Dataset.

Additional file 1 of Surfaceome analyses uncover CD98hc as an antibody drug-conjugate target in triple negative breast cancer [Dataset]

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330848
Digital.CSIC. Repositorio Institucional del CSIC
  • Montero, Juan Carlos
  • Calvo-Jiménez, Elisa
  • Carmen, Sofía del
  • Abad, María del Mar
  • Ocaña, Alberto
  • Pandiella, Atanasio
Additional file 1: Supplementary Figure 1. Schematic flow chart representation of the genomic and proteomic approaches used to identify cell surface proteins in TNBC. Supplementary Figure 2. A) The table shows the data generated form the microarray analyses to identify cell surface proteins upregulated in TNBC. B) Venn diagram showing the number of genes specifically identified in each array and those that are common among them. Supplementary Figure 3. A) Procedure used to obtain enriched plasma membrane microsomal fraction, used to identify plasma membrane proteins in TNBC cell lines. B) The table shows the total number of proteins identified, as well as those that correspond to plasma membrane proteins. C) Venn diagram showing the number of proteins specifically identified in each cell line and those that are common among them. Supplementary Figure 4. A) Schematic representation of the protocol used in cell surface biotinylation experiments. B) The table shows the proteins identified and those that correspond to plasma membrane proteins. C) Venn diagram showing the number of proteins identified in each cell line and those that are common among them. Supplementary Figure 5. BT549 (A and B) and MDA-MB231 (C and D) cells were infected with lentivirus containing the shRNA control (sh-Control) or the shRNA sequences targeting GLUT1 or LAT1. Knockdown efficiency was verified by western (A and C), and the effect of the knockdowns on cell proliferation was analyzed by MTT metabolization (B and D). GAPDH was used as a loading control. Supplementary Figure 6. BT549 and HCC3153 cells were seeded on coverslips and treated with 10 nM of anti-CD98hc for the indicated times. Cells were fixed and stained for CD98hc (red), LAMP1 (green) and DNA (blue). Scale bar = 25 μm. Magnification of one cell at 24 hours of treatment is shown. Scale bar = 10 and 7.5 μm. Supplementary Figure 7. A) Dose-response analyses of the anti-proliferative effect of anti-CD98hc-DM1 in MDA-MB231 CD98hc CRISPR #B3, #G3 and parental MDA-MB231 cells. Cells were treated with anti-CD98hc-DM1 for four days at the indicated doses. Results are shown as the mean ± SD of quadruplicates of an experiment repeated three times. B and D) BT549 (B) and MDA-MB231 (D) cells were infected with lentivirus containing the shRNA control (sh-Control) or two shRNA sequences targeting CD98hc (sh-CD98hc #3 and #7). To verify the knockdown efficiency, levels of CD98hc were analyzed by Western blot. Calnexin was used as a loading control. C and E) BT549 (C) and MDA-MB231 (E) cells infected with lentivirus containing the shRNA control (sh-Control) or two shRNA sequences targeting CD98hc were plated and the MTT metabolization was measured at the times indicated. Supplementary Figure 8. Cell cycle profiles of TNBC cells treated with CD98hc-DM1. Cells were treated for one day with CD98hc-DM1 (10 nM), and then harvested and stained with propidium iodide for cell cycle analysis, following the procedure described in the materials and methods section. Supplementary Figure 9. Graphical representation of the surfaceome and the strategy to develop ADCs against differentially expressed proteins. Genomic as well as proteomic strategies allow the identification of proteins overexpressed or newly expressed by tumors with respect to normal tissue. That information may be used to develop an antibody that targets the differentially expressed protein, and that may be used as a backbone for the preparation of an ADC. Once prepared, in vitro and in vivo models can be used to define the antitumoral activity of the ADC as well as its mechanism of action., Instituto de Salud Carlos III Consejo Superior de Investigaciones Científicas Consejería de Educación, Junta de Castilla y León CRIS Cancer Foundation ACMUMA UCCTA ALMOM, Peer reviewed
 
DOI: http://hdl.handle.net/10261/330848
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330848

HANDLE: http://hdl.handle.net/10261/330848
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330848
 
Ver en: http://hdl.handle.net/10261/330848
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330848

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330848
Dataset. 2022

ADDITIONAL FILE 1 OF SURFACEOME ANALYSES UNCOVER CD98HC AS AN ANTIBODY DRUG-CONJUGATE TARGET IN TRIPLE NEGATIVE BREAST CANCER [DATASET]

Digital.CSIC. Repositorio Institucional del CSIC
  • Montero, Juan Carlos
  • Calvo-Jiménez, Elisa
  • Carmen, Sofía del
  • Abad, María del Mar
  • Ocaña, Alberto
  • Pandiella, Atanasio
Additional file 1: Supplementary Figure 1. Schematic flow chart representation of the genomic and proteomic approaches used to identify cell surface proteins in TNBC. Supplementary Figure 2. A) The table shows the data generated form the microarray analyses to identify cell surface proteins upregulated in TNBC. B) Venn diagram showing the number of genes specifically identified in each array and those that are common among them. Supplementary Figure 3. A) Procedure used to obtain enriched plasma membrane microsomal fraction, used to identify plasma membrane proteins in TNBC cell lines. B) The table shows the total number of proteins identified, as well as those that correspond to plasma membrane proteins. C) Venn diagram showing the number of proteins specifically identified in each cell line and those that are common among them. Supplementary Figure 4. A) Schematic representation of the protocol used in cell surface biotinylation experiments. B) The table shows the proteins identified and those that correspond to plasma membrane proteins. C) Venn diagram showing the number of proteins identified in each cell line and those that are common among them. Supplementary Figure 5. BT549 (A and B) and MDA-MB231 (C and D) cells were infected with lentivirus containing the shRNA control (sh-Control) or the shRNA sequences targeting GLUT1 or LAT1. Knockdown efficiency was verified by western (A and C), and the effect of the knockdowns on cell proliferation was analyzed by MTT metabolization (B and D). GAPDH was used as a loading control. Supplementary Figure 6. BT549 and HCC3153 cells were seeded on coverslips and treated with 10 nM of anti-CD98hc for the indicated times. Cells were fixed and stained for CD98hc (red), LAMP1 (green) and DNA (blue). Scale bar = 25 μm. Magnification of one cell at 24 hours of treatment is shown. Scale bar = 10 and 7.5 μm. Supplementary Figure 7. A) Dose-response analyses of the anti-proliferative effect of anti-CD98hc-DM1 in MDA-MB231 CD98hc CRISPR #B3, #G3 and parental MDA-MB231 cells. Cells were treated with anti-CD98hc-DM1 for four days at the indicated doses. Results are shown as the mean ± SD of quadruplicates of an experiment repeated three times. B and D) BT549 (B) and MDA-MB231 (D) cells were infected with lentivirus containing the shRNA control (sh-Control) or two shRNA sequences targeting CD98hc (sh-CD98hc #3 and #7). To verify the knockdown efficiency, levels of CD98hc were analyzed by Western blot. Calnexin was used as a loading control. C and E) BT549 (C) and MDA-MB231 (E) cells infected with lentivirus containing the shRNA control (sh-Control) or two shRNA sequences targeting CD98hc were plated and the MTT metabolization was measured at the times indicated. Supplementary Figure 8. Cell cycle profiles of TNBC cells treated with CD98hc-DM1. Cells were treated for one day with CD98hc-DM1 (10 nM), and then harvested and stained with propidium iodide for cell cycle analysis, following the procedure described in the materials and methods section. Supplementary Figure 9. Graphical representation of the surfaceome and the strategy to develop ADCs against differentially expressed proteins. Genomic as well as proteomic strategies allow the identification of proteins overexpressed or newly expressed by tumors with respect to normal tissue. That information may be used to develop an antibody that targets the differentially expressed protein, and that may be used as a backbone for the preparation of an ADC. Once prepared, in vitro and in vivo models can be used to define the antitumoral activity of the ADC as well as its mechanism of action., Instituto de Salud Carlos III Consejo Superior de Investigaciones Científicas Consejería de Educación, Junta de Castilla y León CRIS Cancer Foundation ACMUMA UCCTA ALMOM, Peer reviewed




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