Shamis, Suad Ahmad Khalifa and Savioli, Francesca and Ammar, Aula and Al-Badran, Sara S.F. and Hatthakarnkul, Phimmada and Leslie, Holly and Mallon, Elizabeth and Jamieson, Nigel B. and McMillan, Donald C. and Edwards, Joanne (2024) Spatial transcriptomic analysis of tumour with high and low CAIX expression in TNBC tissue samples using GeoMx™ RNA assay. Histology and Histopathology: Cellular and Molecular Biology, 39. pp. 177-200. ISSN 0213-3911
AI Summary:
The study investigated the prognostic significance and gene signatures associated with carbonic anhydrase IX (CAIX) in triple-negative breast cancer (TNBC) patients. The results showed that high CAIX expression was independently associated with poor recurrence-free survival in TNBC patients.AI Topics:
Purpose. Prognostic significance and gene signatures associated with carbonic anhydrase IX (CAIX) was investigated in triple negative breast cancer (TNBC) patients.
Methods. Immunohistochemistry (IHC) for CAIX was performed in tissue microarrays (TMAs) of 136 TNBC patients.In a subset of 52 patients Digital Spatial Profiler (DSP) was performed in tumour (pan-cytokeratin+) and stroma (pan-cytokeratin-). Differentially expressed genes (DEGs) with P<0.05 and fold change ≥1 or ≤-1 were identified. Four genes were validated at the protein level.
Result. Cytoplasmic CAIX expression was independently associated with poor recurrence free survival in TNBC patients [hazard ratio (HR)=6.59, 95% confidence interval (CI): 1.47-29.58, P=0.014]. DEG analysis identified 4 up-regulated genes (CD68, HIF1A, pan-melanocyte, and VSIR) in the tumour region and 9 down-regulated genes in the stromal region (CD86, CD3E, MS4A1, BCL2, CCL5, NKG7, PTPRC, CD27, and FAS) when low versus high CAIX expression was explored. Employing IHC, high CD68 and HIF-1α was associated with poorer prognosis and high BCL2 and CD3 was associated with good prognosis.
Conclusions. DSP technology identified DEGs in TNBC. Selected genes validated by IHC showed involvement of CD3 and BCL2 expression within stroma and HIF-1α, and CD68 expression within tumour. However, further functional analysis is warranted.
Shamis, Suad Ahmad Khalifa
Author
Shamis, Suad A.K. and Quinn, Jean and Al-Badran, Sara and McKenzie, Molly and Hatthakarnkul, Phimmada and Lynch, Gerard and Lian, Guang-Yu and Numprasit, Warapan and Romics Jr, Laszlo and Andersen, Ditte and Mallon, Elizabeth and McMillan, Donald C. and Edwards, Joanne (2024) Elucidation of dysregulated pathways associated with hypoxia in oestrogen receptor-negative breast cancer. Cancer Medicine, 13 (23): e70274. ISSN 2045-7634
Shamis, Suad Ahmad Khalifa and Savioli, Francesca and Ammar, Aula and Al-Badran, Sara S.F. and Hatthakarnkul, Phimmada and Leslie, Holly and Mallon, Elizabeth and Jamieson, Nigel B. and McMillan, Donald C. and Edwards, Joanne (2024) Spatial transcriptomic analysis of tumour with high and low CAIX expression in TNBC tissue samples using GeoMx™ RNA assay. Histology and Histopathology: Cellular and Molecular Biology, 39. pp. 177-200. ISSN 0213-3911
See full publications listSavioli, Francesca
Author
Shamis, Suad Ahmad Khalifa and Savioli, Francesca and Ammar, Aula and Al-Badran, Sara S.F. and Hatthakarnkul, Phimmada and Leslie, Holly and Mallon, Elizabeth and Jamieson, Nigel B. and McMillan, Donald C. and Edwards, Joanne (2024) Spatial transcriptomic analysis of tumour with high and low CAIX expression in TNBC tissue samples using GeoMx™ RNA assay. Histology and Histopathology: Cellular and Molecular Biology, 39. pp. 177-200. ISSN 0213-3911
See full publications listAmmar, Aula
Author
Pennel, Kathryn A.F. and Hatthakarnkul, Phimmada and Wood, Colin S. and Lian, Guang-Yu and Al-Badran, Sara and Quinn, Jean A. and Legrini, Assya and Inthagard, Jitwadee and Alexander, Peter G. and van Wyk, Hester and Kurniawan, Ahmad and Hashmi, Umar and Gillespie, Michael A. and Mills, Megan and Ammar, Aula and Hay, Jennifer and Andersen, Ditte and Nixon, Colin and Rebus, Selma and Chang, David K. and Kelly, Caroline and Harkin, Andrea and Graham, Janet and Church, David and Tomlinson, Ian and Saunders, Mark and Iveson, Tim and Lannagan, Tamsin R. M. and Jackstadt, Rene and Maka, Noori and Horgan, Paul G. and Roxburgh, Campbell S. D. and Sansom, Owen J. and McMillan, Donald C. and Steele, Colin W. and Jamieson, Nigel B. and Park, James H. and Roseweir, Antonia K. and Edwards, Joanne (2024) JAK/STAT3 represents a therapeutic target for colorectal cancer patients with stromal-rich tumors. Journal of Experimental and Clinical Cancer Research, 43: 64. ISSN 1756-9966
Shamis, Suad Ahmad Khalifa and Savioli, Francesca and Ammar, Aula and Al-Badran, Sara S.F. and Hatthakarnkul, Phimmada and Leslie, Holly and Mallon, Elizabeth and Jamieson, Nigel B. and McMillan, Donald C. and Edwards, Joanne (2024) Spatial transcriptomic analysis of tumour with high and low CAIX expression in TNBC tissue samples using GeoMx™ RNA assay. Histology and Histopathology: Cellular and Molecular Biology, 39. pp. 177-200. ISSN 0213-3911
See full publications listAl-Badran, Sara S.F.
Author
Pennel, Kathryn and Kurniawan, Ahmad and Al-Badran, Sara Samir Foad and Schubert Santana, Leonor and Quinn, Jean and Nixon, Colin and Hatthakarnkul, Phimmada and Maka, Noori and Roxburgh, Campbell and McMillan, Donald and Edwards, Joanne (2024) IL6 and IL6R as prognostic biomarkers in colorectal cancer. Biomolecules, 14 (12): 1629. ISSN 2218-273X
Shamis, Suad A.K. and Quinn, Jean and Al-Badran, Sara and McKenzie, Molly and Hatthakarnkul, Phimmada and Lynch, Gerard and Lian, Guang-Yu and Numprasit, Warapan and Romics Jr, Laszlo and Andersen, Ditte and Mallon, Elizabeth and McMillan, Donald C. and Edwards, Joanne (2024) Elucidation of dysregulated pathways associated with hypoxia in oestrogen receptor-negative breast cancer. Cancer Medicine, 13 (23): e70274. ISSN 2045-7634
Galbraith, Norman J. and Quinn, Jean A. and Al-Badran, Sara Sf and Pennel, Kathryn A.F. and Hillson, Lily V.S. and Hatthakarnkul, Phimmada and McKenzie, Molly and Maka, Noori and Loi, Lynette and Frixou, Mikaela and Steele, Colin W. and Roxburgh, Campbell S. and Horgan, Paul G. and McMillan, Donald C. and Edwards, Joanne (2024) TAK1 expression is associated with increased PD-L1 and decreased cancer-specific survival in microsatellite-stable colorectal cancer. Translational Oncology, 48: 102064. ISSN 1944-7124
See full publications listHatthakarnkul, Phimmada
Author
Pennel, Kathryn and Kurniawan, Ahmad and Al-Badran, Sara Samir Foad and Schubert Santana, Leonor and Quinn, Jean and Nixon, Colin and Hatthakarnkul, Phimmada and Maka, Noori and Roxburgh, Campbell and McMillan, Donald and Edwards, Joanne (2024) IL6 and IL6R as prognostic biomarkers in colorectal cancer. Biomolecules, 14 (12): 1629. ISSN 2218-273X
Shamis, Suad A.K. and Quinn, Jean and Al-Badran, Sara and McKenzie, Molly and Hatthakarnkul, Phimmada and Lynch, Gerard and Lian, Guang-Yu and Numprasit, Warapan and Romics Jr, Laszlo and Andersen, Ditte and Mallon, Elizabeth and McMillan, Donald C. and Edwards, Joanne (2024) Elucidation of dysregulated pathways associated with hypoxia in oestrogen receptor-negative breast cancer. Cancer Medicine, 13 (23): e70274. ISSN 2045-7634
Galbraith, Norman J. and Quinn, Jean A. and Al-Badran, Sara Sf and Pennel, Kathryn A.F. and Hillson, Lily V.S. and Hatthakarnkul, Phimmada and McKenzie, Molly and Maka, Noori and Loi, Lynette and Frixou, Mikaela and Steele, Colin W. and Roxburgh, Campbell S. and Horgan, Paul G. and McMillan, Donald C. and Edwards, Joanne (2024) TAK1 expression is associated with increased PD-L1 and decreased cancer-specific survival in microsatellite-stable colorectal cancer. Translational Oncology, 48: 102064. ISSN 1944-7124
See full publications listLeslie, Holly
Author
O’Rourke, Colm J. and Salati, Massimiliano and Rae, Colin and Carpino, Guido and Leslie, Holly and Pea, Antonio and Prete, Maria G. and Bonetti, L.R. and Amato, Francesco and Montal, R. and Upstill-Goddard, Rosie and Nixon, Colin and Sanchon-Sanchez, Paula and Kunderfranco, Paolo and Sia, Daniela and Gaudio, Eugenio and Overi, Diletta and Cascinu, Stefano and Hogdall, Dan and Pugh, Sian and Domingo, Enric and Primrose, John N. and Bridgewater, John and Spallanzi, A. and Gelsomino, F. and Llovet, J.M. and Calvisi, Diego F. and Boulter, Luke and Caputo, F. and Lleo, Ana and Jamieson, Nigel B. and Luppi, G. and Dominici, M. and Andersen, Jesper B. and Braconi, Chiara (2024) Molecular portraits of patients with intrahepatic cholangiocarcinoma who diverge as rapid progressors or long survivors on chemotherapy. Gut, 73 (3). pp. 496-508. ISSN 0017-5749
Shamis, Suad Ahmad Khalifa and Savioli, Francesca and Ammar, Aula and Al-Badran, Sara S.F. and Hatthakarnkul, Phimmada and Leslie, Holly and Mallon, Elizabeth and Jamieson, Nigel B. and McMillan, Donald C. and Edwards, Joanne (2024) Spatial transcriptomic analysis of tumour with high and low CAIX expression in TNBC tissue samples using GeoMx™ RNA assay. Histology and Histopathology: Cellular and Molecular Biology, 39. pp. 177-200. ISSN 0213-3911
See full publications listMallon, Elizabeth
Author
Shamis, Suad A.K. and Quinn, Jean and Al-Badran, Sara and McKenzie, Molly and Hatthakarnkul, Phimmada and Lynch, Gerard and Lian, Guang-Yu and Numprasit, Warapan and Romics Jr, Laszlo and Andersen, Ditte and Mallon, Elizabeth and McMillan, Donald C. and Edwards, Joanne (2024) Elucidation of dysregulated pathways associated with hypoxia in oestrogen receptor-negative breast cancer. Cancer Medicine, 13 (23): e70274. ISSN 2045-7634
Shamis, Suad Ahmad Khalifa and Savioli, Francesca and Ammar, Aula and Al-Badran, Sara S.F. and Hatthakarnkul, Phimmada and Leslie, Holly and Mallon, Elizabeth and Jamieson, Nigel B. and McMillan, Donald C. and Edwards, Joanne (2024) Spatial transcriptomic analysis of tumour with high and low CAIX expression in TNBC tissue samples using GeoMx™ RNA assay. Histology and Histopathology: Cellular and Molecular Biology, 39. pp. 177-200. ISSN 0213-3911
See full publications listJamieson, Nigel B.
Author
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McKenzie, Molly and Lian, Guang-Yu and Pennel, Kathryn A.F. and Quinn, Jean A. and Jamieson, Nigel B. and Edwards, Joanne (2024) NFκB signalling in colorectal cancer: examining the central dogma of IKKα and IKKβ signalling. Heliyon, 10 (12): e32904. ISSN 2405-8440
See full publications listMcMillan, D.C.
Author
Bradley, Nicholas A. and Walter, Amy and Sankey, Chiara and Wilson, Alasdair and Siddiqui, Tamim and Roxburgh, Campbell D. and McMillan, Donald C. and Guthrie, Graeme J.K. (2025) Longitudinal association between statins and changes in CT derived body composition in patients with abdominal aortic aneurysm. Journal of Cachexia, Sarcopenia and Muscle, 16 (2). ISSN 2190-5991
Thompson, Joshua J. and MacLeod, Nicholas and Will, Sarah and O'Rourke, Fraser and McGovern, Josh and Roxburgh, Campbell and Edwards, Joanne and Dolan, Ross D. and McMillan, Donald C. (2025) The prognostic value of a laboratory cachexia score (LCAS) defined by LDH, CRP and albumin in patients with advanced lung cancer. BMC Cancer, 25: 543. ISSN 1471-2407
Dolan, Ross D. and Pennel, Kathryn and Thompson, Joshua and McKenzie, Molly and Alexander, Peter and Richards, Colin and Black, Douglas and Abbass, Tanvir and Maka, Noori and McGovern, Josh and Roseweir, Antonia and McSorley, Stephen T. and Horgan, Paul G. and Roxburgh, Campbell and McMillan, Donald C. and Edwards, Joanne (2025) The relationship between tumour necrosis, systemic inflammation, body composition and survival in patients with colon cancer. BJC Reports, 3 (1): 7. ISSN 2731-9377
See full publications listEdwards, J.
Author
Thompson, Joshua J. and MacLeod, Nicholas and Will, Sarah and O'Rourke, Fraser and McGovern, Josh and Roxburgh, Campbell and Edwards, Joanne and Dolan, Ross D. and McMillan, Donald C. (2025) The prognostic value of a laboratory cachexia score (LCAS) defined by LDH, CRP and albumin in patients with advanced lung cancer. BMC Cancer, 25: 543. ISSN 1471-2407
Dolan, Ross D. and Pennel, Kathryn and Thompson, Joshua and McKenzie, Molly and Alexander, Peter and Richards, Colin and Black, Douglas and Abbass, Tanvir and Maka, Noori and McGovern, Josh and Roseweir, Antonia and McSorley, Stephen T. and Horgan, Paul G. and Roxburgh, Campbell and McMillan, Donald C. and Edwards, Joanne (2025) The relationship between tumour necrosis, systemic inflammation, body composition and survival in patients with colon cancer. BJC Reports, 3 (1): 7. ISSN 2731-9377
Pennel, Kathryn and Kurniawan, Ahmad and Al-Badran, Sara Samir Foad and Schubert Santana, Leonor and Quinn, Jean and Nixon, Colin and Hatthakarnkul, Phimmada and Maka, Noori and Roxburgh, Campbell and McMillan, Donald and Edwards, Joanne (2024) IL6 and IL6R as prognostic biomarkers in colorectal cancer. Biomolecules, 14 (12): 1629. ISSN 2218-273X
See full publications listAvailable under License Creative Commons Attribution.
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