A tale of lineage plasticity: Intense neoadjuvant testosterone lowering therapy in localized prostate cancer (PCa) harboring high-risk genomic signatures

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Background: PCa is driven by androgen receptor (AR) signaling and neoadjuvant therapy with AR inhibitors offer an opportunity to improve cure rates in high-risk PCa particularly with utilization of multiparametric MRI (mpMRI). A loss of AR-regulated lineage characteristics and genomic loss of tumor suppressors RB1 and TP53 or mutations in DNA damage repair (DDR) genes can represent aggressive prostate variants. We conducted a feasibility study using mpMRI to evaluate tumor responses and resistance in newly diagnosed, high-risk PCa (NCT02430480). Methods: Pts were treated with androgen deprivation therapy (ADT) + enzalutamide (enza) 160 mg daily for 6 months (mos). Pts underwent 2 mpMRIs: baseline and post 6 mos treatment (trt). Post-trt mpMRI was followed by radical prostatectomy (RP). Primary endpoint: feasibility of mpMRI for localization and detection of PCa before and after ADT + enza. Results: 39 pts were enrolled on-study with 36 pts completing 6 mos trt and undergoing RP. Of 39 pts, 3 had disease progression. Conclusions: Neoadjuvant intense testosterone lowering therapy shows activity in PCa but a subset of pts not respond to AR-targeted therapies through lineage plasticity enabled by characteristic loss of RB1 and TP53 or due to genetic alterations. Identification of this high-risk patient population, along with development of treatment options, needs further investigation. Clinical trial information: NCT02430480. [Table: see text]

Multiple primary prostate tumors with differential drug sensitivity

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Background: The differential aggressiveness of potentially independent prostate cancer clones remains largely unknown. Appropriate prostate cancer staging using mpMRI and biopsy tissue can be confounded by sampling error. To date, there has been no understanding of whether clonal variability influences management decisions for localized prostate tumors. We sought to identify the sensitivity and genomic profile of distinct localized tumors from a patient following systemic intense neoadjuvant androgen deprivation therapy (ADT). Methods: A 66-year-old man with high risk prostate cancer enrolled in a Phase 2 study of intense neoadjuvant ADT (goserelin + enzalutamide; inADT). Baseline mpMRI showed a single semi-contiguous lesion encompassing the right apical-mid PZ extending into the left distal apical PZ. MR/US-fusion targeted biopsy was performed before 6 months of inADT. A second mpMRI was performed before radical prostatectomy. Whole exome sequencing on microdissected tumor foci identified somatic mutations and copy number alterations, which were further used with immunohistochemistry to assess tumor clonal architecture and genomic/phenotypic evolution of treatment resistant tumor. Results: We found two clonally independent tumors exhibited intrinsic heterogeneity at baseline which correlated with response or resistance. Biopsies of distinct left- and right-sided tumors showed differing histologies. mpMRI and pathology showed near complete response of the left-sided tumor and substantial resistance of the right-sided tumor, which exhibited a large intraductal component. Histology and whole exome data highlighted a divergence in the status of PTEN and TP53, tumor suppressor genes implicated in prostate cancer progression. Conclusions: These data highlight that even nascent prostate cancer is heterogenous and neoadjuvant therapeutic strategies will need to consider this for clinical optimization. Evolutionary trajectories that resulted in tumor heterogeneity in this case likely contributed to our observation that two independent prostate tumor nodules with distinct genetic alterations responded differently to neoadjuvant intense ADT. Clinical trial information: NCT02430480.

Abstract 736: Development of an allele-specific assay for detecting circulating tumor DNA in prostate cancer

Background and Hypothesis

Cancer cells release circulating tumor DNA (ctDNA) into the bloodstream, which has the potential to be clinically relevant as a marker of tumor clonality and a marker of clinical response. This "liquid biopsy" may provide a non-invasive approach to cancer care diagnosis and monitoring. We have optimized a PCR assay for rapid and inexpensive selection and detection of a priori sequenced targets, serving as clonal and subclonal markers of cancer evolution. Our hypothesis is that this assay will allow us to detect circulating free DNA and ctDNA while modeling tumor clonality and measuring clinical response in patients undergoing treatment for metastatic prostate cancer.

Methods

From a given panel of somatic point mutations previously identified via unbiased sequencing of matched tumor and normal samples, multiplex PCR primer mixes were generated using the IonTorrent AmpliSeq Design tool, creating locus-specific primers flanking each point mutation by approximately 60bp on each side. To the 5’ end of each forward primer, a 7-base degenerate unique molecular identifier (UMI) was synthesized, to which an additional 32-base sequence complementary to the forward Illumina Nextera adaptor was further added. To the 3’ end of the reverse primer, a 34-base sequence complementary to the reverse Illumina Nextera adaptor was added. Forward primers for each patient-specific set were pooled and hybridized to aliquots of ctDNA extracted from patient plasma. The tagged product was amplified in exponential PCR with the reverse primer pool and a full-length Nextera i7 Indexing primer. Following purification and size selection, the tagged and partial-adaptor-ligated library was amplified in additional exponential cycles of PCR with full length Nextera i5 and i7 indexing primers. Libraries were then quantified and sequenced via MiSeq.

Results and Conclusions

We have previously shown that for a series of seven patients, primers designed against clonal and subclonal mutations successfully amplified their genomic targets in 269 out of 280 amplicons, averaging 10 amplicons per library and 100,000x target coverage per amplicon. Following duplicate reduction, approximately 1,000 unique molecules were sequenced. Spike-in experiments were utilized to establish the lower limit of reliable detection. This assay is currently being applied to patients with metastatic prostate cancer who had blood drawn across multiple timepoints. We are currently analyzing these samples to model tumor clonality and treatment response across multiple patients.

Relevance and Importance

We have developed a robust, patient-specific assay for detection of ctDNA and monitoring patients over time. This assay has the potential to provide a patient-specific and non-invasive approach for monitoring treatment and remission of metastatic prostate cancer.

Citation Format: Nicholas T. Terrigino, S. Thomas Hennigan, Shana Trostel, Scott C. Wilkinson, Huihui Ye, Adam G. Sowalsky. Development of an allele-specific assay for detecting circulating tumor DNA in prostate cancer [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 736.

LKB1 promotes cell survival by modulating TIF-IA-mediated pre-ribosomal RNA synthesis under uridine downregulated conditions

We analyzed the mechanism underlying 5-aminoimidazole-4-carboxamide riboside (AICAR) mediated apoptosis in LKB1-null non-small cell lung cancer (NSCLC) cells. Metabolic profile analysis revealed depletion of the intracellular pyrimidine pool after AICAR treatment, but uridine was the only nucleotide precursor capable of rescuing this apoptosis, suggesting the involvement of RNA metabolism. Because half of RNA transcription in cancer is for pre-ribosomal RNA (rRNA) synthesis, which is suppressed by over 90% after AICAR treatment, we evaluated the role of TIF-IA-mediated rRNA synthesis. While the depletion of TIF-IA by RNAi alone promoted apoptosis in LKB1-null cells, the overexpression of a wild-type or a S636A TIF-IA mutant, but not a S636D mutant, attenuated AICAR-induced apoptosis. In LKB1-null H157 cells, pre-rRNA synthesis was not suppressed by AICAR when wild-type LKB1 was present, and cellular fractionation analysis indicated that TIF-IA quickly accumulated in the nucleus in the presence of a wild-type LKB1 but not a kinase-dead mutant. Furthermore, ectopic expression of LKB1 was capable of attenuating AICAR-induced death in AMPK-null cells. Because LKB1 promotes cell survival by modulating TIF-IA-mediated pre-rRNA synthesis, this discovery suggested that targeted depletion of uridine related metabolites may be exploited in the clinic to eliminate LKB1-null cancer cells.

Abstract 4770: The regulation of pre-ribosomal RNA synthesis by LKB1

LKB1 is commonly thought of as a tumor suppressor gene, because its hereditary mutation is responsible for a cancer syndrome, and somatic inactivation of LKB1 is found in non-small cell lung cancer, melanoma, and cervical cancers. Unlike other tumor suppressors whose main function is to either suppress cell proliferation or promote cell death, one of the functions of LKB1 is to suppress cell proliferation in order to promote cell survival under energetic stress conditions. We recently discovered that LKB1 promotes pre-ribosomal RNA synthesis under uridine down-regulated condition. The mechanistic basis of this finding is that LKB1 activates TIF-IA-mediated pre-riobosomal RNA synthesis, partly through the control of its cellular localization. Immuno-coprecipitation study revealed that the interaction between TIF-IA and nuclear transportation machinery may be regulated by LKB1. Our finding also has important clinical implication because the suppression of de novo UTP synthesis preferentially promotes apoptosis in LKB1-inactivated cells. This unique, pro-survival function of LKB1 led us to exploit the vulnerability of LKB1-null cells in their defect in sensing intracellular UTP depletion. Such targeted agents represent a novel treatment strategy because they only induce cell killing when LKB1 is absent.

Citation Format: Rui Jin, Faken Liu, Xiuju Liu, Henry Huang, Scott C. Wilkinson, Diansheng Zhong, Fadlo R. Khuri, Haian Fu, Adam I. Marcus, Yulong He, Wei Zhou. The regulation of pre-ribosomal RNA synthesis by LKB1. [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 4770.

The application of machine learning to the modelling of percutaneous absorption: an overview and guide

Machine learning (ML) methods have been applied to the analysis of a range of biological systems. This paper reviews the application of these methods to the problem domain of skin permeability and addresses critically some of the key issues. Specifically, ML methods offer great potential in both predictive ability and their ability to provide mechanistic insight to, in this case, the phenomena of skin permeation. However, they are beset by perceptions of a lack of transparency and, often, once a ML or related method has been published there is little impetus from other researchers to adopt such methods. This is usually due to the lack of transparency in some methods and the lack of availability of specific coding for running advanced ML methods. This paper reviews critically the application of ML methods to percutaneous absorption and addresses the key issue of transparency by describing in detail - and providing the detailed coding for - the process of running a ML method (in this case, a Gaussian process regression method). Although this method is applied here to the field of percutaneous absorption, it may be applied more broadly to any biological system.

Attitudes of community optometrists to smoking cessation: an untapped opportunity overlooked?

AIM

To assess community optometrists' attitudes and current behaviour regarding provision of smoking cessation advice in their practice.

METHODS

A self-completion postal questionnaire was sent to community optometrists in north-west England identified from the General Optical Council's practice lists.

RESULTS

Of 709 optometrists identified, 71.8% (509/709) returned the completed questionnaire. Few community optometrists routinely asked about smoking habits: only 6.2% (95% CI: 4.1-8.3) (n = 31) at new patient consultations, and 2.2% (95% CI: 0.9-3.5) (n=11) at follow-up visits. Reasons for optometrists not routinely providing smoking cessation advice included: not their role (35.4%, n=180), lack of time (22.0%, n=112) and forgetting to ask (21.4%, n=109). Overall 67.6% (95% CI: 63.5-71.7) (n=344) of community optometrists wanted to improve their knowledge of smoking and visual impairment with 56.2% (95% CI: 51.9-60.5) (n=286) requesting further training.

CONCLUSION

Despite low levels of current involvement, many optometrists were keen to receive training on smoking cessation topics. We suggest that there are untapped opportunities to develop brief interventions to promote smoking cessation services in community optometry settings.

Inter‐ and intralaboratory variation of in vitro diffusion cell measurements: An international multicenter study using quasi‐standardized methods and materials

In vitro measurements of skin absorption are an increasingly important aspect of regulatory studies, product support claims, and formulation screening. However, such measurements are significantly affected by skin variability. The purpose of this study was to determine inter- and intralaboratory variation in diffusion cell measurements caused by factors other than skin. This was attained through the use of an artificial (silicone rubber) rate-limiting membrane and the provision of materials including a standard penetrant, methyl paraben (MP), and a minimally prescriptive protocol to each of the 18 participating laboratories. "Standardized" calculations of MP flux were determined from the data submitted by each laboratory by applying a predefined mathematical model. This was deemed necessary to eliminate any interlaboratory variation caused by different methods of flux calculations. Average fluxes of MP calculated and reported by each laboratory (60 +/- 27 microg cm(-2) h(-1), n = 25, range 27-101) were in agreement with the standardized calculations of MP flux (60 +/- 21 microg cm(-2) h(-1), range 19-120). The coefficient of variation between laboratories was approximately 35% and was manifest as a fourfold difference between the lowest and highest average flux values and a sixfold difference between the lowest and highest individual flux values. Intralaboratory variation was lower, averaging 10% for five individuals using the same equipment within a single laboratory. Further studies should be performed to clarify the exact components responsible for nonskin-related variability in diffusion cell measurements. It is clear that further developments of in vitro methodologies for measuring skin absorption are required.

In vitro predictions of skin absorption of caffeine, testosterone, and benzoic acid: a multi-centre comparison study

To obtain better insight into the robustness of in vitro percutaneous absorption methodology, the intra- and inter-laboratory variation in this type of study was investigated in 10 European laboratories. To this purpose, the in vitro absorption of three compounds through human skin (9 laboratories) and rat skin (1 laboratory) was determined. The test materials were benzoic acid, caffeine, and testosterone, representing a range of different physico-chemical properties. All laboratories performed their studies according to a detailed protocol in which all experimental details were described and each laboratory performed at least three independent experiments for each test chemical. All laboratories assigned the absorption of benzoic acid through human skin, the highest ranking of the three compounds (overall mean flux of 16.54+/-11.87 microg/cm(2)/h). The absorption of caffeine and testosterone through human skin was similar, having overall mean maximum absorption rates of 2.24+/-1.43 microg/cm(2)/h and 1.63+/-1.94 microg/cm(2)/h, respectively. In 7 out of 9 laboratories, the maximum absorption rates of caffeine were ranked higher than testosterone. No differences were observed between the mean absorption through human skin and the one rat study for benzoic acid and testosterone. For caffeine the maximum absorption rate and the total penetration through rat skin were clearly higher than the mean value for human skin. When evaluating all data, it appeared that no consistent relation existed between the diffusion cell type and the absorption of the test compounds. Skin thickness only slightly influenced the absorption of benzoic acid and caffeine. In contrast, the maximum absorption rate of testosterone was clearly higher in the laboratories using thin, dermatomed skin membranes. Testosterone is the most lipophilic compound and showed also a higher presence in the skin membrane after 24 h than the two other compounds. The results of this study indicate that the in vitro methodology for assessing skin absorption is relatively robust. A major effort was made to standardize the study performance, but, unlike in a formal validation study, not all variables were controlled. The variation observed may be largely attributed to human variability in dermal absorption and the skin source. For the most lipophilic compound, testosterone, skin thickness proved to be a critical variable.

Visualization of root caries lesions by means of a diazonium dye

A diazonium dye was used to visualize caries lesions in root tissue. Root caries lesions were created in vitro according to a variety of protocols based on methylcellulose gel (6% w/v) and/or lactic acid buffer (0.05 M, pH 4.5). Teeth containing lesions were soaked overnight in an alkaline solution of 2% (w/v) 2-naphthol or resorcinol, rinsed with distilled water, and immersed in a diazonium solution (prepared by titration of aniline with sodium nitrite in 1 M HCl at 5 degrees C) for up to 10 min, prior to being thoroughly rinsed with distilled water. The area of the caries lesion on the anatomical surface was clearly marked with a red/orange color following 5 minutes' incubation in the diazonium solution. The diazonium complex formed with 2-naphthol was found to be more resistant to leaching during rinsing and sectioning than that formed with resorcinol. Microscopic examination of sections taken in the apicalcoronal plane showed that the depth of area of the lesion was also marked by the red/orange coloration. Chemical changes in root mineral monitored during lesion formation showed some degree of correlation between lesion area and mineral dissolution. Visualization of coronal caries by this technique is currently under investigation. The visualization technique provides a simple means of determining the extent and severity of root caries lesions and may be a useful first step in their classification.