Particulate matter exposure during pregnancy is associated with birth weight, but not gestational age, 1962-1992: a cohort study

<p>Abstract</p> <p>Background</p> <p>Exposure to air pollutants is suggested to adversely affect fetal growth, but the evidence remains inconsistent in relation to specific outcomes and exposure windows.</p> <p>Methods</p> <p>Using birth records from the two major maternity hospitals in Newcastle upon Tyne in northern England between 1961 and 1992, we constructed a database of all births to mothers resident within the city. Weekly black smoke exposure levels from routine data recorded at 20 air pollution monitoring stations were obtained and individual exposures were estimated via a two-stage modeling strategy, incorporating temporally and spatially varying covariates. Regression analyses, including 88,679 births, assessed potential associations between exposure to black smoke and birth weight, gestational age and birth weight standardized for gestational age and sex.</p> <p>Results</p> <p>Significant associations were seen between black smoke and both standardized and unstandardized birth weight, but not for gestational age when adjusted for potential confounders. Not all associations were linear. For an increase in whole pregnancy black smoke exposure, from the 1^st(7.4 μg/m³) to the 25^th(17.2 μg/m³), 50^th(33.8 μg/m³), 75^th(108.3 μg/m³), and 90^th(180.8 μg/m³) percentiles, the adjusted estimated decreases in birth weight were 33 g (SE 1.05), 62 g (1.63), 98 g (2.26) and 109 g (2.44) respectively. A significant interaction was observed between socio-economic deprivation and black smoke on both standardized and unstandardized birth weight with increasing effects of black smoke in reducing birth weight seen with increasing socio-economic disadvantage.</p> <p>Conclusions</p> <p>The findings of this study progress the hypothesis that the association between black smoke and birth weight may be mediated through intrauterine growth restriction. The associations between black smoke and birth weight were of the same order of magnitude as those reported for passive smoking. These findings add to the growing evidence of the harmful effects of air pollution on birth outcomes.</p

Abstract 4006: Immune cell profiles and β-catenin signaling in melanoma

Abstract Introduction Immune profiling is a necessary step in understanding tumor microenvironment and predicting the response to immunotherapies. Methods We used the expression of genes exclusively expressed by immune cells in tumors1, to classify 703 formalin-fixed primary melanomas from the Leeds Melanoma Cohort. Transcriptomes were generated from tumor cores using Illumina DASL HT 12.4 array. In the obtained tumor subgroups with differing immune profiles, we tested the hypothesis that β-catenin signaling controls immune suppression in primary tumors as earlier reported in vitro and murine data2. Results We found and validated 6 tumor classes, which showed consistency with other published gene signatures, and predicted melanoma-specific survival (HR=1.8, P=0.003, adjusted for AJCC stage, site, age, sex, ulceration, mitotic rate, BRAF/NRAS mutation). Tumors of good prognosis expressed markedly a large number of markers of T cell cytotoxicity, dendritic cells, macrophages, NK CD56 dim cells and genes coding for checkpoint co-inhibitor molecules (Table 1). They also had upregulation of β-catenin suppressors3 and downregulated β-catenin itself (Table 1). By contrast, poor prognosis tumors (the largest group) lacked both innate and adaptive immunity, and had activation of canonical β-catenin signaling (CTNNB1, its targets and WNT receptors) and WNT-independent β-catenin signaling (Table 1). Conclusion In a large subset of this population-based cohort of primary tumors, we report evidence of immune evasion through β-catenin signaling pathway. These results obtained from archival material suggest that transcriptomic profiling is a viable alternative to flow cytometry in understanding tumor biology and in determining the effectiveness of immunotherapies. Table 1.Immune scores and β-catenin signaling in good/bad prognosis groupsGene expression derived characteristicGood prognosisBad prognosis A. Immune scores from gene expressionCytotoxic T cell (e.g. GZMA, GZMH, KLRB1, KILRD1)updownDendritic cells (e.g. CD1B, CCL13, CCL22, IDO1, IDO2)updownNK CD56 dim (e.g. IL21R, GZMB, KIR2DS5, KIR3DL1)updownMacrophages (e.g. PTGDS, GM2A, CD68, SC5, ATG7)updownB. Checkpoint moleculesPDL1updownCTLA4updownVISTAupdownTIM3updownLAG3updownBTLAupdownC. β-catenin inhibitorsupdownDKK2 (secreted)updownDKK3 (secreted)updownSFRP2 (secreted)updownAXIN2 (intracellular)updownNKD2 (intracellular)updownD. β-catenin, its targets and WNT receptorsCTNNB1 (β-catenin)downupDVL1, DVL2, DVL3downupTCF12, TCF1downupAPC2, APC,c-MyCdownupFZ5, FZ9downupE. WNT-independent β-catenin signaling FGFR4downupPYGO1downupBCL9downupFOXM1downupNUP98downupSMAD4downup References 1. Bindea et al. 2013. Immunity 39 (4): 782-95. 2. Spranger et al. (2015). Nature 523:231-5. 3. MacDonald et al. (2009). Developmental Cell 17(1): 9-26. Citation Format: Jeremie Nsengimana, Sathya Muralidhar, Joanna Pozniak, Jon P. Laye, D T. Bishop, Julia A. Newton-Bishop. Immune cell profiles and β-catenin signaling in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4006. doi:10.1158/1538-7445.AM2017-4006</jats:p

Deep-learning enabled combined measurement of tumour cell density and tumour infiltrating lymphocyte density as a prognostic biomarker in colorectal cancer

BACKGROUND: Within the colorectal cancer (CRC) tumour microenvironment, tumour infiltrating lymphocytes (TILs) and tumour cell density (TCD) are recognised prognostic markers. Measurement of TILs and TCD using deep-learning (DL) on haematoxylin and eosin (HE) whole slide images (WSIs) could aid management. METHODS: HE WSIs from the primary tumours of 127 CRC patients were included. DL was used to quantify TILs across different regions of the tumour and TCD at the luminal surface. The relationship between TILs, TCD, and cancer-specific survival was analysed. RESULTS: Median TIL density was higher at the invasive margin than the luminal surface (963 vs 795 TILs/mm , P = 0.010). TILs and TCD were independently prognostic in multivariate analyses (HR 4.28, 95% CI 1.87-11.71, P = 0.004; HR 2.72, 95% CI 1.19-6.17, P = 0.017, respectively). Patients with both low TCD and low TILs had the poorest survival (HR 10.0, 95% CI 2.51-39.78, P = 0.001), when compared to those with a high TCD and TILs score. CONCLUSIONS: DL derived TIL and TCD score were independently prognostic in CRC. Patients with low TILs and TCD are at the highest risk of cancer-specific death. DL quantification of TILs and TCD could be used in combination alongside other validated prognostic biomarkers in routine clinical practice

Abstract 3388: Copy number alteration in primary melanoma

Abstract The systematic analysis of the genomic characteristics of melanoma primaries has been infeasible given the limited size of these formalin-fixed paraffin embedded (FFPE) lesions. Further studying a clearly ascertained, deeply phenotyped patient population allows meaningful extrapolation of the prevalence of distinct genomic features and investigation of the association of these features with lifestyle exposures and germline profiles. For these reasons, we focused on a recently recruited patient cohort, the Leeds Melanoma Cohort (LMC) consisting of 2184 recruits from a distinct geographical region of Northern England; the only selection applied to recruitment was to only include those whose melanoma was less than 0.75 mm Breslow thickness in the early years of recruitment. Tumor samples from 703 cases have been analyzed for genome-wide gene expression (Pozniak et al, this meeting). For this study, we wanted to explore the prevalence of copy number alterations (CNA) and the mutation profile of tumors (reflecting the association of C&amp;gt;T mutations with UV exposure, the primary environmental risk factor) and so we have adopted a next-generation sequencing (NGS) approach. Tumor blocks were recovered from local pathology laboratories for those cases already deceased at the time that this CNA analysis was initiated plus those surviving more than 5 years post diagnosis at this same time. Blocks at risk of being compromised for clinical purposes by sampling for this research study were excluded from sampling; this amounted to almost 50% of identified samples. A total of 333 NGS libraries were sequenced on an Illumina GAII or HiSeq sequencer to produce &amp;gt;100bp paired-end reads (either 5 or 1 per lane). DNA reads were aligned and mapped achieving approximately 1.8x coverage (9.4x for those at 1 per lane); the number of reads falling within each 10kb window was adjusted for GC content and mappability and compared to a composite normal FFPE sample to determine local copy number. We adopted various approaches to assess the informativeness of the methodology. (i) Replicate samples showed high reproducibility (all p &amp;lt; 0.0001). (ii) Focused analysis of the CDKN2A region with segmentation analyses to determine CNA breakpoints yielded high quality, biologically plausible data revealing multiple copy number events. 67% of samples showed no CNA across the 4 Mb region covering CDKN2A while, as expected, only a small proportion of CNAs did not involve CDKN2A. Four common distinct patterns were observed. Copy number loss ranged from 20kb to &amp;gt; 4 Mb. (iii) A germline CNA could reliably be identified from the tumor data. (iv) CDKN2A expression levels correlated with estimated copy number. We have shown that small FFPE melanomas can be characterized for genomic alterations using NGS opening up the potential for studies associating epidemiological and germline profile with the resulting tumor. 1. Newton-Bishop, J.A., et al. (2009) J Clin Oncol, 27, 5439-5444. Funded by Worldwide Cancer Research and Cancer Research UK. Citation Format: D. Timothy Bishop, Anastasia Filia, Alastair Droop, Joey Diaz, Mark Harland, Jon Laye, Juliette Randerson-Moor, Julia A. Newton-Bishop. Copy number alteration in primary melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3388. doi:10.1158/1538-7445.AM2017-3388</jats:p

High-Resolution Copy Number Patterns From Clinically Relevant FFPE Material

AbstractSystematic tumour profiling is essential for biomarker research and clinically for assessing response to therapy. Solving the challenge of delivering informative copy number (CN) profiles from formalin-fixed paraffin embedded (FFPE) material, the only likely readily available biospecimen for most cancers, involves successful processing of small quantities of degraded DNA. To investigate the potential for analysis of such lesions, whole-genome CNVseq was applied to 300 FFPE primary tumour samples, obtained from a large-scale epidemiological study of melanoma. The quality and the discriminatory power of CNVseq was assessed. Libraries were successfully generated for 93% of blocks, with input DNA quantity being the only predictor of success (success rate dropped to 65% if &lt;20 ng available); 3% of libraries were dropped because of low sequence alignment rates. Technical replicates showed high reproducibility. Comparison with targeted CN assessment showed consistency with the Next Generation Sequencing (NGS) analysis. We were able to detect and distinguish CN changes with a resolution of ≤10 kb. To demonstrate performance, we report the spectrum of genomic CN alterations (CNAs) detected at 9p21, the major site of CN change in melanoma. This successful analysis of CN in FFPE material using NGS provides proof of principle for intensive examination of population-based samples.</jats:p

High-Resolution Copy Number Patterns From Clinically Relevant FFPE Material

Systematic tumour profiling is essential for biomarker research and clinically for assessing response to therapy. Solving the challenge of delivering informative copy number (CN) profiles from formalin-fixed paraffin embedded (FFPE) material, the only likely readily available biospecimen for most cancers, involves successful processing of small quantities of degraded DNA. To investigate the potential for analysis of such lesions, whole-genome CNVseq was applied to 300 FFPE primary tumour samples, obtained from a large-scale epidemiological study of melanoma. The quality and the discriminatory power of CNVseq was assessed. Libraries were successfully generated for 93% of blocks, with input DNA quantity being the only predictor of success (success rate dropped to 65% if <20 ng available); 3% of libraries were dropped because of low sequence alignment rates. Technical replicates showed high reproducibility. Comparison with targeted CN assessment showed consistency with the Next Generation Sequencing (NGS) analysis. We were able to detect and distinguish CN changes with a resolution of ≤10 kb. To demonstrate performance, we report the spectrum of genomic CN alterations (CNAs) detected at 9p21, the major site of CN change in melanoma. This successful analysis of CN in FFPE material using NGS provides proof of principle for intensive examination of population-based samples.status: publishe