Browsing by author "Yuan, Yinyin"
Now showing items 1-20 of 32
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An ecological measure of immune-cancer colocalization as a prognostic factor for breast cancer.
Maley, CC; Koelble, K; Natrajan, R; Aktipis, A; Yuan, Y (BMC, 2015-09-22)INTRODUCTION: Abundance of immune cells has been shown to have prognostic and predictive significance in many tumor types. Beyond abundance, the spatial organization of immune cells in relation to cancer cells may also ... -
Analysis of tumour ecological balance reveals resource-dependent adaptive strategies of ovarian cancer.
Nawaz, S; Trahearn, NA; Heindl, A; Banerjee, S; Maley, CC; et al. (ELSEVIER, 2019-10-21)BACKGROUND: Despite treatment advances, there remains a significant risk of recurrence in ovarian cancer, at which stage it is usually incurable. Consequently, there is a clear need for improved patient stratification. ... -
Artificial intelligence and digital pathology: Opportunities and implications for immuno-oncology.
Sobhani, F; Robinson, R; Hamidinekoo, A; Roxanis, I; Somaiah, N; et al. (ELSEVIER, 2021-02-06)The field of immuno-oncology has expanded rapidly over the past decade, but key questions remain. How does tumour-immune interaction regulate disease progression? How can we prospectively identify patients who will benefit ... -
Biomarkers for site-specific response to neoadjuvant chemotherapy in epithelial ovarian cancer: relating MRI changes to tumour cell load and necrosis.
Winfield, JM; Wakefield, JC; Brenton, JD; AbdulJabbar, K; Savio, A; et al. (SPRINGERNATURE, 2021-03-16)BACKGROUND: Diffusion-weighted magnetic resonance imaging (DW-MRI) potentially interrogates site-specific response to neoadjuvant chemotherapy (NAC) in epithelial ovarian cancer (EOC). METHODS: Participants with newly ... -
Biopsy variability of lymphocytic infiltration in breast cancer subtypes and the ImmunoSkew score.
Khan, AM; Yuan, Y (NATURE PORTFOLIO, 2016-11-04)The number of tumour biopsies required for a good representation of tumours has been controversial. An important factor to consider is intra-tumour heterogeneity, which can vary among cancer types and subtypes. Immune cells ... -
Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci.
Jäger, R; Migliorini, G; Henrion, M; Kandaswamy, R; Speedy, HE; et al. (NATURE PORTFOLIO, 2015-02-19)Multiple regulatory elements distant from their targets on the linear genome can influence the expression of a single gene through chromatin looping. Chromosome conformation capture implemented in Hi-C allows for genome-wide ... -
Classifying the evolutionary and ecological features of neoplasms.
Maley, CC; Aktipis, A; Graham, TA; Sottoriva, A; Boddy, AM; et al. (NATURE PUBLISHING GROUP, 2017-10-01)Neoplasms change over time through a process of cell-level evolution, driven by genetic and epigenetic alterations. However, the ecology of the microenvironment of a neoplastic cell determines which changes provide adaptive ... -
Computational pathology: Exploring the spatial dimension of tumor ecology.
Nawaz, S; Yuan, Y (ELSEVIER IRELAND LTD, 2016-09-28)Tumors are evolving ecosystems where cancer subclones and the microenvironment interact. This is analogous to interaction dynamics between species in their natural habitats, which is a prime area of study in ecology. Spatial ... -
DECONVOLVING CONVOLUTIONAL NEURAL NETWORK FOR CELL DETECTION
Raza, SEA; AbdulJabbar, K; Jamal-Hanjani, M; Veeriah, S; Le Quesne, J; et al. (IEEE, 2019-01-01) -
Evaluation of CDK12 Protein Expression as a Potential Novel Biomarker for DNA Damage Response-Targeted Therapies in Breast Cancer.
Naidoo, K; Wai, PT; Maguire, SL; Daley, F; Haider, S; et al. (AMER ASSOC CANCER RESEARCH, 2018-01-01)Disruption of Cyclin-Dependent Kinase 12 (CDK12) is known to lead to defects in DNA repair and sensitivity to platinum salts and PARP1/2 inhibitors. However, CDK12 has also been proposed as an oncogene in breast cancer. ... -
Geospatial immune variability illuminates differential evolution of lung adenocarcinoma.
AbdulJabbar, K; Raza, SEA; Rosenthal, R; Jamal-Hanjani, M; Veeriah, S; et al. (NATURE PORTFOLIO, 2020-07-01)Remarkable progress in molecular analyses has improved our understanding of the evolution of cancer cells toward immune escape1-5. However, the spatial configurations of immune and stromal cells, which may shed light on ... -
High inter-follicular spatial co-localization of CD8+FOXP3+ with CD4+CD8+ cells predicts favorable outcome in follicular lymphoma.
Hagos, YB; Akarca, AU; Ramsay, A; Rossi, RL; Pomplun, S; et al. (WILEY, 2022-04-22)The spatial architecture of the lymphoid tissue in follicular lymphoma (FL) presents unique challenges to studying its immune microenvironment. We investigated the spatial interplay of T cells, macrophages, myeloid cells ... -
Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer.
Pennycuick, A; Teixeira, VH; AbdulJabbar, K; Raza, SEA; Lund, T; et al. (AMER ASSOC CANCER RESEARCH, 2020-01-01)Before squamous cell lung cancer develops, precancerous lesions can be found in the airways. From longitudinal monitoring, we know that only half of such lesions become cancer, whereas a third spontaneously regress. Although ... -
Investigating the Contribution of Collagen to the Tumor Biomechanical Phenotype with Noninvasive Magnetic Resonance Elastography.
Li, J; Zormpas-Petridis, K; Boult, JKR; Reeves, EL; Heindl, A; et al. (AMER ASSOC CANCER RESEARCH, 2019-11-15)Increased stiffness in the extracellular matrix (ECM) contributes to tumor progression and metastasis. Therefore, stromal modulating therapies and accompanying biomarkers are being developed to target ECM stiffness. Magnetic ... -
Microenvironmental Heterogeneity Parallels Breast Cancer Progression: A Histology-Genomic Integration Analysis.
Natrajan, R; Sailem, H; Mardakheh, FK; Arias Garcia, M; Tape, CJ; et al. (PUBLIC LIBRARY SCIENCE, 2016-02-16)BACKGROUND: The intra-tumor diversity of cancer cells is under intense investigation; however, little is known about the heterogeneity of the tumor microenvironment that is key to cancer progression and evolution. We aimed ... -
Microenvironmental niche divergence shapes BRCA1-dysregulated ovarian cancer morphological plasticity.
Heindl, A; Khan, AM; Rodrigues, DN; Eason, K; Sadanandam, A; et al. (NATURE RESEARCH, 2018-09-25)How tumor microenvironmental forces shape plasticity of cancer cell morphology is poorly understood. Here, we conduct automated histology image and spatial statistical analyses in 514 high grade serous ovarian samples to ... -
MRI Imaging of the Hemodynamic Vasculature of Neuroblastoma Predicts Response to Antiangiogenic Treatment.
Zormpas-Petridis, K; Jerome, NP; Blackledge, MD; Carceller, F; Poon, E; et al. (AMER ASSOC CANCER RESEARCH, 2019-06)Childhood neuroblastoma is a hypervascular tumor of neural origin, for which antiangiogenic drugs are currently being evaluated; however, predictive biomarkers of treatment response, crucial for successful delivery of ... -
Noninvasive MRI Native T1 Mapping Detects Response to MYCN-targeted Therapies in the Th-MYCN Model of Neuroblastoma.
Zormpas-Petridis, K; Poon, E; Clarke, M; Jerome, NP; Boult, JKR; et al. (AMER ASSOC CANCER RESEARCH, 2020-08-15)Noninvasive early indicators of treatment response are crucial to the successful delivery of precision medicine in children with cancer. Neuroblastoma is a common solid tumor of young children that arises from anomalies ... -
Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer.
Kos, Z; Roblin, E; Kim, RS; Michiels, S; Gallas, BD; et al. (NATURE RESEARCH, 2020-05-12)Stromal tumor-infiltrating lymphocytes (sTILs) are important prognostic and predictive biomarkers in triple-negative (TNBC) and HER2-positive breast cancer. Incorporating sTILs into clinical practice necessitates reproducible ... -
Quantitative histology analysis of the ovarian tumour microenvironment.
Lan, C; Heindl, A; Huang, X; Xi, S; Banerjee, S; et al. (NATURE PORTFOLIO, 2015-11-17)Concerted efforts in genomic studies examining RNA transcription and DNA methylation patterns have revealed profound insights in prognostic ovarian cancer subtypes. On the other hand, abundant histology slides have been ...