Journal: Nature genetics

Article Title: A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition

doi: 10.1038/s41588-019-0489-5

Figure Lengend Snippet: a-b) Enrichment of knockouts whose distribution is significantly altered across pseudospace, and therefore EMT progression, in our spontaneous (11,908 cells) (a) and TGF-ß-driven (9,951 cells) (b) conditions. The distribution of cells expressing sgRNAs against EMT genes was compared to the distribution of NTC controls using Chi square (empirically determined FDR < 10%). For targets whose distribution is altered enrichment across each region was determined by calculating the odds ratio. c) Percent E-cadherin (top panels) or vimentin (bottom panels) positive cells in MCF10A colonies exposed to MEK (U0126) and PI3K (LY294002) inhibition after spontaneous (left panels) or TGF-ß-driven (right panels) EMT. Error bars denote standard deviation from the mean (n = 3, two-tailed Student’s t test). d) Percent E-cadherin (top panels) or vimentin (bottom panels) positive cells in MCF10A colonies exposed to EGFR (Erlotinib), MET (Crizotinib), FGFR (Infigratinib) and ITGAV (Cilengitide) inhibition after spontaneous (left panels) or TGF-ß-driven (right panels) EMT. Error bars denote standard deviation from the mean (at left: spontaneous EMT control/EGFRi/ITGAVi n = 7, METi/FGFRi n = 4 independent samples; at right: TGF-ß-driven EMT control n = 4, EGFRi/METi/FGFRi/ITGAVi n = 3 independent samples, two-tailed Student’s t test). e) Inferred EMT regulatory network and putative regulators identified in this study. f) Model depicting the MEK dependent EMT regulatory checkpoint created and its effects on the development of intermediate EMT phenotypes.

Article Snippet: The MEK inhibitor U0126, the PI3K inhibitor LY294002, the EGFR inhibitor erlotinib, the MET inhibitor crizotinib and the FGFR inhibitor infigratinib were purchased from LC Laboratories and resuspended in DMSO.

Techniques: Expressing, Inhibition, Standard Deviation, Two Tailed Test

Journal: The Journal of Pathology: Clinical Research

Article Title: Identifying fibroblast growth factor receptor genetic alterations using RNA‐based assays in patients with metastatic or locally advanced, surgically unresectable, urothelial carcinoma who may benefit from erdafitinib treatment

doi: 10.1002/cjp2.163

Figure Lengend Snippet: Study design and sample selection. *Includes 1 untreated patient in regimen 3. ** n = 600 samples were not eligible for the bridging study (reasons: received before November 28, 2015, no consent for bridging testing, insufficient samples or passing sample store limit). † Includes 1 FGFR+ patient who was not treated but was eligible for the bridging study. ‡ 320 patients were randomly selected and then 120 patients were removed due to a change in the selecting protocol. CDx, companion diagnostic assay; CTA, clinical trial assay; FGFR, fibroblast growth factor receptor; ORR, objective response rate.

Article Snippet: The FGFR inhibitor Clinical Trial Assay (CTA), a RT‐PCR assay developed by Janssen, USA, and performed by Almac Diagnostics (Craigavon, UK) was used to determine the FGFR alteration status in patients enrolled for the erdafitinib phase 2 study.

Techniques: Selection, Diagnostic Assay

Journal: The Journal of Pathology: Clinical Research

Article Title: Identifying fibroblast growth factor receptor genetic alterations using RNA‐based assays in patients with metastatic or locally advanced, surgically unresectable, urothelial carcinoma who may benefit from erdafitinib treatment

doi: 10.1002/cjp2.163

Figure Lengend Snippet: Concordance analysis for CDx and CTA (reference) FGFR gene mutation screening methods

Article Snippet: The FGFR inhibitor Clinical Trial Assay (CTA), a RT‐PCR assay developed by Janssen, USA, and performed by Almac Diagnostics (Craigavon, UK) was used to determine the FGFR alteration status in patients enrolled for the erdafitinib phase 2 study.

Techniques: Mutagenesis

Journal: The Journal of Pathology: Clinical Research

Article Title: Identifying fibroblast growth factor receptor genetic alterations using RNA‐based assays in patients with metastatic or locally advanced, surgically unresectable, urothelial carcinoma who may benefit from erdafitinib treatment

doi: 10.1002/cjp2.163

Figure Lengend Snippet: Investigator‐assessed ORR in erdafitinib‐treated patients who were FGFR+ by both CDx and CTA assays

Article Snippet: The FGFR inhibitor Clinical Trial Assay (CTA), a RT‐PCR assay developed by Janssen, USA, and performed by Almac Diagnostics (Craigavon, UK) was used to determine the FGFR alteration status in patients enrolled for the erdafitinib phase 2 study.

Techniques:

Journal: Journal of Cancer

Article Title: FGF/FGFR signaling pathway involved resistance in various cancer types

doi: 10.7150/jca.40531

Figure Lengend Snippet: Mutations induce resistance to FGFR inhibitors

Article Snippet: V Chell et al revealed that FGFR3 V555M gatekeeper mutation is associated with resistance to FGFR inhibitors, AZD4547 and PD173074 .

Techniques:

Journal: Journal of Cancer

Article Title: FGF/FGFR signaling pathway involved resistance in various cancer types

doi: 10.7150/jca.40531

Figure Lengend Snippet: Signaling pathway induces resistance to FGFR inhibitors

Article Snippet: V Chell et al revealed that FGFR3 V555M gatekeeper mutation is associated with resistance to FGFR inhibitors, AZD4547 and PD173074 .

Techniques:

Journal: EMBO Molecular Medicine

Article Title: Pancreatic cancer intrinsic PI3Kα activity accelerates metastasis and rewires macrophage component

doi: 10.15252/emmm.202013502

Figure Lengend Snippet: A In vitro IC50 of PI3K inhibitors, obtained on recombinant proteins and based on the literature. The Greek letter on the x axis indicates the most potently targeted isoform. B–D (B) Murine pancreatic tumour cells R211 were treated for 15 min with the vehicle, α, β, β/δ, γ‐specific or pan‐PI3K inhibitors at 1 or 10 µM in the presence of 10% FBS and the protein levels of pAkt (Ser473 and Thr308), total Akt and β Actin were observed by Western blot. PAkt on (C) Ser473 and (D) Thr308 were quantified and normalised with β Actin. n = 2 in each group. E Murine pancreatic tumour cells R211 were treated with the vehicle, α, β, β/δ, γ‐specific or pan‐PI3K inhibitors at 0.1 or 1 µM and simultaneously subjected to a Boyden chamber migration assay. Migrating cells were quantified after 24 h. Representative image of filter after Crystal violet staining is shown. Scale = 200 µm. n = 3 in each group. F Murine pancreatic tumour cells R211 were treated with vehicle, BYL‐719 1 µM, AZD4547 2 µM or both treatments and subjected to a Boyden chamber migration assay. Migrating cells were quantified after 24 h. n = 4 in each group. G Murine pancreatic tumour cells R211 were treated with the vehicle, α, β, β/δ, γ‐specific or pan‐PI3K inhibitors, and living cells were quantified after 3 days with a MTT colorimetric assay. Metabolically active cells are considered as living cells. n ≥ 3 in each group. H Murine pancreatic tumour cells R211 were treated with the vehicle, α or pan‐PI3K inhibitors and apoptotic (IncuCyte Annexin V) cells were quantified after 2 days. n = 3 in each group. I Relative p110α, β, γ or δ mRNA expression (compared to scramble siRNA) after inhibition of expression by siRNA targeting p110α or a combination of siRNA targeting each class I PI3K isoform. n ≥ 3 in each group. J R211 and PDAC8661 cells were treated with siRNA scramble, siRNA targeting p110α or a combination of siRNA targeting each class I PI3K isoform (pools) and subjected to a Boyden chamber migration assay. Migrating cells were quantified after 24 h. n = 3 in each group. K Relative p110α or β mRNA expression (compared to scramble shRNA stably transduced cells) in human pancreatic tumour cells PANC‐1 stably transduced with shRNA targeting p110α or β. n = 4 in each group. L PANC‐1‐transduced cells were subjected to a Boyden chamber migration assay. Migrating cells were quantified after 24 h. n = 5 in each group. Data information: Mean ± SEM (* P < 0.05, ** P < 0.01, *** P < 0.001, n ≥ 3 independent experiments except for WB experiment, Student’s t ‐test. When not precised, comparisons are performed with vehicle.

Article Snippet: For in vitro use, all PI3K inhibitors (Knight et al, ; Jackson et al, ; Pomel et al, ; Ali et al, ; Folkes et al, ; Raynaud et al, ; Burger et al, ; Jamieson et al, ; Fritsch et al, ; Barlaam et al, ) (Dataset EV4) and the FGFR inhibitor AZD4547 were purchased (CliniSciences) and dissolved in dimethyl sulfoxide (DMSO) to obtain a stock concentration of 10 mM, subsequently diluted as indicated and compared to the diluted DMSO vehicle (vehicle).

Techniques: In Vitro, Recombinant, Western Blot, Migration, Staining, Colorimetric Assay, Metabolic Labelling, Expressing, Inhibition, shRNA, Stable Transfection, Transduction

Journal: EBioMedicine

Article Title: High throughput profiling of undifferentiated pleomorphic sarcomas identifies two main subgroups with distinct immune profile, clinical outcome and sensitivity to targeted therapies

doi: 10.1016/j.ebiom.2020.103131

Figure Lengend Snippet: Therapeutic potential of FGFR inhibition in a specific subgroup of UPS (A) Assessment of cell viability with pan-FGFR inhibitor JNJ-42756493 in 4 UPS cell lines; Growth curves indicate growth inhibition and IC50 of the 4 UPS cell lines after JNJ-42756493 treatment for 72 h ( n = 6) (**** p < 0.0001, one-way ANOVA). (B) FGFR-inhibitor induces MAPK pathway inhibition in FGFR2 overexpressing cell lines; Phospho-FGFR2/FGFR2 ratio and Phospho-Erk /Erk ratio decrease in FGFR2 overexpressing cell lines after 24 h of treatment with JNJ-42756493 at 1 µM ( n = 3) (* p < 0.05 and ** p < 0.01, two-way ANOVA) (Western-blot). (C) Activity of pan-FGFR inhibitor (JNJ-42756493) on cell cycle of 4 UPS cell lines; Top: cell-cycle profiles after 24 h of treatment with or without JNJ-42756493 at the IC50 analyzed by Propidium Iodide incorporation and flow cytometry; Bottom: cell cycle phase distributions were analyzed with FlowJo software and presented as mean ± SEM of 3 independent experiments ( n = 3) (** p < 0.01 and *** p < 0.001, ns: not significant, two-way ANOVA). (D) Antitumoral effect of a pan-FGFR inhibitor (JNJ-42756493) in two Patient-Derived Xenograft (PDX) models of UPS; Mice were randomly assigned to receive 30 mg/kg of drug or vehicle; Tumor volume progression curves were drawn over 3 to 4 weeks of JNJ-42756493 treatment, arrows represent treatment beginning; The data points represent an average of 11 mice for the JR588 PDX (top) and 8 mice for the KN473 PDX (bottom) per condition (bars, SEM) (*** p < 0.001, two-way ANOVA).

Article Snippet: JNJ-42756493, a pan-FGFR inhibitor, was provided by Johnson&Johnson (New Brunswick, USA), AZD4547 and BGJ398, two other pan-FGFR inhibitors, were purchased from Selleck Chemicals (Houston, USA), prepared as a 10 mmol/L stock solution in DMSO and stored at −20 °C for in vitro studies.

Techniques: Inhibition, Western Blot, Activity Assay, Flow Cytometry, Software, Derivative Assay