Chromosome mapping of the human gene encoding the 68-kDa nuclear antigen (p68) by using the polymerase chain reaction

DEAD-Box RNA Helicases DDX3X and DDX5 as Oncogenes or Oncosuppressors: A Network Perspective

Simple Summary

The transformation of a normal cell into a cancerous one is caused by the deregulation of different metabolic pathways, involving a complex network of protein–protein interactions. The cellular enzymes DDX3X and DDX5 play important roles in the maintenance of normal cell metabolism, but their deregulation can accelerate tumor transformation. Both DDX3X and DDX5 interact with hundreds of different cellular proteins, and depending on the specific pathways in which they are involved, both proteins can either act as suppressors of cancer or as oncogenes. In this review, we summarize the current knowledge about the roles of DDX3X and DDX5 in different tumors. In addition, we present a list of interacting proteins and discuss the possible contribution of some of these protein–protein interactions in determining the roles of DDX3X and DDX5 in the process of cancer proliferation, also suggesting novel hypotheses for future studies.

Abstract

RNA helicases of the DEAD-box family are involved in several metabolic pathways, from transcription and translation to cell proliferation, innate immunity and stress response. Given their multiple roles, it is not surprising that their deregulation or mutation is linked to different pathological conditions, including cancer. However, while in some cases the loss of function of a given DEAD-box helicase promotes tumor transformation, indicating an oncosuppressive role, in other contexts the overexpression of the same enzyme favors cancer progression, thus acting as a typical oncogene. The roles of two well-characterized members of this family, DDX3X and DDX5, as both oncogenes and oncosuppressors have been documented in several cancer types. Understanding the interplay of the different cellular contexts, as defined by the molecular interaction networks of DDX3X and DDX5 in different tumors, with the cancer-specific roles played by these proteins could help to explain their apparently conflicting roles as cancer drivers or suppressors.

The role of DEAD-box RNA helicase p68 (DDX5) in the development and treatment of breast cancer

RNA helicase p68 or DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5) is a unique member of the highly conserved protein family, which is involved in a broad spectrum of biological processes, including transcription, translation, precursor messenger RNA processing or alternative splicing, and microRNA (miRNA) processing. It has been shown that p68 is necessary for cell growth and participates in the early development and maturation of some organs. Interestingly, p68 is a transcriptional coactivator of numerous oncogenic transcription factors, including nuclear factor-κβ (NF-κβ), estrogen receptor α (ERα), β-catenin, androgen receptor, Notch transcriptional activation complex, p53 and signal transducer, and activator of transcription 3 (STAT3). Recent studies on the role of p68 (DDX5) in multiple dysregulated cellular processes in various cancers and its abnormal expression indicate the importance of this factor in tumor development. Discussion of the precise role of p68 in cancer is complex and depends on the cellular microenvironment and interacting factors. In terms of the deregulated expression of p68 in breast cancer and the high prevalence of this cancer among women, it can be informative to review the precise function of this factor in the breast cancer. Therefore, an attempt will be made in this review to clarify the tumorigenic function of p68 in association with its targeting potential for the treatment of breast cancer.

Cyclin-dependent kinase-associated protein Cks2 is associated with bladder cancer progression

In this observational retrospective study, expression of possible cancer-related genes was measured in patients with a pathological diagnosis of superficial bladder cancer. Further measurements were made in those who subsequently developed muscle-invasive cancer. Seven of the 45 patients with superficial bladder cancer progressed to muscle-invasive cancer. Expression of fatty acid binding protein 5 (FABP5), poly(A) binding protein cytoplasmic 1 (PABPC1), DEAD box polypeptide 5 (DDX5), splicing factor 3b subunit 1 (SF3B1), murine mammary tumour integration site 6 (EIF3S6), tropomyosin 2β (TPM2), transgelin (TAGLN) and cyclin-dependent kinase-associated protein (Cks2) genes was measured in bladder samples using real-time reverse transcription-polymerase chain reaction. FABP5, PABPC1, DDX5, SF3B1, EIF3S6 and Cks2 expression levels were significantly increased, and TPM2 and TAGLN were significantly decreased, in superficial bladder cancer compared with normal bladder tissue. In patients who developed muscle-invasive cancer, the Cks2 gene showed significantly increased expression after, compared with before, invasion. The Cks2 gene may have potential as a biomarker for predicting superficial bladder cancer progression to muscle-invasive cancer.

Structure and expression of the human p68 RNA helicase gene

Nuclear DEAD box protein p68 is immunologically related to SV40 large tumour antigen and both proteins possess RNA helicase activity. In this report, we describe the structural organisation of the human p68 gene and aspects of the regulation of its expression. Northern blot and primer extension analyses indicate that, although its level is variable, the p68 RNA helicase appears to be expressed from a single transcription start site in all tissues tested. Sequence analysis revealed that the p68 promoter harbours a 'TATA', a 'CAAT' and an initiator element and contains high affinity binding sites for Sp1, AP-2, CRE and Myc. This and functional promoter analyses in transient expression assays suggest that transcriptional regulation of the p68 gene is complex. Furthermore, there are indications that p68 expression is also regulated post-transcriptionally. Steady-state pools of poly(A)(+)RNA from human cells contain completely spliced p68 mRNA and alternatively spliced forms that contain introns 8-11 or 8-12 (from a total of 12 introns) and are not translated. Analysis of a conditionally p68-overproducing HeLa cell line points to negative autoregulation at the level of splicing, which is confirmed by a recently reported association of p68 with spliceosomes in human cells.

Molecular cloning and characterization of a novel human ribonuclease (RNase k6): increasing diversity in the enlarging ribonuclease gene family

The discovery of Ribonuclease k6 (RNase k6) was an unexpected result of our ongoing efforts to trace the evolutionary history of the ribonuclease gene family. The open reading frame of RNase k6, amplified from human genomic DNA, encodes a 150 amino acid polypeptide with eight cysteines and histidine and lysine residues corresponding to those found in the active site of the prototype, ribonuclease A. The single-copy gene encoding RNase k6 maps to human chromosome 14 and orthologous sequences were detected in both primate and non-primate mammalian species. A single mRNA transcript (1.5 kb) was detected in all human tissues tested, with lung representing the most abundant source. At the cellular level, transcripts encoding RNase k6 were detected in normal human monocytes and neutrophils (but not in eosinophils) suggesting a role for this ribonuclease in host defense. Of the five previously identified human ribonucleases of this group, RNase k6 is most closely related to eosinophil-derived neurotoxin (EDN), with 47% amino acid sequence identity; slight cross-reactivity between RNase k6 and EDN was observed on Western blots probed with polyclonal anti-EDN antiserum. The catalytic constants determined, Km = 5.0 microM and Kcat = 0.13 s-1, indicate that recombinant RNase k6 has approximately 40-fold less ribonuclease activity than recombinant EDN. The identification and characterization of RNase k6 has extended the ribonuclease gene family and suggests the possibility that there are others awaiting discovery.

Human ribonuclease 4 (RNase 4): coding sequence, chromosomal localization and identification of two distinct transcripts in human somatic tissues

We have isolated a unique genomic fragment encoding human ribonuclease 4 (RNase 4) of the mammalian ribonuclease gene family, whose members include pancreatic ribonuclease, eosinophil-derived neurotoxin, eosinophil cationic protein and angiogenin. We have determined that the coding sequence of RNase 4 resides on a single exon found on human chromosome 14. The mRNA encoding RNase 4 was detected by Northern analysis in a number of human somatic tissues, including pancreas, lung, skeletal muscle, heart, kidney and placenta, but not brain; liver represents the most abundant source. Interestingly, the mRNA encoding RNase 4 is approximately 2 kb in length, which is approximately twice as large as the mRNAs encoding other members of this gene family. A larger (approximately 2.4 kb), second transcript was detected in hepatic, pancreatic and renal tissues. The approximately 2 kb RNase 4 mRNA was detected in cells of the human promyelocytic leukemia line, HL-60, that had been treated with dibutyryl-cAMP to promote neutrophilic differentiation. In contrast, no mRNA encoding RNase 4 could be detected in cells treated with phorbol myristic acid (PMA), an agent promoting differentiation toward monocyte/macrophages, suggesting the existence of elements regulating tissue specific expression of this gene.

A somatic cell hybrid map of the long arm of human chromosome 17, containing the familial breast cancer locus (BRCA1)

We describe a detailed somatic cell hybrid map of human chromosome 17q11.2-q23, containing the familial breast and ovarian cancer locus (BRCA1) and highly informative closely linked markers. An X-irradiation panel of 38 hamster/human and mouse/human hybrids with fragments of chromosome 17 was generated and characterized with 22 STS markers from this chromosome. A detailed map of 61 probes onto chromosome 17q, subdividing the chromosome arm into 25 regions, was done by using a panel of hybrids with well-defined breakpoints and nine chromosome-mediated gene transfectants. Our localization of RARA, TOP2, EDH17B1 and 2, and possibly WNT3, between THRA1 and D17S181, two markers known to flank BRCA1, suggests that any of these is a potential candidate for the BRCA1 locus. The marker D17S579 (Mfd188), which is believed to be very close to BRCA1, maps closest to the EDH17B genes.

Cloning, expression and localization of an RNA helicase gene from a human lymphoid cell line with chromosomal breakpoint 11q23.3

A gene encoding a putative human RNA helicase, p54, has been cloned and mapped to the band q23.3 of chromosome 11. The predicted amino acid sequence shares a striking homology (75% identical) with the female germline-specific RNA helicase ME31B gene of Drosophila. Unlike ME31B, however, the new gene expresses an abundant transcript in a large number of adult tissues and its 5' non-coding region was found split in a t(11;14)(q23.3;q32.3) cell line from a diffuse large B-cell lymphoma.

Assignment of eight loci to bovine syntenic groups by use of PCR: extension of a comparative gene map

The polymerase chain reaction (PCR) has been combined with hybrid somatic cell technology to extend the bovine physical map. Eight bovine loci--glycoprotein hormone alpha (CGA), coagulation factor X (F10), chromogranin A (CHGA), low-density lipoprotein receptor (LDLR), human prochymosin pseudogene (CYM), oxytocin (OXT), arginine-vasopressin (ARVP), and cytochrome oxidase c subunit IV pseudogene (COXP)--were assigned to bovine syntenic groups with this approach. CGA was assigned to bovine syntenic group U2, F10 to U27, CHGA to U4 [bovine Chromosome (Chr) 21], LDLR to U22, CYM to U6, OXT and ARVP to U11, and COXP to U3 (bovine Chr 5). Seven of these genes, CGA, F10, CHGA, LDLR, OXT, ARVP, and CYM, further delineate regions of chromosomal conservation on human Chrs 6, 13, 14, 19, 20, 20, and 1, respectively. CHGA, OXT, and ARVP are unmapped in the mouse. Comparative mapping predicts the mouse CHGA will map to Chr 12, and mouse OXT and ARVP will map to mouse Chr 2. Furthermore, human CYM is predicted to be sublocalized to 1p32-q21. The primers developed for these eight loci will be useful for the development of hybrid somatic cell panels in the future as well as establishing a collection of bovine expressed sequence tags.

Use of 3' untranslated sequences of human cDNAs for rapid chromosome assignment and conversion to STSs: implications for an expression map of the genome

A general mapping strategy is described in which the 3'untranslated regions of human cDNAs are used to design PCR primers which will selectively amplify human genomic sequences in a rodent background. When applied to panels of human x hamster somatic cell hybrid DNAs, this approach provides a PCR-based method for rapidly assigning genes to specific chromosomes and chromosomal regions. In addition, it follows from the virtual absence of introns in the 3'untranslated region of vertebrate genes that within this region the cDNA sequences almost always will be identical to those of the genomic DNA and can therefore be used to automatically generate gene-specific sequence-tagged sites (STSs). We have applied this strategy to six human cDNAs and demonstrate that 1) the primers selectively amplify human genomic DNA and 2) the PCR product is of the size predicted from the cDNA. To test this approach further we have utilized it to confirm the known chromosomal location of the retinoblastoma gene. Lastly, we describe how this strategy can readily be applied to unknown human cDNAs, and thereby be integrated into efforts to generate a human STS expression map of the genome. A strategy for production of such a map, using human brain cDNAs as a model, is described.

A novel RNA helicase gene tightly linked to the Triplo-lethal locus of Drosophila

The Triplo-lethal (Tpl) locus of Drosophila is the only known locus which is lethal when present in three copies rather than the normal two. After recovering a hybrid-dysgenesis-induced mutation of Tpl we used a rapid combination of transposon tagging, chromosome microdissection and PCR to clone the P element that had transposed into the Tpl region. That P element is located within the gene for a new and unique member of the RNA helicase family. This new helicase differs from all others known by having glycine-rich repeats at both the amino and carboxyl termini. Curiously, genetic analysis shows that the P element inserted into this gene is not responsible for the Tpl mutant phenotype. We present possible explanations for these findings.