9 Works

Data from: Population-specific genetic modification of Huntington's disease in Venezuela

Michael J. Chao, Kyung-Hee Kim, Jun Wan Shin, Diane Lucente, Vanessa C. Wheeler, Hong Li, Jared C. Roach, Leroy Hood, Nancy S. Wexler, Laura B. Jardim, Peter Holmans, Lesley Jones, Michael Orth, Seung Kwak, James F. Gusella, Marcy E. MacDonald & Jong-Min Lee
Modifiers of Mendelian disorders can provide insights into disease mechanisms and guide therapeutic strategies. A recent genome-wide association (GWA) study discovered genetic modifiers of Huntington's disease (HD) onset in Europeans. Here, we performed whole genome sequencing and GWA analysis of a Venezuelan HD cluster whose families were crucial for the original mapping of the HD gene defect. The Venezuelan HD subjects develop motor symptoms earlier than their European counterparts, implying the potential for population-specific modifiers....

Colorectal cancer scRNA-seq 10xG-format data matrix

Christopher Lausted, Raymond Yeung, Xiaowei Yan, Neda Jabbari, Qiang Tian, Heidi Kenerson, Changting Meng, Dani Bergey, Venu Pillarisetty, Kevin Sullivan, Priyanka Baloni & Leroy Hood
Metastatic colorectal cancer (CRC) is a major cause of cancer-related death and incidence is rising in the younger population (<50 years). Current chemotherapies can achieve response rates above 50%, but immunotherapies have limited value for patients with microsatellite-stable (MSS) cancers. The present study investigates the impact of chemotherapy on the tumor immune microenvironment. We treat human liver metastases slices with 5-Fluorouracil (5FU) plus either irinotecan or oxaliplatin, then perform single-cell transcriptome analyses. Results from eight...

Colorectal cancer interleukin-10 blockade scRNA-seq

Christopher Lausted, Kevin Sulllivan, Xiuyun Jiang, Prajna Guha, Jason Carter, Cynthia Hsu, Kevin Labadie, Karen Kohli, Heidi Kenerson, Sara Daniel, Xiaowei Yan, Changting Meng, Stella Shin, Arezou Abbasi, David Seo, James Park, Nicholas Crispe, Taranjit Gujral, Raymond Yeung, Teresa Kim, Qiang Tian, Steven Katz & Venu Pillarisetty
Objective: PD-1 checkpoint inhibition and adoptive cellular therapy have limited success in patients with microsatellite stable colorectal cancer liver metastases (CRLM). We demonstrate that interleukin-10 (IL-10) blockade enhances endogenous T cell and chimeric antigen receptor T (CAR-T) cell anti-tumor function in CRLM slice cultures.Design: We created organotypic slice cultures from human CRLM (n = 38) and tested the anti-tumor effects of a neutralizing antibody against IL-10 (αIL-10). We evaluated slice cultures with single and multiplex...

The transcriptomic landscape of normal and ineffective erythropoiesis at single cell resolution

Christopher Lausted, Raymond Doty, Adam Munday, Zhantao Yang, Xiaowei Yan, Changting Meng, Qiang Tian & Janis Abkowitz
Ineffective erythropoiesis, the death of maturing erythroid cells, is a common cause of anemia. To better understand why this occurs, we studied the fates and adaptations of single erythroid marrow cells from individuals with Diamond Blackfan anemia (DBA), del(5q) myelodysplastic syndrome (del(5q) MDS), and normal controls, and defined an unhealthy (vs. healthy) differentiation trajectory, using velocity pseudotime and cell surface protein assessment. The pseudotime trajectories diverge immediately after the cells upregulate transferrin receptor (CD71), import...

RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine

E. C. Wood, Amy K. Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, Chunyu Ma, Veronica Flores, Meghamala Sinha, Yodsawalai Chodpathumwan, Arash Termehchy, Jared C. Roach, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki & Stephen A. Ramsey
Abstract Background Biomedical translational science is increasingly using computational reasoning on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome, DrugBank, and SMPDB in order to facilitate discovery of new therapeutic targets and modalities. The NCATS Biomedical Data Translator project is working to federate autonomous reasoning agents and knowledge providers within a distributed system for answering translational questions. Within that project and the broader field, there is a need for a framework that can...

Data from: Divergence in DNA photorepair efficiency among genotypes from contrasting UV radiation environments in nature

Brooks E. Miner, Paige M. Kulling, Karlyn D. Beer & Benjamin Kerr
Populations of organisms routinely face abiotic selection pressures, and a central goal of evolutionary biology is to understand the mechanistic underpinnings of adaptive phenotypes. Ultraviolet radiation (UVR) is one of earth’s most pervasive environmental stressors, potentially damaging DNA in any organism exposed to solar radiation. We explored mechanisms underlying differential survival following UVR exposure in genotypes of the water flea Daphnia melanica derived from natural ponds of differing in UVR intensity. The UVR tolerance of...

Additional file 1 of RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine

E. C. Wood, Amy K. Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, Chunyu Ma, Veronica Flores, Meghamala Sinha, Yodsawalai Chodpathumwan, Arash Termehchy, Jared C. Roach, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki & Stephen A. Ramsey
Additional file 1: Table S1. Ontologies from the OBO Foundry that are included in RTX-KG2

RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine

E. C. Wood, Amy K. Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, Chunyu Ma, Veronica Flores, Meghamala Sinha, Yodsawalai Chodpathumwan, Arash Termehchy, Jared C. Roach, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki & Stephen A. Ramsey
Abstract Background Biomedical translational science is increasingly using computational reasoning on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome, DrugBank, and SMPDB in order to facilitate discovery of new therapeutic targets and modalities. The NCATS Biomedical Data Translator project is working to federate autonomous reasoning agents and knowledge providers within a distributed system for answering translational questions. Within that project and the broader field, there is a need for a framework that can...

Additional file 1 of RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine

E. C. Wood, Amy K. Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, Chunyu Ma, Veronica Flores, Meghamala Sinha, Yodsawalai Chodpathumwan, Arash Termehchy, Jared C. Roach, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki & Stephen A. Ramsey
Additional file 1: Table S1. Ontologies from the OBO Foundry that are included in RTX-KG2

Registration Year

  • 2022
    6
  • 2020
    1
  • 2018
    1
  • 2015
    1

Resource Types

  • Dataset
    5
  • Collection
    2
  • Text
    2

Affiliations

  • Institute for Systems Biology
    9
  • University of Washington
    4
  • Oregon State University
    4
  • Radboud University Nijmegen
    4
  • King Mongkut's University of Technology North Bangkok
    4
  • Pennsylvania State University
    4
  • Massachusetts General Hospital
    1
  • Fred Hutchinson Cancer Research Center
    1
  • Columbia University
    1
  • Ruijin Hospital
    1