Search

Your search keyword '"Mosquera, Juan-Miguel"' showing total 824 results
Start Over Author "Mosquera, Juan-Miguel"
824 results on '"Mosquera, Juan-Miguel"'

1. The interplay of mutagenesis and ecDNA shapes urothelial cancer evolution

Author

Nguyen, Duy D., Hooper, William F., Liu, Weisi, Chu, Timothy R., Geiger, Heather, Shelton, Jennifer M., Shah, Minita, Goldstein, Zoe R., Winterkorn, Lara, Helland, Adrienne, Sigouros, Michael, Manohar, Jyothi, Moyer, Jenna, Al Assaad, Majd, Semaan, Alissa, Cohen, Sandra, Madorsky Rowdo, Florencia, Wilkes, David, Osman, Mohamed, Singh, Rahul R., Sboner, Andrea, Valentine, Henkel L., Abbosh, Phillip, Tagawa, Scott T., Nanus, David M., Nauseef, Jones T., Sternberg, Cora N., Molina, Ana M., Scherr, Douglas, Inghirami, Giorgio, Mosquera, Juan Miguel, Elemento, Olivier, Robine, Nicolas, and Faltas, Bishoy M.

Published
2024
Full Text
View/download PDF

2. Increased translation driven by non-canonical EZH2 creates a synthetic vulnerability in enzalutamide-resistant prostate cancer

Author

Chatterjee, Shankha S., Linares, Juan F., Cid-Diaz, Tania, Duran, Angeles, Khan, Mohd. Imran K., Osrodek, Marta, Brady, Nicholas J., Reina-Campos, Miguel, Marzio, Antonio, Venkadakrishnan, Varadha Balaji, Bakht, Martin K., Khani, Francesca, Mosquera, Juan Miguel, Robinson, Brian D., Moyer, Jenna, Elemento, Olivier, Hsieh, Andrew C., Goodrich, David W., Rickman, David S., Beltran, Himisha, Moscat, Jorge, and Diaz-Meco, Maria T.

Published
2024
Full Text
View/download PDF

3. The evolution of metastatic upper tract urothelial carcinoma through genomic-transcriptomic and single-cell protein markers analysis

Author

Ohara, Kentaro, Rendeiro, André Figueiredo, Bhinder, Bhavneet, Eng, Kenneth Wha, Ravichandran, Hiranmayi, Nguyen, Duy, Pisapia, David, Vosoughi, Aram, Fernandez, Evan, Shohdy, Kyrillus S., Manohar, Jyothi, Beg, Shaham, Wilkes, David, Robinson, Brian D., Khani, Francesca, Bareja, Rohan, Tagawa, Scott T., Ouseph, Madhu M., Sboner, Andrea, Elemento, Olivier, Faltas, Bishoy M., and Mosquera, Juan Miguel

Published
2024
Full Text
View/download PDF

4. Whole genome and transcriptome analysis of pancreatic acinar cell carcinoma elucidates mechanisms of homologous recombination deficiency and unravels novel relevant fusion events

Author

Delgado-de la Mora, Jesús, Al Assaad, Majd, Karaaslan, Selda, Hadi, Kevin, Halima, Ahmed, Deshpande, Aditya, Manohar, Jyothi, Sigouros, Michael, Medina-Martínez, Juan S., Lieberman, Michael D., Sboner, Andrea, Popa, Elizabeta C., Jessurun, José, Elemento, Olivier, Ocean, Allyson J., Hissong, Erika, and Mosquera, Juan Miguel

Published
2025
Full Text
View/download PDF

5. Emerging molecular phenotypes and potential therapeutic targets in esophageal and gastric adenocarcinoma unearthed by whole genome and transcriptome analyses

Author

Windon, Annika, Al Assaad, Majd, Hadi, Kevin, Mendelson, Nicole, Hissong, Erika, Deshpande, Aditya, Tranquille, Marvel, Mclee, Justin, Levine, Max F., Patel, Minal, Medina-Martínez, Juan S., Chiu, Kenrry, Manohar, Jyothi, Sigouros, Michael, Ocean, Allyson J., Sboner, Andrea, Jessurun, José, Elemento, Olivier, Shah, Manish, and Mosquera, Juan Miguel

Published
2025
Full Text
View/download PDF

11. Notch signaling suppresses neuroendocrine differentiation and alters the immune microenvironment in advanced prostate cancer

Author

Ku, Sheng-Yu, Wang, Yanqing, Garcia, Maria Mica, Yamada, Yasutaka, Mizuno, Kei, Long, Mark D., Rosario, Spencer, Chinnam, Meenalakshmi, Assaad, Majd Al, Puca, Loredana, Kim, Min Jin, Bakht, Martin K., Venkadakrishnan, Varadha Balaji, Robinson, Brian D., Acosta, Andres M., Wadosky, Kristine M., Mosquera, Juan Miguel, Goodrich, David W., and Beltran, Himisha

Subjects
Physiological aspects, Health aspects, Cell receptors -- Health aspects, Neuroendocrinology -- Health aspects, Cancer research, Immune system -- Health aspects, Prostate cancer -- Physiological aspects, Cellular signal transduction -- Health aspects, Oncology, Experimental, Cancer -- Research
Abstract

Introduction Phenotypic plasticity is a hallmark of cancer (1-3). In advanced prostate cancer, up to 15%-20% of patients develop resistance to androgen receptor-directed (AR-directed) therapies through conversion from an androgen-driven [...], Notch signaling can have either an oncogenic or tumor-suppressive function in cancer depending on the cancer type and cellular context. While Notch can be oncogenic in early prostate cancer, we identified significant downregulation of the Notch pathway during prostate cancer progression from adenocarcinoma to neuroendocrine (NE) prostate cancer, where it functions as a tumor suppressor. Activation of Notch in NE and Rb1/Trp53-deficient prostate cancer models led to phenotypic conversion toward a more indolent, non-NE state with glandular features and expression of luminal lineage markers. This was accompanied by upregulation of MHC and type I IFN and immune cell infiltration. Overall, these data support Notch signaling as a suppressor of NE differentiation in advanced prostate cancer and provide insights into how Notch signaling influences lineage plasticity and the tumor microenvironment (TME).

Published
2024
Full Text
View/download PDF

14. Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers

Author

Setton, Jeremy, Hadi, Kevin, Choo, Zi-Ning, Kuchin, Katherine S., Tian, Huasong, Da Cruz Paula, Arnaud, Rosiene, Joel, Selenica, Pier, Behr, Julie, Yao, Xiaotong, Deshpande, Aditya, Sigouros, Michael, Manohar, Jyothi, Nauseef, Jones T., Mosquera, Juan-Miguel, Elemento, Olivier, Weigelt, Britta, Riaz, Nadeem, Reis-Filho, Jorge S., Powell, Simon N., and Imieliński, Marcin

Published
2023
Full Text
View/download PDF

15. Multinational, Multicenter Evaluation of Prostate Cancer Tissue in Sub-Saharan Africa: Challenges and Opportunities

Author

van Wyk, Abraham C., Lal, Priti, Ogunbiyi, J. Olufemi, Kyokunda, Lynnette, Hobenu, Fred, Dial, Cherif, Jalloh, Mohamed, Gyasi, Richard, Oluwole, Olabode P., Abrahams, Afua D., Botha, Adam R., Mtshali, Nompumelelo Zamokuhle, Andrews, Caroline, Mante, Sunny, Adusei, Ben, Gueye, Serigne M., Mensah, James E., Adjei, Andrew Anthony, Tettey, Yao, Adebiyi, Akin, Aisuodionoe-Shadrach, Oseremen, Eniola, Sefiu Bolarinwa, Serna, Amparo, Yamoah, Kosj, Chen, Wenlong Carl, Fernandez, Pedro, Robinson, Brian D., Mosquera, Juan Miguel, Hsing, Ann W., Agalliu, Ilir, and Rebbeck, Timothy R.

Published
2024
Full Text
View/download PDF

18. NIPBL NACC1 Fusion Hepatic Carcinoma

Author

Hissong, Erika, Al Assaad, Majd, Bal, Munita, Reed, Katelyn A., Fornelli, Adele, Levine, Max F., Gundem, Gunes, Semaan, Alissa, Orr, Christine E., Sakhadeo, Uma, Manohar, Jyothi, Sigouros, Michael, Wilkes, David, Sboner, Andrea, Montgomery, Elizabeth A., Graham, Rondell P., Medina-Martínez, Juan S., Robine, Nicolas, Fang, Jiayun M., Choi, Eun-Young K., Westerhoff, Maria, Delgado-de la Mora, Jesús, Caudell, Patricia, Yantiss, Rhonda K., Papaemmanuil, Elli, Elemento, Olivier, Sigel, Carlie, Jessurun, José, and Mosquera, Juan Miguel

Published
2023
Full Text
View/download PDF

19. NIPBL: NACC1 Fusion Hepatic Carcinoma

Author

Hissong, Erika, Al Assaad, Majd, Bal, Munita, Reed, Katelyn A., Fornelli, Adele, Levine, Max F., Gundem, Gunes, Semaan, Alissa, Orr, Christine E., Sakhadeo, Uma, Manohar, Jyothi, Sigouros, Michael, Wilkes, David, Sboner, Andrea, Montgomery, Elizabeth A., Graham, Rondell P., Medina-Martínez, Juan S., Robine, Nicolas, Fang, Jiayun M., Choi, Eun-Young K., Westerhoff, Maria, Delgado-de la Mora, Jesús, Caudell, Patricia, Yantiss, Rhonda K., Papaemmanuil, Elli, Elemento, Olivier, Sigel, Carlie, Jessurun, José, and Mosquera, Juan Miguel

Published
2024
Full Text
View/download PDF

21. Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing

Author

Deshpande, Aditya S., Ulahannan, Netha, Pendleton, Matthew, Dai, Xiaoguang, Ly, Lynn, Behr, Julie M., Schwenk, Stefan, Liao, Will, Augello, Michael A., Tyer, Carly, Rughani, Priyesh, Kudman, Sarah, Tian, Huasong, Otis, Hannah G., Adney, Emily, Wilkes, David, Mosquera, Juan Miguel, Barbieri, Christopher E., Melnick, Ari, Stoddart, David, Turner, Daniel J., Juul, Sissel, Harrington, Eoghan, and Imieliński, Marcin

Published
2022
Full Text
View/download PDF

26. Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations

Author

Huang, Franklin W, Mosquera, Juan Miguel, Garofalo, Andrea, Oh, Coyin, Baco, Maria, Amin-Mansour, Ali, Rabasha, Bokang, Bahl, Samira, Mullane, Stephanie A, Robinson, Brian D, Aldubayan, Saud, Khani, Francesca, Karir, Beerinder, Kim, Eejung, Chimene-Weiss, Jeremy, Hofree, Matan, Romanel, Alessandro, Osborne, Joseph R, Kim, Jong Wook, Azabdaftari, Gissou, Woloszynska-Read, Anna, Sfanos, Karen, De Marzo, Angelo M, Demichelis, Francesca, Gabriel, Stacey, Van Allen, Eliezer M, Mesirov, Jill, Tamayo, Pablo, Rubin, Mark A, Powell, Isaac J, and Garraway, Levi A

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Prostate Cancer, Biotechnology, Aging, Cancer, Genetics, Human Genome, Urologic Diseases, Aetiology, 2.1 Biological and endogenous factors, Good Health and Well Being, Black or African American, Animals, Cell Line, Tumor, Class I Phosphatidylinositol 3-Kinases, Exome, Humans, Male, Mice, Mutation, PTEN Phosphohydrolase, Prostatic Neoplasms, Repressor Proteins, Exome Sequencing, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

African-American men have the highest incidence of and mortality from prostate cancer. Whether a biological basis exists for this disparity remains unclear. Exome sequencing (n = 102) and targeted validation (n = 90) of localized primary hormone-naïve prostate cancer in African-American men identified several gene mutations not previously observed in this context, including recurrent loss-of-function mutations in ERF, an ETS transcriptional repressor, in 5% of cases. Analysis of existing prostate cancer cohorts revealed ERF deletions in 3% of primary prostate cancers and mutations or deletions in ERF in 3% to 5% of lethal castration-resistant prostate cancers. Knockdown of ERF confers increased anchorage-independent growth and generates a gene expression signature associated with oncogenic ETS activation and androgen signaling. Together, these results suggest that ERF is a prostate cancer tumor-suppressor gene. More generally, our findings support the application of systematic cancer genomic characterization in settings of broader ancestral diversity to enhance discovery and, eventually, therapeutic applications.Significance: Systematic genomic sequencing of prostate cancer in African-American men revealed new insights into prostate cancer, including the identification of ERF as a prostate cancer gene; somatic copy-number alteration differences; and uncommon PIK3CA and PTEN alterations. This study highlights the importance of inclusion of underrepresented minorities in cancer sequencing studies. Cancer Discov; 7(9); 973-83. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 920.

Published
2017

27. CD38 in Advanced Prostate Cancers

Author

Robinson, Dan, Van Allen, Eliezer M., Wu, Yi-Mi, Schultz, Nikolaus, Lonigro, Robert J., Mosquera, Juan-Miguel, Montgomery, Bruce, Taplin, Mary-Ellen, Pritchard, Colin C., Attard, Gerhardt, Beltran, Himisha, Abida, Wassim, Bradley, Robert K., Vinson, Jake, Cao, Xuhong, Vats, Pankaj, Kunju, Lakshmi P., Hussain, Maha, Tomlins, Scott A., Cooney, Kathleen A., Smith, David C., Brennan, Christine, Siddiqui, Javed, Mehra, Rohit, Chen, Yu, Rathkopf, Dana E., Morris, Michael J., Solomon, Stephen B., Durack, Jeremy C., Reuter, Victor E., Gopalan, Anuradha, Gao, Jianjiong, Loda, Massimo, Lis, Rosina T., Bowden, Michaela, Balk, Stephen P., Gaviola, Glenn, Sougnez, Carrie, Gupta, Manaswi, Yu, Evan Y., Mostaghel, Elahe A., Cheng, Heather H., Mulcahy, Hyojeong, True, Lawrence D., Plymate, Stephen R., Dvinge, Heidi, Ferraldeschi, Roberta, Flohr, Penny, Miranda, Susana, Zafeiriou, Zafeiris, Tunariu, Nina, Mateo, Joaquin, Perez-Lopez, Raquel, Demichelis, Francesca, Robinson, Brian D., Schiffman, Marc, Nanus, David M., Tagawa, Scott T., Sigaras, Alexandros, Eng, Kenneth W., Elemento, Olivier, Sboner, Andrea, Heath, Elisabeth I., Scher, Howard I., Pienta, Kenneth J., Kantoff, Philip, de Bono, Johann S., Rubin, Mark A., Nelson, Peter S., Garraway, Levi A., Sawyers, Charles L., Chinnaiyan, Arul M., Guo, Christina, Crespo, Mateus, Gurel, Bora, Dolling, David, Rekowski, Jan, Sharp, Adam, Petremolo, Antonella, Sumanasuriya, Semini, Rodrigues, Daniel N., Ferreira, Ana, Pereira, Rita, Figueiredo, Ines, Mehra, Niven, Lambros, Maryou B.K., Neeb, Antje, Gil, Veronica, Seed, George, Terstappen, Leon, Alimonti, Andrea, Drake, Charles G., and Yuan, Wei

Published
2021
Full Text
View/download PDF

28. Integration of whole-exome and anchored PCR-based next generation sequencing significantly increases detection of actionable alterations in precision oncology

Author

Beg, Shaham, Bareja, Rohan, Ohara, Kentaro, Eng, Kenneth Wha, Wilkes, David C., Pisapia, David J., Zoughbi, Wael Al, Kudman, Sarah, Zhang, Wei, Rao, Rema, Manohar, Jyothi, Kane, Troy, Sigouros, Michael, Xiang, Jenny Zhaoying, Khani, Francesca, Robinson, Brian D., Faltas, Bishoy M., Sternberg, Cora N., Sboner, Andrea, Beltran, Himisha, Elemento, Olivier, and Mosquera, Juan Miguel

Published
2021
Full Text
View/download PDF

29. Upgrading of Grade Group 1 Prostate Cancer at Prostatectomy: Germline Risk Factors in a Prospective Cohort.

Author

Liss, Michael A., Zeltser, Nicole, Yingye Zheng, Lopez, Camden, Menghan Liu, Patel, Yash, Yamaguchi, Takafumi N., Eng, Stefan E., Mao Tian, Semmes, Oliver J., Lin, Daniel W., Brooks, James D., Wei, John T., Klein, Eric A., Tewari, Ashutosh K., Mosquera, Juan Miguel, Khani, Francesca, Robinson, Brian D., Aasad, Muhammad, and Troyer, Dean A.

Abstract

Background: Localized prostate tumors show significant spatial heterogeneity, with regions of high-grade disease adjacent to lower grade disease. Consequently, prostate cancer biopsies are prone to sampling bias, potentially leading to underestimation of tumor grade. To study the clinical, epidemiologic, and molecular hallmarks of this phenomenon, we conducted a prospective study of grade upgrading: differences in detected prostate cancer grade between biopsy and surgery. Methods: We established a prospective, multi-institutional cohort of men with grade group 1 (GG1) prostate cancer on biopsy who underwent radical prostatectomy. Upgrading was defined as detection of GG2+ in the resected tumor. Germline DNA from 192 subjects was subjected to whole-genome sequencing to quantify ancestry, pathogenic variants in DNA damage response genes, and polygenic risk. Results: Of 285 men, 67% upgraded at surgery. PSA density and percent of cancer in pre-prostatectomy positive biopsy cores were significantly associated with upgrading. No assessed genetic risk factor was predictive of upgrading, including polygenic risk scores for prostate cancer diagnosis. Conclusions: In a cohort of patients with low-grade prostate cancer, a majority upgraded at radical prostatectomy. PSA density and percent of cancer in pre-prostatectomy positive biopsy cores portended the presence of higher-grade disease, while germline genetics was not informative in this setting. Patients with low-risk prostate cancer, but elevated PSA density or percent cancer in positive biopsy cores, may benefit from repeat biopsy, additional imaging or other approaches to complement active surveillance. Impact: Further risk stratification of patients with low-risk prostate cancer may provide useful context for active surveillance decision-making. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

30. Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs

Author

Hadi, Kevin, Yao, Xiaotong, Behr, Julie M., Deshpande, Aditya, Xanthopoulakis, Charalampos, Tian, Huasong, Kudman, Sarah, Rosiene, Joel, Darmofal, Madison, DeRose, Joseph, Mortensen, Rick, Adney, Emily M., Shaiber, Alon, Gajic, Zoran, Sigouros, Michael, Eng, Kenneth, Wala, Jeremiah A., Wrzeszczyński, Kazimierz O., Arora, Kanika, Shah, Minita, Emde, Anne-Katrin, Felice, Vanessa, Frank, Mayu O., Darnell, Robert B., Ghandi, Mahmoud, Huang, Franklin, Dewhurst, Sally, Maciejowski, John, de Lange, Titia, Setton, Jeremy, Riaz, Nadeem, Reis-Filho, Jorge S., Powell, Simon, Knowles, David A., Reznik, Ed, Mishra, Bud, Beroukhim, Rameen, Zody, Michael C., Robine, Nicolas, Oman, Kenji M., Sanchez, Carissa A., Kuhner, Mary K., Smith, Lucian P., Galipeau, Patricia C., Paulson, Thomas G., Reid, Brian J., Li, Xiaohong, Wilkes, David, Sboner, Andrea, Mosquera, Juan Miguel, Elemento, Olivier, and Imielinski, Marcin

Published
2020
Full Text
View/download PDF

33. Feasibility of implementing whole genome sequencing into routine oncology care.

Author

Kasi, Pashtoon Murtaza, primary, Dalton, Emily, additional, Sharaf, Ravi N., additional, Primiano, Michelle, additional, Sternberg, Cora N., additional, Mosquera, Juan Miguel, additional, Guevara, Daniela, additional, Nanus, David M., additional, Manohar, Jyothi, additional, Bapat, Bela, additional, Macdonald, Theresa, additional, Smith, Ryan, additional, and Elemento, Olivier, additional

Published
2024
Full Text
View/download PDF

35. Genomic correlates of clinical outcome in advanced prostate cancer

Author

Abida, Wassim, Cyrta, Joanna, Heller, Glenn, Prandi, Davide, Armenia, Joshua, Coleman, Ilsa, Cieslik, Marcin, Benelli, Matteo, Robinson, Dan, Van Allen, Eliezer M., Sboner, Andrea, Fedrizzi, Tarcisio, Mosquera, Juan Miguel, Robinson, Brian D., De Sarkar, Navonil, Kunju, Lakshmi P., Tomlins, Scott, Wu, Yi Mi, Rodrigues, Daniel Nava, Loda, Massimo, Gopalan, Anuradha, Reuter, Victor E., Pritchard, Colin C., Mateo, Joaquin, Bianchini, Diletta, Miranda, Susana, Carreira, Suzanne, Rescigno, Pasquale, Filipenko, Julie, Vinson, Jacob, Montgomery, Robert B., Beltran, Himisha, Heath, Elisabeth I., Scher, Howard I., Kantoff, Philip W., Taplin, Mary-Ellen, Schultz, Nikolaus, deBono, Johann S., Demichelis, Francesca, Nelson, Peter S., Rubin, Mark A., Chinnaiyan, Arul M., and Sawyers, Charles L.

Published
2019

37. Neuroendocrine Prostate Cancer

Author

Beg, Shaham, Mosquera, Juan Miguel, Cagle, Philip T., Series editor, Robinson, Brian D., editor, Mosquera, Juan Miguel, editor, Ro, Jae Y., editor, and Divatia, Mukul, editor

Published
2018
Full Text
View/download PDF

38. Corrigendum to “Whole genome and transcriptome analysis of pancreatic acinar cell carcinoma elucidates mechanisms of homologous recombination deficiency and unravels novel relevant fusion events” [Pathol. - Res. Pract. 266 (2025) 155798]

Author

Delgado-de la Mora, Jesús, Al Assaad, Majd, Karaaslan, Selda, Hadi, Kevin, Halima, Ahmed, Deshpande, Aditya, Manohar, Jyothi, Sigouros, Michael, Medina-Martínez, Juan S., Lieberman, Michael D., Sboner, Andrea, Popa, Elizabeta C., Jessurun, José, Elemento, Olivier, Ocean, Allyson J., Hissong, Erika, and Mosquera, Juan Miguel

Published
2025
Full Text
View/download PDF

40. Performance Characteristics of a Targeted Sequencing Platform for Simultaneous Detection of Single Nucleotide Variants, Insertions/Deletions, Copy Number Alterations, and Gene Fusions in Cancer Genome

Author

Park, Kyung, Tran, Hung, Eng, Kenneth W., Ramazanoglu, Sinan, Rolon, Rebecca M. Marrero, Scognamiglio, Theresa, Borczuk, Alain, Mosquera, Juan Miguel, Pan, Qiulu, Sboner, Andrea, Rubin, Mark A., Elemento, Olivier, Rennert, Hanna, Fernandes, Helen, and Song, Wei

Subjects
Research, Methods, Molecular diagnostic techniques -- Methods, Cancer research, DNA sequencing -- Methods, RNA sequencing -- Methods, Genetic variation -- Research, Oncology, Experimental, Nucleotide sequencing -- Methods, Cancer -- Research
Abstract

Next-generation sequencing (NGS) has become the major tool in understanding the mutational landscape of many solid tumors and hematologic malignancies. (1,2) Specific genomic alterations in tumors can be used as [...], * Context.--An increasing number of molecular laboratories are implementing next-generation sequencing platforms to identify clinically actionable and relevant genomic alterations for precision oncology. Objective.--To describe the validation studies as per New York State-Department of Health (NYS-DOH) guidelines for the Oncomine Comprehensive Panel v2, which was originally tailored to the National Cancer Institute Molecular Analysis for Therapy Choice (NCIMATCH) trial. Design.--Accuracy, precision, and reproducibility were investigated by using 130 DNA and 18 RNA samples from cytology cell blocks; formalin-fixed, paraffin-embedded tissues; and frozen samples. Analytic sensitivity and specificity were tested by using ATCC and HapMap cell lines. Results.--High accuracy and precision/reproducibility were observed for single nucleotide variants and insertion/ deletions. We also share our experience in the detection of gene fusions and copy number alterations from an amplicon-based sequencing platform. After sequencing analysis, variant annotation and report generation were performed by using the institutional knowledgebase. Conclusions.--This study serves as an example for validating a comprehensive targeted next-generation sequencing assay with both DNASeq and RNASeq components for NYS-DOH. doi: 10.5858/arpa.2019-0162-OA

Published
2020
Full Text
View/download PDF

41. Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer

Author

Beltran, Himisha, Romanel, Alessandro, Conteduca, Vincenza, Casiraghi, Nicola, Sigouros, Michael, Franceschini, Gian Marco, Orlando, Francesco, Fedrizzi, Tarcisio, Ku, Sheng-Yu, Dann, Emma, Alonso, Alicia, Mosquera, Juan Miguel, Sboner, Andrea, Xiang, Jenny, Elemento, Olivier, Nanus, David M., Tagawa, Scott T., Benelli, Matteo, and Demichelis, Francesca

Subjects
Diagnosis, Development and progression, Cancer treatment, Epigenetic inheritance, Cancer genetics -- Diagnosis -- Development and progression, Enzalutamide, Abiraterone, Methylation, Genomes, Genomics, Genetic research, Tumor proteins -- Diagnosis -- Development and progression, DNA, Prostate cancer -- Development and progression -- Diagnosis, Cancer metastasis -- Diagnosis -- Development and progression, Adenocarcinoma, Androgens, Tumors, Sulfites
Abstract

Introduction Prostate cancer is a leading cause of cancer death for men worldwide (1). Despite significant advances in therapy for patients with metastatic disease, the emergence of treatment resistance remains [...], Loss of androgen receptor (AR) signaling dependence occurs in approximately 15%-20% of advanced treatment-resistant prostate cancers, and this may manifest clinically as transformation from a prostate adenocarcinoma histology to a castration-resistant neuroendocrine prostate cancer (CRPC-NE). The diagnosis of CRPC-NE currently relies on a metastatic tumor biopsy, which is invasive for patients and sometimes challenging to diagnose due to morphologic heterogeneity. By studying whole-exome sequencing and whole-genome bisulfite sequencing of cell free DNA (cfDNA) and of matched metastatic tumor biopsies from patients with metastatic prostate adenocarcinoma and CRPC-NE, we identified CRPC-NE features detectable in the circulation. Overall, there was markedly higher concordance between cfDNA and biopsy tissue genomic alterations in patients with CRPC-NE compared with castration-resistant adenocarcinoma, supporting greater intraindividual genomic consistency across metastases. Allele-specific copy number and serial sampling analyses allowed for the detection and tracking of clonal and subclonal tumor cell populations. cfDNA methylation was indicative of circulating tumor content fraction, reflective of methylation patterns observed in biopsy tissues, and was capable of detecting CRPCNE-associated epigenetic changes (e.g., hypermethylation of ASXL3 and SPDEF; hypomethylation of INSM1 and CDH2). A targeted set combining genomic (TP53, RB1, CYLD, AR) and epigenomic (hypo- and hypermethylation of 20 differential sites) alterations applied to ctDNA was capable of identifying patients with CRPC-NE.

Published
2020
Full Text
View/download PDF

42. Clinical features of neuroendocrine prostate cancer

Author

Conteduca, Vincenza, Oromendia, Clara, Eng, Kenneth W., Bareja, Rohan, Sigouros, Michael, Molina, Ana, Faltas, Bishoy M., Sboner, Andrea, Mosquera, Juan Miguel, Elemento, Olivier, Nanus, David M., Tagawa, Scott T., Ballman, Karla V., and Beltran, Himisha

Published
2019
Full Text
View/download PDF

44. Cooperativity of c-MYC with Krüppel-Like Factor 6 Splice Variant 1 induces phenotypic plasticity and promotes prostate cancer progression and metastasis

Author

Izadmehr, Sudeh, primary, Fernandez-Hernandez, Heriberto, additional, Wiredja, Danica, additional, Kirschenbaum, Alexander, additional, Lee-Poturalski, Christine, additional, Tavassoli, Peyman, additional, Yao, Shen, additional, Schlatzer, Daniela, additional, Hoon, Divya, additional, Difeo, Analisa, additional, Levine, Alice C., additional, Mosquera, Juan-Miguel, additional, Galsky, Matthew D., additional, Cordon-Cardo, Carlos, additional, and Narla, Goutham, additional

Published
2024
Full Text
View/download PDF

45. Deciphering the origin and therapeutic targets of cancer of unknown primary: a case report that illustrates the power of integrative whole-exome and transcriptome sequencing analysis

Author

Al Assaad, Majd, primary, Shin, Nara, additional, Sigouros, Michael, additional, Manohar, Jyothi, additional, Antysheva, Zoia, additional, Kotlov, Nikita, additional, Kiriy, Daria, additional, Nikitina, Anastasiia, additional, Kleimenov, Mikhail, additional, Tsareva, Anastasiya, additional, Makarova, Anastasiya, additional, Fomchenkova, Victoria, additional, Dubinina, Julia, additional, Boyko, Alexandra, additional, Almog, Nava, additional, Wilkes, David, additional, Escalon, Joanna G., additional, Saxena, Ashish, additional, Elemento, Olivier, additional, Sternberg, Cora N., additional, Nanus, David M., additional, and Mosquera, Juan Miguel, additional

Published
2024
Full Text
View/download PDF

48. Targeting the epichaperome as an effective precision medicine approach in a novel PML-SYK fusion acute myeloid leukemia

Author

Sugita, Mayumi, Wilkes, David C., Bareja, Rohan, Eng, Kenneth W., Nataraj, Sarah, Jimenez-Flores, Reyna A., Yan, LunBiao, De Leon, Jeanne Pauline, Croyle, Jaclyn A., Kaner, Justin, Merugu, Swathi, Sharma, Sahil, MacDonald, Theresa Y., Noorzad, Zohal, Panchal, Palak, Pancirer, Danielle, Cheng, Shuhua, Xiang, Jenny Z., Olson, Luke, Van Besien, Koen, Rickman, David S., Mathew, Susan, Tam, Wayne, Rubin, Mark A., Beltran, Himisha, Sboner, Andrea, Hassane, Duane C., Chiosis, Gabriela, Elemento, Olivier, Roboz, Gail J., Mosquera, Juan Miguel, and Guzman, Monica L.

Published
2021
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results