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51. Genomic profiling of primary and metastatic thyroid cancers.

Author

Máximo, Valdemar, Melo, Miguel, Yingjie Zhu, Gazzo, Andrea, Sobrinho Simões, Manuel, Da Cruz Paula, Arnaud, and Soares, Paula

Subjects
THYROID cancer, ANAPLASTIC thyroid cancer, LYMPHATIC metastasis, MEDULLARY thyroid carcinoma, BRAF genes, METASTASIS, SOMATIC mutation
Abstract

The genetic repertoire of primary thyroid cancers (TCs) is well documented, but there is a considerable lack of molecular profiling in metastatic TCs. Here, we retrieved and analyzed the molecular and clinical features of 475 primary and metastatic TCs subjected to targeted DNA sequencing, from the cBioPortal database. The cohort included primary and metastatic samples from 276 papillary thyroid carcinomas (PTCs), 5 follicular thyroid carcinomas, 22 Hürthle cell carcinomas (HCCs), 127 poorly differentiated thyroid carcinomas (PDTCs), 30 anaplastic thyroid carcinomas (ATCs) and 15 medullary thyroid carcinomas. The ATCs had the highest tumor mutational burden and the HCCs the highest fraction of the genome altered. Compared to primary PTCs, the metastases had a significantly higher frequency of genetic alterations affecting TERT (51% vs 77%, P < 0.001), CDKN2A (2% vs 10%, P < 0.01), RET (2% vs 7%, P < 0.05), CDKN2B (1% vs 6%, P < 0.05) and BCOR (0% vs 4%, P < 0.05). The distant metastases had a significantly lower frequency of BRAF (64% vs 85%, P < 0.01) and a significantly higher frequency of NRAS (13% vs 3%, P < 0.05) hotspot mutations than the lymph node metastases. Metastases from HCCs and PDTCs were found to be enriched for NF1 (29%) and TP53 (18%) biallelic alterations, respectively. The frequency of subclonal mutations in ATCs was significantly higher than in PTCs (43% vs 25%, P < 0.01) and PDTCs (43% vs 22%, P < 0.01). Metastatic TCs are enriched in clinically informative genetic alterations such as RET translocations, BRAF hotspot mutations and NF1 biallelic losses that may be explored therapeutically. [ABSTRACT FROM AUTHOR]

Published
2024
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52. KIT genetic alterations in breast cancer.

Author

Vahdatinia, Mahsa, Derakhshan, Fatemeh, Da Cruz Paula, Arnaud, Dopeso, Higinio, Marra, Antonio, Gazzo, Andrea M., Brown, David, Selenica, Pier, Ross, Dara S., Razavi, Pedram, Weigelt, Britta, Wen, Hannah Y., Brogi, Edi, Reis-Filho, Jorge S., Pareja, Fresia, and Hong Zhang

Subjects
BREAST, BREAST cancer, SOMATIC mutation, EPIDERMAL growth factor receptors, PROGESTERONE receptors
Published
2024
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54. Data from Cancer-Causative Mutations Occurring in Early Embryogenesis

Author

Pareja, Fresia, primary, Ptashkin, Ryan N., primary, Brown, David N., primary, Derakhshan, Fatemeh, primary, Selenica, Pier, primary, da Silva, Edaise M., primary, Gazzo, Andrea M., primary, Da Cruz Paula, Arnaud, primary, Breen, Kelsey, primary, Shen, Ronglai, primary, Marra, Antonio, primary, Zehir, Ahmet, primary, Benayed, Ryma, primary, Berger, Michael F., primary, Ceyhan-Birsoy, Ozge, primary, Jairam, Sowmya, primary, Sheehan, Margaret, primary, Patel, Utsav, primary, Kemel, Yelena, primary, Casanova-Murphy, Jacklyn, primary, Schwartz, Christopher J., primary, Vahdatinia, Mahsa, primary, Comen, Elizabeth, primary, Borsu, Laetitia, primary, Pei, Xin, primary, Riaz, Nadeem, primary, Abramson, David H., primary, Weigelt, Britta, primary, Walsh, Michael F., primary, Hadjantonakis, Anna-Katerina, primary, Ladanyi, Marc, primary, Offit, Kenneth, primary, Stadler, Zsofia K., primary, Robson, Mark E., primary, Reis-Filho, Jorge S., primary, and Mandelker, Diana, primary

Published
2023
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55. Supplementary Data from Cancer-Causative Mutations Occurring in Early Embryogenesis

Author

Pareja, Fresia, primary, Ptashkin, Ryan N., primary, Brown, David N., primary, Derakhshan, Fatemeh, primary, Selenica, Pier, primary, da Silva, Edaise M., primary, Gazzo, Andrea M., primary, Da Cruz Paula, Arnaud, primary, Breen, Kelsey, primary, Shen, Ronglai, primary, Marra, Antonio, primary, Zehir, Ahmet, primary, Benayed, Ryma, primary, Berger, Michael F., primary, Ceyhan-Birsoy, Ozge, primary, Jairam, Sowmya, primary, Sheehan, Margaret, primary, Patel, Utsav, primary, Kemel, Yelena, primary, Casanova-Murphy, Jacklyn, primary, Schwartz, Christopher J., primary, Vahdatinia, Mahsa, primary, Comen, Elizabeth, primary, Borsu, Laetitia, primary, Pei, Xin, primary, Riaz, Nadeem, primary, Abramson, David H., primary, Weigelt, Britta, primary, Walsh, Michael F., primary, Hadjantonakis, Anna-Katerina, primary, Ladanyi, Marc, primary, Offit, Kenneth, primary, Stadler, Zsofia K., primary, Robson, Mark E., primary, Reis-Filho, Jorge S., primary, and Mandelker, Diana, primary

Published
2023
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56. Data from V211D Mutation in MEK1 Causes Resistance to MEK Inhibitors in Colon Cancer

Author

Gao, Yijun, primary, Maria, Ann, primary, Na, Na, primary, da Cruz Paula, Arnaud, primary, Gorelick, Alexander N., primary, Hechtman, Jaclyn F., primary, Carson, Julianne, primary, Lefkowitz, Robert A., primary, Weigelt, Britta, primary, Taylor, Barry S., primary, Zhao, HuiYong, primary, Reis-Filho, Jorge S., primary, de Stanchina, Elisa, primary, Rosen, Neal, primary, Yao, Zhan, primary, and Yaeger, Rona, primary

Published
2023
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57. Supplementary Data from V211D Mutation in MEK1 Causes Resistance to MEK Inhibitors in Colon Cancer

Author

Gao, Yijun, primary, Maria, Ann, primary, Na, Na, primary, da Cruz Paula, Arnaud, primary, Gorelick, Alexander N., primary, Hechtman, Jaclyn F., primary, Carson, Julianne, primary, Lefkowitz, Robert A., primary, Weigelt, Britta, primary, Taylor, Barry S., primary, Zhao, HuiYong, primary, Reis-Filho, Jorge S., primary, de Stanchina, Elisa, primary, Rosen, Neal, primary, Yao, Zhan, primary, and Yaeger, Rona, primary

Published
2023
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58. Supplementary Data from MAPK Pathway Genetic Alterations Are Associated with Prolonged Overall Survival in Low-Grade Serous Ovarian Carcinoma

Author

Manning-Geist, Beryl, primary, Gordhandas, Sushmita, primary, Liu, Ying L., primary, Zhou, Qin, primary, Iasonos, Alexia, primary, Da Cruz Paula, Arnaud, primary, Mandelker, Diana, primary, Roche, Kara Long, primary, Zivanovic, Oliver, primary, Maio, Anna, primary, Kemel, Yelena, primary, Chi, Dennis S., primary, O'Cearbhaill, Roisin E., primary, Aghajanian, Carol, primary, Weigelt, Britta, primary, Chui, M. Herman, primary, and Grisham, Rachel N., primary

Published
2023
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59. Supplementary Methods from Whole-Exome Sequencing Analysis of the Progression from Non–Low-Grade Ductal Carcinoma In Situ to Invasive Ductal Carcinoma

Author

Pareja, Fresia, primary, Brown, David N., primary, Lee, Ju Youn, primary, Da Cruz Paula, Arnaud, primary, Selenica, Pier, primary, Bi, Rui, primary, Geyer, Felipe C., primary, Gazzo, Andrea, primary, da Silva, Edaise M., primary, Vahdatinia, Mahsa, primary, Stylianou, Anthe A., primary, Ferrando, Lorenzo, primary, Wen, Hannah Y., primary, Hicks, James B., primary, Weigelt, Britta, primary, and Reis-Filho, Jorge S., primary

Published
2023
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60. Supplementary Figure S5 from Whole-Exome Sequencing Analysis of the Progression from Non–Low-Grade Ductal Carcinoma In Situ to Invasive Ductal Carcinoma

Author

Pareja, Fresia, primary, Brown, David N., primary, Lee, Ju Youn, primary, Da Cruz Paula, Arnaud, primary, Selenica, Pier, primary, Bi, Rui, primary, Geyer, Felipe C., primary, Gazzo, Andrea, primary, da Silva, Edaise M., primary, Vahdatinia, Mahsa, primary, Stylianou, Anthe A., primary, Ferrando, Lorenzo, primary, Wen, Hannah Y., primary, Hicks, James B., primary, Weigelt, Britta, primary, and Reis-Filho, Jorge S., primary

Published
2023
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61. Supplementary Table S2 from Whole-Exome Sequencing Analysis of the Progression from Non–Low-Grade Ductal Carcinoma In Situ to Invasive Ductal Carcinoma

Author

Pareja, Fresia, primary, Brown, David N., primary, Lee, Ju Youn, primary, Da Cruz Paula, Arnaud, primary, Selenica, Pier, primary, Bi, Rui, primary, Geyer, Felipe C., primary, Gazzo, Andrea, primary, da Silva, Edaise M., primary, Vahdatinia, Mahsa, primary, Stylianou, Anthe A., primary, Ferrando, Lorenzo, primary, Wen, Hannah Y., primary, Hicks, James B., primary, Weigelt, Britta, primary, and Reis-Filho, Jorge S., primary

Published
2023
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62. KITgenetic alterations in breast cancer

Author

Vahdatinia, Mahsa, Derakhshan, Fatemeh, Da Cruz Paula, Arnaud, Dopeso, Higinio, Marra, Antonio, Gazzo, Andrea M, Brown, David, Selenica, Pier, Ross, Dara S, Razavi, Pedram, Zhang, Hong, Weigelt, Britta, Wen, Hannah Y, Brogi, Edi, Reis-Filho, Jorge S, and Pareja, Fresia

Abstract

AimsActivating somatic mutations or gene amplification of KITresult in constitutive activation of its receptor tyrosine kinase, which is targetable in various solid tumours. Here, we sought to investigate the presence of KITgenetic alterations in breast cancer (BC) and characterise the histological and genomic features of these tumours.MethodsA retrospective analysis of 5,575 BCs previously subjected to targeted sequencing using the FDA-authorised Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Targets (MSK-IMPACT) assay was performed to identify BCs with KITalterations. A histological assessment of KIT-altered BCs was conducted, and their repertoire of genetic alterations was compared with that of BCs lacking KITgenetic alterations, matched for age, histological type, oestrogen receptor/HER2 status and sample type.ResultsWe identified 18 BCs (0.32%), including 9 primary and 9 metastatic BCs, with oncogenic/likely oncogenic genetic alterations affecting KIT, including activating somatic mutations (n=4) or gene amplification (n=14). All KIT-altered BCs were of high histological grade, although no distinctive histological features were observed. When compared with BCs lacking KITgenetic alterations, no distinctive genetic features were identified. In two metastatic KIT-altered BCs in which the matched primary BC had also been analysed by MSK-IMPACT, the KITmutations were found to be restricted to the metastatic samples, suggesting that they were late events in the evolution of these cancers.ConclusionsKITgenetic alterations are vanishingly rare in BC. KIT-altered BCs are of high grade but lack distinctive histological features. Genetic alterations in KITmight be late events in the evolution and/or progression of BC.

Published
2024
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64. Comprehensive analysis of germline drivers in endometrial cancer

Author

Gordhandas, Sushmita, primary, Rios-Doria, Eric, additional, Cadoo, Karen A, additional, Catchings, Amanda, additional, Maio, Anna, additional, Kemel, Yelena, additional, Sheehan, Margaret, additional, Ranganathan, Megha, additional, Green, Dina, additional, Aryamvally, Anjali, additional, Arnold, Angela G, additional, Salo-Mullen, Erin, additional, Manning-Geist, Beryl, additional, Sia, Tiffany, additional, Selenica, Pier, additional, Da Cruz Paula, Arnaud, additional, Vanderbilt, Chad, additional, Misyura, Maksym, additional, Leitao, Mario M, additional, Mueller, Jennifer J, additional, Makker, Vicky, additional, Rubinstein, Maria, additional, Friedman, Claire F, additional, Zhou, Qin, additional, Iasonos, Alexia, additional, Latham, Alicia, additional, Carlo, Maria I, additional, Murciano-Goroff, Yonina R, additional, Will, Marie, additional, Walsh, Michael F, additional, Issa Bhaloo, Shirin, additional, Ellenson, Lora H, additional, Ceyhan-Birsoy, Ozge, additional, Berger, Michael F, additional, Robson, Mark E, additional, Abu-Rustum, Nadeem, additional, Aghajanian, Carol, additional, Offit, Kenneth, additional, Stadler, Zsofia, additional, Weigelt, Britta, additional, Mandelker, Diana L, additional, and Liu, Ying L, additional

Published
2023
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65. Comprehensive Genomic Profiling of Cell-Free Circulating Tumor DNA Detects Response to Ribociclib Plus Letrozole in a Patient with Metastatic Breast Cancer

Author

Silveira, Catarina, primary, Sousa, Ana Carla, additional, Corredeira, Patrícia, additional, Martins, Marta, additional, Sousa, Ana Rita, additional, Da Cruz Paula, Arnaud, additional, Selenica, Pier, additional, Brown, David N., additional, Golkaram, Mahdi, additional, Kaplan, Shannon, additional, Zhang, Shile, additional, Liu, Li, additional, Weigelt, Britta, additional, Reis-Filho, Jorge S., additional, Costa, Luís, additional, and Carmo-Fonseca, Maria, additional

Published
2022
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66. Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples

Author

Martelotto, Luciano G, Baslan, Timour, Kendall, Jude, Geyer, Felipe C, Burke, Kathleen A, Spraggon, Lee, Piscuoglio, Salvatore, Chadalavada, Kalyani, Nanjangud, Gouri, Ng, Charlotte K Y, Moody, Pamela, D'Italia, Sean, Rodgers, Linda, Cox, Hilary, da Cruz Paula, Arnaud, Stepansky, Asya, Schizas, Michail, Wen, Hannah Y, King, Tari A, Norton, Larry, Weigelt, Britta, Hicks, James B, and Reis-Filho, Jorge S

Subjects
Cancer cells -- Genetic aspects -- Health aspects, DNA sequencing -- Methods, Biological sciences, Health
Abstract

A substantial proportion of tumors consist of genotypically distinct subpopulations of cancer cells. This intratumor genetic heterogeneity poses a substantial challenge for the implementation of precision medicine. Single-cell genomics constitutes a powerful approach to resolve complex mixtures of cancer cells by tracing cell lineages and discovering cryptic genetic variations that would otherwise be obscured in tumor bulk analyses. Because of the chemical alterations that result from formalin fixation, single-cell genomic approaches have largely remained limited to fresh or rapidly frozen specimens. Here we describe the development and validation of a robust and accurate methodology to perform whole-genome copy-number profiling of single nuclei obtained from formalin-fixed paraffin-embedded clinical tumor samples. We applied the single-cell sequencing approach described here to study the progression from in situ to invasive breast cancer, which revealed that ductal carcinomas in situ show intratumor genetic heterogeneity at diagnosis and that these lesions may progress to invasive breast cancer through a variety of evolutionary processes., Author(s): Luciano G Martelotto [1]; Timour Baslan [2, 3]; Jude Kendall [2]; Felipe C Geyer [1]; Kathleen A Burke [1]; Lee Spraggon [1]; Salvatore Piscuoglio [1]; Kalyani Chadalavada [4]; Gouri [...]

Published
2017
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68. KITgenetic alterations in breast cancer

Author

Vahdatinia, Mahsa, primary, Derakhshan, Fatemeh, additional, Da Cruz Paula, Arnaud, additional, Dopeso, Higinio, additional, Marra, Antonio, additional, Gazzo, Andrea M, additional, Brown, David, additional, Selenica, Pier, additional, Ross, Dara S, additional, Razavi, Pedram, additional, Zhang, Hong, additional, Weigelt, Britta, additional, Wen, Hannah Y, additional, Brogi, Edi, additional, Reis-Filho, Jorge S, additional, and Pareja, Fresia, additional

Published
2022
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71. Loss-of-function mutations in ATP6AP1 and ATP6AP2 in granular cell tumors

Author

Pareja, Fresia, Brandes, Alissa H., Basili, Thais, Selenica, Pier, Geyer, Felipe C., Fan, Dan, Da Cruz Paula, Arnaud, Kumar, Rahul, Brown, David N., Gularte-Mérida, Rodrigo, Alemar, Barbara, Bi, Rui, Lim, Raymond S., de Bruijn, Ino, Fujisawa, Sho, Gardner, Rui, Feng, Elvin, Li, Anqi, da Silva, Edaise M., Lozada, John R., Blecua, Pedro, Cohen-Gould, Leona, Jungbluth, Achim A., Rakha, Emad A., Ellis, Ian O., Edelweiss, Maria I. A., Palazzo, Juan, Norton, Larry, Hollmann, Travis, Edelweiss, Marcia, Rubin, Brian P., Weigelt, Britta, and Reis-Filho, Jorge S.

Published
2018
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72. High-Sensitivity Mutation Analysis of Cell-Free DNA for Disease Monitoring in Endometrial Cancer

Author

Ashley, Charles W., primary, Selenica, Pier, additional, Patel, Juber, additional, Wu, Michelle, additional, Nincevic, Josip, additional, Lakhman, Yulia, additional, Zhou, Qin, additional, Shah, Ronak H., additional, Berger, Michael F., additional, Da Cruz Paula, Arnaud, additional, Brown, David N., additional, Marra, Antonio, additional, Iasonos, Alexia, additional, Momeni-Boroujeni, Amir, additional, Alektiar, Kaled M., additional, Long Roche, Kara, additional, Zivanovic, Oliver, additional, Mueller, Jennifer J., additional, Zamarin, Dmitriy, additional, Broach, Vance A., additional, Sonoda, Yukio, additional, Leitao, Mario M., additional, Friedman, Claire F., additional, Jewell, Elizabeth, additional, Reis-Filho, Jorge S., additional, Ellenson, Lora H., additional, Aghajanian, Carol, additional, Abu-Rustum, Nadeem R., additional, Cadoo, Karen, additional, and Weigelt, Britta, additional

Published
2022
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73. Risk stratification of stage I grade 3 endometrioid endometrial carcinoma (083)

Author

Zammarrelli, William, primary, Kim, Sarah, additional, Da Cruz Paula, Arnaud, additional, Rios-Doria, Eric, additional, Zhou, Qin, additional, Alektiar, Kaled, additional, Aghajanian, Carol, additional, Makker, Vicky, additional, Leitao, Mario, additional, Abu-Rustum, Nadeem, additional, Ellenson, Lora, additional, Weigelt, Britta, additional, and Mueller, Jennifer, additional

Published
2022
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74. Cell-free DNA analysis as a molecular tool to monitor response to immune checkpoint inhibition in endometrial cancer.

Author

Manning-Geist, Beryl, primary, Patel, Juber Ahamad A, additional, Marra, Antonio, additional, Da Cruz Paula, Arnaud, additional, Hanlon, Etta J, additional, Abu-Rustum, Nadeem, additional, Shah, Ronak H., additional, Berger, Michael F., additional, Hensley, Martee Leigh, additional, Zamarin, Dmitriy, additional, Weigelt, Britta, additional, and Friedman, Claire Frances, additional

Published
2022
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75. Recurrent WWTR1 S89W mutations and Hippo pathway deregulation in clear cell carcinomas of the cervix

Author

Kim, Sarah H, primary, Basili, Thais, additional, Dopeso, Higinio, additional, Da Cruz Paula, Arnaud, additional, Bi, Rui, additional, Issa Bhaloo, Shirin, additional, Pareja, Fresia, additional, Li, Qing, additional, da Silva, Edaise M, additional, Zhu, Yingjie, additional, Hoang, Timothy, additional, Selenica, Pier, additional, Murali, Rajmohan, additional, Chan, Eric, additional, Wu, Michelle, additional, Derakhshan, Fatemeh, additional, Maroldi, Ana, additional, Hanlon, Etta, additional, Ferreira, Carlos Gil, additional, Lapa e Silva, Jose Roberto, additional, Abu‐Rustum, Nadeem R, additional, Zamarin, Dmitriy, additional, Chandarlapaty, Sarat, additional, Matrai, Cathleen, additional, Yoon, Ju‐Yoon, additional, Reis‐Filho, Jorge S, additional, Park, Kay J, additional, and Weigelt, Britta, additional

Published
2022
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76. Hyperthermic intraperitoneal chemotherapy (HIPEC) with carboplatin induces distinct transcriptomic changes in ovarian tumor and normal tissues

Author

Moukarzel, Lea A., primary, Ferrando, Lorenzo, additional, Dopeso, Higinio, additional, Stylianou, Anthe, additional, Basili, Thais, additional, Pareja, Fresia, additional, Da Cruz Paula, Arnaud, additional, Zoppoli, Gabriele, additional, Abu-Rustum, Nadeem R., additional, Reis-Filho, Jorge S., additional, Long Roche, Kara, additional, Tew, William P., additional, Chi, Dennis S., additional, Sonoda, Yukio, additional, Zamarin, Dmitriy, additional, Aghajanian, Carol, additional, O'Cearbhaill, Roisin E., additional, Zivanovic, Oliver, additional, and Weigelt, Britta, additional

Published
2022
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77. MAPK Pathway Genetic Alterations Are Associated with Prolonged Overall Survival in Low-Grade Serous Ovarian Carcinoma

Author

Manning-Geist, Beryl, primary, Gordhandas, Sushmita, additional, Liu, Ying L., additional, Zhou, Qin, additional, Iasonos, Alexia, additional, Da Cruz Paula, Arnaud, additional, Mandelker, Diana, additional, Roche, Kara Long, additional, Zivanovic, Oliver, additional, Maio, Anna, additional, Kemel, Yelena, additional, Chi, Dennis S., additional, O'Cearbhaill, Roisin E., additional, Aghajanian, Carol, additional, Weigelt, Britta, additional, Chui, M. Herman, additional, and Grisham, Rachel N., additional

Published
2022
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78. Cancer-Causative Mutations Occurring in Early Embryogenesis

Author

Pareja, Fresia, primary, Ptashkin, Ryan N., additional, Brown, David N., additional, Derakhshan, Fatemeh, additional, Selenica, Pier, additional, da Silva, Edaise M., additional, Gazzo, Andrea M., additional, Da Cruz Paula, Arnaud, additional, Breen, Kelsey, additional, Shen, Ronglai, additional, Marra, Antonio, additional, Zehir, Ahmet, additional, Benayed, Ryma, additional, Berger, Michael F., additional, Ceyhan-Birsoy, Ozge, additional, Jairam, Sowmya, additional, Sheehan, Margaret, additional, Patel, Utsav, additional, Kemel, Yelena, additional, Casanova-Murphy, Jacklyn, additional, Schwartz, Christopher J., additional, Vahdatinia, Mahsa, additional, Comen, Elizabeth, additional, Borsu, Laetitia, additional, Pei, Xin, additional, Riaz, Nadeem, additional, Abramson, David H., additional, Weigelt, Britta, additional, Walsh, Michael F., additional, Hadjantonakis, Anna-Katerina, additional, Ladanyi, Marc, additional, Offit, Kenneth, additional, Stadler, Zsofia K., additional, Robson, Mark E., additional, Reis-Filho, Jorge S., additional, and Mandelker, Diana, additional

Published
2021
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81. The repertoire of somatic genetic alterations of acinic cell carcinomas of the breast: an exploratory, hypothesis-generating study

Author

Guerini-Rocco, Elena, Hodi, Zsolt, Piscuoglio, Salvatore, Ng, Charlotte KY, Rakha, Emad A, Schultheis, Anne M, Marchiò, Caterina, da Cruz Paula, Arnaud, De Filippo, Maria R, Martelotto, Luciano G, De Mattos-Arruda, Leticia, Edelweiss, Marcia, Jungbluth, Achim A, Fusco, Nicola, Norton, Larry, Weigelt, Britta, Ellis, Ian O, and Reis-Filho, Jorge S

Published
2015
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82. Immune and malignant cell phenotypes of ovarian cancer are determined by distinct mutational processes

Author

Vázquez-García, Ignacio, primary, Uhlitz, Florian, additional, Ceglia, Nicholas, additional, Lim, Jamie L.P., additional, Wu, Michelle, additional, Mohibullah, Neeman, additional, Ruiz, Arvin Eric B., additional, Boehm, Kevin M., additional, Bojilova, Viktoria, additional, Fong, Christopher J., additional, Funnell, Tyler, additional, Grewal, Diljot, additional, Havasov, Eliyahu, additional, Leung, Samantha, additional, Pasha, Arfath, additional, Patel, Druv M., additional, Pourmaleki, Maryam, additional, Rusk, Nicole, additional, Shi, Hongyu, additional, Vanguri, Rami, additional, Williams, Marc J., additional, Zhang, Allen W., additional, Broach, Vance, additional, Chi, Dennis, additional, Da Cruz Paula, Arnaud, additional, Gardner, Ginger J., additional, Kim, Sarah H., additional, Lennon, Matthew, additional, Roche, Kara Long, additional, Sonoda, Yukio, additional, Zivanovic, Oliver, additional, Kundra, Ritika, additional, Viale, Agnes, additional, Derakhshan, Fatemeh N., additional, Geneslaw, Luke, additional, Maroldi, Ana, additional, Nunez, Rahelly, additional, Pareja, Fresia, additional, Stylianou, Anthe, additional, Vahdatinia, Mahsa, additional, Bykov, Yonina, additional, Grisham, Rachel N., additional, Liu, Ying L., additional, Lakhman, Yulia, additional, Nikolovski, Ines, additional, Kelly, Daniel, additional, Gao, Jianjiong, additional, Schietinger, Andrea, additional, Hollmann, Travis J., additional, Bakhoum, Samuel F., additional, Soslow, Robert A., additional, Ellenson, Lora H., additional, Abu-Rustum, Nadeem R., additional, Aghajanian, Carol, additional, Friedman, Claire F., additional, McPherson, Andrew, additional, Weigelt, Britta, additional, Zamarin, Dmitriy, additional, and Shah, Sohrab P., additional

Published
2021
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83. Recurrent WWTR1S89W mutations and Hippo pathway deregulation in clear cell carcinomas of the cervix.

Author

Kim, Sarah H, Basili, Thais, Dopeso, Higinio, Da Cruz Paula, Arnaud, Bi, Rui, Issa Bhaloo, Shirin, Pareja, Fresia, Li, Qing, da Silva, Edaise M, Zhu, Yingjie, Hoang, Timothy, Selenica, Pier, Murali, Rajmohan, Chan, Eric, Wu, Michelle, Derakhshan, Fatemeh, Maroldi, Ana, Hanlon, Etta, Ferreira, Carlos Gil, and Lapa e Silva, Jose Roberto

Subjects
HIPPO signaling pathway, RENAL cell carcinoma, CERVIX uteri tumors, SOMATIC mutation, GENITALIA, GENETIC mutation
Abstract

Clear cell carcinoma (CCC) of the cervix (cCCC) is a rare and aggressive type of human papillomavirus (HPV)‐negative cervical cancer with limited effective treatment options for recurrent or metastatic disease. Historically, CCCs of the lower genital tract were associated with in utero diethylstilbestrol exposure; however, the genetic landscape of sporadic cCCCs remains unknown. Here we sought to define the molecular underpinning of cCCCs. Using a combination of whole‐exome, targeted capture, and RNA‐sequencing, we identified pathogenic genetic alterations in the Hippo signaling pathway in 50% (10/20) of cCCCs, including recurrent WWTR1 S89W somatic mutations in 40% (4/10) of the cases harboring mutations in the Hippo pathway. Irrespective of the presence or absence of Hippo pathway genetic alterations, however, all primary cCCCs analyzed in this study (n = 20) harbored features of Hippo pathway deregulation at the transcriptomic and protein levels. In vitro functional analysis revealed that expression of the WWTR1 S89W mutation leads to reduced binding of TAZ to 14‐3‐3, promoting constitutive nuclear translocation of TAZ and Hippo pathway repression. WWTR1 S89W expression was found to lead to acquisition of oncogenic behavior, including increased proliferation, migration, and colony formation in vitro as well as increased tumorigenesis in vivo, which could be reversed by targeted inhibition of the TAZ/YAP1 complex with verteporfin. Finally, xenografts expressing WWTR1 S89W displayed a shift in tumor phenotype, becoming more infiltrative as well as less differentiated, and were found to be composed of cells with conspicuous cytoplasmic clearing as compared to controls. Our results demonstrate that Hippo pathway alterations are likely drivers of cCCCs and likely contribute to the clear cell phenotype. Therapies targeting this pathway may constitute a new class of treatment for these rare, aggressive tumors. © 2022 The Pathological Society of Great Britain and Ireland. [ABSTRACT FROM AUTHOR]

Published
2022
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84. Genetic characterisation of adult primary pleomorphic uterine rhabdomyosarcoma and comparison with uterine carcinosarcoma

Author

Ashley, Charles W, primary, Da Cruz Paula, Arnaud, additional, Ferrando, Lorenzo, additional, Gularte‐Mérida, Rodrigo, additional, Sebastiao, Ana P M, additional, Brown, David N, additional, Gazzo, Andrea M, additional, Pareja, Fresia, additional, Stylianou, Anthe, additional, Abu‐Rustum, Nadeem R, additional, Reis‐Filho, Jorge S, additional, Buehler, Darya, additional, Weisman, Paul, additional, Chiang, Sarah, additional, and Weigelt, Britta, additional

Published
2021
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85. Identification of recurrent FHL2-GLI2 oncogenic fusion in sclerosing stromal tumors of the ovary

Author

Kim, Sarah H, Da Cruz Paula, Arnaud, Basili, Thais, Dopeso, Higinio, Bi, Rui, Pareja, Fresia, da Silva, Edaise M, Gularte-Mérida, Rodrigo, Sun, Zhen, Fujisawa, Sho, Smith, Caitlin G, Ferrando, Lorenzo, Martins Sebastião, Ana Paula, Bykov, Yonina, Li, Anqi, Silveira, Catarina, Ashley, Charles W, Stylianou, Anthe, Selenica, Pier, Samore, Wesley R, Jungbluth, Achim A, Zamarin, Dmitriy, Abu-Rustum, Nadeem R, Helin, Kristian, Soslow, Robert A, Reis-Filho, Jorge S, Oliva, Esther, Weigelt, Britta, Kim, Sarah H, Da Cruz Paula, Arnaud, Basili, Thais, Dopeso, Higinio, Bi, Rui, Pareja, Fresia, da Silva, Edaise M, Gularte-Mérida, Rodrigo, Sun, Zhen, Fujisawa, Sho, Smith, Caitlin G, Ferrando, Lorenzo, Martins Sebastião, Ana Paula, Bykov, Yonina, Li, Anqi, Silveira, Catarina, Ashley, Charles W, Stylianou, Anthe, Selenica, Pier, Samore, Wesley R, Jungbluth, Achim A, Zamarin, Dmitriy, Abu-Rustum, Nadeem R, Helin, Kristian, Soslow, Robert A, Reis-Filho, Jorge S, Oliva, Esther, and Weigelt, Britta

Abstract

Sclerosing stromal tumor (SST) of the ovary is a rare type of sex cord-stromal tumor (SCST), whose genetic underpinning is currently unknown. Here, using whole-exome, targeted capture and RNA-sequencing, we report recurrent FHL2-GLI2 fusion genes in 65% (17/26) of SSTs and other GLI2 rearrangements in additional 15% (4/26) SSTs, none of which are detected in other types of SCSTs (n = 48) or common cancer types (n = 9,950). The FHL2-GLI2 fusions result in transcriptomic activation of the Sonic Hedgehog (SHH) pathway in SSTs. Expression of the FHL2-GLI2 fusion in vitro leads to the acquisition of phenotypic characteristics of SSTs, increased proliferation, migration and colony formation, and SHH pathway activation. Targeted inhibition of the SHH pathway results in reversal of these oncogenic properties, indicating its role in the pathogenesis of SSTs. Our results demonstrate that the FHL2-GLI2 fusion is likely the oncogenic driver of SSTs, defining a genotypic-phenotypic correlation in ovarian neoplasms.

Published
2020

86. Pleomorphic adenomas and mucoepidermoid carcinomas of the breast are underpinned by fusion genes

Author

Pareja, Fresia; https://orcid.org/0000-0003-3748-8049, Da Cruz Paula, Arnaud, Gularte-Mérida, Rodrigo; https://orcid.org/0000-0002-4383-2523, Vahdatinia, Mahsa, Li, Anqi; https://orcid.org/0000-0003-1409-1858, Geyer, Felipe C, da Silva, Edaise M; https://orcid.org/0000-0003-3281-7333, Nanjangud, Gouri, Wen, Hannah Y, Varga, Zsuzsanna; https://orcid.org/0000-0002-2855-983X, Brogi, Edi, Rakha, Emad A, Weigelt, Britta, Reis-Filho, Jorge S; https://orcid.org/0000-0003-2969-3173, Pareja, Fresia; https://orcid.org/0000-0003-3748-8049, Da Cruz Paula, Arnaud, Gularte-Mérida, Rodrigo; https://orcid.org/0000-0002-4383-2523, Vahdatinia, Mahsa, Li, Anqi; https://orcid.org/0000-0003-1409-1858, Geyer, Felipe C, da Silva, Edaise M; https://orcid.org/0000-0003-3281-7333, Nanjangud, Gouri, Wen, Hannah Y, Varga, Zsuzsanna; https://orcid.org/0000-0002-2855-983X, Brogi, Edi, Rakha, Emad A, Weigelt, Britta, and Reis-Filho, Jorge S; https://orcid.org/0000-0003-2969-3173

Abstract

Primary pleomorphic adenomas (PAs) and mucoepidermoid carcinomas (MECs) of the breast are vanishingly rare. Here we sought to determine whether breast PAs and MECs would be underpinned by the fusion genes reported to occur in their salivary gland counterparts. Our study included three breast PAs and one breast MEC, which were subjected to RNA sequencing (PAs, n = 2; MEC, n = 1) or to Archer FusionPlex sequencing (PA, n = 1). Our analyses revealed the presence of the HMGA2-WIF1 fusion gene in breast PA3, the CTNNB1-PLAG1 fusion gene in breast PA2, and the CRTC1-MAML2 fusion gene in the breast MEC analyzed (1/1). No oncogenic fusion genes were detected in breast PA1, and no additional oncogenic fusion genes were detected in the cases studied. The presence of the fusion genes identified was validated by fluorescence in situ hybridization (n = 1), reverse transcription-PCR (n = 1), or by both methods (n = 1). Taken together, our findings indicate that PAs and MECs arising in the breast resemble their salivary gland counterparts not only phenotypically but also at the genetic level. Furthermore, our data suggest that the molecular analysis of breast PAs and MECs might constitute a useful tool to aid in their differential diagnosis.

Published
2020

87. Whole?exome sequencing and RNA sequencing analyses of acinic cell carcinomas of the breast

Author

Beca, Francisco, Lee, Simon S.K., Pareja, Fresia, da Cruz Paula, Arnaud, Selenica, Pier, Ferrando, Lorenzo, Gularte?Merida, Rodrigo, Wen, Hannah Y, Zhang, Hong, Guerini?Rocco, Elena, Rakha, Emad A., Weigelt, Britta, and Reis?Filho, Jorge S.

Subjects
Histology, General Medicine, Pathology and Forensic Medicine
Abstract

AimsAcinic cell carcinoma of the breast (ACC) is a rare histologic form of triple?negative breast cancer (TNBC). Despite its unique histology, targeted sequencing analysis has failed to identify recurrent genetic alterations other than those found in common forms of TNBC. Here, we subjected three breast ACCs to whole?exome and RNA?sequencing, seeking to define whether they would harbor a pathognomonic genetic alteration.Methods and ResultsTumor and normal DNA and RNA samples from three breast ACCs were subjected to whole?exome sequencing. Somatic mutations, copy number alterations, mutational signatures and fusion genes were determined using state?of?the?art bioinformatics methods. Our analyses revealed TP53 hotspot mutations associated with loss of heterozygosity of the wild?type allele in two cases. Mutations affecting homologous recombination (HR) DNA repair?related genes were found in two cases, and an MLH1 pathogenic germline variant was detected in one case. In addition, copy number analysis revealed the presence of a somatic BRCA1 homozygous deletion and focal amplification of 12q14.3?12q21.1, encompassing MDM2, HMGA2, FRS2 and PTPRB. No oncogenic in?frame fusion transcript was identified in the three breast ACCs analyzed.ConclusionsNo pathognomonic genetic alterations were detected in the ACCs analyzed. These tumors have somatic genetic alterations similar to those of common forms of TNBC and may display HR deficiency or microsatellite instability. These findings provide further insights as to why ACCs which are usually clinically indolent may evolve into or in parallel with high?grade TNBC.

Published
2019

88. The genetic landscape of metaplastic breast cancers and uterine carcinosarcomas

Author

Moukarzel, Lea A., primary, Ferrando, Lorenzo, additional, Da Cruz Paula, Arnaud, additional, Brown, David N., additional, Geyer, Felipe C., additional, Pareja, Fresia, additional, Piscuoglio, Salvatore, additional, Papanastasiou, Anastasios D., additional, Fusco, Nicola, additional, Marchiò, Caterina, additional, Abu‐Rustum, Nadeem R., additional, Murali, Rajmohan, additional, Brogi, Edi, additional, Wen, Hannah Y., additional, Norton, Larry, additional, Soslow, Robert A., additional, Vincent‐Salomon, Anne, additional, Reis‐Filho, Jorge S., additional, and Weigelt, Britta, additional

Published
2021
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89. A Distinctive Adnexal (Usually Paratubal) Neoplasm Often Associated With Peutz-Jeghers Syndrome and Characterized by STK11 Alterations (STK11 Adnexal Tumor)

Author

Bennett, Jennifer A., primary, Young, Robert H., additional, Howitt, Brooke E., additional, Croce, Sabrina, additional, Wanjari, Pankhuri, additional, Zhen, Chaojie, additional, Da Cruz Paula, Arnaud, additional, Meserve, Emily, additional, Schoolmeester, J. Kenneth, additional, Westbom-Fremer, Sofia, additional, Benzi, Eduardo, additional, Patil, Ninad M., additional, Kooreman, Loes, additional, El-Bahrawy, Mona, additional, Zannoni, Gian Franco, additional, Krausz, Thomas, additional, McCluggage, W. Glenn, additional, Weigelt, Britta, additional, Ritterhouse, Lauren L., additional, and Oliva, Esther, additional

Published
2021
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90. Stromal MED12 exon 2 mutations in complex fibroadenomas of the breast

Author

da Silva, Edaise M, primary, Beca, Francisco, additional, Sebastiao, Ana Paula Martins, additional, Murray, Melissa P, additional, Silveira, Catarina, additional, Da Cruz Paula, Arnaud, additional, Pareja, Fresia, additional, Wen, Hannah Y, additional, D'Alfonso, Timothy M, additional, Edelweiss, Marcia, additional, Weigelt, Britta, additional, Brogi, Edi, additional, Reis-Filho, Jorge S, additional, and Zhang, Hong, additional

Published
2020
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91. Whole‐exome sequencing analysis of juvenile papillomatosis and coexisting breast carcinoma

Author

D'Alfonso, Timothy M, primary, Pareja, Fresia, additional, Da Cruz Paula, Arnaud, additional, Vahdatinia, Mahsa, additional, Gazzo, Andrea, additional, Ferrando, Lorenzo, additional, da Silva, Edaise M, additional, Cheng, Esther, additional, Sclafani, Lisa, additional, Chandarlapaty, Sarat, additional, Zhang, Hong, additional, Hoda, Syed A, additional, Wen, Hannah Y, additional, Brogi, Edi, additional, Weigelt, Britta, additional, and Reis‐Filho, Jorge S, additional

Published
2020
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92. Neuroendocrine tumours of the breast: a genomic comparison with mucinous breast cancers and neuroendocrine tumours of other anatomic sites

Author

Pareja, Fresia, primary, Vahdatinia, Mahsa, additional, Marchio, Caterina, additional, Lee, Simon S K, additional, Da Cruz Paula, Arnaud, additional, Derakhshan, Fatemeh, additional, da Silva, Edaise M, additional, Selenica, Pier, additional, Dopeso, Higinio, additional, Chandarlapaty, Sarat, additional, Wen, Hannah Y, additional, Vincent-Salomon, Anne, additional, Brogi, Edi, additional, Weigelt, Britta, additional, and Reis-Filho, Jorge S, additional

Published
2020
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93. Acquisition of APOBEC Mutagenesis and Microsatellite Instability Signatures in the Development of Brain Metastases in Low-Grade, Early-Stage Endometrioid Endometrial Carcinoma

Author

Dessources, Kimberly, primary, Da Cruz Paula, Arnaud, additional, Pareja, Fresia, additional, Stylianou, Anthe, additional, Cybulska, Paulina, additional, Farmanbar, Amir, additional, Chandarlapaty, Sarat, additional, Abu-Rustum, Nadeem R., additional, Reis-Filho, Jorge S., additional, Weigelt, Britta, additional, and Mueller, Jennifer J., additional

Published
2020
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94. Mutant FOXL2C134W Hijacks SMAD4 and SMAD2/3 to Drive Adult Granulosa Cell Tumors

Author

Weis-Banke, Stine E., primary, Lerdrup, Mads, additional, Kleine-Kohlbrecher, Daniela, additional, Mohammad, Faizaan, additional, Sidoli, Simone, additional, Jensen, Ole N., additional, Yanase, Toshihiko, additional, Nakamura, Tomoko, additional, Iwase, Akira, additional, Stylianou, Anthe, additional, Abu-Rustum, Nadeem R., additional, Aghajanian, Carol, additional, Soslow, Robert, additional, Da Cruz Paula, Arnaud, additional, Koche, Richard P., additional, Weigelt, Britta, additional, Christensen, Jesper, additional, Helin, Kristian, additional, and Cloos, Paul A.C., additional

Published
2020
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95. Whole-Exome Sequencing Analysis of the Progression from Non–Low-Grade Ductal Carcinoma In Situ to Invasive Ductal Carcinoma

Author

Pareja, Fresia, primary, Brown, David N., additional, Lee, Ju Youn, additional, Da Cruz Paula, Arnaud, additional, Selenica, Pier, additional, Bi, Rui, additional, Geyer, Felipe C., additional, Gazzo, Andrea, additional, da Silva, Edaise M., additional, Vahdatinia, Mahsa, additional, Stylianou, Anthe A., additional, Ferrando, Lorenzo, additional, Wen, Hannah Y., additional, Hicks, James B., additional, Weigelt, Britta, additional, and Reis-Filho, Jorge S., additional

Published
2020
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96. Oncogenic properties and signaling basis of the PAX8‐GLIS3 fusion gene

Author

Basili, Thais, primary, Dopeso, Higinio, additional, Kim, Sarah H., additional, Ferrando, Lorenzo, additional, Pareja, Fresia, additional, Da Cruz Paula, Arnaud, additional, da Silva, Edaise M., additional, Stylianou, Anthe, additional, Maroldi, Ana, additional, Marchiò, Caterina, additional, Rubin, Brian P., additional, Papotti, Mauro, additional, Weigelt, Britta, additional, Moreira Ferreira, Carlos Gil, additional, Lapa e Silva, José Roberto, additional, and Reis‐Filho, Jorge S., additional

Published
2020
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98. Endometrial Cancers in BRCA1 or BRCA2 Germline Mutation Carriers: Assessment of Homologous Recombination DNA Repair Defects

Author

Smith, Evan S., primary, Da Cruz Paula, Arnaud, additional, Cadoo, Karen A., additional, Abu-Rustum, Nadeem R., additional, Pei, Xin, additional, Brown, David N., additional, Ferrando, Lorenzo, additional, Sebastiao, Ana Paula Martins, additional, Riaz, Nadeem, additional, Robson, Mark E., additional, Soslow, Robert A., additional, Reis-Filho, Jorge S., additional, Mandelker, Diana, additional, and Weigelt, Britta, additional

Published
2019
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99. Stromal MED12 exon 2 mutations in complex fibroadenomas of the breast.

Author

da Silva, Edaise M., Beca, Francisco, Martins Sebastiao, Ana Paula, Murray, Melissa P., Silveira, Catarina, Da Cruz Paula, Arnaud, Pareja, Fresia, Wen, Hannah Y., D'Alfonso, Timothy M., Edelweiss, Marcia, Weigelt, Britta, Brogi, Edi, Reis-Filho, Jorge S., and Hong Zhang

Subjects
FIBROADENOMAS, BREAST, GENETIC mutation, TELOMERASE reverse transcriptase
Published
2022
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100. ESR1hotspot mutations in endometrial stromal sarcoma with high-grade transformation and endocrine treatment

Author

Dessources, Kimberly, Miller, Kathryn M., Kertowidjojo, Elizabeth, Da Cruz Paula, Arnaud, Zou, Youran, Selenica, Pier, da Silva, Edaise M., Benayed, Ryma, Ashley, Charles W., Abu-Rustum, Nadeem R., Dogan, Snjezana, Soslow, Robert A., Hensley, Martee L., Weigelt, Britta, and Chiang, Sarah

Abstract

High-grade endometrial stromal sarcomas (HGESSs) are more aggressive and have higher rates of resistance to endocrine therapy than low-grade endometrial stromal sarcomas (LGESSs). The pathogenesis of hormonal resistance in these lesions has yet to be defined. Here we sought to histologically and genetically characterize 3 LGESSs and their recurrences that underwent histologic high-grade transformation following endocrine therapy. For this, DNA from primary tumors and select subsequent recurrences were subject to massively parallel sequencing targeting 468 cancer-related genes. Somatic mutation analyses were performed using validated bioinformatics methods. In addition, RNA from each case was evaluated for the presence of gene fusions using targeted RNA-sequencing. All patients initially presented with LGESS, developed HGESS recurrences, and received at least 2 lines of hormonal suppressive therapy. Gene fusions classically described as associated with LGESS were identified in all 3 cases, including JAZF1-PHF1, EPC1-PHF1and JAZF1-SUZ12fusions for Cases 1, 2 and 3, respectively. Targeted sequencing analysis revealed that none of the primary LGESS, however the HGESS recurrences of Cases 1 and 3, and the LGESS and HGESS recurrences of Case 2 post endocrine treatment harbored ESR1p.Y537S hotspot mutations. These ESR1ligand-binding domain mutations have been found as a mechanism of acquired endocrine resistance in breast cancer. Also, a reduction in estrogen receptor (ER) expression was observed in recurrences. Our findings suggest that the ESR1p.Y537S hotspot mutation in LGESS with histologic high-grade transformation may be associated with endocrine resistance in these lesions. Furthermore, our data suggest that genetic analyses may be performed in recurrent LGESS following hormonal therapy, development of high-grade morphology, and/or altered/diminished ER expression.

Published
2022
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