Molecular analysis of the rat MHC. II. Isolation of genes that map to the RT1.E-grc region

An initial mapping analysis of growth and reproduction complex (grc) and grc+ genomic DNA identified several restriction fragment length polymorphisms specific for the grc region of the MHC. To analyze further the genomic organization and structure of the grc, a cosmid library was constructed from a grc+-bearing strain (R21). One cosmid cluster, encompassing 41.4 kb of DNA, contained four, or possibly five, class I genes that mapped to the RT1.E-grc region Two unique non-class I fragments were isolated from certain cosmids within this cluster. These fragments were hybridized to genomic DNA derived from five rat strains (BIL/2, R18, R21, R22, and BIL/1), and the results showed that grc-bearing rats have a deletion of at least 3.1 kb of DNA in the region immediately adjacent to the MHC. The loss of the genes in this region is probably the cause of the growth and reproductive defects in these animals and probably also of their increased susceptibility to chemical carcinogens.

Warthin's tumor with malignant lymphoma. DNA analysis of paraffin-embedded tissue

The authors report a case of malignant lymphoma, small lymphocytic type, involving the lymphoid stroma of a Warthin's tumor of the parotid gland. This was confirmed by the presence of a monoclonal immunoglobulin heavy chain gene rearrangement, demonstrated by Southern blot hybridization of DNA extracted from paraffin-embedded tissue. Similar techniques showed only germline immunoglobulin gene bands in two control cases of Warthin's tumor.

Insulin-gene expression in extrafetal membranes of rats

We quantified fetal rat extrapancreatic insulin-gene expression by measuring mRNA in the yolk sac and placenta. Yolk sac makes a significant contribution to the total fetal insulin stores. The placenta contains a much smaller amount of insulin mRNA. Yolk sac insulin mRNA is barely detectable at 16 days gestation but increases markedly to a maximum at 21 days, 1 day before birth. In contrast to the pancreatic 550-nucleotide (n) insulin mRNA, yolk sac has a 720-n mRNA. However, on removal of the terminal poly(A), both transcripts produce a 440-n RNA, the size predicted for a fully processed insulin mRNA.

The pathology of posttransplant lymphoproliferative disorders occurring in the setting of cyclosporine A-prednisone immunosuppression

Posttransplant lymphoproliferative disorders (PTLDs) were diagnosed in 43 patients from the Pittsburgh-Denver series between June 1980 and March 1987. This constitutes a detection rate of 1.7%. Major categories of clinical presentation included a mononucleosislike syndrome, gastrointestinal/abdominal disease, and solid organ disease. The median time of onset in patients initially immunosuppressed with cyclosporine-A (CsA)-containing regimens was 4.4 months after transplant, regardless of tumor clonality. A strong association of PTLD with Epstein-Barr virus (EBV) was observed. A histologic spectrum of lesions from polymorphic to monomorphic was observed. Whereas polymorphic lesions could be either clonal or nonclonal, monomorphic lesions appeared to be clonal in composition. The presence of large atypical cells (atypical immunoblasts) or necrosis did not appreciably worsen the prognosis. Twelve patients had clonal, 13 had nonclonal, and five had both clonal and nonclonal tumors. Clonality was indeterminate in 13 cases. Most patients were treated with a regimen based on reduced immunosuppression and supportive surgery. Almost all nonclonal and about half of the clonal lesions respond to this conservative therapy, indicating that it is an appropriate first line of treatment. This behavior suggests that a spectrum of lesions ranging from infectious mononucleosis to malignant lymphoma constitutes the entity known as PTLD. Some monoclonal tumors can undergo regression, however, apparently in response to host immune control mechanisms. Because of its short latency and strong association with EBV, PTLD is an important model for the study of virus-associated tumor progression in humans.

Albumin and alpha-fetoprotein gene expression and DNA methylation in rat hepatoma cell lines

To define systems for the study of gene control and differentiation in vitro, we analyzed albumin and alpha-fetoprotein (AFP) gene expression and gene methylation in a series of rat hepatoma-derived cell lines and controls. These cell lines had several specific phenotypes: adult (high albumin and low AFP mRNA), fetal (high albumin, high AFP), embryonic (low albumin, high AFP), or undifferentiated (no albumin or AFP). The adult hepatocyte phenotype is marked by a novel 2.2-kb AFP gene transcript and high DNA methylation. In general, tumor cell lines had higher albumin and AFP gene methylation than hepatocytes in vivo. Levels of total DNA methylation did not determine the methylation patterns of specific genes, except for one cell line with hypermethylated and one with hypomethylated DNA. 5'-Hypomethylation of the AFP gene correlated with gene activity in all cases; the albumin gene showed a similar relationship, but with some exceptions. Only adult hepatocytes, not cell lines, have a unique 3'-region of AFP gene demethylation.

Purification and analysis of RNA from paraffin-embedded tissues

We have developed methods for the purification and analysis of RNA from formalin-fixed and paraffin-embedded tissue. The methods allow retrospective analysis of gene expression or viral infection. RNA extraction uses prolonged solubilization of tissue with detergent and protease in the presence of high concentrations of a ribonuclease inhibitor. The purified RNA is moderately degraded but its hybridization behavior is essentially unaffected. We were able to quantify specific mRNAs by dot-blot hybridization.

Analysis of ras genes and linked viral sequences in rat hepatocarcinogenesis

After long-term feeding of a choline-devoid diet to rats, the authors analyzed rasK, rasH, and rasN transcripts and gene structure in livers and liver tumors. They controlled their analysis by studying cell lines derived from chemically induced hepatomas. Transcripts from all three genes were elevated in all tumors, but not in the livers from which they arose. The transcript elevations may represent an effect of active cell proliferation in the tumors. Clone HiHi-3, derived from the Kirsten murine sarcoma virus, detected a large number of hybridization bands, most of which were not part of the rasK-p21 gene. Most tumors had an altered band at 2.6 kb; some had other altered bands. No alterations were seen in liver DNA, and none of the cell lines showed the 2.6 kb band. At low stringency, a rasH probe, which contains a short segment of a similar viral sequence, also detected altered bands in tumors and a single treated liver. These changes in endogenous viral sequences of the rat genome appear to be characteristic of carcinogenesis by a choline-devoid diet.

alpha-Fetoprotein gene methylation and hepatocarcinogenesis in rats fed a choline-devoid diet

We studied the alpha-fetoprotein (AFP) gene methylation of DNA from livers of rats fed choline-devoid or control choline-supplemented diets, and from hepatocellular carcinomas induced by the choline-devoid diet. Chronic choline deficiency caused a reduction in the level but not the pattern of methylation in hepatocytes. The tumors, however, had an altered methylation pattern with a marked increase in methylation at the 3' end, even those tumors that had low average DNA methylation. At the same time, there was a decrease in DNA methylation at the 5' end. The tumor methylation pattern resembled that of the active AFP gene of fetal liver but there was no increase in the steady-state level of AFP mRNA in the tumors. The 3' demethylated region is characteristic of the inactive adult liver AFP gene, but it disappears in the final stages of neoplastic transformation of hepatocytes. The methylation changes are not sufficient to activate the gene.

32P-postlabeling analysis of liver DNA adducts in rats chronically fed a choline-devoid diet

Liver DNA, obtained at various time intervals from rats chronically fed a choline-devoid diet, was analysed for the presence of aromatic or alkyl adducts by the 32P-postlabeling assay. Alkyl adducts were not detected. Aromatic DNA adduct lesions were revealed, but only at levels (1 adduct per 0.5-3 X 10(9) nucleotides) which are at the limits of the extremely high sensitivity of the method used, levels which remained constant throughout the period of feeding. Thus, contamination of the total environment of the animals with chemical carcinogens does not appear to be responsible for the genesis of the hepatocellular carcinomas that develop in rats chronically fed a choline-devoid diet. The diet, therefore, either acts as a complete carcinogen, or promotes the evolution to cancer of endogenous, 'spontaneously' initiated liver cells.

DNA methylation and hepatocarcinogenesis in rats fed a choline-devoid diet

Groups of male Fischer-344 rats were fed either a choline-supplemented or a choline-devoid (CD) diet, for up to 14 months. In rats fed the CD diet, hepatic lesions developed and progressed through two distinct stages, the first characterized by severe steatosis and an increase in cell turnover and the second by gradual clearance of the deposited fat, fibrosis and parenchymal nodularity. Large hepatocellular carcinomas were found in rats killed at 14 months. DNA was purified from the livers of all groups of rats and from the tumors, and its level of methylation was analyzed using the restriction endonucleases HpaII and MspI. DNA undermethylation was detected only in the livers of rats fed the CD diet for 14 months, whether bearing tumors or not, and in three of four hepatocellular carcinomas. Undermethylation of liver total DNA is therefore a late effect of dietary choline deficiency in the rat.

Molecular analysis of the rat MHC. I. Delineation of the major regions in the MHC and in the grc

Southern blot analysis with liver DNA from a unique series of recombinant (R10, R11, R16, R18, R21, and R22), congenic (Y0.1U.grc+, Y0.1U.grc+/Y0.1L.grc, and Y0.1L.grc) and inbred rats has been performed to examine the restriction fragment length polymorphisms of class I genes. After digestion with Xba I or Eco RI, the genomic DNA was resolved on agarose gels, was transferred to nitrocellulose membranes, and was hybridized with murine H-2 cDNA probes. Eighteen to 25 bands of varying intensities could be clearly resolved in any given strain. Analysis of these hybridization patterns detected restriction fragment length polymorphisms that permitted the assignment of 17 specific fragments to regions within the major histocompatibility complex: RT1.A, RT1.B/D, and the RT1.E-grc-T1 alpha region. Fragments have been identified that are specific for grc, grc+, and RT1.E, and mark the junction sites between these loci. In addition, several markers identify the region around the sites of recombination in some strains. The hybridization pattern of the R18 recombinant had a unique band that specified a point of recombination within the grc. The recombinant R11 presented a unique restriction pattern unrelated to either of the parental strains or other related strains. This result suggests that R11 arose from a recombination event(s) undetected by conventional serologic methods.

Molecular analysis of the rat MHC. I. Delineation of the major regions in the MHC and in the grc

Southern blot analysis with liver DNA from a unique series of recombinant (R10, R11, R16, R18, R21, and R22), congenic (Y0.1U.grc+, Y0.1U.grc+/Y0.1L.grc, and Y0.1L.grc) and inbred rats has been performed to examine the restriction fragment length polymorphisms of class I genes. After digestion with Xba I or Eco RI, the genomic DNA was resolved on agarose gels, was transferred to nitrocellulose membranes, and was hybridized with murine H-2 cDNA probes. Eighteen to 25 bands of varying intensities could be clearly resolved in any given strain. Analysis of these hybridization patterns detected restriction fragment length polymorphisms that permitted the assignment of 17 specific fragments to regions within the major histocompatibility complex: RT1.A, RT1.B/D, and the RT1.E-grc-T1 alpha region. Fragments have been identified that are specific for grc, grc+, and RT1.E, and mark the junction sites between these loci. In addition, several markers identify the region around the sites of recombination in some strains. The hybridization pattern of the R18 recombinant had a unique band that specified a point of recombination within the grc. The recombinant R11 presented a unique restriction pattern unrelated to either of the parental strains or other related strains. This result suggests that R11 arose from a recombination event(s) undetected by conventional serologic methods.

Immunogenetics of development and its relationship to carcinogenesis

We have been exploring the classical idea that there is a close relationship between embryogenesis and carcinogenesis. The clinical literature provides evidence for a relationship among the presence of developmental anomalies, an increased incidence of cancer, and genes linked to the major histocompatibility complex (MHC). This relationship was explored experimentally by testing the possibility that rats having the growth and reproduction complex (grc), which causes developmental abnormalities, might be more susceptible to the development of cancer following exposure to a chemical carcinogen. Two groups of animals which were genetically similar except for the presence or absence of the grc were fed the carcinogen 2-aminoacetylfluorene. The animals carrying the grc developed the morphological changes associated with early cancer of the liver, whereas their normal counterparts did not. These susceptible animals also had a number of biochemical alterations, especially in cholesterol biosynthesis, which may be associated with the development of cancer. Molecular analysis of genomic DNA by blot hybridization revealed restriction fragment length polymorphism differences between the DNA from grc and grc+ rats, and these differences may be related to the differential susceptibility of the strains to cancer.

DNaseI sensitivity of the rat albumin and alpha-fetoprotein genes

We have analyzed the DNaseI sensitivity of chromatin from the rat albumin and alpha-fetoprotein genes in the fetal liver (which synthesizes albumin and alpha-fetoprotein), adult liver (which synthesizes albumin), fetal yolk sac (which synthesizes alpha-fetoprotein), and adult kidney (which synthesizes neither). Active genes were much more sensitive than their kidney counterparts, and the adult liver alpha-fetoprotein and fetal yolk sac albumin genes showed intermediate levels of sensitivity. Sensitivity was analyzed as a function of the extent of DNaseI digestion. Rate constants were calculated for the degradation of individual DNA hybridization bands and normalized to the intrinsic rate constants of the same bands degraded in purified DNA. This enabled us to eliminate the inconsistencies that otherwise result from comparing chromatin sensitivity of different DNA sequences, or chromatin sensitivity in different nuclear environments.

Developmental regulation of albumin and alpha-fetoprotein gene expression in the rat

Albumin and AFP comprise a developmentally regulated gene family expressed predominantly in liver and yolk sac. In this study, we have analyzed the developmental changes in the levels of transcripts in liver and yolk sac, and the methylation of the genes in yolk sac. We have previously analyzed the gene methylation in developing liver and non-expressing tissues (Kunnath and Locker, 1983, EMBO J., 2, 317-324). From these analyses we can distinguish 3 active modes of coordinated expression. The adult liver synthesizes albumin, the yolk sac synthesizes AFP, and the fetal liver synthesizes both. In the yolk sac, the relatively inactive albumin gene is hypermethylated, while the active AFP gene is undermethylated. Our data suggest that the genes are activated simultaneously but that subsequent enhancement is specific for tissue and developmental stage.

Extrapancreatic insulin gene expression in the fetal rat

Analysis of gene expression in rat yolk sac, a primitive endodermal structure, revealed a low level of developmentally regulated insulin production. At 14 days of gestation, a 2.4-kilobase (kb) RNA species hybridized to cloned insulin gene probes. This species increased throughout gestation. At 16 days, a second transcript of 0.72 kb became visible and, by 18 days, the 0.72-kb transcript predominated. In the pancreas, the fully processed insulin mRNA is 0.55 kb long. Over the same time period in the fetal liver (also a tissue of endodermal origin, as is the pancreas), only the 2.4-kb transcript was detected; no hybridizing transcripts were detected in adult liver RNA. Gel filtration studies and insulin radioimmunoassay of acid/ethanol-soluble peptides showed approximately equal amounts of proinsulin and insulin in 18-day yolk sac, a result suggesting that the transcripts in this tissue are translated. On the other hand, a lower level of insulin and the lack of proinsulin in fetal liver were compatible with a pancreatic origin of hepatocyte insulin by receptor binding rather than intrahepatic insulin synthesis.

Developmental changes in the methylation of the rat albumin and alpha-fetoprotein genes

We have analyzed methylation of the rat albumin and alpha-fetoprotein (AFP) genes by hydridizing labeled cDNA clones to HpaII and MspI digests of DNA from different stages of development. These CCGG-cutting enzymes distinguish 5-methylcystosine in mCCGG (sensitive to HpaII) and CmCGG (sensitive to MspI). In the liver, the albumin gene is heavily methylated at 18 days gestation and uniformly demethylated in the adult. The AFP gene is also heavily methylated at 18 days gestation, and develops demethylated regions at the 3' half of the gene in the adult. These methylation changes are not observed in other embryonic or adult tissues. We also evaluated expression of these genes by measuring their corresponding mRNAs. The albumin gene is actively transcribed in 18-day fetal liver, when it is heavily methylated, as well as in adult liver, when it is unmethylated. In contrast, the AFP gene is transcribed only in fetal liver, even though it is less methylated in adult liver. These findings suggest that specific methylation changes are associated with changes in gene expression, but that this association is not adequately described by the simple hypothesis that methylation turns genes off.

Characterization of DNA methylation in the rat

In the rat, differentiation and cell proliferation both affect DNA methylation. We studied 5-methylcytosine at the inner cytosine of the sequence C-C-G-G, a common methylation site, using endonuclease MspI (which cleaves C-C-G-G- and C-mC-G-G), and its isoschizomer HpaII (which cleaves only C-C-G-G). DNA from all tissues and cell lines studied was methylated at C-C-G-G, at levels ranging from 45 to 80%, but the methylation sites were not distributed uniformly. Our analysis suggests a model in which cells contain variable amounts of three DNA methylation states, averaging 30-40, 70-80 and 95-100% methylation, respectively. One biological parameter that alters methylation is the proliferative state of the cell. We observed that NRK, a non-transformed cell line, increased its DNA methylation from 45 to 67% when monolayer cultures became confluent and non-dividing. We also observed that a class of repetitive DNA was completely methylated in DNA from all sources except a transformed cell line.

Variable methylation of the ribosomal RNA genes of the rat

Both the pattern and level of rRNA gene methylation vary in the rat. This variation reflects stages in the maturation process and perhaps the level of gene expression in different tissues. We studied methylation at a common site, the inner cytosine of the sequence CCGG, by hybridizing 32P-rRNA to DNA digests obtained with endonuclease Msp I (which cleaves CCGG and CMCGG) and its isochizomer, HpaII (which cleaves only CCGG). In the liver, the changing pattern of rRNA gene methylation reflected the late stages of development: the rRNA genes were mostly unmethylated at 14 days gestation; by 18 days gestation, about 30% of them were methylated, and this level persisted into adulthood. In 18-day DNA, the methylation was uniform, but in adult DNA, the methylation pattern was discontinuous, because otherwise methylated genes contained a demethylated region. Similar developmental changes were observed in brain DNA. In a tissue culture cell line, the change from the continuous to the discontinuous pattern of the methylation could be induced by transformation with Kirsten sarcoma virus. And, in adult tissues, the lowest level of rRNA gene methylation was found in rapidly growing jejunal epithelium, and the highest level, in non-growing spermatozoa.

Transcriptional initiation and processing of the small ribosomal RNA of yeast mitochondria

We have identified the nucleotide at which transcription initiates on the yeast mitochondrial small (14 S) rRNA gene by sequencing of RNA labeled at the 5' initiating triphosphate with vaccinia virus guanylyltransferase [alpha-32P]GTP (in vitro capping reaction). Initiation occurs within the stem of a 12-base palindromic repeat. The initiation sequence has homology with the large (21 S) ribosomal RNA initiation sequence that has been previously determined. We have also sequenced the 5' and 3' ends of the mature 14 S rRNA after labeling with T4 polynucleotide kinase and RNA ligase, respectively. These sequences demonstrate that about 80 nucleotides are cleaved from the 5' end of a precursor to produce the mature 14 S rRNA. This cleavage is imprecise in that the processing occurs at one of five adjacent nucleotides 77 to 81 nucleotides downstream from the 5' initiation site. The 3' ends of this precursor and the mature 14 S rRNA are unique and identical.