Abstract 2623: Variants of CLIP-170 associated with taxane resistance in tumors

Despite its widespread use, the majority of patients with gastric cancer (GC) will not respond to taxane chemotherapy due to resistance mechanisms. Recently, we reported the discovery of a novel truncated variant of the microtubule plus-end binding protein CLIP-170, hereafter CLIP-170S, whose expression is enriched in taxane resistant cell lines and patients with GC. Mass-spec proteomics and 5’-RACE further showed that CLIP-170S lacked the first 155 amino acids, including the Cap-Gly motif required for microtubule plus-end localization. CLIP-170S knockdown reversed taxane resistance in cells and xenografts, whereas its re-expression led to resistance, suggesting causation. Unlike canonical CLIP-170, we showed that CLIP-170S was mislocalized from the MT plus-end to the MT lattice. Computational analysis of RNA-seq data in conjunction with the connectivity map from taxane-sensitive and resistant GC cell lines, predicted imatinib as the top candidate drug to overcome drug resistance. Imatinib treatment completely reversed taxane resistance, as predicted, and did so unexpectedly by selective depletion of CLIP-170S. Other RTK inhibitors also depleted CLIP-170S, suggesting a class effect. We are currently unraveling the molecular mechanisms by which a) CLIP-170S impairs taxane association to its microtubule binding site and b) Imatinib and other RTK inhibitors selectively deplete CLIP-170S. Our data show that CLIP-170S is a clinically prevalent variant that confers taxane resistance in tumors, whereas the discovery of Imatinib as a CLIP-170S inhibitor provides novel therapeutic opportunities for future trials.

Citation Format: Prashant V. Thakkar, Katsuhiro Kita, Urko del Castillo, William G. Stone, Giuseppe Galletti, Neel Madhukar, Elena Vila Navarro, Elena Barasoain, Holly V. Goodson, Dan Sackett, José Fernando Díaz, Yao Lu, Arindam RoyChoudhury, Henrik Molina, Olivier Elemento, Manish A. Shah, Paraskevi Giannakakou. Variants of CLIP-170 associated with taxane resistance in tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2623.

Abstract 1264: CTC-based biomarker analysis and correlation with clinical response to PSMA-TRT in mCRPC

Prostate specific membrane antigen (PSMA)-targeted radionuclide therapies (PSMA-TRTs) is one of the most promising treatments for metastatic castration-resistant prostate cancer (mCRPC) upon progression on androgen receptor signaling inhibitors (ARPi). However, recent studies show that only about half of patients respond to PSMA-TRTs. Expression of PSMA on cancer cells via PET-imaging is of some use as a predictive biomarker of response to PSMA-TRTs, but there are patients with strong PSMA imaging who do not respond and some with poor PSMA imaging that do respond. PSMA imaging does not fully capture response predictability. Currently, the lack of predictive biomarkers of response limits optimal selection of the patient population most likely to benefit from to PSMA-TRTs. PSMA-TRTs radionuclides emit α or β radiations, which induce DNA damage in targeted cells, followed by immunogenic cell death (ICD), evidenced by calreticulin (CRT) plasma membrane accumulation. To investigate the role of PSMA expression and CRT membrane localization as a biomarker of response to PSMA-TRT, we isolated circulating tumor cells (CTCs) from patients with mCRPC, enrolled in a phase I dose escalation trial of 225Ac-J591 (NCT03276572). Thirty-two (32) patients were enrolled (median age 69. 5, range 52-89; PSA 149.1, range 4.8-7168); 78% and 68% of patients received ≥ 2 prior ARPi treatments or chemotherapy, respectively. 69% and 44% of patients experienced any or >50% PSA decline, respectively, with a median PFS of 5.1 months and median OS of 11.1 months. CTCs were isolated before treatment (baseline) from 30/32 of enrolled patients, and 12 weeks after treatment initiation (on-treatment) from 21/32 patients. Enriched CTCs via CD45 depletion were subsequently immunostained for cytokeratin (CK, standard epithelial marker), CD45 (standard marker to identify contaminating leukocytes), PSMA, calreticulin (CRT) and DAPI. CTCs were subjected to multiplex confocal microscopy and identified as CK+/CD45-/DAPI+ cells. For each patient, at each time point, the following parameters are scored: i) total number of CTCs, ii) number of PSMA+ CTCs, iii) number of CRT+ CTCs, iv) number of CTCs with plasma membrane CRT decoration. Percent of PSMA+ CTC at baseline and changes in percentage of CRT+ CTCs and CTCs with plasma membrane CRT decoration between baseline and on treatment timepoints are correlated with clinical response and time to progression upon 225Ac-J591 treatment. Our preliminary results indicate higher expression of plasma membranous CRT in on-treatment CTCs in responders (PFS>12 months; n= 39 CTCs from 3 patients) than in non-responders (PFS<3 months; n= 20 CTCs from 2 patients). Full analysis of CRT and PSMA expression is currently being completed.

Citation Format: Giuseppe Galletti, Prerna Vatsa, Joseph R. Osborne, Neil H. Bander, David M. Nanus, Scott T. Tagawa, Paraskevi Giannakakou. CTC-based biomarker analysis and correlation with clinical response to PSMA-TRT in mCRPC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1264.

Abstract 646: Liquid biopsy transcriptomics identify pathways associated with poor outcomes and immune phenotypes in men with mCRPC

Androgen receptor signaling inhibitors (ARSi) and taxanes are mainstays for patients with metastatic castration-resistant prostate cancer (mCRPC). However, patient response is heterogeneous, and the molecular underpinnings of treatment resistance are not well elucidated.

To identify clinically meaningful mechanisms of treatment resistance, we performed transcriptome analysis of circulating tumor cells (CTCs) isolated from mCRPC patients enrolled in two independent prospective clinical trials: PROPHECY, a clinical study of patients (n=118) treated with abiraterone or enzalutamide followed by docetaxel; and TAXYNERGY where patients were randomized to docetaxel or cabazitaxel treatment. CTCs were obtained at baseline (before treatment), on treatment and at progression and their comprehensive transcriptomic analysis was correlated with clinical outcomes. To uncover potential involvement of the circulating immune macroenvironment (CIME) in treatment resistance, we performed transcriptomic analysis of matching peripheral blood mononuclear cells (PBMCs) using an established, rigorous, blood-derived transcriptional modular framework.

In PROPHECY, CTC RNA-seq identified that RB loss concurrently with enhanced E2F signaling networks were associated with intrinsic ARSi resistance. Using single sample GSEA (ssGSEA) score, we identified that the RB/E2F common signature at baseline was associated with short PFS (median PFS=6.5 months) and OS (median OS=24.5 months) (hazard ratio (HR) = 3.5; 95% CI 1.5-8.2) in men with mCRPC. We further developed a BRCA-loss transcriptional signature, and validated it in the SU2C mCRPC patient cohort, expanding the identification of patients with BRCA-loss phenotypes beyond genomic loss. Applying this signature to PROPHECY baseline samples, we showed that men with high BRCA-loss scores experienced shorter OS (HR=2.42; 95% CI=1-5.9). Through the comparison of CTC transcriptomic profiles at progression with baseline, we identified an inflammatory response signature in CTCs which was significantly associated with acquired ARSi resistance. Transcriptomic PBMC analysis further identified enrichment of inflammasome gene signatures at progression, with concurrent downregulation of CD8+ T and NK cells.

Furthermore, preliminary data from both clinical trials, showed a significant upregulation of TGF-β1 and corresponding TGFβ-Receptor signaling pathway in CTCs from patients at progression following taxane treatment, suggesting a role for TGFβ pathway in clinical response to taxane chemotherapy.

Taken together, these data demonstrate that liquid biopsy transcriptomics of both tumor cells and immune cells can identify molecular pathways associated with treatment resistance paving the way for treatment optimization and the development of novel precision therapies in patients with mCRPC.

Citation Format: Jiaren Zhang, Bob Zimmermann, Giuseppe Galletti, Susan Halabi, Ada Gjyrezi, Qian Yang, Santosh Gupta, Akanksha Verma, Andrea Sboner, Monika Anand, Daniel J. George, Simon G. Gregory, Prerna Mahtani, Seunghee Hong, Virginia Pascual, Clio P. Mavragani, Emmanuel S. Antonarakis, David M. Nanus, Scott T. Tagawa, Olivier Elemento, Andrew J. Armstrong, Paraskevi Giannakakou. Liquid biopsy transcriptomics identify pathways associated with poor outcomes and immune phenotypes in men with mCRPC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 646.

Association of circulating tumor cell RB1 loss RNA signature with outcomes and immune phenotypes in men with mCRPC

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Background: Androgen receptor signaling inhibitors (ARSi) are a mainstay for patients with metastatic castration-resistant prostate cancer (mCRPC). However, patient response is heterogeneous and the molecular underpinnings of ARSi resistance are not well elucidated. Methods: We performed transcriptome analysis of circulating tumor cells (CTCs) and peripheral blood mononuclear cells (PBMC) in the context of PROPHECY, a prospective clinical trial of men (n = 118) with mCRPC treated with abiraterone (Abi) or enzalutamide (Enza). We obtained CTCs at baseline (before treatment) and at the time of progression on Abi/Enza, performed a comprehensive transcriptomic analysis of CTC patient samples (n = 40) and correlated with clinical outcomes to identify mechanisms of ARSi resistance. In addition, we also performed a transcriptomic analysis of matching peripheral blood mononuclear cells (PBMCs) in order to uncover potential involvement of the circulating immune macroenvironment (CIME) in ARSi resistance. The proportional hazard model was used to determine the prognostic significance of these signatures in predicting overall survival (OS) and progression-free survival (PFS). Results: CTC RNA-sequencing identified that RB loss concurrently with enhanced E2F signaling transcriptional networks were associated with intrinsic ARSi resistance. Using single sample GSEA (ssGSEA) score, we identified that the RB/E2F common signature at baseline was associated with short PFS (median PFS = 6.5 months) and OS (median OS = 24.5 months) (hazard ratio (HR) = 3.5; 95% CI 1.5-8.2) in men with mCRPC. We further developed a BRCA loss transcriptional signature which we validated in the SU2C mCRPC patient cohort, by showing that BRCA loss transcriptional network reflected BRCA genomic alterations as it was significantly enriched in the SU2C BRCA-altered patients vs unaltered patients. Generating BRCA loss ssGSEA scores in the PROPHECY cohort we observed that patients with high BRCA loss scores at baseline experienced shorter OS (HR = 2.42; 95% CI = 1-5.9). Through the comparison of CTC transcriptomic profiles at progression with baseline, we identified an inflammatory response signature in CTCs which was significantly associated with acquired ARSi resistance. Transcriptomic analysis of matching PBMCs identified enrichment of inflammasome gene signatures indicative of activated innate immunity at progression, with concurrent downregulation of CD8 T and NK cells. Importantly, CTC gene signatures of RB loss/E2F signaling had a significant positive association with this CIME signatures. Conclusions: Taken together, these data demonstrate that liquid biopsy transcriptomics of both tumor cells and immune cells can identify molecular pathways associated with clinical ARSi resistance paving the way for treatment optimization and the development of novel precision therapies in patients with mCRPC.

CLIP-170S is a microtubule +TIP variant that confers resistance to taxanes by impairing drug-target engagement

Taxanes are widely used cancer chemotherapeutics. However, intrinsic resistance limits their efficacy without any actionable resistance mechanism. We have discovered a microtubule (MT) plus-end-binding CLIP-170 protein variant, hereafter CLIP-170S, which we found enriched in taxane-resistant cell lines and patient samples. CLIP-170S lacks the first Cap-Gly motif, forms longer comets, and impairs taxane access to its MT luminal binding site. CLIP-170S knockdown reversed taxane resistance in cells and xenografts, whereas its re-expression led to resistance, suggesting causation. Using a computational approach in conjunction with the connectivity map, we unexpectedly discovered that Imatinib was predicted to reverse CLIP-170S-mediated taxane resistance. Indeed, Imatinib treatment selectively depleted CLIP-170S, thus completely reversing taxane resistance. Other RTK inhibitors also depleted CLIP-170S, suggesting a class effect. Herein, we identify CLIP-170S as a clinically prevalent variant that confers taxane resistance, whereas the discovery of Imatinib as a CLIP-170S inhibitor provides novel therapeutic opportunities for future trials.

Short communication: Seroprevalence of paratuberculosis in Italian water buffaloes (Bubalus bubalis) in the region of Campania

Paratuberculosis is a chronic enteric disease affecting virtually all ruminants, but only anecdotal information is currently available about the occurrence of this disease in water buffaloes (Bubalus bubalis). We carried out a survey study aimed at determining the prevalence of paratuberculosis in 2 provinces in the region of Campania, Italy, where about half of all Italian buffaloes are reared. From May 2017 to December 2018, we collected 201,175 individual serum samples from 995 buffalo herds. The sera were collected from animals over 24 mo old and were tested using a commercial ELISA test. The herd-level apparent prevalence result was 54.7%, and the animal-level apparent prevalence was 1.8%. The herd-level true prevalence was estimated using a Bayesian approach, demonstrating a high herd-level prevalence of paratuberculosis in water buffaloes from the Campania area. These findings suggest that the urgent adoption of paratuberculosis herd-control programs for water buffaloes in this area would be beneficial.

Phase I trial of apalutamide (Apa) with abiraterone acetate (AA) plus prednisone (P) and docetaxel (Doce) in patients with metastatic castration-resistant prostate cancer (mCRPC)

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Background: The combination of AR inhibition plus taxane chemotherapy has demonstrated clinical benefit in PC ( i.e. CHAARTED, STAMPEDE), indicating efficacy when targeting the AR signaling pathway at different points. We launched a phase I study to test the hypothesis that the combination of Apa (AR signaling inhibitor), AA (CYP17 inhibitor) + P, and Doce (inhibitor of AR translocation to the nucleus) is safe and effective. Previously we reported that the full doses of all drugs were tolerated in combination and the recommended phase II dose (R2PD). Here we present addition of the expansion cohort and longer follow up. Methods: Men were enrolled with progressive mCRPC, intact organ function, and without prior exposure to Doce (within 3 years) or Apa. In the initial dose-escalation portion, standard doses of AA (1000 mg daily), Doce (75 mg/m2 q3 weeks), and P (5 mg BID) were administered initially with different doses of Apa. Cohort 1 = 120 mg/d, Cohort 2 = 240 mg/d in modified 3+3 design. No GCSF was permitted during dose escalation phase. Following initial combo therapy, men could continue Apa/AA+P without Doce. The expansion cohort added men at full doses of all drugs to narrow confidence intervals around efficacy/toxicity. Results: Sixteen men (4 Apa 120 mg, 12 Apa 240 mg) with mCRPC and median age 70 and median PSA 3.45 ug/mL (range 0.07 – 188.97) were treated. Sites of metastases included bone (50%), lymph node (56%), lung and liver (6% each), and other sites (13%). Seven (44%) were low, 5 (31%) were intermediate, and 4 (25%) were high CALGB (Halabi) risk group. During dose escalation, there was 1 DLT of grade (Gr) 3 hypertension. In the overall study including expansion, non-heme AEs included Gr 3 hypertension (2/16), hyperglycemia (1/16), and rash (1/16), and Gr 2 hypertension (3/16), fatigue (3/16), rash (2/16), neuropathy (2/16), and nausea (1/16). Heme AEs included Gr 3 anemia (1) and Gr 4 neutropenia (10/16, 1 febrile neutropenia). 15/16 (93.8%) of subjects had a PSA50, of whom 12 achieved PSA90 (12/16, 75%) and 4 (25%) had PSA decline > 99%. Of 7 evaluable with measureable disease, all had RECIST response. Median rPFS was not reached with median 22.8 month follow up (range 2.8-46.6 mo). 2-year rPFS was 70.1% (95% CI = 32.3%, 89.5%). 9 of 10 evaluated had undetectable CTCs at 12 weeks; 5 of 5 with baseline detectable CTCs converted to undetectable at 12 weeks. Conclusions: The combination of apa, AA+P, and doce at full doses is tolerable. The combination is associated with a high proportion with PSA decline, measurable disease response, CTC count control, and favorable rPFS. Pre-treatment tumor tissue and pre-and post-treatment plasma ctDNA and CTC characterization are being analyzed. [NCT02913196]. Clinical trial information: NCT02913196.

Prospective Multicenter Study of Circulating Tumor Cell AR-V7 and Taxane Versus Hormonal Treatment Outcomes in Metastatic Castration-Resistant Prostate Cancer

PURPOSE

Androgen receptor splice variant 7 (AR-V7) detection in circulating tumor cells (CTCs) is associated with a low probability of response and short progression-free (PFS) and overall survival (OS) in men with metastatic castration-resistant prostate cancer (mCRPC) treated with enzalutamide or abiraterone. However, it is unclear whether such men benefit from taxane chemotherapy.

PATIENTS AND METHODS

PROPHECY is a multicenter prospective blinded study of patients with poor-risk mCRPC starting abiraterone or enzalutamide and observed through subsequent progression and taxane chemotherapy. We assessed AR-V7 status using the Johns Hopkins modified AdnaTest CTC AR-V7 messenger RNA assay and the Epic Sciences CTC nuclear-localized AR-V7 protein assay before treatment. The primary objective was to validate the independent prognostic value of CTC AR-V7 status based on radiographic/clinical PFS. OS, confirmed prostate-specific antigen (PSA), and objective radiologic responses were secondary end points.

RESULTS

We enrolled 118 men with mCRPC treated with abiraterone or enzalutamide, 51 of whom received subsequent docetaxel or cabazitaxel. Pretreatment CTC AR-V7 status by the Johns Hopkins and Epic Sciences assays was independently associated with worse PFS (hazard ratio [HR], 1.7; 95% CI, 1.0 to 2.9 and HR, 2.1; 95% CI, 1.0 to 4.4, respectively) and OS (HR, 3.3; 95% CI, 1.7 to 6.3 and HR, 3.0; 95% CI, 1.4 to 6.3, respectively) and a low probability of confirmed PSA responses, ranging from 0% to 11%, during treatment with abiraterone or enzalutamide. At progression, subsequent CTC AR-V7 detection was not associated with an inferior PSA or radiographic response or worse PFS or OS with subsequent taxane chemotherapy after adjusting for CellSearch CTC enumeration and clinical prognostic factors.

CONCLUSION

Detection of AR-V7 in CTCs by two different blood-based assays is independently associated with shorter PFS and OS with abiraterone or enzalutamide, but such men with AR-V7-positive disease still experience clinical benefits from taxane chemotherapy.

Quantitative analysis of taxane drug target engagement of microtubules in circulating tumor cells from metastatic castration resistant prostate cancer patients treated with CRXL301, a nanoparticle of docetaxel

Aim: We reviewed the radiographic response of three patients with metastatic castration-resistant prostate cancer treated with CRXL301, a docetaxel nanoparticle. For these three patients, we isolated and analyzed circulating tumor cells (CTCs) to explore microtubule (MT) drug-target engagement (MT-DTE) as a biomarker of response to treatment. MT-DTE was based on a quantitative assessment of the MT cytoskeleton in CTCs from pre- and post-treatment patient samples as a potential read-out of CRXL301 activity.

Methods: We isolated CTCs using negative CD45⁺ depletion and subjected them to multiplex confocal microscopy using our established protocol. CTCs were identified as CD45^-/CK⁺/DAPI⁺ cells and MT-DTE was determined using our developed imaging algorithm. We quantified MT bundling in CTCs across multiple time points, from baseline to on-treatment to disease progression. Here, we describe the longitudinal analysis of MT-DTE in CTCs from patients treated with CRXL301 and its correlation with response to treatment.

Results: We collected CTCs at seven time points from three metastatic castration-resistant prostate cancer patients. Clinical response was evaluated by Response Evaluation Criteria in Solid Tumors (RECIST) v.1.1 criteria in those patients with measurable disease. Of the three patients enrolled, one experienced partial response (-50%) to CRXL301 and two patients were unevaluable given bone only disease. Notably, however, these two patients showed stable disease clinically based on bone scans. MT-DTE across all time points revealed that, early time points within four and 24 h of drug administration exhibited the highest levels of drug engagement (MT-DTE) as compared to baseline. However, these early time points did not correlate with clinical response. We observed that the CTCs collected one week after the first or second dose of CRXL301 treatment in the responding patient had numerically higher levels of MT-DTE as compared to the other two patients.

Conclusion: Taxane on-target activity can be detected and analyzed quantitatively in CTCs by tubulin immunofluorescence. Early time points, within 24 h of drug administration, showed high levels of DTE but did not correlate with clinical response. MT-DTE in CTCs collected after one week on treatment correlated best with treatment response. The clinical utility of the 1-week CTC DTE should be tested and validated in future clinical trials involving taxanes.

Abstract 641: Systems biology identifies Gleevec as a specific inhibitor of CLIP-170S, a novel +TIP isoform, which causes taxane resistance in cancer cells and patients by obstructing the Microtubule pore

Taxanes are widely used in the treatment of solid tumor patients including gastric cancer (GC). Post-hoc analysis of the clinical trial that led to docetaxel approval in GC, revealed that patients with diffuse histological subtype were intrinsically resistant to taxanes. As yet, the molecular basis of clinical drug resistance remains poorly elucidated. Using a panel of GC cell lines, we identified a subset with intrinsic taxane resistance due to impaired drug-target engagement, in the absence of tubulin mutations or decreased drug accumulation. We discovered a novel, short variant of the microtubule (MT) +TIP binding protein CLIP-170, hereafter CLIP-170S, which was preferentially expressed in resistant cells. Mass-spec proteomics and 5'RACE showed that CLIP-170S lacked the first 150 amino acids, thus, missing the Cap-Gly domain required for +TIP localization. Microscopy of endogenous or exogenous proteins revealed that CLIP-170S was mislocalized from +TIP to the MT lattice in contrast to the canonical CLIP-170. Stable CLIP-170S knock down (KD) entirely reversed taxane-resistance (300 fold), directly establishing CLIP-170S as the cause of taxane resistance.

Quantitation of Flutax-2 (fluorescently labeled taxane) binding kinetics by live-cell imaging of native cytoskeletons in sensitive and resistant cells, showed that Flutax-2 dissociated faster from MTs in CLIP-170S-expressing resistant cells due to slower association rate. CLIP-170S-KD fully restored Flutax-2 binding to MTs, indicating that CLIP-170S impedes taxane-MT interaction. As taxane binding to MT lumen requires entry via the MT pore, we used chemical probes binding at the outer-only (hexaflutax) or luminal (cyclostreptin) pore sites and showed reduced binding of both compounds to resistant cell cytoskeletons. In contrast, CLIP-170S had no effect on peluroside whose MT binding does not require access through the pore. Together, these data indicate that CLIP-170S obstructs the MT pore, preventing drug access to the MT lumen and causing taxane resistance. Clinically, we found CLIP-170S to be expressed in ~60% of GC patient tumors and that its expression was significantly associated with resistance to cabazitaxel monotherapy. Computational analyses of RNAseq data from sensitive and resistant cells predicted Gleevec (Imatinib) as a drug that could overcome taxane resistance. Indeed, we showed that Gleevec reversed taxane resistance by specific depletion of CLIP-170S protein.

Taken together, these data reveal an entirely novel mechanism of taxane resistance via obstruction of the MT pore by the previously unrecognized CLIP-170S. We further found CLIP-170S to be highly prevalent in patient tumors and identified Gleevec as the first specific inhibitor of CLIP-170S.

Citation Format: Prashant V. Thakkar, Katsuhiro Kita, Giuseppe Galletti, Neel Madhukar, Elena Vila Navarro, Kyle Cleveland, Isabel Barasoain, Holly V. Goodson, Dan Sackett, Jose Fernando Diaz, Olivier Elemento, Manish A. Shah, Paraskevi Giannakakou. Systems biology identifies Gleevec as a specific inhibitor of CLIP-170S, a novel +TIP isoform, which causes taxane resistance in cancer cells and patients by obstructing the Microtubule pore [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 641.

Abstract 3196: Analysis of taxane drug target engagement of microtubules in circulating tumor cells from metastatic castration resistant prostate cancer patients treated with CRLX301, a nanoparticle of docetaxel

We reviewed the radiographic response of three patients with metastatic castration-resistant prostate cancer (mCRPC) treated with CRLX301, a docetaxel nanoparticle. For these three patients, we isolated and analyzed circulating tumor cells (CTC) to explore microtubule (MT) drug-target engagement (MT-DTE) as a biomarker of response to treatment. We quantitatively assessed the MT cytoskeleton in CTCs from pre- and post-treatment patient samples as a potential read-out of CRLX301 activity. We isolated CTCs using negative CD45+ depletion and subjected them to multiplex confocal microscopy using our established protocol. CTCs were identified as CD45-/CK+/DAPI+ cells and MT-DTE was determined using our developed, semi-high-throughput, high-content imaging algorithm to quantify MT bundling in CTCs across multiple time points, from baseline to on-treatment to disease progression. We collected CTCs at seven time points from three mCRPC patients. Clinical response was evaluated by RECIST v.1.1 criteria in those patients with measurable disease. Of the three patients who received CRLX301, one experienced partial response and two patients were unevaluable per RECIST given bone only disease, however showed stable disease clinically per bone scans. MT-DTE across all time points revealed that, early time points within four and 24 hours of drug administration exhibited the highest levels of drug engagement as compared to baseline but did not discriminate the responding patient from the patients with stable disease. However, the limited sample size makes this an observation that warrants validation in a larger cohort of patients. We observed that the CTCs collected one week after the first or second dose of CRLX301 treatment in the responding patient had numerically higher levels of MT-DTE as compared to the other two patients. MT-DTE can be detected and analyzed quantitatively in CTCs by tubulin immunofluorescence. The clinical utility of the 1-week CTC DTE should be tested and validated in future clinical trials involving nanoparticle formulations of taxanes or taxanes in general.

Citation Format: Eiman Mukhtar, Daniel Worroll, Giuseppe Galletti, Shelly Schuster, Sarina A. Piha-Paul, Paraskevi Giannakakou. Analysis of taxane drug target engagement of microtubules in circulating tumor cells from metastatic castration resistant prostate cancer patients treated with CRLX301, a nanoparticle of docetaxel [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3196.

Multicenter Phase II Study of Cabazitaxel in Advanced Gastroesophageal Cancer: Association of HER2 Expression and M2-Like Tumor-Associated Macrophages with Patient Outcome

PURPOSE

We examined cabazitaxel, a novel next-generation taxoid, in patients with metastatic gastric cancer in a multicenter phase II study.

PATIENTS AND METHODS

Patients who have progressed on one or more prior therapies for locally advanced, unresectable, or metastatic disease were eligible, and prior taxane therapy was allowed. Taxane-naïve and pretreated cohorts were analyzed independently for efficacy. The primary endpoint for both cohorts was progression-free survival (PFS) using RECIST 1.1, using a Simon's two-stage design (10% significance and 80% power) for both cohorts. Comprehensive molecular annotation included whole exome and bulk RNA sequencing.

RESULTS

Fifty-three patients enrolled in the taxane-naïve cohort (Arm A) and 23 patients in the prior-taxane cohort (Arm B), from January 8, 2013, to April 8, 2015: median age 61.7 years (range, 35.5-91.8 years), 66% male, 66% Caucasian. The most common adverse events included neutropenia (17% Arm A and 39% Arm B), fatigue/muscle weakness (13%), and hematuria (12%). In Arm A, the 3-month PFS rate was 28% [95% confidence interval (CI), 17%-42%] and did not meet the prespecified efficacy target. The 3-month PFS rate in Arm B was 35% (95% CI, 16%-57%) and surpassed its efficacy target. HER2 amplification or overexpression was associated with improved disease control (P = 0.003), PFS (P = 0.04), and overall survival (P = 0.002). An M2 macrophage signature was also associated with improved survival (P = 0.031).

CONCLUSIONS

Cabazitaxel has modest activity in advanced gastric cancer, including in patients previously treated with taxanes. Her2 amplification/overexpression and M2 high macrophage signature are potential biomarkers for taxane efficacy that warrant further evaluation.

Microtubule Engagement with Taxane Is Altered in Taxane-Resistant Gastric Cancer

PURPOSE

Although taxane-based therapy is standard treatment for advanced gastric cancer, a majority of patients exhibit intrinsic resistance to taxanes. Here, we aim to identify the molecular basis of taxane resistance in gastric cancer.

EXPERIMENTAL DESIGN

We performed a post hoc analysis of the TAX-325 clinical trial and molecular interrogation of gastric cancer cell lines to assess the benefit of docetaxel in diffuse (DIF-GC) versus intestinal (INT-GC) gastric cancer. We assessed drug-induced microtubule stabilization in gastric cancer cells and in biopsies of patients with gastric cancer treated with taxanes. We performed transcriptome analysis in taxane-treated gastric cancer cells and patients to identify molecular drivers of taxane resistance.

RESULTS

Patients with DIF-GC did not derive a clinical benefit from taxane treatment suggesting intrinsic taxane resistance. DIF-GC cell lines displayed intrinsic resistance specific to taxanes because of impaired drug-induced microtubule stabilization, in the absence of tubulin mutations or decreased drug accumulation. Using taxane-treated gastric cancer patient biopsies, we demonstrated that absence of drug-target engagement was correlated with clinical taxane resistance. Taxane-sensitive cell lines displayed faster microtubule dynamics at baseline, implicating proteins that regulate cytoskeletal dynamics in intrinsic taxane resistance. Differential gene expression analysis of untreated and docetaxel-treated gastric cancer lines and patient samples identified kinesins to be associated with taxane sensitivity in vitro and in patient samples.

CONCLUSIONS

Our data reveal that taxane resistance is more prevalent in patients with DIF-GC, support assessment of drug-target engagement as an early read-out of taxane clinical efficacy, and encourage the investigation of kinesins and other microtubule-associated proteins as potentially targetable mediators of taxane resistance in gastric cancer.

Abstract CT097: Phase I trial of apalutamide plus abiraterone acetate, docetaxel, and prednisone in patients with metastatic castration-resistant prostate cancer (mCRPC)

Background: Prostate cancer is driven by the androgen receptor (AR) pathway, which may be targeted by inhibition of androgen synthesis (e.g. abiraterone = Abi), AR signaling (e.g. apalutmide = Apa), and/or translocation of AR to the nucleus (e.g. docetaxel = Doce). The combination of AR inhibition plus taxane chemotherapy has already demonstrated clinical benefit (CHAARTED, STAMPEDE), lending weight to the theory that combining drugs targeting different points in the AR signaling pathway is effective. We hypothesize that the combination of Apa, Abi, and Doce will be safe and efficacious.

Methods: Men with progressive mCRPC, intact organ function, and no prior exposure to Apa (ever) or Doce within 3 years were enrolled. Standard Abi 1000 mg daily, Doce 75 mg/m2 q3 weeks, and prednisone 5 mg BID was administered with different doses of Apa. Cohort 1 = Apa 120 mg daily, Cohort 2 = Apa 240 mg daily, Cohort 3 (if necessary) = Apa 180 mg daily in modified 3+3 design. The primary endpoint of the Phase I dose-escalation portion of the study was determination of dose-limiting toxicity (over 6 weeks) and recommended Phase II dose (RP2D).

Results: Nine men (3 Apa 120 mg, 6 Apa 240 mg) with mCRPC and median age 69, median PSA 8.18 (range 0.07 - 278.5) were treated. 67% with bone, 78% LN, 11% lung, 11% other metastases. No DLT occurred with Apa 120 mg and 1 of 6 with Apa 240 mg had possibly related grade 3 hypertension. All had >95% PSA decline (78% with > 99% decline). Of 5 with measureable disease, 100% had RECIST response. 6 of 7 with post-treatment CTC counts were undetectable.

Conclusions: The combination of apalutamide plus abiraterone, docetaxel, and prednisone at full doses is tolerable, with the RP2D of the regimen Apa 240 mg daily, Abi 1000 mg daily, docetaxel 75 mg/m2 q3 wks, and prednisone 5 mg BID. The combination appears to be associated with a high rate of PSA decline, measurable disease response, and CTC count control. Tumor tissue, plasma ctDNA, and CTCs are being collected for analysis. Enrollment to the expansion phase of study to further refine efficacy and toxicity at PCCTC sites is ongoing including assessment of response and resistance biomarkers [NCT02913196]

Citation Format: Ana Molina, Paul Christos, Amy Hackett, Luke Nordquist, Edward Gelmann, Mark Stein, Cora Sternberg, Himisha Beltran, Lauren Gracey, Giuseppe Galletti, Paraskevi Giannakakou, David M. Nanus, Scott T. Tagawa. Phase I trial of apalutamide plus abiraterone acetate, docetaxel, and prednisone in patients with metastatic castration-resistant prostate cancer (mCRPC) [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 CT097.

Abstract 3817: Systems biology identifies that Gleevec reverses taxane resistance in solid tumors by selective inhibition of a novel +Tip microtubule-binding variant

The microtubule (MT) cytoskeleton is a validated therapeutic target in oncology, evidenced by the wide use of taxanes in solid tumors including gastric cancer (GC). Post-hoc analysis of the clinical trial that led to docetaxel approval in GC, revealed that patients with diffuse histological subtype were intrinsically resistant to taxane chemotherapy. Using a panel of GC cell lines intrinsically sensitive or resistant to taxanes, we showed lack of drug-target engagement in the resistant lines, despite unimpaired intracellular drug accumulation and absence of tubulin mutations. We discovered a novel, truncated variant of the MT +TIP binding protein CLIP1, hereafter CLIP1S, which was significantly enriched in the resistant cells. Mass-spec proteomics and 5’RACE showed that CLIP1S lacked the first 150 amino acids, thus, missing the Cap-Gly domain required for MT +TIP localization. Confocal microscopy of endogenous or exogenous tagged proteins revealed that CLIP1S was indeed mislocalized from the +TIP to the MT lattice in contrast to +TIP localization of canonical CLIP1. Stable CLIP1S-Knock Down (KD) entirely reversed taxane-resistance (~300 fold), establishing causation between CLIP1S and taxane resistance. Quantitation of drug-binding kinetics using live-cell imaging of Flutax-2 (fluorescently-labeled taxane) in native cytoskeletons, showed that CLIP1S caused Flutax-2 to have significantly reduced affinity and increased dissociation rates from MTs, as compared with cells expressing only the canonical CLIP1. CLIP1S-KD, fully restored Flutax-2 binding, implicating CLIP1S in impeding taxane-MT interaction. Co-administration of chemical probes specific for the low affinity taxane binding site on MT surface further implicated CLIP1S in partially obstructing the MT pore thereby restricting taxane access in the MT lumen where the high affinity taxane binding site is located. Computational analyses of RNA-seq data from untreated or taxane-treated sensitive and resistant GC cells using a novel bayesian drug-target identification algorithm predicted Imatinib (Gleevec™) as a drug that could overcome CLIP1S mediated taxane resistance. Indeed, imatinib completely reversed taxane resistance, phenocopying the sensitization observed with the CLIP1S-KD. Most importantly, we showed that imatinib reversed taxane resistance by specific inhibition of CLIP1S in a dose-dependent manner as early as 3 h post-treatment. Taken together, these data identify an entirely novel mechanism of taxane resistance that involves obstruction of the MT pore in the presence of a previously unknown +TIP variant. Through systems biology we identified imatinib as the first specific CLIP1S inhibitor, thereby repurposing imatinib as a novel therapeutic to overcome clinical taxane resistance in GC and beyond.

Citation Format: Prashant V. Thakkar, Katsuhiro Kita, Giuseppe Galletti, Neel S. Madhukar, Kyle Cleveland, Isabel Barasoain, Jose Fernando Diaz, Olivier Elemento, Manish A. Shah, Paraskevi Giannakakou. Systems biology identifies that Gleevec reverses taxane resistance in solid tumors by selective inhibition of a novel +Tip microtubule-binding variant [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 3817.

Abstract 454: Transferrin receptor identifies a novel circulating tumor cell population in patients with pancreatic cancer with a unique metastasis-associated molecular signature

Pancreatic Ductal Adenocarcinomas (PDAC) is the fourth most common cancer, expected to be the second leading cause of cancer mortality by 2030. Most PDAC patients are diagnosed with metastatic disease, with dismal prognosis of less than 1% 5-year survival. A major challenge in PDAC treatment is the absence of actionable molecular targets and the scarcity of available tumor tissue impeding molecular understanding of PDAC progression. Circulating Tumor Cells (CTCs) provide an easily accessible source for tumor tissue. CellSearchTM is the only FDA-cleared platform for CTC isolation based on positive selection of EpCAM+ cells. However, this method performs poorly in PDAC failing to show any prognostic relevance, likely due to EpCAM down-regulation during epithelial-to-mesenchymal transition (EMT), which precedes metastasis. To overcome this limitation, we tested Transferrin Receptor 1 (TfR) in the identification and isolation of CTCs from PDAC patients. TfR is a cell surface protein that mediates iron uptake, is overexpressed in multiple tumors with sustained expression throughout EMT, making it a suitable candidate for CTC isolation. To test this hypothesis, we first assessed TfR expression in a panel of 9 human PDAC cell lines, and we observed that TfR was expressed in 9/9 (100%) in contrast to 6/9 (66.7%) being EpCAM positive. No TfR expression was detected in healthy donor and PDAC patients’ PBMCs. To assess the performance of TfR in CTC identification and isolation from the peripheral blood of PDAC patients, we collected samples from 37 PDAC patients with stage 4 disease, enriched CTCs by negative CD45 depletion (RossetteSepTM) and subsequently stained live CTCs with TfR, EpCAM, and CD45. CTCs were defined as CD45- cells, positive for TfR+ or EpCAM+. We observed that the number of TfR+ CTCs (median: 148, range 2-4182) was significantly higher than EpCAM+ CTCs (median: 68, range 0-1552) within the same patient and across different patients (P-value 0.007). In addition, serial sampling at baseline (chemotherapy-naïve) and at disease progression from 5 PDAC patients revealed that TfR+CTC enumeration correlated with disease progression radiologically and/or CA19-9 (PDAC tumor marker) levels. In contrast, there was no correlation between the number of EpCAM+CTCs and clinical outcomes.

RNA-Sequencing of isolated pools of TfR+ or EpCAM+ CTCs, followed by gene set enrichment analysis, revealed significant enrichment in oncogenic pathways, such as EMT, G2M, MYC and KRAS in TfR+ CTCs as compared with EpCAM+ CTCs. Taken together, our results reveal that TfR identifies a clinically relevant CTC subpopulation which correlates with disease progression and is molecularly distinct. Ongoing studies are focused on the function of TfR in disease progression and the potential use of TfR+ CTC molecular profiles in personalized PDAC treatment.

Citation Format: Ahmed Halima, Jiaren Zhang, Giuseppe Galletti, Allyson J. Ocean, Paraskevi Giannakakou. Transferrin receptor identifies a novel circulating tumor cell population in patients with pancreatic cancer with a unique metastasis-associated molecular signature [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 454.

Androgen receptor nuclear localization correlates with AR-V7 mRNA expression in circulating tumor cells (CTCs) from metastatic castration resistance prostate cancer patients

Androgen receptor (AR) signaling drives prostate cancer (PC) progression and remains active upon transition to castration resistant prostate cancer (CRPC). Active AR signaling is achieved through the nuclear accumulation of AR following ligand binding and through expression of ligand-independent, constitutively active AR splice variants, such as AR-V7, which is the most commonly expressed variant in metastatic CRPC (mCRPC) patients. Most currently approved PC therapies aim to abrogate AR signaling and activity by inhibiting this ligand-mediated nuclear translocation. In a prospective multi-institutional clinical study, we recently showed that taxane based chemotherapy is also capable of impairing AR nuclear localization (ARNL) in circulating tumor cells (CTCs) from CRPC patients, whereas taxane induced decreases in ARNL were associated with response. Thus, quantitative assessment of ARNL in CTCs can be used to monitor therapeutic response in patients and help guide clinical decisions. Here, we describe the development and implementation of quantitative high throughput (QHT) image analysis algorithms to aid in CTC identification and quantitative assessment of percent ARNL (%ARNL). We applied this algorithm to fifteen CRPC patients at the start of taxane chemotherapy, quantified %ARNL in CTCs, and correlated with expression of AR-V7 mRNA (from CTCs enriched via negative, CD45⁺ depletion of peripheral blood) and with biochemical (prostate specific antigen; PSA) response to taxane chemotherapy. We found that CTCs from AR-V7 positive patients had higher baseline %ARNL compared to CTCs from AR-V7 negative patients, consistent with the constitutive nuclear localization of AR-V7. In addition, lower %ARNL in CTCs at baseline was associated with biochemical response to taxane chemotherapy. High inter- and intra-patient heterogeneity was also observed. As ARNL is required for active AR signaling, the QHT algorithms described herein can provide prognostic and/or predictive value in future clinical studies.

Expression of AR-V7 and ARv567es in Circulating Tumor Cells Correlates with Outcomes to Taxane Therapy in Men with Metastatic Prostate Cancer Treated in TAXYNERGY

PURPOSE

Biomarkers aiding treatment optimization in metastatic castration-resistant prostate cancer (mCRPC) are scarce. The presence or absence of androgen receptor (AR) splice variants, AR-V7 and ARv567es, in mCRPC patient circulating tumor cells (CTC) may be associated with taxane treatment outcomes.Experimental Design: A novel digital droplet PCR (ddPCR) assay assessed AR-splice variant expression in CTCs from patients receiving docetaxel or cabazitaxel in TAXYNERGY (NCT01718353). Patient outcomes were examined according to AR-splice variant expression, including prostate-specific antigen (PSA)50 response and progression-free survival (PFS).

RESULTS

Of the 54 evaluable patients, 36 (67%) were AR-V7+, 42 (78%) were ARv567es+, 29 (54%) were double positive, and 5 (9%) were double negative. PSA50 response rates at any time were numerically higher for AR-V7- versus AR-V7+ (78% vs. 58%; P = 0.23) and for ARv567es- versus ARv567es+ (92% vs. 57%; P = 0.04) patients. When AR-V mRNA status was correlated with change in nuclear AR from cycle 1 day 1 to day 8 (n = 24), AR-V7+ patients (n = 16) had a 0.4% decrease versus a 12.9% and 26.7% decrease in AR-V7-/ARv567es- (n = 3) and AR-V7-/ARv567es+ (n = 5) patients, respectively, suggesting a dominant role for AR-V7 over ARv567es. Median PFS was 12.02 versus 8.48 months for AR-V7- versus AR-V7+ (HR = 0.38; P = 0.01), and 12.71 versus 7.29 months for ARv567es- versus ARv567es+ (HR = 0.37; P = 0.02). For AR-V7+, AR-V7-/ARv567es+, and AR-V7-/ARv567es- patients, median PFS was 8.48, 11.17, and 16.62 months, respectively (P = 0.0013 for trend).

CONCLUSIONS

Although detection of both CTC-specific AR-V7 and ARv567es by ddPCR influenced taxane outcomes, AR-V7 primarily mediated the prognostic impact. The absence of both variants was associated with the best response and PFS with taxane treatment.See related commentary by Dehm et al., p. 1696.

Prospective Multicenter Validation of Androgen Receptor Splice Variant 7 and Hormone Therapy Resistance in High-Risk Castration-Resistant Prostate Cancer: The PROPHECY Study

PURPOSE

Androgen receptor splice variant 7 (AR-V7) results in a truncated receptor, which leads to ligand-independent constitutive activation that is not inhibited by anti-androgen therapies, including abiraterone or enzalutamide. Given that previous reports suggested that circulating tumor cell (CTC) AR-V7 detection is a poor prognostic indicator for the clinical efficacy of secondary hormone therapies, we conducted a prospective multicenter validation study.

PATIENTS AND METHODS

PROPHECY (ClinicalTrials.gov identifier: NCT02269982) is a multicenter, prospective-blinded study of men with high-risk mCRPC starting abiraterone acetate or enzalutamide treatment. The primary objective was to validate the prognostic significance of baseline CTC AR-V7 on the basis of radiographic or clinical progression free-survival (PFS) by using the Johns Hopkins University modified-AdnaTest CTC AR-V7 mRNA assay and the Epic Sciences CTC nuclear-specific AR-V7 protein assay. Overall survival (OS) and prostate-specific antigen responses were secondary end points.

RESULTS

We enrolled 118 men with mCRPC who were starting abiraterone or enzalutamide treatment. AR-V7 detection by both the Johns Hopkins and Epic AR-V7 assays was independently associated with shorter PFS (hazard ratio, 1.9 [95% CI, 1.1 to 3.3; P = .032] and 2.4 [95% CI, 1.1 to 5.1; P = .020], respectively) and OS (hazard ratio, 4.2 [95% CI, 2.1 to 8.5] and 3.5 [95% CI, 1.6 to 8.1], respectively) after adjusting for CTC number and clinical prognostic factors. Men with AR-V7–positive mCRPC had fewer confirmed prostate-specific antigen responses (0% to 11%) or soft tissue responses (0% to 6%). The observed percentage agreement between the two AR-V7 assays was 82%.

CONCLUSION

Detection of AR-V7 in CTCs by two blood-based assays is independently associated with shorter PFS and OS with abiraterone or enzalutamide, and such men with mCRPC should be offered alternative treatments.

A method to identify the areas at risk for the introduction of avian influenza virus into poultry flocks through direct contact with wild ducks

Wild dabbling ducks are the main reservoir for avian influenza (AI) viruses and pose an ongoing threat to commercial poultry flocks. Combining the (i) size of that population, (ii) their flight distances and (iii) their AI prevalence, the density of AI-infected dabbling ducks (DID) was calculated as a risk factor for the introduction of AI viruses into poultry holdings of Emilia-Romagna region, Northern Italy. Data on 747 poultry holdings and on 39 AI primary outbreaks notified in Emilia-Romagna between 2000 and 2017 were used to validate that risk factor. A multivariable Bayesian logistic regression was performed to assess whether DID could be associated with the occurrence of AI primary outbreaks. DID value, being an outdoor flock, hobby poultry trading, species reared, length of cycle and flock size were used as explanatory variables. Being an outdoor poultry flock was significantly associated with a higher risk of AI outbreak occurrence. The probability of DID to be a risk factor for AI virus introduction was estimated to be 90%. A DID cut-off of 0.23 was identified to define high-risk areas for AI virus introduction. Using this value, the high-risk area covers 43% of the region. Seventy-four per cent of the primary AI outbreaks have occurred in that area, containing 39% of the regional poultry holdings. Poultry holdings located in areas with a high DID value should be included in a risk-based surveillance programme aimed at AI early detection.

Identification of distinct nanoparticles and subsets of extracellular vesicles by asymmetric flow field-flow fractionation

The heterogeneity of exosomal populations has hindered our understanding of their biogenesis, molecular composition, biodistribution and functions. By employing asymmetric flow field-flow fractionation (AF4), we identified two exosome subpopulations (large exosome vesicles, Exo-L, 90-120 nm; small exosome vesicles, Exo-S, 60-80 nm) and discovered an abundant population of non-membranous nanoparticles termed 'exomeres' (~35 nm). Exomere proteomic profiling revealed an enrichment in metabolic enzymes and hypoxia, microtubule and coagulation proteins as well as specific pathways, such as glycolysis and mTOR signalling. Exo-S and Exo-L contained proteins involved in endosomal function and secretion pathways, and mitotic spindle and IL-2/STAT5 signalling pathways, respectively. Exo-S, Exo-L and exomeres each had unique N-glycosylation, protein, lipid, DNA and RNA profiles and biophysical properties. These three nanoparticle subsets demonstrated diverse organ biodistribution patterns, suggesting distinct biological functions. This study demonstrates that AF4 can serve as an improved analytical tool for isolating extracellular vesicles and addressing the complexities of heterogeneous nanoparticle subpopulations.

Using circulating tumor cells to advance precision medicine in prostate cancer

The field of CTC enrichment has seen many emerging technologies in recent years, which have resulted in the identification and monitoring of clinically relevant, CTC-based biomarkers that can be analyzed routinely without invasive procedures. Several molecular platforms have been used to investigate the molecular profile of the disease, from high throughput gene expression analyses down to single cell biological dissection. The established presence of CTC heterogeneity nevertheless constitutes a challenge for cell isolation as the several subpopulations can potentially display different molecular characteristics; in this scenario, careful consideration must be given to the isolation approach, whereas methods that discriminate against certain subpopulations may result in the exclusion of CTCs that carry biological relevance. In the context of prostate cancer (PC), CTC molecular interrogation can enable longitudinal monitoring of key biological features during treatment with substantial clinical impact, as several biomarkers could predict tumor response to AR signaling inhibitors (abiraterone, enzalutamide) or standard chemotherapy (taxanes). Thus, CTCs represent a valuable opportunity to personalize medicine in current clinical practice.

Abstract 1713: Transferrin receptor 1 (TfR) as marker for circulating tumor cells (CTCs) identification in NSCLC

CTCs are used as a surrogate source of tumor material in solid tumors. Clinical applications of CTCs as liquid biopsy comprise the monitoring of molecular alterations during tumor progression and dynamic evaluation of molecular markers of treatment response. The FDA-cleared method to isolate CTCs in cancer patients (Cell Search) is based on positive selection of EpCAM expressing cells. However, this approach performs poorly in non-small cell lung cancer (NSCLC) as it identifies CTCs in only 7% of the subjects, failing to show any prognostic relevance.

Down-regulation/loss of epithelial markers to isolate (EpCAM) and identify (cytokeratin, CK) CTCs could in part explain the low CTC yield obtained in NSCLC with approaches based on epithelial markers expression. To overcome this challenge we used size-based CTC enrichment (ISET filters) from NSCLC patients’ peripheral blood. As a positive identifier of CTCs we used transferrin receptor 1 (TfR) which is a cell membrane-associated protein, that mediates intracellular iron uptake, and which is expressed at low levels in many normal tissues but over-expressed in cancer cells.

We first analyzed TfR protein expression by immunofluorescence in a panel of NSCLC cell lines and in healthy donor leukocytes. While all NSCLC cells lines analyzed were positive for TfR expression, none of the leukocyte expressed the receptor. Moreover, TfR expression was detected also in EpCAM negative NSCLC cell lines. To determine the clinical applicability of this novel CTC identifier, we determined TfR expression in CTCs isolated from peripheral blood of 35 metastatic NSCLC patients using the ISET filter technology. The isolated CTCs were stained for TfR, CK, CD45 and DAPI. For each patient, one additional ISET filter was stained with Giemsa for morphologic analysis by a pathologist. By using the classic panel of CTC identifiers markers (CK+/CD45-/DAPI+), CTCs were identified in 4/34 (11%) patients, while by using TfR as positive identifier (TfR+/CD45-/DAPI+) CTCs were identified in 31/35 (88%) subjects. The morphologic review of Giemsa stained filters confirmed the presence of tumor cells in 28/34 (82%) samples [0-217 CTCs/sample]. Interestingly, patients with > 6 TfR+ CTCs had a worse overall survival (OS) than patients with < 6 TfR+ CTCs [p=0.048 Log Rank (Mantel-Cox)]. OS did not significantly differ using the same cutoff with CTCs defined based on CK or Giemsa staining.

Overall, our data indicate that TfR is a promising biomarker for the detection of CTCs in NSCLC CTCs, superior to CK or EpCAM. Our data also suggest that TfR may potentially identify CTCs subpopulations with a significant prognostic role in NSCLC. We are currently isolating TfR+ CTCs from early stage and metastatic NSCLC patients for further molecular characterization and determination of clinical significance.

Citation Format: Giuseppe Galletti, Galatea Kallergi, Ashish Saxena, Despoina Aggouraki, Christos Stournaras, Vassilis Georgoulias, Timothy E. McGraw, Nasser Altorki, Paraskevi Giannakakou. Transferrin receptor 1 (TfR) as marker for circulating tumor cells (CTCs) identification in NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1713. doi:10.1158/1538-7445.AM2017-1713

Abstract 4169: A novel, short isoform of the +Tip microtubule binding protein CLIP170 confers taxane resistance in gastric cancer

The microtubule (MT) cytoskeleton is one of the most validated therapeutic targets in clinical oncology, as evidenced by the wide clinical activity of taxanes and other MT inhibitors. However, patients with intrinsic drug resistance do not benefit from taxane chemotherapy, such as patients with diffuse gastric cancer (GC). Currently, the molecular mechanisms underlying clinical taxane resistance remain poorly elucidated. Using a panel of GC cell lines with intrinsic sensitivity or resistance to taxanes, we showed lack of drug-target engagement in the resistant lines, despite unimpaired intracellular accumulation of the drug and in the absence of tubulin mutations or altered tubulin isotype expression. Herein, we show for the first time that the resistant cells expressed a novel, short isoform of the MT plus-end binding protein, CLIP170 (CLIP1). CLIP1 binds to the plus-ends of microtubules (+TIPs) and regulates dynein-mediated MT-based trafficking and the tubulin tyrosination cycle. We showed by both mass-spec proteomics and 5’-RACE that the short CLIP1 isoform (CLIP1S) lacks the first 150 amino acids, thus, missing the first Cap-Gly (Cytoskeleton-Associated Protein-Glycine) domain, which is required for proper +TIP localization. Indeed, confocal microscopy experiments showed that CLIP1S was mislocalized to the microtubule lattice in contrast to the canonical comet-like pattern of CLIP1 seen in taxane sensitive cell lines. CLIP1S expression was specifically correlated with taxane resistance (docetaxel, cabazitaxel) as no correlation was observed with other DNA-damaging agents. Since, CLIP1S expression has never been reported before, to establish causation, we stably knocked down CLIP1 and CLIP1S in taxane-sensitive and resistant cells, respectively. CLIP1SKD entirely reversed taxane-resistance (~300 fold) while CLIP1KD had no effect in the taxane-sensitive cell lines. These data suggest a gain-of-function of CLIP1S that leads to taxane resistance. To study the binding kinetics of taxanes to MTs in the presence or absence of CLIP1S we performed live cell imaging of native cytoskeletons using fluorescently-labeled paclitaxel (Flutax). Our data revealed significantly faster dissociation rates of Flutax from MTs in the resistant cells, indicating transient interaction with MTs. Taxane binding to MTs is a two-step process. First taxanes bind to the MT-pore low affinity surface site, which then facilitates access to the high affinity luminal site. Using a small molecule that binds only to MT-pore site, we showed that we showed that taxol binding to the pore is significantly slower in resistant cells expressing CLIP1S, which together with mislocalization of this variant along the MT lattice suggests that it obstructs access to the MT-pore thus restricting entry of taxane into the lumen of microtubules. This finding will have profound implications for taxane resistance as well as microtubule biology broadly.

Citation Format: Prashant V. Thakkar, Katsuhiro Kita, Giuseppe Galletti, Kyle Cleveland, Isabel Barasoain, Jose Fernando Diaz, Manish A. Shah, Paraskevi Giannakakou. A novel, short isoform of the +Tip microtubule binding protein CLIP170 confers taxane resistance in gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4169. doi:10.1158/1538-7445.AM2017-4169

Abstract 2736: A digital droplet PCR assay for the quantitation of androgen receptor and splice variant expression in CTCs from metastatic castration resistant prostate cancer patients

Prostate cancer (PC) is the second leading cause of cancer death in men in the US. The aberrant functioning of androgen receptor signaling is the central driving force behind prostatic tumorigenesis and its transition into metastatic castration resistant disease. Hence, androgen deprivation therapy (ADT) is the first line of treatment for PC patients. However, many patients progress becoming resistant to ADT therapy, due to the expression of AR splice variants (AR-Vs), which lack the ligand binding domain and are constitutively active in the nucleus. Expression of the AR splice variant, AR-v7, in circulating tumor cells (CTCs) isolated from the blood of PC patients was correlated with resistance to enzalutamide and abiraterone, which are the next generation AR signaling inhibitors in CRPC. Further, there is evidence that AR-Vs may convey cross-resistance, not only to enzalutamide and abiraterone, but also to taxanes, highlighting that their assessment in the clinic may have clinical utility.

We developed a novel, specific and highly sensitive assay to measure mRNA expression of the AR full length (AR-FL) and the splice variants ARv7 and ARv567es, by using Droplet Digital PCR in CTCs isolated from CRPC patients. The analytical specificity of the assay was determined by transfecting cells with plasmids encoding AR-FL, AR-v7 and AR-v567 and showed that each probe detected signal only in cells expressing the respective transcript. No signal was detected against genomic DNA, indicating lack of non-specific binding. Also, the assay detected endogenous expression of AR-FL and AR-v7 in VCAP or 22RV1 cells, while no variant expression was detected in healthy donor blood. The analytical sensitivity of the assay was determined in a series of serial dilution experiments that showed sensitivity down to single cell.

We then used this assay to determine the clinical prevalence and expression pattern of each of these variants in CTCs from about 200 mCRPC patient samples and blood from 40 healthy donors. CTCs were enriched by EpCAM- or PSMA-based positive selection or CD45 negative depletion in an antigen-agnostic manner. AR-FL was detected in ~80% of mCRPC samples irrespective of CTC-enrichment technology. AR-v7 was expressed in 65% of the samples in which in CTCs were enriched either by PSMA-positive selection or by negative depletion. In contrast, EpCAM-based CTC enrichment showed lower AR-v7 expression both in terms of expression levels and prevalence. In addition, CTC enrichment following negative depletion showed that 30% of the samples had higher AR-v7 expression levels as compared to AR-FL. This expression pattern was not observed in the samples using EpCAM-based selection. Collectively, these data suggest distinct CTC subpopulations are present in CRPC patient samples, with differential expression of AR-Vs that could have important predictive and prognostic implications.

Citation Format: Ada Gjyrezi, Giuseppe Galletti, Areti Strati, Seaho Kim, Evi Lianidou, David M. Nanus, Jun Luo, Emmanuel Antonarakis, Scott T. Tagawa, Andrew Armstrong, Paraskevi Giannakakou. A digital droplet PCR assay for the quantitation of androgen receptor and splice variant expression in CTCs from metastatic castration resistant prostate cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2736. doi:10.1158/1538-7445.AM2017-2736

Randomized, Noncomparative, Phase II Trial of Early Switch From Docetaxel to Cabazitaxel or Vice Versa, With Integrated Biomarker Analysis, in Men With Chemotherapy-Naïve, Metastatic, Castration-Resistant Prostate Cancer

Purpose The TAXYNERGY trial ( ClinicalTrials.gov identifier: NCT01718353) evaluated clinical benefit from early taxane switch and circulating tumor cell (CTC) biomarkers to interrogate mechanisms of sensitivity or resistance to taxanes in men with chemotherapy-naïve, metastatic, castration-resistant prostate cancer. Patients and Methods Patients were randomly assigned 2:1 to docetaxel or cabazitaxel. Men who did not achieve ≥ 30% prostate-specific antigen (PSA) decline by cycle 4 (C4) switched taxane. The primary clinical endpoint was confirmed ≥ 50% PSA decline versus historical control (TAX327). The primary biomarker endpoint was analysis of post-treatment CTCs to confirm the hypothesis that clinical response was associated with taxane drug-target engagement, evidenced by decreased percent androgen receptor nuclear localization (%ARNL) and increased microtubule bundling. Results Sixty-three patients were randomly assigned to docetaxel (n = 41) or cabazitaxel (n = 22); 44.4% received prior potent androgen receptor-targeted therapy. Overall, 35 patients (55.6%) had confirmed ≥ 50% PSA responses, exceeding the historical control rate of 45.4% (TAX327). Of 61 treated patients, 33 (54.1%) had ≥ 30% PSA declines by C4 and did not switch taxane, 15 patients (24.6%) who did not achieve ≥ 30% PSA declines by C4 switched taxane, and 13 patients (21.3%) discontinued therapy before or at C4. Of patients switching taxane, 46.7% subsequently achieved ≥ 50% PSA decrease. In 26 CTC-evaluable patients, taxane-induced decrease in %ARNL (cycle 1 day 1 v cycle 1 day 8) was associated with a higher rate of ≥ 50% PSA decrease at C4 ( P = .009). Median composite progression-free survival was 9.1 months (95% CI, 4.9 to 11.7 months); median overall survival was not reached at 14 months. Common grade 3 or 4 adverse events included fatigue (13.1%) and febrile neutropenia (11.5%). Conclusion The early taxane switch strategy was associated with improved PSA response rates versus TAX327. Taxane-induced shifts in %ARNL may serve as an early biomarker of clinical benefit in patients treated with taxanes.

AR nuclear localization and microtubule bundling as markers of docetaxel and cabazitaxel sensitivity in metastatic castration-resistant prostate cancer (mCRPC): Prospective biomarker analysis from TAXYNERGY

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Background: A better understanding of taxane sensitivity/resistance in mCRPC is needed to optimize treatment. Preclinically, taxane efficacy has been linked to the ability of microtubules (MT) to inhibit AR nuclear trafficking. In this prospective biomarker study, we used circulating tumor cells (CTCs) from patients (pts) in TAXYNERGY to perform real-time analysis of AR nuclear localization (ARNL) and MT stabilization (bundling; MTB) in order to predict taxane sensitivity. Methods: TAXYNERGY (NCT01718353) is a phase 2 trial randomizing chemo-naïve mCRPC pts 2:1 to docetaxel or cabazitaxel, with a switch to the alternative taxane in the absence of a ≥ 30% PSA drop by C4. Here we present the co-primary biomarker endpoints. CTCs at baseline (C1D1) were compared to CTCs after 1 week of taxane treatment (C1D8), and were analyzed by multiplex confocal microscopy for %ARNL (integrated AR intensity in the cell and nuclear areas) and MTB (assessed for increase compared to C1D1 on a scale from 0–3 from no to most MTB increase). Associations between %ARNL and MTB with clinical outcomes were sought. Results: Of 63 randomized pts, 26 had evaluable CTCs both at C1D1 and C1D8. At C1D8, mean %ARNL was significantly lower in pts achieving a ≥ 50% PSA drop by C4 vs those without (44% vs 64%; p = 0.004). A taxane-induced decrease in mean %ARNL (C1D8 vs C1D1) was associated with a higher rate of ≥ 50% PSA response (73% vs 13%; p = 0.009); mean %ARNL decreased by 18% in responders and increased by 2% in non-responders (p = 0.02). Finally, a taxane-induced increase in mean MTB trended higher in pts achieving a ≥ 30% PSA drop by C4 vs those without (0.69 vs 0.09; p = 0.09); increase in mean MTB score was indicative of response and observed in pts who did not require a taxane switch after C4 (0.75 vs 0.09; p = 0.06). Conclusions: We provide the first prospective data suggesting that taxane-induced shifts in ARNL and MTB (measured in CTCs) may serve as an early biomarker of taxane sensitivity. Consistent with preclinical data, AR nuclear exclusion caused by microtubule bundling may be a clinically-actionable marker of taxane efficacy. Funding: Sanofi Genzyme. Clinical trial information: NCT01718353.

Abstract 2932: Impaired taxane binding to MT pore sites mediates intrinsic drug resistance in diffuse gastric cancer

Successful clinical application of taxanes (microtubule-stabilizers) is limited due to intrinsic or acquired drug resistance. Thus, it is critical to unveil the molecular mechanisms of taxane resistance to significantly improve clinical outcomes. Retrospective analysis of the TAX-325 gastric cancer (GC) trial revealed that the addition of docetaxel (DTX) to cisplatin/fluorouracil increased progression-free plus overall survival, in intestinal (INT) but not in diffuse (DIF) GC subtypes. Our preclinical data confirmed that DIF GC cell lines are intrinsically resistant to taxanes. The incidence of DTX resistance in DIF GC cell lines was 2.5 times higher than INT GC cell lines. Drug efflux, tubulin posttranslational modification and differential β-tubulin isotype expression were ruled out as potential mechanisms of intrinsic taxane resistance. Thus, a new molecular mechanism must underlie the intrinsic taxane resistance in DIF GC. To quantify the kinetics of taxol binding to cellular MTs, we treated both DIF and INT groups of GC lines with the fluorescein-conjugated paclitaxel analog, Flutax-2. The Flutax-2 staining intensity of cellular MTs was assessed by live-cell confocal microscopy at different time points. Following a 3h incubation, there was less than 20% decrease in Flutax-2 intensity in the sensitive cell lines, compared to 59∼89% decrease in the resistant cell lines. These data suggested different binding kinetics between sensitive and resistant cells. We added 1μM Flutax-2 to sensitive/resistant cells’ native cytoskeletons for 0∼60 seconds to determine the association rate (kon) of Flutax-2 binding to MTs. The kon of Flutax-2 in the sensitive cell lines was significantly higher in sensitive (5.8×104M−1s−1) versus resistant cells (0.3∼2.6×104M−1s−1). Next, we measured the dissociation rates (koff) by competing the pre-bound Flutax-2 with DTX (0∼600 seconds). Although 20∼40% faster koff was observed in resistant cells, it appeared that the association rate of Flutax-2 was the dominant factor of differential taxane binding to MTs in GC cells. The binding mode of taxanes to MTs involves 1) binding to MT pores and 2) internalization to the high-affinity binding site at the MT lumen. To differentiate between the two, we used hexaflutax, which binds exclusively to the MT pores. We observed hexaflutax decorating radial MT arrays in sensitive but not in the resistant cells. As tubulin mutations around the high-affinity taxane binding site or tubulin posttranslational modifications/differential expression of β-tubulin isotype is not the case in DIF GC cell lines, our data suggest that modifications of the MT pore conformation or occlusion of the pore site is responsible for the intrinsic taxane resistance in DIF GC. Determining the origin of the defect at the pores will help design better MT-stabilizing drugs to overcome chemo-resistance, the major obstacle hindering overall survival of patients.

Citation Format: Katsuhiro Kita, Giuseppe Galletti, Kyle Cleveland, Chao Zhang, Isabel Barasoain, J. Fernando Díaz, Doron Betel, Manish A. Shah, Paraskevi Giannakakou. Impaired taxane binding to MT pore sites mediates intrinsic drug resistance in diffuse gastric cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2932.

Abstract 2125: ERG and AR-v7 involvement in taxane resistance of metastatic castration-resistant prostate cancers

While taxane-class drugs remains the only chemotherapy agents shown to improve survival of patients with metastatic castration-resistant prostate cancer (mCRPC), most patients with mCRPC ultimately become refractory due to the development of drug resistance. The molecular mechanisms involved in this resistance remain an unmet need. We previously showed that ERG, an oncogenic transcription factor, directly interacts with soluble tubulin dimers impairing the ability of taxanes to bind to microtubules in vitro and in circulating tumor cells (CTCs) from CRPC patients. We also demonstrated that expression of AR-v7 confers taxane resistance in vitro and in animal models of CRPC, owing to the lack of the microtubule-binding hinge domain which renders AR-v7 insensitive to microtubule stabilization by the taxanes. The purpose of the present study is to evaluate the impact of ERG and AR-v7 co-expression in prostate cells and to characterize their cooperative role in mediating taxane resistance. We generated multiple isogenic cell lines over-expressing ERG alone or in combination with AR-v7, and engineered VCaP cells (harboring endogenous ERG rearrangement and expressing AR-v7) to express a TetOn-shRNA targeting ERG mRNA. We also developed and optimized a Digital Droplet PCR (DD-PCR) assay to quantify the expression of ERG derived from the TMPRSS2-ERG gene fusion and of AR-v7. We tested the sensitivity and specificity of the assays using VCaP cells spiked into healthy donor blood samples. We detected ERG and AR-v7 co-expression in single VCaP cells. We also found that ERG and AR-v7 form a protein complex and we are testing their potential co-binding at common target genes using ChIP-seq. To determine the clinical relevance of our findings we queried available RNAseq data from benign prostate, locally advanced hormone naïve prostate cancer and a subset of the Stand-up-to-Cancer cohort of CRPC patients. We found high levels of AR-v7 expression in CRPC samples and in none of the benign or PCa samples and a co-overexpression of AR-v7 and ERG with 75% of ERG positive CRPC also expressing AR-v7. We are currently using our assays to characterize ERG and AR-v7 co-expression in CTCs of mCRPC patients samples collected at baseline, on treatment and relapse- as part of a fully-enrolled clinical trial (TAXYNERGY). We expect an enrichment overtime of CTCs that are positive for both ERG and AR-v7. In conclusion, determining ERG and AR-v7 status in mCRPC patients and their involvement in taxane resistance mechanism will aid refer ERG and AR-v7 positive mCRPC patients to an effective therapy.

Citation Format: Adeline Berger, Seaho Kim, Ada Gjyrezi, Giuseppe Galletti, Andrea Sboner, Mark A. Rubin, Scott Tagawa, Paraskevi Giannakakou, David S. rickman. ERG and AR-v7 involvement in taxane resistance of metastatic castration-resistant prostate cancers. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2125.

Abstract 4938: Molecular mechanisms of intrinsic resistance to taxanes in gastric cancer

Gastric cancer (GC) is histologically divided into intestinal (INT) and diffuse (DIF) clinical subtypes. Even though these two GC groups are structurally and biologically different, this classification is not used to inform choice of treatment.

Taxanes (paclitaxel, docetaxel (DTX) and cabazitaxel) are widely used for cancer treatment and for GC specifically the TAX-325 study revealed therapeutic benefit when DTX was added to the standard chemotherapy regimen. Despite these improvements, however, patients often exhibit intrinsic or acquired resistance to DTX adversely affecting patient survival. Yet, the molecular basis of clinical drug resistance remains poorly elucidated posing a major barrier for the effective treatment of GC patients.

We performed a post-hoc analysis of the TAX-325 study to examine the potential influence of GC subtypes in clinical response to DTX. We classified randomized patients as diffuse or non-diffuse histology and correlated histology with clinical outcomes using a Cox proportional hazards model. Non-diffuse GC showed a significant improvement in overall survival with the addition of DTX (12.1 v 8.8 mo, p = 0.002), whereas diffuse histology was not associated with an improvement in survival (8.3 v 8.5 mo, p = 0.66). To investigate the molecular mechanism of GC DIF subtype resistance to taxanes, we used a panel of 12 GC cell lines representative of both subtypes (4 intestinal subtype, 8 diffuse subtype). DTX cytotoxicity assays revealed that similarly to what we observed clinically, 63% (5/8) of the DIF GC cell lines were resistant (IC50 > 600 nM) to DTX compared to 25% (1/4) of the INT GC cell lines. Further functional studies revealed that there was minimal DTX drug-target engagement in the DIF GC cells, assessed by confocal microscopy of the microtubule (MT) network and tubulin polymerization assays. These results suggested that DTX interaction with its target, MT, was impaired in the DIF GC cell lines. To rule out multi-drug resistance (MDR) as potential cause of intrinsic DTX resistance in these cells we performed flow cytometric evaluation of P-glycoprotein and found that all of the DIF GC cell lines were negative. Additionally, drug accumulation studies with C-14 radiolabeled DTX revealed that the drug accumulated intracellularly in all of GC cell lines in our panel.

Next generation sequencing of our panel of untreated or DTX-treated GC cell lines revealed 84 significantly differentially expressed genes in drug-sensitive cell lines but no changes in resistant cells. Our analysis showed a significant enrichment and a transcriptional co-regulation after treatment of genes encoding for kinesins, motor proteins associated with MT, in DTX-sensitive cells but not in DTX-resistant cells.

These studies will provide novel insights into mechanism of drug resistance and sensitivity and will ultimately allow us to design more effective targeted therapies to overcome chemo-resistance and eventually prolong patient survival.

Citation Format: Giuseppe Galletti, Chao Zhang, Kyle Cleveland, Doron Betel, Manish Shah, Paraskevi Giannakakou. Molecular mechanisms of intrinsic resistance to taxanes in gastric cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4938.

Abstract 4971: Quantitative image analysis of androgen receptor (AR) and tubulin biomarker profiles in circulating tumor cells (CTCs) from metastatic castration resistant prostate cancer (mCRPC) patients

Background: CTCs represent a real-time, liquid biopsy for analyses of a variety of molecular biomarkers that offer clinically relevant information. In prostate cancer, the AR pathway controls tumor cell growth and survival and is an important therapeutic target. AR becomes biologically active upon translocation from the cytoplasm to the nucleus in a microtubule dependent fashion, resulting in the activation of numerous genes. Real-time analysis of AR and tubulin status in CTCs may provide insight to therapy response in mCRPC patients.

Methods: Androgen sensitive human prostate cancer cells, LNCaP, were treated with and without a synthetic androgen (R1881; 10 nM, 1 hr) and docetaxel, spiked into healthy donor blood, and captured using a prostate specific microfluidic device (GEDI chip), following the same protocol that we use with patient samples. Cells were fixed and stained (N-terminal AR, CD45, CK, DAPI, and tyr-tubulin) directly on the device and imaged using high resolution multiplex confocal microscopy. AR and tubulin status were analyzed using a quantitative image analysis algorithm. Nuclear AR percentage was calculated by integrating fluorescence intensity within regions defining the entire cell and nucleus. H-Score was calculated by multiplying the nuclear AR percentage by the normalized total cell AR intensity. Tubulin status and microtubule bundling were assessed using a variety of quantitative parameters including measurements of tubulin fluorescence intensity and distribution within the cell.

Results: LNCaP cells in the presence of synthetic androgen exhibited higher nuclear AR percentage (p = 0.0004) and H-score (p = 0.003). Docetaxel treatment led to lower nuclear AR percentage (p = 0.04) and lower H-Score (p = 0.03). Cells treated with docetaxel exhibited higher tubulin intensity range (p = 0.008) and standard deviation (p = 0.03), consistent with docetaxel's mechanism of action. We applied these methods of quantitative image analyses to CTCs isolated from a small cohort of mCRPC patients. Single CTC image analysis revealed heterogeneity in AR status. Quantitative evidence for microtubule bundling was observed in patients receiving docetaxel chemotherapy.

Conclusions: We have developed a high throughput quantitative image analysis algorithm to interrogate mCRPC specific biomarkers, such as AR and tubulin status, in single CTCs. These methods of quantitative image analyses will be prospectively validated with CTCs from mCRPC patients followed longitudinally over the course of treatment with AR inhibitors and taxanes, yielding patient specific, clinically relevant information that can guide physicians’ strategies for the clinical management of cancer.

Citation Format: Daniel Worroll, Giuseppe Galletti, David M. Nanus, Scott T. Tagawa, Paraskevi Giannakakou. Quantitative image analysis of androgen receptor (AR) and tubulin biomarker profiles in circulating tumor cells (CTCs) from metastatic castration resistant prostate cancer (mCRPC) patients. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4971.

Abstract 3489: Elucidation of taxane resistance in prostate cancer through RNA-Seq analysis of circulating tumor cells

Prostate cancer is the most commonly diagnosed male cancer in the United States. Taxanes are the only established chemotherapy drugs proven to be effective in improving survival of men with advanced prostate cancer through disruption of the AR-signaling axis downstream of microtubule stabilization. However, there is significant heterogeneity in how patients respond to taxanes and most patients ultimately become refractory due to the development of drug resistance. Currently, the molecular basis of clinical taxane resistance in PC is poorly understood. Prostate cancer circulating tumor cells (P-CTCs) are often found in the peripheral blood of patients suffering from metastatic prostate cancer and have been clinically used as prognostic biomarker for metastatic progression and treatment outcome. The objective of this study is to identify clinically relevant mechanisms of taxane resistance through conducting RNA-Seq analysis in P-CTCs isolated from patients before, during and after they become refractory to taxane chemotherapy.

To show feasibility of RNA-Seq experiments with limiting samples such as CTCs and given the presence of contaminating leucocytes, a pilot experiment was performed in which limiting numbers of prostate cancer cells (LNCaP) either pure or enriched following spiking into healthy donor blood, were analyzed by RNA-Seq. Matching healthy donor blood processed with the same enrichment protocol was used as germline control as well as control for the presence of contaminating leucocytes following CTC enrichment. Trimmed reads were aligned to human reference genome (hg38) using STAR. Determination of Fragments Per Kilobase of exon per Million mapped fragments (FPKM) was performed using Cufflinks and heat map was built based on the value of log10(FPKM+1). Gene expression analysis showed that markers of prostate (such as AR, PSMA, KLK3, KLK2, and AMACR) or epithelial lineage (such as EpCAM, CDH1, KRT8 and KRT18) were detected in both pure LNCaP cells-regardless of amount- as well as limited number of captured LNCaP cells in the presence of contaminating leucocytes. In contrast, healthy donor blood was negative for the prostate and epithelial lineage markers and positive for the leucocyte specific markers (such as CD45 and CD16). Gene set enrichment analysis (GSEA) indicated significant enrichment for Andorgen response, MYC, MTOR and RB related pathways in pure and captured LNCap cells compared with healthy donor blood. These data clearly show that by using RNA-Seq we can detect the prostate and epithelial specific gene signatures of limited number of spiked prostate cancer cells using the microfluidic device. Ongoing work includes RNA-Seq analysis of P-CTCs isolated from patients before and after taxane treatment, in order to detect differentially expressed genes, pathways, and potentially driver somatic mutations associated with clinical taxane resistance.

Citation Format: Jiaren Zhang, Ada Gjyrezi, Prashant Thakkar, Giuseppe Galletti, Akanksha Verma, Olivier Elemento, Paraskevi Giannakakou. Elucidation of taxane resistance in prostate cancer through RNA-Seq analysis of circulating tumor cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3489.

Abstract 3600: Impaired taxane binding to MTs in intrinsically taxane resistant gastric cancer cells without β-tubulin mutation

The taxanes (i.e., paclitaxel, docetaxel (DTX) and cabazitaxel) are microtubule (MT)-stabilizing drugs widely used to treat solid tumor malignancies. Their success is limited by the presence of intrinsic or acquired drug resistance. Understanding the molecular mechanisms of taxane resistance is a key to significantly improve clinical outcomes of taxane-based chemotherapy. In gastric cancer (GC), retrospective analysis of the TAX-325 trial revealed that the addition of docetaxel (DTX) to standard cisplatin/fluorouracil increased progression-free and overall survival, primarily only in intestinal subtype (INT) GC, suggesting that diffuse (DIF) GC may be intrinsically taxane resistant. In fact, our previous data supported this hypothesis; DIF GC cell lines had higher incidence (63%) of DTX resistance than INT GC cell lines (25%). Flow cytometric analyses showed negligible P-glycoprotein expression on the cell surface of all cell types, and accumulation of C14-labeled DTX in cells was observed in both sensitive and resistant GC cell lines. These results ruled out drug efflux as a possible mechanism that confers taxane resistance in DIF GC cells.

Next, we used fluorescein-conjugated paclitaxel (Flutax) as a probe to investigate the affinity of taxanes to MTs. Live cell imaging showed strong binding of Flutax to MTs in a sensitive cell line at least for 60 minutes. In contrast, Flutax failed to stay bound to MTs in resistant GC cell lines,. In addition, discontinuous decoration of MTs with Flutax was seen in resistant but not in sensitive cell lines. Our observation suggests that MTs of resistant GC cell lines have lower affinity for taxanes, and there might be subtle structural changes of MTs. We are currently conducting the competition of Flutax/DTX to quantify the affinity of DTX in both types of GC cell lines.

Because tubulin mutations have been reported in many taxane-resistant cell lines, we sequenced the different tubulin isotypes in GC cell lines using both Sanger and next generation sequencing. No mutations were identified. In addition, we did not see any significant changes in the expression of βIII-tubulin or tubulin post-translational modifications between the sensitive and resistant cell lines. Pathway analyses on the RNA-Seq datasets derived from the panels of sensitive and resistant cell lines before and after taxane treatment is ongoing to identify the key molecular events underlying taxane resistance.Taken together, our data indicate that new molecular pathway(s) or change of overall MT structure and/or function may contribute to the impaired taxane binding to MTs in resistant GC cells. Our study will lead us to novel mechanistic insights in intrinsic drug resistance, and will ultimately allow us to target key molecule(s) to overcome chemo-resistance, the key determinant to improve overall survival of patients.

Citation Format: Katsuhiro Kita, Giuseppe Galletti, Kyle Cleveland, Prashant V. Thakkar, Ada Gjyrezi, Chao Zhang, Isabel Barasoain, J. Fernando Díaz, Doron Betel, Manish A. Shah, Paraskevi Giannakakou. Impaired taxane binding to MTs in intrinsically taxane resistant gastric cancer cells without β-tubulin mutation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3600. doi:10.1158/1538-7445.AM2015-3600

Abstract 4311: Molecular basis of interaction between ERG and microtubule inhibitors in CRPC patients

Microtubules (MTs) are cytoskeletal polymer of α/β tubulin heterodimers that are involved in several cellular functions including mitosis, cell shape and intracellular trafficking. Due to their fundamental role in the maintenance of cell homeostasis, MTs are the target of several chemotherapeutic drugs that act by either stabilizing (taxanes, epothilones) or destabilizing (vinca alkaloids, Eribulin) the MT network.

Taxanes (docetaxel and cabazitaxel) are currently used for first or second line treatment of patients with metastatic castration-resistant prostate caner (CRPC) and are the only class of chemotherapy drugs that improve survival. Despite taxane clinical success, there is significant heterogeneity in how patients respond to taxane therapy and most of CRPC patients eventually become refractory and develop resistance to the treatment. The molecular basis underlying this heterogeneity in treatment response is still to be determined.

ERG (ETS-related gene) is over-expressed by 30-80 fold in at least 50% of prostate cancers as a result of gene fusion with the 5′ promoter of the AR-induced TMPRSS2 gene. ERG rearrangement is an early event in prostate cancer tumorigenesis and represents the most frequent recurrent genetic alteration in prostate cancer. We recently showed that ERG over-expression is associated with decreased taxane sensitivity in prostate cancer cell lines, in vivo xenograft models, and in ERG-positive CRPC patients. Mechanistically, we demonstrated that ERG contributes to taxane resistance by binding tubulin in the cytoplasm, altering MT dynamics towards increased catastrophe rate thereby shifting the dynamic equilibrium between MT polymers (preferred taxane substrate) and soluble tubulin dimers (preferred substrate for MT-depolymerizing drugs) towards soluble tubulin. Tiling mutant co-immunoprecipitation showed that ERG-tubulin physical interaction is mediated by ERG PNT domain, which has been also implicated with ERG homo-oligomerization and heterodimerization. Moreover, MT-cosedimentation assay elucidated that ERG predominantly interacts with tubulin dimers instead of MT-polymers. Finally, we demonstrated that treatment with the MT-depolymerizing drugs nocodazole or Eribulin is associated with lack of resistance or even enhanced sensitivity in ERG-positive cells.

We are currently investigating the molecular basis of the interaction between Eribulin and ERG in CRPC models, in order to elucidate the potential role of Eribulin in the treatment of ERG+ CRPC patients.

Overall, our data strongly suggest a new role for ERG as MT-destabilizing MAP, with significant therapeutic implications in CRPC patients. ERG status could emerge as biomarker predictive of response to MT-inhibitors, driving clinical decisions for patient selection to appropriate therapies.

Citation Format: Giuseppe Galletti, Cynthia Cheung, David S. Rickman, Paraskevi Giannakakou. Molecular basis of interaction between ERG and microtubule inhibitors in CRPC patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4311. doi:10.1158/1538-7445.AM2015-4311

Pattern of care and effectiveness of treatment for glioblastoma patients in the real world: Results from a prospective population-based registry. Could survival differ in a high-volume center?

BACKGROUND

As yet, no population-based prospective studies have been conducted to investigate the incidence and clinical outcome of glioblastoma (GBM) or the diffusion and impact of the current standard therapeutic approach in newly diagnosed patients younger than aged 70 years.

METHODS

Data on all new cases of primary brain tumors observed from January 1, 2009, to December 31, 2010, in adults residing within the Emilia-Romagna region were recorded in a prospective registry in the Project of Emilia Romagna on Neuro-Oncology (PERNO). Based on the data from this registry, a prospective evaluation was made of the treatment efficacy and outcome in GBM patients.

RESULTS

Two hundred sixty-seven GBM patients (median age, 64 y; range, 29-84 y) were enrolled. The median overall survival (OS) was 10.7 months (95% CI, 9.2-12.4). The 139 patients ≤aged 70 years who were given standard temozolomide treatment concomitant with and adjuvant to radiotherapy had a median OS of 16.4 months (95% CI, 14.0-18.5). With multivariate analysis, OS correlated significantly with KPS (HR = 0.458; 95% CI, 0.248-0.847; P = .0127), MGMT methylation status (HR = 0.612; 95% CI, 0.388-0.966; P = .0350), and treatment received in a high versus low-volume center (HR = 0.56; 95% CI, 0.328-0.986; P = .0446).

CONCLUSIONS

The median OS following standard temozolomide treatment concurrent with and adjuvant to radiotherapy given to (72.8% of) patients aged ≤70 years is consistent with findings reported from randomized phase III trials. The volume and expertise of the treatment center should be further investigated as a prognostic factor.

Abstract 923: Analysis of microtubule perturbations and androgen receptor localization in circulating tumor cells from castration resistant prostate cancer patients as predictive biomarkers of clinical response to docetaxel chemotherapy

Although the recent availability of novel treatment for castration resistant prostate cancer (CRPC) has shown improvements in overall survival, CRPC is incurable and lethal disease. It has been recognized that tumor progression despite castrate levels of androgens is still associated with active signaling from the androgen receptor (AR) which affects gene transcription following its nuclear accumulation. Taxanes bind to and stabilize cellular microtubules (MTs) perturbing the fine and intricate organization of the microtubule network thus, impairing MT-based cell processes like cell division and intracellular trafficking. Our recent work showed that AR translocation from the cytoplasm to the nucleus is MT-dependent and that taxane treatment sequesters AR into the cytoplasm inhibiting the receptors transcriptional activity. While this novel mechanism of taxane activity may explain the clinical efficacy of taxanes in CRPC, clinically we still fail to understand the molecular basis of patient response or resistance to taxanes. We hypothesized that engagement of the MT-AR pathway by the taxanes can be used as read-out of effective drug-target engagement in cancer cells and can be used as biomarker predictive of taxane activity in CRPC patients.

To assess the predictive role of these biomarkers, we are currently conducting a prospective clinical study in which we isolate circulating tumor cells (CTCs) from the peripheral blood of CRPC patient undergoing docetaxel treatment. We have enrolled 50 of the 80 total patients, from which we isolated CTCs before (at baseline) and during docetaxel treatment (at day 8 of first cycle of docetaxel and upon relapse) using two different approaches: the EpCAM-based immunomagnetic enrichment (CellSearch) and the ficolling technique to isolate unenriched PBMCs inclusive of CTCs. To avoid issues with leucocyte contamination we subject the EpCAM captured cells are to staining for DAPI , PSMA, CD-45, AR and Tubulin and image them by confocal microscopy. CTCs are defined as nucleated, PSMA+, CD-45- cells. The unenriched PBMC population is also subjected to the same multiplex confocal microscopy protocol. Microtubule network morphology and AR subcellular localization in then assessed in CTCs and each biomarker alone and in combination is correlated with clinical response to docetaxel treatment defined by PCWG2 recommendation. So far we have collected and analyzed baseline and cycle 1-Day 8 samples from all 50 patients and relapse samples from 31 patients.

Determination of effective drug-target engagement on C1D8 may allow early detection of molecular response to treatment, or lack of molecular response, which will ultimately allow for chemotherapy customization for the individual patient.

Citation Format: Shinsuke Tasaki, Matthew Sung, Alexandre Matov, Giuseppe Galletti, Elan Diamond, Neil Bander, Kathy Zhou, Scott Tagawa, David Nanus, Paraskevi Giannakakou. Analysis of microtubule perturbations and androgen receptor localization in circulating tumor cells from castration resistant prostate cancer patients as predictive biomarkers of clinical response to docetaxel chemotherapy. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 923. doi:10.1158/1538-7445.AM2014-923

Circulating tumor cells in prostate cancer diagnosis and monitoring: an appraisal of clinical potential

Circulating tumor cells (CTCs) have emerged as a viable solution to the lack of tumor tissue availability for patients with a variety of solid tumors, including prostate cancer. Different approaches have been used to capture this tumor cell population and several of these techniques have been used to assess the potential role of CTCs as a biological marker to predict treatment efficacy and clinical outcome. CTCs are now considered a strong tool to understand the molecular characteristics of prostate cancer, and to be used and analyzed as a 'liquid biopsy' in the attempt to grasp the biological portrait of the disease in the individual patient.

Isolation of breast cancer and gastric cancer circulating tumor cells by use of an anti HER2-based microfluidic device

Circulating tumor cells (CTCs) have emerged as a reliable source of tumor cells, and their concentration has prognostic implications. CTC capture offers real-time access to cancer tissue without the need of an invasive biopsy, while their phenotypic and molecular interrogation can provide insight into the biological changes of the tumor that occur during treatment. The majority of the CTC capture methods are based on EpCAM expression as a surface marker of tumor-derived cells. However, EpCAM protein expression levels can be significantly down regulated during cancer progression as a consequence of the process of epithelial to mesenchymal transition. In this paper, we describe a novel HER2 (Human Epidermal Receptor 2)-based microfluidic device for the isolation of CTCs from peripheral blood of patients with HER2-expressing solid tumors. We selected HER2 as an alternative to EpCAM as the receptor is biologically and therapeutically relevant in several solid tumors, like breast cancer (BC), where it is overexpressed in 30% of the patients and expressed in 90%, and gastric cancer (GC), in which HER2 presence is identified in more than 60% of the cases. We tested the performance of various anti HER2 antibodies in a panel of nine different BC cell lines with varying HER2 protein expression levels, using immunoblotting, confocal microscopy, live cells imaging and flow cytometry analyses. The antibody associated with the highest capture efficiency and sensitivity for HER2 expressing cells on the microfluidic device was the one that performed best in live cells imaging and flow cytometry assays as opposed to the fixed cell analyses, suggesting that recognition of the native conformation of the HER2 extracellular epitope on living cells was essential for specificity and sensitivity of CTC capture. Next, we tested the performance of the HER2 microfluidic device using blood from metastatic breast and gastric cancer patients. The HER2 microfluidic device exhibited CTC capture in 9/9 blood samples. Thus, the described HER2-based microfluidic device can be considered as a valid clinically relevant method for CTC capture in HER2 expressing solid cancers.

Abstract 2888: Computational analysis of microtubule dynamics for personalized cancer therapy

Metastatic prostate cancer (PC) is treated primarily by means of taxane-based chemotherapy with one of the clinically used taxanes: paclitaxel, docetaxel and cabazitaxel. At the cellular level, the taxanes bind microtubules (MTs), inhibit MT dynamics and alter the spatial organization of the MT network. Thereby the taxanes inhibit the intracellular trafficking of transcription factors critical for tumor survival. In PC, taxanes are the only chemotherapy class shown to improve survival, however, the emergence of clinical taxane resistance hampers their clinical efficacy. In addition, patients resistant to one taxane often respond to another, yet, currently we do not have the ability to match individual patients to a specific taxane. In cells, different taxanes have differential effects on microtubule dynamics which may ultimately pre-determine their efficacy for each individual patient. Thus, we hypothesized that the particular pattern of dynamic behavior of the MT cytoskeleton in individual patients could be exploited therapeutically. Therefore, we looked into dissecting the concrete effects of each of the taxanes for several PC cells lines. Preliminary unpublished data have revealed that PC cells expressing the TMPRSS2-ERG fusion protein exhibit taxane resistance. In addition, we have recently shown that the androgen receptor (AR) binds MTs in order to traffic to the nucleus and that taxane-mediated inhibition of AR nuclear accumulation correlates with patient clinical response to taxane therapy. Moreover, we have shown that the two clinically relevant AR splice variants, ARv567 and ARv7, show differential response to taxane therapy. Therefore, we set out to investigate the hypothesis that ERG fusion and/or AR variants might modulate endogenous microtubule dynamics in a way that determines cellular response to taxane treatment. Xenografts PC models expressing the ARv7 variant exhibit reduced sensitivity to docetaxel treatment. In addition, docetaxel's ability to induce MT stabilization is significantly impaired in ERG+ cells. We have recently established isogenic PC cell line series with inducible ERG (DU145 ERG+ and ERG-), as well as M12 cells without endogenous AR that stably express, wt-AR, ARv567 and ARv7. We then tested in a systematic way endogenous MT dynamics using live cell confocal microscopy of labeled MT tips following EGFP-EB1 lentiviral transduction. We use computer vision algorithms to obtain statistically representative results for the effects of ERG or AR on microtubule homeostasis following treatment with each of the three taxanes. We measure changes in MT behavior as statistically significant shifts in different parameters of MT dynamics measured from >20,000 MTs for each condition. Our preliminary results revealed that the presence of ERG fusion a correlation between MT dynamics and AR variant expression in PC cell lines.

Citation Format: Alexandre Matov, Dragi Kimovski, Giuseppe Galletti, Nancy Chan, Benet Pera, William T. Harkcom, David S. Rickman, Paraskevi Giannakakou. Computational analysis of microtubule dynamics for personalized cancer therapy. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2888. doi:10.1158/1538-7445.AM2013-2888