Androgen receptor blockade promotes response to BRAF/MEK-targeted therapy

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Background: Treatment with BRAF+/-MEK inhibition (BRAF+/-MEKi) has revolutionized treatment in melanoma and other cancers, but resistance is common and innovative treatment strategies are needed. Sexual dimorphism in response to BRAF+/-MEKi have been noted, but mechanisms behind this are poorly understood and hormonal modulation has not been well-studied in this setting. Methods: We examined outcomes by sex in five clinical cohorts of patients (pts) (total n = 792, 362 female, 430 male) with BRAF-mutated melanoma who were treated with BRAF/MEKi in either the neoadjuvant or metastatic setting. Rates of major pathologic response (MPR), clinical benefit (CB), progression free survival (PFS) relapse-free survival (RFS) and overall survival (OS) were assessed. Translational research studies were performed on available pre- and on-treatment tumor samples (n = 27 pts) including RNA sequencing and profiling androgen receptor (AR) expression. Parallel studies were performed in preclinical models to assess the effect of sex and AR modulation on response to BRAF+/-MEKi. Results: In this study, improved rates of MPR, CB, PFS and OS were observed in female vs male pts. Specifically, female patients treated with neoadjuvant BRAF+MEKi showed significantly higher rates of MPR (66% v. 14%, p = 0.001), and improved RFS (64% versus 32% at 2 years, p = 0.021) vs male pts in the neoadjuvant setting (n = 51). These findings were not observed in a 2nd smaller trial of pts (n = 35), but were validated in a cohort of pts with unresectable metastatic melanoma treated with BRAF+MEKi (n = 69), with significantly higher rates of CB (80% v. 68%, p = 0.022) and PFS (12 v. 7 months, p = 0.003) in female vs male pts. Data from several published trials was analyzed (COMBI-D and METRIC trials), demonstrating improved PFS/OS at 2 years in female vs male pts treated with combined BRAF/MEKi (n = 211; p = 0.03 and, p = 0.04) and in female vs male pts treated with MEKi monotherapy (n = 206; p = 0.04 and p = 0.002), but not in female vs male pts treated with BRAFi monotherapy (n = 211; p = 0.21 and 0.095). Significantly higher expression AR expression was observed in available on- vs pre-treatment samples from male pts (p = 0.01), suggesting that treatment with BRAF/MEKi may induce AR expression in tumors. Findings were recapitulated in several preclinical models, and treatment with pharmacologic inhibitors of AR signaling (enzalutamide) in combination with BRAF/MEKi was associated with significantly enhanced anti-tumor activity in both male and female mice (p = 0.003 and p < 0.0001). Conversely, systemic treatment with testosterone was associated with significantly impaired tumor control in male and female mice (p = 0.021 and < 0.001). Conclusions: These data suggest that AR blockade may promote BRAF/MEKi response in melanoma, warranting further investigation in clinical trials. The impact of AR signaling, and modulation should be studied in MAPK-targeted therapy across other cancer types.

Abstract 317: Vecabrutinib inhibits C481 mutated Bruton's tyrosine kinase and its downstream signaling in vitro

Inhibition of Bruton’s Tyrosine Kinase (BTK) by ibrutinib, an irreversible inhibitor, has dramatically improved the outcomes in both previously treated and naïve chronic lymphocytic leukemia (CLL) patients. Ibrutinib inactivates BTK through covalently binding to the cysteine 481 residue (C481) which then leads to the inhibition of autophosphorylation of BTK and the inactivation of downstream survival nexus. Although ibrutinib demonstrated &gt;90% overall and event-free survival, about 25% of patients discontinue ibrutinib due to leukemia progression and intolerance. Patients that initially respond to treatment may develop resistance and the most prevalent resistance mechanism of ibrutinib is described as the point mutation affecting the C481 residue of BTK that results in disruption of ibrutinib binding and acquired ibrutinib resistance. Most common mutations are C481S and C481R. Vecabrutinib is a potent reversible BTK inhibitor that binds to BTK through noncovalent interactions. As vecabrutinib does not require binding to C481 residue, it retains its efficacy with mutant BTK in vitro. To better understand differential biology of Wild-Type (WT) and serine and arginine substituted BTK, we labelled MEC-1 cell line with green fluorescence protein (GFP) and overexpressed either BTKWT, BTKC481Sor BTKC481R that contributes to ibrutinib resistance. We selected MEC-1 cell line as it represents CLL disease and the phenotype of the cells share several characteristics of ex vivo CLL cells. We performed Reverse Phase Protein Array (RPPA) and mRNA-sequencing to determine and compare the proteomic and transcriptomic profiles of the MEC-1 cells harboring WT and mutant BTK. Ingenuity Pathway Analysis (IPA) of RPPA data revealed that overexpression of BTK WT leads to the enrichment of protein alterations involved in cell cycle regulation, B cell receptor signaling, PI3K/AKT signaling, PTEN signaling and ERK/MAPK signaling. IPA of RNAseq data upon BTK WT overexpression unraveled the top canonical pathways that include signaling through axonal guidance, ephrin receptor, c-AMP mediated, CXCR4 signaling and PTEN signaling. Comparative analysis of MEC-1 cells with mutant BTK (C481S vs C481R) using IPA distinguished the activated pathways in BTKC481Sharboring cells from cells that express BTKC481R. These results are being validated by western blot and qRT-PCR assays. Immunoblotting results showed that following 24, 48, and 72 hour of vecabrutinib (at 1 µM) treatment reduced p-BTK (Tyr223), p-PLCG2 (Tyr759) and p-ERK (Thr 202/Tyr 204) levels in MEC-1 cells with mutant BTK. These data indicate that vecabrutinib effectively inhibits BTK and its downstream signaling in the presence of mutant BTK, suggesting that vecabrutinib treatment may be a rational approach to overcome ibrutinib resistance.

Citation Format: Burcu Aslan, Mikhila Mahendra, Michael D Peoples, Joe R. Marszalek, Christopher P Vellano, Xiaofeng Zheng, Jing Wang, Pietro Taverna, Varsha Gandhi. Vecabrutinib inhibits C481 mutated Bruton's tyrosine kinase and its downstream signaling in vitro [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 317.

Abstract GS5-05: Resistance to neoadjuvant chemotherapy in triple negative breast cancer mediated by a reversible drug-tolerant state

Approximately 50% of patients with localized triple negative breast cancer (TNBC) have substantial residual cancer burden following treatment with neoadjuvant chemotherapy (NACT), resulting in distant metastasis and death for most of these patients. While genomic and phenotypic intra-tumor heterogeneity are pervasive features of TNBCs at the time of diagnosis, the functional contributions of heterogeneous tumor cell populations to chemoresistance have not been elucidated.

To investigate tumor evolution accompanying NACT, we employed orthotopic patient-derived xenograft (PDX) models of treatment-naïve TNBC, which retain intra-tumor heterogeneity characteristic of human TNBC. We discovered that some PDX models initially exhibited partial sensitivity to standard front-line NACT (Adriamycin plus Cytoxan, AC). Following AC, residual tumors were resistant to chemotherapy but repopulated tumors with chemo-sensitive cells if left untreated, indicating that tumor cells possessed inherent plasticity. To identify the tumor cell subpopulation(s) conferring chemoresistance, we conducted barcode-mediated clonal tracking in three independent PDX models by introducing a high-complexity pooled lentiviral barcode library into PDX tumor cells which were then orthotopically engrafted into recipient mice. Strikingly, residual tumors maintained the same heterogeneous clonal architecture as naïve tumors. Concordantly, whole-exome sequencing revealed conservation of genomic subclonal architecture throughout treatment. These results were corroborated by genomic sequencing of serial biopsies pre- and post-AC obtained directly from TNBC patients enrolled on an ongoing clinical trial at MD Anderson (ARTEMIS; NCT02276443). Together, these studies revealed that genomically distinct pre-treatment subclones were equally capable of surviving AC to reconstitute tumors after treatment.

To identify functional addictions of residual tumor cells, we conducted histologic and transcriptomic profiling. Residual tumors following AC-treatment exhibited extensive fibrotic desmoplasia and tumor cell pleomorphism in both PDX models and in serial biopsies obtained from TNBC patients enrolled on the ARTEMIS trial. Strikingly, these AC-induced features were reverted upon regrowth of residual tumors in PDXs and in patients' tumors. Similarly, residual tumors exhibited unique transcriptomic features, many of which are also de-regulated in cohorts of human TNBCs undergoing chemotherapy treatment. These features were nearly completely reverted after tumors regrew, suggesting that the residual tumor state may be a unique and transient therapeutic window. Gene set enrichment analyses revealed that residual tumors had increased activation of oxidative phosphorylation and decreased glycolytic signaling. Pharmacologic targeting of oxidative phosphorylation with a small-molecule inhibitor of mitochondrial electron transport chain complex I (IACS-010759) significantly delayed the regrowth of AC-treated residual tumors in three independent PDX models. Collectively, these studies reveal that a reversible phenotypic state can confer chemoresistance in the absence of genomic selection and that the residual tumor state is a novel therapeutic window for chemo-refractory TNBC.

Citation Format: Echeverria GV, Ge Z, Seth S, Jeter-Jones SL, Zhang X, Zhou X, Cai S, Tu Y, McCoy A, Peoples M, Lau R, Shao J, Sun Y, Bristow C, Carugo A, Ma X, Harris A, Wu Y, Moulder S, Symmans WF, Marszalek JR, Heffernan TP, Chang JT, Piwnica-Worms H. Resistance to neoadjuvant chemotherapy in triple negative breast cancer mediated by a reversible drug-tolerant state [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr GS5-05.

Abstract LB-071: Discovery of an imidazopyridine series of potent human IDO1 inhibitors with robust target engagement in a preclinical tumor model

Indoleamine 2,3-dioxygenase (IDO1 and IDO2) and tryptophan dioxygenase (TDO) are heme-containing enzymes that mediate the rate limiting step in the oxidative degradation of L-tryptophan (L-TRP) to kynurenine (KYN) metabolites. Tryptophan catabolism through the KYN metabolic pathway is now recognized as one of many mechanisms involved in tumor cell evasion of the immune surveillance system. Inhibition of the KYN pathway in the tumor microenvironment can lead to improved immune response and tumor growth suppression. Recently, clinical proof of concept of this mechanism has been demonstrated using an Indoleamine 2,3-dioxygenase (IDO1) inhibitor in combination with a PD-1 antagonist in a variety of tumor contexts. Consideration of known low molecular weight heme-co-ordinating ligands identified from the PDB, in conjunction with a virtual screen performed in-silico identified a number of potentially interesting starting points for medicinal chemistry development. Identification of an attractive indazole fragment as a starting point, and expansion into alternative bicyclic cores, resulted in the discovery of a family of imidazopyridines as potent human IDO1 inhibitors with &gt;200 fold selectivity against TDO. Utilizing a structure-based design approach allowed rapid lead optimization that resulted in the identification of IACS-8968. Crystallography studies were conducted, and binding of IACS-8968 to the heme domain of the human IDO1 was confirmed. The homochiral imidazopyridine IACS-8968 displayed cellular IC50= 29 nM in a HeLa cell line expressing human IDO1 and IC50= 21 nM in a PANC02 mouse cell line expressing the murine IDO1 enzyme, showed satisfactory selectivity margin (&gt; 150 fold) versus its CYP450 inhibition profile and good oral bioavailability across species. PK/PD experiments indicated that, at equivalent exposure, IACS-8968 (sodium salt) and epacadostat decreased tumor KYN at comparable levels in CT26 syngeneic mouse model.

Citation Format: Alessia Petrocchi, Naphtali J. Reyna, Faika Mseeh, Connor A. Parker, Simon Yu, Quanyun Xu, Ningping Feng, Paul Leonard, Norma Rogers, Jason B. Cross, Angela L. Harris, Yongying Jiang, Tin Oo Khor, Mikhila G. Mahendra, Jihai Pang, Qi Wu, Andy M. Zuniga, Timothy McAfoos, Timothy McAfoos, Matthew M. Hamilton, Joe R. Marszalek, Keith Mikule, Paul Vancutsem, Keith Wilcoxen, Martin Tremblay, Philip Jones, Richard T. Lewis. Discovery of an imidazopyridine series of potent human IDO1 inhibitors with robust target engagement in a preclinical tumor model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-071.

Genetic evidence for selective transport of opsin and arrestin by kinesin-II in mammalian photoreceptors

To test whether kinesin-II is important for transport in the mammalian photoreceptor cilium, and to identify its potential cargoes, we used Cre-loxP mutagenesis to remove the kinesin-II subunit, KIF3A, specifically from photoreceptors. Complete loss of KIF3A caused large accumulations of opsin, arrestin, and membranes within the photoreceptor inner segment, while the localization of alpha-transducin was unaffected. Other membrane, organelle, and transport markers, as well as opsin processing appeared normal. Loss of KIF3A ultimately caused apoptotic photoreceptor cell death similar to a known opsin transport mutant. The data suggest that kinesin-II is required to transport opsin and arrestin from the inner to the outer segment and that blocks in this transport pathway lead to photoreceptor cell death as found in retinitis pigmentosa.

Understanding the functions of kinesin-II

Species ranging from Chlamydomonas to humans possess the heterotrimeric kinesin-II holoenzyme composed of two different motor subunits and one non-motor accessory subunit. An important function of kinesin-II is that it transports the components needed for the construction and maintenance of cilia and flagella from the site of synthesis in the cell body to the site of growth at the distal tip. Recent work suggests that kinesin-II does not directly interact with these components, but rather via a large protein complex, which has been termed a raft (intraflagellar transport (IFT)). While ciliary transport is the best-established function for kinesin-II, evidence has been reported for possible roles in neuronal transport, melanosome transport, the secretory pathway and during mitosis.

Novel dendritic kinesin sorting identified by different process targeting of two related kinesins: KIF21A and KIF21B

Neurons use kinesin and dynein microtubule-dependent motor proteins to transport essential cellular components along axonal and dendritic microtubules. In a search for new kinesin-like proteins, we identified two neuronally enriched mouse kinesins that provide insight into a unique intracellular kinesin targeting mechanism in neurons. KIF21A and KIF21B share colinear amino acid similarity to each other, but not to any previously identified kinesins outside of the motor domain. Each protein also contains a domain of seven WD-40 repeats, which may be involved in binding to cargoes. Despite the amino acid sequence similarity between KIF21A and KIF21B, these proteins localize differently to dendrites and axons. KIF21A protein is localized throughout neurons, while KIF21B protein is highly enriched in dendrites. The plus end-directed motor activity of KIF21B and its enrichment in dendrites indicate that models suggesting that minus end-directed motor activity is sufficient for dendrite specific motor localization are inadequate. We suggest that a novel kinesin sorting mechanism is used by neurons to localize KIF21B protein to dendrites since its mRNA is restricted to the cell body.

Situs inversus and embryonic ciliary morphogenesis defects in mouse mutants lacking the KIF3A subunit of kinesin-II

The embryonic cellular events that set the asymmetry of the genetic control circuit controlling left-right (L-R) axis determination in mammals are poorly understood. New insight into this problem was obtained by analyzing mouse mutants lacking the KIF3A motor subunit of the kinesin-II motor complex. Embryos lacking KIF3A die at 10 days postcoitum, exhibit randomized establishment of L-R asymmetry, and display numerous structural abnormalities. The earliest detectable abnormality in KIF3A mutant embryos is found at day 7.5, where scanning electron microscopy reveals loss of cilia ordinarily present on cells of the wild-type embryonic node, which is thought to play an important role in setting the initial L-R asymmetry. This cellular phenotype is observed before the earliest reported time of asymmetric expression of markers of the L-R signaling pathway. These observations demonstrate that the kinesin-based transport pathway needed for flagellar and ciliary morphogenesis is conserved from Chlamydomonas to mammals and support the view that embryonic cilia play a role in the earliest cellular determinative events establishing L-R asymmetry.

Identification, partial characterization, and genetic mapping of kinesin-like protein genes in mouse

Microtubule-dependent motors of the kinesin superfamily have undergone structural and functional diversification during evolution and play crucial roles in cell division and intracellular transport. Degenerate oligonucleotides homologous to highly conserved regions of sequence within the motor domain were used in a polymerase chain reaction to isolate five new members (KIF3C, KIFC2, KIFC3, KIFC4, and KIF22) of the kinesin superfamily from a mouse brain cDNA library. Northern analysis showed that KIF3C and KIFC2 are expressed mainly in neural tissues, that KIFC4 and KIF22 are expressed primarily in proliferative tissues and cell lines, and that KIFC3 is apparently ubiquitous. To elucidate the organization of genes encoding kinesin-like motors in the mouse genome and to explore the potential associations of these genes with classical mouse mutations or human genetic diseases, these new genes as well as genes encoding the previously reported KIF3A and KIF3B motors were mapped to mouse chromosomes by using an interspecific backcross panel of DNAs from The Jackson Laboratory. The data indicate that the gene KIFC4 is present in three copies in the mouse genome on chromosomes 13 (KIFC4A), 10 (KIFC4B), and 17 (KIFC4C). The gene KIF22 is present in two copies on chromosomes 7 (KIF22A) and 1 (KIF22B). The genes KIF3A, KIF3B, KIF3C, KIFC2, and KIFC3 are each single loci and map to chromosomes 11, 2, 12, 15, and 8, respectively.

Neurofilament subunit NF-H modulates axonal diameter by selectively slowing neurofilament transport

To examine the mechanism through which neurofilaments regulate the caliber of myelinated axons and to test how aberrant accumulations of neurofilaments cause motor neuron disease, mice have been constructed that express wild-type mouse NF-H up to 4.5 times the normal level. Small increases in NF-H expression lead to increased total neurofilament content and larger myelinated axons, whereas larger increases in NF-H decrease total neurofilament content and strongly inhibit radial growth. Increasing NF-H expression selectively slow neurofilament transport into and along axons, resulting in severe perikaryal accumulation of neurofilaments and proximal axonal swellings in motor neurons. Unlike the situation in transgenic mice expressing modest levels of human NF-H (Cote, F., J.F. Collard, and J.P. Julien. 1993. Cell. 73:35-46), even 4.5 times the normal level of wild-type mouse NF-H does not result in any overt phenotype or enhanced motor neuron degeneration or loss. Rather, motor neurons are extraordinarily tolerant of wild-type murine NF-H, whereas wild-type human NF-H, which differs from the mouse homolog at > 160 residue positions, mediates motor neuron disease in mice by acting as an aberrant, mutant subunit.

Mechanisms of selective motor neuron death in transgenic mouse models of motor neuron disease

To examine the mechanism(s) of disease underlying ALS, transgenic mouse models have been constructed that express aberrant neurofilaments or mutations in the abundant, cytoplasmic enzyme superoxide dismutase 1 (SOD1). In addition to progressive weakness arising from selective motor neuron death, mice expressing a modest level of a point mutant in neurofilament subunit NF-L show most of the pathologic hallmarks observed in familial and sporadic ALS, including perikaryal proximal axonal swellings, axonal degeneration, and severe skeletal muscle atrophy. Additional mice expressing familial ALS-linked mutations in the cytoplasmic enzyme SOD1, the only proven cause of ALS and which accounts for approximately 20% of familial disease, have demonstrated that at least one mutation causes disease through acquisition of an adverse property by the mutant enzyme, rather than elevation or loss of SOD1 activity. These animals not only provide a detailed look at the pathogenic progression of disease, but also represent a tool for testing hypotheses concerning the specific mechanism(s) of neuronal death and for testing therapeutic strategies.

Subunit composition of neurofilaments specifies axonal diameter

Neurofilaments (NFs), which are composed of NF-L, NF-M, and NF-H, are required for the development of normal axonal caliber, a property that in turn is a critical determinant of axonal conduction velocity. To investigate how each subunit contributes to the radial growth of axons, we used transgenic mice to alter the subunit composition of NFs. Increasing each NF subunit individually inhibits radial axonal growth, while increasing both NF-M and NF-H reduces growth even more severely. An increase in NF-L results in an increased filament number but reduced interfilament distance. Conversely, increasing NF-M, NF-H, or both reduces filament number, but does not alter nearest neighbor interfilament distance. Only a combined increase of NF-L with either NF-M or NF-H promotes radial axonal growth. These results demonstrate that both NF-M and NF-H play complementary roles with NF-L in determining normal axonal calibers.

A mutant neurofilament subunit causes massive, selective motor neuron death: implications for the pathogenesis of human motor neuron disease

A direct role of aberrant neurofilament accumulation in the etiology of human motor neuron diseases, including amyotrophic lateral sclerosis, is suggested by the presence of abnormal accumulations of neurofilaments as an early hallmark of the pathogenic process. Furthermore, forcing increased expression of neurofilament subunits in transgenic mouse models leads to motor neuron dysfunction, albeit without the widespread motor neuron death typical of human disease. We now show that accumulation of a modest level of a point mutant in the smallest neurofilament subunit (NF-L) causes massive, selective degeneration of spinal motor neurons accompanied by abnormal accumulations of neurofilaments and severe neurogenic atrophy of skeletal muscles. As in human disease, sensory neurons show only a modest level of degenerative changes. Thus, neurofilament mutations can cause selective motor neuron death, and neurofilamentous abnormalities may be a common toxic intermediate that significantly contributes to the motor neuron death in human disease.