NF-kappaB is dispensable for normal lymphocyte development in bone marrow but required for protection of progenitors from TNFalpha

Improving data interpretability with new differential sample variance gene set tests

BACKGROUND

Gene set analysis methods have played a major role in generating biological interpretations of omics data such as gene expression datasets. However, most methods focus on detecting homogenous pattern changes in mean expression while methods detecting pattern changes in variance remain poorly explored. While a few studies attempted to use gene-level variance analysis, such approach remains under-utilized. When comparing two phenotypes, gene sets with distinct changes in subgroups under one phenotype are overlooked by available methods although they reflect meaningful biological differences between two phenotypes. Multivariate sample-level variance analysis methods are needed to detect such pattern changes.

RESULTS

We used ranking schemes based on minimum spanning tree to generalize the Cramer-Von Mises and Anderson-Darling univariate statistics into multivariate gene set analysis methods to detect differential sample variance or mean. We characterized the detection power and Type I error rate of these methods in addition to two methods developed earlier using simulation results with different parameters. We applied the developed methods to microarray gene expression dataset of prednisolone-resistant and prednisolone-sensitive children diagnosed with B-lineage acute lymphoblastic leukemia and bulk RNA-sequencing gene expression dataset of benign hyperplastic polyps and potentially malignant sessile serrated adenoma/polyps. One or both of the two compared phenotypes in each of these datasets have distinct molecular subtypes that contribute to within phenotype variability and to heterogeneous differences between two compared phenotypes. Our results show that methods designed to detect differential sample variance provide meaningful biological interpretations by detecting specific hallmark gene sets associated with the two compared phenotypes as documented in available literature.

CONCLUSIONS

The results of this study demonstrate the usefulness of methods designed to detect differential sample variance in providing biological interpretations when biologically relevant but heterogeneous changes between two phenotypes are prevalent in specific signaling pathways. Software implementation of the methods is available with detailed documentation from Bioconductor package GSAR. The available methods are applicable to gene expression datasets in a normalized matrix form and could be used with other omics datasets in a normalized matrix form with available collection of feature sets.

Improving data interpretability with new differential sample variance gene set tests

Background

Gene set analysis methods have played a major role in generating biological interpretations from omics data such as gene expression datasets. However, most methods focus on detecting homogenous pattern changes in mean expression and methods detecting pattern changes in variance remain poorly explored. While a few studies attempted to use gene-level variance analysis, such approach remains under-utilized. When comparing two phenotypes, gene sets with distinct changes in subgroups under one phenotype are overlooked by available methods although they reflect meaningful biological differences between two phenotypes. Multivariate sample-level variance analysis methods are needed to detect such pattern changes.

Results

We use ranking schemes based on minimum spanning tree to generalize the Cramer-Von Mises and Anderson-Darling univariate statistics into multivariate gene set analysis methods to detect differential sample variance or mean. We characterize these methods in addition to two methods developed earlier using simulation results with different parameters. We apply the developed methods to microarray gene expression dataset of prednisolone-resistant and prednisolone-sensitive children diagnosed with B-lineage acute lymphoblastic leukemia and bulk RNA-sequencing gene expression dataset of benign hyperplastic polyps and potentially malignant sessile serrated adenoma/polyps. One or both of the two compared phenotypes in each of these datasets have distinct molecular subtypes that contribute to heterogeneous differences. Our results show that methods designed to detect differential sample variance are able to detect specific hallmark signaling pathways associated with the two compared phenotypes as documented in available literature.

Conclusions

The results in this study demonstrate the usefulness of methods designed to detect differential sample variance in providing biological interpretations when biologically relevant but heterogeneous changes between two phenotypes are prevalent in specific signaling pathways. Software implementation of the developed methods is available with detailed documentation from Bioconductor package GSAR. The available methods are applicable to gene expression datasets in a normalized matrix form and could be used with other omics datasets in a normalized matrix form with available collection of feature sets.

The Complex Interplay between DNA Injury and Repair in Enzymatically Induced Mutagenesis and DNA Damage in B Lymphocytes

Lymphocytes are endowed with unique and specialized enzymatic mutagenic properties that allow them to diversify their antigen receptors, which are crucial sensors for pathogens and mediators of adaptive immunity. During lymphocyte development, the antigen receptors expressed by B and T lymphocytes are assembled in an antigen-independent fashion by ordered variable gene segment recombinations (V(D)J recombination), which is a highly ordered and regulated process that requires the recombination activating gene products 1 & 2 (RAG1, RAG2). Upon activation by antigen, B lymphocytes undergo additional diversifications of their immunoglobulin B-cell receptors. Enzymatically induced somatic hypermutation (SHM) and immunoglobulin class switch recombination (CSR) improves the affinity for antigen and shape the effector function of the humoral immune response, respectively. The activation-induced cytidine deaminase (AID) enzyme is crucial for both SHM and CSR. These processes have evolved to both utilize as well as evade different DNA repair and DNA damage response pathways. The delicate balance between enzymatic mutagenesis and DNA repair is crucial for effective immune responses and the maintenance of genomic integrity. Not surprisingly, disturbances in this balance are at the basis of lymphoid malignancies by provoking the formation of oncogenic mutations and chromosomal aberrations. In this review, we discuss recent mechanistic insight into the regulation of RAG1/2 and AID expression and activity in lymphocytes and the complex interplay between these mutagenic enzymes and DNA repair and DNA damage response pathways, focusing on the base excision repair and mismatch repair pathways. We discuss how disturbances of this interplay induce genomic instability and contribute to oncogenesis.

Inhibition of tumor necrosis factor-α enhances apoptosis induced by nuclear factor-κB inhibition in leukemia cells

Inhibition of nuclear factor-κB (NF-κB) results in antitumor activity in leukemia cells, and may be a potential therapeutic strategy for the treatment of leukemia. However, a significant limitation of NF-κB inhibition in the treatment of leukemia is the low efficiency of this technique. NF-κB inhibitor treatment induces apoptosis in leukemia cells; however, it additionally causes inflammatory molecules to induce increased sensitivity of healthy hematopoietic cells to cell death signals, therefore limiting its clinical applications. Tumor necrosis factor-α (TNF-α) is a key regulator of inflammation, and induces a variety of actions in leukemic and healthy hematopoietic cells. TNF-α induces NF-κB-dependent and -independent survival signals, promoting the proliferation of leukemia cells. However, in healthy hematopoietic cells, TNF-α induces death signaling, an effect which is enhanced by the inhibition of NF-κB. Based on these observations, the present study hypothesized that inhibition of TNF-α signaling may be able to protect healthy hematopoietic cells and other tissue cells, while increasing the anti-leukemia effects of NF-κB inhibition on leukemia cells. The role and underlying molecular mechanisms of TNF-α inhibition in the regulation of NF-κB inhibition-induced apoptosis in leukemia cells was therefore investigated in the present study. The results indicated that inhibition of TNF-α enhanced NF-κB inhibition-induced apoptosis in leukemia cells. It was also revealed that protein kinase B was significant in the regulation of TNF-α and NF-κB inhibition-induced apoptosis. During this process, intrinsic apoptotic pathways were activated. A combination of NF-κB and TNF-α inhibition may be a potential specific and effective novel therapeutic strategy for the treatment of leukemia.

NF-κB and AKT signaling prevent DNA damage in transformed pre-B cells by suppressing RAG1/2 expression and activity

In developing lymphocytes, expression and activity of the recombination activation gene protein 1 (RAG1) and RAG2 endonuclease complex is tightly regulated to ensure ordered recombination of the immunoglobulin genes and to avoid genomic instability. Aberrant RAG activity has been implicated in the generation of secondary genetic events in human B-cell acute lymphoblastic leukemias (B-ALLs), illustrating the oncogenic potential of the RAG complex. Several layers of regulation prevent collateral genomic DNA damage by restricting RAG activity to the G1 phase of the cell cycle. In this study, we show a novel pathway that suppresses RAG expression in cycling-transformed mouse pre-B cells and human pre-B B-ALL cells that involves the negative regulation of FOXO1 by nuclear factor κB (NF-κB). Inhibition of NF-κB in cycling pre-B cells resulted in upregulation of RAG expression and recombination activity, which provoked RAG-dependent DNA damage. In agreement, we observe a negative correlation between NF-κB activity and the expression of RAG1, RAG2, and TdT in B-ALL patients. Our data suggest that targeting NF-κB in B-ALL increases the risk of RAG-dependent genomic instability.

Acute disruption of bone marrow hematopoiesis by benzo(a)pyrene is selectively reversed by aryl hydrocarbon receptor-mediated processes

Bone marrow (BM) hematopoietic cells are selectively sensitive to polycyclic aromatic hydrocarbons (PAH) in vivo. 7,12-Dimethylbenz(a)anthracene (DMBA), but not benzo(a)pyrene (BP), depletes BM hematopoietic cells in C57BL/6 mice. This difference is due to a BP-selective aryl hydrocarbon receptor (AhR)-mediated recovery. Colony-forming unit assays show suppression of lymphoid progenitors by each PAH within 6 h but a subsequent recovery, exclusively after BP treatment. Suppression of myeloid progenitors (6 h) occurs only for DMBA. Each progenitor responded equally to DMBA and BP in congenic mice expressing the PAH-resistant AhR (AhR(d)). AhR, therefore, mediates this BP recovery in each progenitor type. These PAH suppressions depend on Cyp1b1-mediated metabolism. Paradoxically, few genes responded to DMBA, whereas 12 times more responded to BP. Progenitor suppression by DMBA, therefore, occurs with minimal effects on the general BM population. Standard AhR-mediated stimulations (Cyp1a1, Cyp1b1, Ahrr) were similar for each PAH and for the specific agonist 2,3,7,8-tetrachlorodibenzo-p-dioxin but were absent in AhR(d) mice. A group of 12 such AhR responses was sustained from 6 to 24 h. A second, larger set of BP responses (chemokines, cytokines, cyclooxygenase 2) differed in two respects; DMBA responses were low and BP responses declined extensively from 6 to 24 h. A third cluster exhibited BP-induced increases in protective genes (Nqo1, GST-mu) that appeared only after 12 h. Conversion of BP to quinones contributes oxidative signaling not seen with DMBA. We propose that genes in this second cluster, which share oxidative signaling and AhR activation, provide the AhR-dependent protection of hematopoietic progenitors seen for BP.

Opposing putative roles for canonical and noncanonical NFκB signaling on the survival, proliferation, and differentiation potential of human embryonic stem cells

The canonical and noncanonical NFκB signaling pathways regulate a variety of cellular activities; however, their functions in human embryonic stem cells (hESCs) have not been fully investigated. Expression studies during hESC differentiation indicated a significant increase in the expression of two key components of the canonical NFκB pathway (p50 and Ser529 phosphorylated form of p65) as well as a significant reduction in expression of key components of the noncanonical NFκB pathway [v-rel reticuloendotheliosis viral oncogene homolog B (RELB), p52, NIK]. Inhibition of canonical NFκB resulted in hESC apoptosis, changes in cell cycle distribution, and reduced hESC proliferation. In addition, inhibition of canonical NFκB was associated with significant changes in NANOG and OCT4 expression, suppression of differentiation toward all primitive extraembryonic and embryonic lineages with the exception of primitive ectoderm and ectodermal lineages. Inhibition of noncanonical NFκB via small interfering RNA-mediated downregulation of RELB resulted in reduced hESC proliferation and opposite changes to expression of key differentiation lineage markers genes when compared with downregulation of canonical NF-κB. Chromatin immunoprecipitation assays indicated binding of p65 and RELB to regulatory regions of key differentiation marker genes suggesting a direct transcriptional role for both branches of this pathway in hESC. These findings coupled with opposing trends in expression of key components during hESC differentiation, suggests a fine and opposing balance between the two branches of NFκB signaling pathways and their involvement in two distinct processes: the canonical pathway regulating hESC differentiation and the noncanonical pathway maintaining hESC pluripotency.

Bone marrow lymphoid and myeloid progenitor cells are suppressed in 7,12-dimethylbenz(a)anthracene (DMBA) treated mice

In this study we used colony forming unit (CFU) assays to demonstrate rapid suppression (within 6h) of lymphoid (CFU-preB) and myeloid (CFU-GM) progenitor cells in DMBA-treated mice. The duration of these changes were consistent with the blood levels of DMBA and its metabolites that were achieved by either IP or oral DMBA administration. CFU-GM and CFU-preB activities returned to control levels by 2 and 7 days after oral DMBA exposure, respectively, but remained suppressed through 7 days after IP DMBA administration. The continued presence of low levels of DMBA in the bloodstream following IP administration was associated with sustained suppression of CFU-preB, total bone marrow lymphoid cells and peripheral blood lymphocytes. The changes noted above were not observed in Cyp1b1 null mice, demonstrating the need for local DMBA metabolism in the bone marrow by Cyp1b1 to impair bone marrow CFU-preB and CFU-GM. Furthermore, these data provide evidence that myeloid-lineage cells are restored more quickly than lymphoid-lineage cells after DMBA exposure.

Roles of the NF-kappaB pathway in lymphocyte development and function

This article focuses on the functions of NF-kappaB that vitally impact lymphocytes and thus adaptive immunity. NF-kappaB has long been known to be essential for many of the responses of mature lymphocytes to invading pathogens. In addition, NF-kappaB has important functions in shaping the immune system so it is able to generate adaptive responses to pathogens. In both contexts, NF-kappaB executes critical cell-autonomous functions within lymphocytes as well as within supportive cells, such as antigen-presenting cells or epithelial cells. It is these aspects of NF-kappaB's physiologic impact that we address in this article.

NF-kappaB activity marks cells engaged in receptor editing

Because of the extreme diversity in immunoglobulin genes, tolerance mechanisms are necessary to ensure that B cells do not respond to self-antigens. One such tolerance mechanism is called receptor editing. If the B cell receptor (BCR) on an immature B cell recognizes self-antigen, it is down-regulated from the cell surface, and light chain gene rearrangement continues in an attempt to edit the autoreactive specificity. Analysis of a heterozygous mutant mouse in which the NF-κB–dependent IκBα gene was replaced with a lacZ (β-gal) reporter complementary DNA (cDNA; IκBα^+/lacZ) suggests a potential role for NF-κB in receptor editing. Sorted β-gal⁺ pre–B cells showed increased levels of various markers of receptor editing. In IκBα^+/lacZ reporter mice expressing either innocuous or self-specific knocked in BCRs, β-gal was preferentially expressed in pre–B cells from the mice with self-specific BCRs. Retroviral-mediated expression of a cDNA encoding an IκBα superrepressor in primary bone marrow cultures resulted in diminished germline κ and rearranged λ transcripts but similar levels of RAG expression as compared with controls. We found that IRF4 transcripts were up-regulated in β-gal⁺ pre–B cells. Because IRF4 is a target of NF-κB and is required for receptor editing, we suggest that NF-κB could be acting through IRF4 to regulate receptor editing.

Cell-autonomous role for NF-kappa B in immature bone marrow B cells

The NF-kappaB transcription factors have many essential functions in B cells, such as during differentiation and proliferation of Ag-challenged mature B cells, but also during final maturation of developing B cells in the spleen. Among the various specific functions NF-kappaB factors carry out in these biologic contexts, their ability to assure the survival of mature and maturing B cells in the periphery stands out. Less clear is what if any roles NF-kappaB factors play during earlier stages of B cell development in the bone marrow. Using mice deficient in both NF-kappaB1 and NF-kappaB2, which are thus partially compromised in both the classical and alternative activation pathways, we demonstrate a B cell-autonomous contribution of NF-kappaB to the survival of immature B cells in the bone marrow. NF-kappaB1 and NF-kappaB2 also play a role during the earlier transition from proB to late preB cells; however, in this context these factors do not act in a B cell-autonomous fashion. Although NF-kappaB1 and NF-kappaB2 are not absolutely required for survival and progression of immature B cells in the bone marrow, they nevertheless make a significant contribution that marks the beginning of the profound cell-autonomous control these factors exert during all subsequent stages of B cell development. Therefore, the lifelong dependency of B cells on NF-kappaB-mediated survival functions is set in motion at the time of first expression of a full BCR.

Cell penetrating peptide inhibitors of nuclear factor-kappa B

The nuclear factor kappa B (NF-kappaB) transcription factors are activated by a range of stimuli including pro-inflammatory cytokines. Active NF-kappaB regulates the expression of genes involved in inflammation and cell survival and aberrant NF-kappaB activity plays pathological roles in certain types of cancer and diseases characterized by chronic inflammation. NF-kappaB signaling is an attractive target for the development of novel anti-inflammatory or anti-cancer drugs and we discuss here how the method of peptide transduction has been used to specifically target NF-kappaB. Peptide transduction relies on the ability of certain small cell-penetrating peptides (CPPs) to enter cells, and a panel of CPP-linked inhibitors (CPP-Is) has been developed to directly inhibit NF-kappaB signaling. Remarkably, several of these NF-kappaB-targeting CPP-Is are effective in vivo and therefore offer exciting potential in the clinical setting.

Lack of nuclear factor-kappa B2/p100 causes a RelB-dependent block in early B lymphopoiesis

Nuclear factor-kappaB (NF-kappaB) transcription factors regulate B-cell development and survival. However, whether they also have a role during early steps of B-cell differentiation is largely unclear. Here, we show that constitutive activation of the alternative NF-kappaB pathway in p100(-/-) knockin mice resulted in a block of early B-cell development at the transition from the pre-pro-B to the pro-B-cell stage due to enhanced RelB activity. Expression of the essential B-cell transcription factors EBF and in particular Pax5 was reduced in p100(-/-) B-cell precursors in a RelB-dependent manner, resulting in reduced mRNA levels of B lineage-specific genes. Moreover, enhanced RelB function in p100(-/-) B-cell precursors was accompanied by increased expression of B lineage-inappropriate genes, such as C/EBP alpha, correlating with a markedly increased myeloid differentiation potential of p100(-/-) progenitor B cells. Ectopic expression of Pax5 in hematopoietic progenitors restored early B-cell development in p100(-/-) bone marrow, suggesting that impaired early B lymphopoiesis in mice lacking the p100 inhibitor may be due to down-regulation of Pax5 expression. Thus, tightly controlled p100 processing and RelB activation is essential for normal B lymphopoiesis and lymphoid/myeloid lineage decision in bone marrow.