Gary F. Temple

GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes.

Publisher Summary Complete genome sequences are available for three model organisms— Escherichia coli , Saccharomyces cerevisiae , and Caenorhabditis elegans —and for several pathogenic microorganisms such as Helicobacter pylori . Complete genome sequences are expected to become available soon for other model organisms and for humans. This information is expected to revolutionize the way biological questions can be addressed. Molecular mechanisms should now be approachable on a more global scale in the context of (nearly) complete sets of genes, rather than by analyzing genes individually. However, most open reading frames (ORFs) predicted from sequencing projects have remained completely uncharacterized at the functional level. The emerging field of functional genomics addresses this limitation by developing methods to characterize the function of large numbers of predicted ORFs simultaneously.

Sexually transmitted papillomaviral infections: I. The anatomic distribution and pathologic grade of neoplastic lesions associated with different viral types☆☆☆

Multiple colposcopic biopsy specimens were collected from 160 women, with sampling of principal cervical and vulvar lesions as well as secondary areas of either minor acetowhitening or normal epithelium. Papillomaviral deoxyribonucleic acid was detected by Southern blot hybridization in 197 (90%) of the 218 principal biopsy specimens and 93 (46%) of 198 secondary biopsy specimens. Although different papillomaviruses were found at different sites in 31 women, only six of 416 specimens contained multiple types within the same sample. Specific viral types were associated with specific disease patterns. Only one of 80 type 6 or 11 infections had a diagnosis greater than cervical intraepithelial neoplasia, grade 2. In contrast, 42 of 48 (90%) biopsy specimens of cervical intraepithelial neoplasia, grade 3, or invasive cancer contained type 16, 18, or 31. Nonetheless, 12 of 124 (10%) cases of condyloma and cervical intraepithelial neoplasia, grade 1, were associated with types 16, 18, and 31 infections. Of 58 women with multicentric disease, 46 had positive hybridizations for both cervical and vulvar lesions (32 showing the same type in both samples and 14 showing different viruses). Differing patterns of papillomavirus-induced disease arise partly from the predilection of specific viral types for certain anatomic sites and partly through variations in host response. Detection of viral deoxyribonucleic acid in 46% of the secondary biopsy specimens suggests that disease expression may represent focal breakdown of host surveillance within a field of latent papillomaviral infection.

Analysis of individual cervical human papillomavirus types in neolasia: A possible role for type 18 in rapid progression

Histologic and molecular analyses of 214 cervical biopsy specimens were performed to test the hypothesis that certain individual human papillomavirus types that are usually grouped together are differentially distributed in various grades of cervical intraepithelial neoplasia and invasive squamous carcinoma. Specifically, types 16 and 18, which are commonly grouped together, were analyzed separately and compared. Biopsies obtained from three different geographic sites in the United States and Brazil were analyzed by Southern blot hybridization and correlated with the histologic diagnosis from the same tissue sample. There was a highly significant correlation between papillomavirus type and histologic grade comparing all grades of cervical intraepithelial neoplasia with invasive cancer ( p p

Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans

The genome sequences of Caenorhabditis elegans, Drosophila melanogaster and Arabidopsis thaliana have been predicted to contain 19,000, 13,600 and 25,500 genes, respectively. Before this information can be fully used for evolutionary and functional studies, several issues need to be addressed. First, the gene number estimates obtained in silico and not yet supported by any experimental data need to be verified. For example, it seems biologically paradoxical that C. elegans would have 50% more genes than Drosophilia. Second, intron/exon predictions need to be tested experimentally. Third, complete sets of open reading frames (ORFs), or “ORFeomes,” need to be cloned into various expression vectors. To address these issues simultaneously, we have designed and applied to C. elegans the following strategy. Predicted ORFs are amplified by PCR from a highly representative cDNA library using ORF-specific primers, cloned by Gateway recombination cloning and then sequenced to generate ORF sequence tags (OSTs) as a way to verify identity and splicing. In a sample (n=1,222) of the nearly 10,000 genes predicted ab initio (that is, for which no expressed sequence tag (EST) is available so far), at least 70% were verified by OSTs. We also observed that 27% of these experimentally confirmed genes have a structure different from that predicted by GeneFinder. We now have experimental evidence that supports the existence of at least 17,300 genes in C. elegans. Hence we suggest that gene counts based primarily on ESTs may underestimate the number of genes in human and in other organisms.

Possible prognostic significance of human papillomavirus type in cervical cancer.

While several different human papillomaviruses (HPV) have been associated with cancer of the cervix, it is yet to be determined if specific HPV types have clinical or prognostic significance. To address this question, 30 cases of invasive carcinoma (squamous carcinoma, adenosquamous carcinoma, and adenocarcinoma) with HPV DNA sequences detectable in the tissue were analyzed. HPV type was determined by Southern blot DNA hybridization. Clinical information was obtained by chart review, and all biopsy and surgical specimens were reviewed microscopically without knowledge of HPV type. HPV 16 was detected in 14 cases, HPV 18 in 6, and HPV 31 in 2. In eight samples there were distinctly different, but as yet uncharacterized, HPV DNAs. Of the factors evaluated, tumor grade was found to have a statistically significant relationship to HPV type. Eighty-three percent of HPV 18-associated tumors were grade 3 tumors (5 of 6) as compared to only 7% of HPV 16-associated tumors (1 of 14) (P = 0.002). Age at diagnosis and nodal status in relation to HPV type exhibited a trend but were not statistically significant. The mean age of the HPV 18 group was 37 years, compared to 49 years for the HPV 16 group. Similarly, among Stage IB cancers, nodal involvement was associated with 60% of HPV 18 cases (3 of 5) as compared with 36% of HPV 16 cases (4 of 11). These observations suggest that HPV 18 may be associated with a more aggressive form of cervical cancer than other HPV types.

Nucleotide sequence of human papillomavirus type 31: a cervical neoplasia-associated virus.

The nucleotide sequence of human papillomavirus (HPV) 31 DNA (7912 bp) was determined and used to deduce the genomic organization of this cervical cancer-associated virus. Based on comparisons of the HPV 31 DNA sequence to other sequenced HPVs, HPV 31 is a typical papillomavirus most related to HPV 16 (70% identical nucleotides). The E6 and E7 open reading frames (ORF) of HPV 31 contain several potential DNA binding motifs (Cys-X-X-Cys), the locations of which are conserved in all HPVs. The E6 ORF also has the potential to code for an E6* protein. The E7 ORF of HPV31 encodes a polypeptide motif which appears to distinguish HPVs associated with cervical cancer, such as types 16, 18, 31, and 33, from HPVs found primarily in benign lesions, such as types 6 and 11.

A new type of papillomavirus associated with cancer of the uterine cervix

A new human papillomavirus (HPV) type was detected by low-stringency Southern blot hybridization analysis of DNA from an endocervical adenocarcinoma. The genomic DNA of the virus, which was obtained as two BamHI fragments of 3.75 and 4.1 kb, was molecularly cloned into lambda L47 and subsequently subcloned into pBR322 for further characterization. Hybridization studies demonstrated that these viral DNA isolates were only distantly related to other HPV and thus represented a new type of HPV, called HPV 35. A restriction enzyme map was prepared which allowed a comparison of the genetic organization of this HPV with that of HPV 6b; the results demonstrated collinearity of the HPV 35 genome with that of HPV 6b. Prevalence studies revealed that HPV 35 was present in 2 of 158 (1%) anogenital intraepithelial neoplasia and in 3 of 69 (4%) anogenital cancers. Thus HPV 35 is a low-prevalence human papillomavirus associated with anogenital intraepithelial neoplasia and cancer.

Temporal associations of human papillomavirus infection with cervical cytologic abnormalities

The relationship between infection with different human papillomavirus types and cervical intraepithelial neoplasia was studied in a group of 398 women seen in a private gynecology practice in Washington, D.C. Each woman was assessed for human papillomavirus infection by Southern blot hybridization analysis of cervical cells obtained by swab. The human papillomavirus results were correlated with the results of Papanicolaou smears taken the same day and with data abstracted from medical records regarding past cervical disease. Subjects with normal cytologic findings at the time of human papillomavirus testing were followed up for an average of 2 to 3 years with additional Papanicolaou smears. At the time of human papillomavirus testing, 58% (19/33) of women with cervical intraepithelial neoplasia had detectable human papillomavirus deoxyribonucleic acid in contrast to 10% (28/289) of women with normal cytologic findings (p less than 0.001). This association persisted after statistical adjustment for age and current use of oral contraceptives, a factor that appeared to increase the detection of human papillomavirus. Among women with no current cytologic evidence of neoplasia, human papillomavirus detection was more likely in those with a history of past genital neoplasia (p = 0.05). In the follow-up study, 15% (3 of 20) of cytologically normal women who were human papillomavirus-positive at baseline subsequently exhibited cervical cells suggestive of cervical intraepithelial neoplasia compared with only 5% (9 of 195) of human papillomavirus-negative women. However, this difference reflected recurrent and not incident neoplasia.

Human Papillomavirus Type 56: a New Virus Detected in Cervical Cancers

A new human papillomavirus type (HPV-56) was identified by low stringency Southern blot analysis with an HPV-31 DNA probe, in a cervical intraepithelial neoplasm (CIN). The DNA of this virus was molecularly cloned and shown to be a new HPV type based on the absence of cross-reactivity to HPV types 1 to 55 under high-stringency hybridization conditions. At low stringency, HPV-56 was most related to HPV types 30 and 45. The deduced organization of the open reading frames of HPV-56, from hybridization and partial nucleotide sequence analyses, reveals a typical HPV genome. HPV-56 was detected in two of 464 normal cervical tissues, in five of 227 cervical condylomas and CIN, and in two of 84 invasive cancers of the cervix.

A comparison study of human papillomavirus prevalence by the polymerase chain reaction in low risk women and in a gynaecology referral group at elevated risk for cervical cancer

The reported prevalence of human papillomavirus (HPV) type 16 in the genital tracts of women with various gynaecological conditions is highly variable. In particular, some results with the polymerase chain reaction (PCR) technique have suggested that HPV-16 is a ubiquitous or very common virus. We undertook this study to help clarify the current confusion. PCR with HPV consensus L1 primers and specific E6 primers was used to study 89 women attending two gynaecology referral clinics, as well as 99 women attending a health maintenance organization (HMO) clinic; 70 of these latter women had no current or prior history of genital HPV disease. HPV-16 was detected in less than 5% of cytologically normal women from either group and in 17% (6/36) and 31% (9/29) of women with cervical intraepithelial neoplasia (CIN) from the referral clinic and the HMO, respectively. The other high-risk or intermediate-risk HPVs (types 18, 31, 33 or 35) were less prevalent than HPV 16 in all groups of women. A majority of the HPV types detected by the L1 primers in normal women were uncharacterized HPVs. Overall these uncharacterized HPVs were detected in 37% (46/123) of the normal women and in 48% (31/65) of the women with CIN. Using the most sensitive PCR product detection method employed in the study, HPV DNA was detected in 36% (4/11) of swab specimens obtained from the external abdomen.