Core C - Functional Genomics and Computational Biology Core
核心 C - 功能基因组学和计算生物学核心
基本信息
- 批准号:10023666
- 负责人:
- 金额:$ 22.49万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2015
- 资助国家:美国
- 起止时间:2015-05-15 至 2025-07-31
- 项目状态:未结题
- 来源:
- 关键词:AffectAntiviral AgentsAutoimmune ProcessAutoimmunityBioinformaticsBiologicalBiologyCD4 Positive T LymphocytesCD8B1 geneCRISPR screenCRISPR/Cas technologyCellsChronicCluster AnalysisComputational BiologyComputer AnalysisConsultationsCoupledDataData AnalysesData FilesData SetDefectDisease modelEmerging TechnologiesEpigenetic ProcessFunctional disorderGene ExpressionGene Expression ProfilingGene TargetingGenerationsGenesGeneticGenetic ScreeningGenetic TranscriptionGenomicsGoalsHIVHepatitis B VirusHepatitis C virusImmunityImmunologicsIndividualInfectionInformaticsLibrariesLymphocytic choriomeningitis virusMalignant NeoplasmsModelingMorbidity - disease rateMouse StrainsMusNatureOutputPathway AnalysisPathway interactionsQuality ControlReporterResearch PersonnelRoleSamplingServicesSignal TransductionSystemT cell responseT-LymphocyteTechnologyTissue-Specific Gene ExpressionTumor ImmunityValidationVariantVertebral columnViralVirusanalytical toolantiviral immunitybasebioinformatics toolchronic infectioncomputational network modelingcomputational suitedata archivedata cleaningdata explorationdata hostingdata integrationdata miningdata qualitydata visualizationdesignexhaustionflexibilityfunctional genomicsgenome-widegenomic dataimmunoregulationimprovedin vivoin vivo evaluationinsightinterestknock-downmortalitymouse modelnovelprogrammed cell death protein 1programsreceptorsingle-cell RNA sequencingsmall hairpin RNAsynergismtranscription factortranscriptomicstumorweb portal
项目摘要
CORE SUMMARY
The overall goal of this PPG application is to compare and contrast the mechanisms by which the inhibitory
receptors PD1 and LAG3 operate on T cells in the context of tolerance and autoimmunity, cancer, and chronic
infection. One major approach to be used throughout the studies is the application of genome-wide
transcriptional profiling. The purpose of the Functional Genomics and Computational Biology Core (Core C) is
to provide essential and centralized sequencing-based genomics services for all three Projects in this Program.
In addition, this Core will operate provide the service of a retroviral (RV)-enforced expression and knockdown
platform that can directly test in vivo individual genes and pathways identified from computational analyses. Thus,
Core C will provide integrated bioinformatic and computational analytical platforms and data integration services
coupled to downstream RV-enforced expression and knockdown as well as in vivo CRISPR/Cas9-focused
genetic screening. The Aims are:
AIM 1: To provide initial data hosting, normalization, preprocessing, and analysis as well as perform
cross-Project data integration and computational network modeling for bulk and single-cell
transcriptomic and epigenetic datasets. Core C will (i) provide raw data QC, data cleaning, pre-processing,
and generation of files for downstream analyses as well as operate a web portal interface for user exploration of
the data; (ii) perform primary and secondary genomics data analyses; and (iii) perform network and integrated
analyses including. The Core also will support and/or develop new analytical tools as technologies become
available (as for scRNA-seq in the last cycle).
AIM 2: To enable in vivo CRISPR/Cas9 screening and provide an RV-enforced expression and
knowckdown platform for downstream in vivo interrogation of genes and pathways regulated by PD-1
and/or LAG3. Core C will aid in design of CRISPR screening libraries for in vivo CRISPR screening platforms
by the Projects as well as downstream data analysis. Core C will also provide an in vivo retroviral platform to
enforce expression or shRNA knock-down of high-priority GOIs.
By its nature, Core C is highly interactive with other components of this PPG. Samples from Projects 1, 2, and
3 will enter Core C, which will analyze samples with input from the Projects and integrate results among the
three Projects. Core C will interact heavily with Cores A, B, and D for administrative support and to identify gene
targets for novel mouse strains and immunostaining analysis.
核心摘要
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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E. John Wherry其他文献
Preferential Loss of Peripheral Non-Naïve CD4+ Lymphocytes in Pediatric Sepsis
- DOI:
10.1016/j.jaci.2020.12.010 - 发表时间:
2021-02-01 - 期刊:
- 影响因子:
- 作者:
Robert Lindell;E. John Wherry;Scott Weiss;Sarah Henrickson - 通讯作者:
Sarah Henrickson
Tu1897 - Human Norovirus-Specific T Cell Responses
- DOI:
10.1016/s0016-5085(17)33394-2 - 发表时间:
2017-04-01 - 期刊:
- 影响因子:
- 作者:
Vesselin Tomov;Olesya Palko;Chi W. Lau;Meenakshi Bewtra;E. John Wherry - 通讯作者:
E. John Wherry
Durable T cell immunity to COVID-19 vaccines in MS patients on B cell depletion therapy
针对接受 B 细胞耗竭疗法的多发性硬化症患者,对 COVID-19 疫苗具有持久的 T 细胞免疫力
- DOI:
10.1038/s41541-025-01151-8 - 发表时间:
2025-05-17 - 期刊:
- 影响因子:6.500
- 作者:
Julia Davis-Porada;Ceren Tozlu;Claudia Aiello;Sokratis A. Apostolidis;Amit Bar-Or;Riley Bove;Diego A. Espinoza;Sugeidy Ferreira Brito;Dina Jacobs;Mihir Kakara;Kaho Onomichi;Adelle Ricci;Joseph J. Sabatino;Elizabeth Walker;E. John Wherry;Lili Zhang;Wen Zhu;Zongqi Xia;Philip De Jager;Sarah Flanagan Wesley;Rebecca Straus Farber;Donna L. Farber - 通讯作者:
Donna L. Farber
CD8sup+/sup T cells in the cancer-immunity cycle
癌症免疫循环中的 CD8 阳性 T 细胞
- DOI:
10.1016/j.immuni.2023.09.005 - 发表时间:
2023-10-10 - 期刊:
- 影响因子:26.300
- 作者:
Josephine R. Giles;Anna-Maria Globig;Susan M. Kaech;E. John Wherry - 通讯作者:
E. John Wherry
The SWI/SNF chromatin remodeling complexes BAF and PBAF differentially regulate epigenetic transitions in exhausted CD8sup+/sup T cells
SWI/SNF 染色质重塑复合物 BAF 和 PBAF 差异调节耗竭 CD8+T 细胞中的表观遗传转变
- DOI:
10.1016/j.immuni.2023.05.008 - 发表时间:
2023-06-13 - 期刊:
- 影响因子:26.300
- 作者:
Amy E. Baxter;Hua Huang;Josephine R. Giles;Zeyu Chen;Jennifer E. Wu;Sydney Drury;Katherine Dalton;Simone L. Park;Leonel Torres;Brandon W. Simone;Max Klapholz;Shin Foong Ngiow;Elizabeth Freilich;Sasikanth Manne;Victor Alcalde;Viktoriya Ekshyyan;Shelley L. Berger;Junwei Shi;Martha S. Jordan;E. John Wherry - 通讯作者:
E. John Wherry
E. John Wherry的其他文献
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{{ truncateString('E. John Wherry', 18)}}的其他基金
Engineering HIV-specific T cells that have improved function and persistence
改造 HIV 特异性 T 细胞,改善其功能和持久性
- 批准号:
9891735 - 财政年份:2020
- 资助金额:
$ 22.49万 - 项目类别:
Engineering HIV-specific T cells that have improved function and persistence
改造 HIV 特异性 T 细胞,改善其功能和持久性
- 批准号:
10617349 - 财政年份:2020
- 资助金额:
$ 22.49万 - 项目类别:
Temporal control of differentiation and epigenetics of Exhausted CD8 T cells by Tox
Tox 对耗竭 CD8 T 细胞的分化和表观遗传学的时间控制
- 批准号:
10685264 - 财政年份:2020
- 资助金额:
$ 22.49万 - 项目类别:
Temporal control of differentiation and epigenetics of Exhausted CD8 T cells by Tox
Tox 对耗竭 CD8 T 细胞的分化和表观遗传学的时间控制
- 批准号:
10096485 - 财政年份:2020
- 资助金额:
$ 22.49万 - 项目类别:
Engineering HIV-specific T cells that have improved function and persistence
改造 HIV 特异性 T 细胞,改善其功能和持久性
- 批准号:
10450648 - 财政年份:2020
- 资助金额:
$ 22.49万 - 项目类别:
Temporal control of differentiation and epigenetics of Exhausted CD8 T cells by Tox
Tox 对耗竭 CD8 T 细胞的分化和表观遗传学的时间控制
- 批准号:
10267763 - 财政年份:2020
- 资助金额:
$ 22.49万 - 项目类别:
Engineering HIV-specific T cells that have improved function and persistence
改造 HIV 特异性 T 细胞,改善其功能和持久性
- 批准号:
10165494 - 财政年份:2020
- 资助金额:
$ 22.49万 - 项目类别:
Temporal control of differentiation and epigenetics of Exhausted CD8 T cells by Tox
Tox 对耗竭 CD8 T 细胞的分化和表观遗传学的时间控制
- 批准号:
10462695 - 财政年份:2020
- 资助金额:
$ 22.49万 - 项目类别:
Project 3: Genetic and epigenetic basis of resistance to RT and ICB
项目3:RT和ICB抗性的遗传和表观遗传基础
- 批准号:
10360425 - 财政年份:2017
- 资助金额:
$ 22.49万 - 项目类别:
Project 3: Genetic and epigenetic basis of resistance to RT and ICB
项目3:RT和ICB抗性的遗传和表观遗传基础
- 批准号:
10005192 - 财政年份:2017
- 资助金额:
$ 22.49万 - 项目类别:
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