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  1. Article: PP2A catalytic subunit alpha is critically required for CD8

    Zhou, Xian / Li, Meilu / Ai, Minji / Li, Yanfeng / Zhu, Xingxing / Hansen, Michael J / Zhong, Jun / Johnson, Kenneth L / Zenka, Roman / Pandey, Akhilesh / Pease, Larry R / Zeng, Hu

    bioRxiv : the preprint server for biology

    2024  

    Abstract: While the functions of tyrosine phosphatases in T cell biology have been extensively studied, our knowledge on the contribution of serine/threonine phosphatases in T cells remains poor. Protein phosphatase 2A (PP2A) is one of the most abundantly ... ...

    Abstract While the functions of tyrosine phosphatases in T cell biology have been extensively studied, our knowledge on the contribution of serine/threonine phosphatases in T cells remains poor. Protein phosphatase 2A (PP2A) is one of the most abundantly expressed serine/threonine phosphatases. It is important in thymocyte development and CD4
    Language English
    Publishing date 2024-02-09
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.02.06.578745
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Retraction. Induction of a gene expression program in dendritic cells with a cross-linking IgM antibody to the co-stimulatory molecule B7-DC.

    Pease, Larry R

    FASEB journal : official publication of the Federation of American Societies for Experimental Biology

    2010  Volume 24, Issue 6, Page(s) 2135–2136

    Language English
    Publishing date 2010-06-01
    Publishing country United States
    Document type Retraction of Publication
    ZDB-ID 639186-2
    ISSN 1530-6860 ; 0892-6638
    ISSN (online) 1530-6860
    ISSN 0892-6638
    DOI 10.1096/fj.06-6171fjeRET
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    Zs.A 2266: Show issues Location:
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  3. Article: Exploring the effect of library preparation on RNA sequencing experiments

    Wang, Lei / Felts, Sara J / Van Keulen, Virginia P / Pease, Larry R / Zhang, Yuji

    Genomics. 2019 Dec., v. 111, no. 6

    2019  

    Abstract: RNA sequencing (RNA-seq) has become the widely preferred choice for surveying the genome-wide transcriptome complexity in many organisms. However, the broad adaptation of this methodology into the clinic still needs further evaluation of potential effect ...

    Abstract RNA sequencing (RNA-seq) has become the widely preferred choice for surveying the genome-wide transcriptome complexity in many organisms. However, the broad adaptation of this methodology into the clinic still needs further evaluation of potential effect of sample preparation factors on its analytical reliability using patient samples. In this study, we examined the impact of three major sample preparation factors (i.e., cDNA library storage time, the quantity of input RNA, and cryopreservation of cell samples) on sequence biases, gene expression profiles, and enriched biological functions using RNAs isolated from primary B cell and CD4+ cell blood samples of healthy subjects. Our comprehensive comparison results suggested that different cDNA library storage time, quantity of input RNA, and cryopreservation of cell samples did not significantly alter gene transcriptional expression profiles generated by RNA-seq experiments. These findings shed new lights on the potential applications of RNA-seq technique to patient samples in a regular clinical setting.
    Keywords B-lymphocytes ; RNA ; blood sampling ; cDNA libraries ; complementary DNA ; cryopreservation ; genes ; patients ; sequence analysis ; storage time ; surveys ; transcription (genetics) ; transcriptome
    Language English
    Dates of publication 2019-12
    Size p. 1752-1759.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 356334-0
    ISSN 1089-8646 ; 0888-7543
    ISSN (online) 1089-8646
    ISSN 0888-7543
    DOI 10.1016/j.ygeno.2018.11.030
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    Zs.A 2367: Show issues Location:
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  4. Article ; Online: Human perforin gene variation is geographically distributed.

    Willenbring, Robin C / Ikeda, Yasuhiro / Pease, Larry R / Johnson, Aaron J

    Molecular genetics & genomic medicine

    2017  Volume 6, Issue 1, Page(s) 44–55

    Abstract: Background: Deleterious mutations in PRF1 result in lethal, childhood disease, familial hemophagocytic lymphohistiocytosis type 2 (FHL 2). However, not all mutations in PRF1 are deleterious and result in FHL 2. Currently, these nondeleterious mutations ... ...

    Abstract Background: Deleterious mutations in PRF1 result in lethal, childhood disease, familial hemophagocytic lymphohistiocytosis type 2 (FHL 2). However, not all mutations in PRF1 are deleterious and result in FHL 2. Currently, these nondeleterious mutations are being investigated in the onset of numerous disorders, such as lymphomas and diabetes. Yet, there is still an overwhelmingly large amount of PRF1 mutations that are not associated with disease.
    Methods: We conducted a post hoc analysis of the PRF1 mutations in the coding region using the recently published Exome Aggregation Consortium genomes, Leiden Open Variation Database, NCBI SNP database, and primary literature to better understand PRF1 variation in the human population.
    Results: This study catalogs 460 PRF1 mutations in the coding region, and demonstrates PRF1 is more variant then previously predicted. We identify key PRF1 mutations with high allelic frequency and are only found in certain populations. Additionally, we define PRF1 SNVs are geographically distributed.
    Conclusions: This study concludes with a novel hypothesis that nondeleterious mutation in PRF1, which decreases perforin expression and/or activity, may be an example of selective advantage in the context of environmental stressors prevalent near the equator. Our studies illustrate how perforin deficiency can be protective from injuries resulting in blood-brain barrier (BBB) disruption.
    MeSH term(s) Alleles ; Amino Acid Sequence/genetics ; Databases, Nucleic Acid ; Ethnic Groups/genetics ; Gene Frequency/genetics ; Genetic Variation ; Geography/methods ; Humans ; Mutation ; Mutation, Missense ; Perforin/genetics ; Pore Forming Cytotoxic Proteins/genetics
    Chemical Substances PRF1 protein, human ; Pore Forming Cytotoxic Proteins ; Perforin (126465-35-8)
    Language English
    Publishing date 2017-12-07
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2734884-2
    ISSN 2324-9269 ; 2324-9269
    ISSN (online) 2324-9269
    ISSN 2324-9269
    DOI 10.1002/mgg3.344
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Exploring the effect of library preparation on RNA sequencing experiments.

    Wang, Lei / Felts, Sara J / Van Keulen, Virginia P / Pease, Larry R / Zhang, Yuji

    Genomics

    2018  Volume 111, Issue 6, Page(s) 1752–1759

    Abstract: RNA sequencing (RNA-seq) has become the widely preferred choice for surveying the genome-wide transcriptome complexity in many organisms. However, the broad adaptation of this methodology into the clinic still needs further evaluation of potential effect ...

    Abstract RNA sequencing (RNA-seq) has become the widely preferred choice for surveying the genome-wide transcriptome complexity in many organisms. However, the broad adaptation of this methodology into the clinic still needs further evaluation of potential effect of sample preparation factors on its analytical reliability using patient samples. In this study, we examined the impact of three major sample preparation factors (i.e., cDNA library storage time, the quantity of input RNA, and cryopreservation of cell samples) on sequence biases, gene expression profiles, and enriched biological functions using RNAs isolated from primary B cell and CD4+ cell blood samples of healthy subjects. Our comprehensive comparison results suggested that different cDNA library storage time, quantity of input RNA, and cryopreservation of cell samples did not significantly alter gene transcriptional expression profiles generated by RNA-seq experiments. These findings shed new lights on the potential applications of RNA-seq technique to patient samples in a regular clinical setting.
    MeSH term(s) Gene Expression Profiling ; Gene Library ; High-Throughput Nucleotide Sequencing ; Humans ; Sequence Analysis, RNA ; Transcriptome
    Language English
    Publishing date 2018-12-06
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 356334-0
    ISSN 1089-8646 ; 0888-7543
    ISSN (online) 1089-8646
    ISSN 0888-7543
    DOI 10.1016/j.ygeno.2018.11.030
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2367: Show issues Location:
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  6. Article ; Online: Stochastic changes in gene expression promote chaotic dysregulation of homeostasis in clonal breast tumors.

    Felts, Sara J / Tang, Xiaojia / Willett, Benjamin / Van Keulen, Virginia P / Hansen, Michael J / Kalari, Krishna R / Pease, Larry R

    Communications biology

    2019  Volume 2, Page(s) 206

    Abstract: Cells within tumors vary in phenotype as a result of changes in gene expression caused by a variety of mechanisms, permitting cancers to evolve under selective pressures from immune and other homeostatic processes. Earlier, we traced apparent losses in ... ...

    Abstract Cells within tumors vary in phenotype as a result of changes in gene expression caused by a variety of mechanisms, permitting cancers to evolve under selective pressures from immune and other homeostatic processes. Earlier, we traced apparent losses in heterozygosity (LOH) of spontaneous breast tumors from first generation (F1) intercrossed mice to atypical epigenetic modifications in the structure of DNA across the tumor genomes. Here, we describe a parallel pattern of LOH in gene expression, revealed through quantitation of parental alleles across a population of clonal tumors. We found variegated patterns of LOH, based on allelic ratio outliers in hundreds of genes, enriched in regulatory pathways typically co-opted by tumors. The frequency of outliers was correlated with transcriptional repression of a large set of homozygous genes. These findings suggest stochastic losses in gene expression across the genome of tumors generate phenotypic variation among cells, allowing clonal selection during tumor development.
    MeSH term(s) Alleles ; Animals ; Crosses, Genetic ; Epigenesis, Genetic ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Germ-Line Mutation ; Homeostasis ; Karyotyping ; Loss of Heterozygosity ; Male ; Mammary Neoplasms, Animal/genetics ; Mammary Neoplasms, Animal/metabolism ; Mice ; Mice, Inbred BALB C ; Mitosis ; Phenotype ; Sequence Analysis, RNA ; Stochastic Processes
    Language English
    Publishing date 2019-06-14
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-019-0460-0
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  7. Article ; Online: Public and private human T-cell clones respond differentially to HCMV antigen when boosted by CD3 copotentiation.

    Becher, Laura R E / Nevala, Wendy K / Sutor, Shari Lee / Abergel, Megan / Hoffmann, Michele M / Parks, Christopher A / Pease, Larry R / Schrum, Adam G / Markovic, Svetomir N / Gil, Diana

    Blood advances

    2021  Volume 4, Issue 21, Page(s) 5343–5356

    Abstract: Human cytomegalovirus (HCMV) induces long-lasting T-cell immune responses that control but do not clear infection. Typical responses involve private T-cell clones, expressing T-cell antigen receptors (TCRs) unique to a person, and public T-cell clones ... ...

    Abstract Human cytomegalovirus (HCMV) induces long-lasting T-cell immune responses that control but do not clear infection. Typical responses involve private T-cell clones, expressing T-cell antigen receptors (TCRs) unique to a person, and public T-cell clones with identical TCRs active in different people. Here, we report the development of a pretherapeutic immunostimulation modality against HCMV for human T cells, CD3 copotentiation, and the clonal analysis of its effects in recall assays at single-cell resolution. CD3 copotentiation of human T cells required identification of an intrinsically inert anti-CD3 Fab fragment that conditionally augmented signaling only when TCR was coengaged with antigen. When applied in recall assays, CD3 copotentiation enhanced the expansion of both public and private T-cell clones responding to autologous HLA-A2(+) antigen-presenting cells and immunodominant NLVPMVATV (NLV) peptide from HCMV pp65 protein. Interestingly, public vs private TCR expression was associated with distinct clonal expansion signatures in response to recall stimulus. This implied that besides possible differences in their generation and selection in an immune response, public and private T cells may respond differently to pharmacoimmunomodulation. Furthermore, a third clonal expansion profile was observed upon CD3 copotentiation of T-cell clones from HLA-A2(-) donors and 1 HLA-A2(+) presumed-uninfected donor, where NLV was of low intrinsic potency. We conclude that human T-cell copotentiation can increase the expansion of different classes of T-cell clones responding to recall antigens of different strengths, and this may be exploitable for therapeutic development against chronic, persistent infections such as HCMV.
    MeSH term(s) CD8-Positive T-Lymphocytes ; Clone Cells ; Cytomegalovirus ; Cytomegalovirus Infections ; HLA-A2 Antigen ; Humans
    Chemical Substances HLA-A2 Antigen
    Language English
    Publishing date 2021-01-28
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2915908-8
    ISSN 2473-9537 ; 2473-9529
    ISSN (online) 2473-9537
    ISSN 2473-9529
    DOI 10.1182/bloodadvances.2020002255
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    Zs.A 7153: Show issues Location:
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  8. Article ; Online: Gene splicing and mutagenesis by PCR-driven overlap extension.

    Heckman, Karin L / Pease, Larry R

    Nature protocols

    2007  Volume 2, Issue 4, Page(s) 924–932

    Abstract: Extension of overlapping gene segments by PCR is a simple, versatile technique for site-directed mutagenesis and gene splicing. Initial PCRs generate overlapping gene segments that are then used as template DNA for another PCR to create a full-length ... ...

    Abstract Extension of overlapping gene segments by PCR is a simple, versatile technique for site-directed mutagenesis and gene splicing. Initial PCRs generate overlapping gene segments that are then used as template DNA for another PCR to create a full-length product. Internal primers generate overlapping, complementary 3' ends on the intermediate segments and introduce nucleotide substitutions, insertions or deletions for site-directed mutagenesis, or for gene splicing, encode the nucleotides found at the junction of adjoining gene segments. Overlapping strands of these intermediate products hybridize at this 3' region in a subsequent PCR and are extended to generate the full-length product amplified by flanking primers that can include restriction enzyme sites for inserting the product into an expression vector for cloning purposes. The highly efficient generation of mutant or chimeric genes by this method can easily be accomplished with standard laboratory reagents in approximately 1 week.
    MeSH term(s) Animals ; Artificial Gene Fusion/methods ; DNA Primers ; Genetic Vectors ; Major Histocompatibility Complex ; Mice ; Mutagenesis, Site-Directed/methods ; Polymerase Chain Reaction/methods ; Transformation, Bacterial
    Chemical Substances DNA Primers
    Language English
    Publishing date 2007
    Publishing country England
    Document type Journal Article
    ZDB-ID 2244966-8
    ISSN 1750-2799 ; 1754-2189
    ISSN (online) 1750-2799
    ISSN 1754-2189
    DOI 10.1038/nprot.2007.132
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  9. Article ; Online: Integrative Genome-Wide Analysis of Long Noncoding RNAs in Diverse Immune Cell Types of Melanoma Patients.

    Wang, Lei / Felts, Sara J / Van Keulen, Virginia P / Scheid, Adam D / Block, Matthew S / Markovic, Svetomir N / Pease, Larry R / Zhang, Yuji

    Cancer research

    2018  Volume 78, Issue 15, Page(s) 4411–4423

    Abstract: Genome-wide identification and characterization of long noncoding RNAs (lncRNA) in individual immune cell lineages helps us better understand the driving mechanisms behind melanoma and advance personalized patient treatment. To elucidate the ... ...

    Abstract Genome-wide identification and characterization of long noncoding RNAs (lncRNA) in individual immune cell lineages helps us better understand the driving mechanisms behind melanoma and advance personalized patient treatment. To elucidate the transcriptional landscape in diverse immune cell types of peripheral blood cells (PBC) in stage IV melanoma, we used whole transcriptome RNA sequencing to profile lncRNAs in CD4
    MeSH term(s) Gene Expression Profiling/methods ; Gene Expression Regulation, Neoplastic/genetics ; Gene Regulatory Networks/genetics ; Genome/genetics ; Humans ; Melanoma/genetics ; Monocytes/physiology ; RNA, Long Noncoding/genetics ; T-Lymphocytes/physiology ; Transcription, Genetic/genetics ; Transcriptome/genetics
    Chemical Substances RNA, Long Noncoding
    Language English
    Publishing date 2018-06-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1432-1
    ISSN 1538-7445 ; 0008-5472
    ISSN (online) 1538-7445
    ISSN 0008-5472
    DOI 10.1158/0008-5472.CAN-18-0529
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Gene splicing by overlap extension: tailor-made genes using the polymerase chain reaction. BioTechniques 8(5):528-535 (November 1990).

    Horton, Robert M / Cai, Zeiling / Ho, Steffan M / Pease, Larry R

    BioTechniques

    2013  Volume 54, Issue 3, Page(s) 129–133

    MeSH term(s) Animals ; Base Sequence ; Cloning, Molecular/methods ; DNA Primers/genetics ; DNA, Recombinant/genetics ; Genes, MHC Class I ; Genes, MHC Class II ; History, 20th Century ; Mice ; Molecular Sequence Data ; Polymerase Chain Reaction/methods
    Chemical Substances DNA Primers ; DNA, Recombinant
    Language English
    Publishing date 2013-03
    Publishing country England
    Document type Biography ; Classical Article ; Historical Article ; Journal Article
    ZDB-ID 48453-2
    ISSN 1940-9818 ; 0736-6205
    ISSN (online) 1940-9818
    ISSN 0736-6205
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