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Ivanova VS, Davies J, Menter T, Wild D, Müller A, Krasniqi F, Stenner F, Papachristofilou A, Dirnhofer S, Tzankov A. Primary bone diffuse large B-cell lymphoma (PB-DLBCL): a distinct extranodal lymphoma of germinal centre origin, with a common EZB-like mutational profile and good prognosis. Histopathology 2024; 84:525-538. [PMID: 37965677 DOI: 10.1111/his.15096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/03/2023] [Accepted: 10/28/2023] [Indexed: 11/16/2023]
Abstract
AIMS Primary bone diffuse large B-cell lymphoma (PB-DLBCL) is not recognized as a separate entity by the current classification systems. Here we define and highlight its distinctive clinical presentation, morphology, phenotype, gene expression profile (GEP), and molecular genetics. METHODS We collected 27 respective cases and investigated their phenotype, performed gDNA panel sequencing covering 172 genes, and carried out fluorescence in situ hybridization to evaluate MYC, BCL2, and BCL6 translocations. We attempted to genetically subclassify cases using the Two-step classifier and performed GEP for cell-of-origin subtyping and in silico comparison to uncover up- and downregulated genes as opposed to other DLBCL. RESULTS Most cases (n = 22) were germinal centre B-cell-like (GCB) by immunohistochemistry and all by GEP. Additionally, PB-DLBCL had a mutational profile similar to follicular lymphoma and nodal GCB-DLBCL, with the exception of more frequent TP53 and B2M mutations. The GEP of PB-DLBCL was unique, and the frequency of BCL2 rearrangements was lower compared to nodal GCB-DLBCL. The Two-step classifier categorized eight of the cases as EZB, three as ST2, and one as MCD. CONCLUSION This study comprehensively characterizes PB-DLBCL as a separate entity with distinct clinical and morpho-molecular features. These insights may aid in developing tailored therapeutic strategies and shed light on its pathogenesis.
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Affiliation(s)
- Vanesa-Sindi Ivanova
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - John Davies
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
| | - Thomas Menter
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Damian Wild
- Divison of Nuclear Medicine, University Hospital Basel, Basel, Switzerland
| | - Anne Müller
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Fatime Krasniqi
- Division of Medical Oncology, University Hospital Basel, Basel, Switzerland
| | - Frank Stenner
- Division of Medical Oncology, University Hospital Basel, Basel, Switzerland
| | | | - Stefan Dirnhofer
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Alexandar Tzankov
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
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2
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Prüschenk S, Majer M, Schlossmann J. Novel Functional Features of cGMP Substrate Proteins IRAG1 and IRAG2. Int J Mol Sci 2023; 24:9837. [PMID: 37372987 DOI: 10.3390/ijms24129837] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
The inositol triphosphate-associated proteins IRAG1 and IRAG2 are cGMP kinase substrate proteins that regulate intracellular Ca2+. Previously, IRAG1 was discovered as a 125 kDa membrane protein at the endoplasmic reticulum, which is associated with the intracellular Ca2+ channel IP3R-I and the PKGIβ and inhibits IP3R-I upon PKGIβ-mediated phosphorylation. IRAG2 is a 75 kDa membrane protein homolog of IRAG1 and was recently also determined as a PKGI substrate. Several (patho-)physiological functions of IRAG1 and IRAG2 were meanwhile elucidated in a variety of human and murine tissues, e.g., of IRAG1 in various smooth muscles, heart, platelets, and other blood cells, of IRAG2 in the pancreas, heart, platelets, and taste cells. Hence, lack of IRAG1 or IRAG2 leads to diverse phenotypes in these organs, e.g., smooth muscle and platelet disorders or secretory deficiency, respectively. This review aims to highlight the recent research regarding these two regulatory proteins to envision their molecular and (patho-)physiological tasks and to unravel their functional interplay as possible (patho-)physiological counterparts.
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Affiliation(s)
- Sally Prüschenk
- Department of Pharmacology and Toxicology, Institute of Pharmacy, University of Regensburg, 93040 Regensburg, Germany
| | - Michael Majer
- Department of Pharmacology and Toxicology, Institute of Pharmacy, University of Regensburg, 93040 Regensburg, Germany
| | - Jens Schlossmann
- Department of Pharmacology and Toxicology, Institute of Pharmacy, University of Regensburg, 93040 Regensburg, Germany
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3
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Kong L, Pokatayev V, Lefkovith A, Carter GT, Creasey EA, Krishna C, Subramanian S, Kochar B, Ashenberg O, Lau H, Ananthakrishnan AN, Graham DB, Deguine J, Xavier RJ. The landscape of immune dysregulation in Crohn's disease revealed through single-cell transcriptomic profiling in the ileum and colon. Immunity 2023; 56:444-458.e5. [PMID: 36720220 PMCID: PMC9957882 DOI: 10.1016/j.immuni.2023.01.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 11/14/2022] [Accepted: 01/06/2023] [Indexed: 01/31/2023]
Abstract
Crohn's disease (CD) is a chronic gastrointestinal disease that is increasing in prevalence worldwide. CD is multifactorial, involving the complex interplay of genetic, immune, and environmental factors, necessitating a system-level understanding of its etiology. To characterize cell-type-specific transcriptional heterogeneity in active CD, we profiled 720,633 cells from the terminal ileum and colon of 71 donors with varying inflammation status. Our integrated datasets revealed organ- and compartment-specific responses to acute and chronic inflammation; most immune changes were in cell composition, whereas transcriptional changes dominated among epithelial and stromal cells. These changes correlated with endoscopic inflammation, but small and large intestines exhibited distinct responses, which were particularly apparent when focusing on IBD risk genes. Finally, we mapped markers of disease-associated myofibroblast activation and identified CHMP1A, TBX3, and RNF168 as regulators of fibrotic complications. Altogether, our results provide a roadmap for understanding cell-type- and organ-specific differences in CD and potential directions for therapeutic development.
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Affiliation(s)
- Lingjia Kong
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Vladislav Pokatayev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ariel Lefkovith
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Grace T Carter
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elizabeth A Creasey
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Chirag Krishna
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sathish Subramanian
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Bharati Kochar
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Orr Ashenberg
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Helena Lau
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jacques Deguine
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114, USA.
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4
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Prüschenk S, Schlossmann J. Function of IRAG2 Is Modulated by NO/cGMP in Murine Platelets. Int J Mol Sci 2022; 23:ijms23126695. [PMID: 35743138 PMCID: PMC9223716 DOI: 10.3390/ijms23126695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
Abstract
Inositol 1,4,5-triphosphate receptor-associated 2 (IRAG2) is a type II membrane protein located at the endoplasmic reticulum. It is a homologue of inositol 1,4,5-triphosphate receptor-associated cGMP kinase substrate 1 (IRAG1), a substrate protein of cGMP-dependent protein kinase I (PKGI), and is among others expressed in platelets. Here, we studied if IRAG2 is also located in platelets and might be a substrate protein of PKGI. IRAG2 was detected in platelets of IRAG2-WT animals but not in those of IRAG2-KO animals. Next, we validated by co-immunoprecipitation studies that IRAG2 is associated with IP3R1-3. No direct stable interaction with PKGIβ or with IRAG1 was observed. Phosphorylation of IRAG2 in murine platelets using a Ser/Thr-specific phospho-antibody was found in vitro and ex vivo upon cGMP stimulation. To gain insight into the function of IRAG2, platelet aggregation studies were performed using thrombin and collagen as agonists for treatment of isolated IRAG2-WT or IRAG2-KO platelets. Interestingly, platelet aggregation was reduced in the absence of IRAG2. Pretreatment of wild type or IRAG2-KO platelets with sodium nitroprusside (SNP) or 8-pCPT-cGMP revealed a further reduction in platelet aggregation in the absence of IRAG2. These results show that IRAG2 is a substrate of PKGI in murine platelets. Furthermore, our results indicate that IRAG2 is involved in the induction of thrombin- or collagen-induced platelet aggregation and that this effect is enhanced by cGMP-dependent phosphorylation of IRAG2. As IRAG1 was previously shown to inhibit platelet aggregation in a cGMP-dependent manner, it can be speculated that IRAG2 exerts an opposing function and might be an IRAG1 counterpart in murine platelets.
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5
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Jin X, Chen L, Zhou N, Ni H, Zu L, He J, Yang L, Zhu Y, Sun X, Li X, Xu S. LRMP Associates With Immune Infiltrates and Acts as a Prognostic Biomarker in Lung Adenocarcinoma. Front Mol Biosci 2021; 8:711928. [PMID: 34901148 PMCID: PMC8661541 DOI: 10.3389/fmolb.2021.711928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
Background: Lymphoid-restricted membrane protein (LRMP) is an endoplasmic reticulum-associated protein that is expressed in a developmentally regulated manner in both B and T cell lineages. However, the role of LRMP in the growth, prognosis and immune infiltration in lung adenocarcinoma (LUAD) remains unclear. Method: The expression levels of LRMP mRNA in tumor and normal tissues were analyzed using Tumor Immune Estimation Resource 2.0 (TIMER 2.0) and Gene Expression Profiling Interactive Analysis 2 (GEPIA 2). LRMP protein expression was examined using the Human Protein Atlas. In vitro experiments, including qRT-PCR Western blot and immunohistochemistry staining were also performed to investigate LRMP expression. GEPIA2 and Kaplan-Meier plotter databases were used to analyze the clinical prognostic significance of LRMP. To further confirm the underlying function of LRMP, the data were analyzed using gene set enrichment analysis. Moreover, we also constructed plasmids to overexpress LRMP and explored the effect of LRMP in A549 cell line. Additionally, Tumor Immune single-cell Hub was used to investigate the distribution of LRMP in the LUAD immune microenvironment; TIMER and CIBERSORT were used to investigate the relationships among LRMP, LRMP co-expressed genes, and tumor-infiltrating immune cells; Finally, the correlations between LRMP and immune checkpoints were analyzed using TIMER 2.0. Results: The expression of LRMP was significantly lower in LUAD tissues and cell lines. High LRMP expression is associated with a better prognosis in patients with LUAD. In vitro experimental studies demonstrated that overexpression of LRMP could decrease the proliferation, migration and invasion in A549 cells, and downregulated multiple oncogenic signaling pathways, including p-STAT3, p-PI3K-p-AKT, p-MEK and EMT pathways. GSEA results showed that immuno-related and cell adhesion pathways were enriched in samples with high LRMP expression. LRMP and its co-expressed genes were positively correlated with various tumor-infiltrating immune cells and their markers. Additionally, LRMP positively correlated with immune checkpoints. Conclusions: Our data suggest that LRMP may act as a tumor suppressor gene and indicates a better prognosis. Moreover, LRMP is associated with immune infiltrates which may be involved in immunotherapy response in LUAD. Further studies are needed to validate these findings.
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Affiliation(s)
- Xin Jin
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Liwei Chen
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Ning Zhou
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Hong Ni
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Lingling Zu
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Jinling He
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Lingqi Yang
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Yifan Zhu
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaoyue Sun
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaojiang Li
- Department of Oncology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Song Xu
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China.,Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
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6
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Prüschenk S, Majer M, Schreiber R, Schlossmann J. IRAG2 Interacts with IP 3-Receptor Types 1, 2, and 3 and Regulates Intracellular Ca 2+ in Murine Pancreatic Acinar Cells. Int J Mol Sci 2021; 22:ijms222413409. [PMID: 34948204 PMCID: PMC8707672 DOI: 10.3390/ijms222413409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 01/18/2023] Open
Abstract
The inositol 1,4,5-triphosphate receptor-associated 2 (IRAG2) is also known as Jaw1 or lymphoid-restricted membrane protein (LRMP) and shares homology with the inositol 1,4,5-triphosphate receptor-associated cGMP kinase substrate 1 (IRAG1). IRAG1 interacts with inositol trisphosphate receptors (IP3 receptors /IP3R) via its coiled-coil domain and modulates Ca2+ release from intracellular stores. Due to the homology of IRAG1 and IRAG2, especially in its coiled-coil domain, it is possible that IRAG2 has similar interaction partners like IRAG1 and that IRAG2 also modulates intracellular Ca2+ signaling. In our study, we localized IRAG2 in pancreatic acinar cells of the exocrine pancreas, and we investigated the interaction of IRAG2 with IP3 receptors and its impact on intracellular Ca2+ signaling and exocrine pancreatic function, like amylase secretion. We detected the interaction of IRAG2 with different subtypes of IP3R and altered Ca2+ release in pancreatic acinar cells from mice lacking IRAG2. IRAG2 deficiency decreased basal levels of intracellular Ca2+, suggesting that IRAG2 leads to activation of IP3R under unstimulated basal conditions. Moreover, we observed that loss of IRAG2 impacts the secretion of amylase. Our data, therefore, suggest that IRAG2 modulates intracellular Ca2+ signaling, which regulates exocrine pancreatic function.
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Affiliation(s)
- Sally Prüschenk
- Department of Pharmacology and Toxicology, Institute of Pharmacy, University of Regensburg, 93040 Regensburg, Germany; (S.P.); (M.M.)
| | - Michael Majer
- Department of Pharmacology and Toxicology, Institute of Pharmacy, University of Regensburg, 93040 Regensburg, Germany; (S.P.); (M.M.)
| | - Rainer Schreiber
- Institute of Physiology, University of Regensburg, 93040 Regensburg, Germany;
| | - Jens Schlossmann
- Department of Pharmacology and Toxicology, Institute of Pharmacy, University of Regensburg, 93040 Regensburg, Germany; (S.P.); (M.M.)
- Correspondence: ; Tel.: +49-941-943-4770
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7
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Kozono T, Sato H, Okumura W, Jogano C, Tamura-Nakano M, Kawamura YI, Rohrer J, Tonozuka T, Nishikawa A. The N-terminal region of Jaw1 has a role to inhibit the formation of organized smooth endoplasmic reticulum as an intrinsically disordered region. Sci Rep 2021; 11:753. [PMID: 33436890 PMCID: PMC7804115 DOI: 10.1038/s41598-020-80258-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/18/2020] [Indexed: 02/07/2023] Open
Abstract
Jaw1/LRMP is a type II integral membrane protein that is localized at the endoplasmic reticulum (ER) and outer nuclear membrane. We previously reported that a function of Jaw1 is to maintain the nuclear shape as a KASH protein via its carboxyl terminal region, a component of linker of nucleoskeleton and cytoskeleton complex in the oligomeric state. Although the oligomerization of some KASH proteins via the cytosolic regions serves to stabilize protein-protein interactions, the issue of how the oligomerization of Jaw1 is regulated is not completely understood. Therefore, we focused on three distinct regions on the cytosolic face of Jaw1: the N-terminal region, the coiled-coil domain and the stem region, in terms of oligomerization. A co-immunoprecipitation assay showed that its coiled-coil domain is a candidate for the oligomerization site. Furthermore, our data indicated that the N-terminal region prevents the aberrant oligomerization of Jaw1 as an intrinsically disordered region (IDR). Importantly, the ectopic expression of an N-terminal region deleted mutant caused the formation of organized smooth ER (OSER), structures such as nuclear karmellae and whorls, in B16F10 cells. Furthermore, this OSER interfered with the localization of the oligomer and interactors such as the type III inositol 1,4,5-triphosphate receptor (IP3R3) and SUN2. In summary, the N-terminal region of Jaw1 inhibits the formation of OSER as an IDR to maintain the homeostatic localization of interactors on the ER membrane.
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Affiliation(s)
- Takuma Kozono
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan.,Department of Gastroenterology, The Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba, 272-8516, Japan
| | - Hiroyuki Sato
- Department of Applied Biological Chemistry, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Wataru Okumura
- Department of Food and Energy Systems Science, Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo, 184-8588, Japan
| | - Chifuyu Jogano
- Department of Applied Biological Chemistry, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Miwa Tamura-Nakano
- Communal Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Yuki I Kawamura
- Department of Gastroenterology, The Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Chiba, 272-8516, Japan
| | - Jack Rohrer
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, CH-8820, Waedenswil, Switzerland
| | - Takashi Tonozuka
- Department of Applied Biological Chemistry, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Atsushi Nishikawa
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan. .,Department of Applied Biological Chemistry, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan. .,Department of Food and Energy Systems Science, Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo, 184-8588, Japan.
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8
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Liu B, Li C, Li Z, Wang D, Ren X, Zhang Z. An entropy-based metric for assessing the purity of single cell populations. Nat Commun 2020; 11:3155. [PMID: 32572028 PMCID: PMC7308400 DOI: 10.1038/s41467-020-16904-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 05/29/2020] [Indexed: 12/26/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a versatile tool for discovering and annotating cell types and states, but the determination and annotation of cell subtypes is often subjective and arbitrary. Often, it is not even clear whether a given cluster is uniform. Here we present an entropy-based statistic, ROGUE, to accurately quantify the purity of identified cell clusters. We demonstrate that our ROGUE metric is broadly applicable, and enables accurate, sensitive and robust assessment of cluster purity on a wide range of simulated and real datasets. Applying this metric to fibroblast, B cell and brain data, we identify additional subtypes and demonstrate the application of ROGUE-guided analyses to detect precise signals in specific subpopulations. ROGUE can be applied to all tested scRNA-seq datasets, and has important implications for evaluating the quality of putative clusters, discovering pure cell subtypes and constructing comprehensive, detailed and standardized single cell atlas.
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Affiliation(s)
- Baolin Liu
- School of Life Sciences, BIOPIC and Beijing Advanced Innovation Centre for Genomics, Peking University, Beijing, China
| | - Chenwei Li
- Peking-Tsinghua Centre for Life Sciences, Peking University, Beijing, China.,Analytical Biosciences Limited, Beijing, China
| | - Ziyi Li
- School of Life Sciences, BIOPIC and Beijing Advanced Innovation Centre for Genomics, Peking University, Beijing, China
| | - Dongfang Wang
- School of Life Sciences, BIOPIC and Beijing Advanced Innovation Centre for Genomics, Peking University, Beijing, China
| | - Xianwen Ren
- School of Life Sciences, BIOPIC and Beijing Advanced Innovation Centre for Genomics, Peking University, Beijing, China
| | - Zemin Zhang
- School of Life Sciences, BIOPIC and Beijing Advanced Innovation Centre for Genomics, Peking University, Beijing, China. .,Peking-Tsinghua Centre for Life Sciences, Peking University, Beijing, China. .,Analytical Biosciences Limited, Beijing, China.
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9
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Kozono T, Tadahira K, Okumura W, Itai N, Tamura-Nakano M, Dohi T, Tonozuka T, Nishikawa A. Jaw1/LRMP has a role in maintaining nuclear shape via interaction with SUN proteins. J Biochem 2018; 164:303-311. [DOI: 10.1093/jb/mvy053] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/28/2018] [Indexed: 12/31/2022] Open
Affiliation(s)
- Takuma Kozono
- Department of Food and Energy Systems Science, Graduate School of Bio-Applications Systems Engineering, 3-5-8 Saiwai-cho, Fuchu, Tokyo, Japan
| | - Kazuko Tadahira
- Division of Applied Biological Chemistry, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, Japan
| | - Wataru Okumura
- Department of Food and Energy Systems Science, Graduate School of Bio-Applications Systems Engineering, 3-5-8 Saiwai-cho, Fuchu, Tokyo, Japan
| | - Nao Itai
- Division of Applied Biological Chemistry, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, Japan
| | - Miwa Tamura-Nakano
- Communal Laboratory, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, Japan
| | - Taeko Dohi
- Department of Gastroenterology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba, Japan
| | - Takashi Tonozuka
- Division of Applied Biological Chemistry, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, Japan
| | - Atsushi Nishikawa
- Department of Food and Energy Systems Science, Graduate School of Bio-Applications Systems Engineering, 3-5-8 Saiwai-cho, Fuchu, Tokyo, Japan
- Division of Applied Biological Chemistry, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, Japan
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10
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Zhao S, Fang S, Liu Y, Li X, Liao S, Chen J, Liu J, Zhao L, Li H, Zhou W, Shen W, Dong X, Xiang R, Wang L, Zhao Y. The long non-coding RNA NONHSAG026900 predicts prognosis as a favorable biomarker in patients with diffuse large B-cell lymphoma. Oncotarget 2018; 8:34374-34386. [PMID: 28423735 PMCID: PMC5470975 DOI: 10.18632/oncotarget.16163] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 02/24/2017] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs are known to be involved in cancer progression, but their biological functions and prognostic values are still largely unexplored in diffuse large B-cell lymphoma. In this study, long non-coding RNAs expression was characterized in 1,403 samples including normal and diffuse large B-cell lymphoma by repurposing 7 microarray datasets. Compared with any stage of normal B cells, NONHSAG026900 expression was significantly decreased in tumor samples. And in germinal center B-cell subtype, the significantly higher expression of NONHSAG026900 indicated it was a favorable prognosis biomarker. Then the prognostic power of NONHSAG026900 was validated with another independent dataset and NONHSAG026900 improved the predictive power of International Prognostic Index as an independent factor. Moreover, functional prediction and validation demonstrated that NONHSAG026900 could inhibit cell cycle activity to restrain tumor proliferation. These findings identified NONHSAG026900 as a novel prognostic biomarker and offered a new therapeutic target for diffuse large B-cell lymphoma patients.
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Affiliation(s)
- Shuangtao Zhao
- Department of Radiation Oncology, National Cancer Center/Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Shuangsang Fang
- The Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Yanhua Liu
- The School of Medicine, Nankai University, Tianjin, China.,The Collaborative Innovation Center for Biotherapy, Nankai University, Tianjin, China.,The Tianjin Key Laboratory of Tumor Microenvironment and Neurovascular Regulation, Tianjin, China
| | - Xixi Li
- The School of Medicine, Nankai University, Tianjin, China.,Department of Pathology, Nankai University, Tianjin, China
| | - Shengyou Liao
- The Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Jinwen Chen
- The Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Jingjia Liu
- The Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Lianhe Zhao
- The Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Hui Li
- The Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Wei Zhou
- The School of Medicine, Nankai University, Tianjin, China.,The Collaborative Innovation Center for Biotherapy, Nankai University, Tianjin, China.,The Tianjin Key Laboratory of Tumor Microenvironment and Neurovascular Regulation, Tianjin, China
| | - Wenzhi Shen
- The School of Medicine, Nankai University, Tianjin, China.,The Collaborative Innovation Center for Biotherapy, Nankai University, Tianjin, China.,The Tianjin Key Laboratory of Tumor Microenvironment and Neurovascular Regulation, Tianjin, China
| | - Xiaoli Dong
- The School of Medicine, Nankai University, Tianjin, China.,The Collaborative Innovation Center for Biotherapy, Nankai University, Tianjin, China.,The Tianjin Key Laboratory of Tumor Microenvironment and Neurovascular Regulation, Tianjin, China
| | - Rong Xiang
- The School of Medicine, Nankai University, Tianjin, China.,The Collaborative Innovation Center for Biotherapy, Nankai University, Tianjin, China.,The Tianjin Key Laboratory of Tumor Microenvironment and Neurovascular Regulation, Tianjin, China
| | - Luhua Wang
- Department of Radiation Oncology, National Cancer Center/Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yi Zhao
- The Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
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11
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Subtype-specific addiction of the activated B-cell subset of diffuse large B-cell lymphoma to FOXP1. Proc Natl Acad Sci U S A 2016; 113:E577-86. [PMID: 26787899 DOI: 10.1073/pnas.1524677113] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
High expression of the forkhead box P1 (FOXP1) transcription factor distinguishes the aggressive activated B cell (ABC) diffuse large B-cell lymphoma (DLBCL) subtype from the better prognosis germinal center B-cell (GCB)-DLBCL subtype and is highly correlated with poor outcomes. A genetic or functional role for FOXP1 in lymphomagenesis, however, remains unknown. Here, we report that sustained FOXP1 expression is vital for ABC-DLBCL cell-line survival. Genome-wide analyses revealed direct and indirect FOXP1 transcriptional enforcement of ABC-DLBCL hallmarks, including the classical NF-κB and MYD88 (myeloid differentiation primary response gene 88) pathways. FOXP1 promoted gene expression underlying transition of the GCB cell to the plasmablast--the transient B-cell stage targeted in ABC-DLBCL transformation--by antagonizing pathways distinctive of GCB-DLBCL, including that of the GCB "master regulator," BCL6 (B-cell lymphoma 6). Cell-line derived FOXP1 target genes that were highly correlated with FOXP1 expression in primary DLBCL accurately segregated the corresponding clinical subtypes of a large cohort of primary DLBCL isolates and identified conserved pathways associated with ABC-DLBCL pathology.
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12
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McKay P, Fielding P, Gallop-Evans E, Hall GW, Lambert J, Leach M, Marafioti T, McNamara C. Guidelines for the investigation and management of nodular lymphocyte predominant Hodgkin lymphoma. Br J Haematol 2015; 172:32-43. [PMID: 26538004 DOI: 10.1111/bjh.13842] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Pamela McKay
- Department of Haematology; Beatson West of Scotland Cancer Centre; Gartnavel Hospital; Glasgow UK
| | - Patrick Fielding
- PETIC; Department of Radiology; University Hospital of Wales; Cardiff UK
| | - Eve Gallop-Evans
- Department of Clinical Oncology; Velindre Cancer Centre; Cardiff UK
| | - Georgina W. Hall
- Paediatric Haematology/Oncology Unit; Children's Hospital; John Radcliffe Hospital; Headington Oxford
| | - Jonathan Lambert
- Department of Haematology; University College London Hospitals; London UK
| | - Mike Leach
- Department of Haematology; Beatson West of Scotland Cancer Centre; Gartnavel Hospital; Glasgow UK
| | - Teresa Marafioti
- Department of Pathology; University College London Hospitals; London UK
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13
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Fernández-Vega I, Quirós LM, Santos-Juanes J, Pane-Foix M, Marafioti T. Bruton’s tyrosine kinase (Btk) is a useful marker for Hodgkin and B cell non-Hodgkin lymphoma. Virchows Arch 2014; 466:229-35. [PMID: 25433814 DOI: 10.1007/s00428-014-1698-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 11/11/2014] [Accepted: 11/19/2014] [Indexed: 12/18/2022]
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14
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Song YY, Tan YH, Yuan Y, Guo W, Pan ZY, Bai O. Current Perspectives in Genetics of “Double-Hit” Lymphoma with Possible Clinical Implications. Cell Biochem Biophys 2013; 69:203-8. [PMID: 24234731 DOI: 10.1007/s12013-013-9790-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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15
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Gene selection and cancer type classification of diffuse large-B-cell lymphoma using a bivariate mixture model for two-species data. Hum Genomics 2013; 7:2. [PMID: 23289441 PMCID: PMC3618031 DOI: 10.1186/1479-7364-7-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 11/14/2012] [Indexed: 11/23/2022] Open
Abstract
A bivariate mixture model utilizing information across two species was proposed to solve the fundamental problem of identifying differentially expressed genes in microarray experiments. The model utility was illustrated using a dog and human lymphoma data set prepared by a group of scientists in the College of Veterinary Medicine at North Carolina State University. A small number of genes were identified as being differentially expressed in both species and the human genes in this cluster serve as a good predictor for classifying diffuse large-B-cell lymphoma (DLBCL) patients into two subgroups, the germinal center B-cell-like diffuse large B-cell lymphoma and the activated B-cell-like diffuse large B-cell lymphoma. The number of human genes that were observed to be significantly differentially expressed (21) from the two-species analysis was very small compared to the number of human genes (190) identified with only one-species analysis (human data). The genes may be clinically relevant/important, as this small set achieved low misclassification rates of DLBCL subtypes. Additionally, the two subgroups defined by this cluster of human genes had significantly different survival functions, indicating that the stratification based on gene-expression profiling using the proposed mixture model provided improved insight into the clinical differences between the two cancer subtypes.
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16
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Hooper SD, Jiao X, Sundström E, Rehman FL, Tellgren-Roth C, Sjöblom T, Cavelier L. Sequence based analysis of U-2973, a cell line established from a double-hit B-cell lymphoma with concurrent MYC and BCL2 rearrangements. BMC Res Notes 2012; 5:648. [PMID: 23171647 PMCID: PMC3534606 DOI: 10.1186/1756-0500-5-648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 11/09/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Double-hit lymphoma is a complex and highly aggressive sub-type of B-cell lymphoma, which has recently been classified and is an area of active research interest due to the poor prognosis for patients with this disease. It is characterized by the presence of both an activating MYC chromosomal translocation and a simultaneous additional oncogenic translocation, often of the BCL2 gene. Recently, a cell line was established from a patient with this complex lymphoma and analyzed using conventional tools revealing it contains both MYC and BCL2 translocation events. FINDINGS In this work, we reanalyzed the genome of the cell line using next generation whole genome sequencing technology in order to catalogue translocations, insertions and deletions which may contribute to the pathology of this lymphoma type. CONCLUSIONS We describe the cell line in much greater detail, and pinpoint the exact locations of the chromosomal breakpoints. We also find several rearrangements within cancer-associated genes, which were not found using conventional tools, suggesting that high throughput sequencing may reveal novel targets for therapy, which could be used concurrently with existing treatments.
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Affiliation(s)
- Sean D Hooper
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, 751 85, Sweden
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17
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Bertram S, Heurich A, Lavender H, Gierer S, Danisch S, Perin P, Lucas JM, Nelson PS, Pöhlmann S, Soilleux EJ. Influenza and SARS-coronavirus activating proteases TMPRSS2 and HAT are expressed at multiple sites in human respiratory and gastrointestinal tracts. PLoS One 2012; 7:e35876. [PMID: 22558251 PMCID: PMC3340400 DOI: 10.1371/journal.pone.0035876] [Citation(s) in RCA: 339] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 03/23/2012] [Indexed: 11/30/2022] Open
Abstract
The type II transmembrane serine proteases TMPRSS2 and HAT activate influenza viruses and the SARS-coronavirus (TMPRSS2) in cell culture and may play an important role in viral spread and pathogenesis in the infected host. However, it is at present largely unclear to what extent these proteases are expressed in viral target cells in human tissues. Here, we show that both HAT and TMPRSS2 are coexpressed with 2,6-linked sialic acids, the major receptor determinant of human influenza viruses, throughout the human respiratory tract. Similarly, coexpression of ACE2, the SARS-coronavirus receptor, and TMPRSS2 was frequently found in the upper and lower aerodigestive tract, with the exception of the vocal folds, epiglottis and trachea. Finally, activation of influenza virus was conserved between human, avian and porcine TMPRSS2, suggesting that this protease might activate influenza virus in reservoir-, intermediate- and human hosts. In sum, our results show that TMPRSS2 and HAT are expressed by important influenza and SARS-coronavirus target cells and could thus support viral spread in the human host.
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Affiliation(s)
| | | | - Hayley Lavender
- Oxfabs, Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | | | - Simon Danisch
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Paula Perin
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Jared M. Lucas
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | | | - Elizabeth J. Soilleux
- Department of Cellular Pathology and Nuffield Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
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18
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Identification of a novel non-immunoglobulin/MYC translocation t(8;12)(q24;p12) involving the LRMP gene in a primary B-cell lymphoma. A case report. Leuk Res 2012; 36:e22-4. [DOI: 10.1016/j.leukres.2011.09.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 09/06/2011] [Accepted: 09/19/2011] [Indexed: 11/20/2022]
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19
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Cleavage and activation of the severe acute respiratory syndrome coronavirus spike protein by human airway trypsin-like protease. J Virol 2011; 85:13363-72. [PMID: 21994442 DOI: 10.1128/jvi.05300-11] [Citation(s) in RCA: 238] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) poses a constant threat to human health. The viral spike protein (SARS-S) mediates host cell entry and is a potential target for antiviral intervention. Activation of SARS-S by host cell proteases is essential for SARS-CoV infectivity but remains incompletely understood. Here, we analyzed the role of the type II transmembrane serine proteases (TTSPs) human airway trypsin-like protease (HAT) and transmembrane protease, serine 2 (TMPRSS2), in SARS-S activation. We found that HAT activates SARS-S in the context of surrogate systems and authentic SARS-CoV infection and is coexpressed with the viral receptor angiotensin-converting enzyme 2 (ACE2) in bronchial epithelial cells and pneumocytes. HAT cleaved SARS-S at R667, as determined by mutagenesis and mass spectrometry, and activated SARS-S for cell-cell fusion in cis and trans, while the related pulmonary protease TMPRSS2 cleaved SARS-S at multiple sites and activated SARS-S only in trans. However, TMPRSS2 but not HAT expression rendered SARS-S-driven virus-cell fusion independent of cathepsin activity, indicating that HAT and TMPRSS2 activate SARS-S differentially. Collectively, our results show that HAT cleaves and activates SARS-S and might support viral spread in patients.
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20
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Dagliyan O, Uney-Yuksektepe F, Kavakli IH, Turkay M. Optimization based tumor classification from microarray gene expression data. PLoS One 2011; 6:e14579. [PMID: 21326602 PMCID: PMC3033885 DOI: 10.1371/journal.pone.0014579] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 12/23/2010] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND An important use of data obtained from microarray measurements is the classification of tumor types with respect to genes that are either up or down regulated in specific cancer types. A number of algorithms have been proposed to obtain such classifications. These algorithms usually require parameter optimization to obtain accurate results depending on the type of data. Additionally, it is highly critical to find an optimal set of markers among those up or down regulated genes that can be clinically utilized to build assays for the diagnosis or to follow progression of specific cancer types. In this paper, we employ a mixed integer programming based classification algorithm named hyper-box enclosure method (HBE) for the classification of some cancer types with a minimal set of predictor genes. This optimization based method which is a user friendly and efficient classifier may allow the clinicians to diagnose and follow progression of certain cancer types. METHODOLOGY/PRINCIPAL FINDINGS We apply HBE algorithm to some well known data sets such as leukemia, prostate cancer, diffuse large B-cell lymphoma (DLBCL), small round blue cell tumors (SRBCT) to find some predictor genes that can be utilized for diagnosis and prognosis in a robust manner with a high accuracy. Our approach does not require any modification or parameter optimization for each data set. Additionally, information gain attribute evaluator, relief attribute evaluator and correlation-based feature selection methods are employed for the gene selection. The results are compared with those from other studies and biological roles of selected genes in corresponding cancer type are described. CONCLUSIONS/SIGNIFICANCE The performance of our algorithm overall was better than the other algorithms reported in the literature and classifiers found in WEKA data-mining package. Since it does not require a parameter optimization and it performs consistently very high prediction rate on different type of data sets, HBE method is an effective and consistent tool for cancer type prediction with a small number of gene markers.
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MESH Headings
- Algorithms
- Calibration
- Electronic Data Processing/standards
- Gene Expression Profiling/methods
- Gene Expression Profiling/standards
- Gene Expression Regulation, Neoplastic
- Humans
- Leukemia/classification
- Leukemia/diagnosis
- Leukemia/genetics
- Lymphoma, Large B-Cell, Diffuse/classification
- Lymphoma, Large B-Cell, Diffuse/diagnosis
- Lymphoma, Large B-Cell, Diffuse/genetics
- Male
- Microarray Analysis/methods
- Microarray Analysis/standards
- Models, Theoretical
- Neoplasms/classification
- Neoplasms/diagnosis
- Neoplasms/genetics
- Pattern Recognition, Automated/methods
- Pattern Recognition, Automated/standards
- Prognosis
- Prostatic Neoplasms/classification
- Prostatic Neoplasms/diagnosis
- Prostatic Neoplasms/genetics
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Affiliation(s)
- Onur Dagliyan
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | | | - I. Halil Kavakli
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Metin Turkay
- Department of Industrial Engineering, Koc University, Istanbul, Turkey
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21
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Hamm CM, Reimers MA, McCullough CK, Gorbe EB, Lu J, Gu CC, Li E, Dieckgraefe BK, Gong Q, Stappenbeck TS, Stone CD, Dietz DW, Hunt SR. NOD2 status and human ileal gene expression. Inflamm Bowel Dis 2010; 16:1649-57. [PMID: 20155851 PMCID: PMC4002261 DOI: 10.1002/ibd.21208] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND NOD2 single nucleotide polymorphisms have been associated with increased risk of ileal Crohn's disease (CD). This exploratory study was conducted to compare ileal mucosal gene expression in CD patients with and without NOD2 risk alleles. METHODS Ileal samples were prospectively collected from 18 nonsmoking CD patients not treated with anti-TNF-α biologics and 9 nonsmoking control patients without inflammatory bowel disease undergoing initial resection and genotyped for the 3 major NOD2 risk alleles (Arg702Trp, Gly908Arg, Leu1007fs). Microarray analysis was performed in samples from 4 NOD2(R) (at least 1 risk allele) CD patients, 4 NOD2(NR) (no risk alleles) CD patients, and 4 NOD2(NR) controls. Candidate genes selected by significance analysis of microarrays (SAM) were confirmed by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) assays of all the samples. RESULTS SAM detected upregulation of 18 genes in affected ileum in NOD2(R) compared to NOD2(NR) CD patients, including genes related to lymphocyte activation. SAM also detected altered ileal gene expression in unaffected NOD2(NR) ileal mucosal CD samples compared to NOD2(NR) control samples. qRT-PCR conducted on all the samples confirmed that increased CD3D expression in affected samples was associated with NOD2(R) status, and that increased MUC1, DUOX2, DMBT1 and decreased C4orf7 expression in unaffected samples was associated with CD, independent of NOD2 status. CONCLUSIONS The results support the concept that NOD2 risk alleles contribute to impaired regulation of inflammation in the ileum. Furthermore, altered ileal gene expression, independent of NOD2 status, is detected in the unaffected proximal margin of resected ileum from CD patients.
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Affiliation(s)
- Christina M Hamm
- Division of Gastroenterology, Washington University, St Louis School of Medicine, St Louis, Missouri, USA
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22
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Schokker D, Smits MA, Hoekman AJW, Parmentier HK, Rebel JMJ. Effects of Salmonella on spatial-temporal processes of jejunal development in chickens. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2010; 34:1090-1100. [PMID: 20541565 DOI: 10.1016/j.dci.2010.05.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 05/25/2010] [Accepted: 05/25/2010] [Indexed: 05/29/2023]
Abstract
To study effects of Salmonella enteritidis on morphological and functional changes in chicken jejunal development, we analysed gene expression profiles at seven points post-infection in 1-21 day-old broiler chickens. Nine clusters with different gene expression patterns were identified, and the genes in each cluster were further analyzed by a functional annotation clustering method (DAVID). Functional and morphological developmental processes dominated in all the nine clusters. Salmonella infection caused delays in several intestinal-morphological processes, whereas functional metabolic processes occurred in a similar spatial-temporal frame compared to normal jejunum development. A clear difference between normal developing- and Salmonella disturbed jejunum was the higher expression of genes involved in cell turn-over at early stages in the infected jejunum. Surprisingly, we found no clustered immune related processes in the infected birds. To compare the immunological processes between control and Salmonella infected chickens, the gene expression data was superimposed on known immunological KEGG pathways. Furthermore an in-depth analysis on the immune gene level was performed. As expected, we did find immunological processes in the Salmonella infected jejunum. Several of these processes could be verified by immunohistochemistry measurements of different immunological cell types. However, the well-ordered spatial-temporal development of the immune system, as observed in control non-infected animals, was completely abolished in the infected animals. Several immunological processes started much earlier in time, whereas other processes are disorganised. These data indicate that normal morphological and immunological development of jejunum is changed dramatically by a disturbance due to Salmonella infection. Due to the disturbance, the well-organized spatial-temporal development of morphological processes are delayed, those of the immunological development are scattered, whereas metabolic functional processes are almost not affected. This demonstrates the flexibility of developmental processes in the broiler chicken intestine.
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Affiliation(s)
- Dirkjan Schokker
- Wageningen UR Livestock Research, Animal Breeding and Genomics Centre, P.O. Box 65, 8200 AB, Lelystad, The Netherlands.
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23
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Rodig SJ, Kutok JL, Paterson JC, Nitta H, Zhang W, Chapuy B, Tumwine LK, Montes-Moreno S, Agostinelli C, Johnson NA, Ben-Neriah S, Farinha P, Shipp MA, Piris MA, Grogan TM, Pileri SA, Gascoyne RD, Marafioti T. The pre-B-cell receptor associated protein VpreB3 is a useful diagnostic marker for identifying c-MYC translocated lymphomas. Haematologica 2010; 95:2056-62. [PMID: 20823132 DOI: 10.3324/haematol.2010.025767] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND During B-cell development, precursor B cells transiently express the pre-B-cell receptor composed of μ heavy chain complexed with VpreB and λ5 surrogate light chain polypeptides. Recent profiling studies unexpectedly revealed abundant transcripts of one member of the VpreB family, VpreB3, in a subset of mature B cells and Burkitt lymphoma. DESIGN AND METHODS Here we used a novel antibody to investigate the normal expression pattern of VpreB3 protein in human hematopoietic and lymphoid tissues, and to determine whether VpreB3 could serve as a useful diagnostic biomarker for select B-cell lymphomas. RESULTS We found that VpreB3 protein is normally expressed by precursor B cells in bone marrow and by a subset of normal germinal center B cells in secondary lymphoid organs. Among lymphoid malignancies, we found an association between VpreB3 expression and B-cell tumors with c-MYC abnormalities. VpreB3 was highly expressed in all cases of Burkitt lymphoma, whether of endemic or sporadic origin (44/44 cases, 100%), all cases of B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and Burkitt lymphoma (5/5 cases, 100%), and the majority of diffuse large B-cell lymphomas harboring a c-MYC translocation (15/18 cases, 83%). The expression of VpreB3 in diffuse large B-cell lymphomas without a c-MYC translocation was associated with c-MYC polysomy in 25/75 cases (33%) but only rarely observed in diffuse large B-cell lymphomas lacking a c-MYC abnormality (9/98 cases, 9%). CONCLUSIONS We conclude that for B-cell tumors with features suggesting a possible c-MYC translocation, such as intermediate to large cell size and high proliferation rate, the presence of VpreB3 should prompt subsequent confirmatory genetic testing, whereas the absence of VpreB3 is virtually always associated with wild-type c-MYC alleles.
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Affiliation(s)
- Scott J Rodig
- Department of Pathology, Brigham & Women's Hospital, Boston, MA, USA
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24
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Ma S, Chan YP, Woolcock B, Hu L, Wong KY, Ling MT, Bainbridge T, Webber D, Chan THM, Guan XY, Lam W, Vielkind J, Chan KW. DNA fingerprinting tags novel altered chromosomal regions and identifies the involvement of SOX5 in the progression of prostate cancer. Int J Cancer 2009; 124:2323-32. [PMID: 19173284 DOI: 10.1002/ijc.24243] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Identification of genomic alterations associated with the progression of prostate cancer may facilitate the better understanding of the development of this highly variable disease. Matched normal, premalignant high-grade prostatic intraepithelial neoplasia and invasive prostate carcinoma cells were procured by laser capture microdissection (LCM) from human radical prostatectomy specimens. From these cells, comparative DNA fingerprints were generated by a modified PCR-based technique called scanning of microdissected archival lesion (SMAL)-PCR. Recurrent polymorphic fingerprint fragments were used in tagging altered chromosomal regions. Altered regions were found at cytobands 1p31.3, 1q44, 2p23.1, 3p26.3, 3q22.3, 4q22.3, 4q35.2, 5q23.2, 8q22.3, 8q24.13, 9q21.3, 9q22.32, 10q11.21, 11p13, 12p12.1, 13q12.1, 16q12.2 and 18q21.31. Candidate genes in the surrounding area that may possibly harbor mutations that change normal prostatic cells to progress into their tumor stages were proposed. Of these fragments, a 420 bp alteration, absent in all 26 normal samples screened, was observed in 2 tumors. This fragment was cloned, sequenced and localized to chromosome 12p12.1. Within this region, candidate gene sex determining region Y-box 5 (SOX5) was proposed. Further studies of SOX5 in cell lines, xenografts and human prostate specimens, at both the RNA and protein levels, found overexpression of the gene in tumors. This overexpression was then subsequently found by fluorescent in situ hybridization to be caused by amplification of the region. In conclusion, our results suggest LCM coupled with SMAL-PCR DNA fingerprinting is a useful method for the screening and identification of chromosomal regions and genes associated with cancer development. Further, overexpression of SOX5 is associated with prostate tumor progression and early development of distant metastasis.
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Affiliation(s)
- Stephanie Ma
- Department of Pathology, The University of Hong Kong, Hong Kong
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25
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Tedoldi S, Mottok A, Ying J, Paterson JC, Cui Y, Facchetti F, van Krieken JHJM, Ponzoni M, Özkal S, Masir N, Natkunam Y, Pileri SA, Hansmann ML, Mason DY, Tao Q, Marafioti T. Selective loss of B-cell phenotype in lymphocyte predominant Hodgkin lymphoma. J Pathol 2007; 213:429-40. [DOI: 10.1002/path.2242] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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26
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27
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Zhang W, Li L, Li X, Jiang W, Huo J, Wang Y, Lin M, Rao S. Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering. BMC Genomics 2007; 8:332. [PMID: 17888167 PMCID: PMC2082044 DOI: 10.1186/1471-2164-8-332] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2006] [Accepted: 09/22/2007] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND It becomes increasingly clear that our current taxonomy of clinical phenotypes is mixed with molecular heterogeneity. Of vital importance for refined clinical practice and improved intervention strategies is to define the hidden molecular distinct diseases using modern large-scale genomic approaches. Microarray omics technology has provided a powerful way to dissect hidden genetic heterogeneity of complex diseases. The aim of this study was thus to develop a bioinformatics approach to seek the transcriptional features leading to the hidden subtyping of a complex clinical phenotype. The basic strategy of the proposed method was to iteratively partition in two ways sample and feature space with super-paramagnetic clustering technique and to seek for hard and robust gene clusters that lead to a natural partition of disease samples and that have the highest functionally conceptual consensus evaluated with Gene Ontology. RESULTS We applied the proposed method to two publicly available microarray datasets of diffuse large B-cell lymphoma (DLBCL), a notoriously heterogeneous phenotype. A feature subset of 30 genes (38 probes) derived from analysis of the first dataset consisting of 4026 genes and 42 DLBCL samples identified three categories of patients with very different five-year overall survival rates (70.59%, 44.44% and 14.29% respectively; p = 0.0017). Analysis of the second dataset consisting of 7129 genes and 58 DLBCL samples revealed a feature subset of 13 genes (16 probes) that not only replicated the findings of the important DLBCL genes (e.g. JAW1 and BCL7A), but also identified three clinically similar subtypes (with 5-year overall survival rates of 63.13%, 34.92% and 15.38% respectively; p = 0.0009) to those identified in the first dataset. Finally, we built a multivariate Cox proportional-hazards prediction model for each feature subset and defined JAW1 as one of the most significant predictor (p = 0.005 and 0.014; hazard ratios = 0.02 and 0.03, respectively for two datasets) for both DLBCL cohorts under study. CONCLUSION Our results showed that the proposed algorithm is a promising computational strategy for peeling off the hidden genetic heterogeneity based on transcriptionally profiling disease samples, which may lead to an improved diagnosis and treatment of cancers.
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Affiliation(s)
- Wei Zhang
- The First Clinical College, Department of Bioinformatics, and the Bio-pharmaceutical Key Laboratory of Heilongjiang Province and State, Harbin Medical University, Harbin 150086, China
| | - Li Li
- Institute of Medical Genetics, Tongji University, Shanghai 200092, China
| | - Xia Li
- The First Clinical College, Department of Bioinformatics, and the Bio-pharmaceutical Key Laboratory of Heilongjiang Province and State, Harbin Medical University, Harbin 150086, China
- Institute of Medical Genetics, Tongji University, Shanghai 200092, China
- Department of Computer Science, Harbin Institute of Technology, Harbin 150080, China
- The Biomedical Engineering Institute, Capital Medical University, Beijing 100054, China
| | - Wei Jiang
- The First Clinical College, Department of Bioinformatics, and the Bio-pharmaceutical Key Laboratory of Heilongjiang Province and State, Harbin Medical University, Harbin 150086, China
| | - Jianmin Huo
- The First Clinical College, Department of Bioinformatics, and the Bio-pharmaceutical Key Laboratory of Heilongjiang Province and State, Harbin Medical University, Harbin 150086, China
| | - Yadong Wang
- Department of Computer Science, Harbin Institute of Technology, Harbin 150080, China
| | - Meihua Lin
- The Biomedical Engineering Institute, Capital Medical University, Beijing 100054, China
- Department of Molecular Cardiology, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Shaoqi Rao
- The First Clinical College, Department of Bioinformatics, and the Bio-pharmaceutical Key Laboratory of Heilongjiang Province and State, Harbin Medical University, Harbin 150086, China
- The Biomedical Engineering Institute, Capital Medical University, Beijing 100054, China
- Department of Molecular Cardiology, Cleveland Clinic, Cleveland, OH 44195, USA
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Mattsson G, Tan SY, Ferguson DJP, Erber W, Turner SH, Marafioti T, Mason DY. Detection of genetic alterations by immunoFISH analysis of whole cells extracted from routine biopsy material. J Mol Diagn 2007; 9:479-89. [PMID: 17690217 PMCID: PMC1975102 DOI: 10.2353/jmoldx.2007.070041] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The detection of genetic abnormalities (eg, translocations, amplifications) in paraffin-embedded samples by the fluorescence in situ hybridization (FISH) technique is usually performed on tissue sections. FISH analysis of nuclei extracted from paraffin-embedded samples is also possible, but the technique is not widely used, principally because of the extra labor involved and the loss of information on tissue architecture. In this article, we report that nuclei extracted from paraffin-embedded tissue often retain at least part of the surrounding cytoplasm. Consequently, immunocytochemical labeling for a range of cellular markers (eg, of lineage or proliferation) can be performed in combination with FISH labeling, allowing specific cell populations to be analyzed for genetic abnormalities. These cell preparations are largely free of the problems associated with tissue sections (eg, truncation artifact, signals in different focal planes) so that interpretation is easy and numerical chromosomal abnormalities are readily assessed. Cells isolated from paraffin sections can be stored in suspension so that arrays can be created as and when needed from a range of neoplasms for investigation by the immunoFISH technique (for example, for studying a new genetic abnormality). This procedure represents a novel methodology, which in some settings offers clear advantages over analysis of tissue sections.
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Affiliation(s)
- Göran Mattsson
- Haematology Department, Level 4, John Radcliffe Hospital, Oxford OX3 9DU, UK
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Svec A. Expression of transmembrane adaptor protein PAG/Cbp in diffuse large B-cell lymphoma: immunohistochemical study of 73 cases. Pathol Res Pract 2007; 203:193-8. [PMID: 17382485 DOI: 10.1016/j.prp.2007.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Revised: 01/17/2007] [Accepted: 01/19/2007] [Indexed: 12/30/2022]
Abstract
PAG/Cbp is a transmembrane adaptor protein involved in proximal immune signaling. It is expressed in reactive germinal centers (GC) of secondary lymphatic follicles and related malignant lymphomas. We studied PAG/Cbp expression in GC-like and non-GC-like diffuse large B-cell lymphoma (DLBCL) subtypes. Seventy-three cases of DLBCL identified among 155 malignant lymphomas were classified as GC-like DLBCL (CD10+ or CD10-, bcl-6+, and MUM1-) and non-GC-like DLBCL (CD10-, MUM1+ or CD10-, bcl-6+, MUM1+). PAG/Cbp was detected by monoclonal antibody MEM-255 following routine immunohistochemical procedures. Thirty-five of 40 GC-like DLBCLs (88%) and 20 of 33 non-GC-like DLBCL cases (61%) expressed PAG/Cbp. Four of 12 bcl-6-negative non-GC-like DLBCL cases (33%) were PAG/Cbp positive, and only 4 of 20 bcl-6-positive non-GC-like DLBCL cases (25%) were PAG/CBP negative. All 37 FL and all 5 Burkitt's lymphomas (BL) expressed PAG/Cbp, whereas all 6 mantle cell lymphomas (MCL) and 4 of 5 chronic lymphocytic leukemias (CLL/SLL) were PAG/Cbp negative. PAG/Cbp is a reliable GC marker. Its expression correlates with GC-like DLBC phenotype in a significant majority of cases. It is typically absent in MCL and SLL/CLL.
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Affiliation(s)
- Alexandr Svec
- Department of Cellular Pathology, James Cook University Hospital, Middlesbrough TS4 3BW, UK.
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Natkunam Y, Zhao S, Mason DY, Chen J, Taidi B, Jones M, Hammer AS, Hamilton Dutoit S, Lossos IS, Levy R. The oncoprotein LMO2 is expressed in normal germinal-center B cells and in human B-cell lymphomas. Blood 2006; 109:1636-42. [PMID: 17038524 PMCID: PMC1794056 DOI: 10.1182/blood-2006-08-039024] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously developed a multivariate model based on the RNA expression of 6 genes (LMO2, BCL6, FN1, CCND2, SCYA3, and BCL2) that predicts survival in diffuse large B-cell lymphoma (DLBCL) patients. Since LMO2 emerged as the strongest predictor of superior outcome, we generated a monoclonal anti-LMO2 antibody in order to study its tissue expression pattern. Immunohistologic analysis of over 1200 normal and neoplastic tissue and cell lines showed that LMO2 protein is expressed as a nuclear marker in normal germinal-center (GC) B cells and GC-derived B-cell lines and in a subset of GC-derived B-cell lymphomas. LMO2 was also expressed in erythroid and myeloid precursors and in megakaryocytes and also in lymphoblastic and acute myeloid leukemias. It was rarely expressed in mature T, natural killer (NK), and plasma cell neoplasms and was absent from nonhematolymphoid tissues except for endothelial cells. Hierarchical cluster analysis of immunohistologic data in DLBCL demonstrated that the expression profile of the LMO2 protein was similar to that of other GC-associated proteins (HGAL, BCL6, and CD10) but different from that of non-GC proteins (MUM1/IRF4 and BCL2). Our results warrant inclusion of LMO2 in multivariate analyses to construct a clinically applicable immunohistologic algorithm for predicting survival in patients with DLBCL.
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Affiliation(s)
- Yasodha Natkunam
- Department of Pathology, Stanford University School of Medicine, CA, USA, and Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, Oxford, UK.
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