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31 results on '"Hernandez, Sharia"'

1. An atlas of epithelial cell states and plasticity in lung adenocarcinoma

Author

Han, Guangchun, Sinjab, Ansam, Rahal, Zahraa, Lynch, Anne M., Treekitkarnmongkol, Warapen, Liu, Yuejiang, Serrano, Alejandra G., Feng, Jiping, Liang, Ke, Khan, Khaja, Lu, Wei, Hernandez, Sharia D., Liu, Yunhe, Cao, Xuanye, Dai, Enyu, Pei, Guangsheng, Hu, Jian, Abaya, Camille, Gomez-Bolanos, Lorena I., Peng, Fuduan, Chen, Minyue, Parra, Edwin R., Cascone, Tina, Sepesi, Boris, Moghaddam, Seyed Javad, Scheet, Paul, Negrao, Marcelo V., Heymach, John V., Li, Mingyao, Dubinett, Steven M., Stevenson, Christopher S., Spira, Avrum E., Fujimoto, Junya, Solis, Luisa M., Wistuba, Ignacio I., Chen, Jichao, Wang, Linghua, and Kadara, Humam

Published
2024
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3. Author Correction: An atlas of epithelial cell states and plasticity in lung adenocarcinoma

Author

Han, Guangchun, Sinjab, Ansam, Rahal, Zahraa, Lynch, Anne M., Treekitkarnmongkol, Warapen, Liu, Yuejiang, Serrano, Alejandra G., Feng, Jiping, Liang, Ke, Khan, Khaja, Lu, Wei, Hernandez, Sharia D., Liu, Yunhe, Cao, Xuanye, Dai, Enyu, Pei, Guangsheng, Hu, Jian, Abaya, Camille, Gomez-Bolanos, Lorena I., Peng, Fuduan, Chen, Minyue, Parra, Edwin R., Cascone, Tina, Sepesi, Boris, Moghaddam, Seyed Javad, Scheet, Paul, Negrao, Marcelo V., Heymach, John V., Li, Mingyao, Dubinett, Steven M., Stevenson, Christopher S., Spira, Avrum E., Fujimoto, Junya, Solis, Luisa M., Wistuba, Ignacio I., Chen, Jichao, Wang, Linghua, and Kadara, Humam

Published
2024
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5. Correlation of cancer testis antigen expression with high type-I interferon signal and prognosis in small bowel neuroendocrine tumors.

Author

Ayabe, Reed I., primary, Seo, Yongwoo David, additional, Melendez, Brenda, additional, Lazcano Segura, Rossana, additional, Fields, Brittany C., additional, Wani, Khalida M., additional, Johnson, Sarah, additional, Witt, Russell, additional, Chelvanambi, Manoj, additional, Hudgens, Courtney, additional, Hernandez, Sharia D., additional, Ajami, Nadim J., additional, Wargo, Jennifer Ann, additional, Lazar, Alexander J., additional, Halperin, Daniel M., additional, Estrella, Jeannelyn, additional, and Maxwell, Jess, additional

Published
2024
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6. Data from The Single-Cell Immunogenomic Landscape of B and Plasma Cells in Early-Stage Lung Adenocarcinoma

Author

Hao, Dapeng, primary, Han, Guangchun, primary, Sinjab, Ansam, primary, Gomez-Bolanos, Lorena Isabel, primary, Lazcano, Rossana, primary, Serrano, Alejandra, primary, Hernandez, Sharia D., primary, Dai, Enyu, primary, Cao, Xuanye, primary, Hu, Jian, primary, Dang, Minghao, primary, Wang, Ruiping, primary, Chu, Yanshuo, primary, Song, Xingzhi, primary, Zhang, Jianhua, primary, Parra, Edwin R., primary, Wargo, Jennifer A., primary, Swisher, Stephen G., primary, Cascone, Tina, primary, Sepesi, Boris, primary, Futreal, Andrew P., primary, Li, Mingyao, primary, Dubinett, Steven M., primary, Fujimoto, Junya, primary, Solis Soto, Luisa M., primary, Wistuba, Ignacio I., primary, Stevenson, Christopher S., primary, Spira, Avrum, primary, Shalapour, Shabnam, primary, Kadara, Humam, primary, and Wang, Linghua, primary

Published
2023
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7. Abstract 4460: Spatial profiling of immune biomarkers in resected treatment-naïve early stage lung adenocarcinoma

Author

Hernandez, Sharia D., primary, Lu, Wei, additional, Serrano, Alejandra G., additional, Arrechedera, Claudio J., additional, Sanchez-Espiridion, Beatriz, additional, Ozirmak, Nejla, additional, Molina, Max, additional, Kostousov, Larisa, additional, Barnes, Sean, additional, Khan, Khaja, additional, Tang, Ximing, additional, Fujimoto, Junya, additional, Parra, Edwin R., additional, Raso, Gabriela, additional, Schmidt, Stephanie T., additional, Behrens, Carmen, additional, Heymach, John, additional, Zhang, Jianjun, additional, Chen, Ken, additional, Sepesi, Boris, additional, Cascone, Tina, additional, Gibbons, Don, additional, Wistuba, Ignacio I., additional, Haymaker, Cara, additional, and Solis, Luisa M., additional

Published
2023
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8. Abstract 113: An atlas of epithelial cell states and plasticity in lung adenocarcinoma

Author

Han, Guangchun, primary, Sinjab, Ansam, additional, Treekitkarnmongkol, Warapen, additional, Rahal, Zahraa, additional, Liu, Yuejiang, additional, Serrano, Alejandra G., additional, Feng, Jiping, additional, Liang, Ke, additional, Khan, Khaja, additional, Lu, Wei, additional, Hernandez, Sharia, additional, Cao, Xuanye, additional, Dai, Enyu, additional, Liu, Yunhe, additional, Pei, Guangsheng, additional, Hu, Jian, additional, Bolanos, Lorena I. Gomez, additional, Parra, Edwin R., additional, Cascone, Tina, additional, Sepesi, Boris, additional, Moghaddam, Seyed Javad, additional, Scheet, Paul, additional, Negrao, Marcelo V., additional, Heymach, John V., additional, Li, Mingyao, additional, Chen, Jichao, additional, Dubinett, Steven M., additional, Fujimoto, Junya, additional, Solis, Luisa M., additional, Wistuba, Ignacio I., additional, Stevenson, Christopher S., additional, Spira, Avrum, additional, Wang, Linghua, additional, and Kadara, Humam, additional

Published
2023
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9. Supplementary Figure from The Single-Cell Immunogenomic Landscape of B and Plasma Cells in Early-Stage Lung Adenocarcinoma

Author

Hao, Dapeng, primary, Han, Guangchun, primary, Sinjab, Ansam, primary, Gomez-Bolanos, Lorena Isabel, primary, Lazcano, Rossana, primary, Serrano, Alejandra, primary, Hernandez, Sharia D., primary, Dai, Enyu, primary, Cao, Xuanye, primary, Hu, Jian, primary, Dang, Minghao, primary, Wang, Ruiping, primary, Chu, Yanshuo, primary, Song, Xingzhi, primary, Zhang, Jianhua, primary, Parra, Edwin R., primary, Wargo, Jennifer A., primary, Swisher, Stephen G., primary, Cascone, Tina, primary, Sepesi, Boris, primary, Futreal, Andrew P., primary, Li, Mingyao, primary, Dubinett, Steven M., primary, Fujimoto, Junya, primary, Solis Soto, Luisa M., primary, Wistuba, Ignacio I., primary, Stevenson, Christopher S., primary, Spira, Avrum, primary, Shalapour, Shabnam, primary, Kadara, Humam, primary, and Wang, Linghua, primary

Published
2023
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10. Supplementary Data from The Single-Cell Immunogenomic Landscape of B and Plasma Cells in Early-Stage Lung Adenocarcinoma

Author

Hao, Dapeng, primary, Han, Guangchun, primary, Sinjab, Ansam, primary, Gomez-Bolanos, Lorena Isabel, primary, Lazcano, Rossana, primary, Serrano, Alejandra, primary, Hernandez, Sharia D., primary, Dai, Enyu, primary, Cao, Xuanye, primary, Hu, Jian, primary, Dang, Minghao, primary, Wang, Ruiping, primary, Chu, Yanshuo, primary, Song, Xingzhi, primary, Zhang, Jianhua, primary, Parra, Edwin R., primary, Wargo, Jennifer A., primary, Swisher, Stephen G., primary, Cascone, Tina, primary, Sepesi, Boris, primary, Futreal, Andrew P., primary, Li, Mingyao, primary, Dubinett, Steven M., primary, Fujimoto, Junya, primary, Solis Soto, Luisa M., primary, Wistuba, Ignacio I., primary, Stevenson, Christopher S., primary, Spira, Avrum, primary, Shalapour, Shabnam, primary, Kadara, Humam, primary, and Wang, Linghua, primary

Published
2023
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11. Supplementary Figure from Diminished Immune Surveillance during Histologic Progression of Intraductal Papillary Mucinous Neoplasms Offers a Therapeutic Opportunity for Cancer Interception

Author

Hernandez, Sharia, primary, Parra, Edwin Roger, primary, Uraoka, Naohiro, primary, Tang, Ximing, primary, Shen, Yu, primary, Qiao, Wei, primary, Jiang, Mei, primary, Zhang, Shanyu, primary, Mino, Barbara, primary, Lu, Wei, primary, Pandurengan, Renganayaki, primary, Haymaker, Cara, primary, Affolter, Kajsa, primary, Scaife, Courtney L., primary, Yip-Schneider, Michele, primary, Schmidt, C. Max, primary, Firpo, Matthew A., primary, Mulvihill, Sean J., primary, Koay, Eugene J., primary, Wang, Huamin, primary, Wistuba, Ignacio I., primary, Maitra, Anirban, primary, Solis, Luisa M., primary, and Sen, Subrata, primary

Published
2023
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12. Supplementary Data from Diminished Immune Surveillance during Histologic Progression of Intraductal Papillary Mucinous Neoplasms Offers a Therapeutic Opportunity for Cancer Interception

Author

Hernandez, Sharia, primary, Parra, Edwin Roger, primary, Uraoka, Naohiro, primary, Tang, Ximing, primary, Shen, Yu, primary, Qiao, Wei, primary, Jiang, Mei, primary, Zhang, Shanyu, primary, Mino, Barbara, primary, Lu, Wei, primary, Pandurengan, Renganayaki, primary, Haymaker, Cara, primary, Affolter, Kajsa, primary, Scaife, Courtney L., primary, Yip-Schneider, Michele, primary, Schmidt, C. Max, primary, Firpo, Matthew A., primary, Mulvihill, Sean J., primary, Koay, Eugene J., primary, Wang, Huamin, primary, Wistuba, Ignacio I., primary, Maitra, Anirban, primary, Solis, Luisa M., primary, and Sen, Subrata, primary

Published
2023
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13. Differential Spatial Gene and Protein Expression Associated with Recurrence Following Chemoradiation for Localized Anal Squamous Cell Cancer

Author

Hernandez, Sharia, primary, Das, Prajnan, additional, Holliday, Emma B., additional, Shen, Li, additional, Lu, Wei, additional, Johnson, Benny, additional, Messick, Craig A., additional, Taniguchi, Cullen M., additional, Skibber, John, additional, Ludmir, Ethan B., additional, You, Y. Nancy, additional, Smith, Grace Li, additional, Bednarski, Brian, additional, Kostousov, Larisa, additional, Koay, Eugene J., additional, Minsky, Bruce D., additional, Tillman, Matthew, additional, Portier, Shaelynn, additional, Eng, Cathy, additional, Koong, Albert C., additional, Chang, George J., additional, Foo, Wai Chin, additional, Wang, Jing, additional, Soto, Luisa Solis, additional, and Morris, Van K., additional

Published
2023
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14. Evaluation of immune exhaustion across the evolution of oligometastatic clear cell renal cell carcinoma using spatially resolved tissue immune profiling: Secondary analysis of a prospective trial.

Author

Hara, Kieko, primary, Corredor-Alonso, Guillermo E, additional, Serrano, Alejandra G, additional, Hernandez, Sharia D, additional, Lu, Wei, additional, Shah, Amishi Yogesh, additional, Jonasch, Eric, additional, Karam, Jose A., additional, Matin, Surena F., additional, Tannir, Nizar M., additional, Msaouel, Pavlos, additional, Sircar, Kanishka, additional, Solis, Luisa Maren, additional, and Tang, Chad, additional

Published
2023
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15. The Single-Cell Immunogenomic Landscape of B and Plasma Cells in Early-Stage Lung Adenocarcinoma

Author

Hao, Dapeng, primary, Han, Guangchun, additional, Sinjab, Ansam, additional, Gomez-Bolanos, Lorena Isabel, additional, Lazcano, Rossana, additional, Serrano, Alejandra, additional, Hernandez, Sharia D., additional, Dai, Enyu, additional, Cao, Xuanye, additional, Hu, Jian, additional, Dang, Minghao, additional, Wang, Ruiping, additional, Chu, Yanshuo, additional, Song, Xingzhi, additional, Zhang, Jianhua, additional, Parra, Edwin R., additional, Wargo, Jennifer A., additional, Swisher, Stephen G., additional, Cascone, Tina, additional, Sepesi, Boris, additional, Futreal, Andrew P., additional, Li, Mingyao, additional, Dubinett, Steven M., additional, Fujimoto, Junya, additional, Solis Soto, Luisa M., additional, Wistuba, Ignacio I., additional, Stevenson, Christopher S., additional, Spira, Avrum, additional, Shalapour, Shabnam, additional, Kadara, Humam, additional, and Wang, Linghua, additional

Published
2022
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18. An atlas of epithelial cell states and plasticity in lung adenocarcinoma

Author

Han, Guangchun, primary, Sinjab, Ansam, additional, Treekitkarnmongkol, Warapen, additional, Lu, Wei, additional, Serrano, Alejandra G., additional, Hernandez, Sharia D., additional, Rahal, Zahraa, additional, Cao, Xuanye, additional, Dai, Enyu, additional, Gomez-Bolanos, Lorena I., additional, Parra, Edwin R., additional, Negrao, Marcelo Vailati, additional, Cascone, Tina, additional, Sepesi, Boris, additional, Moghaddam, Seyed Javad, additional, Chen, Jichao, additional, Dubinett, Steven M., additional, Scheet, Paul, additional, Fujimoto, Junya, additional, Solis, Luisa M., additional, Wistuba, Ignacio I., additional, Stevenson, Christopher S., additional, Spira, Avrum E., additional, Wang, Linghua, additional, and Kadara, Humam, additional

Published
2022
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19. Diminished Immune Surveillance during Histologic Progression of Intraductal Papillary Mucinous Neoplasms Offers a Therapeutic Opportunity for Cancer Interception

Author

Hernandez, Sharia, primary, Parra, Edwin Roger, additional, Uraoka, Naohiro, additional, Tang, Ximing, additional, Shen, Yu, additional, Qiao, Wei, additional, Jiang, Mei, additional, Zhang, Shanyu, additional, Mino, Barbara, additional, Lu, Wei, additional, Pandurengan, Renganayaki, additional, Haymaker, Cara, additional, Affolter, Kajsa, additional, Scaife, Courtney L., additional, Yip-Schneider, Michele, additional, Schmidt, C. Max, additional, Firpo, Matthew A., additional, Mulvihill, Sean J., additional, Koay, Eugene J., additional, Wang, Huamin, additional, Wistuba, Ignacio I., additional, Maitra, Anirban, additional, Solis, Luisa M., additional, and Sen, Subrata, additional

Published
2022
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22. CTIM-04. BIOMARKER IMMUNE CORRELATES IN NEWLY DIAGNOSED GLIOBLASTOMA (GBM) TREATED WITH ATEZOLIZUMAB IN COMBINATION WITH TEMOZOLOMIDE (TMZ) AND RADIATION

Author

Weathers, Shiao-Pei, primary, Knafl, Mark, additional, Parra, Edwin, additional, Hernandez, Sharia, additional, Solis, Luisa, additional, Espiridion, Beatriz Sanchez, additional, Wistuba, Ignacio, additional, Futreal, Andrew, additional, Maru, Dipen, additional, Kamiya-Matsuoka, Carlos, additional, Harrison, Rebecca, additional, Joseph, Victory, additional, Yun, Cindy, additional, Darbonne, Walter, additional, Loghin, Monica, additional, Penas-Prado, Marta, additional, Majd, Nazanin, additional, Yung, W K Alfred, additional, O'Brien, Barbara, additional, Scott, Woodman, additional, and DeGroot, John, additional

Published
2021
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24. Challenges and Opportunities for Immunoprofiling Using a Spatial High-Plex Technology: The NanoString GeoMx® Digital Spatial Profiler.

Author

Hernandez, Sharia, Lazcano, Rossana, Serrano, Alejandra, Powell, Steven, Kostousov, Larissa, Mehta, Jay, Khan, Khaja, Lu, Wei, and Solis, Luisa M.

Subjects
TUMOR microenvironment, IMMUNE complexes, TRANSLATIONAL research, EXPERIMENTAL design, SAMPLE size (Statistics)
Abstract

Characterization of the tumor microenvironment through immunoprofiling has become an essential resource for the understanding of the complex immune cell interactions and the assessment of biomarkers for prognosis and prediction of immunotherapy response; however, these studies are often limited by tissue heterogeneity and sample size. The nanoString GeoMx® Digital Spatial Profiler (DSP) is a platform that allows high-plex profiling at the protein and RNA level, providing spatial and temporal assessment of tumors in frozen or formalin-fixed paraffin-embedded limited tissue sample. Recently, high-impact studies have shown the feasibility of using this technology to identify biomarkers in different settings, including predictive biomarkers for immunotherapy in different tumor types. These studies showed that compared to other multiplex and high-plex platforms, the DSP can interrogate a higher number of biomarkers with higher throughput; however, it does not provide single-cell resolution, including co-expression of biomarker or spatial information at the single-cell level. In this review, we will describe the technical overview of the platform, present current evidence of the advantages and limitations of the applications of this technology, and provide important considerations for the experimental design for translational immune-oncology research using this tissue-based high-plex profiling approach. [ABSTRACT FROM AUTHOR]

Published
2022
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25. Multiplex Immunofluorescence and the Digital Image Analysis Workflow for Evaluation of the Tumor Immune Environment in Translational Research.

Author

Rojas, Frank, Hernandez, Sharia, Lazcano, Rossana, Laberiano-Fernandez, Caddie, and Parra, Edwin Roger

Subjects
IMAGE analysis, TUMOR microenvironment, TRANSLATIONAL research, IMMUNOFLUORESCENCE
Abstract

A robust understanding of the tumor immune environment has important implications for cancer diagnosis, prognosis, research, and immunotherapy. Traditionally, immunohistochemistry (IHC) has been regarded as the standard method for detecting proteins in situ , but this technique allows for the evaluation of only one cell marker per tissue sample at a time. However, multiplexed imaging technologies enable the multiparametric analysis of a tissue section at the same time. Also, through the curation of specific antibody panels, these technologies enable researchers to study the cell subpopulations within a single immunological cell group. Thus, multiplexed imaging gives investigators the opportunity to better understand tumor cells, immune cells, and the interactions between them. In the multiplexed imaging technology workflow, once the protocol for a tumor immune micro environment study has been defined, histological slides are digitized to produce high-resolution images in which regions of interest are selected for the interrogation of simultaneously expressed immunomarkers (including those co-expressed by the same cell) by using an image analysis software and algorithm. Most currently available image analysis software packages use similar machine learning approaches in which tissue segmentation first defines the different components that make up the regions of interest and cell segmentation, then defines the different parameters, such as the nucleus and cytoplasm, that the software must utilize to segment single cells. Image analysis tools have driven dramatic evolution in the field of digital pathology over the past several decades and provided the data necessary for translational research and the discovery of new therapeutic targets. The next step in the growth of digital pathology is optimization and standardization of the different tasks in cancer research, including image analysis algorithm creation, to increase the amount of data generated and their accuracy in a short time as described herein. The aim of this review is to describe this process, including an image analysis algorithm creation for multiplex immunofluorescence analysis, as an essential part of the optimization and standardization of the different processes in cancer research, to increase the amount of data generated and their accuracy in a short time. [ABSTRACT FROM AUTHOR]

Published
2022
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27. Multi-omic molecular profiling reveals potentially targetable abnormalities shared across multiple histologies of brain metastasis

Author

Fukumura, Kazutaka, primary, Malgulwar, Prit Benny, additional, Fischer, Grant M., additional, Hu, Xiaoding, additional, Mao, Xizeng, additional, Song, Xingzhi, additional, Hernandez, Sharia D., additional, Zhang, Xiang H.-F., additional, Zhang, Jianhua, additional, Parra, Edwin Roger, additional, Yu, Dihua, additional, Debeb, Bisrat G., additional, Davies, Michael A., additional, and Huse, Jason T., additional

Published
2021
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28. Procedural Requirements and Recommendations for Multiplex Immunofluorescence Tyramide Signal Amplification Assays to Support Translational Oncology Studies

Author

Parra, Edwin Roger, primary, Jiang, Mei, additional, Solis, Luisa, additional, Mino, Barbara, additional, Laberiano, Caddie, additional, Hernandez, Sharia, additional, Gite, Swati, additional, Verma, Anuj, additional, Tetzlaff, Michael, additional, Haymaker, Cara, additional, Tamegnon, Auriole, additional, Rodriguez-Canales, Jaime, additional, Hoyd, Clifford, additional, Bernachez, Chantale, additional, and Wistuba, Ignacio, additional

Published
2020
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30. Elucidating immune-related gene transcriptional programs via factorization of large-scale RNA-profiles.

Author

He S, Gubin MM, Rafei H, Basar R, Dede M, Jiang X, Liang Q, Tan Y, Kim K, Gillison ML, Rezvani K, Peng W, Haymaker C, Hernandez S, Solis LM, Mohanty V, and Chen K

Abstract

Recent developments in immunotherapy, including immune checkpoint blockade (ICB) and adoptive cell therapy, have encountered challenges such as immune-related adverse events and resistance, especially in solid tumors. To advance the field, a deeper understanding of the molecular mechanisms behind treatment responses and resistance is essential. However, the lack of functionally characterized immune-related gene sets has limited data-driven immunological research. To address this gap, we adopted non-negative matrix factorization on 83 human bulk RNA-seq datasets and constructed 28 immune-specific gene sets. After rigorous immunologist-led manual annotations and orthogonal validations across immunological contexts and functional omics data, we demonstrated that these gene sets can be applied to refine pan-cancer immune subtypes, improve ICB response prediction and functionally annotate spatial transcriptomic data. These functional gene sets, informing diverse immune states, will advance our understanding of immunology and cancer research.

Published
2024
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31. Challenges and Opportunities for Immunoprofiling Using a Spatial High-Plex Technology: The NanoString GeoMx ® Digital Spatial Profiler.

Author

Hernandez S, Lazcano R, Serrano A, Powell S, Kostousov L, Mehta J, Khan K, Lu W, and Solis LM

Abstract

Characterization of the tumor microenvironment through immunoprofiling has become an essential resource for the understanding of the complex immune cell interactions and the assessment of biomarkers for prognosis and prediction of immunotherapy response; however, these studies are often limited by tissue heterogeneity and sample size. The nanoString GeoMx ® Digital Spatial Profiler (DSP) is a platform that allows high-plex profiling at the protein and RNA level, providing spatial and temporal assessment of tumors in frozen or formalin-fixed paraffin-embedded limited tissue sample. Recently, high-impact studies have shown the feasibility of using this technology to identify biomarkers in different settings, including predictive biomarkers for immunotherapy in different tumor types. These studies showed that compared to other multiplex and high-plex platforms, the DSP can interrogate a higher number of biomarkers with higher throughput; however, it does not provide single-cell resolution, including co-expression of biomarker or spatial information at the single-cell level. In this review, we will describe the technical overview of the platform, present current evidence of the advantages and limitations of the applications of this technology, and provide important considerations for the experimental design for translational immune-oncology research using this tissue-based high-plex profiling approach., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Hernandez, Lazcano, Serrano, Powell, Kostousov, Mehta, Khan, Lu and Solis.)

Published
2022
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