Journal: Nature genetics
Article Title: Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis
doi: 10.1038/ng.890
Figure Lengend Snippet: a.) Global survey of PHGDH copy number intensity across 3131 cancers. (left) Plot significance of amplifications (FDR q-value) along chromosome 1p (from Telomere to Centromere) across 3131 samples. Candidate oncogenes (TP73, MYCL1, and JUN) in three peak regions and corresponding FDR q-values are shown. FDR q-value of PHGDH is shown in the fourth peak region. (middle) Copy number intensity along chromosome 1p of 150 cancers containing highest intensity of PHGDH amplification that illustrates the localized intensity near the region of PHGDH. Blue indicates deleted region, white indicates neutral region and red indicates amplified region. (right) Magnification of 4MB region containing PHGDH. Solid line indicates chromosome position of PHGDH coding region. Ratios of ion intensities (fold change) are plotted. b.) Relative cell numbers of T.T. cells upon knockdown with respect to shGFP of GFP, PHGDH, PSAT, and PSPH. Error bars represent the standard deviation of n =3 independent measurements. (below) Interphase FISH analysis showing PHGDH copy number gain in T.T. cells. The green probe maps to 1p12 and includes the PHGDH coding sequence. The red probe maps to the pericentromeric region of chromosome1 (1p11.2-q11.1). (below) Relative protein levels of PHGDH, PSAT, and PSPH (as determined by western blot analysis) in T.T. cells following expression of an shRNA against GFP (shGFP), PHGDH (shPHGDH), PSAT (shPSAT), and PSPH (shPSPH) respectively. c.) PHGDH protein expression and copy number gain in three representative human tissue samples. (upper) PHGDH expression was assessed in tumor samples using Immunohistochemistry (IHC). Nuclei are shown in blue (hematoxylin) and PHGDH antibody staining is shown in brown (3-3’-Diaminobenzidine [DAB]), (lower) panels contain interphase FISH analysis that was carried out as in Fig 2B in matched samples to assess copy number (green) relative to the pericentromeric probe (red).
Article Snippet: Both mouse anti-PSAT antibody (Novus) and rabbit anti-PSPH antibody (Sigma) were used at dilutions of 1:1000.
Techniques: Amplification, Knockdown, Standard Deviation, Sequencing, Western Blot, Expressing, shRNA, Immunohistochemistry, Staining
![a.) Global survey of PHGDH copy number intensity across 3131 cancers. (left) Plot significance of amplifications (FDR q-value) along chromosome 1p (from Telomere to Centromere) across 3131 samples. Candidate oncogenes (TP73, MYCL1, and JUN) in three peak regions and corresponding FDR q-values are shown. FDR q-value of PHGDH is shown in the fourth peak region. (middle) Copy number intensity along chromosome 1p of 150 cancers containing highest intensity of PHGDH amplification that illustrates the localized intensity near the region of PHGDH. Blue indicates deleted region, white indicates neutral region and red indicates amplified region. (right) Magnification of 4MB region containing PHGDH. Solid line indicates chromosome position of PHGDH coding region. Ratios of ion intensities (fold change) are plotted. b.) Relative cell numbers of T.T. cells upon knockdown with respect to shGFP of GFP, PHGDH, <t>PSAT,</t> <t>and</t> <t>PSPH.</t> Error bars represent the standard deviation of n =3 independent measurements. (below) Interphase FISH analysis showing PHGDH copy number gain in T.T. cells. The green probe maps to 1p12 and includes the PHGDH coding sequence. The red probe maps to the pericentromeric region of chromosome1 (1p11.2-q11.1). (below) Relative protein levels of PHGDH, PSAT, and PSPH (as determined by western blot analysis) in T.T. cells following expression of an shRNA against GFP (shGFP), PHGDH (shPHGDH), PSAT (shPSAT), and PSPH (shPSPH) respectively. c.) PHGDH protein expression and copy number gain in three representative human tissue samples. (upper) PHGDH expression was assessed in tumor samples using Immunohistochemistry (IHC). Nuclei are shown in blue (hematoxylin) and PHGDH antibody staining is shown in brown (3-3’-Diaminobenzidine [DAB]), (lower) panels contain interphase FISH analysis that was carried out as in Fig 2B in matched samples to assess copy number (green) relative to the pericentromeric probe (red).](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_7549/pmc03677549/pmc03677549__nihms466512f2a.jpg)