Systemic inflammation, the peripheral blood transcriptome and primary melanoma

Peripheral blood transcriptomes from 383 newly-diagnosed melanoma patients were subjected to differential gene expression analysis. The hypotheses were that impaired systemic immunity is associated with poorer prognosis (thicker tumors and fewer tumor infiltrating lymphocytes (TILs)) and evidence of systemic inflammation (high-sensitivity C-reactive protein (hsCRP) and fibrinogen levels). Higher fibrinogen levels were associated with thicker primaries. In single gene analysis hsCRP levels were significantly associated with higher blood CD274 expression, (coding for PD-L1), but each was independently prognostic, with hsCRP associated with increased mortality, and higher CD274 protective, independent of age. Pathway analysis identified downregulation of immune cell signalling pathways in the blood of people with thicker tumors and notable upregulation of STAT1 in people with brisk TILs. Transcriptomic data provided evidence for increased NFB signalling with higher inflammatory markers but with reduction in expression of HLA class II molecules and higher CD274 suggesting that aberrant systemic inflammation is a significant mediator of reduced immune function in melanoma. In summary, transcriptomic data revealed evidence of reduced immune function in patients with thicker tumors and fewer TILs, at diagnosis. Inflammatory markers were associated with thicker primaries and independently with death from melanoma suggesting that systemic inflammation contributes to that reduced immune function.

Temporal gene signature of myofibroblast transformation in Peyronie's disease: first insights into the molecular mechanisms of irreversibility

BACKGROUND

Transformation of resident fibroblasts to profibrotic myofibroblasts in the tunica albuginea is a critical step in the pathophysiology of Peyronie's disease (PD). We have previously shown that myofibroblasts do not revert to the fibroblast phenotype and we suggested that there is a point of no return at 36 hours after induction of the transformation. However, the molecular mechanisms that drive this proposed irreversibility are not known.

AIM

Identify molecular pathways that drive the irreversibility of myofibroblast transformation by analyzing the expression of the genes involved in the process in a temporal fashion.

METHODS

Human primary fibroblasts obtained from tunica albuginea of patients with Peyronie's disease were transformed to myofibroblasts using transforming growth factor beta 1 (TGF-β1). The mRNA of the cells was collected at 0, 24, 36, 48, and 72 hours after stimulation with TGF-β1 and then analyzed using a Nanostring nCounter Fibrosis panel. The gene expression results were analyzed using Reactome pathway analysis database and ANNi, a deep learning-based inference algorithm based on a swarm approach.

OUTCOMES

The study outcome was the time course of changes in gene expression during transformation of PD-derived fibroblasts to myofibroblasts.

RESULTS

The temporal analysis of the gene expression revealed that the majority of the changes at the gene expression level happened within the first 24 hours and remained so throughout the 72-hour period. At 36 hours, significant changes were observed in genes involved in MAPK-Hedgehog signaling pathways.

CLINICAL TRANSLATION

This study highlights the importance of early intervention in clinical management of PD and the future potential of new drugs targeting the point of no return.

STRENGTHS AND LIMITATIONS

The use of human primary cells and confirmation of results with further RNA analysis are the strengths of this study. The study was limited to 760 genes rather than the whole transcriptome.

CONCLUSION

This study is to our knowledge the first analysis of temporal gene expression associated with the regulation of the transformation of resident fibroblasts to profibrotic myofibroblasts in PD. Further research is warranted to investigate the role of the MAPK-Hedgehog signaling pathways in reversibility of PD.

Global Trends in the Prevalence of Alcohol Consumption Among School-Going Adolescents Aged 12-15 Years

PURPOSE

Adolescent alcohol consumption is detrimental to multiple facets of health. However, there is a scarcity of data available on time trends in adolescents' alcohol consumption particularly from non-Western countries and low- and middle-income countries. Thus, we examined the temporal trend of alcohol use in a large representative sample of school-going adolescents aged 12-15 years from 22 countries in Africa, Asia, and the Americas.

METHODS

Data from the Global School-based Student Health Survey were analyzed. Alcohol consumption referred to consuming alcohol on at least one day in the past 30 days. Crude linear trends of past 30-day alcohol consumption by country were assessed by linear regression models.

RESULTS

Data on 135,426 adolescents aged 12-15 years were analyzed [mean (standard deviation) age 13.8 (1.0) years; 52.0% females]. The overall mean prevalence of past 30-day alcohol consumption was 14.1%. Of the 22 countries included in the study, increasing, decreasing, and stable trends were observed in 3, 8, and 11 countries, respectively. Specifically, significant increases were observed in Benin between 2009 (16.1%) and 2016 (38.6%), Myanmar between 2007 (0.9%) and 2016 (3.6%), and Vanuatu between 2011 (7.6%) and 2016 (12.2%). The most drastic decrease was observed in Samoa between 2011 (34.5%) and 2017 (9.8%), but the rate of decrease was modest in most countries.

DISCUSSION

Among school-going adolescents, decreasing trends in alcohol consumption were more common than increasing trends, but the rate of decrease was limited in most countries, suggesting that more global action is required to curb adolescent alcohol consumption.

Molecular signatures of cortical expansion in the human fetal brain

The third trimester of human gestation is characterised by rapid increases in brain volume and cortical surface area. A growing catalogue of cells in the prenatal brain has revealed remarkable molecular diversity across cortical areas.1,2 Despite this, little is known about how this translates into the patterns of differential cortical expansion observed in humans during the latter stages of gestation. Here we present a new resource, μBrain, to facilitate knowledge translation between molecular and anatomical descriptions of the prenatal developing brain. Built using generative artificial intelligence, μBrain is a three-dimensional cellular-resolution digital atlas combining publicly-available serial sections of the postmortem human brain at 21 weeks gestation3 with bulk tissue microarray data, sampled across 29 cortical regions and 5 transient tissue zones.4 Using μBrain, we evaluate the molecular signatures of preferentially-expanded cortical regions during human gestation, quantified in utero using magnetic resonance imaging (MRI). We find that differences in the rates of expansion across cortical areas during gestation respect anatomical and evolutionary boundaries between cortical types5 and are founded upon extended periods of upper-layer cortical neuron migration that continue beyond mid-gestation. We identify a set of genes that are upregulated from mid-gestation and highly expressed in rapidly expanding neocortex, which are implicated in genetic disorders with cognitive sequelae. Our findings demonstrate a spatial coupling between areal differences in the timing of neurogenesis and rates of expansion across the neocortical sheet during the prenatal epoch. The μBrain atlas is available from: https://garedaba.github.io/micro-brain/ and provides a new tool to comprehensively map early brain development across domains, model systems and resolution scales.

Automated identification of abnormal infant movements from smart phone videos

Cerebral palsy (CP) is the most common cause of physical disability during childhood, occurring at a rate of 2.1 per 1000 live births. Early diagnosis is key to improving functional outcomes for children with CP. The General Movements (GMs) Assessment has high predictive validity for the detection of CP and is routinely used in high-risk infants but only 50% of infants with CP have overt risk factors when they are born. The implementation of CP screening programs represents an important endeavour, but feasibility is limited by access to trained GMs assessors. To facilitate progress towards this goal, we report a deep-learning framework for automating the GMs Assessment. We acquired 503 videos captured by parents and caregivers at home of infants aged between 12- and 18-weeks term-corrected age using a dedicated smartphone app. Using a deep learning algorithm, we automatically labelled and tracked 18 key body points in each video. We designed a custom pipeline to adjust for camera movement and infant size and trained a second machine learning algorithm to predict GMs classification from body point movement. Our automated body point labelling approach achieved human-level accuracy (mean ± SD error of 3.7 ± 5.2% of infant length) compared to gold-standard human annotation. Using body point tracking data, our prediction model achieved a cross-validated area under the curve (mean ± S.D.) of 0.80 ± 0.08 in unseen test data for predicting expert GMs classification with a sensitivity of 76% ± 15% for abnormal GMs and a negative predictive value of 94% ± 3%. This work highlights the potential for automated GMs screening programs to detect abnormal movements in infants as early as three months term-corrected age using digital technologies.

Global time trends of perceived loneliness among adolescents from 28 countries in Africa, Asia, and the Americas

BACKGROUND

Perceived loneliness in adolescence is associated with a plethora of adverse outcomes. However, data on its temporal trends are scarce. Therefore, we aimed to examine the temporal trend of perceived loneliness among school-going adolescents aged 12-15 years from 28 countries in Africa, Asia, and the Americas, where temporal trends of loneliness are largely unknown.

METHODS

Cross-sectional data from the Global School-based Student Health Survey 2003-2017 were analyzed. Perceived loneliness referred to feeling lonely most of the time or always in the past 12 months. Crude linear trends of perceived loneliness by country were assessed by linear regression models.

RESULTS

Data on 180,087 adolescents aged 12-15 years were analyzed [Mean (SD) age 13.7 (1.0) years; 51.4 % females]. The overall prevalence of perceived loneliness was 10.7 %. Among the 28 countries included in the study, significant increasing and decreasing trends were observed in six counties each, with stable trends found in 16 countries. The most drastic increase and decrease were observed in Egypt between 2006 (7.9 %) and 2011 (14.3 %), and in Samoa between 2011 (23.3 %) and 2017 (8.0 %), respectively. Stable trends with high prevalence across time were also common.

CONCLUSION

Our data suggest that perceived loneliness among adolescents is a global phenomenon, which has seen little improvement if any in recent years. It would be prudent to implement nationwide policies to combat loneliness globally.

Unravelling transcriptomic complexity in breast cancer through modulation of DARPP-32 expression and signalling pathways

DARPP-32 is a key regulator of protein-phosphatase-1 (PP-1) and protein kinase A (PKA), with its function dependent upon its phosphorylation state. We previously identified DKK1 and GRB7 as genes with linked expression using Artificial Neural Network (ANN) analysis; here, we determine protein expression in a large cohort of early-stage breast cancer patients. Low levels of DARPP-32 Threonine-34 phosphorylation and DKK1 expression were significantly associated with poor patient prognosis, while low levels of GRB7 expression were linked to better survival outcomes. To gain insight into mechanisms underlying these associations, we analysed the transcriptome of T47D breast cancer cells following DARPP-32 knockdown. We identified 202 differentially expressed transcripts and observed that some overlapped with genes implicated in the ANN analysis, including PTK7, TRAF5, and KLK6, amongst others. Furthermore, we found that treatment of DARPP-32 knockdown cells with 17β-estradiol or PKA inhibitor fragment (6-22) amide led to the differential expression of 193 and 181 transcripts respectively. These results underscore the importance of DARPP-32, a central molecular switch, and its downstream targets, DKK1 and GRB7 in breast cancer. The discovery of common genes identified by a combined patient/cell line transcriptomic approach provides insights into the molecular mechanisms underlying differential breast cancer prognosis and highlights potential targets for therapeutic intervention.

Association between food insecurity and depressive symptoms among adolescents aged 12-15 years from 22 low- and middle-income countries

Food insecurity may be a risk factor for depression in adolescents. However, data on this topic from low- and middle-income countries (LMICs) are scarce, despite food insecurity being most common in LMICs. Therefore, we aimed to examine the association between food-insecurity and depressive symptoms among school-going adolescents from 22 LMICs. Cross-sectional data from the Global school-based Student Health Survey were analyzed. Self-report measures assessed past 12-month depressive symptoms and past 30-day food insecurity (hunger). Multivariable logistic regression and meta-analysis were conducted to assess associations. Data on 48,401 adolescents aged 12-15 years were analyzed [mean (SD) age 13.8 (0.9) years; 51.4 % females]. The prevalence of depressive symptoms was 29.3 %, and those of moderate and severe food insecurity were 45.0 and 6.3 %, respectively. After adjustment for potential confounders, compared to no food insecurity, the pooled OR (95 %CI) of moderate and severe food insecurity were 1.36 (1.30-1.42) and 1.81 (1.67-1.97), respectively. The level of between-country heterogeneity was low. Food insecurity was associated with significantly higher odds for depressive symptoms among adolescents in LMICs. Policies to address food insecurity may also help prevent depression in this population, pending future longitudinal research.

The impact of metabolic endotoxaemia on the browning process in human adipocytes

BACKGROUND

Dysfunctional adipose tissue (AT) is known to contribute to the pathophysiology of metabolic disease, including type 2 diabetes mellitus (T2DM). This dysfunction may occur, in part, as a consequence of gut-derived endotoxaemia inducing changes in adipocyte mitochondrial function and reducing the proportion of BRITE (brown-in-white) adipocytes. Therefore, the present study investigated whether endotoxin (lipopolysaccharide; LPS) directly contributes to impaired human adipocyte mitochondrial function and browning in human adipocytes, and the relevant impact of obesity status pre and post bariatric surgery.

METHODS

Human differentiated abdominal subcutaneous (AbdSc) adipocytes from participants with obesity and normal-weight participants were treated with endotoxin to assess in vitro changes in mitochondrial function and BRITE phenotype. Ex vivo human AbdSc AT from different groups of participants (normal-weight, obesity, pre- and 6 months post-bariatric surgery) were assessed for similar analyses including circulating endotoxin levels.

RESULTS

Ex vivo AT analysis (lean & obese, weight loss post-bariatric surgery) identified that systemic endotoxin negatively correlated with BAT gene expression (p < 0.05). In vitro endotoxin treatment of AbdSc adipocytes (lean & obese) reduced mitochondrial dynamics (74.6% reduction; p < 0.0001), biogenesis (81.2% reduction; p < 0.0001) and the BRITE phenotype (93.8% reduction; p < 0.0001). Lean AbdSc adipocytes were more responsive to adrenergic signalling than obese AbdSc adipocytes; although endotoxin mitigated this response (92.6% reduction; p < 0.0001).

CONCLUSIONS

Taken together, these data suggest that systemic gut-derived endotoxaemia contributes to both individual adipocyte dysfunction and reduced browning capacity of the adipocyte cell population, exacerbating metabolic consequences. As bariatric surgery reduces endotoxin levels and is associated with improving adipocyte functionality, this may provide further evidence regarding the metabolic benefits of such surgical interventions.

Refining the definition of HER2-low class in invasive breast cancer

BACKGROUND

Emerging evidence indicates that breast cancer (BC) patients whose tumours express HER2 protein without HER2 gene amplification (HER2-low), can benefit from antibody-drug conjugates (ADC). However, the current definition of HER2-low BC remains incomplete with low rates of concordance. This study aims to refine HER2-low definition with emphasis on distinguishing HER2 score 0 from score 1+ to identify patients who are eligible for ADC.

METHODS

A BC cohort (n = 363) with HER2 IHC scores 0, 1+ and 2+ (without HER2 gene amplification) and available HER2 mRNA was included. HER2 staining intensity, pattern and subcellular localisation were reassessed. Artificial neural network analysis was applied to cluster the cohort and to distinguish HER2 score 0 from 1+. Reproducibility and reliability of the refined criteria were tested.

RESULTS

HER2 IHC score 1+ was refined as membranous staining in invasive cells as either: (1) faint intensity in ≥ 20% of cells regardless the circumferential completeness, (2) weak complete staining in ≤ 10%, (3) weak incomplete staining in > 10% and (4) moderate incomplete staining in ≤ 10%. Based on this, 63% of the HER2-negative cases were reclassified as positive (HER2-low). The refined score showed perfect observer agreement compared to the moderate agreement in the original clinical scores. Similar results were generated when the refined score was applied on the independent BC cohorts. A proposal to refine the definition of other HER2 classes is presented.

CONCLUSION

This study refined the definition of HER2-low BC based on correlation with HER2 mRNA and distinguished between HER2 IHC score 1+ and score 0 tumours.

Brain charts for the human lifespan

Over the past few decades, neuroimaging has become a ubiquitous tool in basic research and clinical studies of the human brain. However, no reference standards currently exist to quantify individual differences in neuroimaging metrics over time, in contrast to growth charts for anthropometric traits such as height and weight1. Here we assemble an interactive open resource to benchmark brain morphology derived from any current or future sample of MRI data ( http://www.brainchart.io/ ). With the goal of basing these reference charts on the largest and most inclusive dataset available, acknowledging limitations due to known biases of MRI studies relative to the diversity of the global population, we aggregated 123,984 MRI scans, across more than 100 primary studies, from 101,457 human participants between 115 days post-conception to 100 years of age. MRI metrics were quantified by centile scores, relative to non-linear trajectories2 of brain structural changes, and rates of change, over the lifespan. Brain charts identified previously unreported neurodevelopmental milestones3, showed high stability of individuals across longitudinal assessments, and demonstrated robustness to technical and methodological differences between primary studies. Centile scores showed increased heritability compared with non-centiled MRI phenotypes, and provided a standardized measure of atypical brain structure that revealed patterns of neuroanatomical variation across neurological and psychiatric disorders. In summary, brain charts are an essential step towards robust quantification of individual variation benchmarked to normative trajectories in multiple, commonly used neuroimaging phenotypes.

Ulcerated melanoma: Systems biology evidence of inflammatory imbalance towards pro-tumourigenicity

Microscopic ulceration is an independent predictor of melanoma death. Here, we used systems biology to query the role of host and tumour-specific processes in defining the phenotype. Albumin level as a measure of systemic inflammation was predictive of fewer tumour-infiltrating lymphocytes and poorer survival in the Leeds Melanoma Cohort. Ulcerated melanomas were thicker and more mitotically active (with corresponding transcriptomic upregulated cell cycle pathways). Sequencing identified tumoural p53 and APC mutations, and TUBB2B amplification as associated with the phenotype. Ulcerated tumours had perturbed expression of cytokine genes, consistent with protumourigenic inflammation and histological and transcriptomic evidence for reduced adaptive immune cell infiltration. Pathway/network analysis of multiomic data using neural networks highlighted a role for the β-catenin pathway in the ulceration, linking genomic changes in the tumour to immunosuppression and cell proliferation. In summary, the data suggest that ulceration is in part associated with genomic changes but that host factors also predict melanoma death with evidence of reduced immune responses to the tumour.

Abstract P1-08-19: Utilising artificial intelligence (AI) for analysing multiplex genomic and magnetic resonance imaging (MRI) data to develop multimodality predictive system for personalised neoadjuvant treatment of breast cancer (BC)

Background: No effective tool is available to predict response to neoadjuvant chemotherapy (NACT). Aim: to enable an accurate prediction of the treatment response for BC patients, with the aid of machine learning based analysis of tumour histopathological, molecular & imaging features before NACT. Methods: The baseline biopsies were immunohistochemistry (IHC) stained for ER, PR, HER2, Ki67 & SPAG5 and genomically analysed. To build up a genomic profiler & multiplex analysis, a tailored mRNA code set of 450 genes was designed using NanoString nCounter Flex Analysis System. In addition, samples have been analysed for currently used prognostic & predictive genomic panels including: Oncotype DX [Genomic Health], MammaPrint [Agendia], Prosigna [Nanostring Technologies] & MD Anderson Genomic Chemo Sensitivity Predictor. The imaging features were extracted from MRI using radiomics measurements and deep learning methods. Our predictive models were trained in a local cohort of 400 BC (300 HER2 negative (HER2-) received 8 cycles of anthracycline & Taxane & 100 HER2 positive (HER2+) received Trastuzumab, anthracycline &Taxane) & was validated in 150 patients from local clinical trial patients. I-SPY-1 clinal trial genomic & imaging data were used as an external validation. The pathological complete response (pCR) defined as absence of tumor cells in both breast & lymph node was used as endpoint. Results: Compared to HER- BC, HER2+ BC had higher expression of GRB7, ERBB2, SPAG5, FGRF4 & CDC6. While HER2 negative BC showed higher level of CCND1, CDK6, FOXM1, FOXC1, MAI, MYC, ANP32E, SFRP1, ACTR3B, RAD51AP1, MCM3, LIN9, CDCA7 & PMAIP1 (Table 1). In both HER2 positive and negative BC; the reduction of &gt;70% in tumour volume (OR (95% CI)=1.72 (1.35-2.7, p&lt;0.0001) & 1.87 (1.44-2.42, p&lt;0.0001);respectively), high mitotic count (OR (95% CI)=2.6 (1.73-3.91), p&lt;0.0001) & 1.98 (1.49-2.65), p&lt;0.000);respectively), ER- (OR (95% CI)=0.51 (0.41-0.64); p&lt;0.0001 & 0.53 (0.42-0.68; p&lt;0.0001; respectively, IHC), PR- (OR (95% CI)=0.67 (0.57-0.80: p&lt;0.0001 & 0.62 (0.51-0.77; p&lt;0.0001; respectively, IHC), SPAG5+ (OR (95% CI)=2.36 ( 1.77-3.15; p&lt;0.0001) & 2.15 (1.51-3.06); p=&lt;0.0001); respectively, IHC) and over-expressions of ERBB2 (OR (95% CI)=3.51 (2.26-5.45) & 3.32 (2.15-5.10) ; ps&lt;0.0001, respectively), EGFR (OR (95% CI)=1.43. (1.01-2.03; p=0.004) & 1.48 (1.16-1.89); p=0.002; respectively), GRB7 (OR (95% CI)= 3.78 (2.52-5.64) & 3.56 (2.39-5.29); respectively, ps&lt;0.0001), and CDC6 (OR (95% CI)=2.19 1.65-2.90; p=0.0002 & 2.1 (1.60-2.77); p=0.0005; respectively) were associated with higher pCR after receiving NACT. In HER2+ BC, the differential expression of DLC1, EBB4, RUNDC1, ARHGEF9 & PIK3CD were associated with higher response to Trastuzumab (ps&lt;0.01).In HER2- BC: the intensity of histogram skewness in MRI (p=0.03) and low expression of CXXC5, AR, TGFB3, TACC3, TUBA4A, AGR2, ESR1, TP73 and BAG1 were associated with high response to chemotherapy (ps&lt;0.01). Integrated models were developed for predicting response to NACT of HER2- BC (AUC (95% CI)= 0.83 (0.76-0.91; p&lt;0.0001) & to chemotherapy plus Trastuzumab in HER2+ BC (AUC (95% CI) = 0.79 (0.67-0.91; p&lt;0.0001). Conclusions: A predictive model was developed for HER2+ and another for HER2- BC with &gt;= 80% accuracy prediction of pCR. AI & multiplex technology could enable robust biomarker discovery.

ORLower 95% CIUpper 95% CIAdjusted pGRB7-mRNA9.986.7714.706.76E-24ERBB2-mRNA7.765.3011.401.12E-20FOXC1-mRNA0.100.060.166.44E-19MIA-mRNA0.180.110.282.63E-12ANP32E-mRNA0.500.410.622.30E-09MYC-mRNA0.520.410.678.82E-07SFRP1-mRNA0.310.190.491.65E-06CD99-mRNA1.481.261.732.73E-06SPAG5-mRNA1.891.452.474.68E-06PMAIP1-mRNA0.510.390.685.03E-06CDK6-mRNA0.520.390.699.09E-06FGFR4-mRNA2.621.733.979.21E-06CDCA7-mRNA0.400.270.591.13E-05LIN9-mRNA0.610.490.761.25E-05CDC6-mRNA1.941.452.591.44E-05MCM3-mRNA0.660.550.801.55E-05RAD51AP1-mRNA0.570.450.731.58E-05CCND1-mRNA0.450.310.641.93E-05FOXM1-mRNA0.510.380.681.97E-05

Citation Format: Tarek Ma Abdel-Fatah, Graham Ball, Xin Chen, Dalia Mehaisi, Elisabetta Giannotti, Dorothee Auer, Jayakumar Vadakekolathu, Ruizhe Li, Graham Pockley, Stephen Chan. Utilising artificial intelligence (AI) for analysing multiplex genomic and magnetic resonance imaging (MRI) data to develop multimodality predictive system for personalised neoadjuvant treatment of breast cancer (BC) [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-08-19.

Aligned Poly-l-lactic Acid Nanofibers Induce Self-Assembly of Primary Cortical Neurons into 3D Cell Clusters

Relative to two-dimensional (2D) culture, three-dimensional (3D) culture of primary neurons has yielded increasingly physiological responses from cells. Electrospun nanofiber scaffolds are frequently used as a 3D biomaterial support for primary neurons in neural tissue engineering, while hydrophobic surfaces typically induce aggregation of cells. Poly-l-lactic acid (PLLA) was electrospun as aligned PLLA nanofiber scaffolds to generate a structure with both qualities. Primary cortical neurons from E18 Sprague-Dawley rats cultured on aligned PLLA nanofibers generated 3D clusters of cells that extended highly aligned, fasciculated neurite bundles within 10 days. These clusters were viable for 28 days and responsive to AMPA and GABA. Relative to the 2D culture, the 3D cultures exhibited a more developed profile; mass spectrometry demonstrated an upregulation of proteins involved in cortical lamination, polarization, and axon fasciculation and a downregulation of immature neuronal markers. The use of artificial neural network inference suggests that the increased formation of synapses may drive the increase in development that is observed for the 3D cell clusters. This research suggests that aligned PLLA nanofibers may be highly useful for generating advanced 3D cell cultures for high-throughput systems.

Prognostic significance of receptor expression discordance between primary and recurrent breast cancers: a meta-analysis

PURPOSE

This meta-analysis aimed to investigate whether receptor (estrogen receptor [ER], progesterone receptor [PR], and human epidermal growth factor receptor 2 [HER2]) discordances between primary and recurrent breast cancers affect patients' survival.

METHODS

Search terms contained ER, PR, and HER2 status details in both primary and recurrent tumors (local recurrence or distant metastasis) in addition to survival outcome data (overall survival [OS] or post-recurrence survival [PRS]).

RESULTS

Loss of ER or PR in recurrent tumors was significantly associated with shorter OS as compared with receptor-positive concordance (hazard ratio [HR], 1.67; 95% confidence interval [% CI] 1.37-2.04; p < 0.00001 and HR, 1.45; 95% CI 1.21-1.75; p < 0.0001, respectively). Similar trends were observed in groups with only distant metastasis. Gain of ER was a significant predictor of longer PRS as compared with receptor-negative concordance (HR, 0.76; 95% CI 0.59-0.97; p = 0.03). Gain of PR was not a significant predictor of longer survival compared with receptor-negative concordance, but it could be related to better OS at distant metastasis. Both HER2 of loss and gain could be related to poor outcomes.

CONCLUSION

This meta-analysis showed that receptor conversion in recurrent tumors may affect patient survival as compared with receptor concordance.

Visual assessment of mitotic figures in breast cancer: a comparative study between light microscopy and whole slide images

BACKGROUND AND AIMS

Visual assessment of mitotic figures in breast cancer (BC) remains a challenge. This is expected to be more pronounced in the digital pathology era. This study aims to refine the criteria of mitotic figure recognition, particularly in whole slide images (WSI).

METHOD AND RESULTS

Haematoxylin and eosin (H&E)-stained BC sections (n = 506) were examined using light microscopy (LM) and WSI. A set of features for identifying mitosis in WSI and to distinguish true figures from mimickers was developed. Changes in the mitotic count between the two platforms was explored. Morphological features of mitoses were recorded separately, including absence of nuclear membrane, chromatin hairy-like projections, shape, cytoplasmic features, mitotic cell size and relationship to surrounding cells. Each mitotic phase has its own mimickers. Fifty-eight per cent of mitoses showed absent hairy-like projection in WSI; however, 89% retained their ragged nuclear border, which distinguished them from mimickers including apoptotic cells, lymphocytes and dark elongated hyperchromatic structures. Mitosis in WSI showed loss of fine details, and there was a 20% average reduction rate of mitotic counts when compared to the same area on LM. Using refined mitosis recognition criteria in WSI resulted in a twofold improvement of interobserver concordance. However, when compared to LM, 19% of cases were underscored in WSIs.

CONCLUSIONS

All morphological features of mitosis should be considered to enable recognition and differentiation from their mimickers, particularly in WSI, to ensure reliable BC grading. Refining mitotic cut-offs per specific area when using WSI, based on the degree of reduction and association with outcome, is warranted.

α)

AIMS

The mechanisms that drive breast cancer (BC) progression and poor outcome are not fully understood. The human heat shock protein 90 alpha family class A member 1 (HSP90α) encoded by the HSP90ΑA1 gene has a vital role in cellular responses to stress and is implicated in the development and progression of many cancers. The current study aims to explore the clinical and prognostic importance of HSP90α in BC.

METHODS

The Molecular Taxonomy of Breast Cancer International Consortium (n=1980); The Cancer Genome Atlas (n=1097) and the Breast Cancer Gene-Expression Miner (Bc-GenExMiner) BC datasets (n=5056) were used to evaluate HSP90ΑA1 mRNA expression. HSP90α protein expression was further assessed using immunohistochemistry in a large (n=911) well-characterised BC series. The association between mRNA and protein expressions with other clinicopathological parameters and outcome was analysed.

RESULTS

High expression of HSP90ΑA1 both at the mRNA and protein levels was significantly associated with characteristics of BC poor prognosis, including high grade, lymphovascular invasion, poor Nottingham Prognostic Index and positive expression of p53 and PIK3CA. Outcome analysis revealed that high HSP90α protein expression is an independent predictor of shorter BC-specific survival.

CONCLUSION

HSP90α can be used as a potential prognostic marker in BC. Further mechanistic studies are warranted to determine the underlying molecular mechanisms mediated by HSP90α in BC.

Digital breast tomosynthesis: sensitivity for cancer in younger symptomatic women

OBJECTIVE

Full-field digital mammography (FFDM) has limited sensitivity for cancer in younger women with denser breasts. Digital breast tomosynthesis (DBT) can reduce the risk of cancer being obscured by overlying tissue. The primary study aim was to compare the sensitivity of FFDM, DBT and FFDM-plus-DBT in women under 60 years old with clinical suspicion of breast cancer.

METHODS

This multicentre study recruited 446 patients from UK breast clinics. Participants underwent both standard FFDM and DBT. A blinded retrospective multireader study involving 12 readers and 300 mammograms (152 malignant and 148 benign cases) was conducted.

RESULTS

Sensitivity for cancer was 86.6% with FFDM [95% CI (85.2-88.0%)], 89.1% with DBT [95% CI (88.2-90%)], and 91.7% with FFDM+DBT [95% CI (90.7-92.6%)]. In the densest breasts, the maximum sensitivity increment with FFDM +DBT over FFDM alone was 10.3%, varying by density measurement method. Overall specificity was 81.4% with FFDM [95% CI (80.5-82.3%)], 84.6% with DBT [95% CI (83.9-85.3%)], and 79.6% with FFDM +DBT [95% CI (79.0-80.2%)]. No differences were detected in accuracy of tumour measurement in unifocal cases.

CONCLUSIONS

Where available, DBT merits first-line use in the under 60 age group in symptomatic breast clinics, particularly in women known to have very dense breasts.

ADVANCES IN KNOWLEDGE

This study is one of very few to address the accuracy of DBT in symptomatic rather than screening patients. It quantifies the diagnostic gains of DBT in direct comparison with standard digital mammography, supporting informed decisions on appropriate use of DBT in this population.

Identifying playing talent in professional football using artificial neural networks

The aim of the current study was to objectively identify position-specific key performance indicators in professional football that predict out-field players league status. The sample consisted of 966 out-field players who completed the full 90 minutes in a match during the 2008/09 or 2009/10 season in the Football League Championship. Players were assigned to one of three categories (0, 1 and 2) based on where they completed most of their match time in the following season, and then split based on five playing positions. 340 performance, biographical and esteem variables were analysed using a Stepwise Artificial Neural Network approach. The models correctly predicted between 72.7% and 100% of test cases (Mean prediction of models = 85.9%), the test error ranged from 1.0% to 9.8% (Mean test error of models = 6.3%). Variables related to passing, shooting, regaining possession and international appearances were key factors in the predictive models. This is highly significant as objective position-specific predictors of players league status have not previously been published. The method could be used to aid the identification and comparison of transfer targets as part of the due diligence process in professional football.

Development of a Bioinformatics Framework for Identification and Validation of Genomic Biomarkers and Key Immunopathology Processes and Controllers in Infectious and Non-infectious Severe Inflammatory Response Syndrome

Sepsis is defined as dysregulated host response caused by systemic infection, leading to organ failure. It is a life-threatening condition, often requiring admission to an intensive care unit (ICU). The causative agents and processes involved are multifactorial but are characterized by an overarching inflammatory response, sharing elements in common with severe inflammatory response syndrome (SIRS) of non-infectious origin. Sepsis presents with a range of pathophysiological and genetic features which make clinical differentiation from SIRS very challenging. This may reflect a poor understanding of the key gene inter-activities and/or pathway associations underlying these disease processes. Improved understanding is critical for early differential recognition of sepsis and SIRS and to improve patient management and clinical outcomes. Judicious selection of gene biomarkers suitable for development of diagnostic tests/testing could make differentiation of sepsis and SIRS feasible. Here we describe a methodologic framework for the identification and validation of biomarkers in SIRS, sepsis and septic shock patients, using a 2-tier gene screening, artificial neural network (ANN) data mining technique, using previously published gene expression datasets. Eight key hub markers have been identified which may delineate distinct, core disease processes and which show potential for informing underlying immunological and pathological processes and thus patient stratification and treatment. These do not show sufficient fold change differences between the different disease states to be useful as primary diagnostic biomarkers, but are instrumental in identifying candidate pathways and other associated biomarkers for further exploration.

Prognostic significance of nucleolar assessment in invasive breast cancer

AIMS

Nucleolar morphometric features have a potential role in the assessment of the aggressiveness of many cancers. However, the role of nucleoli in invasive breast cancer (BC) is still unclear. The aims of this study were to investigate the optimal method for scoring nucleoli in IBC and their prognostic significance, and to refine the grading of breast cancer (BC) by incorporating nucleolar score.

METHODS AND RESULTS

Digital images acquired from haematoxylin and eosin-stained sections from a large BC cohort were divided into training (n = 400) and validation (n = 1200) sets for use in this study. Four different assessment methods were evaluated in the training set to identify the optimal method associated with the best performance and significant prognostic value. These were: (i) a modified Helpap method; (ii) counting prominent nucleoli (size ≥2.5 µm) in 10 field views (FVs); (iii) counting prominent nucleoli in five FVs; and (iv) counting prominent nucleoli in one FV. The optimal method was applied to the validation set and to an external validation set, i.e. data from The Cancer Genome Atlas (n = 743). Scoring prominent nucleoli in five FVs showed the highest interobserver concordance rate (intraclass correlation coefficient of 0.8) and a significant association with BC-specific survival (P < 0.0001). A high nucleolar score was associated with younger age, larger tumour size, and higher grade. Incorporation of nucleolar score in the Nottingham grading system resulted in a higher significant association with survival than the conventional grade.

CONCLUSIONS

Quantification of nucleolar prominence in five FVs is a cost-efficient and reproducible morphological feature that can predict BC behaviour and can provide an alternative to pleomorphism to improve BC grading performance.

Abstract P3-07-02: Developing a robust multidimensional molecular, pathological and radiological prognostic index (MPRPI) to evaluate the response to neoadjuvant chemotherapy (NACT) and predict clinical outcome of breast cancer (BC)

Background: Recently neoadjuvant chemotherapy (NACT) is regarded as a potential standard approach whenever chemotherapy is indicated in principle and is considered as the preferred treatment approach for stage II/III triple-negative and HER2-positive BC. However, there is an urgent need to develop a more sensitive and robust test that can assess the response for NACT and guide the optimum adjuvant therapy. Aim: Our aim is to identify molecular, radiological and histopathologic criteria that could grade response to NACT and to develop a robust prognostic index that accurately predict clinical outcome of the subsequent adjuvant therapy. Method: Comprehensive histopathological and radiological assessment of consecutive series of 850 BC [T2-4, N0-3, M0] have been centrally carried out at the Nottingham University Hospital (NUH). Furthermore, the immunohistochemistry expression of Ki67 and SPAG5 proliferation biomarkers and the histological evaluation of tumour infiltration lymphocytes (TILs) had been examined in all patients while both volumetric and texture changes detected by magnetic resonance imaging (MRI) were available for 400 cases. Oestrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) were assessed according to the most recent American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP) guidelines. The results were validated in an external cohort of 250 cases. The patient’s characteristics and treatment options are the same between the centres: (68%) has received anthracycline plus Taxane (AC+T) NACT and 32% of patients have received NACT Anthracycline only (AC). Neoadjuvant HER2 targeting agents (Trastuzumab) or (Trastuzumab + Petruzumab) had been prescribed to 16% of patients in addition to AC+T followed by adjuvant Trastuzumab (total=18 cycles). All pre-NACT ER+ patients were given at least 5 year of adjuvant endocrine therapy. The primary end point was disease free survival (DFS). The median follow up was 72 months. Results: Using multivariate Cox proportional hazards models with backward stepwise exclusion for DFS, we found the presence of TILs [(HR (95% CI): 0.68 (0.48-0.94; P=0.022], high SPAG5 expression in post-surgical tumour tissue [(HR (95% CI): 2.58 (1.19-5.63), p=0.017)], the reduction in the primary tumour volume measured by MRI (&gt;30%) [(HR(95% CI): 0.38 (0.16-0.89), p=0.026)], presence of Lymphovascular invasion [(HR(95% CI): 2.92 (1.33-6.40), p=0.008)], presence of chemotherapy induced fibrosis [(HR(95% CI): 0.41 (0.19-0.91), p=0.029)] and the high histological grade [(HR(95% CI): 2.62 (1.19-5.74), p=0.016)] showed statistical significant association with DFS. A prognostic index was calculated using the aforementioned factors after adjusting for both NACT and adjuvant therapy. The receiver-operating characteristic (ROC) curves indicated that this model is a good prognostic test [AUC = 0.854 (95% CI) = 0.777-.0.931; p= 0.00000001] and it outperformed residual cancer burden (RCB score) [AUC = 0. 711 (95% CI) = 0.612-.0.810; P= 0.0003]; and other NACT response grading systems including Miller-Payne system, Clinical-Pathologic Scoring System (CPS) and CPS-ER histological grade (CPS-EG) systems. Conclusion: A prognostic test with high sensitivity and specificity for assessing response to Neo-ACT has been developed and applying this test could guide the choice of the optimal adjuvant therapy.

Citation Format: Tarek M. a. Abdel-Fatah, Xin Chen, Ruizhe Li, Elisabetta Giannotti, Dorothee Auer, Jennifer Walker, Jun Lim, A. Graham Pockley, Graham Ball, Emad Rakhah, Ian Ellis, Arlene Chan, Stephen Chan. Developing a robust multidimensional molecular, pathological and radiological prognostic index (MPRPI) to evaluate the response to neoadjuvant chemotherapy (NACT) and predict clinical outcome of breast cancer (BC) [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-07-02.

Abstract P5-06-06: Clinically significant changes of receptors status (ER, PR and HER2) after receiving neoadjuvant chemotherapy (NACT) in breast cancer (BC) predicts the prognosis and guides the choice of the optimal adjuvant therapy (AT): Retesting of the receptor status should be mandatory

Background: NACT is a standard option for BC (T2-4, N0-3, M0) and certain BC phenotypes. The choice of AT based on the pre-NACT biomarkers status may not be optimum for individual patient because dynamic phenotypic changes induced by NACT may alter the response to treatment. Aim: The aim of this study is to determine the incidence of changes in the receptor status (ER, PR and HER2) and other proliferation biomarkers (Ki67 and SPAG5) before and after NACT and to assess the clinical significance of such changes. Methods Immunohistochemistry staining of ER, PR, HER2, Ki67 and SPAG5 in pre and post NACT tumors tissues from a consecutive series of 850 of BC (T2-4, N0-3, M0) treated at the Nottingham University Hospital (NUH) from 2000 to 2018, have been centrally evaluated according to ASCO guidelines. All cases with conversion in HER2 status had also been retested by HER2-FISH. The results were validated in an external cohort of 250 cases. Treatment options and patients characteristics are the same between the centres: (68%) received anthracycline plus Taxane (AC+T) NACT and 32% of patients have received NACT Anthracycline only (AC). Neoadjuvant HER2 targeting agents (Trastuzumab) or (Trastuzumab + Petruzumab) had been prescribed to 16% of patients in addition to AC+T followed by adjuvant Trastuzumab (total=18 cycles). All pre-NACT ER+ patients were given at least 5 year of adjuvant endocrine therapy (ET). In 2013 NUH started a prospective audit of retesting of receptor status in all post NACT surgical tumour samples. The results of the tests were presented to the weekly tumour board meeting and any change in the receptor status (ER and HER2) from negative (in the pre NACT core biopsies) to positive (in the post NACT surgical specimen) being considered for additional AT (ET for ER+ and Trastuzumab for HER2+ cases).The primary end points for this study are the % changes of biomarker changes and the disease free survival (DFS). The median follow up was 72 months. Results In pre NACT core biopsies 32% and 68% were HER2+ and HER2-; respectively. Twelve percent (12%) of the pre NACT HER2- tumours had a conversion to HER2+ in the post NACT surgical specimens. In this group of patients who subsequently received adjuvant Trastuzumab, 95% 3-year DFS was reported; which was similar to those patients who achieved pCR (3-year DFS; 90%) and was superior to cases which remained HER- in post NACT specimens (3-year DFS; 41%); (p&lt;0.0001). Furthermore, similar group of patients with pre NACT HER- tumour before the 2013 audit, who did not receive Trastuzumab for the change to post NACT HER2+ receptors, has inferior 3-year DFS to those received adjuvant Trastuzumab based on the conversion (HR (95% CI)= 7.40 (1.04-52.86); p=0.046). In pre NACT HER2+ BC, 20% of cases had been converted into HER2- in the post NACT surgical specimens. These patients had better 3y-DFS (94%) compared to those who remained HER2+ in post NACT specimens (3y-DFS=70%; HR (95% CI)= 0.86 (0.77-0.97); p=0.01). Furthermore those patients who received neoadjuvant HER2 targeting therapy had statistically higher incidence of post HER2- conversion (p=0.005) and lower level of post NACT proliferation markers (Ki67 and SPAG5); p=0.01. In pre NACT ER+/PR+ patients, those who has converted into ER+/PR- in post NACT specimens had shorter 5-year DFS (40%) in spite of receiving ET, compared to those who remained ER+/PR+ in post NACT specimen [5-DFS= 72%]; HR (95% CI)= 1.98 (1.18-3.31); p=0.009). Conclusion: To our knowledge, this is the first report, which showed the significant clinical benefit of adjuvant therapy, based on the re-testing of the standard receptors status.

Citation Format: Tarek M. a. Abdel-Fatah, Rebekah Webb, Jennifer Walker, Jun Lim, A. Graham Pockley, Graham Ball, Matthew Griffiths, Ian Ellis, Emad Rakhah, Zsolt Hodi, Andrew Lee, Arlene Chan, Stephen Chan. Clinically significant changes of receptors status (ER, PR and HER2) after receiving neoadjuvant chemotherapy (NACT) in breast cancer (BC) predicts the prognosis and guides the choice of the optimal adjuvant therapy (AT): Retesting of the receptor status should be mandatory [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-06-06.

ERCC1 Is a Predictor of Anthracycline Resistance and Taxane Sensitivity in Early Stage or Locally Advanced Breast Cancers

Genomic instability could be a beneficial predictor for anthracycline or taxane chemotherapy. We interrogated 188 DNA repair genes in the METABRIC cohort (n = 1980) to identify genes that influence overall survival (OS). We then evaluated the clinicopathological significance of ERCC1 in early stage breast cancer (BC) (mRNA expression (n = 4640) and protein level, n = 1650 (test set), and n = 252 (validation)) and in locally advanced BC (LABC) (mRNA expression, test set (n = 2340) and validation (TOP clinical trial cohort, n = 120); and protein level (n = 120)). In the multivariate model, ERCC1 was independently associated with OS in the METABRIC cohort. In ER+ tumours, low ERCC1 transcript or protein level was associated with increased distant relapse risk (DRR). In ER−tumours, low ERCC1 transcript or protein level was linked to decreased DRR, especially in patients who received anthracycline chemotherapy. In LABC patients who received neoadjuvant anthracycline, low ERCC1 transcript was associated with higher pCR (pathological complete response) and decreased DRR. However, in patients with ER−tumours who received additional neoadjuvant taxane, high ERCC1 transcript was associated with a higher pCR and decreased DRR. High ERCC1 transcript was also linked to decreased DRR in ER+ LABC that received additional neoadjuvant taxane. ERCC1 based stratification is an attractive strategy for breast cancers.

Evidence that neoadjuvant anthracycline based combination chemotherapy (NACT) in breast cancer (BC) induces phenotypical changes which guides the optimal adjuvant therapy

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Background: We hereby evaluated the histopathological and radiological alterations of tumor characteristics after receiving NACT and the clinical significance of the changes of adjuvant therapy based on these findings. Methods: A pathological assessment of tumor features including ER, PR, HER2 and proliferation markers (Ki67 and SPAG5) status in pre and post NACT tumors tissue have been centrally evaluated in two cohorts [Nottingham University Hospital (NUH; n=850) and Australian cohort (n=250 patients)]. Since 2013 any change in the ER and HER2 status from negative (-) [in the pre NACT biopsies] to positive (+) [in the post NACT surgical specimens] received additional adjuvant therapy (Endocrine therapy (ET) for ER+ and Trastuzumab for HER2+ cases) in NUH. MRI volumetric and texture changes have been assessed in 400 cases. The primary end point was disease free survival (DFS; median follow-up = 62 months). Results: 10% of pre NACT HER2- cases had been converted to post NACT HER2+ and those cases who subsequently received adjuvant Trastuzumab had achieved 92% 5-year DFS compared to those who remained HER- in post NACT specimens (58% 5-year DFS); (HR (95% CI)= 0.25 (0.08-0.80); p=0.016). While 13% of pre NACT HER2+ tumors were converted into HER2- in post NACT surgical specimens and had similar 5-year DFS to those who remained post NACT HER2+ (5-year DFS= 94% vs., 87%; p=0.613). Loss of PR in the residual disease of pre NACT ER+ BC was associated with shorter 5-year DFS after ET compared to those who remained post NACT PR+ (HR (95% CI)=2.1 (1.25-3.46); p=0.005). After NACT, 40% of pre NACT SPAG5+ cases were converted into post NACT SPAG5- and these patients had prolonged DFS compared to those who remained SPAG5+ in post NACT specimens (27%) [5-year DFS=84% vs 49%; (HR (95% CI)= 3.8 (2.1-6.9); p<0.0001). A prognostic model has been generated including factors in table (AUC = 0.854 (95% CI) = 0.777-.0.931; p= 0.00000001]. Conclusions: We hereby showed evidences a change of treatment strategy based on the changes in the tumor post NACT phenotype gives the optimal choice of treatment eg., the introduction of HER2 targeting therapy for the conversion of HER2– to HER2+ phenotype after NACT improved DFS. Multivariate Cox regression model for 5-year DFS. [Table: see text]

Low expression of G protein-coupled oestrogen receptor 1 (GPER) is associated with adverse survival of breast cancer patients

G protein-coupled oestrogen receptor 1 (GPER), also called G protein-coupled receptor 30 (GPR30), is attracting considerable attention for its potential role in breast cancer development and progression. Activation by oestrogen (17β-oestradiol; E2) initiates short term, non-genomic, signalling events both in vitro and in vivo. Published literature on the prognostic value of GPER protein expression in breast cancer indicates that further assessment is warranted. We show, using immunohistochemistry on a large cohort of primary invasive breast cancer patients (n=1245), that low protein expression of GPER is not only significantly associated with clinicopathological and molecular features of aggressive behaviour but also significantly associated with adverse survival of breast cancer patients. Furthermore, assessment of GPER mRNA levels in the METABRIC cohort (n=1980) demonstrates that low GPER mRNA expression is significantly associated with adverse survival of breast cancer patients. Using artificial neural networks, genes associated with GPER mRNA expression were identified; these included notch-4 and jagged-1. These results support the prognostic value for determination of GPER expression in breast cancer.

Breast cancer histologic grading using digital microscopy: concordance and outcome association

Aims

Virtual microscopy utilising digital whole slide imaging (WSI) is increasingly used in breast pathology. Histologic grade is one of the strongest prognostic factors in breast cancer (BC). This study aims at investigating the agreement between BC grading using traditional light microscopy (LM) and digital WSI with consideration of reproducibility and impact on outcome prediction.

Methods

A large (n=1675) well-characterised cohort of BC originally graded by LM was re-graded using WSI. Two separate virtual-based grading sessions (V1 and V2) were performed with a 3-month washout period. Outcome was assessed using BC-specific and distant metastasis-free survival.

Results

The concordance between LM grading and WSI was strong (LM/WSI Cramer’s V: V1=0.576, and V2=0.579). The agreement regarding grade components was as follows: tubule formation=0.538, pleomorphism=0.422 and mitosis=0.514. Greatest discordance was observed between adjacent grades, whereas high/low grade discordance was uncommon (1.5%). The intraobserver agreement for the two WSI sessions was substantial for grade (V1/V2 Cramer’s V=0.676; kappa=0.648) and grade components (Cramer’s V T=0.628, p=0.573 and M=0.580). Grading using both platforms showed strong association with outcome (all p values <0.001). Although mitotic scores assessed using both platforms were strongly associated with outcome, WSI tends to underestimate mitotic counts.

Conclusions

Virtual microscopy is a reliable and reproducible method for assessing BC histologic grade. Regardless of the observer or assessment platform, histologic grade is a significant predictor of outcome. Continuing advances in imaging technology could potentially provide improved performance of WSI BC grading and in particular mitotic count assessment.

Voxel-wise comparisons of cellular microstructure and diffusion-MRI in mouse hippocampus using 3D Bridging of Optically-clear histology with Neuroimaging Data (3D-BOND)

A key challenge in medical imaging is determining a precise correspondence between image properties and tissue microstructure. This comparison is hindered by disparate scales and resolutions between medical imaging and histology. We present a new technique, 3D Bridging of Optically-clear histology with Neuroimaging Data (3D-BOND), for registering medical images with 3D histology to overcome these limitations. Ex vivo 120 × 120 × 200 μm resolution diffusion-MRI (dMRI) data was acquired at 7 T from adult C57Bl/6 mouse hippocampus. Tissue was then optically cleared using CLARITY and stained with cellular markers and confocal microscopy used to produce high-resolution images of the 3D-tissue microstructure. For each sample, a dense array of hippocampal landmarks was used to drive registration between upsampled dMRI data and the corresponding confocal images. The cell population in each MRI voxel was determined within hippocampal subregions and compared to MRI-derived metrics. 3D-BOND provided robust voxel-wise, cellular correlates of dMRI data. CA1 pyramidal and dentate gyrus granular layers had significantly different mean diffusivity (p > 0.001), which was related to microstructural features. Overall, mean and radial diffusivity correlated with cell and axon density and fractional anisotropy with astrocyte density, while apparent fibre density correlated negatively with axon density. Astrocytes, axons and blood vessels correlated to tensor orientation.

Proteomic Profiling Reveals the Transglutaminase-2 Externalization Pathway in Kidneys after Unilateral Ureteric Obstruction

Increased export of transglutaminase-2 (TG2) by tubular epithelial cells (TECs) into the surrounding interstitium modifies the extracellular homeostatic balance, leading to fibrotic membrane expansion. Although silencing of extracellular TG2 ameliorates progressive kidney scarring in animal models of CKD, the pathway through which TG2 is secreted from TECs and contributes to disease progression has not been elucidated. In this study, we developed a global proteomic approach to identify binding partners of TG2 responsible for TG2 externalization in kidneys subjected to unilateral ureteric obstruction (UUO) using TG2 knockout kidneys as negative controls. We report a robust and unbiased analysis of the membrane interactome of TG2 in fibrotic kidneys relative to the entire proteome after UUO, detected by SWATH mass spectrometry. The data have been deposited to the ProteomeXchange with identifier PXD008173. Clusters of exosomal proteins in the TG2 interactome supported the hypothesis that TG2 is secreted by extracellular membrane vesicles during fibrosis progression. In established TEC lines, we found TG2 in vesicles of both endosomal (exosomes) and plasma membrane origin (microvesicles/ectosomes), and TGF-β1 stimulated TG2 secretion. Knockout of syndecan-4 (SDC4) greatly impaired TG2 exosomal secretion. TG2 coprecipitated with SDC4 from exosome lysate but not ectosome lysate. Ex vivo, EGFP-tagged TG2 accumulated in globular elements (blebs) protruding/retracting from the plasma membrane of primary cortical TECs, and SDC4 knockout impaired bleb formation, affecting TG2 release. Through this combined in vivo and in vitro approach, we have dissected the pathway through which TG2 is secreted from TECs in CKD.

Camptothecin targets WRN protein: mechanism and relevance in clinical breast cancer

Werner syndrome protein (WRN) is a RecQ helicase that participates in DNA repair, genome stability and cellular senescence. The five human RecQ helicases, RECQL1, Bloom, WRN, RECQL4 and RECQL5 play critical roles in DNA repair and cell survival after treatment with the anticancer drug camptothecin (CPT). CPT derivatives are widely used in cancer chemotherapy to inhibit topoisomerase I and generate DNA double-strand breaks during replication. Here we studied the effects of CPT on the stability and expression dynamics of human RecQ helicases. In the cells treated with CPT, we observed distinct effects on WRN compared to other human RecQ helicases. CPT altered the cellular localization of WRN and induced its degradation by a ubiquitin-mediated proteasome pathway. WRN knockdown cells as well as CPT treated cells became senescent and stained positive for senescence-associated β-galactosidase at a higher frequency compared to control cells. However, the senescent phenotype was attenuated by ectopic expression of WRN suggesting functional implication of WRN degradation in CPT treated cells. Approximately 5-23% of breast cancer tumors are known to respond to CPT-based chemotherapy. Interestingly, we found that the extent of CPT-induced WRN degradation correlates with increasing sensitivity of breast cancer cells to CPT. The abundance of WRN decreased in CPT-treated sensitive cells; however, WRN remained relatively stable in CPT-resistant breast cancer cells. In a large clinical cohort of breast cancer patients, we find that WRN and topoisomerase I expression correlate with an aggressive tumor phenotype and poor prognosis. Our novel observations suggest that WRN abundance along with CPT-induced degradation could be a promising strategy for personalizing CPT-based cancer chemotherapeutic regimens.

New Insights into the Anti-pathogenic Potential of Lactococcus garvieae against Staphylococcus aureus Based on RNA Sequencing Profiling

The bio-preservation potential of Lactococcus garvieae lies in its capacity to inhibit the growth of staphylococci, especially Staphylococcus aureus, in dairy products and in vitro. In vitro, inhibition is modulated by the level of aeration, owing to hydrogen peroxide (H₂O₂) production by L. garvieae under aeration. The S. aureus response to this inhibition has already been studied. However, the molecular mechanisms of L. garvieae underlying the antagonism against S. aureus have never been explored. This study provides evidence of the presence of another extracellular inhibition effector in vitro. This effector was neither a protein, nor a lipid, nor a polysaccharide, nor related to an L-threonine deficiency. To better understand the H₂O₂-related inhibition mechanism at the transcriptome level and to identify other mechanisms potentially involved, we used RNA sequencing to determine the transcriptome response of L. garvieae to different aeration levels and to the presence or absence of S. aureus. The L. garvieae transcriptome differed radically between different aeration levels mainly in biological processes related to fundamental functions and nutritional adaptation. The transcriptomic response of L. garvieae to aeration level differed according to the presence or absence of S. aureus. The higher concentration of H₂O₂ with high aeration was not associated with a higher expression of L. garvieae H₂O₂-synthesis genes (pox, sodA, and spxA1) but rather with a repression of L. garvieae H₂O₂-degradation genes (trxB1, ahpC, ahpF, and gpx). We showed that L. garvieae displayed an original, previously undiscovered, H₂O₂ production regulation mechanism among bacteria. In addition to the key factor H₂O₂, the involvement of another extracellular effector in the antagonism against S. aureus was shown. Future studies should explore the relation between H₂O₂-metabolism, H₂O₂-producing LAB and the pathogen they inhibit. The nature of the other extracellular effector should also be determined.

Prognostic stratification of oestrogen receptor-positive HER2-negative lymph node-negative class of breast cancer

AIMS

Multigene assay is recommended currently for prognostic stratification of the clinically indeterminate group of breast cancer (BC) patients defined as lymph node (LN)-negative, oestrogen receptor (ER)-positive, HER2-negative (LN^- /ER⁺ /HER2^- ) to determine the use of chemotherapy. However, this cohort, comprising approximately 40% of BC, is not a homogeneous group and shows variable outcome. This study aims to determine the prognostic value of routinely assessed variables, singly and in combination, in LN^- /ER⁺ /HER2^- BC patients.

METHODS AND RESULTS

A total of 830 LN^- /ER⁺ /HER2^- chemotherapy-naive BCs were investigated. The prognostic value of histological grade, tumour size, lymphovascular invasion (LVI), progesterone receptor (PgR) and Ki67 labelling index (Ki67LI) was assessed. In this series, only 25% of patients received hormone therapy. Median follow-up was 172 months. In the whole cohort, tumour grade, size, LVI, PgR and Ki67LI were correlated highly with outcome in a time-dependent manner. The outcome of this group varied widely from 97% (20% of cases) to 50% survival rate after 10-year follow-up using a combination of these markers. A prognostic index (Nottingham Px) incorporating grade, size, PgR and Ki67LI, was developed. The index can stratify the whole cohort robustly as well as the higher-risk subgroup (NPI score >3.4) into distinct prognostic classes.

CONCLUSION

Current routinely assessed variables can provide additional prognostic information in LN^- /ER⁺ /HER2^- BC. The proposed (Nottingham Px) index can stratify the BC clinically indeterminate group of patients into excellent and poor prognostic subgroups and can be used to identify reliably patients for systemic chemotherapy or further multigene prognostic testing. Performance of prognostic variables in these tumours is time-dependent, and should be considered in future studies.

Does the molecular classification of breast cancer point the way for biomarker identification in prostate cancer?

There is significant variation in clinical outcome between patients diagnosed with prostate cancer (CaP). Although useful, statistical nomograms and risk stratification tools alone do not always accurately predict an individual’s need for and response to treatment. The factors that determine this variation are not fully elucidated. In particular, cellular response to androgen ablation and subsequent paracrine/autocrine adaptation is poorly understood and despite best therapies, median survival in castrate resistant patients is only approximately 35 mo. We propose that one way of understanding this is to look for correlates in other comparable malignancies, such as breast cancer, where markers of at least 4 distinct gene clusters coding for 4 different phenotypic subtypes have been identified. These subtypes have been shown to demonstrate prognostic significance and successfully guide appropriate treatment regimens. In this paper we assess and review the evidence demonstrating parallels in the biology and treatment approach between breast and CaP, and consider the feasibility of patients with CaP being stratified into different molecular classes that could be used to complement prostate specific antigen and histological grading for clinical decision making. We show that there are significant correlations between the molecular classification of breast and CaP and explain how techniques used successfully to predict response to treatment in breast cancer can be applied to the prostate. Molecular phenotyping is possible in CaP and identification of distinct subtypes may allow personalised risk stratification way beyond that currently available.

Temporal Expression of Peripheral Blood Leukocyte Biomarkers in a Macaca fascicularis Infection Model of Tuberculosis; Comparison with Human Datasets and Analysis with Parametric/Non-parametric Tools for Improved Diagnostic Biomarker Identification

A temporal study of gene expression in peripheral blood leukocytes (PBLs) from a Mycobacterium tuberculosis primary, pulmonary challenge model Macaca fascicularis has been conducted. PBL samples were taken prior to challenge and at one, two, four and six weeks post-challenge and labelled, purified RNAs hybridised to Operon Human Genome AROS V4.0 slides. Data analyses revealed a large number of differentially regulated gene entities, which exhibited temporal profiles of expression across the time course study. Further data refinements identified groups of key markers showing group-specific expression patterns, with a substantial reprogramming event evident at the four to six week interval. Selected statistically-significant gene entities from this study and other immune and apoptotic markers were validated using qPCR, which confirmed many of the results obtained using microarray hybridisation. These showed evidence of a step-change in gene expression from an ‘early’ FOS-associated response, to a ‘late’ predominantly type I interferon-driven response, with coincident reduction of expression of other markers. Loss of T-cell-associate marker expression was observed in responsive animals, with concordant elevation of markers which may be associated with a myeloid suppressor cell phenotype e.g. CD163. The animals in the study were of different lineages and these Chinese and Mauritian cynomolgous macaque lines showed clear evidence of differing susceptibilities to Tuberculosis challenge. We determined a number of key differences in response profiles between the groups, particularly in expression of T-cell and apoptotic makers, amongst others. These have provided interesting insights into innate susceptibility related to different host `phenotypes. Using a combination of parametric and non-parametric artificial neural network analyses we have identified key genes and regulatory pathways which may be important in early and adaptive responses to TB. Using comparisons between data outputs of each analytical pipeline and comparisons with previously published Human TB datasets, we have delineated a subset of gene entities which may be of use for biomarker diagnostic test development.

The prognostic significance of STAT3 in invasive breast cancer: analysis of protein and mRNA expressions in large cohorts

Signal transducer and activator of transcription (STAT) transcription factors family are involved in diverse cellular biological functions. Reports regarding the prognostic impact of STAT3 expression in breast cancer (BC) are variable whether being a factor of poor or good prognosis. Immunohistochemical expression of phospho-STAT3 (pSTAT3) was studied in large series of invasive BC (n = 1270). pSTAT3 and STAT3 were quantified using reverse phase protein array (RPPA) on proteins extracted from macro-dissected FFPE tissues (n = 49 cases). STAT3 gene expression in the METABRIC cohort was also investigated. STAT3 gene expression prognostic impact was externally validated using the online BC gene expression data (n = 26 datasets, 4.177 patients). pSTAT3 was expressed in the nuclei and cytoplasm of invasive BC cells. Nuclear pSTAT3 overexpression was positively associated with smaller tumour size, lower grade, good NPI, negative lymphovascular invasion (LVI), ER+, PgR+, p53-, HER2-, and low Ki67LI and an improved breast cancer-specific survival (BCSS), independently of other factors. On RPPA, the mean pSTAT3 and STAT3 expressions were higher in ER+, PgR+, and smaller size tumours. Higher STAT3 transcripts in the METABRIC cohort were observed in cases with favourable prognostic criteria and as well as improved BCSS within the whole cohort, ER+ cohort with and without hormonal therapy, and ER- cohort including those who did not receive adjuvant chemotherapy. Pooled STAT3 gene expression data in the external validation cohort showed an association with improved patients' outcome (P < 0.001, HR = 0.84, 95 % CI 0.79-0.90). Results of this study suggest nuclear localisation of pSTAT3 as favourable prognostic marker in invasive BC, results re-enforced by analysis of STAT3 gene expression data. This good prognostic advantage was maintained in patients who received and who did not receive adjuvant therapy. Therefore, STAT3 could have context-dependent molecular roles of in BC, results which warrant further prospective verification in clinical trials.

RECQL4 helicase has oncogenic potential in sporadic breast cancers

RECQL4 helicase is a molecular motor that unwinds DNA, a process essential during DNA replication and DNA repair. Germ-line mutations in RECQL4 cause type II Rothmund-Thomson syndrome (RTS), characterized by a premature ageing phenotype and cancer predisposition. RECQL4 is widely considered to be a tumour suppressor, although its role in human breast cancer is largely unknown. As the RECQL4 gene is localized to chromosome 8q24, a site frequently amplified in sporadic breast cancers, we hypothesized that it may play an oncogenic role in breast tumourigenesis. To address this, we analysed large cohorts for gene copy number changes (n = 1977), mRNA expression (n = 1977) and protein level (n = 1902). Breast cancer incidence was also explored in 58 patients with type II RTS. DNA replication dynamics and chemosensitivity was evaluated in RECQL4-depleted breast cancer cells in vitro. Amplification or gain in gene copy number (30.6%), high-level mRNA expression (51%) and high levels of protein (23%) significantly associated with aggressive tumour behaviour, including lymph node positivity, larger tumour size, HER2 overexpression, ER-negativity, triple-negative phenotypes and poor survival. RECQL4 depletion impaired the DNA replication rate and increased chemosensitivity in cultured breast cancer cells. Thus, although recognized as a 'safe guardian of the genome', our data provide compelling evidence that RECQL4 is tumour promoting in established breast cancers. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Altered white matter and cortical structure in neonates with antenatally diagnosed isolated ventriculomegaly

Ventriculomegaly (VM) is the most common central nervous system abnormality diagnosed antenatally, and is associated with developmental delay in childhood. We tested the hypothesis that antenatally diagnosed isolated VM represents a biological marker for altered white matter (WM) and cortical grey matter (GM) development in neonates.

25 controls and 21 neonates with antenatally diagnosed isolated VM had magnetic resonance imaging at 41.97(± 2.94) and 45.34(± 2.14) weeks respectively. T₂-weighted scans were segmented for volumetric analyses of the lateral ventricles, WM and cortical GM. Diffusion tensor imaging (DTI) measures were assessed using voxel-wise methods in WM and cortical GM; comparisons were made between cohorts.

Ventricular and cortical GM volumes were increased, and WM relative volume was reduced in the VM group. Regional decreases in fractional anisotropy (FA) and increases in mean diffusivity (MD) were demonstrated in WM of the VM group compared to controls. No differences in cortical DTI metrics were observed. At 2 years, neurodevelopmental delays, especially in language, were observed in 6/12 cases in the VM cohort.

WM alterations in isolated VM cases may be consistent with abnormal development of WM tracts involved in language and cognition. Alterations in WM FA and MD may represent neural correlates for later neurodevelopmental deficits.

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This study compared brain development in neonates with isolated VM to controls.

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Neonates with isolated VM have enlarged cortical volumes compared to controls.

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FA was reduced and MD was increased in the WM of the VM cohort.

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Children with antenatal isolated VM are at increased risk for language delay.