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PubMed2026

Asynchronous transitions from high-risk hepatoblastoma to carcinoma.

BACKGROUND & AIMS: Most pediatric hepatocellular tumors are classified as hepatoblastoma (HB) or hepatocellular carcinoma (HCC), yet a subset exhibits mixed histological and molecular features. These hepatoblastomas with carcinoma features (HBCs) include cases provisionally designated as hepatocellular neoplasm-not otherwise specified (HCN-NOS). Their biology remains poorly understood, with unresolved questions about their cellular composition and outcomes. It is unclear whether HBCs comprise hybrid cells with combined HB and HCC characteristics (HBC cells) or admixtures of distinct HB and HCC cells. We characterized the biology, etiology, cellular composition, and evolutionary dynamics of HBCs. METHODS: We performed multi-omics profiling - including single-nucleus RNA sequencing, single-nucleus DNA sequencing, and multi-region longitudinal bulk RNA and DNA sequencing - to characterize HBC composition, evolution, and treatment response. Two-thirds of our samples were post-chemotherapy resections. RESULTS: HBCs comprise heterogeneous mixtures of HB-like, HBC-like, and HCC-like molecular cell types. Outcomes in HBC are significantly worse than in HB, and HBC cells are more chemoresistant than HB cells, with resistance shaped by their cell identity, genetic alterations, and embryonic differentiation stage. HBC cells originate from HB cells that were arrested at early hepatic stem cell development stages because of aberrant WNT signaling activation. Inhibition of WNT signaling promoted differentiation and enhanced sensitivity to chemotherapy. Furthermore, each analyzed HBC reflected a dynamic process of multiple HB-to-HBC and HBC-to-HCC transitions, underscoring their evolutionary complexity. A limitation of our study is our inability to pinpoint the role of chemotherapy-induced genome modifications. CONCLUSIONS: Multi-omics profiling of HBCs revealed key insights into their biology and composition, demonstrating that they originate from HB precursors at early hepatic stem cell development stages and that their differentiation arrest depends on sustained aberrant WNT signaling activity. IMPACT AND IMPLICATIONS: Hepatoblastomas with carcinoma features (HBCs) represent a poorly understood subset of pediatric liver tumors with mixed characteristics of hepatoblastoma (HB) and hepatocellular carcinoma (HCC). Using multi-omics profiling, we show that HBCs comprise heterogeneous mixtures of HB-like, intermediate HBC-like, and HCC-like cell populations that arise from HB precursors arrested at early hepatic stem cell developmental stages due to aberrant WNT signaling. This differentiation arrest contributes to chemoresistance and poorer clinical outcomes compared with HB. Importantly, pharmacologic inhibition of WNT signaling promoted differentiation and increased chemotherapy sensitivity, suggesting a potential therapeutic strategy. These findings refine the biological classification of HBCs and highlight differentiation-based treatment approaches for this aggressive tumor subtype.

Multiomics↗
PubMed1993

Simple diagnostic statistical tests of models for DNA substitution.

The accuracy of models for DNA substitution used in phylogenetic analyses is becoming more important with the increasing availability and analysis of molecular sequence data. It is natural to look for ways of improving these models, and to do this in a planned manner it is useful to be able to identify features of sequences that may not be described adequately. In this paper, I describe three statistics which may give useful diagnostic information on departures from models' predictions. The statistical distributions of these statistics are discussed and simple significance tests are derived. These tests are based on the (estimated) phylogeny of the sequences and so have the advantage of using the information contained in this tree. Examples are given of the application of the new tests to Markov chain models describing the evolution of primate pseudogene sequences and small-subunit RNA sequences.

Animals↗
PubMedDate not supplied

Prediction of RNA base pairing probabilities on massively parallel computers.

We present an implementation of McCaskill's algorithm for computing the base pair probabilities of an RNA molecule for massively parallel message passing architectures. The program can be used to routinely fold RNA sequences of more than 10,000 nucleotides. Applications to complete viral genomes are discussed.

Algorithms↗
PubMed1985

Nucleotide sequence of cucumber mosaic virus RNA. 1. Presence of a sequence complementary to part of the viral satellite RNA and homologies with other viral RNAs.

The nucleotide sequence of the 3389 residues of RNA 1 (Mr 1.15 X 10(6) of the Q strain of cucumber mosaic virus (CMV) was determined, completing the primary structure of the CMV genome (8617 nucleotides). CMV RNA 1 was sequenced by the dideoxy-chain-termination method using M13 clones carrying RNA 1 sequences as well as synthetic oligonucleotide primers on RNA 1 as a template. At the 5' end of the RNA there are 97 noncoding residues between the cap structure and the first AUG (98-100), which is the start of a single long open-reading frame. This reading frame encodes a translation product of 991 amino acid residues (Mr 110791) and stops 319 nucleotide residues from the 3' end of RNA 1. In addition to the conserved 3' region present in all CMV RNAs (307 residues in RNA 1), RNAs 1 and 2 have highly homologous 5' leader sequences, a 12-nucleotide segment of which is also conserved in the corresponding RNAs of brome mosaic virus (BMV). CMV satellite RNA can form stable base pairs with a region of CMV RNAs 1 and 2 including this 12-nucleotide sequence, implying a regulatory function. This conserved sequence is part of a hairpin structure in RNAs 1 and 2 of CMV and BMV and in CMV satellite RNA. The entire translation products of RNA 1 of CMV and BMV could be aligned with significant homology. Less prominent homologies were found with alfalfa mosaic virus RNA 1 translation product and with tobacco mosaic virus Mr-126000 protein.

Amino Acid Sequence↗
PubMed1996

Software to determine optimal oligonucleotide sequences based on hybridization simulation data.

In the design of oligonucleotide sequences for targeting DNA or RNA sequences, it can be difficult to identify sequences that will hybridize only to the intended target. The term "sequence-specific" or "sequence-nonspecific" is often used to describe the interactions of an oligonucleotide with a mixture of DNA or RNA. Our new computer program, HYBsimulator (formerly OligoProbe DesignStation), creates a set of candidate oligonucleotides from a target gene. For each of the candidate oligonucleotides, a large sequence database is searched for sequences that will hybridize to the oligonucleotide. This is referred to as computer hybridization simulation (CHS). Using the nearest-neighbor model, the HYBsimulator takes into account mismatches in hybridization and calculates the melting temperature (Tm) or free energy for hybridization to all sequences in a database. The specificity of each oligonucleotide is then quantified by the number of genes that may hybridize and the predicted Tms or free energies of hybridization to those genes. The CHS data are used to select oligonucleotides based on their specificity with respect to a database.

Base Sequence↗
PubMed2002

A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure.

BACKGROUND: Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N3) in memory. This is only practical for small RNAs. RESULTS: I describe a divide and conquer variant of the alignment algorithm that is analogous to memory-efficient Myers/Miller dynamic programming algorithms for linear sequence alignment. The new algorithm has an O(N2 log N) memory complexity, at the expense of a small constant factor in time. CONCLUSIONS: Optimal ribosomal RNA structural alignments that previously required up to 150 GB of memory now require less than 270 MB.

Algorithms↗
PubMed1992

Cross-linking of U2 snRNA using nitrogen mustard. Evidence for higher order structure.

Nuclear mRNA precursors are spliced by a large macromolecular complex called the spliceosome which contains, in most eucaryotes, five small nuclear RNAs (snRNAs) each in the form of a small ribonucleoprotein particle (the U1, U2, U5, and U4/U6 snRNPs). Although secondary structures have been derived for all five spliceosomal snRNAs based on phylogenetic, biochemical, and genetic data, little tertiary structure information is available. Here we use the general cross-linking reagent nitrogen mustard [bis-(2-chloroethyl)methylamine] to detect tertiary interactions within U2 snRNA. After the cross-linking of deproteinized HeLa nuclear extract, two intramolecularly cross-linked U2 species with anomalous electrophoretic mobility can be detected (X-U2#1 and X-U2#2). The 3' and 5' boundaries of each cross-link were determined by rapid enzymatic RNA sequencing of end-labeled RNA. X-U2#1 is cross-linked between the region U41-U55 and G105 or G106, X-U2#2 between U53 and G97 or G98. We then tested the ability of the two cross-linked species to bind snRNP proteins in vitro (in nuclear extract or S100) and in vivo (in Xenopus oocytes). X-U2#2 reconstituted efficiently both in vitro and in vivo but X-U2#1 did not, as judged by immunoprecipitation with antibodies specific for Sm- and U2-specific proteins. Since the cross-link in X-U2#2 involves the Sm binding site but does not block snRNP assembly, our data strongly suggest that the Sm binding site lies on the surface of the native snRNP.

Base Sequence↗
PubMed1996

Mutational analysis of RNA structures and sequences postulated to affect 3' processing of M1 RNA, the RNA component of Escherichia coli RNase P.

When the rnpB gene encoding M1 RNA, the RNA component of Escherichia coli RNase P, is transcribed, the primary M1 RNA transcript (pM1 RNA) is produced and subsequently processed at the 3' end to generate the mature M1 RNA. To study features of pM1 RNA thought to be involved in RNA processing, systematic mutations were introduced in sequence elements and secondary structures surrounding the processing site using p23 RNA, a truncated pM1 RNA transcribed from the internally deleted rnpB gene, as a model substrate and the processing of its mutant derivatives was analyzed in vivo and in vitro. Neither the alteration of two bases forming the processing site nor the disruption of secondary structures surrounding the site significantly affected the processing efficiency although the secondary structures were required for maintaining RNA stability. In contrast, mutations at the rne-dependent site, GAUUU, immediately 3' to the processing site inhibited the processing and the extent of the inhibition varied with the altered sequences. Furthermore, the processing of the mutants of the rne-dependent site as well as wild-type p23 RNA was inhibited in an E. coli rnets strain at the nonpermissive temperature.

Base Sequence↗
PubMed1987

RNA design by in vitro RNA recombination and synthesis.

The techniques of in vitro RNA synthesis and recombination are presented. These include the site-specific cleavage of RNA, the manipulation of terminal phosphates, and the ligation of RNA fragments. Areas of promising future research include the establishment of RNA cloning vectors and the use of in vitro transcription of natural or designed RNA genes. The chemical synthesis approach now offers the possibility of making large amounts of biologically active length RNAs and of incorporating modified or reporter nucleotides into RNA sequences for physical studies. The new RNA techniques taken with DNA technology will permit a new approach towards understanding the complexity of RNA metabolism and the relationship of structure to function in RNAs.

Base Sequence↗
PubMed1984

Organ-specific nuclear RNAs in tobacco.

We investigated the developmental regulation of nuclear RNA sequences in tobacco vegetative (leaf, root, stem) and floral (petal, ovary, anther) organ systems using RNA-excess X single-copy DNA hybridization reactions. We found that 18% of the single-copy DNA, equivalent to 1.1 X 10(5) kilobases (kb) of diverse transcripts, is represented in the nuclear RNA of each organ. Each nuclear RNA population has both shared and organ-specific sequences. Depending upon the nuclear RNA, 10-40% of the complexity, or 1.1-4.4 X 10(4) kb of diverse sequence, is organ-specific. Collectively, at least 45% of the single-copy DNA, or 3 X 10(5) kb, is represented in the nuclear RNA of the entire plant. Hybridization experiments with polysomal RNA showed that organ-specific mRNAs are present in both the unique and shared nuclear RNA subsets. Together, our results show that tobacco nuclear RNA sequences are under striking developmental control and that both transcriptional and post-transcriptional processes play a role in regulating plant gene expression.

Base Sequence↗
PubMed1982

Sequence complexity of nuclear RNA from 2-acetylaminofluorene-induced rat hepatomas and host cirrhotic liver.

The sequence complexities of nuclear of RNAs from 2-acetylaminofluorene-induced rat hepatomas and host cirrhotic livers were compared in RNA-driven and host cirrhotic livers were compared in RNA-driven hybridization experiments using iodinated single-copy DNa as a probe. Normal liver nuclei RNA hybridized to 10.0 +/- 0.3+ (mean +/- S.D.) of the DNA, indicating an RNA sequence complexity of 3.8 x 10(8) nucleotides. Although nuclear RNAs from cirrhotic livers displayed a greater variation between animals, the mean values for percent DNA hybridized (9.5 +/- 2.0%) and RNA sequence complexity (3.6 x 10(8) nucleotides) for 5 cirrhotic livers examined did not differ significantly from normal. Analysis of nuclear RNAs from 10 tumors, 8 of which were classified as moderately to well differentiated histologically, revealed a level of hybridization (9.5 +/- 1.8%) and a mean value of RNA sequence complexity (3.6 x 10(8) nucleotides) that were almost identical with those for normal liver. Variation in the complexity amont tumors was slightly less than that among cirrhotic liver RNAs. These results suggest that while growth characteristics, biochemical properties, and physiology are known to vary between hepatomas and normal or cirrhotic liver tissue, there is no substantial or consistent difference in the RNA sequence complexity of chemically-induced hepatoma cells compared with normal or chemically-induced cirrhotic liver.

2-Acetylaminofluorene↗
PubMed1993

Elucidation of a conserved RNA stem-loop structure in the packaging signal of human immunodeficiency virus type 1.

A region of human immunodeficiency virus type 1 (HIV-1) genomic RNA known to interact with the viral nucleocapsid protein is one of the crucial components for retroviral genomic RNA packaging. We have investigated the secondary structure for this RNA packaging signal of HIV-1 using RNA mapping techniques and extensive computer analyses. Our results suggest that the RNA sequence containing the packaging signal conforms to a stable stem-loop structure and that a portion of this structure is conserved among twenty independent HIV-1 isolates. The heterogeneity of the RNA packaging sequence was not correlated with the amino acid sequence variability of the viral nucleocapsid protein. These findings have critical implication in understanding the viral maturation process.

Amino Acid Sequence↗
PubMed1994

Substrate specificity of an RNase III-like activity from Bacillus subtilis.

Bacillus subtilis bacteriophage SP82 codes for several early RNAs that were shown previously to be cleaved by an RNase III-like enzyme called "Bs-RNase III." Cloning of DNA fragments that encode these RNA sequences downstream of a T7 RNA polymerase promoter allowed the synthesis of substrates that were used to test the cleavage specificity of Bs-RNase III, which was purified from a protease-deficient strain of B. subtilis. Single nucleotide changes at or near the cleavage site and deletions upstream and downstream of the cleavage site were constructed. The effects of these changes on the rate of Bs-RNase III cleavage were measured. The activity of Bs-RNase III and Escherichia coli RNase III on heterologous substrates was also tested. Although the local environment of the site of Bs-RNase III cleavage appears very similar to that of E. coli RNase III, there are important differences in their substrate specificity.

Bacillus subtilis↗
PubMed1995

Characterization of the first European isolate of Neospora caninum (Dubey, Carpenter, Speer, Topper and Uggla).

Neospora caninum is an apicomplexan, protozoan parasite, which causes severe disease in dogs and cattle. It has previously been isolated only in the United States. A 5-week-old Boxer pup with a progressive hindlimb paresis was diagnosed as suffering from neosporosis on the basis of clinical signs and the presence of anti-Neospora antibodies in it, 2 litter-mates and its dam. Despite treatment with sulphonamides, the pup was euthanased 3 days later. The diagnosis of neosporosis was confirmed by immunohistochemical examination of muscle and CNS tissue sections from the pup. Parasites were isolated into Vero cell culture from the cerebrum, and confirmed as Neospora caninum by immunofluorescence with specific antibody, tachyzoite ultrastructure and 16S-like ribosomal RNA sequences. This isolate (designated NC-Liverpool) has been continuously passaged every 7-10 days. Its growth characteristics, ultrastructure and antigenic profile, as revealed by immunoblotting, have revealed no major differences from the American NC-1 isolate. Furthermore, no difference was seen when comparing the sequences of 16S-like ribosomal RNA and the ITS1 region of the two isolates.

Animals↗
PubMed2001

Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA.

We studied the evolutionary relationships among basal metazoan lineages by using complete large subunit (LSU) and small subunit (SSU) ribosomal RNA sequences for 23 taxa. After identifying competing hypotheses, we performed maximum likelihood searches for trees conforming to each hypothesis. Kishino-Hasegawa tests were used to determine whether the data (LSU, SSU, and combined) reject any of the competing hypotheses. We also conducted unconstrained tree searches, compared the resulting topologies, and calculated bootstrap indices. Shimodaira-Hasegawa tests were applied to determine whether the data reject any of the topologies resulting from the constrained and unconstrained tree searches. LSU, SSU, and the combined data strongly contradict two assertions pertaining to sponge phylogeny. Hexactinellid sponges are not likely to be the basal lineage of a monophyletic Porifera or the sister group to all other animals. Instead, Hexactinellida and Demospongia form a well-supported clade of siliceous sponges, Silicea. It remains unclear, on the basis of these data alone, whether the calcarean sponges are more closely related to Silicea or to nonsponge animals. The SSU and combined data reject the hypothesis that Bilateria is more closely related to Ctenophora than it is to Cnidaria, whereas LSU data alone do not refute either hypothesis. LSU and SSU data agree in supporting the monophyly of Bilateria, Cnidaria, Ctenophora, and Metazoa. LSU sequence data reveal phylogenetic structure in a data set with limited taxon sampling. Continued accumulation of LSU sequences should increase our understanding of animal phylogeny.

Animal Population Groups↗
PubMed1994

Characterization and partial purification of tRNA processing activities from potato mitochondria.

In plant mitochondria, as in most other genetic systems, several enzymatic processing and modification steps are required to yield mature tRNAs from primary transcripts. Three of the enzymes involved, RNase P, 3'-processing activity, and tRNA nucleotidyl transferase, were identified in potato (Solanum tuberosum) mitochondria and have been separated by several purification steps. RNase P was partially purified, with only a few proteins detectable in active fractions after a final glycerol gradient step. A small RNA molecule present in fractions with RNase P activity contains the heptanucleotide conserved in the other known RNase P RNA sequences and may be a fragment of the RNA moiety of the plant mitochondrial RNase P.

Base Sequence↗
PubMed1985

Expression of long terminal repeat (LTR) sequences in carcinogen-induced murine skin carcinomas.

RNA sequences homologous to the Long Terminal Repeat (LTR) sequence of Moloney Murine Leukemia Virus proviral DNA are expressed in murine squamous cell carcinomas of the skin induced by chemical carcinogens. These transcripts range in size from 8.2 to less than 2.4 kb but their size profile varies between individual tumors. These RNAs are not detected in the poly A+ RNA fraction obtained from the epidermis of control mice or carcinogen induced skin papillomas. The poly A+ RNAs from the livers and spleens of some of the mice with skin carcinomas also revealed LTR related sequences, whereas these RNAs were not detected in the livers and spleens of control mice or of carcinogen-treated mice that did not develop carcinomas. Thus, chemical carcinogenesis in mouse skin is associated with constitutive expression of endogenous retrovirus related sequences in the carcinomas as well as in certain apparently normal host tissues.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed1988

Structure and evolution of the intergenic region in a ribosomal DNA repeat unit of wheat.

The complete nucleotide sequence of the intergenic region between the 25 S and 18 S wheat ribosomal RNA genes has been determined from a 4.6 kb EcoRI-BamHI fragment (1 kb = 10(3) bases or base-pairs) subcloned from the plasmid pTa71. Within this subclone the intergenic DNA is flanked by the 3' end of the 25 S and the 5' end of the 18 S ribosomal RNA sequences. Four repeat families are present within the intergenic region. The major repeat family A, consists of 12 direct repeat units of 135 or 136 base-pairs (bp) flanked by diverged truncated copies. Within each A repeat a subrepeat structure has been revealed. Family B, which is localized to the 5' side of the A repeats, contains three repeat units, one of 152 bp, the second of 150 bp and a truncated unit of 107 bp. Family C, which is localized in the transcribed rRNA precursor, consists of two direct repeat units of 172 and 174 bp and possesses some short subrepeat motifs. The C repeats may have evolved by and diverged from one another by the insertion of short transposable sequences. Family D consists of two direct repeat units of 30 bp located 5' to the start of transcription. Statistical analysis of repeat family A showed that there is a significant association between the similarity of any two repeat units and their distance apart in the array. The near identity of members of the A family is maintained presumably by processes such as unequal crossing over and gene conversion, but the members at each end of the array show more divergence. Sequence motifs in the A and C repeat families and in other regions including the 5' end of 18 S RNA are related, implying that much of the intergenic DNA may have evolved from a few short ancestral sequences. The B and D repeats or their equivalent are not found in a maize ribosomal DNA repeat unit. The DNA in the external transcribed spacer DNA 5' to the 18 S RNA sequence is longer in wheat than in maize. This is due principally to two duplications and insertion of a sequence with dyad symmetry in the wheat gene.

Base Sequence↗