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Investigation on the presence of polyomavirus, herpesvirus, and papillomavirus sequences in colorectal neoplasms and their association with cancer.
No full textDear Sir,
Studies in literature suggest that some human viruses, including JC polyomavirus (JCV),1–3 human cytomegalovirus (HCMV),4 human papillomaviruses (HPVs),5–8 and Epstein-Barr virus (EBV),9, 10 have a pathogenic role in starting or promoting colorectal cancer. However, a revision of the literature indicates that this association between colorectal tumors and viral infection is still matter of debate11–15 and further studies using robust methods to detect viral infection are required. In fact, the prevalence of viral infection in colorectal cancer samples varies widely among series, and this variability appears to be mainly related to technical aspects, such as in the case of JCV, for which the prevalence in colorectal tumors has been reported to range from 011 to 90%1–3, 16 in different studies.
In our study, we used sensitive quantitative real-time PCR analysis and PCR and sequencing to investigate the prevalence of genome sequences not only of JCV, but also of other polyomaviruses which have been involved in human infection, i.e., BK virus (BKV), Simian virus 40 (SV40), and the newly discovered Washington University polyomavirus (WUV), Karolinska Institute polyomavirus (KIV) and Merkel cell carcinoma polyomavirus (MCV),17 in a large series of colorectal adenocarcinomas, adenomas and normal mucosa samples. Moreover, in the same samples, we investigated the presence DNA sequences of the herpesviruses HCMV and EBV and HPVs, which have been also suggested to be associated with colorectal tumorigenesis. A detailed description of methods is reported in the supporting information table. Patients gave informed consent to the study, which was approved by the local ethics committee and performed according to Declaration of Helsinki guidelines.
Originally, the aim of our study was to investigate the prevalence of JCV infection in colorectal cancers from different age groups. To this aim, we first analyzed 144 archival samples of formalin-fixed paraffin-embedded tissues (group 1, Table I), collected at the Department of Medical Diagnostic Sciences and Special Therapies of the University of Padova in the period ranging from 1998 to 2007. Group 1 included colorectal adenocarcinomas and adjacent mucosa, from 72 patients, who were selected on the basis of age (36 patients were ≤45 years, age range 32–45 years; 36 patients were ≥75 years, age range 75–89 years) and matched for gender (14 males and 22 females in both subgroups), tumor site (28 in sigmoid, 30 in ascendent, 11 in descendent, and 3 in rectal colon in both subgroups), and stage (11 stage I-II, 17 stage III, 8 stage 4 in both subgroups). Quite unexpectedly, all samples of group 1 tested negative for JCV DNA at real-time PCR analysis. So, we tried other 3 validated primers and probe sets to detect JCV DNA and investigated whether genome sequences of other polyomaviruses, including the newly discovered viruses, were detectable in colorectal samples. But, no BKV, SV40, KIV, WUV and MCV DNA was detectable in any sample (Table I).
Regarding the study of herpesviruses, 3 cancers and 1 cancer-adjacent mucosa from group 1 were positive for EBV DNA; likewise, 2 cancers and 2 cancer-adjacent mucosa samples were HCMV DNA-positive, without significant differences between age groups and among tumor sites and stages (Table I). Analysis of HPV infection demonstrated that 2 sigmoidal cancers from a male and a female patient <45 years of age were positive for HPV-16 DNA (Table I).
The low frequency of viral DNA detection in this group of archival tumor samples prompted us to subsequently investigate fresh-frozen tissue samples to obtain better quality DNA. In particular, we investigated colorectal biopsies and tissue samples, which were consecutively collected during colonoscopy or surgery performed at the Department of Surgical and Gastroenterological Sciences of the University of Padova in the period ranging from January 2007 to July 2007 (group 2, Table II). Group 2 samples were obtained from 22 patients with colorectal adenomas (2 hyperplastic, 15 tubular, 5 tubulovillous) and 28 patients with colorectal adenocarcinoma (1 stage 0, 5 stage I, 8 stage II, 10 stage III and 4 stage IV). Mean age was 71.6 years (range, 41–92 years), 24 were males and 26 females. Overall, 5 tumors were located in caecum, 8 in ascendent, 1 in transvers, 4 in descendent, 17 in sigmoid colon and 15 in rectum. From each patient, pathologic tissues and tissues at about 3 and 10-cm distance from the lesions were collected. In addition, we analyzed biopsies of rectal, ascending and transverse colonic mucosa, obtained from 15 control subjects without medical history of colorectal pathology and without detection of lesions at colonoscopy (mean age, 58 years; age range, 36–82 years; 10 males, 5 females) (group 3).
Like in group 1, no polyomavirus DNA sequences were detected in any sample of groups 2 and 3 (Table II). Regarding herpesviruses, EBV-DNA was detected in 11 colorectal cancers (including 2 with positive adjacent mucosa), in 5 adenomas (including 4 with positive adjacent mucosa), in 2 samples of 3-cm-adjacent mucosa, and in 1 sample of 10-cm-adjacent mucosa (with negative associated cancer or adenoma samples); HCMV-DNA was detected in 3 carcinomas (including 1 with positive adjacent mucosa) and in 1 sample of 10-cm-adjacent mucosa, but not in adenoma samples (Table II). EBV and HCMV-DNA load in tissue samples, calculated as the number of viral genome equivalents per cell, was very low in both tumor samples and adjacent mucosa (median EBV DNA load, 50 copies/106 cells; range, 10–10,000 copies/106 cells; median HCMV DNA load, 70 copies/106 cells; range, 10–30000 copies/106 cells) and consistent with lymphocyte/macrophage infiltration, rather than infection of tumor cells. The rate of EBV-DNA detection in carcinoma and adenoma samples was significantly higher than in adjacent mucosa (χ2-test, p < 0.05) and was explained by a greater inflammatory cell infiltration in neoplastic tissues than in normal mucosa. In the control group (group 3), EBV-DNA was detected in 5 out of 15 subjects (in the rectal mucosa in 2 cases, in the ascending colon in 2, and in all 3 colon samples in one subject); HCMV-DNA was detected in the rectal mucosa from a patient who was also EBV-positive.
High-risk HPV-16 DNA was detected by both nested PCR/sequencing and real-time PCR in 2 rectal carcinomas and in a sigmoid adenoma of group 2, but not in control group 3 samples (Table III). In the 3 positive cases, the adjacent mucosa was also HPV-16 DNA-positive.
In the literature, JCV genome sequences were detected by PCR amplification and Southern blot hybridization in 90% of colorectal cancers and in the adjacent normal colonic epithelium, with a 10-fold higher viral load in cancers than in adjacent mucosa,1, 2 as well as in 82% of sporadic adenomatous polyps.18 In colorectal mucosa, JCV was suggested to promote tumorigenesis through a direct interaction of its large T antigen (Tag) with β-catenin and p53.2, 3 Since a variant of the JCV Mad-1 strain was preferentially detected in colon cancers, it was hypothesized that this strain might be selectively activated in colonic epithelial cells.19 It cannot however be excluded that detection of a unique JCV strain represented a laboratory contamination, since the same Mad-1 strain was used as positive control in the laboratory.11 In our study, we used real-time PCR to detect viral sequences. This method is very sensitive and specific, but much less susceptible to amplicon contamination than PCR followed by Southern-blot, which was employed in the other studies. A study on large series of colorectal cancer/normal tissue pairs,11 which also employed real-time PCR, failed to demonstrate the presence JCV-DNA sequences in all samples, in agreement with our results. Immunostaining for SV40 TAg has been reported to give problems of false positive results,20 so it cannot be excluded that reported JCV TAg detection in colorectal tissues is also a technical artefact, since the same antibodies against SV40 TAg were employed to investigate JCV expression, exploiting their cross-reactivity with JCV Tag.2, 18
Reports regarding detection of BKV and SV40 in colorectal cancers are conflicting, with negative results in 1 study,21 in agreement with our data, but positive findings in a recent Italian report which demonstrated BKV and SV40 DNA in 6 and 10 out of 66 colorectal carcinomas, respectively.22 Problems of PCR contamination cannot be excluded even in this study, since the primers employed could amplify SV40 DNA sequences which are present in some laboratory plasmids.22 Our data seem also to exclude WUV, KIV and MCV polyomavirus have any role in colorectal tumorigenesis.
HCMV has also been implicated in colorectal tumorigenesis because of its detection in about 80% of tumors, but not in adjacent non-neoplastic mucosa,4, 23 and because of the demonstration that HCMV infection of colorectal cancer cell lines in vitro resulted in induction Bcl2 and cycloxygenase-2 proteins, both of which are involved in important pathways of colorectal cancer progression.4 In contrast, other studies failed to detect HCMV DNA sequences in tumour samples.12–14 Regarding EBV, it has been associated with gastric adenocarcinoma and gastric lymphoepithelioma, whereas its involvement in colorectal tumorigenesis seems to be excluded by several studies which, generally, did not detect EBV-positive cancer cells, even though some EBV-positive tumor infiltrating B lymphocytes were frequently found.9, 24–26 However, we do not rule out the possibility that the occasional presence of EBV and HCMV in infiltrating lymphocytes/monocytes in colorectal mucosa may promote the production and release of cytokines and growth factors or deregulate tumor suppressor genes and thus cooperate with cancer development.
Among candidate oncogenic viruses for colorectal tumorigenesis, HPV is the most reliable, as indicated by the epidemiological evidence of high-risk HPV infection in a relatively high percentage of colorectal tissues from patients with cancer, but not in control subjects without cancer.5–8 Accordingly, we also identified HPV-16 DNA in some cases of distally localized colorectal cancers. Persistent high-risk HPV infection has been definitely demonstrated to be a necessary cause for development of cervical cancer and other anogenital cancers27, 28 and might also be responsible for some cases of colorectal cancer. While waiting for further epidemiological data and for experimental studies to confirm this hypothesis, we can predict anti-HPV vaccination might have an impact on colorectal cancer prevention.
In conclusion, our study, which for the first time systematically investigated the presence of genomic sequences of several putative oncogenic viruses in a large series of colorectal neoplasms, seems to exclude JCV, BKV, SV40, WUV, KIV, MCV, HCMV and EBV have a prominent role in the pathogenesis of colorectal cancer, whereas it suggests high-risk HPV could be involved in some cases of distally localized colorectal carcinoma.
Yours sincerely,
Valentina MILITELLO, Marta TREVISAN, Laura SQUARZON, Maria Angela BIASOLO, Massimo RUGGE, Carmelo MILITELLO, Giorgio PALÚ and Luisa BARZO
Evaluation of the Uro4 HB<M system for the rapid diagnosis of lower respiratory tract infections in intensive care units
No full textRespiratory tract infection is a common and important problem in the intensive care unit (ICU) setting. It has been demonstrated that an appropriate initial regimen or its early modification (within 6-12h from diagnosis) based on microbiological results leads to a higher survival rate. Here we evaluated the Uro4 HB&L automated system for the rapid diagnosis of respiratory tract infections in ICU patients. A total of 644 lower respiratory tract specimens collected from 400 inpatients from nine ICUs at the Padova University hospital were collected during a 12-month period. All samples were processed both with the Uro4 HB&L system and with the reference culture method. Out of 322 samples, 312 were concordant positive, 276 out of 276 were concordant negative, 66 samples were declared uncertain and discarded because of an excess in turbidity. The diagnostic accuracy was good, compared with standard cultures from BAL specimens, in terms of sensitivity (0.972), specificity (1.00), likelihood ratios and diagnostic odds ratio. Ten discordant samples, resulted positive with the reference culture and not detectable with the Uro4 HB&L, were confirmed positive by Gram-stain smear analysis performed after incubation. The Uro4 HB&L system, compared to the standard culture method, revealed a very high sensitivity and a full specificity in identifying clinically relevant microorganisms from lower respiratory tract samples after merely 6h. Overall our results indicate that Uro4 HB&L is a reliable system for the surveillance of the respiratory tract infections in ICUs; it could speed up the laboratory procedures and provide fast, reliable results for clinicians
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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