Identification of two lymphotoxin beta isoforms expressed in human lymphoid cell lines and non-Hodgkin's lymphomas

Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan

Accumulation of mutations in somatic cells has been implicated as a cause of aging since the 1950s. However, attempts to establish a causal relationship between somatic mutations and aging have been constrained by the lack of methods to directly identify mutational events in primary human tissues. Here we provide genome-wide mutation frequencies and spectra of human B lymphocytes from healthy individuals across the entire human lifespan using a highly accurate single-cell whole-genome sequencing method. We found that the number of somatic mutations increases from <500 per cell in newborns to >3,000 per cell in centenarians. We discovered mutational hotspot regions, some of which, as expected, were located at Ig genes associated with somatic hypermutation (SHM). B cell-specific mutation signatures associated with development, aging, or SHM were found. The SHM signature strongly correlated with the signature found in human B cell tumors, indicating that potential cancer-causing events are already present even in B cells of healthy individuals. We also identified multiple mutations in sequence features relevant to cellular function (i.e., transcribed genes and gene regulatory regions). Such mutations increased significantly during aging, but only at approximately one-half the rate of the genome average, indicating selection against mutations that impact B cell function. This full characterization of the landscape of somatic mutations in human B lymphocytes indicates that spontaneous somatic mutations accumulating with age can be deleterious and may contribute to both the increased risk for leukemia and the functional decline of B lymphocytes in the elderly.

Recurrent targets of aberrant somatic hypermutation in lymphoma

Somatic hypermutation (SHM) in the variable region of immunoglobulin genes (IGV) naturally occurs in a narrow window of B cell development to provide high-affinity antibodies. However, SHM can also aberrantly target proto-oncogenes and cause genome instability. The role of aberrant SHM (aSHM) has been widely studied in various non-Hodgkin's lymphoma particularly in diffuse large B-cell lymphoma (DLBCL). Although, it has been speculated that aSHM targets a wide range of genome loci so far only twelve genes have been identified as targets of aSHM through the targeted sequencing of selected genes. A genome-wide study aiming at identifying a comprehensive set of aSHM targets recurrently occurring in DLBCL has not been previously undertaken. Here, we present a comprehensive assessment of the somatic hypermutated genes in DLBCL identified through an analysis of genomic and transcriptome data derived from 40 DLBCL patients. Our analysis verifies that there are indeed many genes that are recurrently affected by aSHM. In particular, we have identified 32 novel targets that show same or higher level of aSHM activity than genes previously reported. Amongst these novel targets, 22 genes showed a significant correlation between mRNA abundance and aSHM.

The multifaceted character of lymphotoxin β in inflammatory myopathies and muscular dystrophies

Lymphotoxin beta (LTβ) regulates some inflammatory mechanisms that could be operative in idiopathic inflammatory myopathies (IM). We studied LTβ and LTβR in inflammatory myopathies, normal and disease controls with immunohistochemistry, Western blotting and in situ hybridisation. LTβ occurs in myonuclei of normal controls, implying its role in normal muscle physiology. LTβ is strongly upregulated in regenerating muscle fibres in all myopathies, but not in denervated myofibres. Normal-appearing myofibres in inflammatory myopathies and muscular dystrophies express LTβ possibly reflecting early myofibre damage, representing a hitherto undescribed pathologic hallmark. Furthermore, we visualised LTβ in several inflammatory cell types in inflammatory myopathies, suggesting its involvement in the different inflammatory mechanisms underlying inflammatory myopathy subgroups.

Identification and expression analysis of lymphotoxin-beta like homologues in rainbow trout Oncorhynchus mykiss

A lymphotoxin-beta (LT-beta) gene has been cloned and sequenced in rainbow trout and provides the first conclusive evidence for the existence of LT-beta in teleost. Two isoforms of LT-beta were isolated. LT-beta1 cDNA was composed of 952 bp (with a 139 bp 5'-UTR and a 201 bp 3'-UTR) and LT-beta2 cDNA was 836 bp (with a 237 bp 5'-UTR and a 197 bp 3'-UTR) both of which translated into a protein of 203 amino acid residues. Both isoforms contained a predicted transmembrane domain of 21 amino acid residues (Leu11-Val31) and the TNF family signature (Val104-Phe120). Homology and phylogenetic analysis of trout LT-beta's with other known TNF family member showed good similarity to TNF-N (teleost) and other LT-beta (mammals and frog). LT-beta1 and TNF-alpha (1 and 2) genes were highly expressed in unstimulated trout head kidney, spleen, gill and intestine, whereas LT-beta2 was weakly expressed only in the gill. The expression of LT-beta1 and -beta2 genes was not found in macrophage (RTS-11) and fibroblast (RTG-2) like cell lines, although the TNF-alpha2 gene was expressed in both cell lines with the TNF-alpha1 gene only expressed in RTS-11 cells. In head kidney cells, expression of LT-beta1 and TNF-alpha (1, 2) genes was increased by stimulation with PHA or LPS. The discovery of trout LT-beta will allow a more complete analysis of fish inflammatory responses.

MCP-1 modulates chemotaxis by follicular lymphoma cells

The localization and establishment of follicular lymphoma (FL) cells in distinct anatomic sites probably involves chemokine and adhesion receptors on the neoplastic cells and appropriate chemokines and adhesion receptor ligands in the microenvironment. Several chemokines play an important role in normal B-cell trafficking and differentiation. Monocyte chemoattractant protein-1 (MCP-1) is a C-C chemokine that induces chemotaxis of a variety of lymphoid cells through its receptor CCR2. CCR2 is also expressed on B cells, and MCP-1 induces chemotaxis of normal B cells. In this report, we investigated expression and function of CCR2 on FL cells. We found FL cells as well as the t(14; 18)+ B-cell lymphoma line H2 expressed CCR2. MCP-1 potentiated SDF-1-induced chemotaxis of FL cells and H2 cells, but MCP-1 alone did not induce chemotaxis. The specificity of the effects of MCP-1 and SDF-1 was demonstrated by antibody blocking studies. Because FL cells are generally associated with follicular dendritic cells (FDCs), FDCs may be an important source of chemokines. We found that cultured FDCs produced MCP-1, and this production was enhanced by tumour necrosis factor. These data implicate MCP-1 in the migration and localization of FL cells.

Functional effects of TNF and lymphotoxin alpha1beta2 on FDC-like cells

Recent studies suggest that tumor necrosis factor (TNF) family members such as TNFalpha and lymphotoxin alphabeta (LTalpha1beta2) are important in the development of follicular dendritic cells (FDCs) and maintenance of FDC function. In this study we used FDC-like cells (FDC-LC) cultured from normal human tonsil and investigated the effects of TNF and LTalpha1beta2 on expression of adhesion molecules and the production of cytokines and chemokines. TNF and LTalpha1beta2 both increased the expression of VCAM-1 and ICAM-1 on FDC-LC. In addition, IL-4 with LTalpha1beta2 synergistically increased the expression of VCAM-1, but not ICAM-1. Cytokine IL-6 and IL-15 mRNAs were induced following stimulation with TNF and LTalpha1beta2. These two cytokines were present in FDC-LC supernatants by ELISA and increased following TNF and LTalpha1beta2 stimulation. We also examined FDC-LC for chemokines, which affect B cells, including IL-8, SDF-1, MIP3beta/ELC, and BCA-1/BLC. SDF-1 mRNA and protein were expressed by FDC-LC, and following stimulation with TNF and LTalpha1beta2, decreases in both were observed. Therefore, TNF and LTalpha1beta2, which are produced by activated B cells, increased the expression of adhesion molecules and cytokines from FDC-LC, potentially providing key signals to support germinal center B cell survival and differentiation.

CD40 regulation of death domains containing receptors and their ligands on lymphoma B cells

Within the tumour necrosis factor (TNF) family the induction of apoptosis is restricted to some ligand-receptors pairs, including TNF-TNF receptor type I (TNFRI/p55), FasL-Fas, TNF-related apoptosis-inducing ligand (TRAIL) and its death-receptors (DR)-4 and -5. The pair CD40L-CD40 belongs to the same family but rescues B cells from apoptosis. To investigate how these opposing actions are cross-linked, purified follicular lymphoma (FL) cells were activated upon a human CD40L-transfected murine fibroblastic layer, then RNA messengers for the above molecules were analysed using RT-PCR. The observed down-modulation of TRAIL and up-regulation of TNF and Fas transcripts might account for CD40-CD40L-mediated FL cell survival.

A new death receptor 3 isoform: expression in human lymphoid cell lines and non-Hodgkin's lymphomas

Two isoforms encoding the full-length transmembrane death receptor 3 (DR3) were isolated from mRNAs of a panel of human cell lines and tumor tissues obtained from patients with follicular non-Hodgkin's lymphoma. A new DR3 variant (DR3 beta) was characterized by 2 insertions of respectively 20- and 7-base pairs (bp) which result in a predictive translated polypeptide differing from the described DR3 molecule by a 28 amino-acid stretch in the extracellular domain. DR3 was shown to be expressed in all cell lines and lymphoma samples tested, whereas DR3 beta expression was restricted to lymphoid T-cell and immature B-cell lines and to selected cases with follicular lymphoma. These data provide new insight into the molecular heterogeneity of DR3, suggesting the presence of several receptor isoforms that can participate in lymphoid cell homeostasis.