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  1. Article ; Online: Stepwise-edited, human melanoma models reveal mutations' effect on tumor and microenvironment.

    Hodis, Eran / Torlai Triglia, Elena / Kwon, John Y H / Biancalani, Tommaso / Zakka, Labib R / Parkar, Saurabh / Hütter, Jan-Christian / Buffoni, Lorenzo / Delorey, Toni M / Phillips, Devan / Dionne, Danielle / Nguyen, Lan T / Schapiro, Denis / Maliga, Zoltan / Jacobson, Connor A / Hendel, Ayal / Rozenblatt-Rosen, Orit / Mihm, Martin C / Garraway, Levi A /
    Regev, Aviv

    Science (New York, N.Y.)

    2022  Volume 376, Issue 6592, Page(s) eabi8175

    Abstract: Establishing causal relationships between genetic alterations of human cancers and specific phenotypes of malignancy remains a challenge. We sequentially introduced mutations into healthy human melanocytes in up to five genes spanning six commonly ... ...

    Abstract Establishing causal relationships between genetic alterations of human cancers and specific phenotypes of malignancy remains a challenge. We sequentially introduced mutations into healthy human melanocytes in up to five genes spanning six commonly disrupted melanoma pathways, forming nine genetically distinct cellular models of melanoma. We connected mutant melanocyte genotypes to malignant cell expression programs in vitro and in vivo, replicative immortality, malignancy, rapid tumor growth, pigmentation, metastasis, and histopathology. Mutations in malignant cells also affected tumor microenvironment composition and cell states. Our melanoma models shared genotype-associated expression programs with patient melanomas, and a deep learning model showed that these models partially recapitulated genotype-associated histopathological features as well. Thus, a progressive series of genome-edited human cancer models can causally connect genotypes carrying multiple mutations to phenotype.
    MeSH term(s) Humans ; Melanocytes/metabolism ; Melanoma/pathology ; Mutation ; Skin Neoplasms/genetics ; Skin Neoplasms/pathology ; Tumor Microenvironment/genetics
    Language English
    Publishing date 2022-04-29
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.abi8175
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Author Correction: Systematic comparison of single-cell and single-nucleus RNA-sequencing methods.

    Ding, Jiarui / Adiconis, Xian / Simmons, Sean K / Kowalczyk, Monika S / Hession, Cynthia C / Marjanovic, Nemanja D / Hughes, Travis K / Wadsworth, Marc H / Burks, Tyler / Nguyen, Lan T / Kwon, John Y H / Barak, Boaz / Ge, William / Kedaigle, Amanda J / Carroll, Shaina / Li, Shuqiang / Hacohen, Nir / Rozenblatt-Rosen, Orit / Shalek, Alex K /
    Villani, Alexandra-Chloé / Regev, Aviv / Levin, Joshua Z

    Nature biotechnology

    2020  Volume 38, Issue 6, Page(s) 756

    Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    Abstract An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    Language English
    Publishing date 2020-04-06
    Publishing country United States
    Document type Journal Article ; Published Erratum
    ZDB-ID 1311932-1
    ISSN 1546-1696 ; 1087-0156
    ISSN (online) 1546-1696
    ISSN 1087-0156
    DOI 10.1038/s41587-020-0534-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Systematic comparison of single-cell and single-nucleus RNA-sequencing methods.

    Ding, Jiarui / Adiconis, Xian / Simmons, Sean K / Kowalczyk, Monika S / Hession, Cynthia C / Marjanovic, Nemanja D / Hughes, Travis K / Wadsworth, Marc H / Burks, Tyler / Nguyen, Lan T / Kwon, John Y H / Barak, Boaz / Ge, William / Kedaigle, Amanda J / Carroll, Shaina / Li, Shuqiang / Hacohen, Nir / Rozenblatt-Rosen, Orit / Shalek, Alex K /
    Villani, Alexandra-Chloé / Regev, Aviv / Levin, Joshua Z

    Nature biotechnology

    2020  Volume 38, Issue 6, Page(s) 737–746

    Abstract: The scale and capabilities of single-cell RNA-sequencing methods have expanded rapidly in recent years, enabling major discoveries and large-scale cell mapping efforts. However, these methods have not been systematically and comprehensively benchmarked. ... ...

    Abstract The scale and capabilities of single-cell RNA-sequencing methods have expanded rapidly in recent years, enabling major discoveries and large-scale cell mapping efforts. However, these methods have not been systematically and comprehensively benchmarked. Here, we directly compare seven methods for single-cell and/or single-nucleus profiling-selecting representative methods based on their usage and our expertise and resources to prepare libraries-including two low-throughput and five high-throughput methods. We tested the methods on three types of samples: cell lines, peripheral blood mononuclear cells and brain tissue, generating 36 libraries in six separate experiments in a single center. To directly compare the methods and avoid processing differences introduced by the existing pipelines, we developed scumi, a flexible computational pipeline that can be used with any single-cell RNA-sequencing method. We evaluated the methods for both basic performance, such as the structure and alignment of reads, sensitivity and extent of multiplets, and for their ability to recover known biological information in the samples.
    MeSH term(s) Animals ; Brain/cytology ; Cells, Cultured ; Humans ; Leukocytes, Mononuclear/cytology ; Mice ; Sequence Analysis, RNA/methods ; Single-Cell Analysis/methods ; Software
    Language English
    Publishing date 2020-04-06
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1311932-1
    ISSN 1546-1696 ; 1087-0156
    ISSN (online) 1546-1696
    ISSN 1087-0156
    DOI 10.1038/s41587-020-0465-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells.

    Singer, Meromit / Wang, Chao / Cong, Le / Marjanovic, Nemanja D / Kowalczyk, Monika S / Zhang, Huiyuan / Nyman, Jackson / Sakuishi, Kaori / Kurtulus, Sema / Gennert, David / Xia, Junrong / Kwon, John Y H / Nevin, James / Herbst, Rebecca H / Yanai, Itai / Rozenblatt-Rosen, Orit / Kuchroo, Vijay K / Regev, Aviv / Anderson, Ana C

    Cell

    2018  Volume 171, Issue 5, Page(s) 1221–1223

    Language English
    Publishing date 2018-02-05
    Publishing country United States
    Document type Journal Article ; Published Erratum
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2017.11.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells.

    Singer, Meromit / Wang, Chao / Cong, Le / Marjanovic, Nemanja D / Kowalczyk, Monika S / Zhang, Huiyuan / Nyman, Jackson / Sakuishi, Kaori / Kurtulus, Sema / Gennert, David / Xia, Junrong / Kwon, John Y H / Nevin, James / Herbst, Rebecca H / Yanai, Itai / Rozenblatt-Rosen, Orit / Kuchroo, Vijay K / Regev, Aviv / Anderson, Ana C

    Cell

    2016  Volume 166, Issue 6, Page(s) 1500–1511.e9

    Abstract: Reversing the dysfunctional T cell state that arises in cancer and chronic viral infections is the focus of therapeutic interventions; however, current therapies are effective in only some patients and some tumor types. To gain a deeper molecular ... ...

    Abstract Reversing the dysfunctional T cell state that arises in cancer and chronic viral infections is the focus of therapeutic interventions; however, current therapies are effective in only some patients and some tumor types. To gain a deeper molecular understanding of the dysfunctional T cell state, we analyzed population and single-cell RNA profiles of CD8(+) tumor-infiltrating lymphocytes (TILs) and used genetic perturbations to identify a distinct gene module for T cell dysfunction that can be uncoupled from T cell activation. This distinct dysfunction module is downstream of intracellular metallothioneins that regulate zinc metabolism and can be identified at single-cell resolution. We further identify Gata-3, a zinc-finger transcription factor in the dysfunctional module, as a regulator of dysfunction, and we use CRISPR-Cas9 genome editing to show that it drives a dysfunctional phenotype in CD8(+) TILs. Our results open novel avenues for targeting dysfunctional T cell states while leaving activation programs intact.
    MeSH term(s) Animals ; CD8-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/pathology ; CRISPR-Cas Systems ; Carcinogenesis/genetics ; Carcinogenesis/immunology ; Female ; GATA3 Transcription Factor/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic/genetics ; Humans ; Lymphocyte Activation/genetics ; Lymphocyte Activation/immunology ; Lymphocytes, Tumor-Infiltrating/immunology ; Lymphocytes, Tumor-Infiltrating/pathology ; Melanoma/immunology ; Melanoma/physiopathology ; Metallothionein/deficiency ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL
    Chemical Substances GATA3 Transcription Factor ; Metallothionein (9038-94-2)
    Language English
    Publishing date 2016-08-17
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2016.08.052
    Database MEDical Literature Analysis and Retrieval System OnLINE

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