All Outputs (28)

Advantages of automated immunostain analyses for complex membranous immunostains: An exemplar investigating loss of E-cadherin expression in colorectal cancer (2024)
Journal Article
Sculthorpe, D., Denton, A., Rusnita, D., Fadhil, W., Ilyas, M., & Mukherjee, A. (2024). Advantages of automated immunostain analyses for complex membranous immunostains: An exemplar investigating loss of E-cadherin expression in colorectal cancer. Pathology - Research and Practice, 260, Article 155470. https://doi.org/10.1016/j.prp.2024.155470

As pathology moves towards digitisation, biomarker profiling through automated image analysis provides potentially objective and time-efficient means of assessment. This study set out to determine how a complex membranous immunostain, E-cadherin, ass... Read More about Advantages of automated immunostain analyses for complex membranous immunostains: An exemplar investigating loss of E-cadherin expression in colorectal cancer.

Mathematical modelling and deep learning algorithms to automate assessment of single and digitally multiplexed immunohistochemical stains in tumoural stroma (2023)
Journal Article
Burrows, L., Sculthorpe, D., Zhang, H., Rehman, O., Mukherjee, A., & Chen, K. (2024). Mathematical modelling and deep learning algorithms to automate assessment of single and digitally multiplexed immunohistochemical stains in tumoural stroma. Journal of Pathology Informatics, 15, Article 100351. https://doi.org/10.1016/j.jpi.2023.100351

Whilst automated analysis of immunostains in pathology research has focused predominantly on the epithelial compartment, automated analysis of stains in the stromal compartment is challenging and therefore requires time-consuming pathological input a... Read More about Mathematical modelling and deep learning algorithms to automate assessment of single and digitally multiplexed immunohistochemical stains in tumoural stroma.

Weakly Supervised Segmentation with Point Annotations for Histopathology Images via Contrast-Based Variational Model (2023)
Presentation / Conference Contribution
Zhang, H., Burrows, L., Meng, Y., Sculthorpe, D., Mukherjee, A., Coupland, S. E., …Zheng, Y. (2023). Weakly Supervised Segmentation with Point Annotations for Histopathology Images via Contrast-Based Variational Model. In 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) (15630-15640). https://doi.org/10.1109/cvpr52729.2023.01500

Image segmentation is a fundamental task in the field of imaging and vision. Supervised deep learning for segmentation has achieved unparalleled success when sufficient training data with annotated labels are available. However, annotation is known t... Read More about Weakly Supervised Segmentation with Point Annotations for Histopathology Images via Contrast-Based Variational Model.

Associations between AI-Assisted Tumor Amphiregulin and Epiregulin IHC and Outcomes from Anti-EGFR Therapy in the Routine Management of Metastatic Colorectal Cancer (2023)
Journal Article
Williams, C. J. M., Elliott, F., Sapanara, N., Aghaei, F., Zhang, L., Muranyi, A., …Quirke, P. (2023). Associations between AI-Assisted Tumor Amphiregulin and Epiregulin IHC and Outcomes from Anti-EGFR Therapy in the Routine Management of Metastatic Colorectal Cancer. Clinical Cancer Research, 29(20), 4153-4165. https://doi.org/10.1158/1078-0432.CCR-23-0859

Purpose: High tumor production of the EGFR ligands, amphiregulin (AREG) and epiregulin (EREG), predicted benefit from anti-EGFR therapy for metastatic colorectal cancer (mCRC) in a retrospective analysis of clinical trial data. Here, AREG/EREG IHC wa... Read More about Associations between AI-Assisted Tumor Amphiregulin and Epiregulin IHC and Outcomes from Anti-EGFR Therapy in the Routine Management of Metastatic Colorectal Cancer.

Autofluorescence-Raman Spectroscopy for Ex Vivo Mapping Colorectal Liver Metastases and Liver Tissue (2023)
Journal Article
Corden, C., Boitor, R., Dusanjh, P. K., Harwood, A., Mukherjee, A., Gomez, D., & Notingher, I. (2023). Autofluorescence-Raman Spectroscopy for Ex Vivo Mapping Colorectal Liver Metastases and Liver Tissue. Journal of Surgical Research, 288, 10-20. https://doi.org/10.1016/j.jss.2023.02.014

Introduction: Identifying colorectal liver metastases (CRLM) during liver resection could assist in achieving clear surgical margins, which is an important prognostic variable for both disease-free and overall survival. The aim of this study was to i... Read More about Autofluorescence-Raman Spectroscopy for Ex Vivo Mapping Colorectal Liver Metastases and Liver Tissue.

Anti-miR-135/SPOCK1 axis antagonizes the influence of metabolism on drug response in intestinal/colon tumour organoids (2022)
Journal Article
Babaei-Jadidi, R., Kashfi, H., Alelwani, W., Bakhtiari, A., Kattan, S. W., Mansouri, O. A., …Nateri, A. S. (2022). Anti-miR-135/SPOCK1 axis antagonizes the influence of metabolism on drug response in intestinal/colon tumour organoids. Oncogenesis, 11, Article 4. https://doi.org/10.1038/s41389-021-00376-1

Little is known about the role of microRNAs (miRNAs) in rewiring the metabolism within tumours and adjacent non-tumour bearing normal tissue and their potential in cancer therapy. This study aimed to investigate the relationship between deregulated m... Read More about Anti-miR-135/SPOCK1 axis antagonizes the influence of metabolism on drug response in intestinal/colon tumour organoids.

High tissue inhibitor of matrix-metalloproteinase 2 expression correlates with poor prognosis in breast cancer (2020)
Presentation / Conference Contribution
Heyman, T., Joseph, C., Craze, M., Green, A., Nolan, C., Rueda, O., …Mukherjee, A. (2020). High tissue inhibitor of matrix-metalloproteinase 2 expression correlates with poor prognosis in breast cancer.

Background & objectives TIMP2, tissue inhibitor of matrix-metalloproteinase 2, inhibits the matrix-metalloproteinase, MMP2, but may activate pro-MMP2. Hence its correlation with prognosis in breast cancer (BC) is contradictory. This study investigat... Read More about High tissue inhibitor of matrix-metalloproteinase 2 expression correlates with poor prognosis in breast cancer.

High micro-vessel density correlates with higher peri-tumoural immune response in colorectal cancer (2020)
Presentation / Conference Contribution
Raghuram, G., Fadhil, W., Sculthorpe, D., Ilyas, M., & Mukherjee, A. (2020). High micro-vessel density correlates with higher peri-tumoural immune response in colorectal cancer.

Background & objectives Microvessels, a significant component of the tumour microenvironment in colorectal cancer (CRC), have traditionally been assessed in full-face sections. This study aimed to assess the microvessel density (MVD) in CRC tissue m... Read More about High micro-vessel density correlates with higher peri-tumoural immune response in colorectal cancer.

Repurposing Antibacterial AM404 as a Potential Anticancer Drug for Targeting Colorectal Cancer Stem-Like Cells (2019)
Journal Article
Ahmed, M., Jinks, N., Babaei-Jadidi, R., Kashfi, H., Castellanos-Uribe, M., May, S. T., …Nateri, A. S. (2019). Repurposing Antibacterial AM404 as a Potential Anticancer Drug for Targeting Colorectal Cancer Stem-Like Cells. Cancers, 12(1), Article 106. https://doi.org/10.3390/cancers12010106

Tumour-promoting inflammation is involved in colorectal cancer (CRC) development and therapeutic resistance. However, the antibiotics and antibacterial drugs and signalling that regulate the potency of anticancer treatment upon forced differentiation... Read More about Repurposing Antibacterial AM404 as a Potential Anticancer Drug for Targeting Colorectal Cancer Stem-Like Cells.

IgG4 Expression Correlates with Poor Prognosis in Pancreatic Adenocarcinoma (2019)
Presentation / Conference Contribution
Budd, W., Mukherjee, A., Lobo, D., & Zaitoun, A. (2019). IgG4 Expression Correlates with Poor Prognosis in Pancreatic Adenocarcinoma. In Supplement: Leeds Pathology 2019. 12th Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland, 2–4 July 2019 (S1-S59). https://doi.org/10.1002/path.5345

Purpose of the study: IgG4, a member of the immunoglobulin family, has been implicated in the pathobiology of inflammatory disease (including autoimmune pancreatitis) and cancers. Its role in pancreatic cancers however remains to be elucidated. This... Read More about IgG4 Expression Correlates with Poor Prognosis in Pancreatic Adenocarcinoma.

Saccharomyces cerevisiae-like 1 (SEC14L1) is a prognostic factor in breast cancer associated with lymphovascular invasion (2018)
Journal Article
Sonbul, S. N., Aleskandarany, M. A., Kurozumi, S., Joseph, C., Toss, M. S., Diez-Rodriguez, M., Nolan, C. C., Mukherjee, A., Martin, S., Caldas, C., Ellis, I. O., Green, A. R., & Rakha, E. A. (in press). Saccharomyces cerevisiae-like 1 (SEC14L1) is a prognostic factor in breast cancer associated with lymphovascular invasion. Modern Pathology, https://doi.org/10.1038/s41379-018-0092-9

Lymphovascular invasion is strongly related to breast cancer metastasis. However, the underlying mechanisms of lymphovascular invasion and its driver molecules in breast cancer remain to be defined. In this study, we explore differential expression o... Read More about Saccharomyces cerevisiae-like 1 (SEC14L1) is a prognostic factor in breast cancer associated with lymphovascular invasion.

Mediator complex (MED) 7: a biomarker associated with good prognosis in invasive breast cancer, especially ER+ luminal subtypes (2018)
Journal Article
Joseph, C., Macnamara, O., Craze, M., Russell, R., Provenzano, E., Nolan, C. C., Diez-Rodriguez, M., Sonbul, S. N., Aleskandarany, M. A., Green, A. R., Rakha, E. A., Ellis, I. O., & Mukherjee, A. (in press). Mediator complex (MED) 7: a biomarker associated with good prognosis in invasive breast cancer, especially ER+ luminal subtypes. British Journal of Cancer, https://doi.org/10.1038/s41416-018-0041-x

Background: Mediator complex (MED) proteins have a key role in transcriptional regulation, some interacting with the oestrogen receptor (ER). Interrogation of the METABRIC cohort suggested that MED7 may regulate lymphovascular invasion (LVI). Thus ME... Read More about Mediator complex (MED) 7: a biomarker associated with good prognosis in invasive breast cancer, especially ER+ luminal subtypes.

Associations between genomic stratification of breast cancer and centrally reviewed tumour pathology in the METABRIC cohort (2018)
Journal Article
Mukherjee, A., Russell, R., Chin, S.-F., Liu, B., Rueda, O., Ali, H., Turashvili, G., Mahler-Araujo, B., Ellis, I., Aparicio, S., Caldas, C., & Provenzano, E. (2018). Associations between genomic stratification of breast cancer and centrally reviewed tumour pathology in the METABRIC cohort. npj Breast Cancer, 4(1), Article 5. https://doi.org/10.1038/s41523-018-0056-8

The integration of genomic and transcriptomic profiles of 2000 breast tumours from the METABRIC [Molecular Taxonomy of Breast Cancer International Consortium] cohort revealed ten subtypes, termed integrative clusters (IntClust/s), characterised by di... Read More about Associations between genomic stratification of breast cancer and centrally reviewed tumour pathology in the METABRIC cohort.

Rho-GTPase activating protein 18: a biomarker associated with good prognosis in invasive breast cancer (2017)
Journal Article
Aleskandarany, M. A., Sonbul, S. N., Surridge, R., Mukherjee, A., Caldas, C., Diez-Rodriguez, M., Ashankyty, I., Albrahim, K. I., Elmouna, A. M., Aneja, R., Martin, S. G., Ellis, I. O., Green, A. R., & Rakha, E. A. (2017). Rho-GTPase activating protein 18: a biomarker associated with good prognosis in invasive breast cancer. British Journal of Cancer, 117(8), 1176-1184. https://doi.org/10.1038/bjc.2017.261

Background: The prognostic value of lymphovascular invasion (LVI) in breast cancer (BC) has been demonstrated in several independent studies. However, identification of driver molecules for LVI remains a challenging task. Large-scale transcriptomic p... Read More about Rho-GTPase activating protein 18: a biomarker associated with good prognosis in invasive breast cancer.

HER2 challenge contest: a detailed assessment of automated HER2 scoring algorithms in whole slide images of breast cancer tissues (2017)
Journal Article
Qaiser, T., Mukherjee, A., Reddy Pb, C., Munugoti, S. D., Tallam, V., Pitkäaho, T., …Rajpoot, N. (2018). HER2 challenge contest: a detailed assessment of automated HER2 scoring algorithms in whole slide images of breast cancer tissues. Histopathology, 72(2), 227-238. https://doi.org/10.1111/his.13333

Aims Evaluating expression of the Human epidermal growth factor receptor 2 (Her2) by visual examination of immunohistochemistry (IHC) on invasive breast cancer (BCa) is a key part of the diagnostic assessment of BCa due to its recognised importanc... Read More about HER2 challenge contest: a detailed assessment of automated HER2 scoring algorithms in whole slide images of breast cancer tissues.

Loss of MED23 leads to poor prognosis in invasive breast cancer (2017)
Presentation / Conference Contribution
cancer. Presented at Belfast Pathology 2017: 10th Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland

Purpose of the study: The molecular mechanism of lymphovascular invasion (LVI) which determines the early metastatic phenotype in breast cancer is still not fully understood. Lead from the METABRIC study revealed that MED23 correlated with negative L... Read More about Loss of MED23 leads to poor prognosis in invasive breast cancer.

Cell division cycle 25C (CDC25C) expression confers poor prognosis in invasive breast cancer (2017)
Presentation / Conference Contribution
Ojiegbe, S., Joseph, C., Provenzano, E., Caldas, C., Nolan, C., Green, A., Rakha, E., Ellis, I., & Mukherjee, A. Cell division cycle 25C (CDC25C) expression confers poor prognosis in invasive breast cancer. Presented at Belfast Pathology 2017: 10th Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland

Background: CDC25C, belonging to the Cdc25 phosphatase family, plays a major role in cell cycle control, impacting on DNA repair and apoptosis. It has been shown that poor prognosis/copy number high Luminal A breast cancers (BCs) are enriched for the... Read More about Cell division cycle 25C (CDC25C) expression confers poor prognosis in invasive breast cancer.

Elevated expression of STK3 mRNA and protein is associated with poor outcome in invasive breast cancer (2017)
Presentation / Conference Contribution
with poor outcome in invasive breast cancer. Presented at Belfast Pathology 2017: 10th Joint Meeting of the British Division of the International Academy of Pathology and the Pathological Society of Great Britain & Ireland

Purpose of the study: The mammalian sterile 20-like kinase (MST2/STK3) and its close homologue MST1(STK4) are members of the germinal centre kinase group II (GCK II) family of mitogen-activated protein kinases (MAPK). High STK3 expression is known to... Read More about Elevated expression of STK3 mRNA and protein is associated with poor outcome in invasive breast cancer.

Phenotypic characterization of breast cancer: the role of CDC42 (2017)
Journal Article
Chrysanthou, E., Gorringe, K. L., Joseph, C., Craze, M. L., Nolan, C. C., Diez-Rodriguez, M., Green, A. R., Rakha, E. A., Ellis, I. O., & Mukherjee, A. (2017). Phenotypic characterization of breast cancer: the role of CDC42. Breast Cancer Research and Treatment, 164(2), https://doi.org/10.1007/s10549-017-4267-8

Purpose: The molecular landscape of breast cancer (BC), especially of the Luminal A subtype, remains to be fully delineated. Transcriptomic data shows that Luminal A tumours are enriched for aberrant expression of genes in the cell division control 4... Read More about Phenotypic characterization of breast cancer: the role of CDC42.

Chemokine (C-C motif) receptor 7 (CCR7) associates with the tumour immune microenvironment but not progression in invasive breast carcinoma (2017)
Journal Article
Sonbul, S. N., Gorringe, K. L., Aleskandarany, M. A., Mukherjee, A., Green, A. R., Ellis, I. O., & Rakha, E. A. (2017). Chemokine (C-C motif) receptor 7 (CCR7) associates with the tumour immune microenvironment but not progression in invasive breast carcinoma. Journal of Pathology: Clinical Research, 3(2), 105-114. https://doi.org/10.1002/cjp2.65

Some previous studies have reported that the chemokine (C-C motif) receptor 7 (CCR7) plays a role in breast cancer, is associated with lymph node metastasis and drives the site of distant metastasis. However, the impact of its expression on patient o... Read More about Chemokine (C-C motif) receptor 7 (CCR7) associates with the tumour immune microenvironment but not progression in invasive breast carcinoma.