PMC8489403_01
Patient treatment timeline and DNA alterations. (A) Patient treatment timeline. (B) Mutant Allelic Frequency (MAF; %) in T1 (sample of 2008), T2 (sample of 2018), and T2-PD (sample of 2019) determined using the VHIO-300 panel. Variants classified as pathogenic or likely pathogenic are highlighted in bold; variants matching APOBEC DNA-sequence signature are underlined. (C) Overlap of somatic mutations between T1, T2, and T2-PD using the VHIO-300 panel and whole-exome sequencing (WES). (D) TMB expressed as mutations/megabase in T1, T2, and T2-PD using the VHIO-300 panel and WES. (E) COSMIC mutational signatures of age, APOBEC defect (APOBEC), defective mismatch repair/microsatellite instability (dMMR/MSI) reflected as small insertions and deletions (INDELs), ultraviolet light (UV), polymerase E defect (POLE), and aflotoxin effect in T1, T2, and T2-PD determined by WES. (F) MAF distribution for APOBEC-related and other mutations in T1, T2, and T2-PD determined by WES.
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The treatment history is summarized in Figure 1A. Genomic analyses revealed a completely different mutational profile of T1 versus T2 and T2-PD; the vast majority of mutations in T2 were also present in T2-PD, while none of them were present in T1, and 34 somatic variants were found exclusively in T2-PD (e.g., RB1 S567* and a nonsense NF1 mutation in residue Q315*) (Figures 1B, C). In addition, TMB was low in T1 compared to T2 and T2-PD (Figure 1D). Analysis of COSMIC mutational signatures from the WES results showed a dominant pattern related to age in T1, while the high TMB in T2 and T2-PD was linked to a sequence context preference of cytosine mutations caused by APOBEC enzymes (Figure 1E). Finally, a study of MAF distribution showed a clonal peak for APOBEC-related mutations in T2, with increased average MAF % in T2-PD, plus a second peak of subclonal mutations also linked to APOBEC defect in the T2-PD (Figure 1F).
Gene expression and molecular and clinical response to atezolizumab and nab-paclitaxel. (A) The Wheel Plots depict the relative expression of each signature for T2 and T2-PD samples determined using the Breast Cancer 360 nCounter-based gene expression panel. Signatures are grouped based on the biological process in which they belong. The Luminal A, Luminal B, HER2-enriched, and Basal-like subtype correlation scores are shown as a radial arc. Signature scores (0-16, low to high) are represented as radial projections. (B) Guardant360 Tumor Response Map showing the highest variant allele fraction (%) and MAF (%) assessed in ctDNA using Guardant360 results before treatment, after 3 weeks of atezolizumab monotherapy, and after combining atezolizumab and nab-paclitaxel. (C) CT scan. Red arrows indicate lesions on the soft tissue of the chest wall (top) and a mammary node (middle) and bone (bottom) during treatment.
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Both T2 and T2-PD were classified as HER2-enriched and showed high expression of immune signatures (i.e., MHC-II, IFN-gamma, TIS, antigen presenting machinery) (Figure 2A). After 1 month of atezolizumab plus nab-paclitaxel, the only mutation detected was ALK R1061Q (VAF = 0.5%) (Figure 2B), and after 2 months, a chest CT scan confirmed a partial response as observed on the soft tissue of the chest wall and a mammary node, and in December 2020, the patient continued in clinical and radiological response (Figure 2C).