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2. Clinical Features Associated with Outcomes and Biomarker Analysis of Dabrafenib plus Trametinib Treatment in Patients with BRAF-Mutant Melanoma Brain Metastases.

Author

Wilmott, James, Tawbi, Hussein, Engh, Johnathan, Amankulor, Nduka, Shivalingam, Brindha, Banerjee, Hiya, Vergara, Ismael, Lee, Hansol, Johansson, Peter, Ferguson, Peter, Saiag, Philippe, Robert, Caroline, Grob, Jean-Jacques, Scolyer, Richard, Kirkwood, John, Long, Georgina, Davies, Michael, and Butterfield, Lisa

Subjects
Humans, Proto-Oncogene Proteins B-raf, Melanoma, Oximes, Pyridones, Brain Neoplasms, Biomarkers, Antineoplastic Combined Chemotherapy Protocols, Mutation, Skin Neoplasms
Abstract

PURPOSE: This study aimed to identify baseline clinical features associated with the outcomes of patients enrolled in the COMBI-MB phase II study of dabrafenib and trametinib treatment in patients with V600 BRAF-mutant metastatic melanoma with melanoma brain metastases (MBM). Exploratory biomarker analysis was also conducted as part of the synergistic COMBI-BRV trial (BRV116521), to identify molecular and immunologic changes associated with dabrafenib in MBMs and extracranial metastases (ECM). PATIENTS AND METHODS: Post hoc analysis was performed for baseline features of patients (n = 125) enrolled in COMBI-MB. Analyses were performed to identify baseline clinical features associated with intracranial response rate (ICRR), progression-free survival (PFS), and overall survival (OS). UNLABELLED: Exploratory biomarker analysis was performed on biospecimen collected in the COMBI-BRV trial in which patients with BRAF-mutant, resectable MBM were treated with dabrafenib for 10 to 14 days prior to craniotomy. Accessible ECM were resected or biopsied at the time of craniotomy. Biospecimens underwent molecular and immunologic profiling for comparative analyses. RESULTS: In COMBI-MB baseline treatment with corticosteroids was independently associated with lower ICRR [39% vs. 63%; OR, 0.323; 95 % confidence interval (CI), 0.105-0.996; P = 0.049] and shorter PFS (HR, 1.93; 95% CI, 1.06-3.51; P = 0.031). Additional significant associations identified in the multivariate analysis were improved PFS in patients with a BRAFV600E genotype (HR, 0.565; 95% CI, 0.321-0.996; P = 0.048) and improved OS in patients with Eastern Cooperative Oncology Group 0 (HR, 0.44; 95% CI, 0.25-0.78; P = 0.005). CONCLUSIONS: Corticosteroid treatment was associated with reduced ICRR and PFS in COMBI-MB, similar to results with immunotherapy for MBMs. Baseline corticosteroid treatment is a key factor to consider in MBM patient management and clinical trial design/interpretation.

Published
2023

3. DNA Methylation Classes of Stage II and III Primary Melanomas and Their Clinical and Prognostic Significance

Author

Conway, Kathleen, Edmiston, Sharon N., Vondras, Amanda, Reiner, Allison, Corcoran, David L., Shen, Ronglai, Parrish, Eloise A., Hao, Honglin, Lin, Lan, Kenney, Jessica M., Ilelaboye, Gbemisola, Kostrzewa, Caroline E., Kuan, Pei Fen, Busam, Klaus J., Lezcano, Cecilia, Lee, Tim K., Hernando, Eva, Googe, Paul B., Ollila, David W., Moschos, Stergios, Gorlov, Ivan, Amos, Christopher I., Ernstoff, Marc S., Cust, Anne E., Wilmott, James S., Scolyer, Richard A., Mann, Graham J., Vergara, Ismael A., Ko, Jennifer, Rees, Judy R., Yan, Shaofeng, Nagore, Eduardo, Bosenberg, Marcus, Rothberg, Bonnie Gould, Osman, Iman, Lee, Jeffrey E., Saenger, Yvonne, Bogner, Paul, Thompson, Cheryl L., Gerstenblith, Meg, Holmen, Sheri L., Funchain, Pauline, Brunsgaard, Elise, Depcik-Smith, Natalie D., Luo, Li, Boyce, Tawny, Orlow, Irene, Begg, Colin B., Berwick, Marianne, Thomas, Nancy E., Berwick, Marianne, Luo, Li, Boyce, Tawny W., Reynolds, Adam Z., Wiggins, Charles, Thomas, Nancy E., Conway, Kathleen, Edmiston, Sharon N., Ollila, David W., Hao, Honglin, Parrish, Eloise, Googe, Paul B., Moschos, Stergios J., Corcoran, David, Vondras, Amanda, Tsai, Yihsuan S., Lin, Lan, Shen, Ronglai, Begg, Colin B., Arora, Arshi, Seshan, Venkatraman, Reiner, Allie, Kostrzewa, Caroline E., Busam, Klaus J., Orlow, Irene, Lezcano, Cecilia, Kenney, Jessica M., Sadeghi, Keimya D., OʼConnell, Kelli, Ilelaboye, Gbemisola Elizabeth, Parmar, Heta, Leong, Siok, Corrales, Sergio, Scolyer, Richard A., Cust, Anne E., Wilmott, James S., Mann, Graham J., Shang, Ping, Burke, Hazel, Ferguson, Peter M., Jakrot, Valerie, Lee, Tim K., Hernando, Eva, Osman, Iman, Hanniford, Douglas, Argibay, Diana, Moran, Una, Heguy, Adriana, Ramaswami, Sitharam, Amos, Christopher I., Gorlov, Ivan P., Zhu, Dakai, Ernstoff, Marc, Bogner, Paul N., Lee, Jeffrey E., Rees, Judy R., Yan, Shaofeng, Gerstenblith, Meg R., Thompson, Cheryl, Ko, Jennifer S., Funchain, Pauline, Ngo, Peter, Bosenberg, Marcus, Gould Rothberg, Bonnie E., Panse, Gauri, Saenger, Yvonne M., Fullerton, Benjamin T., Holmen, Sheri L., Colman, Howard, Brunsgaard, Elise K., Wada, David, Nagore, Eduardo, Manrique-Silva, Esperanza, Requena, Celia, Traves, Victor, Millan-Esteban, David, and Rainka, Michelle

Published
2024
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10. Weakly supervised deep learning image analysis can differentiate melanoma from naevi on haematoxylin and eosin‐stained histopathology slides.

Author

Maher, Nigel G., Danaei Mehr, Homay, Cong, Cong, Adegoke, Nurudeen A., Vergara, Ismael A., Liu, Sidong, and Scolyer, Richard A.

Subjects
BIG data, DEEP learning, IMAGE analysis, SEX distribution, MELANOMA
Abstract

Background: The broad histomorphological spectrum of melanocytic pathologies requires large data sets to develop accurate and generalisable deep learning (DL)‐based diagnostic pathology classifiers. Weakly supervised DL promotes utilisation of larger training data sets compared to fully supervised (patch annotation) approaches. Objectives: To evaluate weakly supervised DL image classifiers for discriminating melanomas from naevi on haematoxylin and eosin (H&E)‐stained pathology slides. Methods: A representative H&E slide for 260 naevi and 260 melanomas from mucocutaneous sites at one tertiary institution was digitized. Clinicopathological features were recorded for each case including thickness and histological subtype. Whole‐slide or whole‐tissue section labels were applied. The ground truth was established by consensus diagnosis from two pathologists. Multiple‐instance learning models, Trans‐MIL, CLAM and DTFD‐MIL were evaluated at 10×, 20× and 40× magnifications using stratified fivefold Monte Carlo cross‐validation, with 80/10/10 splits for training/validation/test groups, to predict melanoma from naevus. Heatmaps were generated to understand model performance. Results: Naevi cases were younger (median age: 51 years; melanoma median age: 71.5 years), with more balanced sex distribution (males: 48.8%, melanoma male subgroup: 64.2%). The most frequent histological subtypes of naevi and melanomas were dysplastic compound (n = 99, 38.1%) and superficial spreading (n = 124, 47.7%), respectively. Average AUC (±1 SD) for Trans‐MIL, CLAM and DTFD‐MIL across test groups were 0.9952 ± 0.006, 0.9925 ± 0.0052 and 0.9708 ± 0.0328, at 20× magnification, respectively. Performance of the models varied according to the magnification used. Heatmaps from the two best performing models, Trans‐MIL and CLAM, generally indicated attention on appropriate tissue regions for interpretation. Conclusions: Weakly supervised DL on pathological slides of common mucocutaneous melanocytic tumours provides highly accurate diagnostic value for discrimination of melanomas and naevi. External validation and further assessment on less frequently occurring histologic subtypes and borderline cases using this method is required. [ABSTRACT FROM AUTHOR]

Published
2024
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11. Author Correction: Tumour gene expression signature in primary melanoma predicts long-term outcomes

Author

Garg, Manik, Couturier, Dominique-Laurent, Nsengimana, Jérémie, Fonseca, Nuno A., Wongchenko, Matthew, Yan, Yibing, Lauss, Martin, Jönsson, Göran B., Newton-Bishop, Julia, Parkinson, Christine, Middleton, Mark R., Bishop, D. Timothy, McDonald, Sarah, Stefanos, Nikki, Tadross, John, Vergara, Ismael A., Lo, Serigne, Newell, Felicity, Wilmott, James S., Thompson, John F., Long, Georgina V., Scolyer, Richard A., Corrie, Pippa, Adams, David J., Brazma, Alvis, and Rabbie, Roy

Published
2022
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12. Correction: Regulation of PRMT5–MDM4 axis is critical in the response to CDK4/6 inhibitors in melanoma

Author

AbuHammad, Shatha, Cullinane, Carleen, Martin, Claire, Bacolas, Zoe, Ward, Teresa, Chen, Huiqin, Slater, Alison, Ardley, Kerry, Kirby, Laura, Chan, Keefe T., Brajanovski, Natalie, Smith, Lorey K., Rao, Aparna D., Lelliott, Emily J., Kleinschmidt, Margarete, Vergara, Ismael A., Papenfuss, Anthony T., Lau, Peter, Ghosh, Prerana, Haupt, Sue, Haupt, Ygal, Sanij, Elaine, Poortinga, Gretchen, Pearson, Richard B., Falk, Hendrik, Curtis, David J., Stupple, Paul, Devlin, Mark, Street, Ian, Davies, Michael A., McArthur, Grant A., and Sheppard, Karen E.

Published
2020

13. Stroma-infiltrating T cell spatiotypes define immunotherapy outcomes in adolescent and young adult patients with melanoma.

Author

Xinyu Bai, Attrill, Grace H., Gide, Tuba N., Ferguson, Peter M., Nahar, Kazi J., Ping Shang, Vergara, Ismael A., Palendira, Umaimainthan, da Silva, Ines Pires, Carlino, Matteo S., Menzies, Alexander M., Long, Georgina V., Scolyer, Richard A., Wilmott, James S., and Quek, Camelia

Abstract

The biological underpinnings of therapeutic resistance to immune checkpoint inhibitors (ICI) in adolescent and young adult (AYA) melanoma patients are incompletely understood. Here, we characterize the immunogenomic profile and spatial architecture of the tumor microenvironment (TME) in AYA (aged ≤ 30 years) and older adult (aged 31–84 years) patients with melanoma, to determine the AYA-specific features associated with ICI treatment outcomes. We identify two ICI-resistant spatiotypes in AYA patients with melanoma showing stroma-infiltrating lymphocytes (SILs) that are distinct from the adult TME. The SILhigh subtype was enriched in regulatory T cells in the peritumoral space and showed upregulated expression of immune checkpoint molecules, while the SILlow subtype showed a lack of immune activation. We establish a young immunosuppressive melanoma score that can predict ICI responsiveness in AYA patients and propose personalized therapeutic strategies for the ICI-resistant subgroups. These findings highlight the distinct immunogenomic profile of AYA patients, and individualized TME features in ICI-resistant AYA melanoma that require patient-specific treatment strategies. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Regulation of PRMT5–MDM4 axis is critical in the response to CDK4/6 inhibitors in melanoma

Author

AbuHammad, Shatha, Cullinane, Carleen, Martin, Claire, Bacolas, Zoe, Ward, Teresa, Chen, Huiqin, Slater, Alison, Ardley, Kerry, Kirby, Laura, Chan, Keefe T., Brajanovski, Natalie, Smith, Lorey K., Rao, Aparna D., Lelliott, Emily J., Kleinschmidt, Margarete, Vergara, Ismael A., Papenfuss, Anthony T., Lau, Peter, Ghosh, Prerana, Haupt, Sue, Haupt, Ygal, Sanij, Elaine, Poortinga, Gretchen, Pearson, Richard B., Falk, Hendrik, Curtis, David J., Stupple, Paul, Devlin, Mark, Street, Ian, Davies, Michael A., McArthur, Grant A., and Sheppard, Karen E.

Published
2019

18. Tumour gene expression signature in primary melanoma predicts long-term outcomes

Author

Garg, Manik, Couturier, Dominique-Laurent, Nsengimana, Jérémie, Fonseca, Nuno A., Wongchenko, Matthew, Yan, Yibing, Lauss, Martin, Jönsson, Göran B., Newton-Bishop, Julia, Parkinson, Christine, Middleton, Mark R., Bishop, D. Timothy, McDonald, Sarah, Stefanos, Nikki, Tadross, John, Vergara, Ismael A., Lo, Serigne, Newell, Felicity, Wilmott, James S., Thompson, John F., Long, Georgina V., Scolyer, Richard A., Corrie, Pippa, Adams, David J., Brazma, Alvis, and Rabbie, Roy

Published
2021
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19. Evolution of late-stage metastatic melanoma is dominated by aneuploidy and whole genome doubling

Author

Vergara, Ismael A., Mintoff, Christopher P., Sandhu, Shahneen, McIntosh, Lachlan, Young, Richard J., Wong, Stephen Q., Colebatch, Andrew, Cameron, Daniel L., Kwon, Julia Lai, Wolfe, Rory, Peng, Angela, Ellul, Jason, Dou, Xuelin, Fedele, Clare, Boyle, Samantha, Arnau, Gisela Mir, Raleigh, Jeanette, Hatzimihalis, Athena, Szeto, Pacman, Mooi, Jennifer, Widmer, Daniel S., Cheng, Phil F., Amann, Valerie, Dummer, Reinhard, Hayward, Nicholas, Wilmott, James, Scolyer, Richard A., Cho, Raymond J., Bowtell, David, Thorne, Heather, Alsop, Kathryn, Cordner, Stephen, Woodford, Noel, Leditschke, Jodie, O’Brien, Patricia, Dawson, Sarah-Jane, McArthur, Grant A., Mann, Graham J., Levesque, Mitchell P., Papenfuss, Anthony T., and Shackleton, Mark

Published
2021
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20. The lncRNAs PCGEM1 and PRNCR1 are not implicated in castration resistant prostate cancer

Author

Prensner, John R, Sahu, Anirban, Iyer, Matthew K, Malik, Rohit, Chandler, Benjamin, Asangani, Irfan A, Poliakov, Anton, Vergara, Ismael A, Alshalalfa, Mohammed, Jenkins, Robert B, Davicioni, Elai, Feng, Felix Y, and Chinnaiyan, Arul M

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Urologic Diseases, Genetics, Cancer, Human Genome, Prostate Cancer, Aging, 2.1 Biological and endogenous factors, Aetiology, Gene Expression Regulation, Neoplastic, High-Throughput Nucleotide Sequencing, Humans, Male, Neoplasm Proteins, Prognosis, Prostate, Prostatic Neoplasms, Castration-Resistant, RNA, Long Noncoding, Receptors, Androgen, Oncology and carcinogenesis
Abstract

Long noncoding RNAs (IncRNAs) are increasingly implicated in cancer biology, contributing to essential cancer cell functions such as proliferation, invasion, and metastasis. In prostate cancer, several lncRNAs have been nominated as critical actors in disease pathogenesis. Among these, expression of PCGEM1 and PRNCR1 has been identified as a possible component in disease progression through the coordination of androgen receptor (AR) signaling (Yang et al., Nature 2013, see ref. [1]). However, concerns regarding the robustness of these findings have been suggested. Here, we sought to evaluate whether PCGEM1 and PRNCR1 are associated with prostate cancer. Through a comprehensive analysis of RNA-sequencing data (RNA-seq), we find evidence that PCGEM1 but not PRNCR1 is associated with prostate cancer. We employ a large cohort of >230 high-risk prostate cancer patients with long-term outcomes data to show that, in contrast to prior reports, neither gene is associated with poor patient outcomes. We further observe no evidence that PCGEM1 nor PRNCR1 interact with AR, and neither gene is a component of AR signaling. Thus, we conclusively demonstrate that PCGEM1 and PRNCR1 are not prognostic lncRNAs in prostate cancer and we refute suggestions that these lncRNAs interact in AR signaling.

Published
2014

21. The IncRNAs PCGEM1 and PRNCR1 are not implicated in castration resistant prostate cancer.

Author

Prensner, John R, Sahu, Anirban, Iyer, Matthew K, Malik, Rohit, Chandler, Benjamin, Asangani, Irfan A, Poliakov, Anton, Vergara, Ismael A, Alshalalfa, Mohammed, Jenkins, Robert B, Davicioni, Elai, Feng, Felix Y, and Chinnaiyan, Arul M

Subjects
Prostate, Humans, Neoplasm Proteins, Receptors, Androgen, Prognosis, Gene Expression Regulation, Neoplastic, Male, High-Throughput Nucleotide Sequencing, RNA, Long Noncoding, Prostatic Neoplasms, Castration-Resistant, Gene Expression Regulation, Neoplastic, Prostatic Neoplasms, Castration-Resistant, RNA, Long Noncoding, Receptors, Androgen, Oncology and Carcinogenesis
Abstract

Long noncoding RNAs (IncRNAs) are increasingly implicated in cancer biology, contributing to essential cancer cell functions such as proliferation, invasion, and metastasis. In prostate cancer, several lncRNAs have been nominated as critical actors in disease pathogenesis. Among these, expression of PCGEM1 and PRNCR1 has been identified as a possible component in disease progression through the coordination of androgen receptor (AR) signaling (Yang et al., Nature 2013, see ref. [1]). However, concerns regarding the robustness of these findings have been suggested. Here, we sought to evaluate whether PCGEM1 and PRNCR1 are associated with prostate cancer. Through a comprehensive analysis of RNA-sequencing data (RNA-seq), we find evidence that PCGEM1 but not PRNCR1 is associated with prostate cancer. We employ a large cohort of >230 high-risk prostate cancer patients with long-term outcomes data to show that, in contrast to prior reports, neither gene is associated with poor patient outcomes. We further observe no evidence that PCGEM1 nor PRNCR1 interact with AR, and neither gene is a component of AR signaling. Thus, we conclusively demonstrate that PCGEM1 and PRNCR1 are not prognostic lncRNAs in prostate cancer and we refute suggestions that these lncRNAs interact in AR signaling.

Published
2014

22. Seasonal patterns of toxicity in melanoma patients treated with combination anti-PD-1 and anti-CTLA-4 immunotherapy

Author

Rogiers, Aljosja, primary, Dimitriou, Florentia, additional, Lobon, Irene, additional, Harvey, Catriona, additional, Vergara, Ismael A., additional, Pires da Silva, Ines, additional, Lo, Serigne N., additional, Scolyer, Richard A., additional, Carlino, Matteo S., additional, Menzies, Alexander M., additional, and Long, Georgina V., additional

Published
2023
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23. Prognostic Significance of Incipient Ulceration in Primary Cutaneous Melanoma

Author

Paver, Elizabeth C., primary, Ahmed, Tasnia, additional, Burke, Hazel, additional, Saw, Robyn P. M., additional, Stretch, Jonathan R., additional, Spillane, Andrew J., additional, Shannon, Kerwin F., additional, Vergara, Ismael A., additional, Elder, David E., additional, Lo, Serigne N., additional, Thompson, John F., additional, and Scolyer, Richard A., additional

Published
2023
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24. The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex

Author

Prensner, John R, Iyer, Matthew K, Sahu, Anirban, Asangani, Irfan A, Cao, Qi, Patel, Lalit, Vergara, Ismael A, Davicioni, Elai, Erho, Nicholas, Ghadessi, Mercedeh, Jenkins, Robert B, Triche, Timothy J, Malik, Rohit, Bedenis, Rachel, McGregor, Natalie, Ma, Teng, Chen, Wei, Han, Sumin, Jing, Xiaojun, Cao, Xuhong, Wang, Xiaoju, Chandler, Benjamin, Yan, Wei, Siddiqui, Javed, Kunju, Lakshmi P, Dhanasekaran, Saravana M, Pienta, Kenneth J, Feng, Felix Y, and Chinnaiyan, Arul M

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Agricultural Biotechnology, Prostate Cancer, Urologic Diseases, Aging, Cancer, Animals, Cell Line, Tumor, Cell Proliferation, Chromosomal Proteins, Non-Histone, DNA-Binding Proteins, Female, Gene Expression Profiling, Humans, Male, Mice, Molecular Sequence Data, Neoplasm Invasiveness, Neoplasm Metastasis, Promoter Regions, Genetic, Prostatic Neoplasms, RNA Interference, RNA, Long Noncoding, RNA, Small Interfering, SMARCB1 Protein, Transcription Factors, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Prostate cancers remain indolent in the majority of individuals but behave aggressively in a minority. The molecular basis for this clinical heterogeneity remains incompletely understood. Here we characterize a long noncoding RNA termed SChLAP1 (second chromosome locus associated with prostate-1; also called LINC00913) that is overexpressed in a subset of prostate cancers. SChLAP1 levels independently predict poor outcomes, including metastasis and prostate cancer-specific mortality. In vitro and in vivo gain-of-function and loss-of-function experiments indicate that SChLAP1 is critical for cancer cell invasiveness and metastasis. Mechanistically, SChLAP1 antagonizes the genome-wide localization and regulatory functions of the SWI/SNF chromatin-modifying complex. These results suggest that SChLAP1 contributes to the development of lethal cancer at least in part by antagonizing the tumor-suppressive functions of the SWI/SNF complex.

Published
2013

26. Classification of the tumor immune microenvironment and associations with outcomes in patients with metastatic melanoma treated with immunotherapies

Author

Adegoke, Nurudeen A, primary, Gide, Tuba N, additional, Mao, Yizhe, additional, Quek, Camelia, additional, Patrick, Ellis, additional, Carlino, Matteo S, additional, Lo, Serigne N, additional, Menzies, Alexander Maxwell, additional, Pires da Silva, Ines, additional, Vergara, Ismael A, additional, Long, Georgina, additional, Scolyer, Richard A, additional, and Wilmott, James S, additional

Published
2023
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29. Supplementary Figure S1 from Intratumoral CD16+ Macrophages Are Associated with Clinical Outcomes of Patients with Metastatic Melanoma Treated with Combination Anti-PD-1 and Anti-CTLA-4 Therapy

Author

Lee, Hansol, primary, Ferguson, Angela L., primary, Quek, Camelia, primary, Vergara, Ismael A., primary, Pires daSilva, Ines, primary, Allen, Ruth, primary, Gide, Tuba Nur, primary, Conway, Jordan W., primary, Koufariotis, Lambros T., primary, Hayward, Nicholas K., primary, Waddell, Nicola, primary, Carlino, Matteo S., primary, Menzies, Alexander M., primary, Saw, Robyn P.M., primary, Shklovskaya, Elena, primary, Rizos, Helen, primary, Lo, Serigne, primary, Scolyer, Richard A., primary, Long, Georgina V., primary, Palendira, Umaimainthan, primary, and Wilmott, James S., primary

Published
2023
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30. Supplementary Table S1 from Intratumoral CD16+ Macrophages Are Associated with Clinical Outcomes of Patients with Metastatic Melanoma Treated with Combination Anti-PD-1 and Anti-CTLA-4 Therapy

Author

Lee, Hansol, primary, Ferguson, Angela L., primary, Quek, Camelia, primary, Vergara, Ismael A., primary, Pires daSilva, Ines, primary, Allen, Ruth, primary, Gide, Tuba Nur, primary, Conway, Jordan W., primary, Koufariotis, Lambros T., primary, Hayward, Nicholas K., primary, Waddell, Nicola, primary, Carlino, Matteo S., primary, Menzies, Alexander M., primary, Saw, Robyn P.M., primary, Shklovskaya, Elena, primary, Rizos, Helen, primary, Lo, Serigne, primary, Scolyer, Richard A., primary, Long, Georgina V., primary, Palendira, Umaimainthan, primary, and Wilmott, James S., primary

Published
2023
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31. Abstract 81: The association between melanoma liver metastases (mets) and the systemic anti-tumor immune profile

Author

Conway, Jordan W., primary, Marsh-Wakefield, Felix, additional, Nahar, Kazi J., additional, Lo, Serigne N., additional, Vergara, Ismael A., additional, Gide, Tuba N., additional, Attrill, Grace H., additional, Braden, Jorja, additional, Carlino, Matteo S., additional, Saw, Robyn P., additional, Thompson, John F., additional, Spillane, Andrew J., additional, Shannon, Kerwin F., additional, Shivalingam, Brindha, additional, Menzies, Alexander M., additional, Palendira, Umaimainthan, additional, Wilmott, James S., additional, Long, Georgina V., additional, Scolyer, Richard A., additional, and Da Silva, Ines Pires, additional

Published
2023
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32. Abstract 2369: Spatial organization of the tumour immune microenvironment (TIME) in primary and metastatic melanoma is associated with patient outcome

Author

Attrill, Grace Heloise, primary, Shteinman, Eva R., additional, Bai, Xinyu, additional, Marsh-Wakefield, Felix, additional, Quek, Camelia, additional, Palendira, Umaimainthan, additional, Vergara, Ismael A., additional, Long, Georgina V., additional, Scolyer, Richard A., additional, and Wilmott, James S., additional

Published
2023
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33. Supplementary Data from Comparative Genomics Provides Etiologic and Biological Insight into Melanoma Subtypes

Author

Newell, Felicity, primary, Johansson, Peter A., primary, Wilmott, James S., primary, Nones, Katia, primary, Lakis, Vanessa, primary, Pritchard, Antonia L., primary, Lo, Serigne N., primary, Rawson, Robert V., primary, Kazakoff, Stephen H., primary, Colebatch, Andrew J., primary, Koufariotis, Lambros T., primary, Ferguson, Peter M., primary, Wood, Scott, primary, Leonard, Conrad, primary, Law, Matthew H., primary, Brooks, Kelly M., primary, Broit, Natasa, primary, Palmer, Jane M., primary, Couts, Kasey L., primary, Vergara, Ismael A., primary, Long, Georgina V., primary, Barbour, Andrew P., primary, Nieweg, Omgo E., primary, Shivalingam, Brindha, primary, Robinson, William A., primary, Stretch, Jonathan R., primary, Spillane, Andrew J., primary, Saw, Robyn P.M., primary, Shannon, Kerwin F., primary, Thompson, John F., primary, Mann, Graham J., primary, Pearson, John V., primary, Scolyer, Richard A., primary, Waddell, Nicola, primary, and Hayward, Nicholas K., primary

Published
2023
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34. Data from Comparative Genomics Provides Etiologic and Biological Insight into Melanoma Subtypes

Author

Newell, Felicity, primary, Johansson, Peter A., primary, Wilmott, James S., primary, Nones, Katia, primary, Lakis, Vanessa, primary, Pritchard, Antonia L., primary, Lo, Serigne N., primary, Rawson, Robert V., primary, Kazakoff, Stephen H., primary, Colebatch, Andrew J., primary, Koufariotis, Lambros T., primary, Ferguson, Peter M., primary, Wood, Scott, primary, Leonard, Conrad, primary, Law, Matthew H., primary, Brooks, Kelly M., primary, Broit, Natasa, primary, Palmer, Jane M., primary, Couts, Kasey L., primary, Vergara, Ismael A., primary, Long, Georgina V., primary, Barbour, Andrew P., primary, Nieweg, Omgo E., primary, Shivalingam, Brindha, primary, Robinson, William A., primary, Stretch, Jonathan R., primary, Spillane, Andrew J., primary, Saw, Robyn P.M., primary, Shannon, Kerwin F., primary, Thompson, John F., primary, Mann, Graham J., primary, Pearson, John V., primary, Scolyer, Richard A., primary, Waddell, Nicola, primary, and Hayward, Nicholas K., primary

Published
2023
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35. Abstract 5701: Predictive biomarker models of immunotherapy response in patients with metastatic melanoma: genomic, transcriptomic, and immune profiles from the Personalised Immunotherapy Program (PIP)

Author

Gide, Tuba N., primary, Adegoke, Nurudeen A., additional, Mao, Yizhe, additional, Lennox, Monica, additional, Raj, Saurab, additional, Quek, Camelia, additional, Vergara, Ismael A., additional, Maher, Nigel, additional, Potter, Alison, additional, Saw, Robyn P., additional, Thompson, John F., additional, Spillane, Andrew J., additional, Shannon, Kerwin F., additional, Carlino, Matteo S., additional, Gonzalez, Maria, additional, Lo, Serigne N., additional, Menzies, Alexander M., additional, da Silva, Inês Pires, additional, Scolyer, Richard A., additional, Long, Georgina V., additional, and Wilmott, James S., additional

Published
2023
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37. Figure S2 from Somatic Hypermutation of the YAP Oncogene in a Human Cutaneous Melanoma

Author

Zhang, Xiaomeng, primary, Tang, Jian Zhong, primary, Vergara, Ismael A., primary, Zhang, Youfang, primary, Szeto, Pacman, primary, Yang, Lie, primary, Mintoff, Christopher, primary, Colebatch, Andrew, primary, McIntosh, Lachlan, primary, Mitchell, Katrina A., primary, Shaw, Evangeline, primary, Rizos, Helen, primary, Long, Georgina V., primary, Hayward, Nicholas, primary, McArthur, Grant A., primary, Papenfuss, Anthony T., primary, Harvey, Kieran F., primary, and Shackleton, Mark, primary

Published
2023
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38. Supplemental Legends from Somatic Hypermutation of the YAP Oncogene in a Human Cutaneous Melanoma

Author

Zhang, Xiaomeng, primary, Tang, Jian Zhong, primary, Vergara, Ismael A., primary, Zhang, Youfang, primary, Szeto, Pacman, primary, Yang, Lie, primary, Mintoff, Christopher, primary, Colebatch, Andrew, primary, McIntosh, Lachlan, primary, Mitchell, Katrina A., primary, Shaw, Evangeline, primary, Rizos, Helen, primary, Long, Georgina V., primary, Hayward, Nicholas, primary, McArthur, Grant A., primary, Papenfuss, Anthony T., primary, Harvey, Kieran F., primary, and Shackleton, Mark, primary

Published
2023
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39. Data from Clinical Features Associated with Outcomes and Biomarker Analysis of Dabrafenib plus Trametinib Treatment in Patients with BRAF-Mutant Melanoma Brain Metastases

Author

Wilmott, James S., primary, Tawbi, Hussein, primary, Engh, Johnathan A., primary, Amankulor, Nduka M., primary, Shivalingam, Brindha, primary, Banerjee, Hiya, primary, Vergara, Ismael A., primary, Lee, Hansol, primary, Johansson, Peter A., primary, Ferguson, Peter M., primary, Saiag, Philippe, primary, Robert, Caroline, primary, Grob, Jean-Jacques, primary, Butterfield, Lisa H., primary, Scolyer, Richard A., primary, Kirkwood, John M., primary, Long, Georgina V., primary, and Davies, Michael A., primary

Published
2023
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40. Supplementary Figure S1 from Clinical Features Associated with Outcomes and Biomarker Analysis of Dabrafenib plus Trametinib Treatment in Patients with BRAF-Mutant Melanoma Brain Metastases

Author

Wilmott, James S., primary, Tawbi, Hussein, primary, Engh, Johnathan A., primary, Amankulor, Nduka M., primary, Shivalingam, Brindha, primary, Banerjee, Hiya, primary, Vergara, Ismael A., primary, Lee, Hansol, primary, Johansson, Peter A., primary, Ferguson, Peter M., primary, Saiag, Philippe, primary, Robert, Caroline, primary, Grob, Jean-Jacques, primary, Butterfield, Lisa H., primary, Scolyer, Richard A., primary, Kirkwood, John M., primary, Long, Georgina V., primary, and Davies, Michael A., primary

Published
2023
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41. Supplementary Tables S6 and S7 from Germline Variants in Asporin Vary by Race, Modulate the Tumor Microenvironment, and Are Differentially Associated with Metastatic Prostate Cancer

Author

Hurley, Paula J., primary, Sundi, Debasish, primary, Shinder, Brian, primary, Simons, Brian W., primary, Hughes, Robert M., primary, Miller, Rebecca M., primary, Benzon, Benjamin, primary, Faraj, Sheila F., primary, Netto, George J., primary, Vergara, Ismael A., primary, Erho, Nicholas, primary, Davicioni, Elai, primary, Karnes, R. Jeffrey, primary, Yan, Guifang, primary, Ewing, Charles, primary, Isaacs, Sarah D., primary, Berman, David M., primary, Rider, Jennifer R., primary, Jordahl, Kristina M., primary, Mucci, Lorelei A., primary, Huang, Jessie, primary, An, Steven S., primary, Park, Ben H., primary, Isaacs, William B., primary, Marchionni, Luigi, primary, Ross, Ashley E., primary, and Schaeffer, Edward M., primary

Published
2023
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42. Supplementary Figure S1 from Germline Variants in Asporin Vary by Race, Modulate the Tumor Microenvironment, and Are Differentially Associated with Metastatic Prostate Cancer

Author

Hurley, Paula J., primary, Sundi, Debasish, primary, Shinder, Brian, primary, Simons, Brian W., primary, Hughes, Robert M., primary, Miller, Rebecca M., primary, Benzon, Benjamin, primary, Faraj, Sheila F., primary, Netto, George J., primary, Vergara, Ismael A., primary, Erho, Nicholas, primary, Davicioni, Elai, primary, Karnes, R. Jeffrey, primary, Yan, Guifang, primary, Ewing, Charles, primary, Isaacs, Sarah D., primary, Berman, David M., primary, Rider, Jennifer R., primary, Jordahl, Kristina M., primary, Mucci, Lorelei A., primary, Huang, Jessie, primary, An, Steven S., primary, Park, Ben H., primary, Isaacs, William B., primary, Marchionni, Luigi, primary, Ross, Ashley E., primary, and Schaeffer, Edward M., primary

Published
2023
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43. Supplementary Figure S5. SPARCL-1 coated beads do not reinforce cellular traction. from Androgen-Regulated SPARCL1 in the Tumor Microenvironment Inhibits Metastatic Progression

Author

Hurley, Paula J., primary, Hughes, Robert M., primary, Simons, Brian W., primary, Huang, Jessie, primary, Miller, Rebecca M., primary, Shinder, Brian, primary, Haffner, Michael C., primary, Esopi, David, primary, Kimura, Yasunori, primary, Jabbari, Javaneh, primary, Ross, Ashley E., primary, Erho, Nicholas, primary, Vergara, Ismael A., primary, Faraj, Sheila F., primary, Davicioni, Elai, primary, Netto, George J., primary, Yegnasubramanian, Srinivasan, primary, An, Steven S., primary, and Schaeffer, Edward M., primary

Published
2023
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44. Supplementary Figure S7. Responses to SPARCL1-coated beads are concentration dependent. from Androgen-Regulated SPARCL1 in the Tumor Microenvironment Inhibits Metastatic Progression

Author

Hurley, Paula J., primary, Hughes, Robert M., primary, Simons, Brian W., primary, Huang, Jessie, primary, Miller, Rebecca M., primary, Shinder, Brian, primary, Haffner, Michael C., primary, Esopi, David, primary, Kimura, Yasunori, primary, Jabbari, Javaneh, primary, Ross, Ashley E., primary, Erho, Nicholas, primary, Vergara, Ismael A., primary, Faraj, Sheila F., primary, Davicioni, Elai, primary, Netto, George J., primary, Yegnasubramanian, Srinivasan, primary, An, Steven S., primary, and Schaeffer, Edward M., primary

Published
2023
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45. Data from Androgen-Regulated SPARCL1 in the Tumor Microenvironment Inhibits Metastatic Progression

Author

Hurley, Paula J., primary, Hughes, Robert M., primary, Simons, Brian W., primary, Huang, Jessie, primary, Miller, Rebecca M., primary, Shinder, Brian, primary, Haffner, Michael C., primary, Esopi, David, primary, Kimura, Yasunori, primary, Jabbari, Javaneh, primary, Ross, Ashley E., primary, Erho, Nicholas, primary, Vergara, Ismael A., primary, Faraj, Sheila F., primary, Davicioni, Elai, primary, Netto, George J., primary, Yegnasubramanian, Srinivasan, primary, An, Steven S., primary, and Schaeffer, Edward M., primary

Published
2023
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46. Supplementary Figure S3 from UV-Associated Mutations Underlie the Etiology of MCV-Negative Merkel Cell Carcinomas

Author

Wong, Stephen Q., primary, Waldeck, Kelly, primary, Vergara, Ismael A., primary, Schröder, Jan, primary, Madore, Jason, primary, Wilmott, James S., primary, Colebatch, Andrew J., primary, De Paoli-Iseppi, Ricardo, primary, Li, Jason, primary, Lupat, Richard, primary, Semple, Timothy, primary, Arnau, Gisela Mir, primary, Fellowes, Andrew, primary, Leonard, J. Helen, primary, Hruby, George, primary, Mann, Graham J., primary, Thompson, John F., primary, Cullinane, Carleen, primary, Johnston, Meredith, primary, Shackleton, Mark, primary, Sandhu, Shahneen, primary, Bowtell, David D.L., primary, Johnstone, Ricky W., primary, Fox, Stephen B., primary, McArthur, Grant A., primary, Papenfuss, Anthony T., primary, Scolyer, Richard A., primary, Gill, Anthony J., primary, Hicks, Rodney J., primary, and Tothill, Richard W., primary

Published
2023
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47. Supplementary Methods and References from UV-Associated Mutations Underlie the Etiology of MCV-Negative Merkel Cell Carcinomas

Author

Wong, Stephen Q., primary, Waldeck, Kelly, primary, Vergara, Ismael A., primary, Schröder, Jan, primary, Madore, Jason, primary, Wilmott, James S., primary, Colebatch, Andrew J., primary, De Paoli-Iseppi, Ricardo, primary, Li, Jason, primary, Lupat, Richard, primary, Semple, Timothy, primary, Arnau, Gisela Mir, primary, Fellowes, Andrew, primary, Leonard, J. Helen, primary, Hruby, George, primary, Mann, Graham J., primary, Thompson, John F., primary, Cullinane, Carleen, primary, Johnston, Meredith, primary, Shackleton, Mark, primary, Sandhu, Shahneen, primary, Bowtell, David D.L., primary, Johnstone, Ricky W., primary, Fox, Stephen B., primary, McArthur, Grant A., primary, Papenfuss, Anthony T., primary, Scolyer, Richard A., primary, Gill, Anthony J., primary, Hicks, Rodney J., primary, and Tothill, Richard W., primary

Published
2023
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48. Data from UV-Associated Mutations Underlie the Etiology of MCV-Negative Merkel Cell Carcinomas

Author

Wong, Stephen Q., primary, Waldeck, Kelly, primary, Vergara, Ismael A., primary, Schröder, Jan, primary, Madore, Jason, primary, Wilmott, James S., primary, Colebatch, Andrew J., primary, De Paoli-Iseppi, Ricardo, primary, Li, Jason, primary, Lupat, Richard, primary, Semple, Timothy, primary, Arnau, Gisela Mir, primary, Fellowes, Andrew, primary, Leonard, J. Helen, primary, Hruby, George, primary, Mann, Graham J., primary, Thompson, John F., primary, Cullinane, Carleen, primary, Johnston, Meredith, primary, Shackleton, Mark, primary, Sandhu, Shahneen, primary, Bowtell, David D.L., primary, Johnstone, Ricky W., primary, Fox, Stephen B., primary, McArthur, Grant A., primary, Papenfuss, Anthony T., primary, Scolyer, Richard A., primary, Gill, Anthony J., primary, Hicks, Rodney J., primary, and Tothill, Richard W., primary

Published
2023
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49. Supplementary Figure S3. The tumor microenvironment in Sparcl1-/- models. from Androgen-Regulated SPARCL1 in the Tumor Microenvironment Inhibits Metastatic Progression

Author

Hurley, Paula J., primary, Hughes, Robert M., primary, Simons, Brian W., primary, Huang, Jessie, primary, Miller, Rebecca M., primary, Shinder, Brian, primary, Haffner, Michael C., primary, Esopi, David, primary, Kimura, Yasunori, primary, Jabbari, Javaneh, primary, Ross, Ashley E., primary, Erho, Nicholas, primary, Vergara, Ismael A., primary, Faraj, Sheila F., primary, Davicioni, Elai, primary, Netto, George J., primary, Yegnasubramanian, Srinivasan, primary, An, Steven S., primary, and Schaeffer, Edward M., primary

Published
2023
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50. Supplementary Figure S6. SPARCL1 engages cell-ECM interactions. from Androgen-Regulated SPARCL1 in the Tumor Microenvironment Inhibits Metastatic Progression

Author

Hurley, Paula J., primary, Hughes, Robert M., primary, Simons, Brian W., primary, Huang, Jessie, primary, Miller, Rebecca M., primary, Shinder, Brian, primary, Haffner, Michael C., primary, Esopi, David, primary, Kimura, Yasunori, primary, Jabbari, Javaneh, primary, Ross, Ashley E., primary, Erho, Nicholas, primary, Vergara, Ismael A., primary, Faraj, Sheila F., primary, Davicioni, Elai, primary, Netto, George J., primary, Yegnasubramanian, Srinivasan, primary, An, Steven S., primary, and Schaeffer, Edward M., primary

Published
2023
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