mouse breast cancer cell line 4t1  (ATCC)

Journal: Nature Communications

Article Title: Paclitaxel drives TREM2 + macrophage expansion underlying its inferior therapeutic efficacy compared to Nab-paclitaxel

doi: 10.1038/s41467-026-69060-5

Figure Lengend Snippet: a Representative immunofluorescence staining of tissues from patients with and without lung metastases. b Quantification of TREM2-expressing macrophages in tissues from patients with and without lung metastases ( n = 5 patients per group). c Schematic of the experimental design in 4T1-Luc breast-tumor-bearing mice treated with DMSO or PTX. Created in BioRender. Xing, Y. (2026) https://BioRender.com/nsp747p d Representative in vivo bioluminescence images of mice that received the indicated treatments ( n = 5 mice per group). e Representative bright-field images (left) and hematoxylin and eosin (H&E) staining (right) of lungs from mice injected orthotopically with 4T1-Luc cells and treated as described in ( c ) ( n = 5 mice per group). f Quantification (right) of the total numbers of lung-surface metastases ( n = 6 mice per group). g Representative flow cytometry analysis showing a histogram (left) and quantification (right) of the proportion of TREM2-expressing macrophages in tumors ( n = 3 mice per group). h Representative immunofluorescence staining of tumors in mice that received the indicated treatments. i Schematic of Nab-PTX treatment in Py8119 breast tumor-bearing mice. Mice were intraperitoneally injected with DMSO, PTX, PBS, or Nab-PTX at the indicated times. Created in BioRender. Xing, Y. (2026) https://BioRender.com/nsp747p j Photographs (left) of tumors in mice that received the indicated treatments on day 14. Tumor weights (right) of mice that received the indicated treatments ( n = 6 mice per group). k Tumor volumes (right) of mice that received the indicated treatments ( n = 6 mice per group). l Representative bright-field images (left) of lungs from mice that received the indicated treatments. Quantification of the total numbers of lung-surface metastases is shown (right) ( n = 6 mice per group). m Representative H&E-stained images of lungs from mice that received the indicated treatments. n , o Representative flow cytometric analysis of pseudo-color plots ( n ) and quantification ( o ) showing the proportion of TREM2-expressing macrophages in tumors ( n = 4 mice per group). Data are shown as means ± S.D. and were analyzed by two-sided unpaired Student’s t test ( b , f and g ), two-sided one-way ANOVA followed by Tukey’s test ( j , l and o ) and two-sided two-way ANOVA followed by Tukey’s test ( k ). Source data are provided as a Source Data file.

Article Snippet: Human breast cancer cell line BT549 (ATCC, HTB-122), Mouse breast cancer cell line 4T1-Luc (ATCC, CRL-2539-LUC2) and human macrophage cell lines THP1 (ATCC, TIB-202) were cultured in RPMI-1640 medium.

Techniques: Immunofluorescence, Staining, Expressing, In Vivo, Injection, Flow Cytometry

Journal: Nature Communications

Article Title: Paclitaxel drives TREM2 + macrophage expansion underlying its inferior therapeutic efficacy compared to Nab-paclitaxel

doi: 10.1038/s41467-026-69060-5

Figure Lengend Snippet: a Representative immunofluorescence staining of tissues from patients with and without lung metastases. b Quantification of TREM2-expressing macrophages in tissues from patients with and without lung metastases ( n = 5 patients per group). c Schematic of the experimental design in 4T1-Luc breast-tumor-bearing mice treated with DMSO or PTX. Created in BioRender. Xing, Y. (2026) https://BioRender.com/nsp747p d Representative in vivo bioluminescence images of mice that received the indicated treatments ( n = 5 mice per group). e Representative bright-field images (left) and hematoxylin and eosin (H&E) staining (right) of lungs from mice injected orthotopically with 4T1-Luc cells and treated as described in ( c ) ( n = 5 mice per group). f Quantification (right) of the total numbers of lung-surface metastases ( n = 6 mice per group). g Representative flow cytometry analysis showing a histogram (left) and quantification (right) of the proportion of TREM2-expressing macrophages in tumors ( n = 3 mice per group). h Representative immunofluorescence staining of tumors in mice that received the indicated treatments. i Schematic of Nab-PTX treatment in Py8119 breast tumor-bearing mice. Mice were intraperitoneally injected with DMSO, PTX, PBS, or Nab-PTX at the indicated times. Created in BioRender. Xing, Y. (2026) https://BioRender.com/nsp747p j Photographs (left) of tumors in mice that received the indicated treatments on day 14. Tumor weights (right) of mice that received the indicated treatments ( n = 6 mice per group). k Tumor volumes (right) of mice that received the indicated treatments ( n = 6 mice per group). l Representative bright-field images (left) of lungs from mice that received the indicated treatments. Quantification of the total numbers of lung-surface metastases is shown (right) ( n = 6 mice per group). m Representative H&E-stained images of lungs from mice that received the indicated treatments. n , o Representative flow cytometric analysis of pseudo-color plots ( n ) and quantification ( o ) showing the proportion of TREM2-expressing macrophages in tumors ( n = 4 mice per group). Data are shown as means ± S.D. and were analyzed by two-sided unpaired Student’s t test ( b , f and g ), two-sided one-way ANOVA followed by Tukey’s test ( j , l and o ) and two-sided two-way ANOVA followed by Tukey’s test ( k ). Source data are provided as a Source Data file.

Article Snippet: Mouse breast cancer cell line Py8119 (ATCC, CRL-3278) was cultured in Ham’s F12K medium.

Techniques: Immunofluorescence, Staining, Expressing, In Vivo, Injection, Flow Cytometry

Journal: Nature Communications

Article Title: Paclitaxel drives TREM2 + macrophage expansion underlying its inferior therapeutic efficacy compared to Nab-paclitaxel

doi: 10.1038/s41467-026-69060-5

Figure Lengend Snippet: a Schematic of the experimental design. Trem2 +/+ and Trem2 −/− mice were orthotopically injected with Py8119 cells and treated with DMSO or PTX, respectively. Created in BioRender. Xing, Y. (2026) https://BioRender.com/nsp747p b Photographs of representative tumors from mice that received the indicated treatments on day 14. c Tumor growth curves (left) and tumor weights (right) of Py8119 tumors in mice that received the indicated treatments ( n = 6 mice per group). d Representative bright-field images (left) of lungs from Py8119 cell-bearing mice that received the indicated treatments. Quantification of the total number of lung-surface metastases is shown (right) ( n = 6 mice per group). e Representative H&E-stained images of lungs from mice. f Representative flow cytometric analysis of histograms showing the proportion of TREM2-expressing macrophages in tumors. g Quantification of flow cytometric analysis showing the proportion of TREM2-expressing macrophages in tumors ( n = 3 mice per group). h Representative flow cytometric analysis of pseudo-color plots showing the proportion of TREM2-expressing macrophages in the PB of mice ( n = 3 mice per group). i Schematic of the experimental design. Trem2 -/- mice were co-injected orthotopically with Py8119 cells and BMDMs. Created in BioRender. Xing, Y. (2026) https://BioRender.com/nsp747p j Photographs of representative tumors from Trem2 -/- mice that received the indicated treatments on day 17. k Tumor growth curves (left) and tumor weights (right) of Py8119 tumors in Trem2 -/- mice ( n = 6 mice per group). l Representative bright-field images (left) of lungs from Trem2 -/- mice that received the indicated inoculations. Quantification of the total number of lung-surface metastases is shown (right) ( n = 6 mice per group). Data are shown as means ± S.D. and were analyzed by two-sided unpaired Student’s t test ( g ), two-sided one-way ANOVA followed by Tukey’s test ( c , d , k and l ) and two-sided two-way ANOVA followed by Tukey’s test ( c and k ). Source data are provided as a Source Data file.

Article Snippet: Mouse breast cancer cell line Py8119 (ATCC, CRL-3278) was cultured in Ham’s F12K medium.

Techniques: Injection, Staining, Expressing

Journal: Nature Communications

Article Title: Paclitaxel drives TREM2 + macrophage expansion underlying its inferior therapeutic efficacy compared to Nab-paclitaxel

doi: 10.1038/s41467-026-69060-5

Figure Lengend Snippet: a Schematic of ASO treatment in Py8119 breast-tumor-bearing mice. Mice were intraperitoneally injected with DMSO or PTX and intratumorally injected with inactive ASOs or Trem2 ASOs at the indicated times. Created in BioRender. Xing, Y. (2026) https://BioRender.com/nsp747p b Photographs (left) and tumor weights (right) of representative tumors in mice that received the indicated treatments on day 14. c Tumor growth curves of mice that received the indicated treatments ( n = 6 mice per group). d Representative bright-field images of lungs from mice that received the indicated treatments. e Representative H&E-stained images (left) of lungs from mice that received the indicated treatments. Quantification of the total number of lung-surface metastases is shown (right) ( n = 6 mice per group). f Survival curves of Py8119 breast tumor-bearing mice that received the indicated treatments ( n = 6 mice per group). Data are shown as means ± S.D. and were analyzed by two-sided one-way ANOVA followed by Tukey’s test ( b and e ), two-way ANOVA followed by Tukey’s test ( c ) and log-rank test ( f ). Source data are provided as a Source Data file.

Article Snippet: Mouse breast cancer cell line Py8119 (ATCC, CRL-3278) was cultured in Ham’s F12K medium.

Techniques: Injection, Staining

Journal: Nature Communications

Article Title: Paclitaxel drives TREM2 + macrophage expansion underlying its inferior therapeutic efficacy compared to Nab-paclitaxel

doi: 10.1038/s41467-026-69060-5

Figure Lengend Snippet: a Schematic of the experimental setup with THP1 or Raw264.7 cells with indicated treatment. Created in BioRender. Xing, Y. (2026) https://BioRender.com/nsp747p b Quantification of proportion of TREM2 in THP1 and Raw264.7 cells with PTX. n = 3 biological independent samples. c Western blot of THP1 and Raw264.7 cells with indicated treatments. The experiment was independently repeated three times with similar results. d Schematic of the experimental strategy. CM was collected from tumor cells with the indicated treatment. TREM2 expression in macrophages incubated with the CM was assessed. Created in BioRender. Xing, Y. (2026) https://BioRender.com/nsp747p e Quantification of proportion of TREM2 in THP1 incubated with CM of BT549 cells, SUM159 cells and MDA-MB-231 cells treated with PTX, in BMDM incubated with CM of Py8119 treated with PTX, in Raw264.7 incubated with CM from 4T1 and Py8119 cells treated with PTX, respectively. n = 3 biological independent samples. f Western blot analysis of TREM2 and related proteins in THP1, BMDMs, and Raw264.7 cells incubated with CM from BT549, SUM159, Py8119, and 4T1 cells, respectively. The experiment was independently repeated three times with similar results. g Representative immunofluorescence staining of THP1 cells incubated with BT549 CM. n = 3 biological independent samples. h Quantification of proportion of TREM2 in THP1 incubated with CM from BT549, SUM159, and MDA-MB-231 cells treated with Nab-PTX, respectively. n = 3 biological independent samples. i Quantification of the proportion of TREM2 in BMDM incubated with CM of Py8119 treated with Nab-PTX. n = 3 biological independent samples. j Cytokine array analysis of CM from BT549 cells treated indicated treatment. k Western blot analysis of the indicated proteins in Raw264.7 cells and BMDMs treated with recombinant FGF2. The experiment was independently repeated three times with similar results. l Quantification of the proportion of TREM2 in Raw264.7 cells and BMDMs treated with recombinant FGF2. n = 3 biological independent samples. m Schematic of the experimental strategy. CM was collected from tumor cells with the indicated treatment, and then pretreatment using an FGF2 neutralizing antibody. TREM2 expression in macrophages incubated with the CM was assessed. Created in BioRender. Xing, Y. (2026) https://BioRender.com/nsp747p n Western blot analysis of the indicated proteins in Raw264.7 and BMDMs incubated with the indicated CM. The experiment was independently repeated three times with similar results. o Quantification of the proportion of TREM2 in Raw264.7 and BMDMs incubated with the indicated CM. n = 3 biological independent samples. p Representative multiplex immunofluorescence staining of CD68, TREM2 and FGF2 in tumors treated with PTX or Nab-PTX ( n = 3 mice per group). The experiment was independently repeated three times with similar results. Data are shown as means ± S.D. and were analyzed by two-sided unpaired Student’s t test ( b , e , h and i ) and two-sided one-way ANOVA followed by Tukey’s test ( l and o ). Source data are provided as a Source Data file.

Article Snippet: Mouse breast cancer cell line Py8119 (ATCC, CRL-3278) was cultured in Ham’s F12K medium.

Techniques: Western Blot, Expressing, Incubation, Immunofluorescence, Staining, Recombinant, Multiplex Assay

Journal: Nature Communications

Article Title: Paclitaxel drives TREM2 + macrophage expansion underlying its inferior therapeutic efficacy compared to Nab-paclitaxel

doi: 10.1038/s41467-026-69060-5

Figure Lengend Snippet: a Overlap of RNA-seq ( n = 3) and PROMO public database analyses to predict transcription factors regulating TREM2 expression. b Correlations between FGF2 and ATF3 expression in breast cancer using TCGA databases. c qPCR analysis of Atf3 expression in the indicated cells. n = 4 (DMSO and PTX) or 3 (PBS and Nab-PTX) biological independent samples. d Western blot analysis of the indicated proteins in Py8119 cells transfected with ATF3-expressing or control vectors. The experiment was independently repeated three times with similar results. e qPCR analysis of Fgf2 expression in Py8119 cells transfected with Atf3 -expressing or control vectors. n = 3 biological independent samples. f Luciferase activity in HEK293T cells transfected with the indicated reporters and Atf3 -expressing or control vectors. n = 3 biological independent samples. g Abundance of Atf3 bound to the Trem2 promoter in Py8119 cells, as assessed by ChIP-qPCR. n = 3 biological independent samples. h ATAC-seq tracks showing the chromatin accessibility in the ATF3 loci for BT549 cells treated by PTX or Nab-PTX. n = 2 samples per group. Data are shown as means ± S.D. and were analyzed by two-sided unpaired Student’s t test ( c, e and f ) and two-sided two-way ANOVA followed by Šídák’s test ( g ). Source data are provided as a Source Data file.

Article Snippet: Mouse breast cancer cell line Py8119 (ATCC, CRL-3278) was cultured in Ham’s F12K medium.

Techniques: RNA Sequencing, Expressing, Western Blot, Transfection, Control, Luciferase, Activity Assay, ChIP-qPCR

Journal: Nature Communications

Article Title: Paclitaxel drives TREM2 + macrophage expansion underlying its inferior therapeutic efficacy compared to Nab-paclitaxel

doi: 10.1038/s41467-026-69060-5

Figure Lengend Snippet: a Overlap of GeneCards and EDCODE public databases analyses to predict transcription factors that regulate TREM2. b Western blot analysis of the indicated proteins in BMDMs and Raw264.7 cells incubated with FGF2 (left) and with CM from Py8119 cells treated with PTX (right). The experiment was independently repeated three times with similar results. c Western blot analysis of the indicated proteins in Raw264.7 cells incubated with the indicated treatment. The experiment was independently repeated three times with similar results. d qPCR analysis of Trem2 expression in BMDMs transfected with Egr1 -expressing vectors. n = 3 biological independent samples. e Western blot analysis of TREM2 expression in BMDMs transfected with Egr1 -expressing vectors. The experiment was independently repeated three times with similar results. f Luciferase activity of HEK293T cells transfected with the indicated reporters and EGR1 -expressing or control vectors. n = 3 biological independent samples. g Abundance of EGR1 bound to the TREM2 promoter in BMDMs assessed by ChIP-qPCR. n = 3 biological independent samples. h Schematic of the Transwell assay. The first CM was collected from tumor cells with indicated treatment, and the second CM was collected from macrophages incubated with the first CM. The migration and invasion capabilities of macrophages incubated with the first CM were assessed. Created in BioRender. Xing, Y. (2026) https://BioRender.com/nsp747p i Quantification of migration and invasion of Py8119 cells induced by BMDM CM incubated with CM from Py8119 cells treated with PTX, and BT549, SUM159, and MDA-MB-231 cells induced by THP1 CM incubated with CM from BT549, SUM159, and MDA-MB-231 cells treated with PTX (left) or Nab-PTX (right), respectively. n = 5 biological independent samples. j Cytokine array analysis of CM from BMDMs with or without TREM2. k Quantification of migration and invasion of Py8119 cells incubated with indicated proteins. n = 3 biological independent samples. l Quantification of migration and invasion of Py8119 cells induced by CM from BMDMs ( Trem2 +/+ ) with CDE-096. n = 3 biological independent samples. m Western blot analysis of EMT- stimulating proteins in BMDMs incubated with indicated proteins. The experiment was independently repeated three times with similar results. n Schematic illustration showing that FGF2 promotes ERK1/2 phosphorylation to upregulate EGR1, which increases TREM2 expression in macrophages. Upregulated TREM2 enhances the secretion of Serpin E1, HGF, CCL3, and CXCL2 from macrophages to tumor cells, facilitating tumor metastasis via EMT. Created in BioRender. Xing, Y. (2026) https://BioRender.com/nsp747p . Data are shown as means ± S.D. and were analyzed by two-sided unpaired Student’s t test ( d, f, i and l ), two-sided one-way ANOVA followed by Tukey’s test ( k ) and two-sided two-way ANOVA followed by Šídák’s test ( g ). Source data are provided as a Source Data file.

Article Snippet: Mouse breast cancer cell line Py8119 (ATCC, CRL-3278) was cultured in Ham’s F12K medium.

Techniques: Western Blot, Incubation, Expressing, Transfection, Luciferase, Activity Assay, Control, ChIP-qPCR, Transwell Assay, Migration, Phospho-proteomics

Journal: Frontiers in Immunology

Article Title: FACS-based genome-wide CRISPR screening platform identifies modulators of CD47

doi: 10.3389/fimmu.2025.1684539

Figure Lengend Snippet: Genome-wide CRISPR-Cas9 screen identifies genetic regulators of CD47 expression in murine cancer cell lines. (A) Schematic of the FACS-based CRISPR screening pipeline. Mouse cancer cells (B16F10A, MC38, and EMT6) were transduced with the mTKO genome-wide CRISPR-Cas9 library, followed by puromycin selection and passaging for 5 days to ensure stable sgRNA integration. Cells were stained with fluorophore-conjugated anti-CD47 antibodies and sorted by FACS into the top 30% (CD47 high ) and bottom 30% (CD47 low ) populations. Genomic DNA was extracted, and sgRNA abundance was determined by NGS and analyzed using DrugZ to calculate NormZ scores. (B) Ranked NormZ scores of sgRNAs in B16F10A, MC38, and EMT6 cells. Negative NormZ scores indicate positive regulators of CD47 (gene knockouts reduce CD47 expression), while positive NormZ scores indicate negative regulators (gene knockouts increase CD47 expression). CD47 itself ranked as the top positive regulator in all three cell lines, validating the screen’s robustness. (C) GO enrichment analysis of significant negative regulators of CD47 expression (|NormZ| > 3) in B16F10A and MC38 cells. Negative regulators were significantly enriched in pathways related to mitochondrial signaling, including oxidative phosphorylation, mitochondrial translation, and respiratory chain complex assembly.

Article Snippet: Mouse melanoma cell line B16F10A, mouse colon cancer cell line MC38, mouse breast cancer cell line EMT6, two mouse macrophage cells J774A-1, RAW264.7 are purchased from the American Type Culture Collection (ATCC).

Techniques: Genome Wide, CRISPR, Expressing, Transduction, Selection, Passaging, Staining, Phospho-proteomics

Journal: Frontiers in Immunology

Article Title: FACS-based genome-wide CRISPR screening platform identifies modulators of CD47

doi: 10.3389/fimmu.2025.1684539

Figure Lengend Snippet: DNAJC13 is a conserved positive regulator of CD47 expression identified across multiple cancer cell lines. (A) Venn diagram of significant positive regulators of CD47 expression identified in the genome-wide CRISPR screen. CD47 and DNAJC13 were the only two genes consistently identified as significant positive regulators (|NormZ| > 3) across all three cell lines (B16F10A, MC38, and EMT6). (B) Correlation of DNAJC13 and CD47 expression in human cancers. Scatter plots generated from TCGA datasets via GEPIA2 show a positive correlation between DNAJC13 and CD47 expression in breast cancer (BRCA), colon adenocarcinoma (COAD), and skin cutaneous melanoma (SKCM). Pearson correlation coefficients (r) and p-values are indicated. (C) Western blot validation of DNAJC13 regulation of CD47 expression. CRISPR-Cas9–mediated DNAJC13 knockout (three independent sgRNAs: DNAJC13#1, #2, #3) markedly reduced CD47 protein levels compared with vector control in B16F10A, MC38, and EMT6 cells. GAPDH was used as a loading control. (D) Flow cytometry analysis of surface CD47 expression. Representative FACS histograms show reduced surface CD47 expression in DNAJC13 KO cells (green, yellow, and orange peaks; three independent sgRNAs) compared with vector controls (red) in B16F10A, MC38, and EMT6 cells. Isotype control is shown in blue. Quantification of Mean fluorescence intensity (MFI) is shown on the right.

Article Snippet: Mouse melanoma cell line B16F10A, mouse colon cancer cell line MC38, mouse breast cancer cell line EMT6, two mouse macrophage cells J774A-1, RAW264.7 are purchased from the American Type Culture Collection (ATCC).

Techniques: Expressing, Genome Wide, CRISPR, Generated, Western Blot, Biomarker Discovery, Knock-Out, Plasmid Preparation, Control, Flow Cytometry, Fluorescence

Journal: Frontiers in Immunology

Article Title: FACS-based genome-wide CRISPR screening platform identifies modulators of CD47

doi: 10.3389/fimmu.2025.1684539

Figure Lengend Snippet: DNAJC13 negatively correlates with macrophage infiltration and regulates macrophage-mediated phagocytosis. (A) Correlation between gene expression and macrophage infiltration in human cancers. Scatter plots generated using TIMER2 show negative correlations between CD47 expression (top row) or DNAJC13 expression (bottom row) and macrophage infiltration levels in breast cancer (BRCA), colon adenocarcinoma (COAD), and skin cutaneous melanoma (SKCM). Spearman’s correlation coefficients (Rho) and p-values are indicated. (B, C) DNAJC13 loss enhances macrophage phagocytosis in vitro . Flow cytometry analysis of macrophage-mediated phagocytosis in co-culture assays. DNAJC13 knockout (KO) or CD47 KO cancer cells (B16F10A, MC38, EMT6) were co-cultured with (B) RAW 264.7 or (C) J774 macrophages for the indicated time. Representative FACS plots show increased phagocytosis (higher engulfment rate) in DNAJC13-KO and CD47-KO groups compared with vector controls.

Article Snippet: Mouse melanoma cell line B16F10A, mouse colon cancer cell line MC38, mouse breast cancer cell line EMT6, two mouse macrophage cells J774A-1, RAW264.7 are purchased from the American Type Culture Collection (ATCC).

Techniques: Gene Expression, Generated, Expressing, In Vitro, Flow Cytometry, Co-Culture Assay, Knock-Out, Cell Culture, Plasmid Preparation