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  1. Article ; Online: Chromosome-level genome editing uncovers aneuploidy addiction in cancer.

    O'Brien, Siobhan / Berger, Alice H

    Cell reports methods

    2023  Volume 3, Issue 10, Page(s) 100618

    Abstract: Publishing in Science, Girish and colleagues achieve chromosome-level genome editing to reveal a requirement for aneuploidy in breast and melanoma cancers. Authors developed and leveraged ReDACT (restoring disomy in aneuploid cells using CRISPR targeting) ...

    Abstract Publishing in Science, Girish and colleagues achieve chromosome-level genome editing to reveal a requirement for aneuploidy in breast and melanoma cancers. Authors developed and leveraged ReDACT (restoring disomy in aneuploid cells using CRISPR targeting) to generate isogenic models of aneuploidy and demonstrate that some cancers are addicted to increased copy number of specific chromosome arms.
    MeSH term(s) Humans ; Gene Editing ; Aneuploidy ; Neoplasms/genetics ; Karyotype
    Language English
    Publishing date 2023-10-10
    Publishing country United States
    Document type Journal Article
    ISSN 2667-2375
    ISSN (online) 2667-2375
    DOI 10.1016/j.crmeth.2023.100618
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: All About That Ras: Novel Fusion Drives Ras Pathway Activation in Lung Cancer.

    Moorthi, Sitapriya / Berger, Alice H

    Clinical cancer research : an official journal of the American Association for Cancer Research

    2022  Volume 28, Issue 14, Page(s) 2983–2985

    Abstract: Lung cancers in never- and light-smokers often harbor targetable oncogenic mutations in Ras pathway genes. Here, a novel OCLN-RASGRF1 fusion is identified in an otherwise Ras wild-type lung tumor. Studying this and other RASGRF1 fusions, the authors show ...

    Abstract Lung cancers in never- and light-smokers often harbor targetable oncogenic mutations in Ras pathway genes. Here, a novel OCLN-RASGRF1 fusion is identified in an otherwise Ras wild-type lung tumor. Studying this and other RASGRF1 fusions, the authors show that these fusions lead to malignant phenotypes that can be reversed by MEK inhibition. See related article by Hunihan et al., p. 3091.
    MeSH term(s) Carcinogenesis/genetics ; Genes, ras ; Humans ; Lung Neoplasms/drug therapy ; Lung Neoplasms/genetics ; Lung Neoplasms/metabolism ; Mitogen-Activated Protein Kinase Kinases/genetics ; Oncogenes ; ras-GRF1/genetics
    Chemical Substances RASGRF1 protein, human ; ras-GRF1 ; Mitogen-Activated Protein Kinase Kinases (EC 2.7.12.2)
    Language English
    Publishing date 2022-05-12
    Publishing country United States
    Document type Editorial ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 1225457-5
    ISSN 1557-3265 ; 1078-0432
    ISSN (online) 1557-3265
    ISSN 1078-0432
    DOI 10.1158/1078-0432.CCR-22-0736
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4223: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article: Genome-wide CRISPR screening reveals novel therapeutic targets in RIT1-driven lung cancer.

    Riley, Amanda K / Berger, Alice H

    Molecular & cellular oncology

    2021  Volume 8, Issue 6, Page(s) 2000318

    Abstract: In recent work, we performed CRISPR/Cas9 screening ... ...

    Abstract In recent work, we performed CRISPR/Cas9 screening in
    Language English
    Publishing date 2021-11-16
    Publishing country United States
    Document type Journal Article
    ISSN 2372-3556
    ISSN 2372-3556
    DOI 10.1080/23723556.2021.2000318
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  4. Article ; Online: Oncogenic KRAS alters splicing factor phosphorylation and alternative splicing in lung cancer.

    Lo, April / McSharry, Maria / Berger, Alice H

    BMC cancer

    2022  Volume 22, Issue 1, Page(s) 1315

    Abstract: Background: Alternative RNA splicing is widely dysregulated in cancers including lung adenocarcinoma, where aberrant splicing events are frequently caused by somatic splice site mutations or somatic mutations of splicing factor genes. However, the ... ...

    Abstract Background: Alternative RNA splicing is widely dysregulated in cancers including lung adenocarcinoma, where aberrant splicing events are frequently caused by somatic splice site mutations or somatic mutations of splicing factor genes. However, the majority of mis-splicing in cancers is unexplained by these known mechanisms. We hypothesize that the aberrant Ras signaling characteristic of lung cancers plays a role in promoting the alternative splicing observed in tumors.
    Methods: We recently performed transcriptome and proteome profiling of human lung epithelial cells ectopically expressing oncogenic KRAS and another cancer-associated Ras GTPase, RIT1. Unbiased analysis of phosphoproteome data identified altered splicing factor phosphorylation in KRAS-mutant cells, so we performed differential alternative splicing analysis using rMATS to identify significantly altered isoforms in lung epithelial cells. To determine whether these isoforms were uniquely regulated by KRAS, we performed a large-scale splicing screen in which we generated over 300 unique RNA sequencing profiles of isogenic A549 lung adenocarcinoma cells ectopically expressing 75 different wild-type or variant alleles across 28 genes implicated in lung cancer.
    Results: Mass spectrometry data showed widespread downregulation of splicing factor phosphorylation in lung epithelial cells expressing mutant KRAS compared to cells expressing wild-type KRAS. We observed alternative splicing in the same cells, with 2196 and 2416 skipped exon events in KRAS
    Conclusion: Proteomic and transcriptomic profiling of lung epithelial cells uncovered splicing factor phosphorylation and mRNA splicing events regulated by oncogenic KRAS. These data suggest that in addition to widespread transcriptional changes, the Ras signaling pathway can promote post-transcriptional splicing changes that may contribute to oncogenic processes.
    MeSH term(s) Humans ; Alternative Splicing ; Proto-Oncogene Proteins p21(ras)/genetics ; Proto-Oncogene Proteins p21(ras)/metabolism ; Phosphorylation ; RNA Splicing Factors/genetics ; RNA Splicing Factors/metabolism ; Proteomics ; Cell Line, Tumor ; Lung Neoplasms/pathology ; Adenocarcinoma of Lung/genetics ; Mutation ; Protein Isoforms/metabolism ; Nerve Tissue Proteins/genetics ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism
    Chemical Substances Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2) ; RNA Splicing Factors ; Protein Isoforms ; KRAS protein, human ; RBM45 protein, human ; Nerve Tissue Proteins ; RNA-Binding Proteins
    Language English
    Publishing date 2022-12-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041352-X
    ISSN 1471-2407 ; 1471-2407
    ISSN (online) 1471-2407
    ISSN 1471-2407
    DOI 10.1186/s12885-022-10311-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: pgMAP: a pipeline to enable guide RNA read mapping from dual-targeting CRISPR screens.

    Parrish, Phoebe C R / Groso, Daniel J / Thomas, James D / Bradley, Robert K / Berger, Alice H

    ArXiv

    2023  

    Abstract: We developed pgMAP, an analysis pipeline to map gRNA sequencing reads from dual-targeting CRISPR screens. pgMAP output includes a dual gRNA read counts table and quality control metrics including the proportion of correctly-paired reads and CRISPR ... ...

    Abstract We developed pgMAP, an analysis pipeline to map gRNA sequencing reads from dual-targeting CRISPR screens. pgMAP output includes a dual gRNA read counts table and quality control metrics including the proportion of correctly-paired reads and CRISPR library sequencing coverage across all time points and samples. pgMAP is implemented using Snakemake and is available open-source under the MIT license at https://github.com/fredhutch/pgmap_pipeline.
    Language English
    Publishing date 2023-06-01
    Publishing country United States
    Document type Preprint
    ISSN 2331-8422
    ISSN (online) 2331-8422
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: The deubiquitinase USP9X regulates RIT1 protein abundance and oncogenic phenotypes.

    Riley, Amanda K / Grant, Michael / Snell, Aidan / Vichas, Athea / Moorthi, Sitapriya / Urisman, Anatoly / Castel, Pau / Wan, Lixin / Berger, Alice H

    bioRxiv : the preprint server for biology

    2023  

    Abstract: ... ...

    Abstract RIT1
    Language English
    Publishing date 2023-12-01
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.11.30.569313
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: CRISPR base editor screens identify variant function at scale.

    Parrish, Phoebe C R / Berger, Alice H

    Molecular cell

    2021  Volume 81, Issue 4, Page(s) 647–648

    Abstract: Cuella-Martin et al. (2021) and Hanna et al. (2021) showcase CRISPR base editing in large-scale pooled screens in human cells to discover both loss- and gain-of-function variants, enabling protein structure/function insights and clinical variant ... ...

    Abstract Cuella-Martin et al. (2021) and Hanna et al. (2021) showcase CRISPR base editing in large-scale pooled screens in human cells to discover both loss- and gain-of-function variants, enabling protein structure/function insights and clinical variant interpretation.
    MeSH term(s) CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Gene Editing ; Humans
    Language English
    Publishing date 2021-03-26
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Comment
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2021.01.036
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5055: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  8. Article: CRISPR base editor screens identify variant function at scale

    Parrish, Phoebe C.R / Berger, Alice H

    Molecular cell. 2021 Feb. 18, v. 81, no. 4

    2021  

    Abstract: Cuella-Martin et al. (2021) and Hanna et al. (2021) showcase CRISPR base editing in large-scale pooled screens in human cells to discover both loss- and gain-of-function variants, enabling protein structure/function insights and clinical variant ... ...

    Abstract Cuella-Martin et al. (2021) and Hanna et al. (2021) showcase CRISPR base editing in large-scale pooled screens in human cells to discover both loss- and gain-of-function variants, enabling protein structure/function insights and clinical variant interpretation.
    Keywords gain-of-function mutation ; humans ; protein structure
    Language English
    Dates of publication 2021-0218
    Size p. 647-648.
    Publishing place Elsevier Inc.
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2021.01.036
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 2005/501: Show issues

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  9. Article ; Online: The Importance of Increasing Surgeon Participation in Hospital Leadership.

    Berger, David H / Goodall, Amanda / Tsai, Alice Y-C

    JAMA surgery

    2019  Volume 154, Issue 4, Page(s) 281–282

    MeSH term(s) Hospital Administration/statistics & numerical data ; Hospitals/standards ; Humans ; Leadership ; Physician Executives/statistics & numerical data ; Quality of Health Care ; Surgeons/education ; Surgeons/psychology ; Surgeons/statistics & numerical data ; United States
    Language English
    Publishing date 2019-02-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2701841-6
    ISSN 2168-6262 ; 2168-6254
    ISSN (online) 2168-6262
    ISSN 2168-6254
    DOI 10.1001/jamasurg.2018.5080
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Uk I Zs.72: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    ab Jg. 2022: Lesesaal (EG)

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  10. Book ; Online: pgMAP

    Parrish, Phoebe C. R. / Groso, Daniel J. / Thomas, James D. / Bradley, Robert K. / Berger, Alice H.

    a pipeline to enable guide RNA read mapping from dual-targeting CRISPR screens

    2023  

    Abstract: We developed pgMAP, an analysis pipeline to map gRNA sequencing reads from dual-targeting CRISPR screens. pgMAP output includes a dual gRNA read counts table and quality control metrics including the proportion of correctly-paired reads and CRISPR ... ...

    Abstract We developed pgMAP, an analysis pipeline to map gRNA sequencing reads from dual-targeting CRISPR screens. pgMAP output includes a dual gRNA read counts table and quality control metrics including the proportion of correctly-paired reads and CRISPR library sequencing coverage across all time points and samples. pgMAP is implemented using Snakemake and is available open-source under the MIT license at https://github.com/fredhutch/pgmap_pipeline.

    Comment: 6 pages, 1 figure, code available at https://github.com/fredhutch/pgmap_pipeline
    Keywords Quantitative Biology - Genomics
    Publishing date 2023-06-01
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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