Additional file 5: of A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels

Evolutionary changes of gene sets described by the four parameters of conservation explained in the manuscript. Sheet 1: results using tissue gene sets. Sheet 2: results using pathway gene sets. Sheet 3: results using disease gene sets. (XLS 552 kb

Additional file 6: of A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels

Novel candidate conserved homologs associated with genes sets. Sheet 1: results using tissue gene sets. Sheet 2: results using pathway gene sets. Sheet 3: results using disease gene sets. Sheets 4, 5 and 6: Same analysis as sheet 1, 2 and 3 but using one-to-one homologous genes only. (XLS 11362 kb

Functional analysis of SETBP1 mutations identified in SGS.

<p><b>A</b>. Fluorescence measurements in live HEK293 cells expressing YFP-tagged SETBP1 variants. (*** p<0.001 versus wild-type and all mutants, ANOVA). All SETBP1 mutations studied displayed a statistically significant difference compared to wild-type and to all other mutations. This graph is representative of 3 independent experiments performed, with 6 technical replicates per experiment. Bars represent the standard error. <b>B</b>. Relative expression of SETBP1 protein variants in live HEK293 cells treated with MG132 proteasome inhibitor or vehicle only. Bars represent the standard error. (*** p<0.001, * p<0.05, NS: not significant, Student’s T test and Mann-Whitney U test). <b>C</b>. ΔΔG values for degron-βTrCP1 interaction for all germline mutations reported in SETBP1 per residue (** p<0.01 D868 versus other residues; ANOVA). <b>D</b>. Immunoblot of whole cell lysates of HEK293 cells expressing FLAG-tagged SETBP1 variants probed with anti-FLAG antibody. <b>E</b>. Immunoblot of whole-cell lysates of fibroblasts probed with anti-SETBP1 antibody. Fibroblasts were derived from two cases of SGS, one carrying the I871T variant and the other carrying the D868N variant, as well as from two unrelated controls. In D and E, blots were stripped and re-probed with anti-β-actin antibody.</p

Genetic and clinical characteristics of individuals with germline <i>SETBP1</i> mutations and Schinzel-Giedion syndrome.

<p><b>A</b>. Schematic representation of the SETBP1 protein, indicating changes found in SGS and in hematologic malignancies. The residues of the canonical degron are highlighted with arrows. Protein domains of SETBP1 are shown in different colors with green corresponding to three AT hooks, purple to the SKI homologous region, blue to the SET binding domain and orange to a repeat domain (modified from Piazza <i>et al</i>.). <b>B</b>. Sequence alignment of the region containing the degron of SETBP1 (in bold) in human (Uniprot accession number Q9Y6X0), chimpanzee (H2QEG8), mouse (Q9Z180), chicken (A0A1D5PT15), african clawed frog (F6TBV9) and zebrafish (B0R147). The consensus motif for βTrCP1 substrates is shown on top, with φ representing a hydrophobic residue and X any amino acid. Residues in which pathogenic germline mutations have been identified in classic SGS are highlighted in blue, while residues in which novel mutations leading to an atypical form of SGS are shown in green. <b>C</b>. Distinctive facial features encountered in classic SGS (current case 9 at 1,5 years of age). <b>D</b>. Typical question mark-shaped ear observed in current case 18. <b>E</b>. Characteristic hand posture with clenched fingers from current case 16. <b>F</b>. Facial features of current case 27 with a mutation in SETBP1 residue S867 at 4 years of age. Note the clenched fingers. <b>G</b>. Facial features of current case 28 with a mutation in SETBP1 residue E862 at 5 years of age. <b>H</b>. Facial features of current case 29 with a mutation in SETBP1 residue T873 at the age of 23 months.</p

Functional effects of germline <i>SETBP1</i> mutations and risk of malignancy.

<p>Degron-βTrCP1 interaction ΔΔG for <i>SETBP1</i> mutations in individuals with SGS who did not develop a malignancy versus those who did (*p<0.05, Mann-Whitney’s U test). The median for each group is marked by an arrowhead. The criteria to be considered negative for the development of a malignancy was either reaching the age of 60 months or dying without developing a malignant tumor or leukemia.</p

On average, <i>SETBP1</i> mutations seen in cancer are more severe than those observed in SGS.

<p><b>A</b>. Distribution of mutations within the SETBP1 degron in SGS and in hematological malignancies. (** p<0.01, Fisher’s test and Bonferroni correction for multiple testing). <b>B</b>. ΔΔG values for protein stability (x-axis) and degron-βTrCP1 interaction (y-axis) for all mutations reported in SETBP1. The size of each circle is proportional to the frequency of the mutation in each condition. <b>C</b>. Difference in free energy of binding in the interaction between βTrCP1 and the degron of variants arising from germline or somatic SETBP1 mutations compared to that of the interaction between βTrCP1 and the wild-type degron (* p <0.05, Mann-Whitney’s U test). The median is highlighted by an arrow head.</p