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PubMed2000

Statistical analysis of the 5' untranslated region of human mRNA using "Oligo-Capped" cDNA libraries.

We constructed 34 types of human "full-length enriched" and "5'-end enriched" cDNA libraries based on the "Oligo-Capping" method. We randomly picked and sequenced 10,000 clones from these libraries. BLAST analysis showed that about 50% of the cDNAs were identical to known genes. Among them, we selected 954 species of cDNA that should represent the entire sequence from the mRNA start sites. Compared with previously reported sequences, they were on average 45 bp longer in the 5'-end. Using these cDNA data, we statistically analyzed the sequence features of the 5'UTR. The average length of the 5'UTR was 125 bp, and there was little correlation with the corresponding mRNA length (correlation coefficient = 0.26). Of the 954 species of 5'UTR, 459 contained no in-frame terminator codon, which is against the common belief. Two hundred seventy-eight species contained at least one ATG codon upstream of the initiator ATG codon. We identified 569 upstream ATGs, in total, 63% of which adequately satisfied Kozak's criteria. These findings are contrary to the typical translation initiation model, which states that translation is initiated from the "first" ATG codon.

5' Untranslated Regions↗
PubMed1997

TCR expression and clonality analysis in peripheral blood and lymph nodes of HIV-infected patients.

We compared the T cell receptor (TCR) V beta gene family repertoire in peripheral blood mononuclear cells (PBMC) and lymph node (LN) cells from 7 human immunodeficiency virus (HIV)-infected patients and 3 seronegative healthy controls. Virtually all the V beta family specificities were represented in patient PBMC and LN cells, and mean values for each specificity were comparable to figures in seronegative controls. In 4 patients, however, some V beta gene segment transcripts were overrepresented in the LN compartment, compared to the peripheral blood counterpart. To ascertain whether this phenomenon was due to polyclonal or oligoclonal expansion of T cells bearing the relevant V beta gene product, we sequenced the entire CDR3 region of a panel of 238 PCR clones corresponding to the V beta transcripts expanded in LN; as control, the same regions were cloned and sequenced in patient's PBMC, and in PBMC and LN cells from seronegative individuals. This analysis disclosed preferential usage of J beta 2 genes in PBMC and LN cells from both seropositive patients and controls, regardless of the V beta gene segment considered, thus indicating that this skewness in the V beta-J beta repertoire could be a consistent feature of at least a part of the V beta repertoire in different lymphoid compartments, regardless of the pathologic conditions. In addition, in LN from HIV seropositive patients we found the presence of recurrent TCR rearrangements, accounting for 8-23% of the generated clones, in each of the 4 V beta specificities analyzed; recurrent sequences were not found in PBMC from patients nor in PBMC and LN cells from seronegative controls. These findings suggest that antigen-driven oligoclonal T cell expansions may occur in vivo in lymphoid organs of HIV seropositive patients.

CD4 Lymphocyte Count↗
PubMed2005

Current efforts in the analysis of RNAi and RNAi target genes.

RNAi is RNA interference by short RNAs. It influences gene-expression by down-regulation of mRNAs, typically by complementarity to the 3' UTR (untranslated region) of the mRNA. microRNAs (miRNAs) are short RNAs acting as natural RNAi. miRNAs mediate down-regulation of many mRNAs from developmental genes and transcription factor genes. Natural examples for this additional level of post-transcriptional control are increasing. Suitable computer-based search strategies for new miRNA candidates include precursor folding as well as different compositional search strategies. Example programs for this are presented. New own and other data are provided for an overview on such strategies. A strategy feasible in plants for miRNA target identification is direct base pairing of miRNAs to potential mRNA target 3' UTRs. Correct identification in animals usually requires comparative genomics and conserved UTR regions pairing to conserved miRNA substructures. A number of example programs and target examples for these tasks are examined. Finally, strategies and programs for artificial gene silencing by designed RNAi are explained.

Animals↗
PubMed2003

Characterisation of yeasts isolated from deep igneous rock aquifers of the Fennoscandian Shield.

The diversity of prokaryotes in the groundwater deep below the surface of the Baltic Sea at the Aspö Hard Rock Laboratory (HRL) in southeast Sweden is well documented. In addition, there is some evidence that eukaryotes, too, are present in the deep groundwater at this site, although their origins are uncertain. To extend the knowledge of eukaryotic life in this environment, five yeast, three yeastlike, and 17 mold strains were isolated from Aspö HRL groundwater between 201 and 444 m below sea level. Phenotypic testing and phylogenetic analysis of 18S rDNA sequences of the five yeast isolates revealed their relationships to Rhodotorula minuta and Cryptococcus spp. Scanning and transmission electron microscopy demonstrated that the strains possessed morphological characteristics typical for yeast, although they were relatively small, with an average length of 3 micro m. Enumeration through direct counting and most probable number methods showed low numbers of fungi, between 0.01 and 1 cells mL(-1), at some sites. Five of the strains were characterized physiologically to determine whether they were adapted to life in the deep biosphere. These studies revealed that the strains grew within a pH range of 4-10, between temperatures of 4 degrees C and 25-30 degrees C, and in NaCl concentrations from 0 to 70 g L(-1). These growth parameters suggest a degree of adaptation to the groundwater at Aspö HRL. Despite the fact that these eukaryotic microorganisms may be transient members of the deep biosphere microbial community, many of the observations of this study suggest that they are capable of growing in this extreme environment.

Adaptation, Physiological↗
PubMed2004

Antigenic and genetic typing of Whataroa viruses in Australia.

We recently characterized three novel alphaviruses isolated from mosquitoes captured in New South Wales, Australia. Initial cross-neutralization studies revealed antigenic similarity to the Sindbis virus (SINV)-like Whataroa virus (WHAV), heretofore found only in New Zealand. Nucleotide sequence analysis showed that the WHAV-like viruses shared >99% nucleotide sequence similarity with each other, and 96-97% similarity with prototype WHAV. Enzyme-linked immunosorbent assay reactions of a panel of monoclonal antibodies to SINV showed that the novel WHAV-like viruses displayed identical binding patterns and were antigenically distinct from all SINV isolates examined. Although these viruses displayed a similar binding pattern to prototype WHAV, three monoclonal antibodies discriminated them from the New Zealand virus. Our results suggest that these novel alphaviruses are antigenic variants of WHAV and represent the first reported isolations of this virus from outside New Zealand. The monoclonal antibodies used in this study will be useful for typing new SINV and SINV-like isolates.

Alphavirus↗
PubMed2001

Phylogenetic analysis of dengue-3 viruses prevalent in Guatemala during 1996-1998.

Dengue is an acute viral disease transmitted by the Aedes aegypti mosquito which is present in most tropical urban areas of the world. There are four antigenically distinct serotypes, designated dengue-1 (DEN-1), dengue-2 (DEN-2), dengue-3 (DEN-3) and dengue-4 virus (DEN-4). In this study, we determined the serotypes of dengue viruses isolated in Guatemala in 1995-1998, and found that DEN-3 viruses appeared in 1995 and became predominant in the following three years. We then sequenced cDNAs from fifteen DEN-3 isolates recovered during 1996-1998. From the nucleic acid sequences and previously determined DEN-3 sequences, a phylogenetic tree was constructed using the neighbor joining method. The tree indicated that all fifteen isolates and other DEN-3 viruses isolated in Sri Lanka, India, Samoa and Mozambique formed subtype III. More than two decades ago, DEN-3 virus was prevalent in the Caribbean, but the isolates obtained at that time belonged to subtype IV. Therefore, we concluded that the 1996-1998 dengue epidemic in Guatemala was caused by DEN-3 strains, imported from a tropical area of Asia or Africa or from a Pacific island.

DNA, Complementary↗
PubMed1998

Experimental infection of chimpanzees with hepatitis G virus and genetic analysis of the virus.

Hepatitis G virus (HGV) was transmitted to 2 chimpanzees by inoculation with human plasma containing approximately 10(8) genome equivalents (GE) of HGV. The infection was characterized by the late appearance (weeks 10 and 11 after inoculation [pi]) of viremia that persisted throughout the 120-week follow-up. Serum HGV titer increased steadily until it plateaued at 10(6)-10(7) GE/mL. However, despite this relatively high titer, neither of the chimpanzees developed hepatitis. The sequence of the viral genome, recovered from each chimpanzee at week 77 pi, differed from that of the inoculum by 5 nt (2 aa) and 27 nt (2 aa). Two more chimpanzees were inoculated with a first-passage plasma pool. The chimpanzee inoculated with approximately 10(6.7) GE of HGV had viremia at week 1 pi. However, the viral titer increased with the same kinetics as observed in the first passage. The second chimpanzee inoculated with approximately 10(4.7) GE of HGV had late appearance (week 7 pi) of viremia.

Amino Acid Substitution↗
PubMed1997

Dominant-negative mutations of the Wilms' tumour predisposing gene (WT1) are infrequent in CML blast crisis and de novo acute leukaemia.

To determine if mutations of the Wilms' tumor predisposing gene (WT1) are associated with haematological malignancies, we have investigated 65 cases of acute leukaemia, including 39 patients in blast crisis of chronic myeloid leukaemia (CML), by amplification of WT1 exons 7, 8 and 9 followed by single-strand conformation polymorphism analysis. WT1 transcripts were detected by RT-PCR in all samples. An exon 7 silent polymorphism (A-->G; Arg 313) was identified in 17 individuals, 5 of whom were homozygous, but no other lesions were found. In 1 sample from a patient with acute lymphoblastic leukaemia a smaller size transcript missing exon 9 was detected; a similar abnormality has been described previously in a patient with Wilms' tumour and the resultant protein shown to act in a dominant-negative manner. No mutations of the exon 9 donor or acceptor splice sites were found in this patient and the basis of the abnormal transcript remains obscure. We conclude that dominant-negative mutations of the zinc finger region of the WT1 gene are uncommon in CML blast crisis. Abnormalities of this gene may, however, contribute to a small proportion of cases of de novo acute leukaemia.

Acute Disease↗
PubMed2005

Alternative usage of Otx2 promoters during mouse development.

Our previous structural analysis of mouse Otx2 transcripts has revealed the existence of three different promoters and suggested that the corresponding mRNAs could exhibit specific expression patterns. Here, we analyze the precise dynamics of their expression throughout mouse development. Their spatial distribution was determined by isoform-specific in situ hybridization and their relative abundance by real-time reverse transcriptase-polymerase chain reaction. Although the three promoters may be used in the same areas, we show that transcription preferentially occurs from the proximal promoter at onset of gene activity in early embryogenesis, and switches to the more distal one in most of the sites of expression in the adult brain. During gestation, their relative utilization becomes inverted. The third promoter, which shows no activity in embryonic stem cells and is moderately expressed during embryogenesis, is mostly used in specific areas derived from the rostral part of the neural tube.

Animals↗
PubMed2005

Analysis of the transcriptome of the protozoan Theileria parva using MPSS reveals that the majority of genes are transcriptionally active in the schizont stage.

Massively parallel signature sequencing (MPSS) was used to analyze the transcriptome of the intracellular protozoan Theileria parva. In total 1,095,000, 20 bp sequences representing 4371 different signatures were generated from T.parva schizonts. Reproducible signatures were identified within 73% of potentially detectable predicted genes and 83% had signatures in at least one MPSS cycle. A predicted leader peptide was detected on 405 expressed genes. The quantitative range of signatures was 4-52,256 transcripts per million (t.p.m.). Rare transcripts (<50 t.p.m.) were detected from 36% of genes. Sequence signatures approximated a lognormal distribution, as in microarray. Transcripts were widely distributed throughout the genome, although only 47% of 138 telomere-associated open reading frames exhibited signatures. Antisense signatures comprised 13.8% of the total, comparable with Plasmodium. Eighty five predicted genes with antisense signatures lacked a sense signature. Antisense transcripts were independently amplified from schizont cDNA and verified by sequencing. The MPSS transcripts per million for seven genes encoding schizont antigens recognized by bovine CD8 T cells varied 1000-fold. There was concordance between transcription and protein expression for heat shock proteins that were very highly expressed according to MPSS and proteomics. The data suggests a low level of baseline transcription from the majority of protein-coding genes.

Animals↗
PubMed1995

Renal expression of the gene encoding the gastric H(+)-K(+)-ATPase beta-subunit.

The gastric mucosal parietal cells and cells of the renal collecting duct both possess H(+)-K(+)-adenosinetriphosphatase (H(+)-K(+)-ATPase) activities. In the stomach, the H(+)-K(+)-ATPase (EC 3.6.1.3) is responsible for acidification of luminal contents. The kidney H(+)-K(+)-ATPase protein(s) contribute to potassium reabsorption and secretion of hydrogen ions to maintain potassium and acid-base homeostasis. The stomach H(+)-K(+)-ATPase is well defined and consists of an alpha-catalytic subunit of apparent molecular mass of 95 kDa and a highly glycosylated beta-subunit of 60-90 kDa. The molecular identity of the protein that mediates the H(+)-K(+)-ATPase activity in the kidney has been addressed in this paper. A combination of RNA hybridizations, polymerase chain reaction analysis of kidney RNA, and sequence analysis of cDNAs indicated that gastric H(+)-K(+)-ATPase beta-subunit mRNA is present in kidney. Immunoblotting with antibodies specific for the gastric H(+)-K(+)-ATPase beta-subunit detected proteins, which, after deglycosylation, had the same molecular mass as the gastric beta-subunit in membrane protein preparations from rabbit, pig, rat, and mouse kidneys. Furthermore, we have used transgenic mice to demonstrate that the gastric H(+)-K(+)-ATPase beta-subunit gene contains cis-acting regulatory sequences that are active in both gastric parietal cells and the renal collecting ducts. Overall, these data indicate that the gastric H(+)-K(+)-ATPase beta-subunit is found in the kidney and probably associates with the gastric H(+)-K(+)-ATPase alpha-subunit and/or other P-type ATPase alpha-subunits, thus contributing to acid-base and potassium homeostasis.

Animals↗
PubMed1997

Molecular analysis of dengue virus attenuation after serial passage in primary dog kidney cells.

The complete nucleotide sequences of the genomes of dengue-1 virus virulent 45AZ5 PDK-O and attenuated vaccine candidate strain 45AZ5 PDK-27 have been determined and compared with the dengue-1 virus Western Pacific (West Pac) 74 parent strain from which 45AZ5 PDK-O was derived. Twenty-five (0.23%) nucleotide and 10 (0.29%) amino acid substitutions occurred between parent strain dengue-1 virus West Pac 74 and virulent strain 45AZ5 PDK-O, which was derived from the parent by serial passage in diploid foetal rhesus lung (FRhL-2) and mutagenized with 5-azacytidine. These substitutions were preserved in the 45AZ5 PDK-27 vaccine. 45AZ5 PDK-O and PDK-27 strains, which differ by 27 passages in primary dog kidney (PDK) cells, show 25 (0.23%) nucleotide and 11 (0.32%) amino acid divergences. These comparative studies suggest that the changes which occurred between the West Pac 74 and 45AZ5 PDK-O strains may alter the biological properties of the virus but may not be important for attenuation. Important nucleotide base changes responsible for attenuation accumulated between 45AZ5 PDK-O and 27.

Animals↗
PubMed2001

The ABC transporter BcatrB from Botrytis cinerea is a determinant of the activity of the phenylpyrrole fungicide fludioxonil.

This study demonstrates that the ATP-binding cassette (ABC) transporter BcatrB from Botrytis cinerea influences the activity of phenlpyrrole fungicides against the pathogen. This conclusion is based on toxicity assays and northern analysis experiments which show that BcatrB replacement mutants, which do not express the BcatrB gene, show an increased sensitivity to the phenylpyrrole fungicides fludioxonil and fenpiclonil. Mutants overexpressing BcatrB exhibit a decreased sensitivity to these fungicides. In addition, accumulation of fludioxonil by BcatrB replacement mutants was higher than by wild-type isolates. For mutants overexpressing BcatrB the reverse was observed. Additional ABC and major facilitator superfamily (MFS) transporter genes were identified in an expressed sequence tag (EST) database, suggesting that B cinerea has gene families of ABC and MFS transporters. Corresponding fragments of ten ABC (BcatrC-BcatrN) and three MFS transporter genes (Bcmfs1-4) were cloned and characterised. Fludioxonil affected the transcript level of some members of these gene families in germlings during a short treatment with the fungicide at sub-lethal concentrations. Hence, other ABC and MFS transporters may affect the activity of phenylpyrrole fungicides as well. Other fungicides such as the anilinopyrimidine fungicide cyprodinil, the azole fungicide tebuconazole, the dicarboximide fungicide iprodione and the strobilurin fungicide trifloxystrobin also induced transcription of some of the ABC and MFS transporter genes identified. Therefore, we propose that various ABC and MFS transporters function in protection of the fungus against fungicides and are involved in multi-drug resistance development.

ATP-Binding Cassette Transporters↗
PubMed2006

Regulation of osmotic stress transcription factor 1 (Ostf1) in tilapia (Oreochromis mossambicus) gill epithelium during salinity stress.

Mechanisms of induction of osmotic stress transcription factor 1 (Ostf1) were analyzed in gill epithelium of tilapia exposed to salinity stress. Experiments with primary cultures of gill epithelial cells revealed that hyperosmotic Ostf1 induction was independent of systemic factors. In addition, the synthetic glucocorticoid receptor agonist dexamethasone did not affect Ostf1 levels, arguing against cortisol being the signal for Ostf1 induction during hyperosmotic stress. Exposure of primary gill cell cultures to a hyperosmotic agent that is cell permeable and non-hypertonic (glycerol) did not trigger Ostf1 induction. However, when gill cells were exposed to hypertonicity (either in the form of NaCl or other forms) Ostf1 was rapidly and significantly induced. Analysis of hnRNA and mRNA levels revealed that Ostf1 upregulation in gill cells of intact fish and primary cultures of gill epithelial cells was mediated by transient mRNA stabilization. In addition to the initial transient mRNA stabilization a subsequent transcriptional induction of Ostf1 was observed. In cultured gill cells increase in Ostf1 mRNA synthesis was stable and very potent, whereas in gill cells of intact fish this increase was transient. This observation suggests positive feedback by Ostf1 or one of its targets and negative feedback by systemic factors on Ostf1 transcription. We conclude that Ostf1 induction in gill epithelial cells of tilapia exposed to salinity stress (1) is independent of cortisol or other systemic factors; (2) depends on hypertonicity as the signal; and (3) is based on transient mRNA stabilization. Moreover, our data on primary cell cultures show that systemic signals are necessary to prevent sustained transcriptional induction of Ostf1 during hyperosmotic stress, indicating feedback regulation and a high degree of complexity of osmosensing and signaling networks in euryhaline fishes.

Animals↗
PubMed1998

Analysis of the envelope region of hepatitis G virus isolated from Korean patients.

The genetic diversity of hepatitis G virus (HGV) was investigated. By using a RT-PCR procedure, 14% of either HBV (hepatitis B virus)- or HCV (hepatitis C virus)-positive Korean hepatitis patients were proved to be HGV positives. Nucleotide sequences in the E1 region of the eight isolates from Korean patients and the six previously reported isolates were compared. Nucleotide substitutions spread uniformly throughout the E1 region. Sequence homology among the Korean isolates was 84-99% and 88-99% at the nucleotide and amino acid sequences, respectively, whereas those from different geographic areas was slightly lower at both levels. At least two genotypes might exist among the Korean HGV isolates. Compared to the corresponding region of HCV, the E1 sequence from HGV is moderately conserved. In addition, as frameshift mutations were observed in most of the Korean isolates compared to the prototype HGV sequence, the Korean isolates might not use the translational initiation site of the prototype HGV for polyprotein translation. Because a putative signal sequence of E1 for entry into endoplasmic reticulum starts from the N-terminus of the polyprotein, and capsid-like peptides composed of basic amino acids could not be detected from the upstream region of E1, the core protein of HGV is absent, or at least not present, at the region next to 5'-UTR. Therefore, HGV could be clearly distinguished from other genera of Flaviviridae.

Amino Acid Sequence↗
PubMed2005

A hepatitis C virus (HCV) internal ribosome entry site (IRES) domain III-IV-targeted aptamer inhibits translation by binding to an apical loop of domain IIId.

The hepatitis C virus (HCV) has a positive single-stranded RNA genome, and translation starts within the internal ribosome entry site (IRES) in a cap-independent manner. The IRES is well conserved among HCV subtypes and has a unique structure consisting of four domains. We used an in vitro selection procedure to isolate RNA aptamers capable of binding to the IRES domains III-IV. The aptamers that were obtained shared the consensus sequence ACCCA, which is complementary to the apical loop of domain IIId that is known to be a critical region of IRES-dependent translation. This convergence suggests that domain IIId is preferentially selected in an RNA-RNA interaction. Mutation analysis showed that the aptamer binding was sequence and structure dependent. One of the aptamers inhibited translation both in vitro and in vivo. Our results indicate that domain IIId is a suitable target site for HCV blockage and that rationally designed RNA aptamers have great potential as anti-HCV drugs.

5' Untranslated Regions↗
PubMed2006

AceView: a comprehensive cDNA-supported gene and transcripts annotation.

BACKGROUND: Regions covering one percent of the genome, selected by ENCODE for extensive analysis, were annotated by the HAVANA/Gencode group with high quality transcripts, thus defining a benchmark. The ENCODE Genome Annotation Assessment Project (EGASP) competition aimed at reproducing Gencode and finding new genes. The organizers evaluated the protein predictions in depth. We present a complementary analysis of the mRNAs, including alternative transcript variants. RESULTS: We evaluate 25 gene tracks from the University of California Santa Cruz (UCSC) genome browser. We either distinguish or collapse the alternative splice variants, and compare the genomic coordinates of exons, introns and nucleotides. Whole mRNA models, seen as chains of introns, are sorted to find the best matching pairs, and compared so that each mRNA is used only once. At the mRNA level, AceView is by far the closest to Gencode: the vast majority of transcripts of the two methods, including alternative variants, are identical. At the protein level, however, due to a lack of experimental data, our predictions differ: Gencode annotates proteins in only 41% of the mRNAs whereas AceView does so in virtually all. We describe the driving principles of AceView, and how, by performing hand-supervised automatic annotation, we solve the combinatorial splicing problem and summarize all of GenBank, dbEST and RefSeq into a genome-wide non-redundant but comprehensive cDNA-supported transcriptome. AceView accuracy is now validated by Gencode. CONCLUSION: Relative to a consensus mRNA catalog constructed from all evidence-based annotations, Gencode and AceView have 81% and 84% sensitivity, and 74% and 73% specificity, respectively. This close agreement validates a richer view of the human transcriptome, with three to five times more transcripts than in UCSC Known Genes (sensitivity 28%), RefSeq (sensitivity 21%) or Ensembl (sensitivity 19%).

Computational Biology↗
PubMed2003

Abnormal splicing of SHP-1 protein tyrosine phosphatase in human T cells. Implications for lymphomagenesis.

OBJECTIVE: SHP-1 protein tyrosine phosphatase has been implicated in suppressing B-lymphocyte and myeloid cell malignancies; however, there are little data on this role of SHP-1 in T-lymphocyte malignancies. We examined malignant human T cells to identify any abnormalities of SHP-1 that would support a role for this molecule in suppressing T lymphomagenesis. MATERIALS AND METHODS: Human T-lymphocyte cell lines and primary blood cells were used to examine the expression of SHP-1 mRNA and protein. Reverse transcriptase polymerase chain reaction was used to amplify particular portions of the SHP-1 mRNA for cloning and sequencing. Gene transfer was used to examine the effects of SHP-1 on cell growth and morphology. Glutathione S-transferase (GST) fusion proteins were generated and used to determine SHP-1-associated proteins. RESULTS: Leukemia- and lymphoma-derived cell lines were identified that did not express SHP-1 protein. Examination of the mRNA from these and other T-cell lines, and from normal peripheral blood mononuclear cells (PBMCs), revealed three distinct transcripts by restriction enzymes, reverse transcriptase polymerase chain reaction, and Southern blot analysis. In addition to the expected wild-type transcript, two novel transcripts were identified. One was a deletion transcript found only in Jurkat leukemia-derived cells, predicted to encode for a 7-kDa protein containing most of the amino-terminal SH2 domain. The second contained an 88-nucleotide insert that is the unspliced second intron resulting in a frame shift and the formation of a noncoding transcript. This mRNA was found in all cells examined but was the only transcript detected in the cell lines lacking SHP-1 protein. Expressing wild-type SHP-1 in these cell lines resulted in a change in the morphology of the cells with a concomitant decrease in their growth. GST fusion constructs showed the 7-kDa variant able to associate with an identical array of proteins as wild-type SHP-1, suggesting that it could compete with the wild-type SHP-1 for substrates. This protein was detectable in the cell line expressing its corresponding mRNA and was able to induce significant changes in cell morphology when transfected into a cell line expressing wild-type SHP-1; however, it did not induce any changes in cell growth. CONCLUSIONS: These data are the first to show the existence of multiple transcripts of SHP-1 in human transformed T lymphocytes and normal PBMCs and supports previous work showing that alternate forms of SHP-1 mRNA are a common finding in other cells. We also show the lack of splicing out of an intron as a novel mechanism of regulation of SHP-1 protein expression in both normal and transformed T cells. Moreover, we provide the first evidence showing a protein product detectable in cells that is translated from an alternatively spliced form of SHP-1 mRNA, a variant truncated SHP-1 protein having potential biologic relevance. This report provides evidence supporting the concept that SHP-1 can negatively regulate growth of malignant human T cells and that lack of SHP-1 protein or function may be associated with lymphomagenesis.

Alternative Splicing↗