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361 results on '"Varma, Sushama"'

1. A human autoimmune organoid model reveals IL-7 function in coeliac disease

Author

Santos, António J. M., van Unen, Vincent, Lin, Zhongqi, Chirieleison, Steven M., Ha, Nhi, Batish, Arpit, Chan, Joshua E., Cedano, Jose, Zhang, Elisa T., Mu, Qinghui, Guh-Siesel, Alexander, Tomaske, Madeline, Colburg, Deana, Varma, Sushama, Choi, Shannon S., Christophersen, Asbjørn, Baghdasaryan, Ani, Yost, Kathryn E., Karlsson, Kasper, Ha, Andrew, Li, Jing, Dai, Hongjie, Sellers, Zachary M., Chang, Howard Y., Dunn, James C. Y., Zhang, Bing M., Mellins, Elizabeth D., Sollid, Ludvig M., Fernandez-Becker, Nielsen Q., Davis, Mark M., and Kuo, Calvin J.

Published
2024
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3. A human lung tumor microenvironment interactome identifies clinically relevant cell-type cross-talk

Author

Gentles, Andrew J, Hui, Angela Bik-Yu, Feng, Weiguo, Azizi, Armon, Nair, Ramesh V, Bouchard, Gina, Knowles, David A, Yu, Alice, Jeong, Youngtae, Bejnood, Alborz, Forgó, Erna, Varma, Sushama, Xu, Yue, Kuong, Amanda, Nair, Viswam S, West, Rob, van de Rijn, Matt, Hoang, Chuong D, Diehn, Maximilian, and Plevritis, Sylvia K

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Cancer, Biotechnology, Human Genome, Lung, Rare Diseases, Lung Cancer, Clinical Research, Genetics, 2.1 Biological and endogenous factors, Adenocarcinoma, Carcinoma, Non-Small-Cell Lung, Cell Communication, Cell Line, Tumor, Fibroblasts, Humans, Intercellular Signaling Peptides and Proteins, Lung Neoplasms, Primary Cell Culture, Receptor Cross-Talk, Tumor Microenvironment, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundTumors comprise a complex microenvironment of interacting malignant and stromal cell types. Much of our understanding of the tumor microenvironment comes from in vitro studies isolating the interactions between malignant cells and a single stromal cell type, often along a single pathway.ResultTo develop a deeper understanding of the interactions between cells within human lung tumors, we perform RNA-seq profiling of flow-sorted malignant cells, endothelial cells, immune cells, fibroblasts, and bulk cells from freshly resected human primary non-small-cell lung tumors. We map the cell-specific differential expression of prognostically associated secreted factors and cell surface genes, and computationally reconstruct cross-talk between these cell types to generate a novel resource called the Lung Tumor Microenvironment Interactome (LTMI). Using this resource, we identify and validate a prognostically unfavorable influence of Gremlin-1 production by fibroblasts on proliferation of malignant lung adenocarcinoma cells. We also find a prognostically favorable association between infiltration of mast cells and less aggressive tumor cell behavior.ConclusionThese results illustrate the utility of the LTMI as a resource for generating hypotheses concerning tumor-microenvironment interactions that may have prognostic and therapeutic relevance.

Published
2020

4. Gene Expression Profiling of Head and Neck Tumors Identifies FOXP1 and SOX10 Expression as Useful for Distinguishing Ameloblastoma From Basaloid Salivary Gland Tumors

Author

Ko, Yen Chen Kevin, Varma, Sushama, Zhu, Chun Fang, Zhu, Shirley Xiaolei, Vennam, Sujay, Poh, Catherine F, Jordan, Richard C, Kong, Christina, Pollack, Jonathan R, and West, Robert B

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Dental/Oral and Craniofacial Disease, Cancer, Clinical Research, Genetics, Digestive Diseases, Ameloblastoma, Biomarkers, Tumor, British Columbia, Carcinoma, Diagnosis, Differential, Forkhead Transcription Factors, Gene Expression Profiling, Humans, Immunohistochemistry, Predictive Value of Tests, Repressor Proteins, SOXE Transcription Factors, Salivary Gland Neoplasms, San Francisco, Transcriptome, odontogenic tumors, salivary gland tumors, FOXP1, SOX10, ameloblastoma, gene expression profile, Clinical Sciences, Pathology, Clinical sciences
Abstract

Odontogenic tumors show considerable morphologic heterogeneity and at times the diagnosis can be challenging. Ameloblastoma, the most common odontogenic tumor, can have morphologic similarity to some salivary gland tumors and therefore we sought to identify biomarkers that might aid in the diagnosis by performing transcriptome wide gene expression profiling of 80 odontogenic and salivary gland neoplasms. These data identified the FOXP1/SOX10 expression profile as characteristic of many odontogenic tumors including ameloblastoma but largely absent in salivary gland tumors. We then assessed 173 salivary gland tumors and 108 odontogenic tumors by immunohistochemistry for FOXP1 and SOX10 expression and found that 34/35 (97%) cases of ameloblastomas were diffusely positive for FOXP1 but completely negative for SOX10. None of the basaloid salivary neoplasms (basal cell adenoma, adenoid cystic carcinoma, polymorphous adenocarcinoma, and myoepitheloma) demonstrated FOXP1/SOX10 expression pattern. Taken together, the results of this study suggest that the FOXP1/SOX10 immunophenotype is common in odontogenic tumors including ameloblastoma and might be useful distinguishing these from similar appearing basaloid salivary gland tumors.

Published
2020

5. Molecular classification and biomarkers of clinical outcome in breast ductal carcinoma in situ: Analysis of TBCRC 038 and RAHBT cohorts

Author

Strand, Siri H., Rivero-Gutiérrez, Belén, Houlahan, Kathleen E., Seoane, Jose A., King, Lorraine M., Risom, Tyler, Simpson, Lunden A., Vennam, Sujay, Khan, Aziz, Cisneros, Luis, Hardman, Timothy, Harmon, Bryan, Couch, Fergus, Gallagher, Kristalyn, Kilgore, Mark, Wei, Shi, DeMichele, Angela, King, Tari, McAuliffe, Priscilla F., Nangia, Julie, Lee, Joanna, Tseng, Jennifer, Storniolo, Anna Maria, Thompson, Alastair M., Gupta, Gaorav P., Burns, Robyn, Veis, Deborah J., DeSchryver, Katherine, Zhu, Chunfang, Matusiak, Magdalena, Wang, Jason, Zhu, Shirley X., Tappenden, Jen, Ding, Daisy Yi, Zhang, Dadong, Luo, Jingqin, Jiang, Shu, Varma, Sushama, Anderson, Lauren, Straub, Cody, Srivastava, Sucheta, Curtis, Christina, Tibshirani, Rob, Angelo, Robert Michael, Hall, Allison, Owzar, Kouros, Polyak, Kornelia, Maley, Carlo, Marks, Jeffrey R., Colditz, Graham A., Hwang, E. Shelley, and West, Robert B.

Published
2022
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7. Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma

Author

Risom, Tyler, Glass, David R., Averbukh, Inna, Liu, Candace C., Baranski, Alex, Kagel, Adam, McCaffrey, Erin F., Greenwald, Noah F., Rivero-Gutiérrez, Belén, Strand, Siri H., Varma, Sushama, Kong, Alex, Keren, Leeat, Srivastava, Sucheta, Zhu, Chunfang, Khair, Zumana, Veis, Deborah J., Deschryver, Katherine, Vennam, Sujay, Maley, Carlo, Hwang, E. Shelley, Marks, Jeffrey R., Bendall, Sean C., Colditz, Graham A., West, Robert B., and Angelo, Michael

Published
2022
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9. Chromosomal copy number alterations for associations of ductal carcinoma in situ with invasive breast cancer

Author

Afghahi, Anosheh, Forgó, Erna, Mitani, Aya A, Desai, Manisha, Varma, Sushama, Seto, Tina, Rigdon, Joseph, Jensen, Kristin C, Troxell, Megan L, Gomez, Scarlett Lin, Das, Amar K, Beck, Andrew H, Kurian, Allison W, and West, Robert B

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Women's Health, Cancer, Breast Cancer, 4.1 Discovery and preclinical testing of markers and technologies, Adult, Aged, Aged, 80 and over, Biomarkers, Tumor, Breast Neoplasms, Carcinoma, Intraductal, Noninfiltrating, Chromosome Aberrations, DNA Copy Number Variations, Female, Genetic Predisposition to Disease, Humans, In Situ Hybridization, Fluorescence, Middle Aged, Neoplasm Grading, Neoplasm Invasiveness, Neoplasm Staging, Young Adult, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

IntroductionScreening mammography has contributed to a significant increase in the diagnosis of ductal carcinoma in situ (DCIS), raising concerns about overdiagnosis and overtreatment. Building on prior observations from lineage evolution analysis, we examined whether measuring genomic features of DCIS would predict association with invasive breast carcinoma (IBC). The long-term goal is to enhance standard clinicopathologic measures of low- versus high-risk DCIS and to enable risk-appropriate treatment.MethodsWe studied three common chromosomal copy number alterations (CNA) in IBC and designed fluorescence in situ hybridization-based assay to measure copy number at these loci in DCIS samples. Clinicopathologic data were extracted from the electronic medical records of Stanford Cancer Institute and linked to demographic data from the population-based California Cancer Registry; results were integrated with data from tissue microarrays of specimens containing DCIS that did not develop IBC versus DCIS with concurrent IBC. Multivariable logistic regression analysis was performed to describe associations of CNAs with these two groups of DCIS.ResultsWe examined 271 patients with DCIS (120 that did not develop IBC and 151 with concurrent IBC) for the presence of 1q, 8q24 and 11q13 copy number gains. Compared to DCIS-only patients, patients with concurrent IBC had higher frequencies of CNAs in their DCIS samples. On multivariable analysis with conventional clinicopathologic features, the copy number gains were significantly associated with concurrent IBC. The state of two of the three copy number gains in DCIS was associated with a risk of IBC that was 9.07 times that of no copy number gains, and the presence of gains at all three genomic loci in DCIS was associated with a more than 17-fold risk (P = 0.0013).ConclusionsCNAs have the potential to improve the identification of high-risk DCIS, defined by presence of concurrent IBC. Expanding and validating this approach in both additional cross-sectional and longitudinal cohorts may enable improved risk stratification and risk-appropriate treatment in DCIS.

Published
2015

16. Cell volume expansion and local contractility drive collective invasion of the basement membrane in breast cancer

Author

Chang, Julie, primary, Saraswathibhatla, Aashrith, additional, Song, Zhaoqiang, additional, Varma, Sushama, additional, Sanchez, Colline, additional, Alyafei, Naomi Hassan Kahtan, additional, Indana, Dhiraj, additional, Slyman, Raleigh, additional, Srivastava, Sucheta, additional, Liu, Katherine, additional, Bassik, Michael C., additional, Marinkovich, M. Peter, additional, Hodgson, Louis, additional, Shenoy, Vivek, additional, West, Robert B., additional, and Chaudhuri, Ovijit, additional

Published
2023
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17. TMIC-75. SPATIALLY-RESOLVED TRANSCRIPTOME ANALYSIS OF BRAIN METASTATIC BREAST CANCER REVEAL KEY MEDIATORS OF BRAIN-TROPIC METASTATIC POTENTIAL

Author

Umeh-Garcia, Maxine, primary, Godfrey, Bryanna, additional, Perez, Pablo Nunez, additional, Varma, Sushama, additional, Ahmadian, Saman, additional, Toland, Angus, additional, Granucci, Monica, additional, Averbukh, Inna, additional, Tian, Lu, additional, West, Robert, additional, Angelo, Michael, additional, Plevritis, Sylvia, additional, and Gephart, Melanie Hayden, additional

Published
2023
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18. Single Cell Expression Analysis of Ductal Carcinoma in Situ Identifies Alterations in Epithelial Integrity

Author

Qin, Xiaodi, primary, Strand, Siri H, additional, Lee, Marissa R., additional, van Ijzendoorn, David G. P., additional, Zhu, ChunFang, additional, Vennam, Sujay, additional, Varma, Sushama, additional, Hall, Allison, additional, King, Lorraine, additional, Simpson, Lunden, additional, Luo, Xiaoke, additional, Colditz, Graham A., additional, Jiang, Shu, additional, Hwang, E. Shelley, additional, Marks, Jeffrey R., additional, Owzar, Kouros, additional, and West, Robert B., additional

Published
2023
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20. The HTN3-MSANTD3 Fusion Gene Defines a Subset of Acinic Cell Carcinoma of the Salivary Gland

Author

Andreasen, Simon, Varma, Sushama, Barasch, Nicholas, Thompson, Lester D.R., Miettinen, Markku, Rooper, Lisa, Stelow, Edward B., Agander, Tina K., Seethala, Raja R., Chiosea, Simion I., Homøe, Preben, Wessel, Irene, Larsen, Stine R., Erentaite, Daiva, Bishop, Justin A., Ulhøi, Benedicte P., Kiss, Katalin, Melchior, Linea C., Pollack, Jonathan R., and West, Robert B.

Published
2018
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27. Supplementary Figure from Interactions in CSF1-Driven Tenosynovial Giant Cell Tumors

Author

van IJzendoorn, David G.P., primary, Matusiak, Magdalena, primary, Charville, Gregory W., primary, Spierenburg, Geert, primary, Varma, Sushama, primary, Colburg, Deana R.C., primary, van de Sande, Michiel A.J., primary, van Langevelde, Kirsten, primary, Mohler, David G., primary, Ganjoo, Kristen N., primary, Bui, Nam Q., primary, Avedian, Raffi S., primary, Bovée, Judith V.M.G., primary, Steffner, Robert, primary, West, Robert B., primary, and van de Rijn, Matt, primary

Published
2023
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28. Supplementary Table from Interactions in CSF1-Driven Tenosynovial Giant Cell Tumors

Author

van IJzendoorn, David G.P., primary, Matusiak, Magdalena, primary, Charville, Gregory W., primary, Spierenburg, Geert, primary, Varma, Sushama, primary, Colburg, Deana R.C., primary, van de Sande, Michiel A.J., primary, van Langevelde, Kirsten, primary, Mohler, David G., primary, Ganjoo, Kristen N., primary, Bui, Nam Q., primary, Avedian, Raffi S., primary, Bovée, Judith V.M.G., primary, Steffner, Robert, primary, West, Robert B., primary, and van de Rijn, Matt, primary

Published
2023
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29. Supplementary Data from Multiomics Analysis of Spatially Distinct Stromal Cells Reveals Tumor-Induced O-Glycosylation of the CDK4–pRB Axis in Fibroblasts at the Invasive Tumor Edge

Author

Bouchard, Gina, primary, Garcia-Marques, Fernando Jose, primary, Karacosta, Loukia Georgiou, primary, Zhang, Weiruo, primary, Bermudez, Abel, primary, Riley, Nicholas McIlvain, primary, Varma, Sushama, primary, Mehl, Lindsey Catherine, primary, Benson, Jalen Anthony, primary, Shrager, Joseph B., primary, Bertozzi, Carolyn Ruth, primary, Pitteri, Sharon J., primary, Giaccia, Amato J., primary, and Plevritis, Sylvia Katina, primary

Published
2023
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32. Data from Multiomics Analysis of Spatially Distinct Stromal Cells Reveals Tumor-Induced O-Glycosylation of the CDK4–pRB Axis in Fibroblasts at the Invasive Tumor Edge

Author

Bouchard, Gina, primary, Garcia-Marques, Fernando Jose, primary, Karacosta, Loukia Georgiou, primary, Zhang, Weiruo, primary, Bermudez, Abel, primary, Riley, Nicholas McIlvain, primary, Varma, Sushama, primary, Mehl, Lindsey Catherine, primary, Benson, Jalen Anthony, primary, Shrager, Joseph B., primary, Bertozzi, Carolyn Ruth, primary, Pitteri, Sharon J., primary, Giaccia, Amato J., primary, and Plevritis, Sylvia Katina, primary

Published
2023
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33. Supplementary Figures S1-S5 from Clinically Relevant Molecular Subtypes in Leiomyosarcoma

Author

Guo, Xiangqian, primary, Jo, Vickie Y., primary, Mills, Anne M., primary, Zhu, Shirley X., primary, Lee, Cheng-Han, primary, Espinosa, Inigo, primary, Nucci, Marisa R., primary, Varma, Sushama, primary, Forgó, Erna, primary, Hastie, Trevor, primary, Anderson, Sharon, primary, Ganjoo, Kristen, primary, Beck, Andrew H., primary, West, Robert B., primary, Fletcher, Christopher D., primary, and van de Rijn, Matt, primary

Published
2023
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34. Supplementary Tables S1-S9 from Clinically Relevant Molecular Subtypes in Leiomyosarcoma

Author

Guo, Xiangqian, primary, Jo, Vickie Y., primary, Mills, Anne M., primary, Zhu, Shirley X., primary, Lee, Cheng-Han, primary, Espinosa, Inigo, primary, Nucci, Marisa R., primary, Varma, Sushama, primary, Forgó, Erna, primary, Hastie, Trevor, primary, Anderson, Sharon, primary, Ganjoo, Kristen, primary, Beck, Andrew H., primary, West, Robert B., primary, Fletcher, Christopher D., primary, and van de Rijn, Matt, primary

Published
2023
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46. Interactions in CSF1-Driven Tenosynovial Giant Cell Tumors

Author

van IJzendoorn, David G.P., primary, Matusiak, Magdalena, additional, Charville, Gregory W., additional, Spierenburg, Geert, additional, Varma, Sushama, additional, Colburg, Deana R.C., additional, van de Sande, Michiel A.J., additional, van Langevelde, Kirsten, additional, Mohler, David G., additional, Ganjoo, Kristen N., additional, Bui, Nam Q., additional, Avedian, Raffi S., additional, Bovée, Judith V.M.G., additional, Steffner, Robert, additional, West, Robert B., additional, and van de Rijn, Matt, additional

Published
2022
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47. Collective invasion of the basement membrane in breast cancer driven by forces from cell volume expansion and local contractility

Author

Chang, Julie, primary, Saraswathibhatla, Aashrith, additional, Song, Zhaoqiang, additional, Varma, Sushama, additional, Sanchez, Colline, additional, Srivastava, Sucheta, additional, Liu, Katherine, additional, Bassik, Michael C., additional, Marinkovich, M. Peter, additional, Hodgson, Louis, additional, Shenoy, Vivek, additional, West, Robert B., additional, and Chaudhuri, Ovijit, additional

Published
2022
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50. The microdissected gene expression landscape of nasopharyngeal cancer reveals vulnerabilities in FGF and noncanonical NF-κB signaling

Author

Tay, Joshua K., primary, Zhu, Chunfang, additional, Shin, June Ho, additional, Zhu, Shirley X., additional, Varma, Sushama, additional, Foley, Joseph W., additional, Vennam, Sujay, additional, Yip, Yim Ling, additional, Goh, Chuan Keng, additional, Wang, De Yun, additional, Loh, Kwok Seng, additional, Tsao, Sai Wah, additional, Le, Quynh-Thu, additional, Sunwoo, John B., additional, and West, Robert B., additional

Published
2022
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