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192 results on '"Rathi, Komal S."'

1. OpenPBTA: The Open Pediatric Brain Tumor Atlas

Author

Shapiro, Joshua A., Gaonkar, Krutika S., Spielman, Stephanie J., Savonen, Candace L., Bethell, Chante J., Jin, Run, Rathi, Komal S., Zhu, Yuankun, Egolf, Laura E., Farrow, Bailey K., Miller, Daniel P., Yang, Yang, Koganti, Tejaswi, Noureen, Nighat, Koptyra, Mateusz P., Duong, Nhat, Santi, Mariarita, Kim, Jung, Robins, Shannon, Storm, Phillip B., Mack, Stephen C., Lilly, Jena V., Xie, Hongbo M., Jain, Payal, Raman, Pichai, Rood, Brian R., Lulla, Rishi R., Nazarian, Javad, Kraya, Adam A., Vaksman, Zalman, Heath, Allison P., Kline, Cassie, Scolaro, Laura, Viaene, Angela N., Huang, Xiaoyan, Way, Gregory P., Foltz, Steven M., Zhang, Bo, Poetsch, Anna R., Mueller, Sabine, Ennis, Brian M., Prados, Michael, Diskin, Sharon J., Zheng, Siyuan, Guo, Yiran, Kannan, Shrivats, Waanders, Angela J., Margol, Ashley S., Kim, Meen Chul, Hanson, Derek, Van Kuren, Nicholas, Wong, Jessica, Kaufman, Rebecca S., Coleman, Noel, Blackden, Christopher, Cole, Kristina A., Mason, Jennifer L., Madsen, Peter J., Koschmann, Carl J., Stewart, Douglas R., Wafula, Eric, Brown, Miguel A., Resnick, Adam C., Greene, Casey S., Rokita, Jo Lynne, and Taroni, Jaclyn N.

Published
2023
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2. Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design

Author

Rokita, Jo Lynne, Rathi, Komal S, Cardenas, Maria F, Upton, Kristen A, Jayaseelan, Joy, Cross, Katherine L, Pfeil, Jacob, Egolf, Laura E, Way, Gregory P, Farrel, Alvin, Kendsersky, Nathan M, Patel, Khushbu, Gaonkar, Krutika S, Modi, Apexa, Berko, Esther R, Lopez, Gonzalo, Vaksman, Zalman, Mayoh, Chelsea, Nance, Jonas, McCoy, Kristyn, Haber, Michelle, Evans, Kathryn, McCalmont, Hannah, Bendak, Katerina, Böhm, Julia W, Marshall, Glenn M, Tyrrell, Vanessa, Kalletla, Karthik, Braun, Frank K, Qi, Lin, Du, Yunchen, Zhang, Huiyuan, Lindsay, Holly B, Zhao, Sibo, Shu, Jack, Baxter, Patricia, Morton, Christopher, Kurmashev, Dias, Zheng, Siyuan, Chen, Yidong, Bowen, Jay, Bryan, Anthony C, Leraas, Kristen M, Coppens, Sara E, Doddapaneni, HarshaVardhan, Momin, Zeineen, Zhang, Wendong, Sacks, Gregory I, Hart, Lori S, Krytska, Kateryna, Mosse, Yael P, Gatto, Gregory J, Sanchez, Yolanda, Greene, Casey S, Diskin, Sharon J, Vaske, Olena Morozova, Haussler, David, Gastier-Foster, Julie M, Kolb, E Anders, Gorlick, Richard, Li, Xiao-Nan, Reynolds, C Patrick, Kurmasheva, Raushan T, Houghton, Peter J, Smith, Malcolm A, Lock, Richard B, Raman, Pichai, Wheeler, David A, and Maris, John M

Subjects
Biological Sciences, Pediatric, Rare Diseases, Genetics, Human Genome, Pediatric Cancer, Pediatric Research Initiative, Clinical Research, Orphan Drug, Biotechnology, Cancer, Development of treatments and therapeutic interventions, 5.1 Pharmaceuticals, 2.1 Biological and endogenous factors, Aetiology, Good Health and Well Being, Animals, Cell Line, Tumor, Central Nervous System Neoplasms, Child, Clinical Trials as Topic, Disease Models, Animal, Genomics, Humans, Mice, Mutation, Neuroblastoma, Neurofibromin 1, Osteosarcoma, Precursor Cell Lymphoblastic Leukemia-Lymphoma, Recurrence, Rhabdomyosarcoma, Sarcoma, Ewing, Tumor Suppressor Protein p53, Exome Sequencing, Wilms Tumor, Xenograft Model Antitumor Assays, classifier, copy number profiling, patient-derived xenograft, pediatric cancer, preclinical testing, relapse, transcriptome sequencing, whole-exome sequencing, Pediatric cancer, whole exome sequencing, Biochemistry and Cell Biology, Medical Physiology, Biological sciences
Abstract

Accelerating cures for children with cancer remains an immediate challenge as a result of extensive oncogenic heterogeneity between and within histologies, distinct molecular mechanisms evolving between diagnosis and relapsed disease, and limited therapeutic options. To systematically prioritize and rationally test novel agents in preclinical murine models, researchers within the Pediatric Preclinical Testing Consortium are continuously developing patient-derived xenografts (PDXs)-many of which are refractory to current standard-of-care treatments-from high-risk childhood cancers. Here, we genomically characterize 261 PDX models from 37 unique pediatric cancers; demonstrate faithful recapitulation of histologies and subtypes; and refine our understanding of relapsed disease. In addition, we use expression signatures to classify tumors for TP53 and NF1 pathway inactivation. We anticipate that these data will serve as a resource for pediatric oncology drug development and will guide rational clinical trial design for children with cancer.

Published
2019

3. A GPC2 antibody-drug conjugate is efficacious against neuroblastoma and small-cell lung cancer via binding a conformational epitope

Author

Raman, Swetha, Buongervino, Samantha N., Lane, Maria V., Zhelev, Doncho V., Zhu, Zhongyu, Cui, Hong, Martinez, Benjamin, Martinez, Daniel, Wang, Yanping, Upton, Kristen, Patel, Khushbu, Rathi, Komal S., Navia, Carmen T., Harmon, Daniel B., Li, Yimei, Pawel, Bruce, Dimitrov, Dimiter S., Maris, John M., Julien, Jean-Philippe, and Bosse, Kristopher R.

Published
2021
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4. NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data

Author

Overbey, Eliah G., Saravia-Butler, Amanda M., Zhang, Zhe, Rathi, Komal S., Fogle, Homer, da Silveira, Willian A., Barker, Richard J., Bass, Joseph J., Beheshti, Afshin, Berrios, Daniel C., Blaber, Elizabeth A., Cekanaviciute, Egle, Costa, Helio A., Davin, Laurence B., Fisch, Kathleen M., Gebre, Samrawit G., Geniza, Matthew, Gilbert, Rachel, Gilroy, Simon, Hardiman, Gary, Herranz, Raúl, Kidane, Yared H., Kruse, Colin P.S., Lee, Michael D., Liefeld, Ted, Lewis, Norman G., McDonald, J. Tyson, Meller, Robert, Mishra, Tejaswini, Perera, Imara Y., Ray, Shayoni, Reinsch, Sigrid S., Rosenthal, Sara Brin, Strong, Michael, Szewczyk, Nathaniel J., Tahimic, Candice G.T., Taylor, Deanne M., Vandenbrink, Joshua P., Villacampa, Alicia, Weging, Silvio, Wolverton, Chris, Wyatt, Sarah E., Zea, Luis, Costes, Sylvain V., and Galazka, Jonathan M.

Published
2021
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5. Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality

Author

Dang, Mai T., Gonzalez, Michael V., Gaonkar, Krutika S., Rathi, Komal S., Young, Patricia, Arif, Sherjeel, Zhai, Li, Alam, Zahidul, Devalaraja, Samir, To, Tsun Ki Jerrick, Folkert, Ian W., Raman, Pichai, Rokita, Jo Lynne, Martinez, Daniel, Taroni, Jaclyn N., Shapiro, Joshua A., Greene, Casey S., Savonen, Candace, Mafra, Fernanda, Hakonarson, Hakon, Curran, Tom, and Haldar, Malay

Published
2021
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6. Comprehensive Multi-omics Analysis Reveals Mitochondrial Stress as a Central Biological Hub for Spaceflight Impact

Author

da Silveira, Willian A., Fazelinia, Hossein, Rosenthal, Sara Brin, Laiakis, Evagelia C., Kim, Man S., Meydan, Cem, Kidane, Yared, Rathi, Komal S., Smith, Scott M., Stear, Benjamin, Ying, Yue, Zhang, Yuanchao, Foox, Jonathan, Zanello, Susana, Crucian, Brian, Wang, Dong, Nugent, Adrienne, Costa, Helio A., Zwart, Sara R., Schrepfer, Sonja, Elworth, R.A. Leo, Sapoval, Nicolae, Treangen, Todd, MacKay, Matthew, Gokhale, Nandan S., Horner, Stacy M., Singh, Larry N., Wallace, Douglas C., Willey, Jeffrey S., Schisler, Jonathan C., Meller, Robert, McDonald, J. Tyson, Fisch, Kathleen M., Hardiman, Gary, Taylor, Deanne, Mason, Christopher E., Costes, Sylvain V., and Beheshti, Afshin

Published
2020
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9. Hedgehog actively maintains adult lung quiescence and regulates repair and regeneration.

Author

Peng, Tien, Frank, David B, Kadzik, Rachel S, Morley, Michael P, Rathi, Komal S, Wang, Tao, Zhou, Su, Cheng, Lan, Lu, Min Min, and Morrisey, Edward E

Subjects
Lung, Epithelial Cells, Mesoderm, Animals, Mice, Regeneration, Wound Healing, Paracrine Communication, Cell Proliferation, Down-Regulation, Homeostasis, Male, Hedgehog Proteins, Lung Injury, Feedback, Physiological, Feedback, Physiological, General Science & Technology
Abstract

Postnatal tissue quiescence is thought to be a default state in the absence of a proliferative stimulus such as injury. Although previous studies have demonstrated that certain embryonic developmental programs are reactivated aberrantly in adult organs to drive repair and regeneration, it is not well understood how quiescence is maintained in organs such as the lung, which displays a remarkably low level of cellular turnover. Here we demonstrate that quiescence in the adult lung is an actively maintained state and is regulated by hedgehog signalling. Epithelial-specific deletion of sonic hedgehog (Shh) during postnatal homeostasis in the murine lung results in a proliferative expansion of the adjacent lung mesenchyme. Hedgehog signalling is initially downregulated during the acute phase of epithelial injury as the mesenchyme proliferates in response, but returns to baseline during injury resolution as quiescence is restored. Activation of hedgehog during acute epithelial injury attenuates the proliferative expansion of the lung mesenchyme, whereas inactivation of hedgehog signalling prevents the restoration of quiescence during injury resolution. Finally, we show that hedgehog also regulates epithelial quiescence and regeneration in response to injury via a mesenchymal feedback mechanism. These results demonstrate that epithelial-mesenchymal interactions coordinated by hedgehog actively maintain postnatal tissue homeostasis, and deregulation of hedgehog during injury leads to aberrant repair and regeneration in the lung.

Published
2015

10. A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma

Author

Hamilton, Amber K., Radaoui, Alexander B., Tsang, Matthew, Martinez, Daniel, Conkrite, Karina L., Patel, Khushbu, Sidoli, Simone, Delaidelli, Alberto, Modi, Apexa, Rokita, Jo Lynne, Lane, Maria V., Hartnett, Nicholas, Lopez, Raphael D., Zhang, Bo, Zhong, Chuwei, Ennis, Brian, Miller, Daniel P., Brown, Miguel A., Rathi, Komal S., Raman, Pichai, Pogoriler, Jennifer, Bhatti, Tricia, Pawel, Bruce, Glisovic-Aplenc, Tina, Teicher, Beverly, Erickson, Stephen W., Earley, Eric J., Bosse, Kristopher R., Sorensen, Poul H., Krytska, Kateryna, Mosse, Yael P., Havenith, Karin E., Zammarchi, Francesca, van Berkel, Patrick H., Smith, Malcolm A., Garcia, Benjamin A., Maris, John M., and Diskin, Sharon J.

Published
2024
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12. Long noncoding RNAs are spatially correlated with transcription factors and regulate lung development

Author

Herriges, Michael J, Swarr, Daniel T, Morley, Michael P, Rathi, Komal S, Peng, Tien, Stewart, Kathleen M, and Morrisey, Edward E

Subjects
Human Genome, Lung, Biotechnology, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Animals, Cell Differentiation, Cell Line, Endoderm, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Knockdown Techniques, Genome, HEK293 Cells, Humans, Mice, Nuclear Proteins, RNA, Long Noncoding, Thyroid Nuclear Factor 1, Transcription Factors, Wnt Signaling Pathway, Nkx2.1, Wnt signaling, development, lncRNA, lung, retinoic acid, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology
Abstract

Long noncoding RNAs (lncRNAs) are thought to play important roles in regulating gene transcription, but few have well-defined expression patterns or known biological functions during mammalian development. Using a conservative pipeline to identify lncRNAs that have important biological functions, we identified 363 lncRNAs in the lung and foregut endoderm. Importantly, we show that these lncRNAs are spatially correlated with transcription factors across the genome. In-depth expression analyses of lncRNAs with genomic loci adjacent to the critical transcription factors Nkx2.1, Gata6, Foxa2 (forkhead box a2), and Foxf1 mimic the expression patterns of their protein-coding neighbor. Loss-of-function analysis demonstrates that two lncRNAs, LL18/NANCI (Nkx2.1-associated noncoding intergenic RNA) and LL34, play distinct roles in endoderm development by controlling expression of critical developmental transcription factors and pathways, including retinoic acid signaling. In particular, we show that LL18/NANCI acts upstream of Nkx2.1 and downstream from Wnt signaling to regulate lung endoderm gene expression. These studies reveal that lncRNAs play an important role in foregut and lung endoderm development by regulating multiple aspects of gene transcription, often through regulation of transcription factor expression.

Published
2014

13. A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma

Author

Weiner, Amber K., primary, Radaoui, Alexander B., additional, Tsang, Matthew, additional, Martinez, Daniel, additional, Sidoli, Simone, additional, Conkrite, Karina L., additional, Delaidelli, Alberto, additional, Modi, Apexa, additional, Rokita, Jo Lynne, additional, Patel, Khushbu, additional, Lane, Maria V., additional, Zhang, Bo, additional, Zhong, Chuwei, additional, Ennis, Brian, additional, Miller, Daniel P., additional, Brown, Miguel A., additional, Rathi, Komal S., additional, Raman, Pichai, additional, Pogoriler, Jennifer, additional, Bhatti, Tricia, additional, Pawel, Bruce, additional, Glisovic-Aplenc, Tina, additional, Teicher, Beverly, additional, Erickson, Stephen W., additional, Earley, Eric Jay, additional, Bosse, Kristopher R., additional, Sorensen, Poul H., additional, Krytska, Kateryna, additional, Mosse, Yael P., additional, Havenith, Karin E., additional, Zammarchi, Francesca, additional, van Berkel, Patrick H., additional, Smith, Malcolm A., additional, Garcia, Benjamin A., additional, Maris, John M., additional, and Diskin, Sharon J., additional

Published
2023
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14. Identification of GPC2 as an Oncoprotein and Candidate Immunotherapeutic Target in High-Risk Neuroblastoma

Author

Bosse, Kristopher R., Raman, Pichai, Zhu, Zhongyu, Lane, Maria, Martinez, Daniel, Heitzeneder, Sabine, Rathi, Komal S., Kendsersky, Nathan M., Randall, Michael, Donovan, Laura, Morrissy, Sorana, Sussman, Robyn T., Zhelev, Doncho V., Feng, Yang, Wang, Yanping, Hwang, Jennifer, Lopez, Gonzalo, Harenza, Jo Lynne, Wei, Jun S., Pawel, Bruce, Bhatti, Tricia, Santi, Mariarita, Ganguly, Arupa, Khan, Javed, Marra, Marco A., Taylor, Michael D., Dimitrov, Dimiter S., Mackall, Crystal L., and Maris, John M.

Published
2017
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16. Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality

Author

Dang, Mai T., primary, Gonzalez, Michael V., additional, Gaonkar, Krutika S., additional, Rathi, Komal S., additional, Young, Patricia, additional, Arif, Sherjeel, additional, Zhai, Li, additional, Alam, Zahidul, additional, Devalaraja, Samir, additional, Jerrick To, Tsun Ki, additional, Folkert, Ian W., additional, Raman, Pichai, additional, Rokita, Jo Lynne, additional, Martinez, Daniel, additional, Taroni, Jaclyn N., additional, Shapiro, Joshua A., additional, Greene, Casey S., additional, Savonen, Candace, additional, Mafra, Fernanda, additional, Hakonarson, Hakon, additional, Curran, Tom, additional, and Haldar, Malay, additional

Published
2023
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17. Figures S1-7 from Evaluation of the DLL3-targeting Antibody–Drug Conjugate Rovalpituzumab Tesirine in Preclinical Models of Neuroblastoma

Author

Krytska, Kateryna, primary, Casey, Colleen E., primary, Pogoriler, Jennifer, primary, Martinez, Daniel, primary, Rathi, Komal S., primary, Farrel, Alvin, primary, Berko, Esther R., primary, Tsang, Matthew, primary, Sano, Renata R., primary, Kendsersky, Nathan, primary, Erickson, Stephen W., primary, Teicher, Beverly A., primary, Isse, Kumiko, primary, Saunders, Laura, primary, Smith, Malcolm A., primary, Maris, John M., primary, and Mossé, Yael P., primary

Published
2023
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18. Supplementary Data from MYC Levels Regulate Metastatic Heterogeneity in Pancreatic Adenocarcinoma

Author

Maddipati, Ravikanth, primary, Norgard, Robert J., primary, Baslan, Timour, primary, Rathi, Komal S., primary, Zhang, Amy, primary, Saeid, Asal, primary, Higashihara, Taku, primary, Wu, Feng, primary, Kumar, Angad, primary, Annamalai, Valli, primary, Bhattacharya, Saurav, primary, Raman, Pichai, primary, Adkisson, Christian A., primary, Pitarresi, Jason R., primary, Wengyn, Maximilian D., primary, Yamazoe, Taiji, primary, Li, Jinyang, primary, Balli, David, primary, LaRiviere, Michael J., primary, Ngo, Tuong-Vi C., primary, Folkert, Ian W., primary, Millstein, Ian D., primary, Bermeo, Jonathan, primary, Carpenter, Erica L., primary, McAuliffe, John C., primary, Oktay, Maja H., primary, Brekken, Rolf A., primary, Lowe, Scott W., primary, Iacobuzio-Donahue, Christine A., primary, Notta, Faiyaz, primary, and Stanger, Ben Z., primary

Published
2023
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19. Supplementary Figure from MYC Levels Regulate Metastatic Heterogeneity in Pancreatic Adenocarcinoma

Author

Maddipati, Ravikanth, primary, Norgard, Robert J., primary, Baslan, Timour, primary, Rathi, Komal S., primary, Zhang, Amy, primary, Saeid, Asal, primary, Higashihara, Taku, primary, Wu, Feng, primary, Kumar, Angad, primary, Annamalai, Valli, primary, Bhattacharya, Saurav, primary, Raman, Pichai, primary, Adkisson, Christian A., primary, Pitarresi, Jason R., primary, Wengyn, Maximilian D., primary, Yamazoe, Taiji, primary, Li, Jinyang, primary, Balli, David, primary, LaRiviere, Michael J., primary, Ngo, Tuong-Vi C., primary, Folkert, Ian W., primary, Millstein, Ian D., primary, Bermeo, Jonathan, primary, Carpenter, Erica L., primary, McAuliffe, John C., primary, Oktay, Maja H., primary, Brekken, Rolf A., primary, Lowe, Scott W., primary, Iacobuzio-Donahue, Christine A., primary, Notta, Faiyaz, primary, and Stanger, Ben Z., primary

Published
2023
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20. Data from MYC Levels Regulate Metastatic Heterogeneity in Pancreatic Adenocarcinoma

Author

Maddipati, Ravikanth, primary, Norgard, Robert J., primary, Baslan, Timour, primary, Rathi, Komal S., primary, Zhang, Amy, primary, Saeid, Asal, primary, Higashihara, Taku, primary, Wu, Feng, primary, Kumar, Angad, primary, Annamalai, Valli, primary, Bhattacharya, Saurav, primary, Raman, Pichai, primary, Adkisson, Christian A., primary, Pitarresi, Jason R., primary, Wengyn, Maximilian D., primary, Yamazoe, Taiji, primary, Li, Jinyang, primary, Balli, David, primary, LaRiviere, Michael J., primary, Ngo, Tuong-Vi C., primary, Folkert, Ian W., primary, Millstein, Ian D., primary, Bermeo, Jonathan, primary, Carpenter, Erica L., primary, McAuliffe, John C., primary, Oktay, Maja H., primary, Brekken, Rolf A., primary, Lowe, Scott W., primary, Iacobuzio-Donahue, Christine A., primary, Notta, Faiyaz, primary, and Stanger, Ben Z., primary

Published
2023
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21. Data from Evaluation of the DLL3-targeting Antibody–Drug Conjugate Rovalpituzumab Tesirine in Preclinical Models of Neuroblastoma

Author

Krytska, Kateryna, primary, Casey, Colleen E., primary, Pogoriler, Jennifer, primary, Martinez, Daniel, primary, Rathi, Komal S., primary, Farrel, Alvin, primary, Berko, Esther R., primary, Tsang, Matthew, primary, Sano, Renata R., primary, Kendsersky, Nathan, primary, Erickson, Stephen W., primary, Teicher, Beverly A., primary, Isse, Kumiko, primary, Saunders, Laura, primary, Smith, Malcolm A., primary, Maris, John M., primary, and Mossé, Yael P., primary

Published
2023
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22. Data from Targeting PARP-1 with Alpha-Particles Is Potently Cytotoxic to Human Neuroblastoma in Preclinical Models

Author

Makvandi, Mehran, primary, Lee, Hwan, primary, Puentes, Laura N., primary, Reilly, Sean W., primary, Rathi, Komal S., primary, Weng, Chi-Chang, primary, Chan, Ho Sze, primary, Hou, Catherine, primary, Raman, Pichai, primary, Martinez, Daniel, primary, Xu, Kuiying, primary, Carlin, Sean D., primary, Greenberg, Roger A., primary, Pawel, Bruce R., primary, Mach, Robert H., primary, Maris, John M., primary, and Pryma, Daniel A., primary

Published
2023
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23. Supplementary Figures 1-10; Supplemental Tables 1-6; and Supplemental Materials and Methods from Targeting PARP-1 with Alpha-Particles Is Potently Cytotoxic to Human Neuroblastoma in Preclinical Models

Author

Makvandi, Mehran, primary, Lee, Hwan, primary, Puentes, Laura N., primary, Reilly, Sean W., primary, Rathi, Komal S., primary, Weng, Chi-Chang, primary, Chan, Ho Sze, primary, Hou, Catherine, primary, Raman, Pichai, primary, Martinez, Daniel, primary, Xu, Kuiying, primary, Carlin, Sean D., primary, Greenberg, Roger A., primary, Pawel, Bruce R., primary, Mach, Robert H., primary, Maris, John M., primary, and Pryma, Daniel A., primary

Published
2023
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24. OpenPBTA: The Open Pediatric Brain Tumor Atlas

Author

Shapiro, Joshua A, Gaonkar, Krutika S; https://orcid.org/0000-0003-0838-2405, Spielman, Stephanie J, Savonen, Candace L, Bethell, Chante J, Jin, Run, Rathi, Komal S, Zhu, Yuankun, Egolf, Laura E, Farrow, Bailey K, Miller, Daniel P, Yang, Yang; https://orcid.org/0000-0001-6645-2454, Koganti, Tejaswi, Noureen, Nighat, Koptyra, Mateusz P, Duong, Nhat, Santi, Mariarita, Kim, Jung, Robins, Shannon, Storm, Phillip B, Mack, Stephen C, Lilly, Jena V, Xie, Hongbo M, Jain, Payal; https://orcid.org/0000-0002-5914-9083, Raman, Pichai, Rood, Brian R, Lulla, Rishi R, Nazarian, Javad; https://orcid.org/0000-0002-1951-9828, Kraya, Adam A, Vaksman, Zalman, et al, Shapiro, Joshua A, Gaonkar, Krutika S; https://orcid.org/0000-0003-0838-2405, Spielman, Stephanie J, Savonen, Candace L, Bethell, Chante J, Jin, Run, Rathi, Komal S, Zhu, Yuankun, Egolf, Laura E, Farrow, Bailey K, Miller, Daniel P, Yang, Yang; https://orcid.org/0000-0001-6645-2454, Koganti, Tejaswi, Noureen, Nighat, Koptyra, Mateusz P, Duong, Nhat, Santi, Mariarita, Kim, Jung, Robins, Shannon, Storm, Phillip B, Mack, Stephen C, Lilly, Jena V, Xie, Hongbo M, Jain, Payal; https://orcid.org/0000-0002-5914-9083, Raman, Pichai, Rood, Brian R, Lulla, Rishi R, Nazarian, Javad; https://orcid.org/0000-0002-1951-9828, Kraya, Adam A, Vaksman, Zalman, and et al

Abstract

Pediatric brain and spinal cancers are collectively the leading disease-related cause of death in children; thus, we urgently need curative therapeutic strategies for these tumors. To accelerate such discoveries, the Children's Brain Tumor Network (CBTN) and Pacific Pediatric Neuro-Oncology Consortium (PNOC) created a systematic process for tumor biobanking, model generation, and sequencing with immediate access to harmonized data. We leverage these data to establish OpenPBTA, an open collaborative project with over 40 scalable analysis modules that genomically characterize 1,074 pediatric brain tumors. Transcriptomic classification reveals universal TP53 dysregulation in mismatch repair-deficient hypermutant high-grade gliomas and TP53 loss as a significant marker for poor overall survival in ependymomas and H3 K28-mutant diffuse midline gliomas. Already being actively applied to other pediatric cancers and PNOC molecular tumor board decision-making, OpenPBTA is an invaluable resource to the pediatric oncology community.

Published
2023

25. Clinical utility of custom-designed NGS panel testing in pediatric tumors

Author

Surrey, Lea F., MacFarland, Suzanne P., Chang, Fengqi, Cao, Kajia, Rathi, Komal S., Akgumus, Gozde T., Gallo, Daniel, Lin, Fumin, Gleason, Adam, Raman, Pichai, Aplenc, Richard, Bagatell, Rochelle, Minturn, Jane, Mosse, Yael, Santi, Mariarita, Tasian, Sarah K., Waanders, Angela J., Sarmady, Mahdi, Maris, John M., Hunger, Stephen P., and Li, Marilyn M.

Published
2019
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31. Supplementary Data from OBI-3424, a Novel AKR1C3-Activated Prodrug, Exhibits Potent Efficacy against Preclinical Models of T-ALL

Author

Evans, Kathryn, primary, Duan, JianXin, primary, Pritchard, Tara, primary, Jones, Connor D., primary, McDermott, Lisa, primary, Gu, Zhaohui, primary, Toscan, Cara E., primary, El-Zein, Narimanne, primary, Mayoh, Chelsea, primary, Erickson, Stephen W., primary, Guo, Yuelong, primary, Meng, Fanying, primary, Jung, Donald, primary, Rathi, Komal S., primary, Roberts, Kathryn G., primary, Mullighan, Charles G., primary, Shia, Chi-Sheng, primary, Pearce, Tillman, primary, Teicher, Beverly A., primary, Smith, Malcolm A., primary, and Lock, Richard B., primary

Published
2023
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32. Supplementary Data from GAS7 Deficiency Promotes Metastasis in MYCN-Driven Neuroblastoma

Author

Dong, Zhiwei, primary, Yeo, Kok Siong, primary, Lopez, Gonzalo, primary, Zhang, Cheng, primary, Dankert Eggum, Erin N., primary, Rokita, Jo Lynne, primary, Ung, Choong Yong, primary, Levee, Taylor M., primary, Her, Zuag Paj, primary, Howe, Cassie J., primary, Hou, Xiaonan, primary, van Ree, Janine H., primary, Li, Shuai, primary, He, Shuning, primary, Tao, Ting, primary, Fritchie, Karen, primary, Torres-Mora, Jorge, primary, Lehman, Julia S., primary, Meves, Alexander, primary, Razidlo, Gina L., primary, Rathi, Komal S., primary, Weroha, S. John, primary, Look, A. Thomas, primary, van Deursen, Jan M., primary, Li, Hu, primary, Westendorf, Jennifer J., primary, Maris, John M., primary, and Zhu, Shizhen, primary

Published
2023
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33. Evaluation of the DLL3-targeting Antibody–Drug Conjugate Rovalpituzumab Tesirine in Preclinical Models of Neuroblastoma

Author

Krytska, Kateryna, primary, Casey, Colleen E., additional, Pogoriler, Jennifer, additional, Martinez, Daniel, additional, Rathi, Komal S., additional, Farrel, Alvin, additional, Berko, Esther R., additional, Tsang, Matthew, additional, Sano, Renata R., additional, Kendsersky, Nathan, additional, Erickson, Stephen W., additional, Teicher, Beverly A., additional, Isse, Kumiko, additional, Saunders, Laura, additional, Smith, Malcolm A., additional, Maris, John M., additional, and Mossé, Yael P., additional

Published
2022
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35. MYC Levels Regulate Metastatic Heterogeneity in Pancreatic Adenocarcinoma

Author

Maddipati, Ravikanth, primary, Norgard, Robert J., additional, Baslan, Timour, additional, Rathi, Komal S., additional, Zhang, Amy, additional, Saeid, Asal, additional, Higashihara, Taku, additional, Wu, Feng, additional, Kumar, Angad, additional, Annamalai, Valli, additional, Bhattacharya, Saurav, additional, Raman, Pichai, additional, Adkisson, Christian A., additional, Pitarresi, Jason R., additional, Wengyn, Maximilian D., additional, Yamazoe, Taiji, additional, Li, Jinyang, additional, Balli, David, additional, LaRiviere, Michael J., additional, Ngo, Tuong-Vi C., additional, Folkert, Ian W., additional, Millstein, Ian D., additional, Bermeo, Jonathan, additional, Carpenter, Erica L., additional, McAuliffe, John C., additional, Oktay, Maja H., additional, Brekken, Rolf A., additional, Lowe, Scott W., additional, Iacobuzio-Donahue, Christine A., additional, Notta, Faiyaz, additional, and Stanger, Ben Z., additional

Published
2021
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36. Targeted gene expression profiling of inverted papilloma and squamous cell carcinoma

Author

Tong, Charles C. L., primary, Koptyra, Mateusz, additional, Raman, Pichai, additional, Rathi, Komal S., additional, Choudhari, Namrata, additional, Lin, Xiang, additional, Seckar, Tyler, additional, Wei, Zhi, additional, Kohanski, Michael A., additional, O'Malley, Bert W., additional, Cohen, Noam A., additional, Kennedy, David W., additional, Adappa, Nithin D., additional, Robertson, Erle S., additional, Baranov, Esther, additional, Kuan, Edward C., additional, Papagiannopoulos, Peter, additional, Jalaly, Jalal B., additional, Feldman, Michael D., additional, Storm, Phillip B., additional, Resnick, Adam C., additional, and Palmer, James N., additional

Published
2021
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37. NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data

Author

National Aeronautics and Space Administration (US), Biotechnology and Biological Sciences Research Council (UK), Centre for Musculoskeletal Ageing Research (UK), Agencia Estatal de Investigación (España), Nottingham Biomedical Research Centre (UK), Overbey, Eliah G. [0000-0002-2866-8294], Fogle, Homer [0000-0002-5579-5432], Beheshti, Afshin [0000-0003-4643-531X], Berrios, Daniel C. [0000-0003-4312-9552], Cekanaviciute, Egle [0000-0003-3306-1806], Davin, Laurence B. [0000-0002-3248-6485], Gebre, Samrawit [0000-0002-8963-4856], Geniza, Matthew [0000-0003-4828-7891], Gilroy, Simon [0000-0001-9597-6839], Hardiman, Gary [0000-0003-4558-0400], Herranz, Raúl [0000-0002-0246-9449], Kruse, Colin P. S. [0000-0001-7070-8889], Mishra, Tejaswini [0000-0001-9931-1260], Perera, Imara Y. [0000-0001-9421-1420], Ray, Shayoni [0000-0003-1911-7738], Reinsch, Sigrid [0000-0002-6484-7521], Rosenthal, Sara Brin [0000-0002-6548-9658], Strong, Michael [0000-0002-3247-6260], Szewczyk, Nathaniel [0000-0003-4425-9746], Tahimic, Candice G. T. [0000-0001-5862-2652], Taylor, Deanne M. [0000-0002-3302-4610], Villacampa, Alicia [0000-0002-7398-8545], Weging, Silvio [0000-0002-8484-4352], Wolverton, Chris [0000-0003-2248-474X], Wyatt, Sarah E. [0000-0001-7874-0509], Costes, Sylvain V. [0000-0002-8542-2389], Galazka, Jonathan M. [0000-0002-4153-0249], Overbey, Eliah G., Saravia-Butler, Amanda M., Zhang, Zhe, Rathi, Komal S., Fogle, Homer, da Silveira, William A., Barker, Richard, Bass, Joseph J., Beheshti, Afshin, Berrios, Daniel C., Blaber, Elizabeth A., Cekanaviciute, Egle, Costa, Helio A., Davin, Laurence B., Fisch, Kathleen M., Gebre, Samrawit, Geniza, Matthew, Gilbert, Rachel, Gilroy, Simon, Hardiman, Gary, Herranz, Raúl, Kidane, Yared H., Kruse, Colin P. S., Lee, Michael D., Liefeld, Ted, Lewis, Norman G., McDonald, J. Tyson, Meller, Robert, Mishra, Tejaswini, Perera, Imara Y., Ray, Shayoni, Reinsch, Sigrid, Rosenthal, Sara Brin, Strong, MichaelSzewczyk, Nathaniel, Tahimic, Candice G. T., Taylor, Deanne M., Vandenbrink, Joshua P., Villacampa, Alicia, Weging, Silvio, Wolverton, Chris, Wyatt, Sarah E., Zea, Luis, Costes, Sylvain V., Galazka, Jonathan M., National Aeronautics and Space Administration (US), Biotechnology and Biological Sciences Research Council (UK), Centre for Musculoskeletal Ageing Research (UK), Agencia Estatal de Investigación (España), Nottingham Biomedical Research Centre (UK), Overbey, Eliah G. [0000-0002-2866-8294], Fogle, Homer [0000-0002-5579-5432], Beheshti, Afshin [0000-0003-4643-531X], Berrios, Daniel C. [0000-0003-4312-9552], Cekanaviciute, Egle [0000-0003-3306-1806], Davin, Laurence B. [0000-0002-3248-6485], Gebre, Samrawit [0000-0002-8963-4856], Geniza, Matthew [0000-0003-4828-7891], Gilroy, Simon [0000-0001-9597-6839], Hardiman, Gary [0000-0003-4558-0400], Herranz, Raúl [0000-0002-0246-9449], Kruse, Colin P. S. [0000-0001-7070-8889], Mishra, Tejaswini [0000-0001-9931-1260], Perera, Imara Y. [0000-0001-9421-1420], Ray, Shayoni [0000-0003-1911-7738], Reinsch, Sigrid [0000-0002-6484-7521], Rosenthal, Sara Brin [0000-0002-6548-9658], Strong, Michael [0000-0002-3247-6260], Szewczyk, Nathaniel [0000-0003-4425-9746], Tahimic, Candice G. T. [0000-0001-5862-2652], Taylor, Deanne M. [0000-0002-3302-4610], Villacampa, Alicia [0000-0002-7398-8545], Weging, Silvio [0000-0002-8484-4352], Wolverton, Chris [0000-0003-2248-474X], Wyatt, Sarah E. [0000-0001-7874-0509], Costes, Sylvain V. [0000-0002-8542-2389], Galazka, Jonathan M. [0000-0002-4153-0249], Overbey, Eliah G., Saravia-Butler, Amanda M., Zhang, Zhe, Rathi, Komal S., Fogle, Homer, da Silveira, William A., Barker, Richard, Bass, Joseph J., Beheshti, Afshin, Berrios, Daniel C., Blaber, Elizabeth A., Cekanaviciute, Egle, Costa, Helio A., Davin, Laurence B., Fisch, Kathleen M., Gebre, Samrawit, Geniza, Matthew, Gilbert, Rachel, Gilroy, Simon, Hardiman, Gary, Herranz, Raúl, Kidane, Yared H., Kruse, Colin P. S., Lee, Michael D., Liefeld, Ted, Lewis, Norman G., McDonald, J. Tyson, Meller, Robert, Mishra, Tejaswini, Perera, Imara Y., Ray, Shayoni, Reinsch, Sigrid, Rosenthal, Sara Brin, Strong, MichaelSzewczyk, Nathaniel, Tahimic, Candice G. T., Taylor, Deanne M., Vandenbrink, Joshua P., Villacampa, Alicia, Weging, Silvio, Wolverton, Chris, Wyatt, Sarah E., Zea, Luis, Costes, Sylvain V., and Galazka, Jonathan M.

Abstract

With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility, and reusability of pipeline data; to provide a template for data processing of future spaceflight-relevant datasets; and to encourage cross-analysis of data from other databases with the data available in GeneLab.

Published
2021

38. Additional file 1 of annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

Author

Gaonkar, Krutika S., Marini, Federico, Rathi, Komal S., Jain, Payal, Zhu, Yuankun, Chimicles, Nicholas A., Brown, Miguel A., Naqvi, Ammar S., Zhang, Bo, Storm, Phillip B., Maris, John M., Raman, Pichai, Resnick, Adam C., Strauch, Konstantin, Taroni, Jaclyn N., and Rokita, Jo Lynne

Abstract

Additional file 1: Figure S1. Fusions found in more than 1 histology. Barplots represent the number of histologies in which each fusion was observed. Dotted line represents the cut off (> 4 counts) used to remove potential false positives and fusions containing pseudogenes. Figure S2. Distribution of spanningDelta for annoFuse prioritized fusions from TCGA and PBTA cohorts. The spanningFragCountFilter and mean are plotted for each filtering cutoff of 10, 20, 30, 40, 50, 100, 150, and 200 spanningDelta for TCGA (N = 160 samples) (A) and PBTA (N = 1028 samples) (B) fusions. Figure S3. Sensitivity of TCGA fusions retained by annoFuse. At a spanningDelta of 100, annoFuse achieved a sensitivity of 96.35% for fusions in the TCGA final call set. The x-axis represents the cutoff for spanningFragCountFilter used and y-axis represents the sensitivity of the fusions retained after fusion_filtering_QC. Figure S4. Distribution of kinase genes fused in 5' and 3' genes per histologies. For each broad histology, pie charts represent the percentage of fusions in which Gene1A (5’) or Gene1B (3’) retain their kinase domains.

Published
2020
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39. Epigenetic regulator BMI1 promotes alveolar rhabdomyosarcoma proliferation and constitutes a novel therapeutic target

Author

Shields, Cara E., primary, Potlapalli, Sindhu, additional, Cuya‐Smith, Selma M., additional, Chappell, Sarah K., additional, Chen, Dongdong, additional, Martinez, Daniel, additional, Pogoriler, Jennifer, additional, Rathi, Komal S., additional, Patel, Shiv A., additional, Oristian, Kristianne M., additional, Linardic, Corinne M., additional, Maris, John M., additional, Haynes, Karmella A., additional, and Schnepp, Robert W., additional

Published
2021
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40. GAS7 Deficiency Promotes Metastasis in MYCN-Driven Neuroblastoma

Author

Dong, Zhiwei, primary, Yeo, Kok Siong, additional, Lopez, Gonzalo, additional, Zhang, Cheng, additional, Dankert Eggum, Erin N., additional, Rokita, Jo Lynne, additional, Ung, Choong Yong, additional, Levee, Taylor M., additional, Her, Zuag Paj, additional, Howe, Cassie J., additional, Hou, Xiaonan, additional, van Ree, Janine H., additional, Li, Shuai, additional, He, Shuning, additional, Tao, Ting, additional, Fritchie, Karen, additional, Torres-Mora, Jorge, additional, Lehman, Julia S., additional, Meves, Alexander, additional, Razidlo, Gina L., additional, Rathi, Komal S., additional, Weroha, S. John, additional, Look, A. Thomas, additional, van Deursen, Jan M., additional, Li, Hu, additional, Westendorf, Jennifer J., additional, Maris, John M., additional, and Zhu, Shizhen, additional

Published
2021
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41. MYCcontrols metastatic heterogeneity in pancreatic cancer

Author

Maddipati, Ravikanth, primary, Norgard, Robert J., additional, Baslan, Timour, additional, Rathi, Komal S., additional, Zhang, Amy, additional, Raman, Pichai, additional, Pitarresi, Jason R., additional, Wengyn, Maximilian D., additional, Yamazoe, Taiji, additional, Li, Jinyang, additional, Balli, David, additional, LaRiviere, Michael J., additional, Folkert, Ian W., additional, Millstein, Ian D., additional, Bermeo, Jonathan, additional, Carpenter, Erica L., additional, Lowe, Scott, additional, Iacobuzio-Donahue, Christine, additional, Notta, Faiyaz, additional, and Stanger, Ben Z., additional

Published
2021
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42. Abstract PO-053: MYC Influences metastatic heterogeneity in pancreatic cancer

Author

Maddipati, Ravikanth, primary, Norgard, Robert J., additional, Baslan, Timour, additional, Rathi, Komal S., additional, Zhang, Amy, additional, Raman, Pichai, additional, Wengyn, Max D., additional, Yamazoe, Taiji, additional, Li, Jinyang, additional, Balli, David, additional, LaRiviere, Michael J., additional, Folkert, Ian W., additional, Millstein, Ian D., additional, Bermeo, Jonathan, additional, Carpenter, Erica L., additional, Lowe, Scott, additional, Iacobuzio-Donahue, Christine, additional, Notta, Faiyaz, additional, and Stanger, Ben Z., additional

Published
2020
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43. NASA GeneLab RNA-Seq Consensus Pipeline: Standardized Processing of Short-Read RNA-Seq Data

Author

Overbey, Eliah G., primary, Saravia-Butler, Amanda M., additional, Zhang, Zhe, additional, Rathi, Komal S., additional, Fogle, Homer, additional, da Silveira, Willian A., additional, Barker, Richard J., additional, Bass, Joseph J., additional, Beheshti, Afshin, additional, Berrios, Daniel C., additional, Blaber, Elizabeth A., additional, Cekanaviciute, Egle, additional, Costa, Helio A., additional, Davin, Laurence B., additional, Fisch, Kathleen M., additional, Gebre, Samrawit G., additional, Geniza, Matthew, additional, Gilbert, Rachel, additional, Gilroy, Simon, additional, Hardiman, Gary, additional, Herranz, Raúl, additional, Kidane, Yared H., additional, Kruse, Colin P.S., additional, Lee, Michael D., additional, Liefeld, Ted, additional, Lewis, Norman G., additional, McDonald, J. Tyson, additional, Meller, Robert, additional, Mishra, Tejaswini, additional, Perera, Imara Y., additional, Ray, Shayoni, additional, Reinsch, Sigrid S., additional, Rosenthal, Sara Brin, additional, Strong, Michael, additional, Szewczyk, Nathaniel J, additional, Tahimic, Candice G.T., additional, Taylor, Deanne M., additional, Vandenbrink, Joshua P., additional, Villacampa, Alicia, additional, Weging, Silvio, additional, Wolverton, Chris, additional, Wyatt, Sarah E., additional, Zea, Luis, additional, Costes, Sylvain V., additional, and Galazka, Jonathan M., additional

Published
2020
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45. Somatic structural variation targets neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in neuroblastoma

Author

Lopez, Gonzalo, primary, Conkrite, Karina L., additional, Doepner, Miriam, additional, Rathi, Komal S., additional, Modi, Apexa, additional, Vaksman, Zalman, additional, Farra, Lance M., additional, Hyson, Eric, additional, Noureddine, Moataz, additional, Wei, Jun S., additional, Smith, Malcolm A., additional, Asgharzadeh, Shahab, additional, Seeger, Robert C., additional, Khan, Javed, additional, Auvil, Jaime Guidry, additional, Gerhard, Daniela S., additional, Maris, John M., additional, and Diskin, Sharon J., additional

Published
2020
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46. Epigenetic regulator BMI1 promotes fusion-positive rhabdomyosarcoma proliferation and constitutes a novel therapeutic target

Author

Shields, Cara E., primary, Potlapalli, Sindhu, additional, Cuya-Smith, Selma M., additional, Chappell, Sarah K., additional, Chen, Dongdong, additional, Martinez, Daniel, additional, Pogoriler, Jennifer, additional, Rathi, Komal S., additional, Patel, Shiv A., additional, Maris, John M., additional, and Schnepp, Robert W., additional

Published
2020
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47. CAMKV Is a Candidate Immunotherapeutic Target in MYCN Amplified Neuroblastoma

Author

Sussman, Robyn T., primary, Rokita, Jo Lynne, additional, Huang, Kevin, additional, Raman, Pichai, additional, Rathi, Komal S., additional, Martinez, Daniel, additional, Bosse, Kristopher R., additional, Lane, Maria, additional, Hart, Lori S., additional, Bhatti, Tricia, additional, Pawel, Bruce, additional, and Maris, John M., additional

Published
2020
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48. Mitochondrial DNA Haplogroups and Susceptibility to Neuroblastoma

Author

Chang, Xiao, primary, Bakay, Marina, additional, Liu, Yichuan, additional, Glessner, Joseph, additional, Rathi, Komal S, additional, Hou, Cuiping, additional, Qu, Huiqi, additional, Vaksman, Zalman, additional, Nguyen, Kenny, additional, Sleiman, Patrick M A, additional, Diskin, Sharon J, additional, Maris, John M, additional, and Hakonarson, Hakon, additional

Published
2020
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49. Single-cell transcriptomic profile reveals macrophage heterogeneity in medulloblastoma and their treatment-dependent recruitment

Author

Dang, Mai T., primary, Gonzalez, Michael, additional, Gaonkar, Krutika S., additional, Rathi, Komal S., additional, Young, Patricia, additional, Arif, Sherjeel, additional, Zhai, Li, additional, Alam, Md Zahidul, additional, Devalaraja, Samir, additional, To, Tsun Ki, additional, Folkert, Ian W., additional, Ramen, Pichai, additional, Rokita, Jo Lynne, additional, Martinez, Daniel, additional, Taroni, Jaclyn N., additional, Shapiro, Joshua, additional, Greene, Casey S., additional, Savonen, Candace, additional, Hakonarson, Hakon, additional, Curran, Tom, additional, and Haldar, Malay, additional

Published
2020
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50. NASA GeneLab Platform Utilized for Biological Response to Space Radiation in Animal Models

Author

McDonald, J. Tyson, primary, Stainforth, Robert, additional, Miller, Jack, additional, Cahill, Thomas, additional, Silveira, Willian A. da, additional, Rathi, Komal S., additional, Hardiman, Gary, additional, Taylor, Deanne, additional, Costes, Sylvain V., additional, Chauhan, Vinita, additional, Meller, Robert, additional, and Beheshti, Afshin, additional

Published
2020
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