Superpixel-based conditional random fields (SuperCRF) : incorporating global and local context for enhanced deep learning in melanoma histopathology

Computational pathology-based cell classification algorithms are revolutionizing the study of the tumor microenvironment and can provide novel predictive/prognosis biomarkers crucial for the delivery of precision oncology. Current algorithms used on hematoxylin and eosin slides are based on individual cell nuclei morphology with limited local context features. Here, we propose a novel multi-resolution hierarchical framework (SuperCRF) inspired by the way pathologists perceive regional tissue architecture to improve cell classification and demonstrate its clinical applications. We develop SuperCRF by training a state-of-art deep learning spatially constrained- convolution neural network (SC-CNN) to detect and classify cells from 105 high-resolution (20×) H&E-stained slides of The Cancer Genome Atlas melanoma dataset and subsequently, a conditional random field (CRF) by combining cellular neighborhood with tumor regional classification from lower resolution images (5, 1.25×) given by a superpixel-based machine learning framework. SuperCRF led to an 11.85% overall improvement in the accuracy of the state-of-art deep learning SC-CNN cell classifier. Consistent with a stroma-mediated immune suppressive microenvironment, SuperCRF demonstrated that (i) a high ratio of lymphocytes to all lymphocytes within the stromal compartment (p = 0.026) and (ii) a high ratio of stromal cells to all cells (p < 0.0001 compared to p = 0.039 for SC-CNN only) are associated with poor survival in patients with melanoma. SuperCRF improves cell classification by introducing global and local context-based information and can be implemented in combination with any single-cell classifier. SuperCRF provides valuable tools to study the tumor microenvironment and identify predictors of survival and response to therapy

Geometric characteristics of collagen have independent prognostic significance in breast ductal carcinoma in situ: an image analysis study

Collagen plays a key role in normal and malignant tissue homeostasis. While the prognostic significance of collagen fibre remodeling in invasive breast cancer has been studied, its role in ductal carcinoma in situ (DCIS) remains poorly defined. Using image analysis, we aimed to evaluate the prognostic significance of the geometric characteristics of collagen surrounding DCIS. A large well-characterized cohort of DCIS comprising pure DCIS (n=610) and DCIS co-existing with invasive carcinoma (n=180) were histochemically stained for collagen using picrosirius red. ImageJ software was used to assess collagen density, degree of collagen fibre dispersion and directionality in relation to DCIS ducts’ boundary. We developed a collagen prognostic index and evaluated its prognostic significance. A poor index was observed in 24% of the pure DCIS and was associated with determinants of high-risk DCIS including higher grade, comedo necrosis, hormonal receptor negativity, HER2 positivity and high proliferation index. High index was associated with overexpression of the collagen remodeling protein prolyl-4-hydroxlase alpha 2 and the hypoxia inducible factor 1α. DCIS co-existing with invasive carcinoma had a higher collagen prognostic index than pure DCIS (

Serum-derived extracellular vesicles from breast cancer patients contribute to differential regulation of T-cell-mediated immune-escape mechanisms in breast cancer subtypes

Background: Intracellular communication within the tumour is complex and extracellular vesicles (EVs) have been identified as major contributing factors for the cell-to-cell communication in the local and distant tumour environments. Here, we examine the differential effects of breast cancer (BC) subtype-specific patient serum and cell-line derived EVs in the regulation of T cell mediated immune responses. Methods: Ultracentrifugation was used to isolate EVs from sera of 63 BC patients, 15 healthy volunteers and 4 human breast cancer cell lines. Longitudinal blood draws for EV isolation for patients on neoadjuvant chemotherapy was also performed. Characterization of EVs was performed by Nanoparticle Tracking Analysis (NTA), transmission electron microscopy (TEM) and immunoblotting. CD63 staining was performed on a tissue microarray of 218 BC patients. In-house bioinformatics algorithms were utilized for the computation of EV associated expression scores within The Cancer Genome Atlas (TCGA) and correlated with tumour infiltrating lymphocyte (TIL) scores. In vitro stimulation of PBMCs with EVs from serum and cell-line derived EVs was performed and changes in the immune phenotypes characterized by flow cytometry. Cytokine profiles were assessed using a 105-plex immunoassay or IL10 ELISA. Results: Patients with triple negative breast cancers (TNBCs) exhibited the lowest number of EVs in the sera; whilst the highest was detected in ER+HER2+ cancers; reflected also in the higher level of CD63+ vesicles found within the ER+HER2+ local tumour microenvironment. Transcriptomic analysis of the TCGA data identified that samples assigned with lower EV scores had significantly higher abundance of CD4+ memory activated T cells, T follicular cells and CD8 T cells, plasma, and memory B cells; whilst samples with high EV scores were more enriched for anti-inflammatory M2 macrophages and mast cells. A negative correlation between EV expression scores and stromal TIL counts was also observed. In vitro experiments confirmed that circulating EVs within breast cancer subtypes have functionally differing immunomodulatory capabilities, with EVs from patients with the most aggressive breast cancer subtype (TNBCs) demonstrating the most immune-suppressive phenotype (decreased CD3+HLA-DR+ but increased CD3+PD-L1 T cells, increased CD4+CD127-CD25hi T regulatory cells with associated increase in IL10 cytokine production). In depth assessment of the cytokine modulation triggered by the serum/cell line derived exosomes confirmed differential inflammatory cytokine profiles across differing breast cancer subtypes. Studies using the MDA-231 TNBC breast cancer cell-line derived EVs provided further support that TNBC EVs induced the most immunosuppressive response within PBMCs. Discussion: Our study supports further investigations into how tumour derived EVs are a mechanism that cancers can exploit to promote immune suppression; and breast cancer subtypes produce EVs with differing immunomodulatory capabilities. Understanding the intracellular/extracellular pathways implicated in alteration from active to suppressed immune state may provide a promising way forward for restoring immune competence in specific breast cancer patient populations

Integrated Pharmacodynamic Analysis Identifies Two Metabolic Adaption Pathways to Metformin in Breast Cancer.

Late-phase clinical trials investigating metformin as a cancer therapy are underway. However, there remains controversy as to the mode of action of metformin in tumors at clinical doses. We conducted a clinical study integrating measurement of markers of systemic metabolism, dynamic FDG-PET-CT, transcriptomics, and metabolomics at paired time points to profile the bioactivity of metformin in primary breast cancer. We show metformin reduces the levels of mitochondrial metabolites, activates multiple mitochondrial metabolic pathways, and increases 18-FDG flux in tumors. Two tumor groups are identified with distinct metabolic responses, an OXPHOS transcriptional response (OTR) group for which there is an increase in OXPHOS gene transcription and an FDG response group with increased 18-FDG uptake. Increase in proliferation, as measured by a validated proliferation signature, suggested that patients in the OTR group were resistant to metformin treatment. We conclude that mitochondrial response to metformin in primary breast cancer may define anti-tumor effect

Serum-derived extracellular vesicles from breast cancer patients contribute to differential regulation of T-cell-mediated immune-escape mechanisms in breast cancer subtypes

BackgroundIntracellular communication within the tumour is complex and extracellular vesicles (EVs) have been identified as major contributing factors for the cell-to-cell communication in the local and distant tumour environments. Here, we examine the differential effects of breast cancer (BC) subtype-specific patient serum and cell-line derived EVs in the regulation of T cell mediated immune responses. MethodsUltracentrifugation was used to isolate EVs from sera of 63 BC patients, 15 healthy volunteers and 4 human breast cancer cell lines. Longitudinal blood draws for EV isolation for patients on neoadjuvant chemotherapy was also performed. Characterization of EVs was performed by Nanoparticle Tracking Analysis (NTA), transmission electron microscopy (TEM) and immunoblotting. CD63 staining was performed on a tissue microarray of 218 BC patients. In-house bioinformatics algorithms were utilized for the computation of EV associated expression scores within The Cancer Genome Atlas (TCGA) and correlated with tumour infiltrating lymphocyte (TIL) scores. In vitro stimulation of PBMCs with EVs from serum and cell-line derived EVs was performed and changes in the immune phenotypes characterized by flow cytometry. Cytokine profiles were assessed using a 105-plex immunoassay or IL10 ELISA. ResultsPatients with triple negative breast cancers (TNBCs) exhibited the lowest number of EVs in the sera; whilst the highest was detected in ER+HER2+ cancers; reflected also in the higher level of CD63+ vesicles found within the ER+HER2+ local tumour microenvironment. Transcriptomic analysis of the TCGA data identified that samples assigned with lower EV scores had significantly higher abundance of CD4+ memory activated T cells, T follicular cells and CD8 T cells, plasma, and memory B cells; whilst samples with high EV scores were more enriched for anti-inflammatory M2 macrophages and mast cells. A negative correlation between EV expression scores and stromal TIL counts was also observed. In vitro experiments confirmed that circulating EVs within breast cancer subtypes have functionally differing immunomodulatory capabilities, with EVs from patients with the most aggressive breast cancer subtype (TNBCs) demonstrating the most immune-suppressive phenotype (decreased CD3+HLA-DR+ but increased CD3+PD-L1 T cells, increased CD4+CD127-CD25hi T regulatory cells with associated increase in IL10 cytokine production). In depth assessment of the cytokine modulation triggered by the serum/cell line derived exosomes confirmed differential inflammatory cytokine profiles across differing breast cancer subtypes. Studies using the MDA-231 TNBC breast cancer cell-line derived EVs provided further support that TNBC EVs induced the most immunosuppressive response within PBMCs.DiscussionOur study supports further investigations into how tumour derived EVs are a mechanism that cancers can exploit to promote immune suppression; and breast cancer subtypes produce EVs with differing immunomodulatory capabilities. Understanding the intracellular/extracellular pathways implicated in alteration from active to suppressed immune may provide a promising way forward for restoring immune competence in specific breast cancer patient populations

The role of HER4 in relation to trastuzumab resistance and prognosis in HER2 positive breast cancer

Background Trastuzumab resistance imposes a major limitation to the successful treatment of HER2 positive breast cancer. The expression of HER4 and its prognostic value is controversial in breast cancer. Furthermore, its role in trastuzumab treatment and resistance in HER2 positive breast cancer has not been reported. Methods The effects of trastuzumab on HER4 cleavage and its localisation were studied in both parental and trastuzumab-resistant SKBR3 and BT474 cells using western blot, RT-PCR, nuclear fractionation and confocal microscopy. Tissue microarrays consisting of a cohort of HER2 positive breast cancer patients were stained for HER4 by immunohistochemistry and the results were correlated with patients’ outcome. This study also assessed HER4 expression in the tumor samples from a window study of trastuzumab alone or in combination with neoadjuvant chemotherapy in HER2 positive breast cancer patients. Results Trastuzumab treatment upregulated HER4 mRNA, and increased expression of both 80 and 180 kDa HER4 protein isoforms, and induced nuclear translocation of 80kDa HER4 protein isoforms, which the results similar to heregulin stimulation. This was also seen in trastuzumab resistant cells although HER480kDa and nuclear HER4 decreased upon overnight withdrawal of trastuzumab in resistant cell lines. In addition, knockdown of HER4 protein expression by specific siRNAs increased trastuzumab sensitivity and reversed trastuzumab resistance in SKBR3 and BT474 cells, confirming the importance of HER4 in trastuzumab response. This study also showed that trastuzumab-induced HER4 nuclear translocation is due to HER4 activation and cleavage since &gamma;-secretase inhibitor (GSi) and neratinib prevented the process when combined with trastuzumab treatment, correlating with an increased apoptosis and decreased cell viability. There was also increased nuclear HER4 expression in tumors from both BT474 xenografts and from patients with breast cancer treated with trastuzumab monotherapy. Furthermore, nuclear HER4 predicted poor clinical response to trastuzumab monotherapy in patients undergoing a window study and was a poor prognostic factor in HER2 positive breast cancer. Conclusions This study suggests HER4 activation, cleavage and nuclear translocation play a key role in trastuzumab resistance in HER2 positive breast cancer. Nuclear HER4 could be a novel predictive and prognostic biomarker in HER2 positive breast cancer patients.This thesis is not currently available in OR

ADGRL4/ELTD1 expression in breast cancer cells induces vascular normalization and immune suppression

SEARCH, a machine learning methodology developed by our lab, has been previously used to discover ELTD1 as driver of angiogenesis. We confirmed that its expression is increased in the vasculature and associated with good prognosis in multiple cancer types. Here we show that 35% of primary human breast tumours is positive for ELTD1 expression. Using immunocompetent, syngeneic mouse breast cancer models we found that tumours expressing recombinant murine Eltd1 grow faster and have enhanced ability to metastasize and promote systemic immune effects. Eltd1-expressing tumours have larger and better perfused vessels and tumour-endothelial cell interaction leading to the release of pro-angiogenic and immune modulating factors. The results in this study suggest that ELTD1 expression may enhance delivery of therapeutic antibodies to reverse the immunosuppression and increase response to chemotherapy and radiotherapy