonstrating splicing of EIF4A2 mRNA within the region encompassing exons 8-11 and 3’UTR in RNA from anti-TIAR RIP. Alternative splice site usage marked by the purple line, and the percent usage ± ME (n=3) in numbers by the lines, reads coverage from 0-145 shown in grey, alternatively spliced exon marked by shaded yellow. Gene region scheme in the top. (H) Percent transcripts with TIAR-dependent alternative exon inclusion in K562 cells from xenografts treated with IM. Student’s t-test was used to compare results from three experiments (each dot) for the mean value marked with a thick black line; * p = 0.021.

Journal: bioRxiv

Article Title: TIAR-dependent coordination of alternative splicing and lipid peroxidation is required for CML cell resistance to imatinib in the bone marrow stroma

doi: 10.64898/2026.05.29.728710

Figure Lengend Snippet: (A) Scheme explaining experimental setup to determine proteomic changes using the quantitative BONCAT (QuaNCAT). K562 cells expressing shNEG or shTIAR growing in co-culture with HS-5 cells under hypoxia (1.5% O2) for 1.5 days were treated with imatinib (IM) for 18h before the bioorthogonal noncanonical amino acid tagging (BONCAT) of nascent proteins synthesized in cells for 4h. (B) Upper panel - number of genes and nascent proteins showing increased (UP; log₂ fold change [Log₂FC] ≥ 0.6) or decreased (DOWN; Log₂FC ≤ −0.6) abundance in IM-treated shTIAR cells compared with shNEG cells, with a significance threshold of p ≤ 0.05. In total, 2186 nascent proteins were quantified in the BONCAT experiment. Lower panel - scatter plot showing intensity-based absolute quantification (iBAQ), used as an estimate of relative protein molar abundance, plotted against Log₂FC values for BONCAT-identified proteins in shTIAR versus shNEG cells. Purple dots indicate hits with significant changes at both the protein and mRNA levels. Dashed vertical lines mark the Log₂FC thresholds of −0.6 and 0.6. (C) Functional annotation Gene Ontology Molecular Function enrichment analysis of UP (brown) or DOWN (purple) proteins with ClueGO/CytoScape, displaying proteins annotated with the term; only one side enriched terms with FDR < 0.05. (D) Lower panel - number of proteins that upon shTIAR are UP and DOWN regulated, for which mRNA was detected in the RNA immunoprecipitated (IP) in TIAR protein complexes (RIP), enriched in samples obtained with anti-TIAR antibody versus the same isotype non-binding antibody (ISO) (n=3647). Upper panel - example Image of Western blotting analysis of IP, with a sample of cell lysate used for IP loaded for reference (input). (E) Changes in the mRNA level, determined by real-time PCR and quantified using the ddCT method, expressed as log2 of change between IM-treated versus untreated cells, detected in samples from whole cells (upper panel) and anti-TIAR RIP (lower panel). Mean of 3 independent experiments with ± range is presented. Student’s t-test two-way was used to compare the difference between IM to C; * p ≤ 0.05, ** p≤0.005. (F) Number of genes identified in anti-TIAR RIP that show significant changes in intron retention (RI) or cassette exon alternative splicing (CE) in shTIAR versus shNEG alternative splicing analysis of RNA from IM-treated cells. Number of genes in the intersection provided above the bar; comparisons indicated by the black dot. (G) Sashimi plot (middle panel) demonstrating splicing of EIF4A2 mRNA within the region encompassing exons 8-11 and 3’UTR in RNA from anti-TIAR RIP. Alternative splice site usage marked by the purple line, and the percent usage ± ME (n=3) in numbers by the lines, reads coverage from 0-145 shown in grey, alternatively spliced exon marked by shaded yellow. Gene region scheme in the top. (H) Percent transcripts with TIAR-dependent alternative exon inclusion in K562 cells from xenografts treated with IM. Student’s t-test was used to compare results from three experiments (each dot) for the mean value marked with a thick black line; * p = 0.021.

Techniques: Expressing, Co-Culture Assay, Synthesized, Quantitative Proteomics, Functional Assay, Immunoprecipitation, Binding Assay, Western Blot, Real-time Polymerase Chain Reaction, Alternative Splicing

$(A) Expression level of genes analyzed at the scdbm for CD34 + cells subtype; patient classification explained in . (B-H) Impact of shTIAR compared to shNEG analyzed in K562 cells that were co-cultured with HS-5 cells under hypoxia (1.5%O2) 2 days before initiation of 18h culture with imatinib (IM) treatment or without (C). (B) Protein level in whole cell extracts analyzed by Western blot, representative images of immunoblots (n=3) presented. (C) Mitochondrial (mit.) membrane potential measured using JC-1 probe; values for signal from probe aggregates (red) in polarized mitochondria expressed as % of signal from the probe in the cells (n=3), and carbonyl cyanide 3-chlorophenylhydrazone (CCCP) used as a control. (C,D,F,H) Bars represent the mean of values from independent experiments (indicated by dots) with ± SD. Student’s t-test was used to determine the significance of the difference shTIAR vs shNEG (#) and IM vs C (*); * - p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.005, **** p ≤ 0.001 (D) Lipid peroxidation measured with click-it chemistry by flow cytometry. Fluorescence intensity GeoMean expressed as fold change of value in the untreated shNEG cells (n=5). (E-H) Presentation on the cluster of cell differentiation (CD) surface protein markers CD45 and CD235a on K562 cells with shNEG or shTIAR isolated from co-culture established in hypoxia (1.5%O2) a day before initiation of treatment with IM for 48h (E-G) or FACS-sorted K562/luc GFP positive cells from xenografts (H) . (E-F,H) Percentage of parental live cell subpopulations that are: double positive for CD45 and CD235a (CD235a&CD45), positive only for CD45, or only for CD235a, or negative for both CD markers. Representative scatter plots in (E) , summary of independent co-culture experiments (n=4) in (F) . (G) Fluorescence intensity of surface CD36 protein staining in the fraction of cells positive for CD235a or CD45. Numbers correspond to fold change in shTIAR to shNEG ± ME (n=2). (H) Percent GFP and hCD45-positive cells from different xenografts (n=4) that are positive for CD235a. Two-way ANOVA test was used to for comparison of shNEG_C to other variants (@), and p=0.0046.$

Journal: bioRxiv

Article Title: TIAR-dependent coordination of alternative splicing and lipid peroxidation is required for CML cell resistance to imatinib in the bone marrow stroma

doi: 10.64898/2026.05.29.728710

Figure Lengend Snippet: (A) Expression level of genes analyzed at the scdbm for CD34 + cells subtype; patient classification explained in . (B-H) Impact of shTIAR compared to shNEG analyzed in K562 cells that were co-cultured with HS-5 cells under hypoxia (1.5%O2) 2 days before initiation of 18h culture with imatinib (IM) treatment or without (C). (B) Protein level in whole cell extracts analyzed by Western blot, representative images of immunoblots (n=3) presented. (C) Mitochondrial (mit.) membrane potential measured using JC-1 probe; values for signal from probe aggregates (red) in polarized mitochondria expressed as % of signal from the probe in the cells (n=3), and carbonyl cyanide 3-chlorophenylhydrazone (CCCP) used as a control. (C,D,F,H) Bars represent the mean of values from independent experiments (indicated by dots) with ± SD. Student’s t-test was used to determine the significance of the difference shTIAR vs shNEG (#) and IM vs C (*); * - p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.005, **** p ≤ 0.001 (D) Lipid peroxidation measured with click-it chemistry by flow cytometry. Fluorescence intensity GeoMean expressed as fold change of value in the untreated shNEG cells (n=5). (E-H) Presentation on the cluster of cell differentiation (CD) surface protein markers CD45 and CD235a on K562 cells with shNEG or shTIAR isolated from co-culture established in hypoxia (1.5%O2) a day before initiation of treatment with IM for 48h (E-G) or FACS-sorted K562/luc GFP positive cells from xenografts (H) . (E-F,H) Percentage of parental live cell subpopulations that are: double positive for CD45 and CD235a (CD235a&CD45), positive only for CD45, or only for CD235a, or negative for both CD markers. Representative scatter plots in (E) , summary of independent co-culture experiments (n=4) in (F) . (G) Fluorescence intensity of surface CD36 protein staining in the fraction of cells positive for CD235a or CD45. Numbers correspond to fold change in shTIAR to shNEG ± ME (n=2). (H) Percent GFP and hCD45-positive cells from different xenografts (n=4) that are positive for CD235a. Two-way ANOVA test was used to for comparison of shNEG_C to other variants (@), and p=0.0046.

Techniques: Expressing, Cell Culture, Western Blot, Membrane, Control, Flow Cytometry, Fluorescence, Cell Differentiation, Isolation, Co-Culture Assay, Staining, Comparison

Generation of key components and validation of the core anti-tumor mechanism. (A) Plasmid map for overexpression of anti-TGF-βRII gene. (B) Immunoblot and densitometry of pSMAD2 signaling, downstream of TGF-β, in A549 cells, treated with recombinant TGF-β1 and A549 cells infected with plasmid-anti-TGF-βRII, or mock-infected. (C) The scheme of Ad-null (control) and Ad-anti-TGF-βRII. (D) The percentage of in vitro -cultured NK cells (CD3 − CD56 + ) on day 14 was detected by flow cytometry. The cytotoxic activity of NK cells was assessed against K562 cells (24 h co-culture) (E) and A549 cells (F) target cells at various effector-to-target (E:T) ratios. (G) Dose-dependent oncolytic activity of Ad-null and Ad-anti-TGF-βRII in A549 cells 48 h post-infection. (H) RT-qPCR analysis confirming specific upregulation of anti-TGF-βRII mRNA in A549 cells infected with Ad-anti-TGF-βRII, but not Ad-null. (I) Western blot analysis demonstrating that Ad-anti-TGF-βRII infection, but not Ad-null, significantly reduces pSMAD2 levels in A549 cells. *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001; ns means no significance by one-way ANOVA or two-way ANOVA with Tukey’s multiple comparison test. Error bars indicate SDs (n=3).

Journal: Frontiers in Immunology

Article Title: Oncolytic adenovirus encoding a TGF-β inhibitor synergizes with PD-1 blockade to potentiate NK cell cytotoxicity against NSCLC

doi: 10.3389/fimmu.2026.1759236

Figure Lengend Snippet: Generation of key components and validation of the core anti-tumor mechanism. (A) Plasmid map for overexpression of anti-TGF-βRII gene. (B) Immunoblot and densitometry of pSMAD2 signaling, downstream of TGF-β, in A549 cells, treated with recombinant TGF-β1 and A549 cells infected with plasmid-anti-TGF-βRII, or mock-infected. (C) The scheme of Ad-null (control) and Ad-anti-TGF-βRII. (D) The percentage of in vitro -cultured NK cells (CD3 − CD56 + ) on day 14 was detected by flow cytometry. The cytotoxic activity of NK cells was assessed against K562 cells (24 h co-culture) (E) and A549 cells (F) target cells at various effector-to-target (E:T) ratios. (G) Dose-dependent oncolytic activity of Ad-null and Ad-anti-TGF-βRII in A549 cells 48 h post-infection. (H) RT-qPCR analysis confirming specific upregulation of anti-TGF-βRII mRNA in A549 cells infected with Ad-anti-TGF-βRII, but not Ad-null. (I) Western blot analysis demonstrating that Ad-anti-TGF-βRII infection, but not Ad-null, significantly reduces pSMAD2 levels in A549 cells. *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001; ns means no significance by one-way ANOVA or two-way ANOVA with Tukey’s multiple comparison test. Error bars indicate SDs (n=3).

Article Snippet: The human embryonic kidney cell line HEK293, the A549 lung adenocarcinoma cell line, and the human chronic myeloid leukemia cell line K562 were obtained from Procell Biotechnology Co., Ltd. (Wuhan, China).

Techniques: Biomarker Discovery, Plasmid Preparation, Over Expression, Western Blot, Recombinant, Infection, Control, In Vitro, Cell Culture, Flow Cytometry, Activity Assay, Co-Culture Assay, Quantitative RT-PCR, Comparison

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