Transcriptomic rationale for synthetic lethality-targeting ERCC1 and CDKN1A in chronic myelomonocytic leukaemia

Data S1. Supplementary methods.

Figure S1. Transcriptome assessment of genes involved in DNA repair: differences between patiens and healthy controls in CMML RNA-seq experiment (upper panel) and complex karyotype AML MILE study extracted data (lower panel).

Figure S2. Bone marrow CD34+ cells: CDKN1A, ERCC1, PARP1 and BAP1 RT-qPCR expression in 12 CMML, 15 MDS and 15 healthy donors.

Figure S3. Mutational landscape of recurrently mutated genes in CMML in 57 patients from the validation cohort.

Figure S4. Transcriptome assessment of genes involved in DNA repair extracted from the MILE study: differences between MDS patients and healthy controls.

Figure S5. Venn diagram showing the overlap between dysregulated genes in CMML, MDS and ckAML.

Table SI. Probes used in the RT-qPCR validation experiment.

Table SII. Probes sequences in the pyrosequencing experiment.

Table SIII Targeted amplicon sequencing design.

Table SIV. Significant gene expression differences by RNA-Seq in DNA repair genes between CMML patient and healthy controls.

Table SV. Gene expression differences of CDKN1A, ERCC1, PARP1 and BAP1 by direct and global techniques in CMML discovery and validation, and myeloid extension cohorts.

Table SVI. Cellular compartment size in 18 bone marrow samples from the CMML discovery cohort and analysis of potential correlation with the expression of our 4 main candidate genes.

Table SVII. Methylation status of CpG sites within the promoter regions of 26 RNA-seq differently expressed DNA repair genes.

Table SVIII. Methylation status of CpG sites within the promoter regions of ERCC1 and CDK1NA by pyrosequencing in CMML patients.

Table SIX. Mutations found in the targeted amplicon sequencing approach in the CMML validation cohort.

Table SX. Skipped exons.

Table SXI. Mutually exclusive exons.

Table SXII. Alternative 3′ splice sites.

Table SXIII. Alternative 5′ splice sites.

Table SXIV. Retained introns.

Table SXV. Clinical associations of validated DEGs in our CMML extended cohort.

Table SXVI. Baseline characteristics of MDS patients included in the RT-qPCR validations cohort.

Table SXVII. Characteristics of AML patients included in the rt-qPCR cohort (n=53).

Table SXVIII. Significant gene expression differences in DNA repair genes between MDS patient and healthy controls obtained from the MILE Study.

Table SXIX. Significant gene expression differences in DNA repair genes between ckAML patients and healthy controls obtained from MILE Study.