feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    In: JCI Insight, American Society for Clinical Investigation, Vol. 6, No. 12 ( 2021-6-22)
    Type of Medium: Online Resource
    ISSN: 2379-3708
    Language: English
    Publisher: American Society for Clinical Investigation
    Publication Date: 2021
    detail.hit.zdb_id: 2874757-4
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 2
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 74, No. 19_Supplement ( 2014-10-01), p. 2375-2375
    Abstract: Duplications and deletions of large-scale genomic regions, including whole chromosomes, are a hallmark of malignant tumors and represent an important predictor of outcome for many tumor types. In multiple myeloma, a core set of structural variants are regularly used for disease prognosis (e.g., del17p, t(4;14), t(14,16)). The presence of one or more of these lesions is predictive of a more aggressive disease and poorer outcomes for patients. The application of next-generation sequencing (NGS) to cancer samples has enhanced our ability to detect prognostic and predictive copy number aberrations (CNAs). However, most NGS-based methods for the identification of CNAs in tumors require whole genome sequencing (WGS). Relatively fewer methods exist for the detection of CNAs from exome sequencing and, to our knowledge, these methods all rely on having matched normal data. However, WES is still far more common than WGS and matched normal samples are frequently not available. Therefore, we have developed a novel method for the identification of CNAs from single-sample WES data. Our method combines LOWESS smoothing and discrete-wavelet-transformation to normalize the exome coverage data with an HMM for coverage segmentation. We have applied our new method to WES data from 40 myeloma cell-lines for which aCGH copy number calls were also available for training and validation. Our method shows a high correlation with the aCGH calls (mean = 95%). In addition we have currently analyzed 42 (of 102) tumor samples that were collected during screening of relapsed/refractory multiple myeloma patients on three Onyx-sponsored Phase 2 clinical trials of the proteasome inhibitor carfilzomib (PX-171-003,PX-171-004, PX-171-005). Based on analysis of the completed subset we find that the frequency of known and novel lesions within these samples is similar to what has previously been observed in other publically available myeloma CNA datasets. The most frequent event that we find is loss of chr13 followed by gains on chr1q and chr15 all at near 40% frequency. We also find gains of chr3, chr5, chr9 and chr11 in ∼30% of patients. These results indicate that we can apply this new method to our larger set of clinical samples in order to discover new prognostic markers for patient outcomes and response to therapy in MM. Citation Format: Jeremiah D. Degenhardt, Kenneth B. Hoehn, Kevin A. Kwei, Kristi Stephenson, Jonathan J. Keats, Chris J. Kirk, Brian B. Tuch. A method to identify copy number aberrations (CNAs) from whole exome sequence (WES) data and its application to multiple myeloma cell lines and patient samples. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2375. doi:10.1158/1538-7445.AM2014-2375
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2014
    detail.hit.zdb_id: 2036785-5
    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 3
    In: Journal of Experimental Medicine, Rockefeller University Press, Vol. 220, No. 5 ( 2023-05-01)
    Abstract: Age-associated B cells (ABCs) are formed under inflammatory conditions and are considered a type of memory B cell (MBC) expressing the transcription factor T-bet. In SLE, ABC frequency is correlated with disease, and they are thought to be the source of autoantibody-secreting cells. However, in inflammatory conditions, whether autoreactive B cells can become resting MBCs is uncertain. Further, the phenotypic identity of ABCs and their relationship to other B cell subsets, such as plasmablasts, is unclear. Whether ABCs directly promote disease is untested. Here we report, in the MRL/lpr SLE model, unexpected heterogeneity among ABC-like cells for expression of the integrins CD11b and CD11c, T-bet, and memory or plasmablast markers. Transfer and labeling studies demonstrated that ABCs are dynamic, rapidly turning over. scRNA-seq identified B cell clones present in multiple subsets, revealing that ABCs can be plasmablast precursors or undergo cycles of reactivation. Deletion of CD11c-expressing B cells revealed a direct role for ABC-like B cells in lupus pathogenesis.
    Type of Medium: Online Resource
    ISSN: 0022-1007 , 1540-9538
    RVK:
    Language: English
    Publisher: Rockefeller University Press
    Publication Date: 2023
    detail.hit.zdb_id: 1477240-1
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 4
    In: Blood, American Society of Hematology, Vol. 122, No. 21 ( 2013-11-15), p. 4881-4881
    Abstract: Duplications and deletions of large-scale genomic regions, including whole chromosomes, are a hallmark of many malignant tumors. Gross cytogenetic changes of this type were among the earliest genomic lesions to be observed in tumors and represent an important predictor of outcome for many tumor types. In multiple myeloma, a core set of structural variants are regularly used for disease prognosis (e.g., del17p, t(4;14), t(14,16)). The presence of one or more of these lesions is predictive of a more aggressive disease type and poor outcomes for patients. The application of next-generation sequencing (NGS) to cancer samples has enhanced our ability to detect copy number aberrations (CNAs) and identify driver mutations. The NGS approach can generate higher resolution maps of these mutations than traditional methods, which in turn enables faster identification of the functionally relevant genes they harbor. Most NGS-based methods for the identification of CNAs in tumors require whole genome sequencing (WGS) as input. Relatively fewer methods exist for the detection of CNAs from exome sequencing and, to our knowledge, these methods all rely on having matched normal data. However, WES is still far more common than WGS and matched normal samples are frequently not available. Therefore, we have developed a novel method for the identification of CNAs from single-sample WES data. Our method combines LOWESS smoothing & discrete-wavelet-transformation to normalize the exome coverage data with an HMM for coverage segmentation. We have applied our new method to WES data from 32 myeloma cell-lines for which aCGH copy number calls were also available for training and validation. Our method shows a high correlation with the aCGH calls (mean = 95%). We are currently applying the method to a set of 102 CD138+ tumor cell samples that were collected during patient screening on three Onyx-sponsored Phase 2 clinical trials of the proteasome inhibitor carfilzomib. We will report on the frequency of known and novel lesions in these samples, comparing to what we’ve observed in cell lines and other publically available CNA datasets. Disclosures: Degenhardt: Onyx Pharmaceuticals: Employment, Equity Ownership. Hoehn:Onyx Pharmaceuticals: Employment. Kwei:Onyx Pharmaceuticals: Employment, Equity Ownership. Kirk:Onyx Pharmaceuticals: Employment, Equity Ownership. Tuch:Onyx Pharmaceuticals: Employment, Equity Ownership.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2013
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 5
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2022-01-21)
    Abstract: Dysregulated immune responses against the SARS-CoV-2 virus are instrumental in severe COVID-19. However, the immune signatures associated with immunopathology are poorly understood. Here we use multi-omics single-cell analysis to probe the dynamic immune responses in hospitalized patients with stable or progressive course of COVID-19, explore V(D)J repertoires, and assess the cellular effects of tocilizumab. Coordinated profiling of gene expression and cell lineage protein markers shows that S100A hi /HLA-DR lo classical monocytes and activated LAG-3 hi T cells are hallmarks of progressive disease and highlights the abnormal MHC-II/LAG-3 interaction on myeloid and T cells, respectively. We also find skewed T cell receptor repertories in expanded effector CD8 + clones, unmutated IGHG + B cell clones, and mutated B cell clones with stable somatic hypermutation frequency over time. In conclusion, our in-depth immune profiling reveals dyssynchrony of the innate and adaptive immune interaction in progressive COVID-19.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2553671-0
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 6
    In: Frontiers in Immunology, Frontiers Media SA, Vol. 12 ( 2021-10-14)
    Abstract: In order to better understand how the immune system interacts with environmental triggers to produce organ-specific disease, we here address the hypothesis that B and plasma cells are free to migrate through the mucosal surfaces of the upper and lower respiratory tracts, and that their total antibody repertoire is modified in a common respiratory tract disease, in this case atopic asthma. Using Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) we have catalogued the antibody repertoires of B cell clones retrieved near contemporaneously from multiple sites in the upper and lower respiratory tract mucosa of adult volunteers with atopic asthma and non-atopic controls and traced their migration. We show that the lower and upper respiratory tracts are immunologically connected, with trafficking of B cells directionally biased from the upper to the lower respiratory tract and points of selection when migrating from the nasal mucosa and into the bronchial mucosa. The repertoires are characterized by both IgD-only B cells and others undergoing class switch recombination, with restriction of the antibody repertoire distinct in asthmatics compared with controls. We conclude that B cells and plasma cells migrate freely throughout the respiratory tract and exhibit distinct antibody repertoires in health and disease.
    Type of Medium: Online Resource
    ISSN: 1664-3224
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2606827-8
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 7
    Online Resource
    Online Resource
    The Royal Society ; 2015
    In:  Philosophical Transactions of the Royal Society B: Biological Sciences Vol. 370, No. 1676 ( 2015-09-05), p. 20140241-
    In: Philosophical Transactions of the Royal Society B: Biological Sciences, The Royal Society, Vol. 370, No. 1676 ( 2015-09-05), p. 20140241-
    Abstract: Advances in immunoglobulin (Ig) sequencing technology are leading to new perspectives on immune system dynamics. Much research in this nascent field has focused on resolving immune responses to viral infection. However, the dynamics of B-cell diversity in early HIV infection, and in response to anti-retroviral therapy, are still poorly understood. Here, we investigate these dynamics through bulk Ig sequencing of samples collected over 2 years from a group of eight HIV-1 infected patients, five of whom received anti-retroviral therapy during the first half of the study period. We applied previously published methods for visualizing and quantifying B-cell sequence diversity, including the Gini index, and compared their efficacy to alternative measures. While we found significantly greater clonal structure in HIV-infected patients versus healthy controls, within HIV patients, we observed no significant relationships between statistics of B-cell clonal expansion and clinical variables such as viral load and CD4 + count. Although there are many potential explanations for this, we suggest that important factors include poor sampling resolution and complex B-cell dynamics that are difficult to summarize using simple summary statistics. Importantly, we find a significant association between observed Gini indices and sequencing read depth, and we conclude that more robust analytical methods and a closer integration of experimental and theoretical work is needed to further our understanding of B-cell repertoire diversity during viral infection.
    Type of Medium: Online Resource
    ISSN: 0962-8436 , 1471-2970
    RVK:
    Language: English
    Publisher: The Royal Society
    Publication Date: 2015
    detail.hit.zdb_id: 1462620-2
    SSG: 12
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 8
    Online Resource
    Online Resource
    Wiley ; 2006
    In:  ELECTROPHORESIS Vol. 27, No. 8 ( 2006-04), p. 1584-1597
    In: ELECTROPHORESIS, Wiley, Vol. 27, No. 8 ( 2006-04), p. 1584-1597
    Abstract: The anthrax lethal toxin (LeTx) is composed of two proteins, protective antigen and lethal factor, which bind and enter the cell through a host receptor termed the anthrax toxin receptor (ATR). In the cell, LeTx targets p38, part of the MAP kinase signaling pathway. The toxin appears to initiate an apoptotic pathway in infected cells, indicating additional downstream targets of the toxin. We have applied a proteomics approach to investigate these downstream targets and the affected processes. In this study we have used an improved strategy for fractionation based on protein p I , off‐gel electrophoresis, employed in conjunction with relative quantitation using the mass labeling approach. In our survey, 67 proteins were observed and quantified from the cytosol of RAW 264.7 cells with respect to control versus toxin‐treated cells. Many of these proteins are involved in the oxidative stress response, as well as apoptosis, and thus likely to be relevant to the effects of anthrax in infected cells. Our results indicate that the tumor necrosis factor‐α‐mediated pathway is compromised in intoxicated cells. The knowledge of such changes and the pathways leading to the changes should be of great value in understanding and combating this disease.
    Type of Medium: Online Resource
    ISSN: 0173-0835 , 1522-2683
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2006
    detail.hit.zdb_id: 1475486-1
    SSG: 12
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 9
    In: Blood, American Society of Hematology, Vol. 138, No. Supplement 1 ( 2021-11-05), p. 359-359
    Abstract: Somatic missense mutations of BTG1 are exclusive to germinal center (GC)-derived B cell lymphomas (~12% of DLBCLs) and are most prevalent in ABC-DLBCL (p=0.0184 vs GCB-DLBCL), particularly in the MCD/cluster 5 subtype, which features extranodal dissemination and unfavorable outcome. However, the relevance, mechanism of action and biological contribution of BTG1 mutations have not been studied. Using a rigorous genomic covariate analysis, we identified BTG1 mutations as a top genetic driver in DLBCL. Furthermore, molecular dynamics simulations indicated that BTG1 recurrent mutations, including the most frequent Q36H, disrupted the protein structure, with likely deleterious functional consequences. To investigate the effect of BTG1 mutation in GC B cells, we generated a conditional Btg1Q36H knock in mouse crossed to the B cell specific Cd19Cre line. Surprisingly, there was no apparent phenotype in GC B cells or other B cell populations. However, placing Btg1 Q36H and WT GC B cells in competition within the same mouse through adoptive transfer revealed a dramatic competitive advantage of Btg1 Q36H cells, virtually taking over the GC reaction. To gain further insight into this striking fitness advantage, we performed RNAseq in Btg1 Q36H GCs, which showed marked enrichment for genes induced in positively selected GC B cells, including MYC targets and biosynthetic pathways. The same genes were also enriched in BTG1 mutant DLBCL patients in 2 independent cohorts. Furthermore, Btg1 Q36H GC B cells displayed greater RNA content and cell size, reflecting increased fitness. Positive selection normally triggers a brief Myc pulse in GC B cells. We therefore crossed our Btg1Q36H mice to the MycGFPprotein fusion reporter and observed higher proportion of Myc GFP+ cells in Btg1 Q36H GCs. For mechanistic studies, we generated isogenic BTG1 Q36H or BTG1 WT human DLBCL cell lines. BTG1 Q36H cells exhibited enrichment for the same positively selected GC B and MYC target genes, as well as greater RNA content and cell size. BTG1 family members were suggested to interact with RNA. Performing RNA-immunoprecipitation, we discovered that ~800 transcripts associated with BTG1 WT, but not BTG1 Q36H. Notably, these corresponded to the same positively selected GC B and MYC target genes, including MYC itself. BTG1 was shown to regulate mRNA stability in other cell types. However, BTG1 Q36H did not alter MYC mRNA stability and instead facilitated MYC protein synthesis, thus disrupting a novel GC context-specific checkpoint mechanism, whereby BTG1 normally attenuates spurious MYC translation to tightly restrict fitness potential. In GC B cells, Myc induction coincides with S phase entry, but G2/M progression requires re-entry into the proliferative dark zone. To characterize GC dynamics in vivo, we performed targeted single cell RNAseq in competing Btg1 Q36H and WT GC B cells and noted earlier and higher proportion of positively selected Btg1 Q36H GC B cells having committed to G2/M and the proliferative program. We confirmed faster S phase completion in competing Btg1 Q36H GC B cells by in vivo EdU/BrdU labelling and greater re-entry into the proliferative dark zone by in vivo antigen delivery to synchronize GC B cells at the time of positive selection. Given that MCD-DLBCLs express high levels of BCL2, we crossed our Btg1Q36H mice to the VavP-Bcl2 model. As compared to VavP-Bcl2, VavP-Bcl2+Btg1 Q36H mice displayed shorter survival (p=0.0005), earlier onset of lymphoma, dysplastic B cell infiltration into non lymphoid organs and they contained highly mutated, selected and clonal tumor B cells. Moribund VavP-Bcl2+Btg1 Q36H mice uniquely featured sheets of large, immunoblastic lymphoma cells, characteristic of ABC-DLBCLs. Most notably, examining ABC-DLBCLs from 5 independent cohorts showed inferior clinical outcome for BTG1 mutant patients (p=0.0011) and independent association of BTG1 mutation with inferior overall survival by multivariable Cox regression (p=0.0190). Collectively, we find that BTG1 mutations mediate lymphomagenesis through an entirely novel mechanism of action that recapitulates the embryonic MYC-dependent "super-competitive" phenotype originally described in Drosophila imaginal disc cells. In the GC, "super-competition" is provided by BTG1 mutation via a subtle acceleration of MYC induction and GC dynamics, conferring dramatic fitness and the potential to transform into aggressive lymphomas. Disclosures Hoehn: Prellis Biologics: Consultancy. Elemento: Janssen: Research Funding; Freenome: Consultancy, Other: Current equity holder in a privately-held company; Volastra Therapeutics: Consultancy, Other: Current equity holder, Research Funding; Owkin: Consultancy, Other: Current equity holder; Champions Oncology: Consultancy; One Three Biotech: Consultancy, Other: Current equity holder; Eli Lilly: Research Funding; AstraZeneca: Research Funding; Johnson and Johnson: Research Funding. Scott: NanoString Technologies: Patents & Royalties: Patent describing measuring the proliferation signature in MCL using gene expression profiling.; BC Cancer: Patents & Royalties: Patent describing assigning DLBCL COO by gene expression profiling--licensed to NanoString Technologies. Patent describing measuring the proliferation signature in MCL using gene expression profiling. ; AstraZeneca: Consultancy; Abbvie: Consultancy; Celgene: Consultancy; Incyte: Consultancy; Janssen: Consultancy, Research Funding; Rich/Genentech: Research Funding. Melnick: Constellation: Consultancy; Epizyme: Consultancy; Daiichi Sankyo: Research Funding; Sanofi: Research Funding; Janssen Pharmaceuticals: Research Funding; KDAC Pharma: Membership on an entity's Board of Directors or advisory committees.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2021
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 10
    In: Cell Reports, Elsevier BV, Vol. 42, No. 1 ( 2023-01), p. 111895-
    Type of Medium: Online Resource
    ISSN: 2211-1247
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 2649101-1
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. Further information can be found on the KOBV privacy pages