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4. Risk Factors for New Neurologic Diagnoses in Hospitalized Patients With COVID-19: A Case-Control Study in New York City.

Author

Thakur, Kiran, Chu, Victoria, Hughes, Christine, Kim, Carla, Fleck-Derderian, Shannon, Barrett, Catherine, Matthews, Elizabeth, Balbi, Alanna, Bilski, Amanda, Chomba, Mashina, Lieberman, Ori, Jacobson, Samuel, Agarwal, Sachin, Roh, David, Park, Soojin, Ssonko, Vivian, Silver, Wendy, Vargas, Wendy, Geneslaw, Andrew, Bell, Michelle, Waters, Brandon, Rao, Agam, Claassen, Jan, Boehme, Amelia, Willey, Joshua, Elkind, Mitchell, Sobieszczyk, Magdalena, Zucker, Jason, McCollum, Andrea, and Sejvar, James

Abstract

BACKGROUND AND OBJECTIVES: There have been numerous reports of neurologic manifestations identified in hospitalized patients infected with SARS-CoV-2, the virus that causes COVID-19. Here, we identify the spectrum of associated neurologic symptoms and diagnoses, define the time course of their development, and examine readmission rates and mortality risk posthospitalization in a multiethnic urban cohort. METHODS: We identify the occurrence of new neurologic diagnoses among patients with laboratory-confirmed SARS-CoV-2 infection in New York City. A retrospective cohort study was performed on 532 cases (hospitalized patients with new neurologic diagnoses within 6 weeks of positive SARS-CoV-2 laboratory results between March 1, 2020, and August 31, 2020). We compare demographic and clinical features of the 532 cases with 532 controls (hospitalized COVID-19 patients without neurologic diagnoses) in a case-control study with one-to-one matching and examine hospital-related data and outcomes of death and readmission up to 6 months after acute hospitalization in a secondary case-only analysis. RESULTS: Among the 532 cases, the most common new neurologic diagnoses included encephalopathy (478, 89.8%), stroke (66, 12.4%), and seizures (38, 7.1%). In the case-control study, cases were more likely than controls to be male (58.6% vs 52.8%, p = 0.05), had baseline neurologic comorbidities (36.3% vs 13.0%, p < 0.0001), and were to be treated in an intensive care unit (62.0% vs 9.6%, p < 0.0001). Of the 394 (74.1%) cases who survived acute hospitalization, more than half (220 of 394, 55.8%) were readmitted within 6 months, with a mortality rate of 23.2% during readmission. DISCUSSION: Hospitalized patients with SARS-CoV-2 and new neurologic diagnoses have significant morbidity and mortality postdischarge. Further research is needed to define the effect of neurologic diagnoses during acute hospitalization on longitudinal post-COVID-19-related symptoms including neurocognitive impairment.

Published
2022

7. SARS-CoV-2 infection of primary human lung epithelium for COVID-19 modeling and drug discovery

Author

Mulay, Apoorva, Konda, Bindu, Garcia, Gustavo, Yao, Changfu, Beil, Stephen, Villalba, Jaquelyn M, Koziol, Colin, Sen, Chandani, Purkayastha, Arunima, Kolls, Jay K, Pociask, Derek A, Pessina, Patrizia, de Aja, Julio Sainz, Garcia-de-Alba, Carolina, Kim, Carla F, Gomperts, Brigitte, Arumugaswami, Vaithilingaraja, and Stripp, Barry R

Subjects
Biological Sciences, Coronaviruses Therapeutics and Interventions, Lung, Emerging Infectious Diseases, Infectious Diseases, Coronaviruses, 2.1 Biological and endogenous factors, Infection, Respiratory, Good Health and Well Being, Adenosine Monophosphate, Adult, Aged, Alanine, Alveolar Epithelial Cells, COVID-19, Child, Preschool, Drug Discovery, Epithelial Cells, Epithelium, Female, Fibroblasts, Humans, Male, Middle Aged, Models, Biological, Primary Cell Culture, Respiratory Mucosa, SARS-CoV-2, Virus Replication, COVID-19 Drug Treatment, adult lung epithelium, alveolar type 2 cells, alveoli, drug discovery, interferon, primary in vitro model, remdesivir, Biochemistry and Cell Biology, Medical Physiology, Biological sciences
Abstract

Coronavirus disease 2019 (COVID-19) is the latest respiratory pandemic caused by severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). Although infection initiates in the proximal airways, severe and sometimes fatal symptoms of the disease are caused by infection of the alveolar type 2 (AT2) cells of the distal lung and associated inflammation. In this study, we develop primary human lung epithelial infection models to understand initial responses of proximal and distal lung epithelium to SARS-CoV-2 infection. Differentiated air-liquid interface (ALI) cultures of proximal airway epithelium and alveosphere cultures of distal lung AT2 cells are readily infected by SARS-CoV-2, leading to an epithelial cell-autonomous proinflammatory response with increased expression of interferon signaling genes. Studies to validate the efficacy of selected candidate COVID-19 drugs confirm that remdesivir strongly suppresses viral infection/replication. We provide a relevant platform for study of COVID-19 pathobiology and for rapid drug screening against SARS-CoV-2 and emergent respiratory pathogens.

Published
2021

8. Organoids Model Transcriptional Hallmarks of Oncogenic KRAS Activation in Lung Epithelial Progenitor Cells

Author

Dost, Antonella FM, Moye, Aaron L, Vedaie, Marall, Tran, Linh M, Fung, Eileen, Heinze, Dar, Villacorta-Martin, Carlos, Huang, Jessie, Hekman, Ryan, Kwan, Julian H, Blum, Benjamin C, Louie, Sharon M, Rowbotham, Samuel P, Sainz de Aja, Julio, Piper, Mary E, Bhetariya, Preetida J, Bronson, Roderick T, Emili, Andrew, Mostoslavsky, Gustavo, Fishbein, Gregory A, Wallace, William D, Krysan, Kostyantyn, Dubinett, Steven M, Yanagawa, Jane, Kotton, Darrell N, and Kim, Carla F

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Genetics, Stem Cell Research - Nonembryonic - Non-Human, Stem Cell Research - Induced Pluripotent Stem Cell - Human, Rare Diseases, Stem Cell Research - Induced Pluripotent Stem Cell, Lung Cancer, Cancer, Stem Cell Research, Stem Cell Research - Nonembryonic - Human, Lung, Biotechnology, 2.1 Biological and endogenous factors, Animals, Humans, Induced Pluripotent Stem Cells, Mice, Organoids, Proteomics, Proto-Oncogene Proteins p21(ras), KRAS, alveolar, developmental programs, early-stage lung cancer, iPSC, loss of differentiation, organoid, single-cell RNA sequencing, stage IA lung adenocarcinoma, tumor progression, Biological Sciences, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

Mutant KRAS is a common driver in epithelial cancers. Nevertheless, molecular changes occurring early after activation of oncogenic KRAS in epithelial cells remain poorly understood. We compared transcriptional changes at single-cell resolution after KRAS activation in four sample sets. In addition to patient samples and genetically engineered mouse models, we developed organoid systems from primary mouse and human induced pluripotent stem cell-derived lung epithelial cells to model early-stage lung adenocarcinoma. In all four settings, alveolar epithelial progenitor (AT2) cells expressing oncogenic KRAS had reduced expression of mature lineage identity genes. These findings demonstrate the utility of our in vitro organoid approaches for uncovering the early consequences of oncogenic KRAS expression. This resource provides an extensive collection of datasets and describes organoid tools to study the transcriptional and proteomic changes that distinguish normal epithelial progenitor cells from early-stage lung cancer, facilitating the search for targets for KRAS-driven tumors.

Published
2020

9. The Geometry of Ijo Temple: Bridging Cultural Heritage and Mathematical Learning through Ethnomathematics.

Author

Kim Carla, Olly Orva Peggy, Ishartono, Naufal, and Eko Putri, Rizky Oktaviana

Subjects
EMBEDDINGS (Mathematics), CULTURAL property, RESEARCH questions, TRAPEZOIDS, ACADEMIC discourse, ETHNOLOGY
Abstract

Ethnomathematics examines the relationship between mathematics and cultural practices, highlighting mathematical concepts embedded within diverse cultural contexts. Ijo Temple, located approximately 4 km southeast of Ratu Boko Temple and 18 km east of Yogyakarta, stands as a prominent cultural site in Indonesia. While prior studies have explored mathematical elements within cultural heritage, limited attention has been given to the geometric concepts inherent in Ijo Temple's architecture. This study bridges this gap by analyzing the temple's architectural geometry through an ethnographic lens, guided by four key research questions: "Where do I observe?", "How do I investigate?", "How do I identify significant findings?", and "How do I interpret these findings?". The investigation uncovers various geometric sub-concepts, validated in collaboration with geometry experts. These include (1) planar geometry, encompassing triangles, rectangles, squares, trapezoids, and circles; (2) spatial geometry, such as cubes, rectangular prisms, and cylinders; (3) geometric transformations, including translation, reflection, and dilation; and (4) congruence principles. Beyond contributing to the academic discourse on geometric applications within cultural heritage, this research underscores the potential of culturally contextualized learning to enhance students' mathematical understanding. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Clinical review of cerebral venous thrombosis in the context of COVID-19 vaccinations: Evaluation, management, and scientific questions

Author

Thakur, Kiran T., Tamborska, Arina, Wood, Greta K., McNeill, Emily, Roh, David, Akpan, Imo J., Miller, Eliza C., Bautista, Alyssa, Claassen, Jan, Kim, Carla Y., Guekht, Alla, Pardo, Carlos A., Williams, Olajide, García-Azorín, David, Prasad, Kameshwar, Schmutzhard, Erich, Michael, Benedict D., Chou, Sherry H.-Y., Winkler, Andrea S., Solomon, Tom, and Elkind, Mitchell S.

Published
2021
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13. The Epithelial Sodium Channel Is a Modifier of the Long-Term Nonprogressive Phenotype Associated with F508del CFTR Mutations

Author

Agrawal, Pankaj B, Wang, Ruobing, Li, Hongmei Lisa, Schmitz-Abe, Klaus, Simone-Roach, Chantelle, Chen, Jingxin, Shi, Jiahai, Louie, Tin, Sheng, Shaohu, Towne, Meghan C, Brainson, Christine F, Matthay, Michael A, Kim, Carla F, Bamshad, Michael, Emond, Mary J, Gerard, Norma P, Kleyman, Thomas R, and Gerard, Craig

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Human Genome, Orphan Drug, Cystic Fibrosis, Rare Diseases, Pediatric, Lung, 2.1 Biological and endogenous factors, Aetiology, Congenital, Amino Acid Sequence, Animals, Cystic Fibrosis Transmembrane Conductance Regulator, Epithelial Sodium Channels, Female, Humans, Male, Sequence Deletion, Xenopus, Xenopus laevis, cystic fibrosis, ENaC, epithelial sodium channel, genetic modifier, SCNN1D, Cardiorespiratory Medicine and Haematology, Respiratory System, Biochemistry and cell biology, Cardiovascular medicine and haematology
Abstract

Cystic fibrosis (CF) remains the most lethal genetic disease in the Caucasian population. However, there is great variability in clinical phenotypes and survival times, even among patients harboring the same genotype. We identified five patients with CF and a homozygous F508del mutation in the CFTR gene who were in their fifth or sixth decade of life and had shown minimal changes in lung function over a longitudinal period of more than 20 years. Because of the rarity of this long-term nonprogressive phenotype, we hypothesized these individuals may carry rare genetic variants in modifier genes that ameliorate disease severity. Individuals at the extremes of survival time and lung-function trajectory underwent whole-exome sequencing, and the sequencing data were filtered to include rare missense, stopgain, indel, and splicing variants present with a mean allele frequency of

Published
2017

15. Genomic and evolutionary classification of lung cancer in never smokers

Author

Zhang, Tongwu, Joubert, Philippe, Ansari-Pour, Naser, Zhao, Wei, Hoang, Phuc H., Lokanga, Rachel, Moye, Aaron L., Rosenbaum, Jennifer, Gonzalez-Perez, Abel, Martínez-Jiménez, Francisco, Castro, Andrea, Muscarella, Lucia Anna, Hofman, Paul, Consonni, Dario, Pesatori, Angela C., Kebede, Michael, Li, Mengying, Gould Rothberg, Bonnie E., Peneva, Iliana, Schabath, Matthew B., Poeta, Maria Luana, Costantini, Manuela, Hirsch, Daniela, Heselmeyer-Haddad, Kerstin, Hutchinson, Amy, Olanich, Mary, Lawrence, Scott M., Lenz, Petra, Duggan, Maire, Bhawsar, Praphulla M. S., Sang, Jian, Kim, Jung, Mendoza, Laura, Saini, Natalie, Klimczak, Leszek J., Islam, S. M. Ashiqul, Otlu, Burcak, Khandekar, Azhar, Cole, Nathan, Stewart, Douglas R., Choi, Jiyeon, Brown, Kevin M., Caporaso, Neil E., Wilson, Samuel H., Pommier, Yves, Lan, Qing, Rothman, Nathaniel, Almeida, Jonas S., Carter, Hannah, Ried, Thomas, Kim, Carla F., Lopez-Bigas, Nuria, Garcia-Closas, Montserrat, Shi, Jianxin, Bossé, Yohan, Zhu, Bin, Gordenin, Dmitry A., Alexandrov, Ludmil B., Chanock, Stephen J., Wedge, David C., and Landi, Maria Teresa

Published
2021
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17. Clinical Characteristics and Risk Factors for Cryptococcal Meningitis in Diverse Patient Populations in New York City.

Author

Sardar, Zomer, Kim, Carla Y, and Thakur, Kiran T

Subjects
*CHRONIC lymphocytic leukemia, *IMMUNOCOMPROMISED patients, *HIV, *SYSTEMIC lupus erythematosus, *HIV-positive persons
Abstract

Background Cryptococcal meningitis (CM) is responsible for 15%–20% of human immunodeficiency virus (HIV)–associated mortalities. CM prevalence has also increased in other immunocompromised populations of transplant recipients, patients with cancer, and individuals on immunomodulatory medication. Methods This retrospective review included 51 definitive patients with CM hospitalized at a tertiary academic medical center in New York City between 2010 and 2023. We assessed clinical features and outcomes of CM, with additional analysis of factors related to antiretroviral therapy (ART) adherence in HIV-infected cases and immunomodulatory medication history of HIV-negative cases. Results The cohort had a mean (standard deviation) age of 47.1 ± 15.1 years, and was predominantly male (37, 72.5%). Of 32 patients with HIV, 3 (9.4%) were newly diagnosed with HIV at the time of CM hospitalization, 5 (15.6%) had recurrent CM, and 2 (6.3%) had a CM relapse. The majority (30, 93.8%) of patients with HIV were ART nonadherent. Of 19 HIV-negative patients, 8 (42.1%) were solid-organ transplant recipients, 5 (26.3%) had autoimmune conditions of sarcoidosis or systemic lupus erythematosus, and 3 (15.8%) had chronic lymphocytic leukemia. Six (11.8%) patients died during hospitalization, 4 of whom had HIV. Conclusions The burden of CM in people with HIV and immunocompromised patients continues even in settings with accessible standard antifungal treatment though interventions of increased ART adherence for those with HIV and antifungal prophylaxis may improve morbidity and mortality. [ABSTRACT FROM AUTHOR]

Published
2024
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18. Sociodemographic and Clinical Factors Associated With Clinical Outcome in Neuroinfectious Diseases: A Multicenter Retrospective Cohort Study.

Author

Boubour, Alexandra, Kim, Carla Y., Torres, Sarah, Jia, Dan T., Hess, Evan, Liu, Sibei, Sun, Yifei, Fong, Kathryn, Epstein, Samantha, Yan, Helena, Luche, Nicole, Gao, Kerry, Glassberg, Brittany, Harmon, Michael, Hoang, Hai, Navis, Allison, Schorr, Emily, Gofshteyn, Jacqueline S., Yeshokumar, Anusha K., and Thakur, Kiran T.

Published
2024
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19. Human Airway and Alveolar Organoids from Bronchoalveolar Lavage Fluid

Author

Liu, Monica Yun, primary, Chen, Belinda, additional, Borji, Mehdi, additional, Garcia de Alba Rivas, Carolina, additional, Dost, Antonella F. M., additional, Moye, Aaron L., additional, Movval Abdulla, Nusrath, additional, Paschini, Margherita, additional, Rollins, Stuart D., additional, Wang, Ruobing, additional, Schnapp, Lynn M, additional, Khalil, Hassan A, additional, Wu, Catherine J., additional, Sharma, Nirmal S, additional, and Kim, Carla F, additional

Published
2024
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22. Airway injury induces alveolar epithelial and mesenchymal responses mediated by macrophages

Author

Wong, Irene G., primary, Stark, Jillian, additional, Ya, VanNashlee, additional, Moye, Aaron L., additional, Vazquez, Alan Baez, additional, Dang, Susanna M., additional, Shehaj, Andrea, additional, Rouhani, Maral J., additional, Bronson, Roderick, additional, Janes, Sam M., additional, Rowbotham, Samuel P., additional, Paschini, Margherita, additional, Franklin, Ruth A., additional, and Kim, Carla F, additional

Published
2024
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25. Human Airway and Alveolar Organoids from BAL Fluid

Author

Hubrecht Institute with UMC, Liu, Monica Yun, Chen, Belinda, Borji, Mehdi, de Alba Rivas, Carolina Garcia, Dost, Antonella F.M., Moye, Aaron L., Abdulla, Nusrath Movval, Paschini, Margherita, Rollins, Stuart D., Wang, Ruobing, Schnapp, Lynn M., Khalil, Hassan A., Wu, Catherine J., Sharma, Nirmal S., Kim, Carla F., Hubrecht Institute with UMC, Liu, Monica Yun, Chen, Belinda, Borji, Mehdi, de Alba Rivas, Carolina Garcia, Dost, Antonella F.M., Moye, Aaron L., Abdulla, Nusrath Movval, Paschini, Margherita, Rollins, Stuart D., Wang, Ruobing, Schnapp, Lynn M., Khalil, Hassan A., Wu, Catherine J., Sharma, Nirmal S., and Kim, Carla F.

Published
2024

26. Adult mouse intralobar airway stem cells

Author

Dabrowska, Catherine, primary, Li, Jingyun, additional, Mulay, Apoorva, additional, Carraro, Gianni, additional, Gupta, Manav, additional, Kim, Carla F., additional, Lee, Joo-Hyeon, additional, and Stripp, Barry R., additional

Published
2021
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28. Human Airway and Alveolar Organoids from BAL Fluid.

Author

Liu, Monica Yun, Chen, Belinda, Borji, Mehdi, Garcia de Alba Rivas, Carolina, Dost, Antonella F. M., Moye, Aaron L., Movval Abdulla, Nusrath, Paschini, Margherita, Rollins, Stuart D., Wang, Ruobing, Schnapp, Lynn M., Khalil, Hassan A., Wu, Catherine J., Sharma, Nirmal S., and Kim, Carla F.

Subjects
ORGANOIDS, BRONCHOALVEOLAR lavage
Abstract

The article focuses on establishing efficient methods for deriving airway and alveolar organoids from human bronchoalveolar lavage (BAL) samples. It is reported that these organoids recapitulate diverse cell types found in the lung epithelium, offering versatile models for studying lung diseases and personalized therapeutics.

Published
2024
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31. Clinical and Diagnostic Features of West Nile Virus Neuroinvasive Disease in New York City.

Author

Roberts, Jackson A., Kim, Carla Y., Dean, Amy, Kulas, Karen E., St. George, Kirsten, Hoang, Hai E., and Thakur, Kiran T.

Subjects
WEST Nile fever, FEVER, ACUTE flaccid paralysis, IMMUNOGLOBULIN M, WEST Nile virus, MAGNETIC resonance imaging, ACADEMIC medical centers
Abstract

West Nile virus (WNV) neuroinvasive disease (WNND) occurs in approximately 1 percent of WNV-infected patients and typically presents as encephalitis, meningitis, or acute flaccid paralysis (AFP). WNND remains a difficult inpatient diagnosis, creating significant challenges for prognostication and therapy selection. We characterized the clinical and diagnostic features of WNND cases at two major academic medical centers in New York City in routine clinical practice. We retrospectively reviewed the charts of thirty-six patients with WNND, including twenty-six encephalitis, four meningitis, and six AFP cases. The most common presenting symptoms were fever (86.1%) and gastrointestinal symptoms (38.9%) in addition to altered mental status (72.2%), lethargy (63.9%), gait disturbances (46.2%), and headache (44.4%). Fourteen (48.3%) patients displayed acute magnetic resonance imaging (MRI) findings, particularly T2 hyperintensities in the bilateral thalami, brainstem, and deep white matter. New York State Department of Health WNV CSF IgM testing was utilized for diagnosis in 58.3% of patients; however, just 38.1% had the result by discharge, compared to 85.6% of those who underwent serum IgM testing. The median length of stay was 13.5 days, 38.9% were intubated, and three patients (8.9%) died during acute hospitalization. Our findings underscore the morbidity, mortality, and diagnostic challenges of WNND, suggesting the potential utility of serum IgM testing in combination with confirmatory CSF testing to expedite diagnosis in the acute setting. [ABSTRACT FROM AUTHOR]

Published
2024
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34. 7.342 Cancer Biology: From Basic Research to the Clinic, Fall 2004

Author

Kim, Carla, Haigis, Kevin, Kim, Carla, and Haigis, Kevin

Abstract

This course is one of many Advanced Undergraduate Seminars offered by the Biology Department at MIT. These seminars are tailored for students with an interest in using primary research literature to discuss and learn about current biological research in a highly interactive setting. In 1971, President Nixon declared the "War on Cancer," but after three decades the war is still raging. How much progress have we made toward winning the war and what are we doing to improve the fight? Understanding the molecular and cellular events involved in tumor formation, progression, and metastasis is crucial to the development of innovative therapy for cancer patients. Insights into these processes have been gleaned through basic research using biochemical, molecular, and genetic analysis in yeast, C. elegans, mice, and cell culture models. We will explore the laboratory tools and techniques used to perform cancer research, major discoveries in cancer biology, and the medical implications of these breakthroughs. A focus of the class will be critical analysis of the primary literature to foster understanding of the strengths and limitations of various approaches to cancer research. Special attention will be made to the clinical implications of cancer research performed in model organisms and the prospects for ending the battle with this devastating disease.

Published
2023

37. CUT&RUN Supplementary Data from Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung

Author

Concepcion, Carla P., primary, Ma, Sai, primary, LaFave, Lindsay M., primary, Bhutkar, Arjun, primary, Liu, Manyuan, primary, DeAngelo, Lydia P., primary, Kim, Jonathan Y., primary, Del Priore, Isabella, primary, Schoenfeld, Adam J., primary, Miller, Manon, primary, Kartha, Vinay K., primary, Westcott, Peter M.K., primary, Sánchez-Rivera, Francisco J., primary, Meli, Kevin, primary, Gupta, Manav, primary, Bronson, Roderick T., primary, Riely, Gregory J., primary, Rekhtman, Natasha, primary, Rudin, Charles M., primary, Kim, Carla F., primary, Regev, Aviv, primary, Buenrostro, Jason D., primary, and Jacks, Tyler, primary

Published
2023
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38. Supplementary Table S1 from Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung

Author

Concepcion, Carla P., primary, Ma, Sai, primary, LaFave, Lindsay M., primary, Bhutkar, Arjun, primary, Liu, Manyuan, primary, DeAngelo, Lydia P., primary, Kim, Jonathan Y., primary, Del Priore, Isabella, primary, Schoenfeld, Adam J., primary, Miller, Manon, primary, Kartha, Vinay K., primary, Westcott, Peter M.K., primary, Sánchez-Rivera, Francisco J., primary, Meli, Kevin, primary, Gupta, Manav, primary, Bronson, Roderick T., primary, Riely, Gregory J., primary, Rekhtman, Natasha, primary, Rudin, Charles M., primary, Kim, Carla F., primary, Regev, Aviv, primary, Buenrostro, Jason D., primary, and Jacks, Tyler, primary

Published
2023
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39. Supplementary Figures S1-S7 from Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung

Author

Concepcion, Carla P., primary, Ma, Sai, primary, LaFave, Lindsay M., primary, Bhutkar, Arjun, primary, Liu, Manyuan, primary, DeAngelo, Lydia P., primary, Kim, Jonathan Y., primary, Del Priore, Isabella, primary, Schoenfeld, Adam J., primary, Miller, Manon, primary, Kartha, Vinay K., primary, Westcott, Peter M.K., primary, Sánchez-Rivera, Francisco J., primary, Meli, Kevin, primary, Gupta, Manav, primary, Bronson, Roderick T., primary, Riely, Gregory J., primary, Rekhtman, Natasha, primary, Rudin, Charles M., primary, Kim, Carla F., primary, Regev, Aviv, primary, Buenrostro, Jason D., primary, and Jacks, Tyler, primary

Published
2023
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40. RNA-seq (cell line) Supplementary Data from Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung

Author

Concepcion, Carla P., primary, Ma, Sai, primary, LaFave, Lindsay M., primary, Bhutkar, Arjun, primary, Liu, Manyuan, primary, DeAngelo, Lydia P., primary, Kim, Jonathan Y., primary, Del Priore, Isabella, primary, Schoenfeld, Adam J., primary, Miller, Manon, primary, Kartha, Vinay K., primary, Westcott, Peter M.K., primary, Sánchez-Rivera, Francisco J., primary, Meli, Kevin, primary, Gupta, Manav, primary, Bronson, Roderick T., primary, Riely, Gregory J., primary, Rekhtman, Natasha, primary, Rudin, Charles M., primary, Kim, Carla F., primary, Regev, Aviv, primary, Buenrostro, Jason D., primary, and Jacks, Tyler, primary

Published
2023
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41. RNA-seq (primary tumors) Supplementary Data from Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung

Author

Concepcion, Carla P., primary, Ma, Sai, primary, LaFave, Lindsay M., primary, Bhutkar, Arjun, primary, Liu, Manyuan, primary, DeAngelo, Lydia P., primary, Kim, Jonathan Y., primary, Del Priore, Isabella, primary, Schoenfeld, Adam J., primary, Miller, Manon, primary, Kartha, Vinay K., primary, Westcott, Peter M.K., primary, Sánchez-Rivera, Francisco J., primary, Meli, Kevin, primary, Gupta, Manav, primary, Bronson, Roderick T., primary, Riely, Gregory J., primary, Rekhtman, Natasha, primary, Rudin, Charles M., primary, Kim, Carla F., primary, Regev, Aviv, primary, Buenrostro, Jason D., primary, and Jacks, Tyler, primary

Published
2023
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42. Bulk ATAC-seq Supplementary Data from Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung

Author

Concepcion, Carla P., primary, Ma, Sai, primary, LaFave, Lindsay M., primary, Bhutkar, Arjun, primary, Liu, Manyuan, primary, DeAngelo, Lydia P., primary, Kim, Jonathan Y., primary, Del Priore, Isabella, primary, Schoenfeld, Adam J., primary, Miller, Manon, primary, Kartha, Vinay K., primary, Westcott, Peter M.K., primary, Sánchez-Rivera, Francisco J., primary, Meli, Kevin, primary, Gupta, Manav, primary, Bronson, Roderick T., primary, Riely, Gregory J., primary, Rekhtman, Natasha, primary, Rudin, Charles M., primary, Kim, Carla F., primary, Regev, Aviv, primary, Buenrostro, Jason D., primary, and Jacks, Tyler, primary

Published
2023
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43. Data from Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung

Author

Concepcion, Carla P., primary, Ma, Sai, primary, LaFave, Lindsay M., primary, Bhutkar, Arjun, primary, Liu, Manyuan, primary, DeAngelo, Lydia P., primary, Kim, Jonathan Y., primary, Del Priore, Isabella, primary, Schoenfeld, Adam J., primary, Miller, Manon, primary, Kartha, Vinay K., primary, Westcott, Peter M.K., primary, Sánchez-Rivera, Francisco J., primary, Meli, Kevin, primary, Gupta, Manav, primary, Bronson, Roderick T., primary, Riely, Gregory J., primary, Rekhtman, Natasha, primary, Rudin, Charles M., primary, Kim, Carla F., primary, Regev, Aviv, primary, Buenrostro, Jason D., primary, and Jacks, Tyler, primary

Published
2023
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44. Data from Oncogenic Deregulation of EZH2 as an Opportunity for Targeted Therapy in Lung Cancer

Author

Zhang, Haikuo, primary, Qi, Jun, primary, Reyes, Jaime M., primary, Li, Lewyn, primary, Rao, Prakash K., primary, Li, Fugen, primary, Lin, Charles Y., primary, Perry, Jennifer A., primary, Lawlor, Matthew A., primary, Federation, Alexander, primary, De Raedt, Thomas, primary, Li, Yvonne Y., primary, Liu, Yan, primary, Duarte, Melissa A., primary, Zhang, Yanxi, primary, Herter-Sprie, Grit S., primary, Kikuchi, Eiki, primary, Carretero, Julian, primary, Perou, Charles M., primary, Reibel, Jacob B., primary, Paulk, Joshiawa, primary, Bronson, Roderick T., primary, Watanabe, Hideo, primary, Brainson, Christine Fillmore, primary, Kim, Carla F., primary, Hammerman, Peter S., primary, Brown, Myles, primary, Cichowski, Karen, primary, Long, Henry, primary, Bradner, James E., primary, and Wong, Kwok-Kin, primary

Published
2023
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45. Supplementary Figures S1 - S5, Tables S1 - S2 from Oncogenic Deregulation of EZH2 as an Opportunity for Targeted Therapy in Lung Cancer

Author

Zhang, Haikuo, primary, Qi, Jun, primary, Reyes, Jaime M., primary, Li, Lewyn, primary, Rao, Prakash K., primary, Li, Fugen, primary, Lin, Charles Y., primary, Perry, Jennifer A., primary, Lawlor, Matthew A., primary, Federation, Alexander, primary, De Raedt, Thomas, primary, Li, Yvonne Y., primary, Liu, Yan, primary, Duarte, Melissa A., primary, Zhang, Yanxi, primary, Herter-Sprie, Grit S., primary, Kikuchi, Eiki, primary, Carretero, Julian, primary, Perou, Charles M., primary, Reibel, Jacob B., primary, Paulk, Joshiawa, primary, Bronson, Roderick T., primary, Watanabe, Hideo, primary, Brainson, Christine Fillmore, primary, Kim, Carla F., primary, Hammerman, Peter S., primary, Brown, Myles, primary, Cichowski, Karen, primary, Long, Henry, primary, Bradner, James E., primary, and Wong, Kwok-Kin, primary

Published
2023
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46. Supplementary Table 3 from Oncogenic Deregulation of EZH2 as an Opportunity for Targeted Therapy in Lung Cancer

Author

Zhang, Haikuo, primary, Qi, Jun, primary, Reyes, Jaime M., primary, Li, Lewyn, primary, Rao, Prakash K., primary, Li, Fugen, primary, Lin, Charles Y., primary, Perry, Jennifer A., primary, Lawlor, Matthew A., primary, Federation, Alexander, primary, De Raedt, Thomas, primary, Li, Yvonne Y., primary, Liu, Yan, primary, Duarte, Melissa A., primary, Zhang, Yanxi, primary, Herter-Sprie, Grit S., primary, Kikuchi, Eiki, primary, Carretero, Julian, primary, Perou, Charles M., primary, Reibel, Jacob B., primary, Paulk, Joshiawa, primary, Bronson, Roderick T., primary, Watanabe, Hideo, primary, Brainson, Christine Fillmore, primary, Kim, Carla F., primary, Hammerman, Peter S., primary, Brown, Myles, primary, Cichowski, Karen, primary, Long, Henry, primary, Bradner, James E., primary, and Wong, Kwok-Kin, primary

Published
2023
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47. Supplementary Methods from Oncogenic Deregulation of EZH2 as an Opportunity for Targeted Therapy in Lung Cancer

Author

Zhang, Haikuo, primary, Qi, Jun, primary, Reyes, Jaime M., primary, Li, Lewyn, primary, Rao, Prakash K., primary, Li, Fugen, primary, Lin, Charles Y., primary, Perry, Jennifer A., primary, Lawlor, Matthew A., primary, Federation, Alexander, primary, De Raedt, Thomas, primary, Li, Yvonne Y., primary, Liu, Yan, primary, Duarte, Melissa A., primary, Zhang, Yanxi, primary, Herter-Sprie, Grit S., primary, Kikuchi, Eiki, primary, Carretero, Julian, primary, Perou, Charles M., primary, Reibel, Jacob B., primary, Paulk, Joshiawa, primary, Bronson, Roderick T., primary, Watanabe, Hideo, primary, Brainson, Christine Fillmore, primary, Kim, Carla F., primary, Hammerman, Peter S., primary, Brown, Myles, primary, Cichowski, Karen, primary, Long, Henry, primary, Bradner, James E., primary, and Wong, Kwok-Kin, primary

Published
2023
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48. Supplementary Table 5 from BRG1 Loss Predisposes Lung Cancers to Replicative Stress and ATR Dependency

Author

Gupta, Manav, primary, Concepcion, Carla P., primary, Fahey, Caroline G., primary, Keshishian, Hasmik, primary, Bhutkar, Arjun, primary, Brainson, Christine F., primary, Sanchez-Rivera, Francisco J., primary, Pessina, Patrizia, primary, Kim, Jonathan Y., primary, Simoneau, Antoine, primary, Paschini, Margherita, primary, Beytagh, Mary C., primary, Stanclift, Caroline R., primary, Schenone, Monica, primary, Mani, D.R., primary, Li, Chendi, primary, Oh, Audris, primary, Li, Fei, primary, Hu, Hai, primary, Karatza, Angeliki, primary, Bronson, Roderick T., primary, Shaw, Alice T., primary, Hata, Aaron N., primary, Wong, Kwok-Kin, primary, Zou, Lee, primary, Carr, Steven A., primary, Jacks, Tyler, primary, and Kim, Carla F., primary

Published
2023
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49. Figure S4 from BRG1 Loss Predisposes Lung Cancers to Replicative Stress and ATR Dependency

Author

Gupta, Manav, primary, Concepcion, Carla P., primary, Fahey, Caroline G., primary, Keshishian, Hasmik, primary, Bhutkar, Arjun, primary, Brainson, Christine F., primary, Sanchez-Rivera, Francisco J., primary, Pessina, Patrizia, primary, Kim, Jonathan Y., primary, Simoneau, Antoine, primary, Paschini, Margherita, primary, Beytagh, Mary C., primary, Stanclift, Caroline R., primary, Schenone, Monica, primary, Mani, D.R., primary, Li, Chendi, primary, Oh, Audris, primary, Li, Fei, primary, Hu, Hai, primary, Karatza, Angeliki, primary, Bronson, Roderick T., primary, Shaw, Alice T., primary, Hata, Aaron N., primary, Wong, Kwok-Kin, primary, Zou, Lee, primary, Carr, Steven A., primary, Jacks, Tyler, primary, and Kim, Carla F., primary

Published
2023
Full Text
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50. Supplementary Table 3 from BRG1 Loss Predisposes Lung Cancers to Replicative Stress and ATR Dependency

Author

Gupta, Manav, primary, Concepcion, Carla P., primary, Fahey, Caroline G., primary, Keshishian, Hasmik, primary, Bhutkar, Arjun, primary, Brainson, Christine F., primary, Sanchez-Rivera, Francisco J., primary, Pessina, Patrizia, primary, Kim, Jonathan Y., primary, Simoneau, Antoine, primary, Paschini, Margherita, primary, Beytagh, Mary C., primary, Stanclift, Caroline R., primary, Schenone, Monica, primary, Mani, D.R., primary, Li, Chendi, primary, Oh, Audris, primary, Li, Fei, primary, Hu, Hai, primary, Karatza, Angeliki, primary, Bronson, Roderick T., primary, Shaw, Alice T., primary, Hata, Aaron N., primary, Wong, Kwok-Kin, primary, Zou, Lee, primary, Carr, Steven A., primary, Jacks, Tyler, primary, and Kim, Carla F., primary

Published
2023
Full Text
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