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: The FGF2 protein (HY-P73052AF) was purchased from MedChemExpress and used with indicated concentration.

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: The FGF2 protein (HY-P73052AF) was purchased from MedChemExpress and used with indicated concentration.

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: The FGF2 protein (HY-P73052AF) was purchased from MedChemExpress and used with indicated concentration.

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

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: PTX, but not Nab-PTX, promotes lung metastasis by inducing TREM2 + macrophage recruitment. Mechanistically, PTX enhances the ATF3-FGF2 axis in breast cancer cells; secreted FGF2 activates the EGR1–TREM2–EMT cytokine axis in macrophages. Created in BioRender. Xing, Y. (2026) https://BioRender.com/6hxlbow .

Article Snippet: The FGF2 protein (HY-P73052AF) was purchased from MedChemExpress and used with indicated concentration.

Techniques:

Journal:

Article Title: Spi-B can functionally replace PU.1 in myeloid but not lymphoid development

doi: 10.1093/emboj/21.9.2220

Figure Lengend Snippet: Fig. 1. Comparison of functional domains between PU.1, Spi-B and Ets-1.

Article Snippet: The blot was first probed with anti-human Spi-B antibody ( Su et al., 1996 ) and subsequently reprobed with anti-PU.1 antibody (Santa Cruz Biotechnology). ( D ) RT–PCR of RNA isolated from splenic B cells.

Techniques: Functional Assay

Journal:

Article Title: Spi-B can functionally replace PU.1 in myeloid but not lymphoid development

doi: 10.1093/emboj/21.9.2220

Figure Lengend Snippet: Fig. 2. Generation of homozygous knock-in ES cell clones. (A) Schematic representation of the targeting strategy. (B) RT–PCR of RNA isolated from in vitro differentiated heterozygous knock-in clones. Primers correspond to the 5′ prime epitope tag and the 3′ prime polyadenylation sequences. Forty cycles of PCR were used to amplify target cDNAs. (C) Western blot of protein isolated from clone 13, U937 and splenic PU.1+/Spi-B cells. A total of 500 000 cell equivalents were loaded per lane. The blot was first probed with anti-human Spi-B antibody (Su et al., 1996) and subsequently reprobed with anti-PU.1 antibody (Santa Cruz Biotechnology). (D) RT–PCR of RNA isolated from splenic B cells. The B-cell preparation was >95% CD19+/B200+ as determined by FACS analysis. Amplification of cDNA was performed as previously stated. (E) Western blot of lysates prepared from splenic B cells. Approximately 150 µg of total cellular protein was loaded per well. The human Spi-B (h-Spi-B) antibody does not recognize murine Spi-B. The blot was first probed with anti-hSpiB and subsequently reprobed with anti-PU.1 and anti-CREB. CREB expression is shown to demonstrate approximately equivalent loading of cell lysate. The asterisk denotes a non-specific immunoreactive band.

Article Snippet: The blot was first probed with anti-human Spi-B antibody ( Su et al., 1996 ) and subsequently reprobed with anti-PU.1 antibody (Santa Cruz Biotechnology). ( D ) RT–PCR of RNA isolated from splenic B cells.

Techniques: Knock-In, Clone Assay, Reverse Transcription Polymerase Chain Reaction, Isolation, In Vitro, Western Blot, Amplification, Expressing

Journal:

Article Title: Spi-B can functionally replace PU.1 in myeloid but not lymphoid development

doi: 10.1093/emboj/21.9.2220

Figure Lengend Snippet: Fig. 6. Examination of macrophage colonies. (A) Macrophage colonies from each genotype were isolated from methylcellulose cultures, cytocentrifuged onto glass slides and stained with May–Grunwald–Giemsa. Magnification = 1000×. (B) RNA was isolated from hematopoietic cultures and subjected to RT–PCR analysis. Cultures derived from two independent clones of PU.1Ets-1/Ets-1 and PU.1Spi-B/Spi-B ES cells were used. Primer pairs specific for M-CSFR, CD11b or CD18 did not generate appropriate size fragments when genomic DNA was used as the template (data not shown).

Article Snippet: The blot was first probed with anti-human Spi-B antibody ( Su et al., 1996 ) and subsequently reprobed with anti-PU.1 antibody (Santa Cruz Biotechnology). ( D ) RT–PCR of RNA isolated from splenic B cells.

Techniques: Isolation, Staining, Reverse Transcription Polymerase Chain Reaction, Derivative Assay, Clone Assay

Journal:

Article Title: Spi-B can functionally replace PU.1 in myeloid but not lymphoid development

doi: 10.1093/emboj/21.9.2220

Figure Lengend Snippet: Fig. 7. Examination of granulocyte colonies. (A) Granulocyte colonies from each genotype were isolated from methylcellulose cultures, cytocentrifuged onto glass slides and stained with May–Grunwald–Giemsa. Magnification = 1000×. (B) Cytospin preparations were stained for MPO activity using a diagnostic kit (Sigma). Dark brown staining indicates the presence of MPO activity. Magnification = 200×. (C) RNA isolated from entire hematopoietic cultures was subjected to RT–PCR analysis. Cultures derived from two independent clones of PU.1+/–, PU.1Et-1/Ets-1 and PU.1Spi-B/Spi-B ES cells were used. For the upper two panels (MPO and HPRT), RNA prepared from one PU.1+/+ culture was used instead of two PU.1+/– cultures. Primer pairs specific for MPO, lysozyme, lactoferrin, C/EBPε and HPRT did not generate the predicted fragment when genomic DNA and/or mock reverse-transcribed RNA was used as the template (data not shown).

Article Snippet: The blot was first probed with anti-human Spi-B antibody ( Su et al., 1996 ) and subsequently reprobed with anti-PU.1 antibody (Santa Cruz Biotechnology). ( D ) RT–PCR of RNA isolated from splenic B cells.

Techniques: Isolation, Staining, Activity Assay, Diagnostic Assay, Reverse Transcription Polymerase Chain Reaction, Derivative Assay, Clone Assay

Journal:

Article Title: Spi-B can functionally replace PU.1 in myeloid but not lymphoid development

doi: 10.1093/emboj/21.9.2220

Figure Lengend Snippet: Fig. 8. Analysis of potential lymphoid rescue of RAG-2–/– mice. (A and B) PU.1Spi-B/Spi-B, PU.1+/–or PU.1–/– ES cells were injected into RAG-2–/– blastocysts to produce control and experimental chimeras. Flow cytometric analysis of blood cell lineages within various tissues of chimeric mice was performed. This figure represents chimeric mice analyzed at 8 weeks of age. (A) Analysis of B220/IgM and IgM/IgD staining revealed no contribution to B-cell populations by PU.1Spi-B/Spi-B or PU.1–/– ES cells, while PU.1+/– contributed significantly to both bone marrow and splenic B cells. (B) Analysis of CD4/CD8 staining showed no contribution to either immature DP or mature SP T cells in the thymus or spleen of PU.1Spi-B/Spi-B or PU.1–/– chimeras, while PU.1+/– contributed to all populations.

Article Snippet: The blot was first probed with anti-human Spi-B antibody ( Su et al., 1996 ) and subsequently reprobed with anti-PU.1 antibody (Santa Cruz Biotechnology). ( D ) RT–PCR of RNA isolated from splenic B cells.

Techniques: Injection, Staining

Journal:

Article Title: Spi-B can functionally replace PU.1 in myeloid but not lymphoid development

doi: 10.1093/emboj/21.9.2220

Figure Lengend Snippet: Fig. 9. Spi-B weakly transactivates the 3′ κ light chain enhancer. NIH 3T3 cells were transfected with the CoreLBKCAT and pGL2 control reporter plasmids along with plasmids expressing c-Jun, c-Fos and PIP. PU.1 and Spi-B expression plasmids were included in the transfections as indicated in the figure. Fold induction of CAT activity is relative to the transfection without PU.1 or Spi-B and is normalized to relative luciferase activity. Values obtained are an average of three independent transfections. Error bars represent standard deviations from the mean.

Article Snippet: The blot was first probed with anti-human Spi-B antibody ( Su et al., 1996 ) and subsequently reprobed with anti-PU.1 antibody (Santa Cruz Biotechnology). ( D ) RT–PCR of RNA isolated from splenic B cells.

Techniques: Transfection, Expressing, Activity Assay, Luciferase

Journal: Oncotarget

Article Title: Epigenomic study identifies a novel mesenchyme homeobox2-GLI1 transcription axis involved in cancer drug resistance, overall survival and therapy prognosis in lung cancer patients

doi: 10.18632/oncotarget.17715

Figure Lengend Snippet: (A) mRNA expression analysis was performed for the A427 and A549 lung adenocarcinoma cell lines in the presence or absence of cisplatinum-based treatment, and the effects of negative control scramble siRNAs and specific anti-MEOX2 siRNAs were assessed. The results are shown for two representative biological experiments performed in triplicate, with * p ≤0.05, and ** p ≤0.01. (B) A427 and A549 lung adenocarcinoma cells exhibited a cisplatinum-inducible GLI-1 protein expression pattern at IC:12.5 (8 μM), while reduced inducible GLI-1 expression was observed following transfection with anti-MEOX2 siRNA in the presence of 8 μM cisplatinum. Western blot statistical analyses, assessed via quantitative densitometry, were performed to determine * p ≤0.05 and ** p ≤0.005 using Student's t -test as well as one-way ANOVA with Dunnett's and Tukey's multiple comparison tests. Western blot bands were quantified as the pixel total intensity rate and expressed as a Change Index normalized to GAPDH. Images are representative of 3 biological replicates. Quantification analyses were performed using cisplatinum (0 μM) treatment as a negative control reference. Images were obtained using a C-DIGIT device (LICOR). Pixel quantification and data analyses were carried out using Image Studio software; the total pixel intensity for each specific protein product was normalized to GAPDH.

Article Snippet: Two non-human related siRNAs obtained from Santa Cruz Biotechnology (Dallas, TX, USA) were used as negative controls (sc-37007 and sc-44230).

Techniques: Expressing, Negative Control, Transfection, Western Blot, Comparison, Software

Journal: Oncotarget

Article Title: Epigenomic study identifies a novel mesenchyme homeobox2-GLI1 transcription axis involved in cancer drug resistance, overall survival and therapy prognosis in lung cancer patients

doi: 10.18632/oncotarget.17715

Figure Lengend Snippet: (A) A549 and H1975 lung cancer cells demonstrated an inducible GLI-1 protein expression pattern following treatment with 8 μM cisplatinum and reduced GLI-1 inducible expression following the application of specific anti-MEOX2 siRNA and/or anti-MEOX2 siRNA plus anti-GLI1 siRNA in the presence of 8 μM cisplatinum. Western blot statistical analyses, assessed via quantitative densitometry, were performed to determine * p ≤0.05 by one-way ANOVA and Dunnett's test for multiple comparisons to identify significant differences with respect to controls. Student's t -test was performed to identify significant differences between control and cisplatinum treatment. Quantification analyses were normalized to scrambled siRNA as a negative control for gene silencing. Images were obtained using a C-DIGIT device (LICOR), and pixel quantification and data analyses were carried out using Image Studio software. Total pixel intensity for each specific protein product was normalized to GAPDH. (B) Cell culture images and graphs showing the quantitative analysis of cellular migration as a percentage (transwell migration assays) indicated significant MEOX2 and GLI-1 protein-dependent functions following the individual and combined application of anti-MEOX2 and anti-GLI1 siRNAs in A549, NH2347 and H1975 lung adenocarcinoma cells; ** p ≤0.005 and *** p ≤0.0001 based on one-way ANOVA and Dunnett's multiple comparisons test. (C) Cell culture images and graphs showing the quantitative analysis of cellular proliferation (clonogenic assays) indicated significant MEOX2 and GLI-1 protein-dependent functions following the individual and combined application of anti-MEOX2 and anti-GLI1 siRNAs in A549, NH2347 and H1975 lung adenocarcinoma cells; ** p ≤0.005 and *** p ≤0.0001 based on one-way ANOVA and Dunnett's multiple comparisons test. Transwell migration index and colony growth (clonogenic assays) rates were normalized and quantified using the ImageJ Colony Number plugin tool (see Materials and Methods).

Article Snippet: Two non-human related siRNAs obtained from Santa Cruz Biotechnology (Dallas, TX, USA) were used as negative controls (sc-37007 and sc-44230).

Techniques: Expressing, Western Blot, Control, Negative Control, Software, Cell Culture, Migration