scholarly journals Plasticity of extrachromosomal and intrachromosomal BRAF amplifications in mediating targeted therapy dosage challenges

2021 ◽  
Author(s):  
Kai Song ◽  
Jenna K. Minami ◽  
William P. Crosson ◽  
Jesus Salazar ◽  
Eli Pazol ◽  
...  

Cancer cells display two modes of focal amplifications (FAs), extrachromosomal DNA/double-minutes (ecDNA/DMs) and intrachromosomal homogenously staining regions (HSRs). Understanding the plasticity of these two modes is critical for preventing targeted therapy resistance. We developed a combined BRAF plus MEK inhibitor resistance melanoma model that bears high BRAF amplifications through both DM and HSR modes, and investigated FA dynamics in the context of drug resistance plasticity. Cells harboring FAs displayed mode switching between DMs and HSRs, from both de novo genetic changes and selection of pre-existing subpopulations. We found that copy number plasticity is not exclusive to DMs. Single cell-derived clones with HSRs also exhibit BRAF copy number and corresponding HSR length plasticity that allows them to respond to dose reduction and recover from drug addiction. Upon kinase inhibitor escalation, we observed reproducible selection for cells with BRAF kinase domain duplications residing on DMs. In sum, the plasticity of FAs allows cancer cells to respond to drug dose changes through a myriad of mechanisms. These mechanisms include increases or decreases in DMs, shortening of HSRs, acquisition of secondary resistance mechanisms, and expression of alternative slicing oncogene variants. These results highlight the challenges in targeting the cellular vulnerabilities tied to focal amplifications.

2018 ◽  
Vol 62 (4) ◽  
pp. 583-593 ◽  
Author(s):  
Peter T. Harrison ◽  
Paul H. Huang

Drug resistance remains one of the greatest challenges facing precision oncology today. Despite the vast array of resistance mechanisms that cancer cells employ to subvert the effects of targeted therapy, a deep understanding of cancer signalling networks has led to the development of novel strategies to tackle resistance both in the first-line and salvage therapy settings. In this review, we provide a brief overview of the major classes of resistance mechanisms to targeted therapy, including signalling reprogramming and tumour evolution; our discussion also focuses on the use of different forms of polytherapies (such as inhibitor combinations, multi-target kinase inhibitors and HSP90 inhibitors) as a means of combating resistance. The promise and challenges facing each of these polytherapies are elaborated with a perspective on how to effectively deploy such therapies in patients. We highlight efforts to harness computational approaches to predict effective polytherapies and the emerging view that exceptional responders may hold the key to better understanding drug resistance. This review underscores the importance of polytherapies as an effective means of targeting resistance signalling networks and achieving durable clinical responses in the era of personalised cancer medicine.


2019 ◽  
Vol 21 (1) ◽  
pp. 237 ◽  
Author(s):  
Husain Yar Khan ◽  
James Ge ◽  
Misako Nagasaka ◽  
Amro Aboukameel ◽  
Gabriel Mpilla ◽  
...  

Lenvatinib is a multitargeted tyrosine kinase inhibitor (TKI) that shows improved median progression-free survival (PFS) in patients with thyroid carcinomas. However, virtually all patients ultimately progress, indicating the need for a better understanding of the mechanisms of resistance. Here, we examined the molecular profile of anaplastic thyroid cancer cells (8505C) exposed to lenvatinib and found that long-term exposure to lenvatinib caused phenotypic changes. Consistent with change toward mesenchymal morphology, activation of pro-survival signaling, nuclear exporter protein exportin 1 (XPO1) and Rho GTPase effector p21 activated kinases (PAK) was also observed. RNA-seq analysis showed that prolonged lenvatinib treatment caused alterations in numerous cellular pathways and several oncogenes such as CEACAM (carcinoembryonic antigen-related cell adhesion molecule) and NUPR1 (Nuclear protein 1) were also upregulated. Further, we evaluated the impact of XPO1 and PAK4 inhibition in the presence or absence of lenvatinib. Targeted inhibition of XPO1 and PAK4 could sensitize the 8505C cells to lenvatinib. Both XPO1 and PAK4 inhibitors, when combined with lenvatinib, showed superior anti-tumor activity in 8505C sub-cutaneous xenograft. These studies bring forward novel drug combinations to complement lenvatinib for treating anaplastic thyroid cancer. Such combinations may possibly reduce the chances of lenvatinib resistance in thyroid cancer patients.


2001 ◽  
Vol 276 (50) ◽  
pp. 47131-47135 ◽  
Author(s):  
Carl E. Clay ◽  
Gen-ichi Atsumi ◽  
Kevin P. High ◽  
Floyd H. Chilton

Cyclopentenone prostaglandin derivatives of arachidonic acid are potent inducers of apoptosis in a variety of cancer cell types. Several investigators have shown that the terminal derivative of prostaglandin J2(PGJ2) metabolism, 15-deoxy-Δ12,14-PGJ2(15dPGJ2), induces apoptosis in breast cancer cells and is a potent activator of the nuclear hormone receptor peroxisome proliferator-activated receptor γ (PPARγ), but 15dPGJ2effects can be mediated by PPARγ-dependent and PPARγ-independent mechanisms. Here we report that 15dPGJ2regulates early gene expression critical to apoptosis. Specifically, 15dPGJ2induces potent and irreversible S phase arrest that is correlated with expression of genes critical to cell cycle arrest and apoptosis, including the cyclin-dependent kinase inhibitor p21Waf1/Cip1(p21). Inhibition of RNA or protein synthesis abrogates apoptosis induced by 15dPGJ2in breast cancer cells but potentiates apoptosis induced by tumor necrosis factor-α or CD95/Fas ligand. Additionally, 15dPGJ2induces caspase activation that is blocked by peptide caspase inhibitors. These data show thatde novogene transcription is necessary for 15dPGJ2-induced apoptosis in breast cancer cells. Critical candidate genes are likely to be revealed through analysis of differential cDNA array expression.


2017 ◽  
Author(s):  
Marco Ranzani ◽  
Kristel Kemper ◽  
Magali Michaut ◽  
Oscar Krijgsman ◽  
Nanne Aben ◽  
...  

AbstractDespite recent therapeutic advances in the management ofBRAFV600-mutant melanoma, there is still a compelling need for more effective treatments for patients who developedBRAF/NRASwild type disease. Since the activity of single targeted agents is limited by innate and acquired resistance, we performed a high-throughput drug screen using 180 drug combinations to generate over 18,000 viability curves, with the aim of identifying agents that synergise to killBRAF/NRASwild type melanoma cells. From this screen we observed strong synergy between the tyrosine kinase inhibitor nilotinib and MEK inhibitors and validated this combination in an independent cell line collection. We found that AXL expression was associated with synergy to the nilotinib/MEK inhibitor combination, and that both drugs work in concert to suppress pERK. This finding was supported by genome-wide CRISPR screening which revealed that resistance mechanisms converge on regulators of the MAPK pathway. Finally, we validated the synergy of nilotinib/trametinib combinationin vivousing patient-derived xenografts. Our results indicate that a nilotinib/MEK inhibitor combination may represent an effective therapy inBRAF/NRASwild type melanoma patients.


2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Lun-Xi Peng ◽  
Guang-Ling Jie ◽  
An-Na Li ◽  
Si-Yang Liu ◽  
Hao Sun ◽  
...  

Abstract Background MET amplification plays an important role in the development of non-small-cell lung cancer (NSCLC) either de novo or in resistance to epidermal growth factor receptor tyrosine–kinase inhibitor (EGFR-TKI) settings. Fluorescence in situ hybridization (FISH) is the standard method for MET amplification. With more and more discoveries of oncogenic driver genes, next-generation sequencing (NGS) plays a significant role in precision oncology. Meanwhile, the role of NGS in MET amplification remains uncertain. Methods Forty patients diagnosed with advanced NSCLC were included. FISH and NGS were conducted prior to MET inhibitors treatment. MET amplification by FISH was defined as a MET/CEP7 ratio of  >  2.0 and/or copy number (CN)  >  5. MET amplification by NGS was defined as gene copy number (GCN)  ≥  5. Results The concordance rate among FISH and NGS was 62.5% (25/40). MET amplification identified by FISH showed the optimal predictive value. The partial response (PR) rate was 68.0% (17/25 with MET amplification) vs. 6.7% (1/15 without MET amplification); the median progression-free survival (PFS) was 5.4 months versus 1.0 months (P  < 0.001). MET amplification identified by NGS failed to distinguish significant clinical outcomes. The PR rate was 60.0% (6/10, with MET GCN  ≥ 5) vs. 40.0% (12/30, with MET GCN  < 5); the median PFS was 4.8 months vs. 2.2 months (P  = 0.357). The PR rate was 68.8% (11/16) and the median PFS was 4.8 months in patients with focal amplification by NGS. Conclusions MET amplification identified by FISH remains the optimal biomarker to identify suitable candidates for MET-TKI therapy. In comparison, amplification identified by NGS seems not as robust to be effective predictive biomarker. Further exploration is needed regarding the focal amplification by NGS in predicting the efficacy.


2019 ◽  
Vol 33 (S1) ◽  
Author(s):  
Paula Rocío Vigo‐Morales ◽  
Luis Daniel Borrero‐Garcia ◽  
Maria Del Mar Maldonado ◽  
Suranganie Dharmawardhane

2018 ◽  
Vol 144 (3) ◽  
pp. 545-557 ◽  
Author(s):  
Denise Treue ◽  
Michael Bockmayr ◽  
Albrecht Stenzinger ◽  
Daniel Heim ◽  
Svenja Hester ◽  
...  

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Massimo Pancione ◽  
Guido Giordano ◽  
Andrea Remo ◽  
Antonio Febbraro ◽  
Lina Sabatino ◽  
...  

Over the past decade, growing evidence indicates that the tumor microenvironment (TME) contributes with genomic/epigenomic aberrations of malignant cells to enhance cancer cells survival, invasion, and dissemination. Many factors, produced orde novosynthesized by immune, stromal, or malignant cells, acting in a paracrine and autocrine fashion, remodel TME and the adaptive immune response culminating in metastasis. Taking into account the recent accomplishments in the field of immune oncology and using metastatic colorectal cancer (mCRC) as a model, we propose that the evasion of the immune surveillance and metastatic spread can be achieved through a number of mechanisms that include (a) intrinsic plasticity and adaptability of immune and malignant cells to paracrine and autocrine stimuli or genotoxic stresses; (b) alteration of positional schemes of myeloid-lineage cells, produced by factors controlling the balance between tumour-suppressing and tumour-promoting activities; (c) acquisition by cancer cells of aberrant immune-phenotypic traits (NT5E/CD73, CD68, and CD163) that enhance the interactions among TME components through the production of immune-suppressive mediators. These properties may represent the driving force of metastatic progression and thus clinically exploitable for cancer prevention and therapy. In this review we summarize results and suggest new hypotheses that favour the growing impact of tumor-infiltrating immune cells on tumour progression, metastasis, and therapy resistance.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 2041-2041
Author(s):  
Heike Pfeifer ◽  
Sylvia Wystub ◽  
Barbara Wassmann ◽  
Jaqueline Maier ◽  
Thoralf Lange ◽  
...  

Abstract Abstract 2041 Poster Board II-18 Background: Patients with newly diagnosed and recurrent Philadelphia chromosome positive acute lymphoblastic leukemia (Ph+ALL) differ profoundly in their responsiveness to imatinib: whereas nearly all imatinib-naïve patients with de novo Ph+ALL initially achieve a complete remission (CR), eventually followed by secondary resistance, imatinib rarely induces a CR in patients with disease recurrence after chemotherapy. Mutations in the BCR-ABL tyrosine kinase domain (KD) are commonly associated with acquired imatinib resistance, but their role in primary resistance is not known. Recently, we determined that the same mutation found at relapse could already be detected prior to first imatinib exposure in 30% to 40% of patients with de novo Ph+ALL but surprisingly was not associated with an inferior response to imatinib monotherapy, which resulted in a CR rate exceeding 90%. Possible reasons for the inferior response of patients with recurrent Ph+ALL include a higher frequency of pre-existing mutations, a preponderance of mutations with greater transforming activity, a larger mutant clone or the contribution of non-mutational resistance mechanisms. To elucidate the potential role of these resistance mechanisms, we compared patients with de novo Ph+ALL and patients who had failed prior chemotherapy with respect to the frequency and pattern of pre-existing mutations, the level of mutant clones, the outgrowth kinetics of mutations during the first 4 weeks of imatinib monotherapy and the concordance between mutations detected prior to imatinib and at the time of relapse. Patients and methods: By denaturing high-performance liquid chromatography (D-HPLC; sensitivity 0.1-1%), ligation PCR (sensitivity 0.1-0.005%) and cDNA sequencing, we examined bone marrow and/or peripheral blood samples collected pre-treatment, during therapy and at relapse from 91 patients with Ph+ lymphoid leukemias who were enrolled in the initial phase II studies of imatinib for treatment of BCR-ABL positive leukemias after chemotherapy failure (n=65), or in a prospective, randomized clinical trial assessing front-line imatinib therapy in elderly patients with newly diagnosed Ph+ALL (n=26). Results: Prior to imatinib treatment, the frequency of TKD mutations did not differ significantly between patients with de novo and recurrent Ph+ ALL, respectively (30 % vs. 46%; p=n.s.) as detected by highly sensitive DHPLC and ligation PCR. P-loop mutations predominated in both patient groups (92% and 85% of detected mutations). The T315I gatekeeper mutation was identified in 4 patients, mutations in the activation loop were uncommon. Following only four weeks imatinib, the prevalence of detectable mutations increased substantially in patients with recurrent (to 75%) but not with de novo Ph+ALL (38%). Moreover, the median mutated bcr-abl transcript levels after 4 weeks of imatinib treatment were significantly higher in patients with recurrent than with de novo Ph+ALL (median 10%, [range 0-100] versus median 0%;range [0-7]). Conspicuously, we observed good concordance between the type of bcr-abl mutation detected prior to imatinib and at relapse. Conclusions: The incidence, pattern and levels of TKD mutations detected prior to imatinib and at relapse are similar in advanced and newly diagnosed Ph+ALL. In contrast, the outgrowth kinetics of cells with TKD mutations were far more rapid in patients with recurrent disease. These data provide clinical-translational evidence for a cooperative effect between mutational and non-mutational resistance mechanisms in Ph+ALL, and highlight the importance of early mutation monitoring using highly sensitive methodology. Disclosures: Hochhaus: Novartis : Research Funding. Ottmann:Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees; BMS: Honoraria.


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