Therapy resistance: opportunities created by adaptive responses to targeted therapies in cancer

Abstract

Normal cells explore multiple states to survive stresses encountered during development and self-renewal as well as environmental stresses such as starvation, DNA damage, toxins or infection. Cancer cells co-opt normal stress mitigation pathways to survive stresses that accompany tumour initiation, progression, metastasis and immune evasion. Cancer therapies accentuate cancer cell stresses and invoke rapid non-genomic stress mitigation processes that maintain cell viability and thus represent key targetable resistance mechanisms. In this Review, we describe mechanisms by which tumour ecosystems, including cancer cells, immune cells and stroma, adapt to therapeutic stresses and describe three different approaches to exploit stress mitigation processes: (1) interdict stress mitigation to induce cell death; (2) increase stress to induce cellular catastrophe; and (3) exploit emergent vulnerabilities in cancer cells and cells of the tumour microenvironment. We review challenges associated with tumour heterogeneity, prioritizing actionable adaptive responses for optimal therapeutic outcomes, and development of an integrative framework to identify and target vulnerabilities that arise from adaptive responses and engagement of stress mitigation pathways. Finally, we discuss the need to monitor adaptive responses across multiple scales and translation of combination therapies designed to take advantage of adaptive responses and stress mitigation pathways to the clinic.

Figure 1:. Therapeutic opportunities created by adaptive responses due to tumor cell endogenous stress, engagement of stress mitigation pathways and interactions in the tumor ecosystem.

(A) Stresses associated with tumor initiation and stress mitigation programs that are engaged to allow cancer cells to survive and proliferate. (B) Adaptation to therapeutic stress and engagement of stress mitigation pathways in the tumor ecosystem (tumor, stromal and immune cells) provide three therapeutic options: a) induce tumor cell death by interdicting stress mitigation pathways that allow tumor cell survival, b) overwhelm the mitigation pathways by increasing existing stress that results in stress-induced catastrophe, c) exploit emergent vulnerabilities in the tumor ecosystem by targeting tumor-host interactions. The difference in stress levels and stress mitigation programs between normal and tumor cells provides an opportunity for increased therapeutic index.

Figure 2:. Adaptive response programs in tumor cells and in the tumor ecosystem.

(A) Examples of adaptive responses that bypass inhibition of the PI3K/mTOR pathway: 1) Transcriptional upregulation of RTKs via FOXO transcription factors, 2) secretion of autocrine growth factors via release of the mTOR-driven IRS1 negative feedback loop and 3) utilization of a non-targeted isoform of PI3K. We also highlight another example of signaling rewiring following EGFR inhibition due to downregulation of negative mediators in the PI3K pathway such as PTEN. Purple bolded arrows indicate adaptive responses following each targeted therapy (e.g. EGFRi, PI3Ki, PARPi, MEKi). (B) Engagement of DNA repair pathways to mitigate DNA damage and replication stress. DNA damaging anti-cancer therapies (examples of chemotherapy and PARP inhibition) induce activation of DNA integrity sensors ATM/ATR that induce cell cycle arrest and active DNA repair pathways. PI3K inhibition promotes DNA damage by depletion of nucleoside availability that is required for DNA repair. MEK inhibition represents another example that decreases the levels of DNA repair pathway members resulting in elevated DNA damage. (C) Stress response pathways feed into kinases that phosphorylate eIF2α to induce cap-independent translation of transcription factors that regulate stress homeostasis (integrated stress response). For example, BRAF inhibition mediates metabolic stress via upregulating the upstream kinase GCN2, while RTK inhibition results in PERK upregulation and endoplasmic reticulum (ER) stress. Targeted therapies (e.g. BRAFi) can also result in unbalanced generation of reactive oxygen species (ROS) that via the same eIF2α kinases engage ROS-mitigation programs that are regulated by transcription factors such as NRF2 and NFkB. (D) Tumor-immune paracrine signaling following BRAF inhibition that mediates immunoevasion (proliferation of pro-tumor M2 macrophages) and reactivation of ERK in tumor cells via macrophage-derived VEGF. BRAF inhibition has also been shown to reactivate focal adhesion kinase-driven ERK in melanoma cells via cancer associated fibroblast-mediated extracellular matrix remodeling. Purple bolded arrows indicate adaptive responses resulting from cell-cell communication.

Figure 2:. Adaptive response programs in tumor cells and in the tumor ecosystem.

(A) Examples of adaptive responses that bypass inhibition of the PI3K/mTOR pathway: 1) Transcriptional upregulation of RTKs via FOXO transcription factors, 2) secretion of autocrine growth factors via release of the mTOR-driven IRS1 negative feedback loop and 3) utilization of a non-targeted isoform of PI3K. We also highlight another example of signaling rewiring following EGFR inhibition due to downregulation of negative mediators in the PI3K pathway such as PTEN. Purple bolded arrows indicate adaptive responses following each targeted therapy (e.g. EGFRi, PI3Ki, PARPi, MEKi). (B) Engagement of DNA repair pathways to mitigate DNA damage and replication stress. DNA damaging anti-cancer therapies (examples of chemotherapy and PARP inhibition) induce activation of DNA integrity sensors ATM/ATR that induce cell cycle arrest and active DNA repair pathways. PI3K inhibition promotes DNA damage by depletion of nucleoside availability that is required for DNA repair. MEK inhibition represents another example that decreases the levels of DNA repair pathway members resulting in elevated DNA damage. (C) Stress response pathways feed into kinases that phosphorylate eIF2α to induce cap-independent translation of transcription factors that regulate stress homeostasis (integrated stress response). For example, BRAF inhibition mediates metabolic stress via upregulating the upstream kinase GCN2, while RTK inhibition results in PERK upregulation and endoplasmic reticulum (ER) stress. Targeted therapies (e.g. BRAFi) can also result in unbalanced generation of reactive oxygen species (ROS) that via the same eIF2α kinases engage ROS-mitigation programs that are regulated by transcription factors such as NRF2 and NFkB. (D) Tumor-immune paracrine signaling following BRAF inhibition that mediates immunoevasion (proliferation of pro-tumor M2 macrophages) and reactivation of ERK in tumor cells via macrophage-derived VEGF. BRAF inhibition has also been shown to reactivate focal adhesion kinase-driven ERK in melanoma cells via cancer associated fibroblast-mediated extracellular matrix remodeling. Purple bolded arrows indicate adaptive responses resulting from cell-cell communication.

Figure 3. Strategies to induce tumor cell death by exploiting stress adaptation, accentuating existing stress and targeting emergent vulnerabilities in the tumor ecosystem

(A) Example of therapeutic opportunities emerging from therapy-induced stress. PARP inhibitors induce DNA damage and replication stress that results in cell cycle arrest and engagement of DNA repair pathways. This diagram show strategies involving combination therapies to enhance the efficacy of PARP inhibition that increase stress via radiation or chemotherapy. In addition, there are multiple approaches to interdict the stress mitigation process via 1) blocking anti-apoptotic survival proteins such as BCL-XL, 2) inhibiting upstream mediators of DNA repair (RAS/ERK inhibition) or cell cycle checkpoints (ATR), 3) blocking epigenetic reprograming (HDAC/BET) and 4) stress mitigation programs (e.g. anti-oxidant NRF2, NFkB). (B) Targeting emergent opportunities in the tumor ecosystem represents another approach to develop rational combination therapies. Tumor cells in therapy-resistant tumor ecosystems can be targeted by 1) inhibiting immune checkpoints to augment anti-tumor immunity that is mediated via tumor-immune paracrine signaling, 2) blocking therapy-induced extracellular matrix remodeling that enhances recruitment of cytotoxic immune cells, 3) targeting anti-apoptotic signaling that is induced via stromal-derived cytokines and extracellular matrix remodeling, and 4) blocking angiogenesis to normalize blood vessels and enhance immune cell recruitment.

Figure 4. Potential approach to deliver personalized combination therapies in real time.

Liquid biopsy and tumor samples are collected at diagnosis. A suite of CLIA assays are performed to establish the baseline tumor phenotype and genotype of the tumor and select an initial therapy. After a short treatment period, a second liquid biopsy and tumor samples are collected and re-analyzed. The on-treatment tumor phenotype and genotype is established and the therapy is reassessed for one of three scenarios. (1) If sensitivity to therapy is suspected, no changes are made in terms of treatment. (2) If targetable adaptive responses are induced, a second drug is added to generate a patient-specific combination therapy. (3) If the tumor is indifferent to therapy or displays acquired resistance, a new treatment will be selected. Importantly, during the whole process, the progression of the disease is monitored regularly. In case of progression, new samples are acquired and analyzed for therapy reassessment.