Additional file 2 of Genomic and transcriptomic profiling of combined small-cell lung cancer through microdissection: unveiling the transformational pathway of mixed subtype

Additional file 2. Figure S1. An overview of the design of this study. A) Schematic diagram of study design; B) Schematic diagram of laser microdissection, left picture represents the IHC staining of cSCLCs before laser microdissection, the right represents the IHC staining of cSCLCs after laser microdissection, the yellow dotted line represents the lung adenocarcinoma component to be separated. Figure S2. Genomic biomakers in cSCLCs. A) Distribution of the 96 mutation types combined across cSCLCs; Mutational signatures B) between LCC and paired SCLC components; C) between ADC/SCC and paired SCLC components; D) between different tumor types; E) between L-SCLC and AS-SCLC; Boxplot in TMB F) and TNB G) between L-SCLC and AS-SCLC; Boxplot in TMB H) and TNB I) at the tumor types level; wGII comparisions J) at the tumor types level, and K) between L-SCLC and AS-SCLC. The percentage of occurred whole genome doubling L) between LCC and paired SCLC components; M) between ADC/SCC and paired SCLC components. Figure S3. Copy number variations profile of cSCLCs. Frequencies of copy number variations in chromosome arm-level of A) SCLC and paired ADC/SCC, B) SCLC and paired LCC. Recurrent focal CNVs in C) SCLC and paired LCC, D) SCLC and paired ADC/SCC, with potential CNV drivers annotated on the circos plot. Focal amplications were marked by red color, Focal deletions were marked by blue color. Figure S4. Driver genes between pure tumors and cSCLCs. A) The MutSigCV p-value of drivers A) between LCC components and pure LCC tumors; B) between ADC/SCC components and pure LUAD/LUSC tumors; C) between SCLC components and pure SCLC tumors; D) between LCC components and paried SCLC components; E) between ADC/SCC components and paired SCLC tumors. F) The tumor mutation burden between pure tumors and cSCLC. The frequency of G) TP53, H) RB1, I) EGFR between pure tumors and cSCLC. J) Hierarchical clustering based on mutational spectrum on cSCLC and the corresponding pure tumors. K) SCLC subtypes in SCLC components and pure SCLC tumors. Figure S5. Enrichment of Immune-related pathways and immune cell infiltration in CSCLCs. The comparisions of A) immune cell infiltration, B) tumor immune microenvironment, and C) TIS between L-SCLC and AS-SCLC components; D) The enrichment score heatmap of immune-related pathways in CSCLCs, and statistics p-value between different components; E) The comparisions of enrichment scores of immune-related pathways between L-SCLC and AS-SCLC components. Figure S6. Clonality in CSCLCs. The bar plots showed clonal types of each driver genes in different components of A) SCLC-LCC subtypes and B) SCLC-ADC/SCC subtypes; C) The distribution of somatic mutations clonality between different components in each cSCLC tumor; The comparisions of D) no selection, E) positive selection in non-SCLC components, and F) positive selection in SCLC components between SCLC-LCC subtypes and SCLC-ADC/SCC subtypes; The assocations between G) tumor purity, H) LCC/SCC tumor proporition, I) ADC/SCC/SCLC tumor proporition, J) tumor stages of non-SCLC components, K) tumor stages of SCLC components and the ccorresponding subclonal ratios. Figure S7. Epithelial cell components of cSCLCs and tranformation modes in CSCLCs. A) the proportion of epithelial cell components in cSCLCs; B) subclonal structure of patients which are transformed from ADCs to SCLCs; C) subclonal structure of patients which are transformed from SCLCs to SCCs; D) The evolutionary fishplot of P12 patient; E) 3D reconstruction of P14's CT scan; F) IHC staining of primary tumor and recurrent tumor of P14. G) subclonal structure of patients which cannot be inferred the transformation direction. Figure S8. Neoantigen depletion in CSCLCs. The odds ratio to occur neoantigen expressed in A) different tumor subtypes and B) different levels immune cell infiltration. The odds ratio to generate neoantigen in consistently expressed genes C) different tumor subtypes and D) different levels immune cell infiltration. The odds ratio to neoantigen occurred in all copy number loss region in E) different tumor subtypes and F) different levels immune cell infiltration. The odds ratio to neoantigen occurred in clonal copy number loss region in G) different tumor subtypes and H) different levels immune cell infiltration. The likely to neoantigen occurred in subclonal copy number loss region in I) different tumor subtypes and J) different levels immune cell infiltration. Figure S9. The associates between RB1 and genomic biomarkers in cSCLCs. A) The correlation between immune distance and the pairwise genomic distance. The weighted chromosome instability comparisons between different TP53 and RB1 alterations status B) in the whole cohort and C) SCLC-ADC/SCC cohort. Comparisons of the whole genome doubling between different TP53 and RB1 alterations status D) in the whole cohort and E) SCLC-ADC/SCC cohort. H) DDR pathways alterations between SCLC components and LCC/ADC/SCC components. I) Differently expressed genes of DDR pathways in SCLC versus ADC/SCC. J) The enrichment score of DDR pathways among tumors with different alteration status of TP53 and RB1.