HPB P11 Ex vivo human pancreatic cancer avatars; establishing a platform to evaluate chemotherapeutic sensitivity

Background

A significant variation is observed in the response rate to chemotherapy amongst patients with pancreatic cancer. Current guidelines advocate treatment regimes based purely on the patient's level of fitness. Such an approach fails to acknowledge the individual's tumour biology. Our aim was to assess whether patient derived cancer avatars could be used to deliver personalised therapy.

Methods

Individual avatars were created from resected tumours and were cultured ex vivo either under novel perfusion culture conditions or conventional static culture. Serial assessment of avatar proliferation capacity and metabolic function was performed to determine viability over time. Avatars were treated with chemotherapy and treatment sensitivity was determined. Avatar response to chemotherapy was subsequently compared to the patient's response in order to determine whether the patient's avatar could predict a clinically meaningful response to therapy.

Results

Patient derived cancer avatars (n=13) were successfully cultured for 12 days ex vivo. Perfusion culture of avatars was associated with a preservation of proliferative capacity (p < 0.01), metabolic function (p < 0.01) and a reduction in apoptosis rates (p < 0.05) when compared to conventional static culture. Avatars were treated with Gemcitabine and different response rates were observed varying from treatment sensitivity to resistance. A positive correlation was noted between the avatar's response and the patient's clinical response whilst on adjuvant Gemcitabine therapy.

Conclusions

Patient derived cancer avatars provide a window of insight into the tumour's response to chemotherapy and may allow for a paradigm shift in the long-term survival rates for this disease.

53BP1-mediated recruitment of RASSF1A to ribosomal DNA breaks promotes local ATM signaling

DNA lesions occur across the genome and constitute a threat to cell viability; however, damage at specific genomic loci has a relatively greater impact on overall genome stability. The ribosomal RNA gene repeats (rDNA) are emerging fragile sites. Recent progress in understanding how the rDNA damage response is organized has highlighted a key role of adaptor proteins. Here, we show that the scaffold tumor suppressor RASSF1A is recruited to rDNA breaks. RASSF1A recruitment to double-strand breaks is mediated by 53BP1 and depends on RASSF1A phosphorylation at Serine 131 by ATM kinase. Employing targeted rDNA damage, we uncover that RASSF1A recruitment promotes local ATM signaling. RASSF1A silencing, a common epigenetic event during malignant transformation, results in persistent breaks, rDNA copy number alterations and decreased cell viability. Overall, we identify a novel role for RASSF1A at rDNA break sites, provide mechanistic insight into how the DNA damage response is organized in a chromatin context, and provide further evidence for how silencing of the RASSF1A tumor suppressor contributes to genome instability.

Predicting Early Disease Recurrence of Pancreatic Cancer following Surgery: Determining the Role of NUDT15 as a Prognostic Biomarker

Surgical resection remains the only curative treatment strategy for Pancreatic Ductal Adenocarcinoma (PDAC). A proportion of patients succumb to early disease recurrence post-operatively despite receiving adjuvant chemotherapy. The ability to identify these high-risk individuals at their initial diagnosis, prior to surgery, could potentially alter their treatment algorithm. This unique patient cohort may benefit from neo-adjuvant chemotherapy, even in the context of resectable disease, as this may secure systemic control over their disease burden. It may also improve patient selection for surgery. Using the Cancer Genome Atlas dataset, we first confirmed the poor overall survival associated with early disease recurrence (p < 0.0001). The transcriptomic profiles of these tumours were analysed, and we identified key aberrant signalling pathways involved in early disease relapse; downregulation across several immune signalling pathways was noted. Differentially expressed genes that could serve as biomarkers were identified (BPI, C6orf58, CD177, MCM7 and NUDT15). Receiver operating characteristic curves were constructed in order to identify biomarkers with a high diagnostic ability to identify patients who developed early disease recurrence. NUDT15 expression had the highest discriminatory capability as a biomarker (AUC 80.8%). Its expression was confirmed and validated in an independent cohort of patients with resected PDAC (n = 13). Patients who developed an early recurrence had a statistically higher tumour expression of NUDT15 when compared to patients who did not recur early (p < 0.01). Our results suggest that NUDT15 can be used as a prognostic biomarker that can stratify patients according to their risk of developing early disease recurrence.

TET2 Drives 5hmc Marking of GATA6 and Epigenetically Defines Pancreatic Ductal Adenocarcinoma Transcriptional Subtypes

BACKGROUND & AIMS

Pancreatic ductal adenocarcinoma (PDAC) is characterized by advanced disease stage at presentation, aggressive disease biology, and resistance to therapy, resulting in an extremely poor 5-year survival rate of <10%. PDAC is classified into transcriptional subtypes with distinct survival characteristics, although how these arise is not known. Epigenetic deregulation, rather than genetics, has been proposed to underpin progression, but exactly why is unclear and is hindered by the technical limitations of analyzing clinical samples.

METHODS

We performed genome-wide epigenetic mapping of DNA modifications 5-methylcytosine and 5-hydroxymethylcytosine (5hmc) using oxidative bisulfite sequencing from formalin-embedded sections. We identified overlap with transcriptional signatures in formalin-fixed, paraffin-embedded tissue from resected patients, via bioinformatics using iCluster and mutational profiling and confirmed them in vivo.

RESULTS

We found that aggressive squamous-like PDAC subtypes result from epigenetic inactivation of loci, including GATA6, which promote differentiated classical pancreatic subtypes. We showed that squamous-like PDAC transcriptional subtypes are associated with greater loss of 5hmc due to reduced expression of the 5-methylcytosine hydroxylase TET2. Furthermore, we found that SMAD4 directly supports TET2 levels in classical pancreatic tumors, and loss of SMAD4 expression was associated with reduced 5hmc, GATA6, and squamous-like tumors. Importantly, enhancing TET2 stability using metformin and vitamin C/ascorbic acid restores 5hmc and GATA6 levels, reverting squamous-like tumor phenotypes and WNT-dependence in vitro and in vivo.

CONCLUSIONS

We identified epigenetic deregulation of pancreatic differentiation as an underpinning event behind the emergence of transcriptomic subtypes in PDAC. Our data showed that restoring epigenetic control increases biomarkers of classical pancreatic tumors that are associated with improved therapeutic responses and survival.

Circulating biomarkers and outcomes from a randomised phase 2 trial of gemcitabine versus capecitabine-based chemoradiotherapy for pancreatic cancer

BACKGROUND

The Phase 2 SCALOP trial compared gemcitabine with capecitabine-based consolidation chemoradiotherapy (CRT) in locally advanced pancreatic cancer (LAPC).

METHODS

Thirty-five systematically identified circulating biomarkers were analysed in plasma samples from 60 patients enroled in SCALOP. Each was measured in triplicate at baseline (prior to three cycles of gemcitabine-capecitabine induction chemotherapy) and, for a subset, prior to CRT. Association with overall survival (OS) was determined using univariable Cox regression and optimal thresholds delineating low to high values identified using time-dependent ROC curves. Independence from known prognostic factors was assessed using Spearman correlation and the Wilcoxon rank sum test prior to multivariable Cox regression modelling including independent biomarkers and known prognostic factors.

RESULTS

Baseline circulating levels of C-C motif chemokine ligand 5 (CCL5) were significantly associated with OS, independent of other clinicopathological characteristics. Patients with low circulating CCL5 (CCL5low) had a median OS of 18.5 (95% CI 11.76-21.32) months compared to 11.3 (95% CI 9.86-15.51) months in CCL5high; hazard ratio 1.95 (95% CI 1.04-8.65; p = 0.037).

CONCLUSIONS

CCL5 is an independent prognostic biomarker in LAPC. Given the known role of CCL5 in tumour invasion, metastasis and the induction of an immunosuppressive micro-environment, targeting of CCL5-mediated pathways may offer therapeutic potential in pancreatic cancer.

CLINICAL TRIAL REGISTRATION

The SCALOP trial was registered with ISRCTN, number 96169987 (registered 29 May 2008).

Translational analysis from SCALOP trial: CCL5 as a prognostic biomarker and a potentially actionable target in locally advanced pancreatic cancer (LAPC)

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Background: SCALOP was a multi-centre phase II RCT where 114 patients with LAPC were received 3 cycles of Gemcitabine and Capecitabine (GEMCAP) and those with stable/responding disease (n = 74) were randomised to Gem-RT or Cap-RT. The trial showed superiority of Cap-RT. Baseline blood samples of randomised patients were analysed for 35 circulating biomarkers. In vivo study was undertaken with candidate biomarker (CCL5) to test actionability. Methods: Patient bloods were tested using R&D multiplexed magnetic Luminex assays and IGF-1, TGF-b1 and b-NGF DuoSet ELISA. Orthotropic KrasG12D;P53R172H;PDXcre (KPC) tumors were implanted in Bl6-mice and treated with Gem, CCR5-inhibitor (CCR5i) maraviroc (MV), PD1 inhibitor (PD1i), PD1i+MV alone and in combination with MRI guided small animal Radiotherapy (RT). Immunophenotyping was performed by IHC and Aurora Cytek spectral flow cytometry. Results: Baseline biomarker data was available on 63/74 randomised patients. Of the 35 biomarkers tested, only CCL5 was found to be significantly associated with OS with a median OS of 18.5 (95% CI: 11.76-21.32) vs 11.3 (9.86-15.51) months (low vs high), and HR 1.37 (95% CI:1.04-3.65; p = 0.037) in the Cox multivariable model. Treatment of orthotopic KPC tumors revealed that combination of MV+PD1i+RT resulted in tumour growth inhibition and a switch of tumour macrophages from M2 to M1 accompanied by increase in infiltration of cytotoxic CD8+ Tcells and NK cells. Conclusions: Previous pre-clinical studies reported CCL5-CCR5 axis as a poor prognostic marker and a possible cause of immune-resistance in pancreatic cancer. Herein we have demonstrated in prospectively collected clinical trial blood samples that high circulating CCL5 is associated with poor prognosis in LAPC. CCR5 inhibitor in combination with RT+PD1i may overcome immune-resistance, and should be tested in clinical trials. Clinical trial information: 96169987 .

Dual-specificity protein phosphatase DUSP4 regulates response to MEK inhibition in BRAF wild-type melanoma

Background

Aiming to improve treatment options for BRAF wild-type melanoma, we previously conducted the DOC-MEK study of docetaxel with MEK inhibitor (MEKi) selumetinib or placebo, revealing trends to prolongation of progression-free survival (hazard ratio 0.75, P = 0.130), and improved response rates (32% vs 14%, P = 0.059) with docetaxel plus selumetinib. NRAS status did not associate with outcome. Here, the aim was to identify novel biomarkers of response to MEKi.

Methods

A MEK 6 gene signature was quantified using NanoString and correlated with clinical outcomes. Two components of the gene signature were investigated by gene silencing in BRAF/NRAS wild-type melanoma cells.

Results

In melanomas of patients on the selumetinib but not the placebo arm, two gene signature components, dual-specificity protein phosphatase 4 (DUSP4) and ETS translocation variant 4 (ETV4), were expressed more highly in responders than non-responders. In vitro, ETV4 depletion inhibited cell survival but did not influence sensitivity to MEKi selumetinib or trametinib. In contrast, DUSP4-depleted cells showed enhanced cell survival and increased resistance to both selumetinib and trametinib.

Conclusions

ETV4 and DUSP4 associated with clinical response to docetaxel plus selumetinib. DUSP4 depletion induced MEKi resistance, suggesting that DUSP4 is not only a biomarker but also a mediator of MEKi sensitivity.

Clinical Trial Registration

DOC-MEK (EudraCT no: 2009-018153-23).

Abstract C42: Cell culture under perfusion conditions reduces cellular metabolic stress and mimics the in vivo physiologic environment in pancreatic cancer

Introduction: Tumor responsiveness to chemotherapy in PDAC varies significantly across patients, and some patients may succumb to very early recurrent disease (within 6 months). This reinforces the need to establish an accurate model that preserves the tumor microenvironment in the ex vivo, allowing a personalized drug screen for patients to identify optimal regime of therapy. Many aspects of tumor biology are difficult to reproduce in ex vivo, e.g., the tumor-host interaction and tumor vascularity. The current standard of 2D cell culture is that the medium is exchanged at defined time points (i.e., static culture). However, this is not a physiologically representative model as cells are maintained in either a nutrient and substrate “hyper-replete” or deplete environment, rather than an epistatic supply. Moreover, episodic media replacement creates significant and abrupt changes to the culture environment and availability of substrates, which induces cellular metabolic stress. We evaluated the role of perfusion culture to establish whether this technique reduced metabolic stress and created a physiologically representative model of the in vivo tumor environment by comparing in vitro cell responses to core biopsies from patients with pancreatic cancer.

Methods: Cells were cultured and maintained either in static culture (serving as a control, with media exchange every 72 hours) or in a nutritionally replete condition with a constant low perfusion rate of media exchange over 7 days. Daily media extraction was performed in order to evaluate the metabolic activity and viability of cells in addition to quantify the availability of metabolic substrates. Core biopsies were temporarily fixed in low melting agarose gel prior to creating multiple tissue slices through the tumor. Tissue slices were then cultured either in static culture (as control) or under perfusion conditions. Tumors were also subjected to histologic assessment of the tissue morphology, cellular function, and components of the microenviroment.

Results: Under conventional static culture, a decrease in the quantity of metabolic substrates was observed over time, indicating metabolic activity of cells in static culture was suppressed (noted by downregulation of mTOR pathway products, notably phosphorylated S6). Under perfusion conditions, glucose concentration was maintained over 7 days, indicating cells were able to maintain metabolic activity. Tissue sections were similarly evaluated for metabolic stress and will be presented.

Conclusion: This platform highlights the considerable metabolic stress that cells undergo while under conventional static culture. Perfusion culture serves as a technique to reduce cellular metabolic stress in addition to creating a physiologically representative model ex vivo.

Citation Format: Daniel Hughes, Frances Willenbrock, Zahir Soonawalla, Srikanth Reddy, Michael Silva, Somnath Mukherjee, Eric O'Neill. Cell culture under perfusion conditions reduces cellular metabolic stress and mimics the in vivo physiologic environment in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr C42.

Abstract B40: High circulating CCL5 is associated with poor prognosis in locally advanced pancreatic cancer (LAPC): Biomarker analysis from the randomized phase II SCALOP trial

Background: SCALOP recruited 114 patients with LAPC. Induction chemotherapy consisted of 3 cycles of gemcitabine and capecitabine (GEMCAP). Patients with nonprogression (n=74) were randomized to GEM or CAP based CRT (50.4Gy/28 fractions). Blood samples collected at baseline were analyzed for 35 angiogenic and immune biomarkers reported to be of prognostic/predictive value in pancreatic cancer.

Methods: IGF-1, TGF-b1, and b-NGF were analyzed using R & D DuoSet ELISA systems and the signal detected using a POLARstar Omega plate reader. The remaining biomarkers were assessed using R & D multiplexed magnetic Luminex assays and measured using a Luminex Magpix. Assays were performed in triplicate.

Statistical Analysis: Univariate Cox proportional hazard models were used as continuous variable to determine the association with overall survival (OS). Multiple comparisons were adjusted using the False Discovery Rate (FDR). Those found to be significant at the q value &lt;0.2 were then further investigated for independence from existing clinical characteristics (i.e., CA19-9, WHO PS and age). Of those found to be independent, optimal thresholds delineating low to high values were found using the R “survivalROC” package based on time-dependent ROC curves from censored survival data and their corresponding area under the curve (AUC). The dichotomized biomarkers, split at the optimal threshold, were then associated with OS using univariate and multivariable Cox proportional hazard models.

Results: Biomarker data were available on 63/74 patients. 57% (36/63) were male, 56% (35/63) were age &lt;65, 59% (37/63) had WHO PS 0 compared to 1, 51% (32/63) received gemcitabine, median CA19.9 was 233IU/L (IQR 75,801) and median tumor diameter was 3.8cm (IQR 3, 4.8). Of the 35 biomarkers tested, only CCL5, IL3, and IFN had significant associations with OS. CCL5 and IL3 were then found to be independent of existing clinical characteristics and were taken forward, where their optimal thresholds were found to be 1.27 micg/ml (sensitivity 64%; specificity 100%) and 57.75 pg/ml (sensitivity 83%; specificity 100%), respectively. CCL5, but not IL3, was found to be significantly associated with OS once dichotomized at its optimal threshold, with a median OS of 18.5 (95% CI: 11.76-21.32) vs. 11.3 (9.86-15.51) months, HR 1.37 (95% CI:1.04-3.65; p=0.037) in the Cox multivariable model. Moreover, biomarker signatures incorporating both CCL5 and IL3 (continuous variable) with age, PS and CA19.9 were prognostic: CCL5 signature:19.2 vs. 10.8 mo (HR 2.79, p=0.001) IL3 signature: 18.5 vs. 11.2 mo (HR 2.35, p=0.006) CCL5/IL3 signature: 18.7 vs. 11.2 mo, (HR 2.25, p=0.11).

Conclusion: High circulating CCL5 has a significantly worse prognosis. This is consistent with preclinical literature that demonstrates the role of CCL5 in tumor invasion/metastasis and induction of an immunosuppressive microenvironment through Treg infiltration. We are currently conducting in vivo experiments involving CCR5 antagonists and immunotherapy in orthotopic mouse models.

Citation Format: Frances Willenbrock, Catrin Cox, Charlotte Wilhelm-Benartzi, Aswin Abraham, Robert Owens, Ahmad Sabbagh, Chris Hurt, Tim Maughan, Eric O'Neill, Somnath Mukherjee. High circulating CCL5 is associated with poor prognosis in locally advanced pancreatic cancer (LAPC): Biomarker analysis from the randomized phase II SCALOP trial [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr B40.

Abstract PR02: Loss of TET2 activity results in epigenetic instability and drives PDAC molecular subtypes

Background: mRNA datasets have defined two molecular subtypes of pancreatic ductal adenocarcinoma (PDAC), classical and squamous, with distinct clinical characteristics and raising the possibility of subtype specific therapies (Collisson et al., 2019). The aggressive squamous subtype is characterized by poorer patient survival and loss of endodermal differentiation markers GATA6 and PDX1, but neither PDAC subtypes nor metastasis can be explained by genetic mutations alone (Reiter et al., 2018). Conversely, widespread epigenetic reprogramming is associated with progression to more aggressive phenotypes (McDonald et al., 2017), suggesting that aggressive molecular subtype is likely to be epigenetically driven. The role of DNA 5’methylcytosine (5’mc) in PDAC has been previously unclear due to an inability to distinguish this mark from the reciprocal activation mark DNA 5’hydroxymethylcytosine (5’hmC), mediated by Ten-eleven-translocation (TET) enzymes. Moreover, 5’hmc is dynamically regulated during pancreatic differentiation, but a role during PDAC initiation or progression has not been previously addressed.

Methods: PDAC patients who underwent surgical resection at the Churchill Hospital, Oxford (n=146) had FFPE tumor tissue mutation comprehensively profiled by illumina hotspot array (300X), mRNA microarray, and the first epigenetic separation of 5’mc and 5’hmc on FFPE via oxidative bisulphite sequencing (oxBS) and illumina EPIC arrays. iCluster was used to highlight epigenetic PDAC subtypes and compare to existing TCGA datasets. Orthotopic models were employed to test whether the Squamous subtype is defined by 5’hmc loss and if this can be converted to the classical subtype in vivo.

Results: Compared to healthy tissue, PDAC tumors demonstrate loss of 5’hmC at genes critical for pancreatic development and associated with PDAC progression, including MAPK signaling and TP53 targets. 5’hmC was preferentially lost in aggressive molecular subtypes (squamous) compared to the classical subtypes and was associated with SMAD4 mutations and reduced TET2. Overexpression of TET2 in squamous tumor cells restored 5’hmc and the expression of classical associated genes (e.g., GATA6 and PDX1), suggesting that 5’hmC is a master epigenetic regulator of PDAC molecular subtypes. Notably, we find TET2 stability is regulated by glucose levels, implying the widespread hypoglycemia seen in PDAC patients may contribute to progression of aggressive subtypes through loss of 5’hmC. Concomitantly, as metformin and vitamin C independently enhance endogenous TET2 activity, we find that this combination acts synergistically on squamous tumors to increase 5’hmC and expression of a classical-subtype phenotype, suggesting subtype switching is achievable in vitro and in vivo.

Conclusion: These results identify 5’hmC as a regulator of molecular subtype that can be targeted in vivo using well-tolerated drugs.

This abstract is also being presented as Poster A39.

Citation Format: Michael Eyres, Simone Lanfredini, Frances Willenbrock, Asmita Thapa, Andrew Blake, Adam Burns, Ahmad Sabbagh, Aswin Abraham, Timothy Maughan, Zahir Soonawalla, Anna Schuh, Somnath Mukhergee, Eric O'Neill. Loss of TET2 activity results in epigenetic instability and drives PDAC molecular subtypes [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr PR02.

RAPTOR up-regulation contributes to resistance of renal cancer cells to PI3K-mTOR inhibition

The outlook for patients with advanced renal cell cancer (RCC) has been improved by targeted agents including inhibitors of the PI3 kinase (PI3K)-AKT-mTOR axis, although treatment resistance is a major problem. Here, we aimed to understand how RCC cells acquire resistance to PI3K-mTOR inhibition. We used the RCC4 cell line to generate a model of in vitro resistance by continuous culture in PI3K-mTOR kinase inhibitor NVP-BEZ235 (BEZ235, Dactolisib). Resistant cells were cross-resistant to mTOR inhibitor AZD2014. Sensitivity was regained after 4 months drug withdrawal, and resistance was partially suppressed by HDAC inhibition, supporting an epigenetic mechanism. BEZ235-resistant cells up-regulated and/or activated numerous proteins including MET, ABL, Notch, IGF-1R, INSR and MEK/ERK. However, resistance was not reversed by inhibiting or depleting these pathways, suggesting that many induced changes were passengers not drivers of resistance. BEZ235 blocked phosphorylation of mTOR targets S6 and 4E-BP1 in parental cells, but 4E-BP1 remained phosphorylated in resistant cells, suggesting BEZ235-refractory mTORC1 activity. Consistent with this, resistant cells over-expressed mTORC1 component RAPTOR at the mRNA and protein level. Furthermore, BEZ235 resistance was suppressed by RAPTOR depletion, or allosteric mTORC1 inhibitor rapamycin. These data reveal that RAPTOR up-regulation contributes to PI3K-mTOR inhibitor resistance, and suggest that RAPTOR expression should be included in the pharmacodynamic assessment of mTOR kinase inhibitor trials.

Aruncin B: Synthetic Studies, Structural Reassignment and Biological Evaluation

A ring-closing alkene metathesis (RCM)/ oxyselenation-selenoxide elimination sequence was established to the sodium salts E- and Z-25 of the originally proposed structure for the recently isolated cytotoxin aruncin B (1), as well as to the sodium salt Z-34 of a related ethyl ether regioisomer; however, none of their corresponding free acids could be obtained. Their acid sensitivity, together with detailed analysis of the spectroscopic data indicated that profound structural revision was necessary. This led to reassignment of aruncin B as a Z-γ-alkylidenebutenolide Z-36. Although a related RCM/ oxyselenation-selenoxide elimination sequence was used to confirm the γ-alkylidenebutenolide motif, a β-iodo Morita-Baylis-Hillman reaction/ Sonogashira cross-coupling-5-exo-dig lactonisation sequence was subsequently developed, due to its brevity and flexibility for diversification. Aruncin B (36), together with 14 γ-alkylidenebutenolide analogues, were generated for biological evaluation.

Perfused Three-dimensional Organotypic Culture of Human Cancer Cells for Therapeutic Evaluation

Pharmaceutical research requires pre-clinical testing of new therapeutics using both in-vitro and in-vivo models. However, the species specificity of non-human in-vivo models and the inadequate recapitulation of physiological conditions in-vitro are intrinsic weaknesses. Here we show that perfusion is a vital factor for engineered human tissues to recapitulate key aspects of the tumour microenvironment. Organotypic culture and human tumour explants were allowed to grow long-term (14-35 days) and phenotypic features of perfused microtumours compared with those in the static culture. Differentiation status and therapeutic responses were significantly different under perfusion, indicating a distinct biological response of cultures grown under static conditions. Furthermore, heterogeneous co-culture of tumour and endothelial cells demonstrated selective cell-killing under therapeutic perfusion versus episodic delivery. We present a perfused 3D microtumour culture platform that sustains a more physiological tissue state and increased viability for long-term analyses. This system has the potential to tackle the disadvantages inherit of conventional pharmaceutical models and is suitable for precision medicine screening of tumour explants, particularly in hard-to-treat cancer types such as brain cancer which suffer from a lack of clinical samples.

Synthesis and bioactivity of fused- and spiro-β-lactone-lactam systems

An investigation of the formation of fused- and spiro-β-lactone annulate to γ-lactams has shown that the fused systems are formed preferentially, under standard conditions, but that spiro systems are accessible only when the formation of the fused system is blocked and require careful optimisation of reaction conditions. These systems display both weak antibacterial activity and proteasome inhibition.

Abstract 3593: Raptor upregulation contributes to maintenance of 4EBP1 phosphorylation and TORC kinase resistance in renal cancer cells

Advanced renal cell cancer (RCC) is incurable, but recent advances in targeted treatment have improved the prognosis. Rapalogue inhibitors of the mammalian target of rapamycin (mTOR) are licensed for treatment of advanced RCC, although clinical benefit is modest. Novel mTOR kinase inhibitors show more complete blockade of mTOR downstream targets, and greater in vitro anti proliferative activity, although resistance remains a problem. The aim of this study was to create a model of in vitro resistance to PI3K-mTOR kinase inhibitor BEZ235, in order to identify biomarkers and mediators of resistance.

After 5 months continuous culture in BEZ235, resistance to 20nM BEZ235 was induced in the RCC4 cell line, generating subline RCC4B20. These cells had 14 fold higher BEZ235 growth inhibitory 50 (GI50) concentration compared to sensitive cells (99 nM vs. 7 nM). There was cross-resistance to alternative mTOR kinase inhibitor AZD2014 (GI50 1131 vs. 166 nM), but not to PI3K, AKT or allosteric mTORC1 inhibitors, suggesting that resistance was primarily directed at mTOR kinase. RCC4B20 cells were screened at the protein level by antibody array, and RNA level by microarray, and hits were validated by western blotting and qRT-PCR.

Proteins and pathways found to be up-regulated in RCC4B20 cells included MET, pMET, ABL, and MEK/ERK by antibody array, and NOTCH signalling by microarray. These were validated as showing altered regulation, but BEZ235 resistance was not blocked by depletion or inhibition of these targets, suggesting that these changes were correlates, but not mediators of resistance. An hypothesis-led approach directed attention to the mTORC1 pathway. In BEZ235 resistant cells, the mTORC1 target 4E-BP1 was re-phosphorylated, despite on-going mTOR blockade as evidenced by suppressed S6 phosphorylation. Recovery of 4E-BP1 phosphorylation was associated with 4.2 ± 0.3 fold increase in levels of RAPTOR, a scaffolding protein for mTOR substrates. Phosphorylation of 4E-BP1 was suppressed by rapamycin, or by RAPTOR depletion, both interventions partially reversing BEZ235 resistance. Finally, RCC4B20 cells lost resistance after 8 weeks of drug withdrawal, suggesting that resistance may have been associated with reversible changes in gene expression due to histone modification. Indeed, histone deacetylase inhibitor panobinostat partially reversed resistance to BEZ235.

In summary, the acquisition of resistance to mTOR kinase inhibition was accompanied by complex molecular changes, many of which were passengers, not drivers of resistance. Resistance was partially suppressed by interventions directed at raptor up-regulation and histone modification, suggesting that these changes do mediate resistance. The combination of BEZ235 with rapamyin or panobinostat warrant further investigation to evaluate potential to overcome resistance to mTOR kinase inhibition in RCC.

Citation Format: Philip Earwaker, Frances Willenbrock, Andrew Protheroe, Valentine Macaulay. Raptor upregulation contributes to maintenance of 4EBP1 phosphorylation and TORC kinase resistance in renal cancer cells. [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 3593. doi:10.1158/1538-7445.AM2015-3593

Novel automated tracking analysis of particles subjected to shear flow: kindlin-3 role in B cells

Shear flow assays are used to mimic the influence of physiological shear force in diverse situations such as leukocyte rolling and arrest on the vasculature, capture of nanoparticles, and bacterial adhesion. Analysis of such assays usually involves manual counting, is labor-intensive, and is subject to bias. We have developed the Leukotrack program that incorporates a novel (to our knowledge) segmentation routine capable of reliable detection of cells in phase contrast images. The program also automatically tracks rolling cells in addition to those that are more firmly attached and migrating in random directions. We demonstrate its use in the analysis of lymphocyte arrest mediated by one or more active conformations of the integrin LFA-1. Activation of LFA-1 is a multistep process that depends on several proteins including kindlin-3, the protein that is mutated in leukocyte adhesion deficiency-III patients. We find that the very first stage of LFA-1-mediated attaching is unable to proceed in the absence of kindlin-3. Our evidence indicates that kindlin-3-mediated high-affinity LFA-1 controls both the early transient integrin-dependent adhesions in addition to the final stable adhesions made under flow conditions.

The Gαq/11 proteins contribute to T lymphocyte migration by promoting turnover of integrin LFA-1 through recycling

The role of Gαi proteins coupled to chemokine receptors in directed migration of immune cells is well understood. In this study we show that the separate class of Gαq/11 proteins is required for the underlying ability of T cells to migrate both randomly and in a directed chemokine-dependent manner. Interfering with Gαq or Gα11 using dominant negative cDNA constructs or siRNA for Gαq causes accumulation of LFA-1 adhesions and stalled migration. Gαq/11 has an impact on LFA-1 expression at plasma membrane level and also on its internalization. Additionally Gαq co-localizes with LFA-1- and EEA1-expressing intracellular vesicles and partially with Rap1- but not Rab11-expressing vesicles. However the influence of Gαq is not confined to the vesicles that express it, as its reduction alters intracellular trafficking of other vesicles involved in recycling. In summary vesicle-associated Gαq/11 is required for the turnover of LFA-1 adhesion that is necessary for migration. These G proteins participate directly in the initial phase of recycling and this has an impact on later stages of the endo-exocytic pathway.

The specificity of TIMP-2 for matrix metalloproteinases can be modified by single amino acid mutations

Residues 1-127 of human TIMP-2 (N-TIMP-2), comprising three of the disulfide-bonded loops of the TIMP-2 molecule, is a discrete protein domain that folds independently of the C-terminal domain. This domain has been shown to be necessary and sufficient for metalloproteinase inhibition and contains the major sites of interaction with the catalytic N-terminal domain of active matrix metalloproteinases (MMPs). Residues identified as being involved in the interaction with MMPs by NMR chemical shift perturbation studies and TIMP/MMP crystal structures have been altered by site-directed mutagenesis. We show, by measurement of association rates and apparent inhibition constants, that the specificity of these N-TIMP-2 mutants for a range of MMPs can be altered by single site mutations in either the TIMP "ridge" (Cys1-Cys3 and Ser68-Cys72) or the flexible AB loop (Ser31-Ile41). This work demonstrates that it is possible to engineer TIMPs with altered specificity and suggests that this form of protein engineering may be useful in the treatment of diseases such as arthritis and cancer where the selective inhibition of key MMPs is desirable.

Human tissue inhibitor of metalloproteinases 3 interacts with both the N- and C-terminal domains of gelatinases A and B. Regulation by polyanions

We compared the association constants of tissue inhibitor of metalloproteinases (TIMP)-3 with various matrix metalloproteinases with those for TIMP-1 and TIMP-2 using a continuous assay. TIMP-3 behaved more like TIMP-2 than TIMP-1, showing rapid association with gelatinases A and B. Experiments with the N-terminal domain of gelatinase A, the isolated C-terminal domain, or an inactive progelatinase A mutant showed that the hemopexin domain of gelatinase A makes an important contribution to the interaction with TIMP-3. The exchange of portions of the gelatinase A hemopexin domain with that of stromelysin revealed that residues 568-631 of gelatinase A were required for rapid association with TIMP-3. The N-terminal domain of gelatinase B alone also showed slower association with TIMP-3, again implying significant C-domain interactions. The isolation of complexes between TIMP-3 and progelatinases A and B on gelatin-agarose demonstrated that TIMP-3 binds to both proenzymes. We analyzed the effect of various polyanions on the inhibitory activity of TIMP-3 in our soluble assay. The association rate was increased by dextran sulfate, heparin, and heparan sulfate, but not by dermatan sulfate or hyaluronic acid. Because TIMP-3 is sequestered in the extracellular matrix, the presence of certain heparan sulfate proteoglycans could enhance its inhibitory capacity.

Kinetic analysis of the mechanism of interaction of full-length TIMP-2 and gelatinase A: evidence for the existence of a low-affinity intermediate

We have undertaken a detailed analysis of the mechanism of inhibition of matrix metalloproteinase-2 (gelatinase A) by tissue inhibitor of metalloproteinase-2 (TIMP-2). Quenched fluorescent substrates have been used to analyze the rate of inhibition of gelatinase A by TIMP-2 over a wide range of TIMP-2 concentrations. When the values of the observed rate constant for the inhibition are plotted against TIMP-2 concentration, saturation is observed at high concentrations, providing evidence for formation of an intermediate in the pathway. Rate constants for the formation and dissociation of the intermediate are 5.9 x 10(6) M-1 s-1 and 6.3 s-1 respectively, giving a Ki for the initial step of approximately 1 microM. The rate constant for the association of the final complex is 33 s-1. By studying the dissociation of 125I-labeled TIMP-2 from a gelatinase A-TIMP-2 complex using ligand exchange experiments, we obtained a rate constant for the dissociation of the final stable complex of 2 x 10(-)8 s-1. This gives a value for the overall dissociation constant of approximately 0.6 fM.

Evidence for the importance of weakly bound water for matrix metalloproteinase activity

The effects of organic cosolvents on the kinetic characteristics of two matrix metalloproteinases, gelatinase A and stromelysin 1, were investigated. In each case, addition of the cosolvent resulted in a decrease in the apparent kcat/Km for the catalyzed hydrolysis of fluorogenic peptide substrates. Two factors were identified as being responsible for this decrease in catalytic activity: hydrophobic partitioning of the substrate in favor of the bulk solvent and decrease in the water content of the enzyme. The former reflects the hydrophobic nature of the enzyme-substrate interaction and the effect can be corrected for by using the solvent to water partition coefficient of the substrate in the mixed solvent systems. The catalyzed hydrolysis of substrate, corrected for the effect of hydrophobic partitioning, was demonstrated to be sixth order in water for gelatinase A and third order in water for stromelysin 1. Variation in water concentration did not produce saturation even at concentrations close to 55.5 M. The results indicate that weakly bound water molecules are essential to mediate the interaction between substrate and enzyme. The sensitivity of these enzymes to water concentration could be an important mechanism for regulating catalytic activity in vivo.

The second zinc atom in the matrix metalloproteinase catalytic domain is absent in the full-length enzymes: a possible role for the C-terminal domain

Domain deletion mutants of the matrix metalloproteinases consisting of the catalytic domain only contain two zinc atoms per molecule. One is essential for catalysis, while the other may fulfil a structural role. We have analysed the zinc contents of both the full-length and the truncated mutants of prostromelysin-1 and progelatinase A and report that the second zinc atom is not present in the full-length form of the proenzymes. Thus it seems likely that the role proposed for this zinc atom in maintaining the structure of the enzyme catalytic domain is performed by the C-terminal domain in the full-length enzyme.

Structure-function relationships in the tissue inhibitors of metalloproteinases

The tissue inhibitors of metalloproteinases (TIMPs) are proteins that specifically inhibit the matrix metalloproteinases. They consist of two distinct structural and functional domains. In order to elucidate the role of these domains, we have prepared mutants of TIMP-1 and TIMP-2 that lack a C-terminal domain. The N-terminal domain alone is an efficient inhibitor of all the matrix metalloproteinases through interaction with the enzyme catalytic domain. The C-terminal domain has at least two separate enzyme binding sites, one for gelatinase A and the other for stromelysin-1. The rate of inhibition of either enzyme is increased by interaction with the TIMP C-terminal domain. As no conformational change is observed, we propose that the rate enhancement is due to an anchoring effect in which binding of the TIMP C-terminal domain aligns the TIMP N-terminal domain with the enzyme active site. Site-directed mutagenesis of TIMP-1 has demonstrated that the N-terminal amino acids, His7 and Gln9, are important for inhibition.

Mutation of the active site glutamic acid of human gelatinase A: effects on latency, catalysis, and the binding of tissue inhibitor of metalloproteinases-1

Human gelatinase A, a member of the matrix metalloproteinase family, is secreted from cells as the M(r) 72,000 latent precursor, progelatinase A. The autolytic removal of an N-terminal propeptide generates the M(r) 66,000 active form. Mutants of recombinant progelatinase A, altered such that the proposed active site glutamic acid residue (E375) was replaced by either an aspartic acid (proE375-->D), an alanine (proE375-->A) or a glutamine (proE375-->Q), were purified from medium conditioned by transfected NS0 mouse myeloma cells. Like wild-type progelatinase A, the mutant proenzymes were inactive and could bind tissue inhibitor of metalloproteinases (TIMP)-2 but not TIMP-1 to their C-terminal domains. Their rates of autolytic processing induced by the organomercurial (4-aminophenyl) mercuric acetate, however, were markedly slower and, of the three M(r) 66,000 forms so produced, only E375-->D displayed any proteolytic activity against either a synthetic substrate (kcat/Km = 10% that of the wild-type enzyme) or denatured type I collagen (specific activity = 0.9% that of the wild-type enzyme). ProE375-->A and proE375-->Q could be more rapidly processed to their M(r) 66,000 forms by incubation with a deletion mutant of gelatinase A that has full catalytic activity but lacks the C-terminal domain [delta (418-631) gelatinase A]. These two M(r) 66,000 forms displayed low activity on a gelatin zymogram (approximately 0.01% that of the wild-type enzyme) but, like E375-->D were able to bind TIMP-1 with an affinity equal to that of the activated wild-type enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of the role of the COOH-terminal domain in the activation, proteolytic activity, and tissue inhibitor of metalloproteinase interactions of gelatinase B

Recombinant human progelatinase B and a COOH terminally truncated version, pro-delta426-688 gelatinase B have been prepared from a myeloma cell expression system. Both proenzymes could be processed to active forms by stromelysin-1 to give an NH2 terminus of Phe88, or by treatment with 4-aminophenylmercuric acetate resulting in an NH2-terminal Met75. The kinetics of activation using either treatment was not affected by removal of the enzyme COOH-terminal domain. The specific activities of both gelatinase B and delta426-688 gelatinase B, activated using either method, were found to be similar using either a quenched fluorescent peptide or gelatin as the substrate. Fibroblast monolayers were shown to mediate processing of both progelatinases at similar rates in the presence of either plasminogen or prostromelysin-1. Active wild-type gelatinase B was inhibited by tissue inhibitor of metalloproteinase (TIMP) -1 at a much faster rate than TIMP-2. COOH-terminal truncation of either enzyme or inhibitor gave a marked reduction in the rate constant for TIMP-1 inhibition but had no effect on the rate of TIMP-2 binding. It can be concluded that the COOH-terminal domain of progelatinase B is not involved in autolytic or cellular activation and does not affect the catalytic activity of the enzyme. However, COOH-terminal domain interactions between active gelatinase B and TIMP-1 significantly enhance the rate of complex formation.

Assessment of the role of the fibronectin-like domain of gelatinase A by analysis of a deletion mutant

The properties of a deletion mutant delta V191-Q364 of gelatinase A, which represents the removal of the fibronectin-like type II repeats defined by exons 5-7, were compared with those of full-length gelatinase A. Both enzymes underwent self-activation over a similar time course in the presence of 4-aminophenylmercuric acetate. The fully active enzymes had similar kcat/Km values for the cleavage of an octapeptide substrate, but the deletion mutant had 50% of the activity of wild type gelatinase A against beta-casein and 10% of the activity against gelatin. The cleavage pattern for gelatin was similar for both enzymes but differed for type IV collagen. Comparison of the rates of association of the tissue inhibitors of metalloproteinase (TIMP)-1 and TIMP-2 and their N-terminal domains to both forms of gelatinase indicated that the fibronectin-like domain plays little role in TIMP binding. The deletion mutant failed to bind to collagen, while the wild type gelatinase bound tightly, indicating that the fibronectin-like domain is the sole site of collagen binding. Both gelatinases could be activated by concanavalin A-activated fibroblasts, suggesting that the fibronectin-like domain is not required for the membrane-mediated activation process.

Different domain interactions are involved in the binding of tissue inhibitors of metalloproteinases to stromelysin-1 and gelatinase A

The matrix metalloproteinases gelatinase A and stromelysin-1 have definable N-terminal (catalytic) and C-terminal domains. In order to analyze their interactions with the N- and C-terminal domains of the tissue inhibitors of metalloproteinases TIMP-1 and -2, mutants of both the enzymes and the inhibitors were prepared in which the C-terminal domains had been deleted. Since the Ki values for TIMP inhibition of the matrix metalloproteinases are in the picomolar range, it was not possible to measure these accurately within the sensitivity of available activity assays. Rate constants for the association of the wild-type proteins were therefore determined and systematically compared with those for the deletion mutants. It was found that TIMP-1 binds more rapidly than TIMP-2 to stromelysin-1 and that the C-terminal domain of the enzyme does not affect the rate of association of enzyme and inhibitor. This is in contrast to gelatinase A, where the C-terminal domain has been shown to play an important role in increasing the rate of complex formation with the TIMPs (Willenbrock et al., 1993). The TIMPs are also comprised of an N- and C-terminal domain. By deletion mutagenesis, we found that the C-terminal domain of both TIMPs contributed less to the rate of complex formation with stromelysin-1 than to that with gelatinase A. Hybrids of the N- and C-terminal domains of gelatinase A and stromelysin-1 were prepared and used to analyze further the differences in domain interactions with the TIMPs. They demonstrated that the interactions between the C-terminal domains of enzyme and inhibitor can occur irrespective of the nature of the N-terminal domain. We can conclude that the TIMPs have two major binding regions which associate in different ways with the domains of the enzymes gelatinase A and stromelysin-1. The N-terminal domains of the TIMPs bind to the enzyme catalytic domains to inhibit activity. The TIMP C-terminal domain acts to increase the association rate constant by binding to the N-terminal domain of stromelysin or the C-terminal domain of gelatinase A.

The activity of the tissue inhibitors of metalloproteinases is regulated by C-terminal domain interactions: a kinetic analysis of the inhibition of gelatinase A

The cloning and expression of the full-length tissue inhibitor of metalloproteinase 2 (TIMP-2), delta 187-194TIMP-2, and delta 128-194TIMP-2 and the purification of these inhibitors and a cleaved version of TIMP-2 lacking nine C-terminal amino acids (delta 186-194TIMP-2) are described. The mechanism of inhibition of gelatinase A by the TIMPs was investigated by comparing the kinetics of association of TIMP-1, TIMP-2, the C-terminal deletions, and the mutants of both TIMPs which consisted of the N-terminal domain only. The full-length TIMPs inhibited gelatinase A rapidly with association constants of 3.2 x 10(6) M-1 s-1 for TIMP-1 and 2.1 x 10(7) M-1 s-1 for TIMP-2 at I = 0.2. The C-terminal peptide of TIMP-2 is proposed to exist as an exposed "tail" responsible for binding to progelatinase A and for increasing the rate of inhibition of active gelatinase A through electrostatic interactions with the C-terminal domain of the enzyme. The C-terminal domains of both TIMP-1 and TIMP-2 participate in low-affinity interactions with the C-terminal domain of gelatinase A which increase the rate of association by a factor of about 100 in both cases.

Site-directed mutations that alter the inhibitory activity of the tissue inhibitor of metalloproteinases-1: importance of the N-terminal region between cysteine 3 and cysteine 13

The tissue inhibitor of metalloproteinases-1 (TIMP-1) was subjected to single-site mutations within the N-terminal three loops using an oligonucleotide-directed polymerase chain reaction method. All the histidines, and a number of other residues conserved between TIMP-1 and TIMP-2, were individually modified and the mutant TIMPs expressed in mammalian cells. Purified mutant TIMPs were shown to be correctly folded by measuring the effect of guanidine hydrochloride on intrinsic fluorescence. Kinetic analyses of mutants using a quenched fluorescent peptide substrate and the metalloproteinase PUMP indicated that mutation of His7 and Gln9 caused an increase in the apparent dissociation constant, largely due to an increase in the rate of dissociation of complexes. The data indicate that the anchored sequence between Cys 3 and Cys 13 is a key region for interaction of TIMP-1 with metalloproteinases.

Biochemical characterization of matrilysin. Activation conforms to the stepwise mechanisms proposed for other matrix metalloproteinases

The latent precursor of matrilysin (EC 3.4.24.23; punctuated metalloproteinase (PUMP) was purified from transfected mouse myeloma cell conditioned medium and was found to contain one zinc atom per molecule which was essential for catalytic activity. Promatrilysin could be activated to the same specific activity by (4-aminophenyl)mercuric acetate, trypsin, and incubation at elevated temperatures (heat activation). Active matrilysin hydrolyzed the fluorescent substrate 2,4-dinitrophenyl-Pro-Leu-Gly-Leu-Trp-Ala-D-Arg-NH2 at the Gly-Leu bond with a maximum value for kcat/Km of 1.3 x 10(4) M-1 s-1 at the pH optimum of 6.5 and pKa values of 4.60 and 8.65. Activity is inhibited by the tissue inhibitor of metalloproteinases-1 in a 1:1 stoichiometric interaction. Analysis by sodium dodecyl sulfate polyacrylamide gel electrophoresis in conjunction with N-terminal sequencing revealed that, as with all other matrix metalloproteinases similarly studied, promatrilysin activation was accompanied by the stepwise proteolytic removal of an M(r) 9000 propeptide from the N-terminus. The intermediates generated were dependent on the mode of activation used but, in all cases studied, activation terminated with an autocatalytic cleavage at E77-Y78 to yield the final M(r) 19,000 active matrilysin. From an analysis of the stability of the various intermediates, we propose that the sequence L13-K33 is particularly important in protecting the E77-Y78 site from autocatalytic cleavage, thereby maintaining the latency of the proenzyme.

The role of the C-terminal domain in collagenase and stromelysin specificity

Recombinant human interstitial collagenase, an N-terminal truncated form, delta 243-450 collagenase, recombinant human stromelysin-1, and an N-terminal truncated form, delta 248-460 stromelysin, have been stably expressed in myeloma cells and purified. The truncated enzymes were similar in properties to their wild-type counterparts with respect to activation requirements and the ability to degrade casein, gelatin, and a peptide substrate, but truncated collagenase failed to cleave native collagen. Removal of the C-terminal domain from collagenase also modified its interaction with tissue inhibitor of metalloproteinases-1. Hybrid enzymes consisting of N-terminal (1-242) collagenase.C-terminal (248-460) stromelysin and N-terminal (1-233) stromelysin.C-terminal (229-450) collagenase, representing an exchange of the complete catalytic and C-terminal domains of the two enzymes, were expressed in a transient system using Chinese hamster ovary cells and purified. Both proteins showed similar activity to their N-terminal parent and neither was able to degrade collagen. Analysis of the ability of the different forms of recombinant enzyme to bind to collagen by ELISA showed that both pro and active stromelysin and N-terminal collagenase.C-terminal stromelysin bound to collagen equally well. In contrast, only the active forms of collagenase and N-terminal stromelysin.C-terminal collagenase bound well to collagen, as compared with their pro forms.

The C-terminal domain of 72 kDa gelatinase A is not required for catalysis, but is essential for membrane activation and modulates interactions with tissue inhibitors of metalloproteinases

Recombinant 72 kDa gelatinase A and a truncated form lacking the C-terminal domain were shown to be activated by organomercurials and to possess similar activities towards a number of substrates. The truncated proenzyme differed from the full-length gelatinase in that it could not be activated by a membrane activator and did not bind tissue inhibitor of metalloproteinase (TIMP)-2. Kinetic studies also showed that the inhibition of the activated truncated enzyme, by both TIMP-1 and TIMP-2, was considerably decreased compared with the full-length enzyme. We conclude that the C-terminal domain plays an important role in the regulation of gelatinase A by a potential physiological activator and inhibitors.

A novel coumarin-labelled peptide for sensitive continuous assays of the matrix metalloproteinases

(7-methoxycoumarin-4-yl)Acetyl-Pro-Leu-Gly-Leu-(3-[2,4-dinitrophenyl]-L- 2,3-diaminopropionyl)-Ala-Arg-NH2 (Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2) has been synthesised as a fluorogenic substrate for the matrix metalloproteinases. The highly fluorescent 7-methoxycoumarin group is efficiently quenched by energy transfer to the 2,4-dinitrophenyl group. The punctuated metalloproteinase (PUMP, EC 3.4.24.23) cleaves the substrate at the Gly-Leu bond with a 190-fold increase in fluorescence (lambda cx 328 nm, lambda cm 393 nm). In assays of the human matrix metalloproteinases. Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 is about 50 to 100 times more sensitive than dinitrophenyl-Pro-Leu-Gly-Leu-Trp-Ala-D-Arg-NH2 and continuous assays can be made at enzyme concentrations comparable to those used with macromolecular substrates. Specificity constants (kcat/Km) are reported for both synthetic substrates with PUMP, collagenase, stromelysin and 72 kDa gelatinase.

Purification of a hybrid plasminogen activator protein

Recombinant DNA technology has been employed to produce a hybrid gene in which the kringle and serine protease domains of tissue plasminogen activator are linked to the heavy-chain Fd region of a fibrin-specific antibody. The hybrid gene is co-expressed with antibody light chains. This communication describes a purification procedure for the hybrid protein, involving affinity and ion-exchange chromatography. The purified hybrid protein has been used in vivo and in vitro clot lysis experiments and has been shown to be effective at clot dissolution.

Supracrystallographic resolution of interactions contributing to enzyme catalysis by use of natural structural variants and reactivity-probe kinetics

1. The influence on the reactivities of the catalytic sites of papain (EC 3.4.22.2) and actinidin (3.4.22.14) of providing for interactions involving the S1-S2 intersubsite regions of the enzymes was evaluated by using as a series of thiol-specific two-hydronic-state reactivity probes: n-propyl 2-pyridyl disulphide (I) (a 'featureless' probe), 2-(acetamido)ethyl 2'-pyridyl disulphide (II) (containing a P1-P2 amide bond), 2-(acetoxy)ethyl 2'-pyridyl disulphide (III) [the ester analogue of probe (II)] and 2-carboxyethyl 2'-pyridyl disulphide N-methylamide (IV) [the retroamide analogue of probe (II)]. Syntheses of compounds (I), (III) and (IV) are reported. 2. The reactivities of the two enzymes towards the four reactivity probes (I)-(IV) and also that of papain towards 2-(N'-acetyl-L-phenylalanylamino)ethyl 2'-pyridyl disulphide (VII) (containing both a P1-P2 amide bond and an L-phenylalanyl side chain as an occupant for the S2 subsite), in up to four hydronic (previously called protonic) states, were evaluated by analysis of pH-dependent stopped-flow kinetic data (for the release of pyridine-2-thione) by using an eight-parameter rate equation [described in the Appendix: Brocklehurst & Brocklehurst (1988) Biochem. J. 256, 556-558] to provide pH-independent rate constants and macroscopic pKa values. The analysis reveals the various ways in which the two enzymes respond very differently to the binding of ligands in the S1-S2 intersubsite regions despite the virtually superimposable crystal structures in these regions of the molecules. 3. Particularly striking differences between the behaviour of papain and that of actinidin are that (a) only papain responds to the presence of a P1-P2 amide bond in the probe such that a rate maximum at pH 6-7 is produced in the pH-k profile in place of the rate minimum, (b) only in the papain reactions does the pKa value of the alkaline limb of the pH-k profile change from 9.5 to approx. 8.2 [the value characteristic of a pH-(kcat./Km) profile] when the probe contains a P1-P2 amide bond, (c) only papain reactivity is affected by two positively co-operative hydronic dissociations with pKI congruent to pKII congruent to 4 and (d) modulation of the reactivity of the common -S(-)-ImH+ catalytic-site ion-pair (Cys-25/His-159 in papain and Cys-25/His-162 in actinidin) by hydronic dissociation with pKa approx. 5 is more marked and occurs more generally in reactions of actinidin than is the case for papain reactions.(ABSTRACT TRUNCATED AT 400 WORDS)

Consequences of molecular recognition in the S1-S2 intersubsite region of papain for catalytic-site chemistry. Change in pH-dependence characteristics and generation of an inverse solvent kinetic isotope effect by introduction of a P1-P2 amide bond into a two-protonic-state reactivity probe

1. The pH-dependences of the second-order rate constant (k) for the reactions of papain (EC 3.4.22.2) with 2-(acetamido)ethyl 2'-pyridyl disulphide and with ethyl 2-pyridyl disulphide and of k for the reaction of benzimidazol-2-ylmethanethiol (as a minimal model of cysteine proteinase catalytic sites) with the former disulphide were determined in aqueous buffers at 25 degrees C at I 0.1. 2. Of these three pH-k profiles only that for the reaction of papain with 2-(acetamido)ethyl 2'-pyridyl disulphide has a rate maximum at pH approx. 6; the others each have a rate minimum in this pH region and a rate maximum at pH 4, which is characteristic of reactions of papain with other 2-pyridyl disulphides that do not contain a P1-P2 amide bond in the non-pyridyl part of the molecule. 3. The marked change in the form of the pH-k profile consequent upon introduction of a P1-P2 amide bond into the probe molecule for the reaction with papain but not for that with the minimal catalytic-site model is interpreted in terms of the induction by binding of the probe in the S1-S2 intersubsite region of the enzyme of a transition-state geometry in which nucleophilic attack by the -S- component of the catalytic site is assisted by association of the imidazolium ion component with the leaving group. 4. The greater definition of the rate maximum in the pH-k profile for the reaction of papain with an analogous 2-pyridyl disulphide reactivity probe containing both a P1-P2 amide bond and a potential occupant for the S2 subsite [2-(N'-acetyl-L-phenylalanylamino)ethyl 2'-pyridyl disulphide [Brocklehurst, Kowlessur, O'Driscoll, Patel, Quenby, Salih, Templeton, Thomas & Willenbrock (1987) Biochem. J. 244, 173-181]) suggests that a P2-S2 interaction substantially increases the population of transition states for the imidazolium ion-assisted reaction. 5. The overall kinetic solvent 2H-isotope effect at pL 6.0 was determined to be: for the reaction of papain with 2,2'-dipyridyl disulphide, 0.96 (i.e. no kinetic isotope effect), for its reaction with the probe containing only the P1-P2 amide bond, 0.75, for its reaction with the probe containing both the P1-P2 amide bond and the occupant for the S2 subsite, 0.61, and for kcat./Km for its catalysis of the hydrolysis of N-methoxycarbonylglycine 4-nitrophenyl ester, 0.67.(ABSTRACT TRUNCATED AT 400 WORDS)

Substrate-derived two-protonic-state electrophiles as sensitive kinetic specificity probes for cysteine proteinases. Activation of 2-pyridyl disulphides by hydrogen-bonding

1. 2-(N'-Acetyl-L-phenylalanylamino)ethyl 2'-pyridyl disulphide [compound (III)] and 2-(acetamido)ethyl 2'-pyridyl disulphide [compound (IV)] were synthesized by acylation of the common intermediate, 2-aminoethyl 2'-pyridyl disulphide, to provide examples of chromogenic thiol-specific substrate-derived two-protonic-state electrophilic probe reagents. These two reagents, together with n-propyl 2-pyridyl disulphide [compound (II)], provide structural variation in the non-pyridyl part of the molecule from a simple hydrocarbon side chain in compound (II) to a P1-P2 amide bond in compound (IV) and further to both a P1-P2 amide bond and a hydrophobic side chain (of phenylalanine) at P2 as a potential occupant of S2 subsites. 2. These disulphides were used as reactivity probes to investigate specificity and binding-site-catalytic-site signalling in a number of cysteine proteinases by determining (a) the reactivity at pH 6.0 at 25 degrees C at I 0.1 of compound (III) (a close analogue of a good papain substrate) towards 2-mercaptoethanol, benzimidazol-2-ylmethanethiol [compound (V), as a minimal catalytic-site model], chymopapains B1-B3, chymopapain A, papaya proteinase omega, actinidin, cathepsin B and papain, (b) the effect of changing the structure of the probe as indicated above on the reactivities of compound (V) and of the last five of these enzymes, and (c) the forms of pH-dependence of the reactivities of papain and actinidin towards compound (III). 3. The kinetic data suggest that reagents of the type investigated may be sensitive probes of molecular recognition features in this family of enzymes and are capable not only of detecting differences in binding ability of the various enzymes but also of identifying enzyme-ligand contacts that provide for binding-site-catalytic-site signalling mechanisms. 4. The particular value of this class of probe appears to derive from the possibility of activating the 2-mercaptopyridine leaving group not only by formal protonation, as was recognized previously [see Brocklehurst (1982) Methods Enzymol. 87C, 427-469], but also by hydrogen-bonding to the pyridyl nitrogen atom when the appropriate geometry in the catalytic site is provided by enzyme-ligand contacts involving the non-pyridyl part of the molecule.(ABSTRACT TRUNCATED AT 400 WORDS)

Chemical evidence for the pH-dependent control of ion-pair geometry in cathepsin B. Benzofuroxan as a reactivity probe sensitive to differences in the mutual disposition of the thiolate and imidazolium components of cysteine proteinase catalytic sites

Benzofuroxan reacts with the catalytic-site thiol group of cathepsin B (EC 3.4.22.1) to produce stoichiometric amount of the chromophoric reduction product, o-benzoquinone dioxime. In a study of the pH-dependence of the kinetics of this reaction, most data were collected for the bovine spleen enzyme, but the more limited data collected for the rat liver enzyme were closely similar both in the magnitude of the values of the second-order rate constants (k) and in the shape of the pH-k profile. In acidic and weakly alkaline media, the reaction is faster than the reactions of benzofuroxan with some other cysteine proteinases. For example, in the pH region around 5-6, the reaction of cathepsin B is about 10 times faster than that of papain, 15 times faster than that of stem bromelain and 6 times faster than that of ficin. The pH-dependence of k for the reaction of cathepsin B with benzofuroxan was determined in the pH range 2.7-8.3. In marked contrast with the analogous reactions of papain, ficin and stem bromelain [reported by Shipton & Brocklehurst (1977) Biochem. J. 167, 799-810], the pH-k profile for the cathepsin B reaction contains a sigmoidal component with pKa 5.2 in which k increases with decrease in pH. This modulation of the reactivity of the catalytic-site -S-/-ImH+ ion-pair state of cathepsin B (produced by protonic dissociation from -SH/-ImH+ with pKa approx. 3) towards a small, rigid, electrophilic reagent, in a reaction that appears to involve both components of the ion-pair for efficient reaction, suggests that the state of ionization of a group associated with a molecular pKa of approx. 5 may control ion-pair geometry. This might account for the remarkable finding [reported by Willenbrock & Brocklehurst (1984) Biochem. J. 222, 805-814] that, although the ion-pair appears to be generated in cathepsin B as the pH is increased across pKa 3.4, catalytic competence is not generated until the pH is increased across pKa 5-6.