Now showing items 1-20 of 28

    • An ecological measure of immune-cancer colocalization as a prognostic factor for breast cancer. 

      Maley, CC; Koelble, K; Natrajan, R; Aktipis, A; Yuan, Y (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 have ...
    • Analysis of tumour ecological balance reveals resource-dependent adaptive strategies of ovarian cancer. 

      Nawaz, S; Trahearn, NA; Heindl, A; Banerjee, S; Maley, CC; Sottoriva, A; Yuan, Y (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. ...
    • 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; Freeman, S; Pace, E; Lutchman-Singh, K; Vroobel, KM; Yuan, Y; Banerjee, S; Porta, N; Ahmed Raza, SE; deSouza, NM (2021-01-04)
      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 diagnosed ...
    • Biopsy variability of lymphocytic infiltration in breast cancer subtypes and the ImmunoSkew score. 

      Khan, AM; Yuan, Y (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; Heindl, A; Whiffin, N; Carnicer, MJ; Broome, L; Dryden, N; Nagano, T; Schoenfelder, S; Enge, M; Yuan, Y; Taipale, J; Fraser, P; Fletcher, O; Houlston, RS (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; Janiszewska, M; Silva, AS; Gerlinger, M; Yuan, Y; Pienta, KJ; Anderson, KS; Gatenby, R; Swanton, C; Posada, D; Wu, C-I; Schiffman, JD; Hwang, ES; Polyak, K; Anderson, ARA; Brown, JS; Greaves, M; Shibata, D (2017-10)
      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 (2016-09)
      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; Swanton, C; Yuan, Y (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; Kriplani, D; Campbell, J; Mirza, H; Grigoriadis, A; Tutt, A; Moseley, PM; Abdel-Fatah, TMA; Chan, SYT; Madhusudan, S; Rhaka, EA; Ellis, IO; Lord, CJ; Yuan, Y; Green, AR; Natrajan, R (2018-01)
      Disruption of Cyclin-Dependent Kinase 12 (<i>CDK12</i>) is known to lead to defects in DNA repair and sensitivity to platinum salts and PARP1/2 inhibitors. However, <i>CDK12</i> has also been proposed as an oncogene in ...
    • Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer. 

      Pennycuick, A; Teixeira, VH; AbdulJabbar, K; Raza, SEA; Lund, T; Akarca, AU; Rosenthal, R; Kalinke, L; Chandrasekharan, DP; Pipinikas, CP; Lee-Six, H; Hynds, RE; Gowers, KHC; Henry, JY; Millar, FR; Hagos, YB; Denais, C; Falzon, M; Moore, DA; Antoniou, S; Durrenberger, PF; Furness, AJ; Carroll, B; Marceaux, C; Asselin-Labat, M-L; Larson, W; Betts, C; Coussens, LM; Thakrar, RM; George, J; Swanton, C; Thirlwell, C; Campbell, PJ; Marafioti, T; Yuan, Y; Quezada, SA; McGranahan, N; Janes, SM (2020-10)
      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 ...
    • Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer. 

      Zhang, AW; McPherson, A; Milne, K; Kroeger, DR; Hamilton, PT; Miranda, A; Funnell, T; Little, N; de Souza, CPE; Laan, S; LeDoux, S; Cochrane, DR; Lim, JLP; Yang, W; Roth, A; Smith, MA; Ho, J; Tse, K; Zeng, T; Shlafman, I; Mayo, MR; Moore, R; Failmezger, H; Heindl, A; Wang, YK; Bashashati, A; Grewal, DS; Brown, SD; Lai, D; Wan, ANC; Nielsen, CB; Huebner, C; Tessier-Cloutier, B; Anglesio, MS; Bouchard-Côté, A; Yuan, Y; Wasserman, WW; Gilks, CB; Karnezis, AN; Aparicio, S; McAlpine, JN; Huntsman, DG; Holt, RA; Nelson, BH; Shah, SP (2018-06)
      High-grade serous ovarian cancer (HGSC) exhibits extensive malignant clonal diversity with widespread but non-random patterns of disease dissemination. We investigated whether local immune microenvironment factors shape ...
    • 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; Vinci, M; Lopes, F; Cummings, C; Springer, CJ; Chesler, L; Jones, C; Bamber, JC; Yuan, Y; Sinkus, R; Jamin, Y; Robinson, SP (2019-11)
      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; Dowsett, M; Bakal, C; Yuan, Y (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; Orbegoso, C; Punta, M; Sottoriva, A; Lise, S; Banerjee, S; Yuan, Y (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; Clarke, M; McErlean, CM; Barone, G; Koers, A; Vaidya, SJ; Marshall, LV; Pearson, ADJ; Moreno, L; Anderson, J; Sebire, N; McHugh, K; Koh, D-M; Yuan, Y; Chesler, L; Robinson, SP; Jamin, Y (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 ...
    • Non-Invasive Prostate Cancer Characterization with Diffusion-Weighted MRI: Insight from In silico Studies of a Transgenic Mouse Model. 

      Hill, DK; Heindl, A; Zormpas-Petridis, K; Collins, DJ; Euceda, LR; Rodrigues, DN; Moestue, SA; Jamin, Y; Koh, D-M; Yuan, Y; Bathen, TF; Leach, MO; Blackledge, MD (2017-01)
      Diffusion-weighted magnetic resonance imaging (DWI) enables non-invasive, quantitative staging of prostate cancer via measurement of the apparent diffusion coefficient (ADC) of water within tissues. In cancer, more advanced ...
    • Noninvasive MRI Native T<sub>1</sub> Mapping Detects Response to <i>MYCN</i>-targeted Therapies in the Th-<i>MYCN</i> Model of Neuroblastoma. 

      Zormpas-Petridis, K; Poon, E; Clarke, M; Jerome, NP; Boult, JKR; Blackledge, MD; Carceller, F; Koers, A; Barone, G; Pearson, ADJ; Moreno, L; Anderson, J; Sebire, N; McHugh, K; Koh, D-M; Chesler, L; Yuan, Y; Robinson, SP; Jamin, Y (2020-08)
      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 ...
    • Quantitative histology analysis of the ovarian tumour microenvironment. 

      Lan, C; Heindl, A; Huang, X; Xi, S; Banerjee, S; Liu, J; Yuan, Y (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 ...
    • Relevance of Spatial Heterogeneity of Immune Infiltration for Predicting Risk of Recurrence After Endocrine Therapy of ER+ Breast Cancer. 

      Heindl, A; Sestak, I; Naidoo, K; Cuzick, J; Dowsett, M; Yuan, Y (2018-02)
      Background Despite increasing evidence supporting the clinical utility of immune infiltration in the estrogen receptor-negative (ER-) subtype, the prognostic value of immune infiltration for ER+ disease is not well ...
    • Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group. 

      Amgad, M; Stovgaard, ES; Balslev, E; Thagaard, J; Chen, W; Dudgeon, S; Sharma, A; Kerner, JK; Denkert, C; Yuan, Y; AbdulJabbar, K; Wienert, S; Savas, P; Voorwerk, L; Beck, AH; Madabhushi, A; Hartman, J; Sebastian, MM; Horlings, HM; Hudeček, J; Ciompi, F; Moore, DA; Singh, R; Roblin, E; Balancin, ML; Mathieu, M-C; Lennerz, JK; Kirtani, P; Chen, I-C; Braybrooke, JP; Pruneri, G; Demaria, S; Adams, S; Schnitt, SJ; Lakhani, SR; Rojo, F; Comerma, L; Badve, SS; Khojasteh, M; Symmans, WF; Sotiriou, C; Gonzalez-Ericsson, P; Pogue-Geile, KL; Kim, RS; Rimm, DL; Viale, G; Hewitt, SM; Bartlett, JMS; Penault-Llorca, F; Goel, S; Lien, H-C; Loibl, S; Kos, Z; Loi, S; Hanna, MG; Michiels, S; Kok, M; Nielsen, TO; Lazar, AJ; Bago-Horvath, Z; Kooreman, LFS; van der Laak, JAWM; Saltz, J; Gallas, BD; Kurkure, U; Barnes, M; Salgado, R; Cooper, LAD; International Immuno-Oncology Biomarker Working Group (2020-01)
      Assessment of tumor-infiltrating lymphocytes (TILs) is increasingly recognized as an integral part of the prognostic workflow in triple-negative (TNBC) and HER2-positive breast cancer, as well as many other solid tumors. ...