Corrigendum: VIDIIA Hunter: a low-cost, smartphone connected, artificial intelligence-assisted COVID-19 rapid diagnostic platform approved for medical use in the UK

[This corrects the article DOI: 10.3389/fmolb.2023.1144001.].

VIDIIA Hunter diagnostic platform: a low-cost, smartphone connected, artificial intelligence-assisted COVID-19 rapid diagnostics approved for medical use in the UK

Introduction: Accurate and rapid diagnostics paired with effective tracking and tracing systems are key to halting the spread of infectious diseases, limiting the emergence of new variants and to monitor vaccine efficacy. The current gold standard test (RT-qPCR) for COVID-19 is highly accurate and sensitive, but is time-consuming, and requires expensive specialised, lab-based equipment. Methods: Herein, we report on the development of a SARS-CoV-2 (COVID-19) rapid and inexpensive diagnostic platform that relies on a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay and a portable smart diagnostic device. Automated image acquisition and an Artificial Intelligence (AI) deep learning model embedded in the Virus Hunter 6 (VH6) device allow to remove any subjectivity in the interpretation of results. The VH6 device is also linked to a smartphone companion application that registers patients for swab collection and manages the entire process, thus ensuring tests are traced and data securely stored. Results: Our designed AI-implemented diagnostic platform recognises the nucleocapsid protein gene of SARS-CoV-2 with high analytical sensitivity and specificity. A total of 752 NHS patient samples, 367 confirmed positives for coronavirus disease (COVID-19) and 385 negatives, were used for the development and validation of the test and the AI-assisted platform. The smart diagnostic platform was then used to test 150 positive clinical samples covering a dynamic range of clinically meaningful viral loads and 250 negative samples. When compared to RT-qPCR, our AI-assisted diagnostics platform was shown to be reliable, highly specific (100%) and sensitive (98-100% depending on viral load) with a limit of detection of 1.4 copies of RNA per µL in 30 min. Using this data, our CE-IVD and MHRA approved test and associated diagnostic platform has been approved for medical use in the United Kingdom under the UK Health Security Agency's Medical Devices (Coronavirus Test Device Approvals, CTDA) Regulations 2022. Laboratory and in-silico data presented here also indicates that the VIDIIA diagnostic platform is able to detect the main variants of concern in the United Kingdom (September 2023). Discussion: This system could provide an efficient, time and cost-effective platform to diagnose SARS-CoV-2 and other infectious diseases in resource-limited settings.

Rectified Classifier Chains for Prediction of Antibiotic Resistance From Multi-Labelled Data With Missing Labels

Predicting Antimicrobial Resistance (AMR) from genomic data has important implications for human and animal healthcare, and especially given its potential for more rapid diagnostics and informed treatment choices. With the recent advances in sequencing technologies, applying machine learning techniques for AMR prediction have indicated promising results. Despite this, there are shortcomings in the literature concerning methodologies suitable for multi-drug AMR prediction and especially where samples with missing labels exist. To address this shortcoming, we introduce a Rectified Classifier Chain (RCC) method for predicting multi-drug resistance. This RCC method was tested using annotated features of genomics sequences and compared with similar multi-label classification methodologies. We found that applying the eXtreme Gradient Boosting (XGBoost) base model to our RCC model outperformed the second-best model, XGBoost based binary relevance model, by 3.3% in Hamming accuracy and 7.8% in F1-score. Additionally, we note that in the literature machine learning models applied to AMR prediction typically are unsuitable for identifying biomarkers informative of their decisions; in this study, we show that biomarkers contributing to AMR prediction can also be identified using the proposed RCC method. We expect this can facilitate genome annotation and pave the path towards identifying new biomarkers indicative of AMR.

Prevalence of asthma and its symptoms in Sri Lankan adults

BACKGROUND

Data on adult asthma is scarce in Sri Lanka. The objective of this study was to estimate the prevalence of asthma and its symptoms in adult Sri Lankans.  METHODS: A cross-sectional study using a translated version of the European Community Respiratory Health Survey screening questionnaire on subjects ≥ 18 years from 7 provinces in Sri Lanka was conducted. The asthma was defined as "wheezing in the past 12 months (current wheeze)", self-reported asthma attack in the past 12 months or on current asthma medication use.

RESULTS

Among 1872 subjects (45.1% males, 48.8% between 18-44 years of age), the prevalence of current wheeze was 23.9% (95%CI: 22.0%-25.9%), self-reported asthma was 11.8% (95%CI: 10.3%-13.2%) and current asthma medication use was 11.1% (95% CI: 9.6%-12.5%). The prevalences were higher in adults > 44 years, 31.4% positively responded to any of the above questions (95%CI: 29.3%-33.4%) and 60.9% of current wheezers did not report having asthma whilst 38.2% used asthma medication. Among current wheezers, 80.1% had at least one other symptom, cough being the commonest. Those with no current wheeze, self-reported asthma and on current asthma medication use, 30%, 35.9% and 36.6%, respectively, reported at least one other symptom. Smokers comprises 22% current wheezers, 20.6% of self-reported asthmatics and 18.7% of current asthma medication users.

CONCLUSIONS

The prevalence of asthma in Sri Lankan adults is higher than the other South Asian countries and higher in the older age group. A significant percentage of symptomatic individuals did not report having asthma or being on medication.

Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (AI-LAMP) for Rapid Detection of SARS-CoV-2

Until vaccines and effective therapeutics become available, the practical solution to transit safely out of the current coronavirus disease 19 (CoVID-19) lockdown may include the implementation of an effective testing, tracing and tracking system. However, this requires a reliable and clinically validated diagnostic platform for the sensitive and specific identification of SARS-CoV-2. Here, we report on the development of a de novo, high-resolution and comparative genomics guided reverse-transcribed loop-mediated isothermal amplification (LAMP) assay. To further enhance the assay performance and to remove any subjectivity associated with operator interpretation of results, we engineered a novel hand-held smart diagnostic device. The robust diagnostic device was further furnished with automated image acquisition and processing algorithms and the collated data was processed through artificial intelligence (AI) pipelines to further reduce the assay run time and the subjectivity of the colorimetric LAMP detection. This advanced AI algorithm-implemented LAMP (ai-LAMP) assay, targeting the RNA-dependent RNA polymerase gene, showed high analytical sensitivity and specificity for SARS-CoV-2. A total of ~200 coronavirus disease (CoVID-19)-suspected NHS patient samples were tested using the platform and it was shown to be reliable, highly specific and significantly more sensitive than the current gold standard qRT-PCR. Therefore, this system could provide an efficient and cost-effective platform to detect SARS-CoV-2 in resource-limited laboratories.

Abstract P5-04-27: Investigating the incidence of ESR1 gene amplification in breast cancers resistant to multiple endocrine agents

Background: Around 70% of all breast cancers (BCs) are estrogen receptor positive (ER+), but some do not respond to endocrine therapy (ET) and many eventually develop resistance. ESR amplification (ESRA) linked to an increase in ESR1 gene expression is known to occur in some cancers that are endocrine resistant. However, the incidence of ESRA has been the object of debate and its clinical significance remains unclear. This study aimed to investigate the incidence of ESRA in BCs resistant to multiple sequential ETs and optimise a fluorescence in-situ hybridisation (FISH) methodology to robustly detect ESRA.

Methods: Two unique cohorts have been studied:

(A) 20 post-menopausal women with ER+ BC with acquired resistance to letrozole, subsequently treated with up to 4 different lines of ET. Serial RNA and DNA from 3-5 cancer samples per patient (58 samples from 20 patients) were analysed by Ribo0-RNAseq and DNA exome sequencing;

(B) 18 post-menopausal women who developed ER+ BC recurrences on 1st line adjuvant letrozole, then on 2nd line tamoxifen and subsequently on 3rd line exemestane. Tissues were collected at the time of each surgery.

We have optimised a FISH method to assess ESRA in these tissues.

Results: In cohort A, 6/20 patients developed ESR1 gene amplification (ESRA) at some point during treatment. In 5 of these cases, ESRA was only found while on 2nd or 3rd line exemestane but was not present on acquired resistance to previous letrozole or tamoxifen. 1 patient had ESRA at the time of first recurrence on letrozole.

The FISH method showed concordance with the genomic analysis. This suggests that ESRA may be associated with BCs that are treated with and then become resistant to exemestane.

ESRA is also evident in samples from Cohort B, which includes 18 exemestane resistant cases. The complete analysis is ongoing.

Conclusions:

· ESRA can be seen in ER+ recurrent BCs.

· ESRA may be associated with BCs treated with 2nd or 3rd line exemestane.

· The frequency of ESRA in endocrine and exemestane resistance can now be ascertained using an optimised FISH-based method, which is more cost-effective than alternative genomic and biochemical methods.

Citation Format: Turnbull AK, Martinez-Perez C, Mok S, Tanioka M, Fernando A, Renshaw L, Keys J, Wheless A, Garrett A, Parker J, He X, Sims AH, Carey LA, Perou CM, Dixon JM. Investigating the incidence of ESR1 gene amplification in breast cancers resistant to multiple endocrine agents [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-04-27.

Abstract P5-04-14: Tracking ESR1 mutation clonal evolution in breast cancer using in situ mutation detection

Background: Approximately 70% of breast cancers (BCs) are estrogen receptor positive (ER+). Not all ER+ cancers respond to endocrine therapy (ET) and many eventually develop acquired resistance. Next-generation sequencing (NGS) has shown ESR1 mutations (ESRMs) are present in 10-50% of recurrent/metastatic cancers treated with aromatase inhibitors (AIs). Many of these mutations are located in the ligand-binding domain of ER, so they can lead to constitutive activation. This suggests ESRMs are a major mechanism of acquired resistance to endocrine therapy (ET) and numerous studies have shown a link between ESRMs and reduced sensitivity to 2nd line ET. The aim of this project was to investigate the incidence and clonal evolution of common ESRMs in BCs resistant to multiple sequential ETs using NGS, as well as novel PCR and in situ mutation detection methods.

Methods: We have optimised an allele-specific real-time PCR (rtPCR) assay and an in situ mutation detection method (ER-ISMD) for the assessment of ESRMs. Both have been designed to identify a missense gain-of-function D538G mutation with a single nucleotide-resolution in formalin-fixed paraffin-embedded (FFPE) BC tissues.

Two unique cohorts have been studied:

(A) 20 post-menopausal women (PMW) with ER+ BC who acquired resistance to letrozole and were treated with up to 4 subsequent lines of ET. Serial RNA and DNA from 3-5 cancer samples per patient (58 samples from 20 patients) were analysed by Ribo0-RNAseq, DNA exome sequencing, rtPCR and ER-ISMD.

(B) 150 PMW with ER+ BC who developed local (n=79), lymph node (n=59) or distant (n=12) recurrences on 1st line adjuvant letrozole, anastrozole or tamoxifen. Of these, 48 patients developed subsequent recurrences on 2nd line ET. Tissue samples from each recurrence and matched primary BC were collected.

Results: In cohort A, 5/20 patients (20%) had expansion of a D538G ESR1 mutation clone at time of resistance 1st line ET (3:letrozole, 1:anastrozole, 1:tamoxifen). The mutant allele frequency (MAF) increased further in the 4 BCs treated with 2nd line ET (2:tamoxifen, 2:exemestane) and further still in the 1 BC who received 3rd line exemestane. 0/6 patients with ESRM responded to subsequent ET. Allele-specific rtPCR and ER-ISMD have been used to validate these findings and also identified low frequency ESRM clones in the sequential samples prior to the development of clinical resistance, that were not reported by NGS. Both methods have also been applied to screen tissues from patients in cohort B, where ESRMs have also been identified in recurrent samples. Complete analysis is currently ongoing.

Conclusions:

· ESRMs develop and expand in some BCs as a mechanism for acquired resistance to ET and are associated with a lack of response to subsequent standard ETs.

· Allele-specific rtPCR can detect ESRMs and is more cost-effective and easier to use than NGS for ER mutation analysis.

· Some ESRMs predate clinical resistance.

· ER-ISMD is a novel approach that allows for identification and visualisation of the distribution of mutant clones in morphologically intact FFPE tissue.

· ER-ISMD has the potential to become a clinically useful tool to help direct the use of 2nd line ET in routine care.

Citation Format: Martinez-Perez C, Turnbull AK, Tanioka M, Fernando A, Renshaw L, Keys J, Wheless A, Garrett A, Parker J, He X, Sims AH, Carey LA, Perou CM, Dixon JM. Tracking ESR1 mutation clonal evolution in breast cancer using in situ mutation detection [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-04-14.

Abstract P5-18-03: A predictive model for local recurrence in patients treated for ductal carcinoma in situ of the breast (DCIS)

Background: Ductal carcinoma in situ (DCIS) is a heterogeneous precursor, non-invasive breast lesion. There is a lack of specific DCIS molecular predictors of in breast tumour recurrence (IBTR) or progression to invasive breast cancer (IBC) after breast conserving surgery (BCS) +/- radiotherapy (RT). The aim of this was to identify novel biomarkers and combine these with clinical parameters to develop a new model to predict IBTR in patients treated by BCS for DCIS.

Methods: A single institution DCIS biomarker discovery study included a case-control matched series of 180 patients (median age 61, range 35-94) treated at the Edinburgh Breast Unit between 2000 and 2010:

· 88 patients with low/intermediate grade DCIS treated with BCS alone; 18 recurred within 10 years.

· 92 patients with high grade DCIS treated by BCS and RT; 22 recurred within 10 years.

Median follow-up was 7.4 years. RNA was extracted from DCIS lesions and whole-genome transcriptomics analysis was performed using Lexogen QuantSeq. Predictive models were generated based upon the most informative genes. Independent validation cohorts are also available and are currently being used for validation.

Results: The models developed predict risk of IBTR in patients with low or intermediate grade DCIS treated with BCS alone and high grade DCIS treated with DCIS plus RT. The models were found to be independent of grade and stratify patients into binary groups of high and low risk of recurrence.

A promising model was developed based on the expression of 5 genes combined with tumour diameter ≤15mm or >15mm.

• In low/intermediate grade DCIS expression levels of a solute carrier family gene, kinetochore associated gene and an immunomodulatory gene are predictive of recurrence.

• In high grade DCIS an additional solute carrier and a glutathione S-transferase related gene are predictive of recurrence.

• In the training sets the models have 96% (high-grade) and 92% (low/intermediate grade) accuracy of prediction of subsequent recurrence and estimates of IBTR-free survival were highly significant in both groups (<0.0001). Validation of the model by RT-PCR and immunohistochemistry is underway in both the training cohort and an independent validation cohort.

Conclusions:

· Promising models to predict risk of IBTR in patients treated for DCIS have been developed.

· Novel biomarkers that predict recurrence have been identified using new technologies that may have clinical potential.

· Independent validation is currently underway.

Citation Format: Martinez-Perez C, Turnbull AK, Fernando A, Ekatah GE, Arthur LM, Cartlidge CW, Johns N, Sims AH, Thomas JS, Dixon JM. A predictive model for local recurrence in patients treated for ductal carcinoma in situ of the breast (DCIS) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-18-03.

Abstract P5-04-03: Molecular characterisation of ER+ breast cancer dormancy and acquired resistance using a clinical model: Potential involvement of epigenetic regulation

Background: The risk of recurrence for oestrogen receptor positive (ER+) breast cancer patients treated with 5 years of adjuvant endocrine therapy persists for many years or even decades following surgery and apparently successful adjuvant therapy. This period of dormancy and acquired resistance is inherently difficult to investigate. Therefore, previous efforts have been limited to in vitro or in vivo approaches. In this study sequential tumour samples from patients receiving extended neoadjuvant endocrine treatment were characterised as a novel clinical model of ER+ breast cancer dormancy and acquired resistance.

Methods: Consecutive tumour samples from 62 patients undergoing extended (4-45 months) neoadjuvant letrozole therapy were subjected to transcriptomic and proteomic analysis, representing pre- (before treatment), early-on (13-120 days) and long-term (>120 days) neoadjuvant letrozole treatment. Patients with at least a 40% initial reduction in tumour size by 4 months of treatment were included. Of these, 42 patients with no subsequent progression were classified as “dormant”, and the remaining 20 patients as “acquired resistant”. Expression analysis was performed by using Illumina BeadChips. R and BioConductor packages were used for analysis. Differentially expressed genes were determined by using paired Rank Products (FDR, 5%).

Results: Multidimensional scaling using most variant 500 genes demonstrated that long-term treated dormant samples clustered separately from their matched pre- and early-on samples whereas long-term treated resistant samples were indistinguishable from their pre-treatment counterparts. Therapy-induced changes in resistant tumours were common features of treatment, rather than being specific to resistant phenotype. Comparative analysis of long-term treated dormant and resistant tumours highlighted changes in epigenetics pathways including DNA methylation and histone acetylation. DNA methylation marks 5-methylcytosine and 5-hydroxymethylcytosine were significantly reduced in resistant tumours compared to dormant tissues after extended letrozole treatment. Decrease in 5-hydroxymethylcytosine were significant early-on.

Conclusions: This is the first patient-matched gene expression study investigating long-term aromatase inhibitor-induced dormancy and acquired resistance in breast cancer. Dormant tumors exhibit distinct molecular changes under extended treatment whereas acquired resistant tumors are more similar to matched diagnostic samples supporting the molecular concordance between primary tumors and metastases. Global loss of DNA methylation was observed in resistant tumours under extended treatment which can be predicted within first 4 months of therapy. Epigenetic alterations may lead to escape from dormancy and drive acquired resistance in a subset of patients supporting a potential role for therapy targeted at these epigenetic alterations in the management of endocrine resistant breast cancer.

Funding: This work was supported by Marie Skłodowska-Curie Individual Fellowship [H2020-MSCA-IF, 658170] and Welcome Trust Institutional Fund (ISSF3) to CS and AHS, Breast Cancer Now to AHS.

Citation Format: Selli C, Turnbull AK, Pearce D, Fernando A, Renshaw L, Thomas JS, Dixon MJ, Sims AH. Molecular characterisation of ER+ breast cancer dormancy and acquired resistance using a clinical model: Potential involvement of epigenetic regulation [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-04-03.

Abstract P3-10-26: Predicting benefit from HER2-targeted therapies in patients with ER+/HER2+ breast cancer

Background: ER+/HER2+ accounts for up to 10% of all breast cancers (BCs) and most are treated with endocrine therapy (ET) after surgery to reduce the recurrence risk. We developed and validated an immunohistochemistry (IHC) based test (EA2Clin) that incorporates baseline IL6ST, clinical variables and on-treatment measurement of MCM4. Responders (Rs) and non-responders (NRs) to ET are identified and it accurately estimates recurrence-free survival (RFS) and BC-specific overall survival (BCSS). The aim was to determine if EA2Clin could accurately predict ER+/HER2+ patients likely to benefit from ET and to determine if it can identify those for whom HER2-targeted therapies are required.

Methods: 3 cohorts were studied:

A: 32 post-menopausal women (PMW) with large ER+/HER2+ BC treated with neoadjuvant (3-6 months) then adjuvant letrozole. 5 also received adjuvant chemotherapy plus Herceptin. Neoadjuvant clinical response was assessed by changes in tumour volume. Tumour core biopsies were taken at 0, 14 days and 3 months. Gene expression analysis using Illumina HT12 whole-genome beadarrays was performed on a subset (n=17) where fresh tissue was available.

B: 13 PMW with ER+/HER2+ BC who were treated by surgery without neoadjuvant therapy. RNA was extracted from excision tissues and analysed using whole-genome Affymetrix U133A microarrays.

C: 15 PMW with ER+/HER2+ BC treated with 2-weeks of pre-operative letrozole (n=7) or anastrozole (n=8). All received adjuvant letrozole. Tissues were collected at pre-treatment and at surgery. None received Herceptin or chemotherapy.

All patients were followed-up after surgery (median follow-up = 6.4 years).

Results: In cohort A, half (16/32) of the patients responded to ET with tumour volume reductions of >70% with neoadjuvant treatment. Innate resistance was apparent in 3 patients with continued tumour growth on ET, whereas 13 patients developed resistance after a period of response. EAClin2 predicted neoadjuvant response with a 92% accuracy. There was increased expression of phospho-AKT and phospho-ERK in NRs, not seen in Rs. Half (8/16) of the NR cancers expressed phospho-ER; but was not seen in any responsive cancer. Gene expression analysis in 17 patients showed increased MAPK and PI3K pathway activity in the 9 NR compared with the 8 R tumours. These results were recapitulated in cohort B where MAPK and PI3K activity were associated with low levels of IL6ST.

In the 16/32 patients who responded well to neoadjuvant ET the actuarial recurrence rate was 0% at 5 and 10 years. The rate of recurrence in the NR was 30% at both 5 and 10 years. Of the 5 patients who received chemotherapy plus Herceptin, none recurred despite a poor response to neoadjuvant letrozole (median length to last follow-up was 6.1 years). Initial data suggest that in cohort B EA2Clin identifies a group of ER+/HER2+ cancers that can be managed by ET alone.

Conclusions:

· The EA2Clin test identifies ER+/HER2+ BCs who respond well to ET alone and those with a poor clinical response who have higher risk of recurrence.

· NR to ET have increased expression of PI3K and MAPK pathways, consistent with active HER2 signalling.

· There is potential role for EA2Clin in selecting ER+/HER2+ patients that require and benefit from HER2-targeted therapies.

Citation Format: Turnbull AK, Webber V, McStay D, Arthur L, Martinez-Perez C, Fernando A, Renshaw L, Keys J, Clarke R, Sims AH, Dixon JM. Predicting benefit from HER2-targeted therapies in patients with ER+/HER2+ breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-10-26.

Abstract P3-06-17: Unlocking the transcriptomic potential of formalin-fixed paraffin embedded breast cancer tissues for high-throughput genomic analysis

Background: Transcriptomic analyses of clinical samples can help improve our understanding of disease aetiology, drug effectiveness, assign molecular subtypes and derive prognostic signatures for clinical decision-making. The success of early microarray studies relied heavily on sample quality and predominantly fresh frozen (FF) tissues to generate reliably robust data. The emergence of next-generation microarray and sequencing-based technologies from formalin-fixed paraffin-embedded (FFPE) tissues provides an opportunity to study archival clinical tissues with long-term follow-up. Here we assess 9 technologies, which vary in resolution, cost and RNA requirements, with matched FF and FFPE tissues from the same patient.

Methods: Sequential tumour biopsies were taken pre-treatment and on-treatment (at 14-days and 3-months) from 11 postmenopausal patients with oestrogen receptor positive breast cancer treated with 3 months of neoadjuvant letrozole. Half of each sample was snap frozen in liquid nitrogen and half was FFPE, RNA was extracted from both. Transcriptomic analyses were performed using 9 technologies: Illumina Beadarray, Affymetrix U133A, Affymetrix Clariom S, NanoString nCounter, AmpliSeq Transcriptome, Lexogen QuantSeq and IonXpress RNAseq, Tempo-Seq BioSpyder and Qiagen UPX3'.

Results: Success rates for generating robust expression profiles from FFPE tissues were 100% all except the Illumina BeadChip (22%) and AmpliSeq Transcriptome (83%) , which varied by the age of tissue. With the total number and position of probes/primers/counts varying widely between approaches, in total 7305 genes were represented across all of the whole-genome technologies tested.

Clear batch effects were evident when comparing data from FF and FFPE tissues and when comparing between different technologies. Standard batch correction approaches such as XPN and ComBat minimised technical bias effect and increased the correlations between matched samples (FF and FFPE) to R>0.9, irrespective of the technology used.

When analysed by multi-dimensional scaling following batch correction, samples clustered by treatment time-point. When ranked by expression of 60 proliferation genes, reported by us to change with letrozole treatment, samples ordered again by time-point, consistent with our previous findings, and paired samples clustered together.

Conclusions:

· Robust gene expression profiles can be reliably generated from FFPE tissues and are comparable to those derived from FF tissue using established transcriptomic approaches.

· A range of new technologies are available for the study of FFPE tissues; these vary in cost, resolution and RNA requirements to fit the user's needs.

· Gene expression data from biologically similar studies, generated using different technologies, can be reliably integrated for robust meta-analysis, subject to appropriate batch correction analysis.

Citation Format: Turnbull AK, Selli C, Martinez-Perez C, Fernando A, Renshaw L, Keys J, Figueroa JD, He X, Tanioka M, Munro A, Murphy L, Fawkes A, Clark R, Coutts A, Perou CM, Carey LA, Dixon JM, Sims AH. Unlocking the transcriptomic potential of formalin-fixed paraffin embedded breast cancer tissues for high-throughput genomic analysis [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-06-17.

Abstract P5-11-03: Measurement of on-treatment proliferation biomarkers in nodal metastasis improves prediction of endocrine therapy response using the EA2CliN test

Background: The majority of patients with early-stage estrogen receptor positive (ER+) breast cancer (BC) are treated with adjuvant endocrine therapy (ET) after surgery to reduce the risk of recurrence. Recently, we have developed and validated an immunohistochemistry (IHC) based assay (EndoAdjuvant2 Clinical; EA2Clin) that measures pre-treatment IL6ST level together with clinical variables and on-treatment MCM4 to assess proliferation. We have previously shown that it can accurately identify responders and non-responders to ET and predicts recurrence-free survival (RFS) and BC-specific overall survival (BCSS). We postulated that measuring on-treatment proliferation in lymph node metastases (LN+) rather in the primary cancer might further improve the accuracy of the test for these patients. The aim was to test and validate this in cohorts of pre- and post-menopausal women (preMW & PMW) treated with preoperative ET (tamoxifen (T), fulvestrant (F), letrozole (L) or anastrozole (A)) and subsequent adjuvant ET.

Methods: Cohorts: (1) 137 PMW with ER+ BC, 59 were LN+, treated with neoadjuvant L (median duration 4.8 months, range 1-33), then surgery followed by adjuvant L (n=109) or other ET (n=28); (2) 148 PMW with ER+ BC, 55 were LN+, treated with 2 weeks of preoperative L (n=76) or A (n=72), then surgery followed by adjuvant L (n=69) or T (n=79); (3) 52 preMW with ER+ BC, 24 were LN+, treated with 2 weeks of preoperative T (n=26) or 1x750mg dose of F (n=26), then surgery followed by adjuvant T. All LN+ patients had sentinel node biopsies or clearance. The median follow-up was 6.5 years (cohort 1), 6.3 years (cohort 2) and 10.2 years (cohort 3).

EA2Clin: Patients are classified as:

· Low risk: ER+ and LN-negative and <2cm or pre-treatment IL6ST 2+/3+ (IHC) and post-treatment MCM4 in the primary has <20% positive nuclear staining.

· High risk: ER+ LN+ grade 3 BCs >2cm or pre-treatment IL6ST is 0 or 1+, or IL6ST is 2+ or 3+ and MCM4 in the primary has >10% positive nuclear staining.

EA2CliN uses the post-treatment level of MCM4 in the nodes, rather than the primary cancer.

Results: In cohort 1, EA2Clin (using primary tumour MCM4) was significantly associated with both RFS (P=0.0003, HR=13.17, 95%CI=5.48-13.61) and BCSS (P=0.005, HR=11.91, 95%CI=8.73-31.42). The 5 and 10 year actuarial recurrence rates were 5%/5% and 48%/64% for the low and high-risk groups respectively.

In the same cohort, using the MCM4 level in the node (EA2CliN) there was an even more significant association with both RFS (P<0.00009, HR=18.16, 95%CI=12.59-19.46) and BCSS (P=0.002, HR=12.93, 95%CI=5.43-25.62). The 5 and 10 year actuarial recurrence rates were 0%/0% and 48%/72% for the low and high-risk groups respectively. Further validation of EA2CliN in cohorts 2 and 3 is underway.

Discussion:

· Direct measurement of on-treatment proliferation biomarkers in LN metastases improves prediction of outcomes to ET in women with BC.

· This tests identifies a group of low risk women that are node negative and node positive with a 100% RFS and BCSS.

· This is the most impressive predictive test for patients with ER+ breast cancer yet developed.

Citation Format: Turnbull AK, Mok S, Martinez-Perez C, Fernando A, Renshaw L, Keys J, Sims AH, Dixon JM. Measurement of on-treatment proliferation biomarkers in nodal metastasis improves prediction of endocrine therapy response using the EA2CliN test [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-11-03.

Abstract P4-08-03: EA2Clin: A novel immunohistochemical prognostic and predictive test for patients with estrogen receptor-Positive breast cancer

Background: The majority of patients with early-stage estrogen receptor positive (ER+) breast cancer (BC) are treated with adjuvant endocrine therapy (ET) after primary surgery to reduce the risk of recurrence. A variety of tests are available to predict outcomes on ET but most require gene-level measurements and are expensive. Recently, we developed an immunohistochemistry (IHC) based test (EA2Clin) using levels of pre-treatment IL6ST together with clinical variables and on-treatment proliferation. The aim was to validate this test in cohorts of both pre- and post-menopausal women treated with two weeks of a variety of endocrine treatments (tamoxifen, fulvestrant or an aromatase inhibitor) prior to surgery.

Methods: The cohorts are: (A) 186 post-menopausal women (PMW) with ER+ BC treated with at least 2 weeks of preoperative or neoadjuvant letrozole or anastrozole, then surgery followed by adjuvant letrozole (n=132) or tamoxifen (n=54); (B) 51 pre-menopausal women (preMW) with ER+ BC treated with 2 weeks of either neoadjuvant tamoxifen (n=24) or one 750mg dose of faslodex (n=27), then surgery followed by adjuvant tamoxifen. The median follow-up was 5.4 years for cohort A and 10.2 years for cohort B. IHC analysis was performed using a Leica BOND III autostainer and the EA2Clin algorithm was used to stratify patients in binary high or low-risk groups.

Results: In the cohort of PMW, EA2Clin was highly significantly associated with both recurrence-free survival (RFS) (P<0.0001, HR=13.26, 95%CI=5.59-13.46) and breast cancer specific survival (BCSS) (P<0.0001, HR=12.93, 95%CI=4.43-37.72). The 5 and 10 year actuarial recurrence rates were 7%/22% and 46%/73% for the low and high risk groups, respectively. The actuarial breast cancer-related death rate for the low risk group was 5% at both 5 and 10 years, whereas for the high risk group was 33%/38%. Confounding factors were not found to be significant.

In the cohort of preMW, our test was significantly associated with both RFS (P=0.002, HR=5.71, 95%CI=1.91-17.05) and BCSS (P=0.016, HR=4.81, 95%CI=1.34-17.26). The 5 and 10 year actuarial recurrence rates were 12%/29% and 27%/77% for the low and high risk groups, respectively. The 5 and 10 year actuarial breast cancer-related death rates were 7%/19% and 9%/58% for low and high risk groups, respectively.

Discussion:

· This study has validated EA2Clin as the first predictive tool to incorporate clinical data with pre and on-treatment immunohistochemical biomarkers to predict accurately the outcome of patients with ER positive breast cancer treated with adjuvant ET.

· This test predicts both RFS and BCSS in pre- and PMW treated with a variety of endocrine agents.

· Because this test incorporates clinical variables with simple IHC, it can be performed locally in any pathology lab.

Citation Format: Turnbull AK, Fernando A, Renshaw L, Keys J, Thomas JS, Sims AH, Dixon JM. EA2Clin: A novel immunohistochemical prognostic and predictive test for patients with estrogen receptor-Positive breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-08-03.

Abstract P5-11-02: Predicting local recurrence in patients treated for ductal carcinoma in situ of the breast (DCIS)

Background: Ductal carcinoma in situ (DCIS) of the breast represents a heterogeneous group of precursor, non-invasive breast lesions. Currently we lack accurate tools to stratify DCIS patients according to inherent risk of in breast tumour recurrence (IBTR) or progression to invasive breast cancer (IBC).Most DCIS patients are treated by breast-conversing surgery (BCS), followed by whole-breast radiotherapy (RT) for the majority of high-grade DCIS. The aim of this study was to identify novel biomarkers which predict recurrence after BCS +/- RT.

Methods: A single institution study of 466 consecutive patients (median age 61, range 35-94) with DCIS treated by BCS between 2000 and 2010 was carried out. 271 patients with grade 3 DCIS received RT and 155 with grade 1/2 DCIS did not receive RT.

For biomarker discovery, a case-control matched series of 200 patients (mean age = 61, range = 36-84) from the above audit that met the following criteria was selected:

· 120 with low/intermediate-grade DCIS treated with BCS alone: 30 have recurred, 90 patients matched 3:1 have not recurred by 10 years.

· 80 with high-grade DCIS treated by BCS plus RT: 20 have recurred, 60 patients matched 3:1 have not recurred by 10 years.

Median follow-up was 7.4 years. RNA has been extracted and Affymetrix Clariom S whole-genome analysis has been performed and is currently being analysed.

Results:

In the cohort of 466 patients, 271 patients with high grade DCIS had BCS plus RT. Actuarial IBTR and IBC-IBTR in this group were 10% and 4% at 5 years and 18% and 6% at 10 years, respectively. 155 patients with low/intermediate grade DCIS had BCS alone. Actuarial overall IBTR and IBC-IBTR in this group were 6% and 2% at 5 years and 13% and 2% at 10 years respectively.

In the high-grade, RT treated group, lesion size (P<0.001, P=0.003), presence of comedo necrosis (P=0.018, P=0.025) and the Van Nuys Prognostic Index (VNPI) (P=0.02, P=0.004) were significantly associated with overall IBTR and DCIS-IBTR. No factor was significantly associated with IBS-IBTR in the high grade group and no factor predicted for any IBTR in the low/intermediate group.

Full genomic analysis of the 240 patient case-control matched cohort is underway and will be presented.

Discussion:

· This is the first DCIS biomarker discovery study using whole genome analysis and the matched cohort design looking separately at BCS + RT for high-grade DCIS and BCS only for low/intermediate grade DCIS.

· Clinical parameters alone may have insufficient sensitivity to identify high-grade, RT-treated patients at risk of developing IBC-IBTR.

· While recurrence rates in the low/intermediate grade DCIS group are lower than in the high-grade group, some patients do recur and there is a need to develop new tools which can identify low grade patients with a sufficiently high risk of recurrence to warrant additional treatment.

Citation Format: Martinez-Perez C, Turnbull AK, Ekatah GE, Arthur LM, Fernando A, Sims AH, Thomas JS, Dixon JM. Predicting local recurrence in patients treated for ductal carcinoma in situ of the breast (DCIS) [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-11-02.

Abstract P4-08-02: Understanding the mechanisms of action underlying the role of IL6ST, a key biomarker for prediction of response to endocrine therapy

Introduction: IL6ST is regarded as a putative ER target gene. Recently it has been recognised as a key biomarker for prediction of response to endocrine therapy (ET), having been included as the primary biomarker in our EA2Clin test and as an ER-signalling gene in the EndoPredict test. In both tests higher IL6ST expression is associated with a better response to ET and better prognosis. Despite its importance as a biomarker, little is known about its functional role in breast cancer (BC).

Methods: Pre- and on-treatment (at 14-days and at surgery) samples were collected from 102 post-menopausal women with ER+ BC, treated with 3-6 months of neoadjuvant ET. RNA was extracted for whole-genome expression analysis. From a subset with available fresh frozen tissue (28 patients, 83 samples) protein was extracted and proteome analysis using mass spectrometry is currently underway – results available for SABCS 2017. Immunohistochemistry was performed on FFPE tissue microarrays (TMAs) comprising pre-treatment samples from 102 patients. Cytoplasmic/membrane staining was scored using a graduated scale (0-3+) and nuclear staining was graded using an Immunoscore.

Results: IL6ST exists in membrane-bound and soluble forms of varying size. The full-length membrane bound molecule comprises 8 domains: 6 extracellular, 1 transmembrane and 1 cytoplasmic. In the EA2Clin test, pre-treatment BC tissues are stained for IL6ST with an antibody specific for a region spanning the transmembrane and cytoplasmic domains. TMAs were stained for IL6ST with both this and a second antibody binding the extracellular part, detecting both full-length and most soluble isoforms. Levels of both were correlated (R=0.82, P<0.0001).

IL6ST is known to mediate the action of cytokines including IL6, OSM and LIF via downstream regulation of pathways such as JAK/STAT. TMAs were stained for antibodies against IL6ST, OSM, IL6, total STAT3, pSTAT3 (Tyr705) and pSTAT3 (Ser727). IL6ST was scored as low (0/1+) or high (2+/3+). There was a positive association between levels of IL6ST and IL6 (P=0.02) and total STAT3 (P=0.003). There was no association between IL6ST and OSM or either pSTAT3.

Supervised gene expression analysis comparing pre-treatment samples with high and low IL6ST levels revealed increased levels of STAT3-regulated genes: cell cycle (CEBPD, CDKN1B), apoptosis (NFIL3, ATF3, BCL2), extracellular matrix remodelling (ADM, SEPRINE1-3) and interferon signalling (IFIT1, IFI44, IFI27). Unsupervised gene enrichment analysis revealed increased expression of genes involved with JAK/STAT, PI3K, mTOR and ERBB1 signalling in tumours expressing higher IL6ST levels. Lower levels were associated with increased energy generation, cellular metabolism and epithelial-mesenchymal transition.

Conclusions:

• This is the first matched whole-genome and mass spectrometry proteome analysis of sequential ET-treated BC patients

• IL6ST predicts response to ET – it is used in2 independent assays

• Levels of full-length IL6ST appear to be the most important for ET response prediction

• IL6ST may have an active role in BC cells, mediating signalling of cytokines such as IL6 through the JAK/STAT pathway and subsequent downstream transcriptional regulation.

Citation Format: Turnbull AK, Fernando A, Martinez-Perez C, Finch AJ, von Kriegsheim A, Wills J, Quinn N, Selli C, Mosley D, Langdon SP, Sims AH, Dixon JM. Understanding the mechanisms of action underlying the role of IL6ST, a key biomarker for prediction of response to endocrine therapy [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-08-02.

Abstract P4-04-02: Characterising the effects of neoadjuvant endocrine therapy on primary cancers and nodal metastasis

Background: Approximately 40% of ER+ breast cancer present with nodal metastasis. To date, there has been no comparison of the molecular response of primary cancers and metastases to ET. Recent evidence suggests that nodal metastases have different clones and subclones compared to the primary tumour. The aim of this study is to characterise the molecular response of primaries and nodal metastases to ET.

Methods: A unique set of 7 post-menopausal women with ER-positive breast cancer had biopsies taken from the primary tumour and a positive lymph node at diagnosis and at surgery following 3-12 months of neoadjuvant letrozole. 14-day and 3-6 month on-treatment biopsies from the primary tumour and involved nodes were also taken from the same patients, giving a total of 75 samples. Lymph node FFPE blocks were stained for cytokeratin and macro-dissected to enrich for tumour tissue. RNA and DNA were extracted and Ribo0-RNAseq, DNA exome sequencing and somatic mutation detection using UNCeqR performed. Whole-transcriptome AmpliSeq targeted-sequencing has been analysed for 4 patients.

Results: Multi-dimensional scaling and hierarchical clustering analysis based on all transcripts and the 500 most variably expressed genes revealed that primaries and nodal metastases are strongly associated at diagnosis but some nodes diverge during ET treatment. Analysis of estrogen-responsive proliferation-associated genes (n=60) in nodal metastasis revealed a reduction in expression of the majority of genes with ET. However, the expression levels of some remained high in the on-treatment node samples in all 4 patients analysed compared with the matched primary tumour on treatment. In particular, expression of genes involved in DNA replication and regulation of cell cycle including MCM6 and RRM2 (DNA replication), ASPM and CEP55 (mitosis) and CDKN3 (regulation of cell cycle) persisted at high levels in nodal metastases, but reduced in the primary cancers. Similarly, primary tumours had increased levels of ECM remodeling genes (n=60) as treatment continued, while levels in the nodal metastasis were heterogeneous on-treatment. Full genome sequencing results will be available by December 2017.

Discussion

· This is the first study to investigate genomic and transcriptomic changes with ET in both primary cancers and nodal metastases.

· On-treatment changes in nodal disease are heterogeneous between patients and within the same patient.

· Nodal metastases do respond to ET with reduced levels of proliferation-associated genes.

· Some proliferation-associated genes appear to maintain higher expression in nodal disease.

· Patterns of gene expression observed in some nodal metastases are consistent with profiles previously described by us for ET resistance and recurrent disease.

· Nodal metastases may accumulate mutations during treatment with ET and on-going analysis will clarify this.

Citation Format: Dixon JM, Turnbull AK, Tanioka M, Parker J, He X, Fernando A, Renshaw L, Keys J, Thomas JS, Sims AH, Carey LA, Perou CM. Characterising the effects of neoadjuvant endocrine therapy on primary cancers and nodal metastasis [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-04-02.

Abstract P6-01-21: Novel CD146-downstream signaling pathway involved in breast tumor suppression

This abstract was not presented at the symposium.

Comparative pharmacokinetics and bioavailability of brimonidine following ocular and dermal administration of brimonidine tartrate ophthalmic solution and gel in patients with moderate-to-severe facial erythema associated with rosacea

BACKGROUND

Persistent facial erythema is the most common primary pathological feature of rosacea, the only treatment for which is brimonidine tartrate (BT) gel.

OBJECTIVES

To assess the relative bioavailability of topical BT gel in comparison with the ophthalmic BT solution.

METHODS

A pharmacokinetic study was conducted to compare intraindividual systemic exposures after dermal application of BT gel (0·07%, 0·18% and 0·5%) under maximal use conditions in patients with moderate-to-severe facial erythema associated with rosacea, and administration of BT ophthalmic solution 0·2%.

RESULTS

Patients who received BT ophthalmic solution 0·2% three times a day for 1 day had a mean Cmax of 54 ± 28 pg mL(-1) and a mean 0-24-h area under the curve (AUC0-24 h ) of 568 ± 277 pg h mL(-1) . Topical application of BT gel for 29 days resulted in quantifiable systemic exposure in 22%, 48%, 71% and 79% of patients who received BT gel 0·07% twice daily, 0·18% once daily, 0·18% twice daily and 0·5% once daily, respectively. The mean Cmax values for the BT gels ranged between 13 and 25 pg mL(-1) , and mean AUC0-24 h values ranged between 42 and 290 pg h mL(-1) . Systemic exposure increased with applied dose, with no drug accumulation for the duration of treatment. The systemic exposure observed with the highest dose of BT gel (0·5% once daily) was significantly lower than the systemic levels observed for the ophthalmic solution. 0·2% apply for all the concentrations.

CONCLUSIONS

The systemic safety profile of BT gel may be considered better than that of the ophthalmic solution.

Divergent effects of D₂/₃ receptor activation in the nucleus accumbens core and shell on impulsivity and locomotor activity in high and low impulsive rats

RATIONALE

Previously we demonstrated reduced D2/3 receptor availability in the ventral striatum of hyper-impulsive rats on the five-choice serial reaction time task (5-CSRTT). However, the anatomical locus of D2/3 receptor dysfunction in high impulsive (HI) rats is unknown.

OBJECTIVE

In the present study, we investigated whether D2/3 receptor dysfunction in HI rats is localised to the core or shell sub-regions of the nucleus accumbens (NAcb).

METHODS

Rats were selected for low (low impulsive, LI) and high impulsivity on the 5-CSRTT and implanted with guide cannulae targeting the NAcb core and shell. The D2/3 receptor agonist quinpirole was locally injected in the NAcb (0.1, 0.3 and 1 μg per infusion) and its effects investigated on the performance of LI and HI rats on the 5-CSRTT as well as spontaneous locomotor activity in an open field.

RESULTS

Intra-NAcb core quinpirole increased premature responding in HI rats but not in LI rats. In contrast, intra-NAcb shell quinpirole strongly increased locomotor activity in HI rats, unlike LI rats. This effect was blocked by intra-NAcb shell infusions of the D2/3 receptor antagonist nafadotride (0.03 μg). However, nafadotride was ineffective in blocking the effects of intra-NAcb core quinpirole on premature responding in HI rats.

CONCLUSIONS

These findings indicate that impulsivity and hyperactivity are separately regulated by core and shell sub-regions of the NAcb and that HI rats show an enhanced response to D2/3 receptor activation in these regions. These results suggest that the symptom clusters of hyperactivity and impulsivity in attention-deficit hyperactivity disorder may be neurally dissociable at the level of the NAcb.

Abstract P4-06-14: CD146-suppresses breast tumor invasion via a novel transcription target TIMPv

The function of the cell adhesion receptor CD146, a recently discovered marker of endothelial cells and a tumor promoter of melanoma and other cancers, is controversial in breast cancer (BC). However several lines of evidence supports its role as a tumor suppressor in BC. Further, the molecular mechanisms underpinning this suppression are unknown, neither has the ligand for CD146 been identified. Using a novel validated Enhanced Green Fluorescent Protein (EGFP)-inducible systems of CD146 expression both in vitro and in vivo, we provide here molecular and functional evidence of CD146 and its novel transcriptional target TIMPv (a variant of tissue inhibitor of metallo-proteinases) in underpinning the suppression of BC invasion.

Tetracycline (tet-on) CD146 system was developed in both MCF-7 and MDA-231 BC founder cell lines, and validated using time course RT-PCR and western blot analyses, and fluorescent microscopy. In functional experiments, induction of CD146 inhibited BC cell migration and invasion. TIMPv, the only endogenous protein inhibitor known for metallocarboxypeptidases, was identified by expression profiling as a novel transcriptional target of CD146-signaling, an association validated by quantitative PCR and immunoblotting experiments in a range of breast and melanoma cancer cells. However, siRNA inhibition of CD146 in the SKMel-28 melanoma cell line increased TIMPv expression, suggesting that while TIMPv is a positive transcriptional target of CD146 in BC cells, it is negatively regulated in melanoma cells. Furthermore, using invasion assay, the functional relevance of TIMPv to CD146-suppressed metastasis was demonstrated by selective suppression of TIMPv in CD146-expressing BC inducible cells using RNAi. More interestingly, induction of CD146 expression in vivo, using the tet-on CD146 expression system in BC Xenograft model resulted in suppression of breast tumor growth. Further, Clinical analysis of breast tissue samples by Immunohistochemistry showed that TIMPv expression patterns paralleled those of CD44s during breast tumor progression. Pharmacological and molecular approaches revealed that the activation of NFκB via Akt pathway couples CD146 to the transcription of TIMPv in BC cells.

Our study is the first report to provide a functional molecular link of a novel transcriptional target of CD146, TIMPv, to cancer via a unique axis that underpin CD146-suppressed BC progression; TIMPv is a potential target for guiding the development of novel therapeutic strategies for BC.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-06-14.

P2-01-26: TIMPv: a novel downstream transcriptional target gene that underpins CD146-suppressed breast tumor invasion

Background: CD146, a marker of endothelial cells, promotes tumor progression of many cancers including melanoma and prostate. Strikingly, several lines of evidence suggest that it is a suppressor of breast cancer (BC) progression. Not only the ligand(s) has not been identified, but CD146-downstream signaling mechanisms remain unknown.

Material and Methods: Here, we report the functional importance of CD146 and that of a novel transcriptional target of CD146-signaling, variant of tissue inhibitor of metalloproteinases (TIMPv) identified by microarray analysis, in underpinning the suppression of BC invasion, using novel validated Enhanced Green Fluorescent Protein (EGFP)-inducible systems of CD146 expression both in vitro and in vivo. Results: In functional experiments, induction of CD146 inhibited BC cell migration and invasion. TIMPv was identified by expression profiling as a novel transcriptional target of CD146-signaling, an association validated by quantitative PCR and immunoblotting experiments in a range of breast and melanoma cancer cells. However, siRNA inhibition of CD146 in the SKMel-28 melanoma cell line increased TIMPv expression, suggesting that while TIMPv is a positive transcriptional target of CD146 in BC cells, it is negatively regulated in melanoma cells. Furthermore, the functional relevance of TIMPv to CD146-suppressed metastasis was demonstrated by selective suppression of TIMPv in CD146-expressing BC inducible cells using RNAi. More interestingly, induction of CD146 expression in vivo using mouse EGFP-inducible system of CD146 expression resulted in suppression of breast tumor growth.

Discussion: Our study is the first report to provide a functional molecular link of TIMPv to cancer via unique axis that underpin CD146-suppressed BC progression, thus identifying TIMPv as a potential target for guiding the development of novel therapeutic strategies for BC.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P2-01-26.

Health status of primary schoolchildren in Sri Lanka

OBJECTIVE

To assess health status of 9-10-year old school children in Sri Lanka.

DESIGN

A cross-sectional, descriptive study. Schools were selected to obtain a sample representative at national and provincial levels and 20 children were randomly selected from Grade 5 classes in each school.

MEASUREMENTS

Children were examined for Bitot's spots and goitre. Height, weight, and visual acuity were measured according to standard procedures. Haemoglobin level was measured using finger-prick blood and a HemoCue meter. Geohelminth infections were quantified by faecal examination using the modified Kato-Katz technique. Height for age Z-scores (HAZ) and body mass index (BMI) were calculated as indicators of nutritional status.

RESULTS

Two thousand five hundred and twenty eight children (1351 boys) from 144 schools (140 state schools and four private schools) were examined. Nationally, 15.5% of children were stunted (HAZ lower than -2.0 SD); 52.6% were thin (BMI < 5th centile of age- and sex-matched reference population); 3.1% were overweight (BMI > 85th centile); 12.1% were anaemic; 0.3% had Bitot's spots; 3% had a visible or palpable goitre; 4.6% were shortsighted; and 6.9% had one or more soil-transmitted nematode infection. Among children on whom anthropometry, haemoglobin and faecal examinations were all done, 64.6% (1332/2063) were thin, stunted, anaemic or infected with worms. A much higher proportion of children in the Northern and Eastern provinces had health problems when compared to the other provinces.

CONCLUSIONS

The majority of older primary schoolchildren in Sri Lanka are undernourished. Anaemia, vitamin A deficiency, iodine deficiency and soil-transmitted nematode infections affect a much smaller proportion of them.

Neonatal thymectomy identifies two major pools of sessile and recirculating peripheral T cells which appear to be under separate homeostatic control

In this study the role of the thymus in the development of sessile T cell populations resident in spleen and lymph nodes (LN) was contrasted with the development of recirculating T cell populations trafficking between blood and lymph. Extensive analysis of the composition and the rate of growth of the secondary lymphoid tissues and recirculating lymphocyte pool coupled with neonatal thymectomy revealed that the sessile and recirculating T cell populations showed different degrees of thymic dependency and increased in size at different rates, suggesting these two populations might be under separate homeostatic control. Neonatal thymectomy also resulted in a much greater depletion of CD8+ and gammadelta TCR+ T cell subsets compared with CD4+ T cells in the sessile and recirculating T cell pools, and greatly reduced the number of T cells homing to peripheral lymph nodes compared with those homing to the gut.

Use of imposex (pseudohermaphroditism) as indicator of the occurrence of organotin compounds in Portuguese coastal waters--Sado and Mira estuaries

Organotin compounds, including tributyltin (TBT), are a class of the most toxic xenobiotics occurring in aquatic systems. High concentration levels in waters and sediments are mainly due to their extensive use as biocides and high persistence when present in sediments under anaerobic conditions. Toxicity studies have revealed the acute effects of TBT for aquatic organisms at concentrations as low as 1 microgram/L, and the induction of imposex at levels below 0.5 ng/L TBT (as Sn). At 20 ng/L TBT (as Sn) causes sterility and is followed with the disappearance of the most sensitive neogastropods on a given shore. Imposex is the most sensitive response of all known pathological conditions for nontarget organisms following an exposure to tributyltin. In this study results are discussed that were obtained from two monitoring sites with different anthropogenic background using imposex monitoring as an indicator of TBT concentrations, as well as chemical analysis of tissue of Hinia (= Nassarius) reticulata (L.) (Gastropoda).

Comparative evaluation of European methods for sampling and sample preparation of soils--the Portuguese contribution

The main purpose of this work was to prepare a Portuguese sampling strategy, according to the existing Portuguese recommendations, for the soil sampling exercise at Dornach in the framework of the CEEM soil project of the SMT Programme of the EU. Within this project, the results obtained from the Dornach study were compared with the results obtained by other European participants and also with the reference sampling. The objective of this comparison was to validate the method used and to evaluate possible factors of uncertainty that may arise from the application of our national guideline as well as possible advantages. Another objective, also important, was to provide information regarding the need for a harmonised procedure within the European Union related to soil sampling and sample preparation of soils. The results obtained were consistent with the results obtained by other participants, however, in the Portuguese recommendations there is a general lack of specific information that may complicate its application to polluted scenarios. In fact, those guidelines are valuable to detect the average contamination of the soil, but they are not useful to identify hot spots or the edge influence in a contaminated land. As a conclusion, the results obtained by the CEEM soil project helped to evaluate the Portuguese sampling plan. This may provide a basis for further standardisation of soil sampling for specific purposes, e.g. contaminated land, and to establish a technical support for criteria used in the accreditation of laboratories for soil sampling.