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5. FIGURE 4 from FASN Gene Methylation is Associated with Fatty Acid Synthase Expression and Clinical-genomic Features of Prostate Cancer

Author

Dairo, Oluwademilade, primary, DePaula Oliveira, Lia, primary, Schaffer, Ethan, primary, Vidotto, Thiago, primary, Mendes, Adrianna A., primary, Lu, Jiayun, primary, Huynh, Sophie Vo, primary, Hicks, Jessica, primary, Sowalsky, Adam G., primary, De Marzo, Angelo M., primary, Joshu, Corrine E., primary, Hanratty, Brian, primary, Sfanos, Karen S., primary, Isaacs, William B., primary, Haffner, Michael C., primary, and Lotan, Tamara L., primary

Published
2024
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6. Supplementary Figure S2 from FASN Gene Methylation is Associated with Fatty Acid Synthase Expression and Clinical-genomic Features of Prostate Cancer

Author

Dairo, Oluwademilade, primary, DePaula Oliveira, Lia, primary, Schaffer, Ethan, primary, Vidotto, Thiago, primary, Mendes, Adrianna A., primary, Lu, Jiayun, primary, Huynh, Sophie Vo, primary, Hicks, Jessica, primary, Sowalsky, Adam G., primary, De Marzo, Angelo M., primary, Joshu, Corrine E., primary, Hanratty, Brian, primary, Sfanos, Karen S., primary, Isaacs, William B., primary, Haffner, Michael C., primary, and Lotan, Tamara L., primary

Published
2024
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7. FIGURE 3 from FASN Gene Methylation is Associated with Fatty Acid Synthase Expression and Clinical-genomic Features of Prostate Cancer

Author

Dairo, Oluwademilade, primary, DePaula Oliveira, Lia, primary, Schaffer, Ethan, primary, Vidotto, Thiago, primary, Mendes, Adrianna A., primary, Lu, Jiayun, primary, Huynh, Sophie Vo, primary, Hicks, Jessica, primary, Sowalsky, Adam G., primary, De Marzo, Angelo M., primary, Joshu, Corrine E., primary, Hanratty, Brian, primary, Sfanos, Karen S., primary, Isaacs, William B., primary, Haffner, Michael C., primary, and Lotan, Tamara L., primary

Published
2024
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8. Data from FASN Gene Methylation is Associated with Fatty Acid Synthase Expression and Clinical-genomic Features of Prostate Cancer

Author

Dairo, Oluwademilade, primary, DePaula Oliveira, Lia, primary, Schaffer, Ethan, primary, Vidotto, Thiago, primary, Mendes, Adrianna A., primary, Lu, Jiayun, primary, Huynh, Sophie Vo, primary, Hicks, Jessica, primary, Sowalsky, Adam G., primary, De Marzo, Angelo M., primary, Joshu, Corrine E., primary, Hanratty, Brian, primary, Sfanos, Karen S., primary, Isaacs, William B., primary, Haffner, Michael C., primary, and Lotan, Tamara L., primary

Published
2024
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9. Supplementary Tables S1-S7 from FASN Gene Methylation is Associated with Fatty Acid Synthase Expression and Clinical-genomic Features of Prostate Cancer

Author

Dairo, Oluwademilade, primary, DePaula Oliveira, Lia, primary, Schaffer, Ethan, primary, Vidotto, Thiago, primary, Mendes, Adrianna A., primary, Lu, Jiayun, primary, Huynh, Sophie Vo, primary, Hicks, Jessica, primary, Sowalsky, Adam G., primary, De Marzo, Angelo M., primary, Joshu, Corrine E., primary, Hanratty, Brian, primary, Sfanos, Karen S., primary, Isaacs, William B., primary, Haffner, Michael C., primary, and Lotan, Tamara L., primary

Published
2024
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10. FIGURE 5 from FASN Gene Methylation is Associated with Fatty Acid Synthase Expression and Clinical-genomic Features of Prostate Cancer

Author

Dairo, Oluwademilade, primary, DePaula Oliveira, Lia, primary, Schaffer, Ethan, primary, Vidotto, Thiago, primary, Mendes, Adrianna A., primary, Lu, Jiayun, primary, Huynh, Sophie Vo, primary, Hicks, Jessica, primary, Sowalsky, Adam G., primary, De Marzo, Angelo M., primary, Joshu, Corrine E., primary, Hanratty, Brian, primary, Sfanos, Karen S., primary, Isaacs, William B., primary, Haffner, Michael C., primary, and Lotan, Tamara L., primary

Published
2024
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11. FIGURE 6 from FASN Gene Methylation is Associated with Fatty Acid Synthase Expression and Clinical-genomic Features of Prostate Cancer

Author

Dairo, Oluwademilade, primary, DePaula Oliveira, Lia, primary, Schaffer, Ethan, primary, Vidotto, Thiago, primary, Mendes, Adrianna A., primary, Lu, Jiayun, primary, Huynh, Sophie Vo, primary, Hicks, Jessica, primary, Sowalsky, Adam G., primary, De Marzo, Angelo M., primary, Joshu, Corrine E., primary, Hanratty, Brian, primary, Sfanos, Karen S., primary, Isaacs, William B., primary, Haffner, Michael C., primary, and Lotan, Tamara L., primary

Published
2024
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12. FIGURE 2 from FASN Gene Methylation is Associated with Fatty Acid Synthase Expression and Clinical-genomic Features of Prostate Cancer

Author

Dairo, Oluwademilade, primary, DePaula Oliveira, Lia, primary, Schaffer, Ethan, primary, Vidotto, Thiago, primary, Mendes, Adrianna A., primary, Lu, Jiayun, primary, Huynh, Sophie Vo, primary, Hicks, Jessica, primary, Sowalsky, Adam G., primary, De Marzo, Angelo M., primary, Joshu, Corrine E., primary, Hanratty, Brian, primary, Sfanos, Karen S., primary, Isaacs, William B., primary, Haffner, Michael C., primary, and Lotan, Tamara L., primary

Published
2024
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13. TABLE 2 from FASN Gene Methylation is Associated with Fatty Acid Synthase Expression and Clinical-genomic Features of Prostate Cancer

Author

Dairo, Oluwademilade, primary, DePaula Oliveira, Lia, primary, Schaffer, Ethan, primary, Vidotto, Thiago, primary, Mendes, Adrianna A., primary, Lu, Jiayun, primary, Huynh, Sophie Vo, primary, Hicks, Jessica, primary, Sowalsky, Adam G., primary, De Marzo, Angelo M., primary, Joshu, Corrine E., primary, Hanratty, Brian, primary, Sfanos, Karen S., primary, Isaacs, William B., primary, Haffner, Michael C., primary, and Lotan, Tamara L., primary

Published
2024
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14. TABLE 1 from FASN Gene Methylation is Associated with Fatty Acid Synthase Expression and Clinical-genomic Features of Prostate Cancer

Author

Dairo, Oluwademilade, primary, DePaula Oliveira, Lia, primary, Schaffer, Ethan, primary, Vidotto, Thiago, primary, Mendes, Adrianna A., primary, Lu, Jiayun, primary, Huynh, Sophie Vo, primary, Hicks, Jessica, primary, Sowalsky, Adam G., primary, De Marzo, Angelo M., primary, Joshu, Corrine E., primary, Hanratty, Brian, primary, Sfanos, Karen S., primary, Isaacs, William B., primary, Haffner, Michael C., primary, and Lotan, Tamara L., primary

Published
2024
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15. FIGURE 1 from FASN Gene Methylation is Associated with Fatty Acid Synthase Expression and Clinical-genomic Features of Prostate Cancer

Author

Dairo, Oluwademilade, primary, DePaula Oliveira, Lia, primary, Schaffer, Ethan, primary, Vidotto, Thiago, primary, Mendes, Adrianna A., primary, Lu, Jiayun, primary, Huynh, Sophie Vo, primary, Hicks, Jessica, primary, Sowalsky, Adam G., primary, De Marzo, Angelo M., primary, Joshu, Corrine E., primary, Hanratty, Brian, primary, Sfanos, Karen S., primary, Isaacs, William B., primary, Haffner, Michael C., primary, and Lotan, Tamara L., primary

Published
2024
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16. FASN Gene Methylation is Associated with Fatty Acid Synthase Expression and Clinical-Genomic Features of Prostate Cancer

Author

Dairo, Oluwademilade O, primary, DePaula Oliveira, Lia, additional, Schaffer, Ethan, additional, Vidotto, Thiago, additional, Mendes, Adrianna A A, additional, Lu, Jiayun, additional, Huynh, Sophie Vo, additional, Hicks, Jessica L., additional, Sowalsky, Adam G., additional, De Marzo, Angelo M, additional, Joshu, Corinne E, additional, Hanratty, Brian, additional, Sfanos, Karen S, additional, Isaacs, William B., additional, Haffner, Michael C., additional, and Lotan, Tamara L, additional

Published
2023
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18. Plasma cells are enriched in localized prostate cancer in Black men and are associated with improved outcomes

Author

Weiner, Adam B., Vidotto, Thiago, Liu, Yang, Mendes, Adrianna A., Salles, Daniela C., Faisal, Farzana A., Murali, Sanjana, McFarlane, Matthew, Imada, Eddie L., Zhao, Xin, Li, Ziwen, Davicioni, Elai, Marchionni, Luigi, Chinnaiyan, Arul M., Freedland, Stephen J., Spratt, Daniel E., Wu, Jennifer D., Lotan, Tamara L., and Schaeffer, Edward M.

Published
2021
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21. PD27-11 COMPARISON OF PROSTATE BIOPSY GRADE OBTAINED BY HUMAN PATHOLOGISTS VERSUS AN ARTIFICIAL INTELLIGENCE ALGORITHM FOR PREDICTING BIOCHEMICAL RECURRENCE AFTER RADICAL PROSTATECTOMY

Author

Calle, Claire de la, primary, Vidotto, Thiago, additional, Erak, Eric, additional, Salles, Daniela, additional, Dairo, Oluwademilade, additional, Pavlovich, Christian, additional, Han, Misop, additional, Cho, Joonyoung, additional, Suh, In Hye, additional, Chang, Hye Yoon, additional, Kim, Sun Woo, additional, Gorin, Michael, additional, and Lotan, Tamara, additional

Published
2023
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22. Supplementary Data from CDKN1B Deletions are Associated with Metastasis in African American Men with Clinically Localized, Surgically Treated Prostate Cancer

Author

Faisal, Farzana A., primary, Murali, Sanjana, primary, Kaur, Harsimar, primary, Vidotto, Thiago, primary, Guedes, Liana B., primary, Salles, Daniela Correia, primary, Kothari, Vishal, primary, Tosoian, Jeffrey J., primary, Han, Sumin, primary, Hovelson, Daniel H., primary, Hu, Kevin, primary, Spratt, Daniel E., primary, Baras, Alexander S., primary, Tomlins, Scott A., primary, Schaeffer, Edward M., primary, and Lotan, Tamara L., primary

Published
2023
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24. Association of self-identified race and genetic ancestry with the immunogenomic landscape of primary prostate cancer

Author

Vidotto, Thiago, primary, Imada, Eddie L., additional, Faisal, Farzana, additional, Murali, Sanjana, additional, Mendes, Adrianna A., additional, Kaur, Harsimar, additional, Zheng, Siqun, additional, Xu, Jianfeng, additional, Schaeffer, Edward M., additional, Isaacs, William B., additional, Sfanos, Karen S., additional, Marchionni, Luigi, additional, and Lotan, Tamara L., additional

Published
2023
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28. Reciprocal YAP1 loss and INSM1 expression in neuroendocrine prostate cancer

Author

Asrani, Kaushal, primary, Torres, Alba FC, additional, Woo, Juhyung, additional, Vidotto, Thiago, additional, Tsai, Harrison K, additional, Luo, Jun, additional, Corey, Eva, additional, Hanratty, Brian, additional, Coleman, Ilsa, additional, Yegnasubramanian, Srinivasan, additional, De Marzo, Angelo M, additional, Nelson, Peter S, additional, Haffner, Michael C, additional, and Lotan, Tamara L, additional

Published
2021
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33. Additional file 2 of Transcriptional landscape of PTEN loss in primary prostate cancer

Author

Imada, Eddie Luidy, Sanchez, Diego Fernando, Dinalankara, Wikum, Vidotto, Thiago, Ebot, Ericka M., Tyekucheva, Svitlana, Franco, Gloria Regina, Mucci, Lorelei Ann, Loda, Massimo, Schaeffer, Edward Matthew, Lotan, Tamara, and Marchionni, Luigi

Abstract

Additional file 2: Supplementary Figures. PDF file containing the raw results of all bioinformatics analysis. Figure S1. Cross-study of differential gene expression in PTEN-null vs PTEN-intact in ERG+ samples. Meta-analysis of HPFS/PHS and NH cohorts with Bayesian Hierarchical Model for DGE using XDE showing the top 25 most concordant differentially up- and down-regulated genes. PTEN status were based on IHC assays. Figure S2. PTEN expression levels stratified by CNV. Figure shows PTEN expression levels distribution by copy number variation (CNV), called by GISTIC algorithm. Figure S3. Correspondence-at-the-top (CAT) plot between TCGA CNV-based calls and the Bayesian Hierarchical Model approach (BHM). Agreement of genes ranked by t-statistics (TCGA) and average Bayesian Effect Size (BHM). Lines represent agreement between tested cohorts for PTEN-intact vs PTEN-null. Black-to-light grey shades represent the decreasing probability of agreeing by chance based on the hypergeometric distribution, with intervals ranging from 0.999999 (light grey) to 0.95 (dark grey). Lines outside this range represent agreement in different cohorts with a higher agreement than expected by chance. Figure S4. Expression of AC009478.1 is shown to be highly specific to PRAD, BLCA, to a lesser extent in UECA and BRCA. Figure shows raw expression values of SchLAP1 and AC009478.1 across cancer types. Pearson correlations and p-values are shown in red. Figure S5. Expression of FANTOM-CAT lncRNAs genes (top) and close coding genes (bottom) stratified by PTEN status. Significances based on t-test between PTEN-null and PTEN-intact using log2 CPM + 1 value. Significance cutoffs: * 0.05; **≤0.01; ***≤0.0001. Figure S6. Person correlation gene CATG00000038715 and CYP4F2 across cancer types. CATG00000038715 and CYP4F2 expression are shown to be highly correlated in PCa. Moreover, CATG00000038715 expression is shown to be highly specific to PCa. With exception of leukemia cells, none of the other tumors expressed high levels of CATG00000038715. Figure S7. Gene set enrichment for Androgen repressed genes. Gene set enrichment analysis of gene signature showing positive enrichment of genes repressed by dihydrotestosterone after 6 h of exposure obtained from Schaeffer et al. Enrichment for BHM-signature is shown in panel A and TCGA-signature in panel B.

Published
2021
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36. GPNMB expression identifies TSC1/2/mTOR‐associated and MiT family translocation‐driven renal neoplasms.

Author

Salles, Daniela C, Asrani, Kaushal, Woo, Juhyung, Vidotto, Thiago, Liu, Hans B, Vidal, Igor, Matoso, Andres, Netto, George J, Argani, Pedram, and Lotan, Tamara L

Subjects
KIDNEY tumors, RENAL cell carcinoma, ANGIOMYOLIPOMA, GENOME editing, IMAGE analysis, CELL tumors
Abstract

GPNMB (glycoprotein nonmetastatic B) and other TFE3/TFEB transcriptional targets have been proposed as markers for microphthalmia (MiT) translocation renal cell carcinomas (tRCCs). We recently demonstrated that constitutive mTORC1 activation via TSC1/2 loss leads to increased activity of TFE3/TFEB, suggesting that the pathogenesis and molecular markers for tRCCs and TSC1/2‐associated tumors may be overlapping. We examined GPNMB expression in human kidney and angiomyolipoma (AML) cell lines with TSC2 and/or TFE3/TFEB loss produced using CRISPR–Cas9 genome editing as well as in a mouse model of Tsc2 inactivation‐driven renal tumorigenesis. Using an automated immunohistochemistry (IHC) assay for GPNMB, digital image analysis was employed to quantitatively score expression in clear cell RCC (ccRCC, n = 87), papillary RCC (papRCC, n = 53), chromophobe RCC (chRCC, n = 34), oncocytoma (n = 4), TFE3‐ or TFEB‐driven tRCC (n = 56), eosinophilic solid and cystic RCC (ESC, n = 6), eosinophilic vacuolated tumor (EVT, n = 4), and low‐grade oncocytic tumor (LOT, n = 3), as well as AML (n = 29) and perivascular epithelioid cell tumors (PEComas, n = 8). In cell lines, GPNMB was upregulated following TSC2 loss in a MiT/TFE‐ and mTORC1‐dependent fashion. Renal tumors in Tsc2+/− A/J mice showed upregulation of GPNMB compared with normal kidney. Mean GPNMB expression was significantly higher in tRCC than in ccRCC (p < 0.0001), papRCC (p < 0.0001), and chRCC (p < 0.0001). GPNMB expression in TSC1/2/MTOR alteration‐associated renal tumors (including ESC, LOT, AML, and PEComa) was comparable to that in tRCC. The immunophenotype of tRCC and TSC1/2/MTOR alteration‐associated renal tumors is highly overlapping, likely due to the increased activity of TFE3/TFEB in both, revealing an important caveat regarding the use of TFE3/TFEB‐transcriptional targets as diagnostic markers. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland. [ABSTRACT FROM AUTHOR]

Published
2022
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39. Transcriptional landscape of PTEN loss in primary prostate cancer

Author

Imada, Eddie Luidy, primary, Sanchez, Diego Fernando, additional, Dinalankara, Wikum, additional, Vidotto, Thiago, additional, Ebot, Ericka M, additional, Tyekucheva, Svitlana, additional, Franco, Gloria Regina, additional, Mucci, Lorelei, additional, Loda, Massimo, additional, Schaeffer, Edward M, additional, Lotan, Tamara, additional, and Marchionni, Luigi, additional

Published
2020
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41. CDKN1B Deletions are Associated with Metastasis in African American Men with Clinically Localized, Surgically Treated Prostate Cancer

Author

Faisal, Farzana A., primary, Murali, Sanjana, additional, Kaur, Harsimar, additional, Vidotto, Thiago, additional, Guedes, Liana B., additional, Salles, Daniela Correia, additional, Kothari, Vishal, additional, Tosoian, Jeffrey J., additional, Han, Sumin, additional, Hovelson, Daniel H., additional, Hu, Kevin, additional, Spratt, Daniel E., additional, Baras, Alexander S., additional, Tomlins, Scott A., additional, Schaeffer, Edward M., additional, and Lotan, Tamara L., additional

Published
2020
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43. Risk Stratification of Prostate Cancer Through Quantitative Assessment of PTEN Loss (qPTEN)

Author

Jamaspishvili, Tamara, primary, Patel, Palak G, additional, Niu, Yi, additional, Vidotto, Thiago, additional, Caven, Isabelle, additional, Livergant, Rachel, additional, Fu, Winnie, additional, Kawashima, Atsunari, additional, How, Nathan, additional, Okello, John B, additional, Guedes, Liana B, additional, Ouellet, Veronique, additional, Picanço, Clarissa, additional, Koti, Madhuri, additional, Reis, Rodolfo B, additional, Saad, Fred, additional, Mes-Masson, Anne-Marie, additional, Lotan, Tamara L, additional, Squire, Jeremy A, additional, Peng, Yingwei P, additional, Siemens, D Robert, additional, and Berman, David M, additional

Published
2020
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47. Serotonin synthesis protects the mouse colonic crypt from DNA damage and colorectal tumorigenesis

Author

Sakita, Juliana Y, primary, Bader, Michael, additional, Santos, Emerson S, additional, Garcia, Sergio B, additional, Minto, Stefania B, additional, Alenina, Natalia, additional, Brunaldi, Mariângela O, additional, Carvalho, Milene C, additional, Vidotto, Thiago, additional, Gasparotto, Bianca, additional, Martins, Ronaldo B, additional, Silva, Wilson A, additional, Brandão, Marcus L, additional, Leite, Caio A, additional, Cunha, Fernando Q, additional, Karsenty, Gerard, additional, Squire, Jeremy A, additional, Uyemura, Sergio A, additional, and Kannen, Vinicius, additional

Published
2019
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48. PTEN‐deficient prostate cancer is associated with an immunosuppressive tumor microenvironment mediated by increased expression of IDO1 and infiltrating FoxP3+ T regulatory cells

Author

Vidotto, Thiago, primary, Saggioro, Fabiano P., additional, Jamaspishvili, Tamara, additional, Chesca, Deise L., additional, Picanço de Albuquerque, Clarissa G., additional, Reis, Rodolfo B., additional, Graham, Charles H., additional, Berman, David M., additional, Siemens, D. Robert, additional, Squire, Jeremy A., additional, and Koti, Madhuri, additional

Published
2019
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49. MP28-02 QUANTITATIVE MEASUREMENT OF PTEN LOSS IMPROVES RISK ASSESSMENT IN PROSTATE CANCER

Author

Jamaspishvili*, Tamara, primary, Patel, Palak, additional, Niu, Yi, additional, Vidotto, Thiago, additional, Caven, Isabelle, additional, Livergant, Rachel, additional, Fu, Winnie, additional, Ouellet, Veronique, additional, Picanço, Clarissa, additional, Koti, Madhuri, additional, How, Nathan, additional, Saad, Fred, additional, Mes-Masson, Anne-Marie, additional, Lotan, Tamara, additional, Squire, Jeremy, additional, Peng, Yingwei, additional, Berman, David, additional, and Reis, Rodolfo, additional

Published
2019
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