Journal: PLoS ONE

Article Title: Investigation of FOXM1 as a Potential New Target for Melanoma

doi: 10.1371/journal.pone.0144241

Figure Lengend Snippet: PANC1 cells were used as a positive control. (a) The results of the quantitative RT-PCR analyses of FOXM1 mRNA expression. The relative transcript levels of FOXM1 normalized to the level in PANC1 are shown. (b) The expression of FOXM1 proteins in the malignant melanoma cell lines and NHEM. (c) The results of the quantitative RT-PCR analyses of the miR-370 mRNA expression. (d) The results of the semiquantitative RT-PCR using primers that can detect three splicing variants: FOXM1a (472bp), FOXM1b (323bp) and FOXM1c (368bp).

Article Snippet: Sections of paraffin-embedded melanomas and nevus tissue samples were stained with a monoclonal mouse anti-FOXM1 antibody (clone 3A9; Abnova, Taipei, Taiwan), monoclonal mouse anti-BRAFV600E antibody (clone VE1; Spring Bioscience, Pleasanton, CA) and monoclonal rabbit anti-phospho-AKT (Ser473) antibody (Cell Signaling Technologies, Tokyo, Japan).

Techniques: Positive Control, Quantitative RT-PCR, Expressing, Reverse Transcription Polymerase Chain Reaction

Journal: PLoS ONE

Article Title: Investigation of FOXM1 as a Potential New Target for Melanoma

doi: 10.1371/journal.pone.0144241

Figure Lengend Snippet: The FOXM1 expression (normalized to GAPDH) in the patients with primary melanoma (n = 25), metastatic melanoma (n = 9) and nevi (n = 10) is shown. The bars indicate the median values.

Article Snippet: Sections of paraffin-embedded melanomas and nevus tissue samples were stained with a monoclonal mouse anti-FOXM1 antibody (clone 3A9; Abnova, Taipei, Taiwan), monoclonal mouse anti-BRAFV600E antibody (clone VE1; Spring Bioscience, Pleasanton, CA) and monoclonal rabbit anti-phospho-AKT (Ser473) antibody (Cell Signaling Technologies, Tokyo, Japan).

Techniques: Expressing

Journal: PLoS ONE

Article Title: Investigation of FOXM1 as a Potential New Target for Melanoma

doi: 10.1371/journal.pone.0144241

Figure Lengend Snippet: Representative images of the immunohistochemical staining for FOXM1 in primary malignant melanoma (a, b, c, d, e) and nevus tissues samples (f, g, h). Hematoxylin and eosin staining (a, f: × 40) and FOXM1 immunohistochemistry (b, g: × 40, c, h: × 400). Negative controls using an isotype monoclonal antibody were presented in d and e (d: × 40, e: × 400). Melanin granules are indicated by blue staining, although they did not exhibit FOXM1 expression. Bars: 500 μm (a, b, d, f, g), 50 μm (c, e, h).

Article Snippet: Sections of paraffin-embedded melanomas and nevus tissue samples were stained with a monoclonal mouse anti-FOXM1 antibody (clone 3A9; Abnova, Taipei, Taiwan), monoclonal mouse anti-BRAFV600E antibody (clone VE1; Spring Bioscience, Pleasanton, CA) and monoclonal rabbit anti-phospho-AKT (Ser473) antibody (Cell Signaling Technologies, Tokyo, Japan).

Techniques: Immunohistochemical staining, Staining, Immunohistochemistry, Expressing

Journal: PLoS ONE

Article Title: Investigation of FOXM1 as a Potential New Target for Melanoma

doi: 10.1371/journal.pone.0144241

Figure Lengend Snippet: The results of the immunohistochemical analysis of FOXM1.

Article Snippet: Sections of paraffin-embedded melanomas and nevus tissue samples were stained with a monoclonal mouse anti-FOXM1 antibody (clone 3A9; Abnova, Taipei, Taiwan), monoclonal mouse anti-BRAFV600E antibody (clone VE1; Spring Bioscience, Pleasanton, CA) and monoclonal rabbit anti-phospho-AKT (Ser473) antibody (Cell Signaling Technologies, Tokyo, Japan).

Techniques: Immunohistochemical staining

Journal: PLoS ONE

Article Title: Investigation of FOXM1 as a Potential New Target for Melanoma

doi: 10.1371/journal.pone.0144241

Figure Lengend Snippet: The results of the immunohistochemical analysis of FOXM1, BRAFV600E and p-AKT.

Article Snippet: Sections of paraffin-embedded melanomas and nevus tissue samples were stained with a monoclonal mouse anti-FOXM1 antibody (clone 3A9; Abnova, Taipei, Taiwan), monoclonal mouse anti-BRAFV600E antibody (clone VE1; Spring Bioscience, Pleasanton, CA) and monoclonal rabbit anti-phospho-AKT (Ser473) antibody (Cell Signaling Technologies, Tokyo, Japan).

Techniques: Immunohistochemical staining

Journal: PLoS ONE

Article Title: Investigation of FOXM1 as a Potential New Target for Melanoma

doi: 10.1371/journal.pone.0144241

Figure Lengend Snippet: The correlation between FOXM1 expression and the tumor thickness.

Article Snippet: Sections of paraffin-embedded melanomas and nevus tissue samples were stained with a monoclonal mouse anti-FOXM1 antibody (clone 3A9; Abnova, Taipei, Taiwan), monoclonal mouse anti-BRAFV600E antibody (clone VE1; Spring Bioscience, Pleasanton, CA) and monoclonal rabbit anti-phospho-AKT (Ser473) antibody (Cell Signaling Technologies, Tokyo, Japan).

Techniques: Expressing

Journal: PLoS ONE

Article Title: Investigation of FOXM1 as a Potential New Target for Melanoma

doi: 10.1371/journal.pone.0144241

Figure Lengend Snippet: A comparison of the overall survival between the patients positive for FOXM1 and those negative for expression, as determined using immunohistochemical staining. The p -values were determined using the log-rank test.

Article Snippet: Sections of paraffin-embedded melanomas and nevus tissue samples were stained with a monoclonal mouse anti-FOXM1 antibody (clone 3A9; Abnova, Taipei, Taiwan), monoclonal mouse anti-BRAFV600E antibody (clone VE1; Spring Bioscience, Pleasanton, CA) and monoclonal rabbit anti-phospho-AKT (Ser473) antibody (Cell Signaling Technologies, Tokyo, Japan).

Techniques: Comparison, Expressing, Immunohistochemical staining, Staining

Journal: PLoS ONE

Article Title: Investigation of FOXM1 as a Potential New Target for Melanoma

doi: 10.1371/journal.pone.0144241

Figure Lengend Snippet: The human melanoma cell lines, MeWo and SK-MEL28, were transfected with control and FOXM1 siRNA. Twenty-four hours after treatment, the quantitative RT-PCR analyses were carried out (a,). Seventy-two hours after treatment, a Western blotting analysis and the BrdU cell proliferation assay were performed (b, c). The p -values were determined using the Mann–Whitney U-test. * p < 0.05.

Article Snippet: Sections of paraffin-embedded melanomas and nevus tissue samples were stained with a monoclonal mouse anti-FOXM1 antibody (clone 3A9; Abnova, Taipei, Taiwan), monoclonal mouse anti-BRAFV600E antibody (clone VE1; Spring Bioscience, Pleasanton, CA) and monoclonal rabbit anti-phospho-AKT (Ser473) antibody (Cell Signaling Technologies, Tokyo, Japan).

Techniques: Transfection, Control, Quantitative RT-PCR, Western Blot, BrdU Cell Proliferation Assay, MANN-WHITNEY

Journal: PLoS ONE

Article Title: Investigation of FOXM1 as a Potential New Target for Melanoma

doi: 10.1371/journal.pone.0144241

Figure Lengend Snippet: The expression of FOXM1 was assessed using a Western blotting analysis. The human melanoma cell lines were treated with 10 μM of MEK1 siRNA for 72 hours.

Article Snippet: Sections of paraffin-embedded melanomas and nevus tissue samples were stained with a monoclonal mouse anti-FOXM1 antibody (clone 3A9; Abnova, Taipei, Taiwan), monoclonal mouse anti-BRAFV600E antibody (clone VE1; Spring Bioscience, Pleasanton, CA) and monoclonal rabbit anti-phospho-AKT (Ser473) antibody (Cell Signaling Technologies, Tokyo, Japan).

Techniques: Expressing, Western Blot

Journal: PLoS ONE

Article Title: Investigation of FOXM1 as a Potential New Target for Melanoma

doi: 10.1371/journal.pone.0144241

Figure Lengend Snippet: (a) The expression of activated AKT was assessed by a Western blotting analysis using phospho-specific anti-AKT antibodies. (b) The results of the Western blotting analysis of the cell lysates from the human melanoma cell lines treated with LY294002 (30 μM) and an AKT inhibitor (20 μM) for 24 hours. The levels of FOXM1, p-AKT (ser 473) and AKT were determined. (c) Melanoma cell lines were transfected with control or FOXM1 siRNA, and a Western blotting was carried out with p-AKT (ser 473), AKT and FOXM1 antibodies 72 hours after treatment.

Article Snippet: Sections of paraffin-embedded melanomas and nevus tissue samples were stained with a monoclonal mouse anti-FOXM1 antibody (clone 3A9; Abnova, Taipei, Taiwan), monoclonal mouse anti-BRAFV600E antibody (clone VE1; Spring Bioscience, Pleasanton, CA) and monoclonal rabbit anti-phospho-AKT (Ser473) antibody (Cell Signaling Technologies, Tokyo, Japan).

Techniques: Expressing, Western Blot, Transfection, Control

Journal: Nature Communications

Article Title: Senescent tumor cells lead the collective invasion in thyroid cancer

doi: 10.1038/ncomms15208

Figure Lengend Snippet: ( a ) Scheme of a leader-cell assay. PTC tissues were digested with collagenase to obtain small fragments of cancer tissues, and fragments were cultured in collagen I containing matrigel for 96 h, followed by SA-β-Gal staining (left panel). SA-β-Gal-positive migrating cells emerged from the tumour organoid (right panel). ‘1', ‘2' and ‘3' indicate the high-magnification field of the original figure. ( b ) CXCLs/CCLs and their receptor expression in cancer invasive region. Experimental scheme was same as . Raw data of mRNA expression is summarized in . ( c ) Expression of CXCLs and their receptors in BRAFV600E-expressing PTC. Expression of CXCLs and CXCRs was analysed in the normal region and PTC by real-time PCR and represented as a dot graph ( n =13, left panel). The values indicate the relative value compared to that of a normal follicle. Expression of CXCL12 and CXCR4 was analysed in the centre and invasive area of cancer by real-time PCR and represented as a bar graph ( n =9, right panel). ‘Cen' and ‘Inv' indicate the centre and invasive area of cancer, respectively. ( d ) Immunohistochemical analysis of CXCL12, CXCR4 and p16 INK4A expression in BRAFV600E-expressing PTC ( n =13). Normal, centre and collective invasive regions of cancer were serially sectioned, and CXCL12, CXCR4 and p16 INK4A expression was analysed by H score. ‘N.S' indicates not significant. ( e ) Expression of CXCLs/CXCRs in BRAFV600E -induced senescent thyrocytes ( n =2, average value). Experimental scheme was same as . Secreted CXCL12 protein was measured by ELISA ( n =3, right lower panel). The P value shown ( d ) was calculated by Wilcoxon signed rank test and the others were calculated by Student's t- test. Bars indicate 50 μm ( a ), 100 μm ( d ), respectively. Error bars, s.d.

Article Snippet: The primary antibodies used were as follows: anti-BRAFV600E (VE1), predilution (#790-4855,Ventana Medical Systems Inc); p16 INK4A , predilution (#705-4713, Ventana Medical Systems Inc); Anti-Human Ki67 antigen, clone MIB-1, 1:100 (M7240, Dako Denmark A/S, Glostrup, Denmark); TTF-1, clone 8G7G3/1, 1:50 (343M-95, Cell Marque, Rocklin, USA); D2-40 (Podoplanin), 1:100 (322M-15, Cell Marque); MMP1, 1:100 (GTX100534, GeneTex, Irvine, CA, USA); MMP3, 1:100 (GTX100723, GeneTex); MMP9, 1:100 (GTX100458,GeneTex); CXCR4, 1:100 (MAB172, R&D System, Minneapolis, MN, USA); CXCL12, 1:100 (MAB350, R&D System); E-cadherin, 1:100 (ab15148, Abcam, Cambridge, MA, USA); Twist1, 1;100 (ab50887, Abcam); Zeb1, 1;100 (NBP1-05987, Novus Biologicals, Littleton, CO, USA).

Techniques: Cell Culture, Staining, Expressing, Real-time Polymerase Chain Reaction, Immunohistochemical staining, Enzyme-linked Immunosorbent Assay

Journal: Nature Communications

Article Title: Senescent tumor cells lead the collective invasion in thyroid cancer

doi: 10.1038/ncomms15208

Figure Lengend Snippet: ( a ) In vitro cell-migration assay. Normal/SNU790- CXCR4 , BRAFV600E /SNU790- CXCR4 and BRAFV600E-shCXCL12 /SNU790- CXCR4 cells were seeded. After 24 h, cell migration was measured. One set of BRAFV600E /SNU790- CXCR4 cells was treated with 1μM of AMD3100. Bar graph indicates the average of independent measurements ( n =3). ( b ) Transwell assay. SNU790- CXCR4 cells suspended in medium were seeded in transwell. Control, BRAFV600E , BRAFV600E / shCXCL12 or BRAFV600E /AMD3100 treated cells were seeded at the bottom. After 24 h, cells that invaded the lower surface of the filters were counted. The number of migrated cells was counted in the 40-fold magnification field, and presented in the bar graph ( n =3, right panel). ( c ) Three-dimensional invasion assay. SNU790- CXCR4 cells were co-cultured with normal or BRAFV600E -induced thyrocytes on the top of collagen I containing matrigel for 48 h (upper panel). Cell invasion was assessed by HE staining (lower panel). Bar graph indicates the average of independent experiments ( n =3). ( d ) mCherry lentivirus-infected SNU790- CXCR4 cells were co-cultured with GFP lentivirus-infected normal (upper panel), BRAFV600E (middle panel) or BRAFV600E/shCXCL12 thyrocytes (lower panel) on the top of collagen I containing matrigel for 48 h. Independent experiments were performed and data are presented in the bar graph ( n =3). The P values were calculated by Student's t- test. Bars indicate 50 μm ( c , d ) and 100 μm ( a , b ), respectively. Error bars, s.d.

Article Snippet: The primary antibodies used were as follows: anti-BRAFV600E (VE1), predilution (#790-4855,Ventana Medical Systems Inc); p16 INK4A , predilution (#705-4713, Ventana Medical Systems Inc); Anti-Human Ki67 antigen, clone MIB-1, 1:100 (M7240, Dako Denmark A/S, Glostrup, Denmark); TTF-1, clone 8G7G3/1, 1:50 (343M-95, Cell Marque, Rocklin, USA); D2-40 (Podoplanin), 1:100 (322M-15, Cell Marque); MMP1, 1:100 (GTX100534, GeneTex, Irvine, CA, USA); MMP3, 1:100 (GTX100723, GeneTex); MMP9, 1:100 (GTX100458,GeneTex); CXCR4, 1:100 (MAB172, R&D System, Minneapolis, MN, USA); CXCL12, 1:100 (MAB350, R&D System); E-cadherin, 1:100 (ab15148, Abcam, Cambridge, MA, USA); Twist1, 1;100 (ab50887, Abcam); Zeb1, 1;100 (NBP1-05987, Novus Biologicals, Littleton, CO, USA).

Techniques: In Vitro, Cell Migration Assay, Migration, Transwell Assay, Invasion Assay, Cell Culture, Staining, Infection

Journal: Nature Communications

Article Title: Senescent tumor cells lead the collective invasion in thyroid cancer

doi: 10.1038/ncomms15208

Figure Lengend Snippet: ( a ) The epithelial marker E-cadherin is retained in cancer emboli in lymphatic channels. PTC specimens were serially immunostained with TTF-1 (brown colour in nuclei)/D2-40 (red colour in cytoplasm), E-cadherin, CXCR4, CXCL12 and p16 INK4A . White triangles indicated D2-40 stained lymphatic vessels. ( b ) Metastatic tumour cells at lymph nodes were stained with CXCR4 and CXCL12, respectively. ( c ) Anoikis inhibitory function of senescent cells. Control, BRAFV600E /shCon, BRAFV600E/shCXCL12 or BRAFV600E /AMD3100 treated cells were co-cultured with thyroid carcinoma cells (SNU790- CXCR4 ) in HEMA-coated plates for 12 h, and cell death was determined by Calcein AM and EthD-1 staining, ( d ) caspase activity and ( e ) apoptosis related proteins expression. Independent experiments were performed and data are presented in the bar graph ( n =3). Thick bars indicate 1 mm ( b ) and thin bars indicate 50 μm ( a – c ), respectively. The P values were calculated by Student's t- test. Error bars, s.d.

Article Snippet: The primary antibodies used were as follows: anti-BRAFV600E (VE1), predilution (#790-4855,Ventana Medical Systems Inc); p16 INK4A , predilution (#705-4713, Ventana Medical Systems Inc); Anti-Human Ki67 antigen, clone MIB-1, 1:100 (M7240, Dako Denmark A/S, Glostrup, Denmark); TTF-1, clone 8G7G3/1, 1:50 (343M-95, Cell Marque, Rocklin, USA); D2-40 (Podoplanin), 1:100 (322M-15, Cell Marque); MMP1, 1:100 (GTX100534, GeneTex, Irvine, CA, USA); MMP3, 1:100 (GTX100723, GeneTex); MMP9, 1:100 (GTX100458,GeneTex); CXCR4, 1:100 (MAB172, R&D System, Minneapolis, MN, USA); CXCL12, 1:100 (MAB350, R&D System); E-cadherin, 1:100 (ab15148, Abcam, Cambridge, MA, USA); Twist1, 1;100 (ab50887, Abcam); Zeb1, 1;100 (NBP1-05987, Novus Biologicals, Littleton, CO, USA).

Techniques: Marker, Staining, Cell Culture, Activity Assay, Expressing

Journal: Scientific Reports

Article Title: Novel computational method for predicting polytherapy switching strategies to overcome tumor heterogeneity and evolution

doi: 10.1038/srep44206

Figure Lengend Snippet: ( A ) Computed tomography indicates the clinical course and timeline of disease in the patient with rapid progression on EGFR TKI therapy and shows the EGFR-mutant lung adenocarcinoma (red arrows) analyzed both prior to erlotinib treatment and upon resistance at 4 months. ( B ) Key somatic mutations identified by exon-capture and deep sequencing of the pre- and post-treatment tumor in ( A ) demonstrating concurrent alterations in EGFR and BRAF and the frequency of each mutation in pre- and post- treatment tumor samples. P-values indicated as determined by a two-tailed Fischer’s exact test. ( C ) DNA copy number alterations inferred from exon-capture and sequencing data indicate the focal amplification of the EGFRL858R-mutant allele was lost upon acquired resistance while the patient’s resistant tumor gained a focal amplification of MET, with no change in BRAF (relative positions indicated, chromosome 7).

Article Snippet: For immunoblots, the following antibodies were used: anti-total EGFR (1:1000 dilution, Bethyl Laboratories, Inc., Montgomery TX), anti-pEGFR, anti-total Met, anti-pMet, anti-total Mek, anti-pMek, anti-total Akt, anti-pAkt, anti-total Erk, anti-pErk (1:1000, Cell Signaling Technology Inc., Danvers, MA), BRAFV600E Monoclonal Antibody (Clone VE1, 1:1000, Spring Bioscience, Pleasonton, CA), BRAF WT (1:1000, Santa Cruz Biotech, Santa Cruz, CA) and anti-actin (1:5000 dilution, Sigma-Aldrich, Saint Loius, MO), HRP-conjugated anti-rabbit Ig (used at a 1:3000 dilution, Cell Signaling), and HRP-conjugated anti-mouse IgG (used at a 1:3000 dilution, Cell Signaling).

Techniques: Computed Tomography, Mutagenesis, Sequencing, Two Tailed Test, Amplification

Journal: Scientific Reports

Article Title: Novel computational method for predicting polytherapy switching strategies to overcome tumor heterogeneity and evolution

doi: 10.1038/srep44206

Figure Lengend Snippet: ( A ) Drug efficacy as measured by the effect of 1.5 μ M erlotinib or 0.5 μ M afatinib in combination with either 0.5 μ M MET inhibitor crizotinib, 0.5 μ M MEK inhibitor trametinib or 5 μ M BRAF inhibitor vemurafenib on cell growth (SI, Equation S1) of parental 11–18 EGFRL858R-positive lung adenocarcinoma cells or those cells engineered to express mutations listed above and treated with 0 or 50 ng/ml HGF. ( B ) Concentrations of EGFR TKIs afatinib and erlotinib in combination with either 0.5 μ M crizotinib, 0.5 μ M trametinib or 5 μ M vemurafenib that guarantee progression free tumor reduction for any HGF− or HGF+ initial tumor subpopulations according to the model, measured by the minimum concentration of erlotinib or afatinib that results in exponential stability of the evolutionary dynamics model (SI, Section 3.2). ( C ) Simulations of the lung adenocarcinoma model for combinations of 0.5M afatinib + 0.5 μ M trametinib and 1.5 μ M erlotinib + 0.5 μ M μ crizotinib for the HGF− and HGF+ tumors specified. ( D ) (Left) Simulations of the evolutionary dynamics of different HGF− lung adenocarcinoma initial tumor subpopulations with a constant treatment of 0.7 μ M, 0.5, 0.3 or 0.1 μ M afatinib in combination with 0.5 μ M of trametinib (red) and of different HGF+ lung adenocarcinoma initial tumor subpopulations with a constant treatment of 8.32 μ M, 3.2 μ M, 1.5 μ M or 0.75 μ M erlotinib in combination with 0.5 μ M crizotinib (blue). (Right) Maximum eigenvalue decompositions (SI, Section 3.2) classify which subpopulations can lead to progression at different concentrations of EGFR TKI for the afatinib + trametinib combination and the erlotinib + crizotinib combination.

Article Snippet: For immunoblots, the following antibodies were used: anti-total EGFR (1:1000 dilution, Bethyl Laboratories, Inc., Montgomery TX), anti-pEGFR, anti-total Met, anti-pMet, anti-total Mek, anti-pMek, anti-total Akt, anti-pAkt, anti-total Erk, anti-pErk (1:1000, Cell Signaling Technology Inc., Danvers, MA), BRAFV600E Monoclonal Antibody (Clone VE1, 1:1000, Spring Bioscience, Pleasonton, CA), BRAF WT (1:1000, Santa Cruz Biotech, Santa Cruz, CA) and anti-actin (1:5000 dilution, Sigma-Aldrich, Saint Loius, MO), HRP-conjugated anti-rabbit Ig (used at a 1:3000 dilution, Cell Signaling), and HRP-conjugated anti-mouse IgG (used at a 1:3000 dilution, Cell Signaling).

Techniques: Concentration Assay

Journal: Scientific Reports

Article Title: Novel computational method for predicting polytherapy switching strategies to overcome tumor heterogeneity and evolution

doi: 10.1038/srep44206

Figure Lengend Snippet: Optimal drug scheduling strategies solved by Algorithm 1 (SI, Section 2.2) for representative initial tumor cell distributions ( A ),( C ), for a 30 day timeframe and 30, 15, 10, 5, 3 and 1 day minimum switching horizons, give one EGFR TKI, either 1.5 μ M erlotinib (ERL) or 0.5 μ M afatinib (AFA) in combination with either 5 μ M vemurafenib (VEM), 0.5 μ M trametinib (TRA) or 0.5 μ M crizotinib (CRI) and corresponding simulations ( B , D ) of the lung adenocarcinoma evolutionary dynamics for a subset of optimal drug scheduling strategies.

Article Snippet: For immunoblots, the following antibodies were used: anti-total EGFR (1:1000 dilution, Bethyl Laboratories, Inc., Montgomery TX), anti-pEGFR, anti-total Met, anti-pMet, anti-total Mek, anti-pMek, anti-total Akt, anti-pAkt, anti-total Erk, anti-pErk (1:1000, Cell Signaling Technology Inc., Danvers, MA), BRAFV600E Monoclonal Antibody (Clone VE1, 1:1000, Spring Bioscience, Pleasonton, CA), BRAF WT (1:1000, Santa Cruz Biotech, Santa Cruz, CA) and anti-actin (1:5000 dilution, Sigma-Aldrich, Saint Loius, MO), HRP-conjugated anti-rabbit Ig (used at a 1:3000 dilution, Cell Signaling), and HRP-conjugated anti-mouse IgG (used at a 1:3000 dilution, Cell Signaling).

Techniques:

Journal: Scientific Reports

Article Title: Novel computational method for predicting polytherapy switching strategies to overcome tumor heterogeneity and evolution

doi: 10.1038/srep44206

Figure Lengend Snippet: ( A ) Switching strategies are more beneficial to tumor cell populations with more initial heterogeneity. (Left) Fold change in final lung adenocarcinoma tumor cell populations at day 30 versus day 0 over the course of the optimal 30, 15, 10, 5, 3, and 1 day treatment strategies solved by algorithm 1 (SI, Section 2.2) and normalized by fold change in final tumor cell population for the constant 30 day treatment strategy for an initial tumor cell population comprised of (90% EGFRL858R, 10% H1975 EGFRL858R, T790M) and another comprised of (89% EGFRL858R, 10% BRAFV600E, 1% EGFRL858R, T790M) subclones. (Right) Sum of fold change for the final lung adenocarcinoma populations (SI, Equation S5) for select initial tumor cell distributions ( , ) and their corresponding optimal 30, 15, 10, 5, 3, and 1 day treatment strategies, categorized by the number of subclones in the initial tumor cell population. Smaller fold change sums indicate that more switching is beneficial to reduce final populations, whereas larger fold changes indicate that more switching does not necessarily help in reducing the final tumor populations. ( B ) EGFR TKI dose perturbations. (Left) Fold change in number of lung adenocarcinoma cells between day 30 and day 0, as a function of percent EGFR TKI dose reduction for the optimal 30, 15, 10, 5 and 1 day strategies solved by algorithm 1 (SI, Section 2.2) for tumor cell populations indicated above. The shaded areas indicate the regions of the perturbation space where the treatment strategy reduces the initial tumor cell population by more than 30% (response, light blue), increases the size of the original tumor population size by more than 20% (progression, red), or maintains the original tumor population size between the two (stability, white). (Right) Bar graphs indicate the maximum reduction in EGFR TKI dose supported by the optimal strategy such that there is still reduction in tumor size at day 30 with respect to day 0 for the V600E and the pretreatment MET tumor. ( C ) The average maximum percent EGFR TKI dose reduction supported before progression for lung adenocarcinoma tumors with different number of initial tumor cell subpopulations and for predicted optimal 30, 15, 10, 5, and 1 day switching strategies.

Article Snippet: For immunoblots, the following antibodies were used: anti-total EGFR (1:1000 dilution, Bethyl Laboratories, Inc., Montgomery TX), anti-pEGFR, anti-total Met, anti-pMet, anti-total Mek, anti-pMek, anti-total Akt, anti-pAkt, anti-total Erk, anti-pErk (1:1000, Cell Signaling Technology Inc., Danvers, MA), BRAFV600E Monoclonal Antibody (Clone VE1, 1:1000, Spring Bioscience, Pleasonton, CA), BRAF WT (1:1000, Santa Cruz Biotech, Santa Cruz, CA) and anti-actin (1:5000 dilution, Sigma-Aldrich, Saint Loius, MO), HRP-conjugated anti-rabbit Ig (used at a 1:3000 dilution, Cell Signaling), and HRP-conjugated anti-mouse IgG (used at a 1:3000 dilution, Cell Signaling).

Techniques:

Journal: Acta neuropathologica communications

Article Title: ATRX loss in adult gliomas lacking H3 alterations or IDH mutations, an exceptional situation for exceptional diagnoses: the experience of Sainte-Anne hospital.

doi: 10.1186/s40478-025-02044-6

Figure Lengend Snippet: Fig. 1 Imaging, histopathological and molecular features of the case #4. (A) A capsulo-thalamic infiltrating lesion without initial enhancement after gadolinium injection but FLAIR hyperintensity (B). This tumor was non-homogeneously enhanced after gadolinium injection during the following MRI of the follow-up (C). (D) A diffuse glial proliferation composed of astrocytic and multinucleated cells with numerous mitoses (HPS, magnification × 400). (E) No immunoexpression for IDH1R132H (magnification × 400). (F) A loss of ATRX expression (magnification × 400). (G) No overexpression of p53 (magnification × 400). (H) Elevated proliferative index (MIB1, magnification × 400). (I) A preserved expression of FH (magnification × 400). (J) Copy number variation analysis showing a homozygous deletion of the CDKN2A gene. Black scale bars represent 60 µm. HPS: Hematoxylin Phloxin Saffron

Article Snippet: The following primary antibodies were used: OLIG2 (1:500, clone EP112, Roche Diagnostics GmbH, Mannheim, Deutschland), neurofilament protein (NF) (1:100, clone 2F11, Dako, Glostrup, Denmark), Synaptophysin (1:150, clone DAK-SYNAP, Dako, Glostrup, Denmark), H3K27me3 (1:2500, polyclonal, Diagenode, Liege, Belgium), EZHIP (1:75, polyclonal, Sigma-Aldrich, Bromma, Sweden), H3K27M (1:5000, clone EPR18340, Abcam, Cambridge, United Kingdom), H3G34R (1:1000, clone EPR23519, Abcam, Cambridge, United Kingdom), BRAFV600E (1:100; clone VE1, Spring Biosciences, Pleasanton, United States of America), p53 (1:5000, clone DO-1, Santa Cruz Biotechnology, Dallas, United States of America), FGFR3 (1:150, clone B-9, Santa Cruz Biotechnology, Dallas, United States of America), RB1 (1:200, clone G3-245, Becton Dickinson, Rungis, France), MSH2 (pre-diluted, clone FE11, Dako, Glostrup, Denmark), MSH6 (pre-diluted, clone 44, Dako, Glostrup, Denmark), MLH1 (pre-diluted, clone E505, Dako, Glostrup, Denmark), PMS2 (prediluted, clone EPR3947, Dako, Glostrup, Denmark), and Fumarate Hydratase (FH) (1:500, clone J-13, Santa Cruz Biotechnology, Dallas, United States of America).

Techniques: Imaging, Injection, Expressing, Over Expression

Journal: Acta neuropathologica communications

Article Title: ATRX loss in adult gliomas lacking H3 alterations or IDH mutations, an exceptional situation for exceptional diagnoses: the experience of Sainte-Anne hospital.

doi: 10.1186/s40478-025-02044-6

Figure Lengend Snippet: Fig. 2 Imaging, histopathological and molecular features of case #2. Axial T1 sequence before (A) and after contrast injection (B) displayed a large right hemispheric lesion with slight subcortical enhancement (arrow in B), associated with mass effect and brain herniation under the falx cerebri. T2-weighted sequence (C) and T2-FLAIR sequence (D) displayed a hyper-intense liquid central contingent (arrow in D) in T2 and signal suppression in FLAIR. (E) A diffuse astrocytoma (HPS, magnification × 400) with a low proliferative index (F, magnification × 400), and loss of ATRX expression (G, magnification × 400). Two years after the initial surgery, diffusion-weighted imaging (H) displayed a rim with diffusion restriction (arrows), suggesting hypercellularity. Relative Cerebral Volume (rCBV) map (I) computed from Perfusion-Weighted Imaging, displayed a hyperperfused area in the frontal region (rCBV = 5), suggesting the presence of an intermediate or high grade component. Axial T1 sequence after contrast injection (J) displayed a large mass (star) posterior to the postoperative cavity (arrow) with partial enhancement suggesting intratumoral necrosis. Susceptibility imaging (K) displayed hemorrhagic areas (arrow). The recurrent tumor was histopathologically different, composed of solid nodules showing immature cells with numerous mitoses (L). (M) Focal expression of OLIG2 (magnification × 400), and diffuse immunoreactivity for synaptophysin (N, magnification × 400). (O) Overexpression of p53 (magnification × 400). P loss of ATRX expression (magnification × 400). Q High-level amplification of MYCN locus (magnification × 400, MYCN locus: green signals, centromere of chromosome 2: orange signals). Black scale bars represent 60 µm. HPS: Hematoxylin Phloxin Saffron

Article Snippet: The following primary antibodies were used: OLIG2 (1:500, clone EP112, Roche Diagnostics GmbH, Mannheim, Deutschland), neurofilament protein (NF) (1:100, clone 2F11, Dako, Glostrup, Denmark), Synaptophysin (1:150, clone DAK-SYNAP, Dako, Glostrup, Denmark), H3K27me3 (1:2500, polyclonal, Diagenode, Liege, Belgium), EZHIP (1:75, polyclonal, Sigma-Aldrich, Bromma, Sweden), H3K27M (1:5000, clone EPR18340, Abcam, Cambridge, United Kingdom), H3G34R (1:1000, clone EPR23519, Abcam, Cambridge, United Kingdom), BRAFV600E (1:100; clone VE1, Spring Biosciences, Pleasanton, United States of America), p53 (1:5000, clone DO-1, Santa Cruz Biotechnology, Dallas, United States of America), FGFR3 (1:150, clone B-9, Santa Cruz Biotechnology, Dallas, United States of America), RB1 (1:200, clone G3-245, Becton Dickinson, Rungis, France), MSH2 (pre-diluted, clone FE11, Dako, Glostrup, Denmark), MSH6 (pre-diluted, clone 44, Dako, Glostrup, Denmark), MLH1 (pre-diluted, clone E505, Dako, Glostrup, Denmark), PMS2 (prediluted, clone EPR3947, Dako, Glostrup, Denmark), and Fumarate Hydratase (FH) (1:500, clone J-13, Santa Cruz Biotechnology, Dallas, United States of America).

Techniques: Imaging, Sequencing, Injection, Expressing, Diffusion-based Assay, Over Expression, Amplification

Journal: Acta neuropathologica communications

Article Title: ATRX loss in adult gliomas lacking H3 alterations or IDH mutations, an exceptional situation for exceptional diagnoses: the experience of Sainte-Anne hospital.

doi: 10.1186/s40478-025-02044-6

Figure Lengend Snippet: Fig. 4 Imaging, histopathological and molecular features of case #4. Axial T2-FLAIR sequence (A) displayed a mass centered on the left part of the corpus callosum splenium (star in A), associated with a left hemispheric infiltration with high FLAIR intensity (arrow in A). After contrast injection, axial T1 sequence (B) displayed a diffuse, non-necrotic enhancement on the mass bulk (arrows in B). Diffusion Weighted Imaging (C) displayed high intensity areas inside the mass, suggesting tumoral hypercellularity. Relative Cerebral Volume (rCBV) map (D) computed from Perfusion-Weighted Imaging, displayed a hyper-perfused area in the periventricular region (rCBV = 2.5), suggesting the presence of an intermediate or high grade contingent. Spectroscopic analysis with long Echo Time (TE = 144 ms) (E) displayed a myoinositol peak suggestive of a glial origin, an increase of choline, and a decrease of N-Acetyl-Aspartate, suggestive of hypercellularity and lactate peaks, suggestive of anaerobic metabolism. (F) A diffuse glioma with an astrocytic proliferation, showing atypicalities, multinucleated cells and a microvascular proliferation (HPS, magnification × 400, insert HPS magnification × 400). (G) No immunopositivity for IDH1R132H (magnification × 400). (H) Loss of expression of ATRX (magnification × 400). (I) No overexpression of p53 (magnification × 400). (J) Eleavted proliferative index (MIB1, magnification × 400). (K) Preserved expression of FH (magnification × 400). (L) The copy number variation analysis showed a gain of chromosome 7, without a loss of chromosome 10, and amplifications of the MDM2 and CDK4 genes without EGFR amplification. Black scale bars represent 60 µm. HPS: Hematoxylin Phloxin Saffron

Article Snippet: The following primary antibodies were used: OLIG2 (1:500, clone EP112, Roche Diagnostics GmbH, Mannheim, Deutschland), neurofilament protein (NF) (1:100, clone 2F11, Dako, Glostrup, Denmark), Synaptophysin (1:150, clone DAK-SYNAP, Dako, Glostrup, Denmark), H3K27me3 (1:2500, polyclonal, Diagenode, Liege, Belgium), EZHIP (1:75, polyclonal, Sigma-Aldrich, Bromma, Sweden), H3K27M (1:5000, clone EPR18340, Abcam, Cambridge, United Kingdom), H3G34R (1:1000, clone EPR23519, Abcam, Cambridge, United Kingdom), BRAFV600E (1:100; clone VE1, Spring Biosciences, Pleasanton, United States of America), p53 (1:5000, clone DO-1, Santa Cruz Biotechnology, Dallas, United States of America), FGFR3 (1:150, clone B-9, Santa Cruz Biotechnology, Dallas, United States of America), RB1 (1:200, clone G3-245, Becton Dickinson, Rungis, France), MSH2 (pre-diluted, clone FE11, Dako, Glostrup, Denmark), MSH6 (pre-diluted, clone 44, Dako, Glostrup, Denmark), MLH1 (pre-diluted, clone E505, Dako, Glostrup, Denmark), PMS2 (prediluted, clone EPR3947, Dako, Glostrup, Denmark), and Fumarate Hydratase (FH) (1:500, clone J-13, Santa Cruz Biotechnology, Dallas, United States of America).

Techniques: Imaging, Sequencing, Injection, Diffusion-based Assay, Expressing, Over Expression, Amplification