Generalizing about GC (hypoxia): Dys- & Dat-Informatica Comment on “Germinal center B cells selectively oxidize fatty acids for energy while conducting minimal glycolysis”

AbstractSteadily accumulating evidence supports the concept that the outputs of immune responses are influenced by local nutrient and metabolite conditions or concentrations, as well as by the molecular programming of intermediary metabolism within immune cells. Humoral immunity and germinal center reactions are one setting in which these factors are under active investigation. Hypoxia has been highlighted as one example of how a particular nutrient is distributed in primary and secondary follicles during an antibody response, and how its sensors could impact the qualities of antibody output after immunization. Based on a bio-informatic analysis of mRNA levels in germinal center and other B cells, recently published work challenges the concept that there is any hypoxia or that it has any influence. In this perspective, we perform new analyses of published genomics data to explore potential sources of disparity and elucidate aspects of what on the surface might seem to be conflicting conclusions. In particular, the replicability and variance among data sets derived from different naïve as well as germinal center B cells are considered. The results of the investigation highlight several broader issues that merit consideration, especially at a time of heightened focus on scientific reports in the realm of immunity and antibody responses. From one finding of this re-analysis, it is proposed that a standard should be expected in which the relationship of new data sets compared to prior “fingerprints” of cell types should be reported transparently to referees and readers. In light of the strong evidence for diversity in the constituencies within germinal centers elicited by protein immunization, it also is proposed that a core practice should be to avoid overly broad conclusions about germinal centers in general when experimental systems are subject to substantial constraints imposed by technical features.

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Over-Generalizing About GC (Hypoxia): Pitfalls of Limiting Breadth of Experimental Systems and Analyses in Framing Informatics Conclusions

Frontiers in Immunology ◽

10.3389/fimmu.2021.664249 ◽

2021 ◽

Vol 12 ◽

Author(s):

Mark R. Boothby ◽

Ariel Raybuck ◽

Sung Hoon Cho ◽

Kristy R. Stengel ◽

Volker H. Haase ◽

...

Keyword(s):

B Cells ◽

Cell Types ◽

Germinal Centers ◽

Nutrient Concentrations ◽

Data Sets ◽

Mrna Levels ◽

Independent Evidence ◽

Experimental Systems ◽

Protein Immunization ◽

Technical Features

Accumulating evidence suggests that many immune responses are influenced by local nutrient concentrations in addition to the programming of intermediary metabolism within immune cells. Humoral immunity and germinal centers (GC) are settings in which these factors are under active investigation. Hypoxia is an example of how a particular nutrient is distributed in lymphoid follicles during an antibody response, and how oxygen sensors may impact the qualities of antibody output after immunization. Using exclusively a bio-informatic analysis of mRNA levels in GC and other B cells, recent work challenged the concept that there is any hypoxia or that it has any influence. To explore this proposition, we performed new analyses of published genomics data, explored potential sources of disparity, and elucidated aspects of the apparently conflicting conclusions. Specifically, replicability and variance among data sets derived from different naïve as well as GC B cells were considered. The results highlight broader issues that merit consideration, especially at a time of heightened focus on scientific reports in the realm of immunity and antibody responses. Based on these analyses, a standard is proposed under which the relationship of new data sets should be compared to prior “fingerprints” of cell types and reported transparently to referees and readers. In light of independent evidence of diversity within and among GC elicited by protein immunization, avoidance of overly broad conclusions about germinal centers in general when experimental systems are subject to substantial constraints imposed by technical features also is warranted.

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miRNA Profiling of B Cell Subsets: Specific miRNA Profile for Germinal Center B Cells with a Marked Variation Between Centroblast and Centrocytes.

Blood ◽

10.1182/blood.v112.11.1459.1459 ◽

2008 ◽

Vol 112 (11) ◽

pp. 1459-1459

Author(s):

Lu Ping Tan ◽

Miao Wang ◽

Jan-Lukas Robertus ◽

Rikst Nynke Schakel ◽

Johan H Gibcus ◽

...

Keyword(s):

B Cells ◽

B Cell ◽

Germinal Center ◽

Germinal Centers ◽

Memory B Cells ◽

Mirna Profile ◽

Mantle Zone ◽

Tissue Sections ◽

Germinal Center B Cell ◽

Germinal Center B Cells

Abstract MiRNAs are a new class of small RNAs, of 19–23 nucleotides that were discovered less than two decades ago. These tiny RNAs can negatively regulate genes at the post-transcriptional level by either triggering translational repression or direct cleavage of mRNAs. It has become evident that miRNAs are involved in hematopoiesis and that the aberrant expression of miRNAs may give rise to hematopoietic malignancies. The aim of our study was to characterize the miRNA profile of naïve, germinal center and memory B cells sorted from tonsils and review expression of selected miRNAs in tonsils and in B cell malignancies by miRNA in situ hybridization (ISH). Quantitative (q)RT-PCR profiling revealed that several miRNAs were elevated in germinal center B cells, including miR-17–5p, miR-106a and miR-181b. miR-150 was one of the most abundant miRNAs in all subsets, but the expression level was more than 10 fold lower in germinal center B cell as compared to the other two subsets. MiRNA ISH on tonsillar tissue sections confirmed findings from the profiling work, and at the same time depicted differences in staining intensities within germinal centers. According to miRNA ISH, expression levels of miR-17-5p, miR-106a, and miR-181b were indeed higher in germinal center B cells as compared to naïve and memory B cells in the mantle zone. Surprisingly, we also observed gradual decrease of miR-17-5p, miR-106a, and miR-181b staining from dark to light zone in the germinal centers. Moreover, miRNA ISH with a probe for miR-150 demonstrated an interesting staining pattern in lymph node tissue sections. Naïve and memory B cells located in the mantle zone showed a higher miR-150 expression as compared to most of the cells in the germinal centers. However, within the germinal centers a minority of cells showed a much stronger cytoplasmic staining in part of the blasts located specifically in the dark zone. This indicated that part of the centroblasts have a high expression level of miR-150. The level of miR-150 was surprisingly low in 22 B cell lymphoma cell lines, irrespective of germinal center or non germinal center B cell origin. This seemingly negative association of miR-150 with proliferation suggests a role in B cell growth/death. We observed an inverse expression pattern of miR-150 and Survivin in the germinal centers by miRNA ISH and immunohistochemistry. Moreover, induction of miR-150 using synthetic mature miR-150 duplex resulted in reduced Survivin expression levels. Our results suggested that aside the experimentally proven target c-Myb, Survivin may also be regulated by miR-150. In conclusion, we have revealed a unique miRNA profile of naïve, germinal center and memory B cells sorted from normal tonsils and the results were confirmed by miRNA ISH. Within the germinal centers a marked difference was observed between the light zone and the dark zone.

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In situ studies of the primary immune response to (4-hydroxy-3-nitrophenyl)acetyl. III. The kinetics of V region mutation and selection in germinal center B cells.

Journal of Experimental Medicine ◽

10.1084/jem.178.4.1293 ◽

1993 ◽

Vol 178 (4) ◽

pp. 1293-1307 ◽

Cited By ~ 254

Author(s):

J Jacob ◽

J Przylepa ◽

C Miller ◽

G Kelsoe

Keyword(s):

B Cells ◽

Germinal Center ◽

Somatic Hypermutation ◽

Point Mutations ◽

Variable Region ◽

Germinal Centers ◽

Primary Immune Response ◽

Kinetics Of ◽

Mutation And Selection ◽

Germinal Center B Cells

In the murine spleen, germinal centers are the anatomic sites for antigen-driven hypermutation and selection of immunoglobulin (Ig) genes. To detail the kinetics of Ig mutation and selection, 178 VDJ sequences from 16 antigen-induced germinal centers were analyzed. Although germinal centers appeared by day 4, mutation was not observed in germinal center B cells until day 8 postimmunization; thereafter, point mutations favoring asymmetrical transversions accumulated until day 14. During this period, strong phenotypic selection on the mutant B lymphocytes was inferred from progressively biased distributions of mutations within the Ig variable region, the loss of crippling mutations, decreased relative clonal diversity, and increasingly restricted use of canonical gene segments. The period of most intense selection on germinal center B cell populations preceded significant levels of mutation and may represent a physiologically determined restriction on B cells permitted to enter the memory pathway. Noncanonical Ig genes recovered from germinal centers were mostly unmutated although they probably came from antigen-reactive cells. Together, these observations demonstrate that the germinal center microenvironment is rich and temporally complex but may not be constitutive for somatic hypermutation.

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Histone deacetylase 3 controls a transcriptional network required for B cell maturation

Nucleic Acids Research ◽

10.1093/nar/gkz816 ◽

2019 ◽

Vol 47 (20) ◽

pp. 10612-10627 ◽

Cited By ~ 1

Author(s):

Kristy R Stengel ◽

Srividya Bhaskara ◽

Jing Wang ◽

Qi Liu ◽

Jacob D Ellis ◽

...

Keyword(s):

B Cells ◽

B Cell ◽

Histone Deacetylase ◽

Germinal Center ◽

Hdac Inhibitors ◽

Germinal Centers ◽

Cell Of Origin ◽

Histone Deacetylase 3 ◽

Germinal Center B Cells

Abstract Histone deacetylase 3 (Hdac3) is a target of the FDA approved HDAC inhibitors, which are used for the treatment of lymphoid malignancies. Here, we used Cd19-Cre to conditionally delete Hdac3 to define its role in germinal center B cells, which represent the cell of origin for many B cell malignancies. Cd19-Cre-Hdac3−/− mice showed impaired germinal center formation along with a defect in plasmablast production. Analysis of Hdac3−/− germinal centers revealed a reduction in dark zone centroblasts and accumulation of light zone centrocytes. RNA-seq revealed a significant correlation between genes up-regulated upon Hdac3 loss and those up-regulated in Foxo1-deleted germinal center B cells, even though Foxo1 typically activates transcription. Therefore, to determine whether gene expression changes observed in Hdac3−/− germinal centers were a result of direct effects of Hdac3 deacetylase activity, we used an HDAC3 selective inhibitor and examined nascent transcription in germinal center-derived cell lines. Transcriptional changes upon HDAC3 inhibition were enriched for light zone gene signatures as observed in germinal centers. Further comparison of PRO-seq data with ChIP-seq/exo data for BCL6, SMRT, FOXO1 and H3K27ac identified direct targets of HDAC3 function including CD86, CD83 and CXCR5 that are likely responsible for driving the light zone phenotype observed in vivo.

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Germinal Center Marker GL7 Probes Activation-Dependent Repression of N-Glycolylneuraminic Acid, a Sialic Acid Species Involved in the Negative Modulation of B-Cell Activation

Molecular and Cellular Biology ◽

10.1128/mcb.02047-06 ◽

2007 ◽

Vol 27 (8) ◽

pp. 3008-3022 ◽

Cited By ~ 120

Author(s):

Yuko Naito ◽

Hiromu Takematsu ◽

Susumu Koyama ◽

Shizu Miyake ◽

Harumi Yamamoto ◽

...

Keyword(s):

Sialic Acid ◽

T Cell ◽

B Cells ◽

B Cell ◽

Germinal Center ◽

Cell Activation ◽

Germinal Centers ◽

Negative Regulator ◽

B Cell Activation ◽

Germinal Center B Cells

ABSTRACT Sialic acid (Sia) is a family of acidic nine-carbon sugars that occupies the nonreducing terminus of glycan chains. Diversity of Sia is achieved by variation in the linkage to the underlying sugar and modification of the Sia molecule. Here we identified Sia-dependent epitope specificity for GL7, a rat monoclonal antibody, to probe germinal centers upon T cell-dependent immunity. GL7 recognizes sialylated glycan(s), the α2,6-linked N-acetylneuraminic acid (Neu5Ac) on a lactosamine glycan chain(s), in both Sia modification- and Sia linkage-dependent manners. In mouse germinal center B cells, the expression of the GL7 epitope was upregulated due to the in situ repression of CMP-Neu5Ac hydroxylase (Cmah), the enzyme responsible for Sia modification of Neu5Ac to Neu5Gc. Such Cmah repression caused activation-dependent dynamic reduction of CD22 ligand expression without losing α2,6-linked sialylation in germinal centers. The in vivo function of Cmah was analyzed using gene-disrupted mice. Phenotypic analyses showed that Neu5Gc glycan functions as a negative regulator for B-cell activation in assays of T-cell-independent immunization response and splenic B-cell proliferation. Thus, Neu5Gc is required for optimal negative regulation, and the reaction is specifically suppressed in activated B cells, i.e., germinal center B cells.

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Human t(14;18)positive germinal center B cells: a new step in follicular lymphoma pathogenesis?

Blood ◽

10.1182/blood-2013-12-545954 ◽

2014 ◽

Vol 123 (22) ◽

pp. 3462-3465 ◽

Cited By ~ 31

Author(s):

Julie Tellier ◽

Cedric Menard ◽

Sandrine Roulland ◽

Nadine Martin ◽

Céline Monvoisin ◽

...

Keyword(s):

B Cells ◽

Follicular Lymphoma ◽

Germinal Center ◽

Germinal Centers ◽

Lymphoid Tissues ◽

Healthy Individuals ◽

Key Points ◽

Germinal Center B Cells

Key Points Follicular lymphoma-like cells found in healthy individuals accumulate within germinal centers in reactive lymphoid tissues. Follicular lymphoma-like cells are nonproliferating cells in situ and in vitro.

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