Targeting the Heterogeneous Genomic Landscape in Triple-Negative Breast Cancer through Inhibitors of the Transcriptional Machinery

Abstract

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer defined by lack of the estrogen, progesterone and human epidermal growth factor receptor 2. Although TNBC tumors contain a wide variety of oncogenic mutations and copy number alterations, the direct targeting of these alterations has failed to substantially improve therapeutic efficacy. This efficacy is strongly limited by interpatient and intratumor heterogeneity, and thereby a lack in uniformity of targetable drivers. Most of these genetic abnormalities eventually drive specific transcriptional programs, which may be a general underlying vulnerability. Currently, there are multiple selective inhibitors, which target the transcriptional machinery through transcriptional cyclin-dependent kinases (CDKs) 7, 8, 9, 12 and 13 and bromodomain extra-terminal motif (BET) proteins, including BRD4. In this review, we discuss how inhibitors of the transcriptional machinery can effectively target genetic abnormalities in TNBC, and how these abnormalities can influence sensitivity to these inhibitors. These inhibitors target the genomic landscape in TNBC by specifically suppressing MYC-driven transcription, inducing further DNA damage, improving anti-cancer immunity, and preventing drug resistance against MAPK and PI3K-targeted therapies. Because the transcriptional machinery enables transcription and propagation of multiple cancer drivers, it may be a promising target for (combination) treatment, especially of heterogeneous malignancies, including TNBC.

Keywords: bromodomain and extra-terminal (BET) proteins; transcription-associated cyclin-dependent kinases (CDKs); transcriptional machinery; triple-negative breast cancer.

Figure 1

Genomic alterations of frequently altered pathways and the transcriptional machinery (TM) in TNBC. (a) Copy number alterations and (b) mutations in genes from TNBC patients from the METABRIC study (TNBC and other BC) or TCGA (pan-cancer) derived from cBioportal. Shown are the most frequently altered genes within cell cycle, DNA damage response (DDR) and growth factor signaling pathways.

Figure 2

Overview of the use of TM inhibitors (TMi’s) to tackle the genomic landscape in TNBC. TMi’s can suppress super-enhancer (SE) driven MYC expression and interfere with MYC-driven transcription (Section 3). As TMi’s can improve p53 function and thereby synergize with DNA damaging agents, genomic loss of TP53 in TNBC can reduce the efficacy of these combination therapies (Section 4). TNBC is characterized by frequent homologous recombination deficiencies and TMi’s further induce genomic instability, thereby sensitizing cells to DNA damaging agents and PARP inhibitors. Despite their genomic instability that could evoke immune responses, TNBCs suppress this, for example through PD-L1 overexpression (Section 6). TMi’s further induce genomic instability and prevent immune suppressive gene expression, improving anti-cancer immunity and anti-PD-L1 therapy. Furthermore, TMi’s can improve therapies directed against the elevated levels of growth factor or AR signaling pathways in TNBC, such as PI3K and MEK inhibitors (Section 7). This figure was created with BioRender.com (accessed on 8 August 2022).

Figure 3

Effects of CDK7 and BET inhibition on super-enhancer driven transcription. (a) BRD4 is enriched at super-enhancers, and its inhibition preferentially disrupts this enrichment and expression driven by super-enhancers, not normal enhancers. (b) CDK7 inhibition preferentially reduces RNA polymerase II binding to the transcription start site of genes driven by super-enhancers. This figure was created with BioRender.com (accessed on 8 August 2022).

Figure 4

Effects of TMi’s on DNA damage and the DNA damage response. (a) CDK7 and BET inhibitors suppress the expression of mitotic genes (e.g., MCM2, PLK1), and thereby functioning of the replication machinery, causing replication fork stalling, transcription-replication conflicts and DNA damage. In TNBC, CDK6 and CCND1 amplifications (amp), and RB1 mutations (mut) or losses, cause further instability of the replication machinery. (b) In addition to this replication stress from improper functioning of the replication machinery, BET and CDK9 inhibitors cause stalling of the TM, thereby causing R loop formation, transcription-replication conflicts and, subsequently, DNA damage. In TNBC, these conflicts are further driven by MYC amplifications that drive high transcriptional activity and replication stress. (c) Although these R loops and DNA double strand breaks may be repaired through proper functioning of DNA damage response and repair, these pathways are impaired in homologous recombination deficient TNBC. TMi’s also suppress the expression of DNA damage response genes (e.g., BRCA1, RAD51), preventing DNA damage repair and thus inducing further DNA damage, all together leading to mitotic catastrophe and cell death. This figure was created with BioRender.com, accessed on 8 August 2022.

Figure 5

Effects of TMi’s on anti-cancer immunity. TMi’s improve anti-cancer immunity by suppressing expression of anti-inflammatory cytokines and PD-L1 in cancer cells, but also in immune cells directly, thereby inducing inflammatory type 1 immune responses. TMi’s also induce pro-inflammatory IFN-y responses in cancer cells, induce sensitivity to TNFα-mediated cell death and induce immunogenic cell death. CDK8 inhibition mostly improves anti-cancer immunity by enhancing natural killer (NK) cell cytotoxicity. This figure was created with BioRender.com (accessed on 8 August 2022).