Epigenomic analysis of the HOX gene loci reveals mechanisms that may control canonical expression patterns in AML and normal hematopoietic cells.

HOX genes are highly expressed in many acute myeloid leukemia (AML) samples, but the patterns of expression and associated regulatory mechanisms are not clearly understood. We analyzed RNA sequencing data from 179 primary AML samples and normal hematopoietic cells to understand the range of expression patterns in normal versus leukemic cells. HOX expression in AML was restricted to specific genes in the HOXA or HOXB loci, and was highly correlated with recurrent cytogenetic abnormalities. However, the majority of samples expressed a canonical set of HOXA and HOXB genes that was nearly identical to the expression signature of normal hematopoietic stem/progenitor cells. Transcriptional profiles at the HOX loci were similar between normal cells and AML samples, and involved bidirectional transcription at the center of each gene cluster. Epigenetic analysis of a subset of AML samples also identified common regions of chromatin accessibility in AML samples and normal CD34(+) cells that displayed differences in methylation depending on HOX expression patterns. These data provide an integrated epigenetic view of the HOX gene loci in primary AML samples, and suggest that HOX expression in most AML samples represents a normal stem cell program that is controlled by epigenetic mechanisms at specific regulatory elements.

IgG2a and igA co-expression by the natural autoantibody-producing murine B lymphoma T560.

The T560 B lymphoma produces polyreactive IgG2a with the features of natural autoantibody. All T560 cells bear and secrete IgG2a but a small fraction spontaneously co-express IgA. Cells secreting IgA alone cannot be detected. IgA secretion is enhanced by interaction of T560 cells either with activated T cells and cognate antigen, or with LPS, but not with cytokines, including IL-5 and TGF-beta. IgA and IgG2a mRNAs have identical V186.2. DFL 16 and JH1 sequences from framework 2 through JH1. PCR analysis reveals that previous recombination events have led to deletion of the mu, gamma3, gamma1, gamma2b constant region genes from both the productive and the unproductive chromosome but the former has retained gamma2a, epsilon and alpha, the latter only alpha. Digestion-circularization (DC)-PCR experiments provide formal proof of DNA recombination between Ca and the intron upstream of Cmu. Evidently, the productive chromosome has switched only as far as gamma2a, the unproductive all the way to the alpha constant region gene. The unproductive allele is transcriptionally active as evidenced by the presence of mRNA encoding Calphal inappropriately spliced to a cryptic splice site in the downstream intron of DQ52 (eliminated from the productive chromosome). A specific RT-PCR using oligonucleotide primers derived from the upstream initiation site of the Ialpha exon and from Calpha1 discloses that T560 cells contain alpha-germ line mRNA, presumably transcribed from the Ialpha-region of the productive chromosome, spliced to Calpha. Treatment with LPS stops production of these spliced transcripts suggesting that it may promote either DNA recombination in cells spontaneously transcribing Ialpha or a change in splicing such that Ialpha sequence is no longer joined to Calpha. Verification of the DC-PCR product by sequencing reveals that the T560 and B10.A IgA (Ig2b allotype) hinge is different from the BALB/c IgA (Ig2a allotype) hinge: it has two extra Cys and has eliminated the first Thr, a potential glycosylation site in BALB/c IgA.

The IgG2a/IgA produced by the murine T560 B lymphoma that arose during a graft-versus-host reaction is polyreactive and somatically mutated.

In mice undergoing a graft-versus-host (GVH) reaction, donor T cells responding to the host's MHC antigens induce polyclonal activation of the host's B cells and secretion of their antibodies and autoantibodies. T560, a CD5- B lymphoma that arose in the gut-associated lymphoid tissue (GALT) of a (B10 x B10.H2aH4(b)pWts) F1 hybrid mouse that had been injected with parental B10.H2aH4b splenocytes, is of particular interest because it produces switched, heavily mutated, but, nevertheless, polyreactive immunoglobulin. T560 bears and contains IgG2a but switches to IgA spontaneously. The T560 Ig variable region is encoded by a V186.2-related VH gene, juxtaposed to DFL 16 and J(H)1, and by a Vkappa gene of the Vkappa 4/5 group juxtaposed to Jkappa1. Both VH and VK are heavily mutated. The IgA binds to polystyrene, to p-azophenyl-phosphorylcholine (PC)-conjugated keyhole limpet hemocyanin (KLH) (PC-KLH), to 2,4,6 trinitrophenylated (TNP)-KLH and to human TNF-beta but not to KLH, human TNF-alpha, or any of several other Ags tested. Hapten inhibition experiments indicate that the polystyrene, PC- and TNP-binding sites do not overlap. The switched isotypes and heavy load of somatic mutations found in the T560 IgG2a/IgA suggest that T cell-dependant somatic selection of the T560 precursor B cell may have been superimposed on polyclonal B cell activation originally associated with the GVH.

Mechanisms that limit the diversity of antibody: three sequentially acting mechanisms that favor the spontaneous production of germline encoded anti-phosphatidyl choline.

Antibody to phosphatidyl choline (PtC) is produced spontaneously in mice, by approximately 2-10% of naturally occurring CD5+ (B1) B cells in the peritoneum. Much of this antibody is encoded by the VH11 gene associated with a specific V kappa 9 gene. Constraints on the size and structure of the H chain CDR3 have been defined from nucleotide sequences of genes expressed by hybridomas and lymphomas derived from adult mice. All employ JH1 and all encode tyrosine as the first amino acid in CDR3, which is either nine or 10 amino acids long; the last six are always the same, start with tyrosine, and are rich in aromatic amino acids. Those with nine amino acids in CDR3 have glycine or serine in the second position and asparagine, serine or proline in the third; those with 10 have an additional aspartate or glycine inserted after the first tyrosine. DSP2 genes are used by 80% and DFL16 by 20%. Productively rearranged VH11 genes in neonates and in 18 day fetal liver display a greater, but still limited degree of diversity. All four JH genes are used and the length of CDR3 varies from three to 12 amino acids, but the first is tyrosine in 58 of 61 and DSP2 genes are used by 80% of these productive VDJ assemblies. Non-productive rearrangements of VH11 in fetal liver show a different pattern; 41% use DFL16 genes and only 40% have a TAx codon in the first position of CDR3. All rearrangements show evidence of a bias in favor of joining the VH11 gene to D genes at positions of matching nucleotide overlap.(ABSTRACT TRUNCATED AT 250 WORDS)

Isolation of a chick cytokeratin cDNA clone indicative of regional specialization in early embryonic ectoderm.

During early vertebrate development, a series of inductive tissue interactions appear to be involved in establishing regional specializations that are eventually elaborated in the basic body plan of the embryo. These early inductive interactions are particularly difficult to study because they often occur in the absence of any associated morphological changes. In the chick embryo, the regional subdivision of the early ectoderm is evidenced by a marked lens-forming bias in the head ectoderm, which is absent from the presumptive dorsal epidermis of the trunk region. This striking divergence in developmental state is present long before any differentiation into lens or epidermal phenotypes can be detected. As a strategy for isolating genes whose differential expression might be a reflection of this regional subdivision, a cDNA library was prepared from early embryos and screened for differential hybridization to radiolabelled probes prepared from head ectoderm and trunk ectoderm. Two related cDNA clones were isolated that hybridize to transcripts present at much higher levels in trunk ectoderm than in head ectoderm. Sequence analysis of one of these clones revealed a high degree of similarity to members of the type II subfamily of intermediate filament cytokeratins. This clone (pCKse1) was used to examine cytokeratin gene expression in ectodermal tissues. A large increase in the level of CKse1 transcripts was found to take place in trunk ectoderm, approximately coordinate with neurulation, contrasting sharply with the much lower levels detected in head ectoderm and neural ectoderm at all stages tested. These results indicate that differential cytokeratin gene expression can occur within a contiguous layer of simple embryonic epithelia, and that this expression pattern coincides closely to the subdivision of the early ectoderm into regions with distinct developmental potencies. This type of regulation has not been described previously for members of the cytokeratin gene family.

Four-dimensional chemical shift MR imaging of phosphorus metabolites of normal and diseased human liver.

Four dimensional chemical shift imaging was used to map the relative peak heights of phosphorus metabolites of the liver and overlying skeletal muscle of a normal subject and two patients. The technique provides 31P spectra localised on a voxel-by-voxel basis and may be valuable in mapping heterogeneous structural and metabolic changes in disease.