Additional file 1 of It is not all about the alpha: elevated expression of p53β variants is associated with lower probability of survival in a retrospective melanoma cohort
Creators: name: Groen, Kira
name: Steffens Reinhardt, Luiza
name: Bourdon, Jean-Christophe
name: Avery-Kiejda, Kelly A.
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Cancer

description: Additional file 1: Table S1: Melanoma cohort characteristics. Figure S1: Expression of p53 isoforms in metastatic samples by metastatic site. A. Nuclear and B. cytoplasmic expression of p53 isoforms in metastatic melanoma samples obtained from lymph nodes (n = 13), the skin (n = 21), the brain (n = 8), the lungs (n = 3) and the gastrointestinal tract (incl. the mouth (n = 5). Two metastatic samples, one from the liver and one from the abdomen, were not included. Significance was determined by Kruskal-Wallis test corrected for multiple comparisons with Dunn’s multiple comparisons test. GIT – gastrointestinal tract; * - p &lt; 0.05. Figure S2: Correlation between the expression of different p53 isoforms in the nucleus and cytoplasm. A. Correlations between p53β and other p53 isoform H-scores, B. correlations between Δ40p53 and other N-terminal p53 isoform H-scores, and C. correlation between Δ133p53 and TAp53 H-scores in the nucleus (left) and cytoplasm (right). R2 of the linear regressions and associated p-values are shown under each graph. Figure S3: Relative expression of truncated p53 isoforms. A. Relative expression of p53β, Δ40p53, and Δ133p53 to TAp53 of all melanomas in the nucleus (n = 119) and cytoplasm (n = 110). Relative B. nuclear and C. cytoplasmic expression of truncated p53 isoforms to TAp53 in primary (nucleus n = 69; cytoplasm n = 64) and metastatic melanomas (nucleus n = 50, cytoplasm n = 46). D. Relative nuclear and E. cytoplasmic expression of p53 isoforms in metastatic melanoma samples obtained from lymph nodes (nucleus n = 12, cytoplasm n = 11), the skin (nucleus n = 20, cytoplasm n = 18), the brain (nucleus n= 8, cytoplasm n = 8), the lungs (nucleus n = 3, cytoplasm n = 2) and the gastrointestinal tract (incl. the mouth (nucleus n = 3, cytoplasm n = 5). Two metastatic samples, one from the liver and one from the abdomen, are not included. Significance was determined through Friedman test (matched samples A) or Kruskal-Wallis test (unmatched samples B-E), corrected for multiple comparisons with Dunn’s multiple comparisons test. GIT – gastrointestinal tract; * - p &lt; 0.05;** - p &lt; 0.01; *** - p &lt; 0.001; **** - p &lt; 0.0001. Figure S4: p53 isoform expression in matched primary and metastatic melanomas. A. Nuclear and B. cytoplasmic p53 isoform H-scores in matched primary and metastatic melanoma samples (n = 21). C. Relative nuclear and D. cytoplasmic p53 isoform expression in matched primary and metastatic melanoma samples (n = 17). p-values of comparisons nearing statistical significance are shown. Figure S5: Probability of survival based on p53 isoform expression in primary and metastatic melanoma. Kaplan-Meier plots of probability of melanoma-specific survival in primary melanomas (n = 59) based on A. nuclear TAp53 H-scores &gt; 63.04 (n = 16) or &lt; 63.04 (n = 42), B. nuclear p53β H-scores &gt; 60.57 (n = 19) or &lt; 60.57 (n = 40), C. nuclear Δ40p53 H-scores &gt; 44.30 (n = 10) or &lt; 44.30 (n = 49), D. nuclear Δ133p53 H-scores &gt; 17.03 (n = 10) or &lt; 17.03 (n = 49), E. relative nuclear p53β expression &gt;1.318 (n =26) or &lt; 1.318 (n = 32), F. relative nuclear Δ40p53 &gt; 0.2325(n =40) or &lt; 0.2325 (n = 18), G. relative nuclear Δ133p53 expression &gt;1.252 (n = 10) or &lt; 1.252 (n = 48), H. cytoplasmic TAp53 H-scores &gt; 20.08 (n = 12) or &lt; 20.08 (n = 46), I. cytoplasmic p53β H-scores &gt; 18.84 (n = 10) or &lt; 18.84 (n = 49), J. cytoplasmic Δ40p53 H-scores &gt; 5.252 (n = 11) or &lt; 5.252 (n = 48), K. cytoplasmic Δ133p53 H-scores &gt; 0.535 (n = 16) or &lt; 0.535 (n = 43), L. relative cytoplasmic p53β expression &gt; 0.0425 (n = 42) or &lt; 0.0425 (n = 13), M. relative cytoplasmic Δ40p53 expression &gt; 0.001 (n = 34) or &lt; 0.001 (n = 21), N. relative cytoplasmic Δ133p53 &gt; 1.303 (n = 46) or &lt; 1.303 (n = 9), and in metastatic melanomas (n = 42) based on O. nuclear TAp53 H-scores &gt; 66.63 (n = 13) or &lt; 66.63 (n = 28), P. nuclear p53β H-scores &gt; 50.35 (n = 18) or &lt; 50.35 (n = 24), Q. nuclear Δ40p53 H-scores &gt; 12.49 (n = 18) or &lt; 12.49 (n = 24), R. nuclear Δ133p53 H-scores &gt; 18.70 (n = 10) or &lt; 18.70 (n = 32), S. relative nuclear p53β expression &gt; 0.6186 (n = 30) or &lt; 0.6186 (n = 11), T. relative nuclear Δ40p53 &gt; 0.6444 (n =16) or &lt; 0.6444 (n = 25), U. relative nuclear Δ133p53 expression &gt; 0.2982 (n = 20) or &lt; 0.2989 (n = 21), V. cytoplasmic TAp53 H-scores &gt; 6.488 (n = 16) or &lt; 6.488 (n = 25), W. cytoplasmic p53β H-scores &gt; 1.043 (n = 20) or &lt; 1.043 (n = 22), X. cytoplasmic Δ40p53 H-scores &gt; 0.0265 (n = 26) or &lt; 0.0265 (n = 16), Y. cytoplasmic Δ133p53 H-scores &gt; 0.591 (n = 17) or &lt; 0.591 (n = 25), Z. relative cytoplasmic p53β expression &gt; 0.2384 (n = 24) or &lt; 0.2384 (n = 14), AA. relative cytoplasmic Δ40p53 expression &gt; 0.3022 (n = 12) or &lt; 0.3022 (n = 26), AB. relative cytoplasmic Δ133p53 &gt; 0.2548 (n = 16) or &lt; 0.2548 (n = 22). Significance was determined by Log-rank (Mantel-Cox) tests. ns – not significant; * - p &lt; 0.05; ** - p &lt; 0.01; *** - p &lt; 0001; **** - p &lt; 0.0001. Figure S6: Association of TP53 mutation status with clinical parameters. A. Percentage of melanoma cases with wild-type (n = 8) or mutated (n = 19) TP53 divided according to the p53 isoform composite biomarker classes. B. Kaplan-Meier plots of probability of melanoma-specific survival in primary melanomas (n = 27) based on TP53 mutation status. C. Kaplan-Meier plots of probability of metastasis-free survival in primary melanomas (n = 27) based on TP53 mutation status. D. Breslow thickness and E. Clarke’s microanatomical level in samples with mutant and wild-type TP53. In A and B Significance was determined by Log-rank (Mantel-Cox) tests. p-values as indicated. In C and D significance was determined by Kruskal-Wallis test. ns – not significant; mut – mutant; WT – wild-type.