Mutational Signatures in Mandibular Ameloblastoma Correlate with Smoking.

Ameloblastoma is a rare tumor of odontogenic epithelium, the low incidence rate of which precludes statistical determination of its molecular characterizations. Despite recent genomic and transcriptomic profiling, the etiology of ameloblastomas remains poorly understood. Risk factors of ameloblastoma development are also largely unknown. Whole exome sequencing was performed on 11 mandibular ameloblastoma samples. We identified 2 convergent mutational signatures in ameloblastoma: 1) a signature found in multiple types of lung cancers with probable etiology of tobacco carcinogens (COSMIC signature 4) and 2) a signature present in gingivobuccal oral squamous cell carcinoma and correlated with tobacco-chewing habits (COSMIC signature 29). These mutational signatures highlight tobacco usage or related mutagens as one possible risk factor of ameloblastoma, since the association of BRAF mutations and smoking was demonstrated in multiple studies. In addition to BRAF hotspot mutations (V600E), we observed clear inter- and intratumor heterogeneities. Interestingly, prior to BRAF mutation, important genes regulating odontogenesis mutated (e.g., corepressor BCOR), possibly playing important roles in tumorigenesis. Furthermore, recurrent mutations in the CDC73 gene, the germline mutations of which predispose patients to the development of jaw tumors, were found in 2 patients, which may lead to recurrence if not targeted by therapeutic drugs. Our unbiased profiling of coding regions of ameloblastoma genomes provides insights to the possible etiology of mandibular ameloblastoma and highlights potential disease risk factors for screening and prevention, especially for Asian patients. Because of the limited sample size and incomplete habitual, dietary, and occupational data, a causal link between tobacco usage and ameloblastoma still requires further investigations.

Preoperative downstaging chemoradiation with concurrent irinotecan and capecitabine in MRI-defined locally advanced rectal cancer: a phase I trial (NWCOG-2).

BACKGROUND: The aim of this study was to investigate the safety of neoadjuvant chemoradiation using radiotherapy (RT) combined with concurrent capecitabine and irinotecan for locally advanced rectal cancer before surgery. METHODS: Forty-six patients were recruited and treated on the basis that MRI scanning had shown poor-risk tumours with threatening (< or =1 mm) or involvement of the mesorectal fascia. Conformal RT was given using 3 or 4 fields at daily fractions of 1.8 Gy on 5 days per week to a total dose of 45 Gy. Concurrently oral capecitabine was given twice daily throughout radiotherapy continuously from days 1 to 35 and intravenous irinotecan was given once per week during weeks 1 to 4 of RT. Dose levels were gradually escalated as follows. Dose level 1: capecitabine 650 mg m(-2) b.i.d. and irinotecan 50 mg m(-2); Dose level 2: capecitabine 650 mg m(-2) b.i.d. and irinotecan 60 mg m(-2); Dose level 3: capecitabine 825 mg m(-2) b.i.d. and irinotecan 60 mg m(2); Dose level 4: capecitabine 825 mg m(-2) b.i.d. and irinotecan 70 mg m(-2). RESULTS: Diarrhoea (grade 3, no grade 4) was the main serious acute toxicity with lesser degrees of fatigue, neutropenia, anorexia and palmar-plantar erythrodysesthesia. The recommended dose for future study was dose level 2 at which 3 of 14 patients (21%) developed grade 3 diarrhoea. Postoperative complications included seven pelvic or wound infections and two anastomotic and two perineal wound dehiscences. There were no deaths in the first 30 days postoperatively. Of 41 resected specimens, 11 (27%) showed a pathological complete response (pCR) and five (12%) showed an involved circumferential resection margin (defined as < or =1 mm). The 3-year disease-free survival (intent-to-treat) was 53.2%. CONCLUSION: In patients with poor-risk MRI-defined locally advanced rectal cancer threatening or involving the mesorectal fascia, preoperative chemoradiation based on RT at 45 Gy in 25 daily fractions over 5 weeks with continuous daily oral capecitabine at 650 mg m(-2) b.i.d. days 1-35 and weekly IV irinotecan at 60 mg m(-2) weeks 1-4, provides acceptable acute toxicity and postoperative morbidity with encouraging response and curative resection rates.

Irinotecan+5-fluorouracil with concomitant pre-operative radiotherapy in locally advanced non-resectable rectal cancer: a phase I/II study.

In the UK, 10% of patients diagnosed with rectal cancer have inoperable disease at presentation. This study ascertained whether the resectability rate of inoperable locally advanced rectal cancer was improved by administration of intravenous irinotecan, 5-fluorouracil (5-FU) and pelvic radiotherapy. During phase I of the trial (n=12), the dose of irinotecan was escalated in three-patient cohorts from 50 mg m(-2) to 60 mg m(-2) to 70 mg m(-2) to identify the maximum tolerated dose (60 mg m(-2)). In phase II, 31 patients with non-resectable disease received 45 Gy radiotherapy and 5-FU infusions (200 mg m(-2) per day) for 5 weeks. Irinotecan (60 mg m(-2)) was given on days 1, 8, 15 and 22. After treatment, patients were operated on if possible. Thirty patients completed the protocol, 28 underwent surgery. Before surgery, MRI restaging of 24 patients showed that 19 (79%) had a reduction in tumour stage after treatment (seven complete clinical response and 12 partial). Of 27 patients followed up after surgery, 22 (81%) had clear circumferential resection margins. Disease-free and overall survival estimates at 3 years were 65 and 90%, respectively. The regimen was well tolerated. Irinotecan, 5-FU and radiotherapy results in tumour downgrading, allowing resection of previously inoperable tumour with acceptable toxicity.

Risk factors for hospital-acquired urinary tract infection in a large English teaching hospital: a case-control study.

About 10% of patients in hospital develop a hospital-acquired infection (HAI); the most commonly affected site is the urinary tract. Many studies have examined risk factors for HAI but few have adjusted for confounding and interaction. We performed a prospective case-control study on six acute wards of a busy English teaching hospital to assess risk factors for hospital-acquired urinary tract infection (HAUTI). Over a 2-year period, 136 cases were identified (2.8% of all patient episodes) along with 408 controls. Multiple logistic regression revealed that female sex, increased length of stay, elective admission, surgical operation, and transurethral and repeated intermittent catheterization were all significant independent risk factors for HAUTI. However, specialty of admission was also a significant risk factor when added to the model and, under these conditions, only length of stay and catheterization also remained significant. We detected significant interactions suggesting that the risk of HAUTI is maximal among women undergoing elective surgery, especially those who are catheterized; however, the overall risk of HAUTI among patients admitted electively was greater than for patients admitted as emergencies.

PCR sequencing of the spike genes of geographically and chronologically distinct human coronaviruses 229E.

A reverse transcription nested PCR (RT-PCR) sequencing methodology was developed and used to generate sequence data from the spike genes of three geographically and chronologically distinct human coronaviruses 229E. These three coronaviruses were isolated originally from the USA in the 1960s (human coronavirus 229E strain ATCC VR-74), the UK in the 1990s (human coronavirus 229E LRI 281) and Ghana (human coronavirus 229E A162). Upon translation and alignment with the published spike protein sequence of human coronavirus 229E 'LP' (isolated in the UK in the 1970s), it was found that variation within the translated protein sequences was rather limited. In particular, minimal variation was observed between the translated spike protein sequence of human coronaviruses 229E LP and ATCC VR-74 (1/1012 amino acid differences), whilst most variation was observed between the translated spike protein sequence of human coronaviruses 229E LP and A162 (47/1012 amino acid changes). Further, the translated spike protein sequence of human coronavirus 229E A162 showed three clusters of amino acid changes, situated within the 5' half of the translated spike protein sequence.

Sequence variation in the early genes E1E4, E6 and E7 of human papilloma virus type 6.

The majority of condylomata acuminata (anogenital warts) are caused by infection with Human Papilloma Virus type 6 (HPV-6). We have sequenced the HPV-6 early genes, E1-E4, E6 and E7 from wart biopsy DNA samples sourced from the UK and USA and derived a consensus sequence for these genes and the proteins they encode. When compared to the prototype HPV-6b sequence, published over 12 years ago, the E1-E4 consensus sequence showed 3/91 (3.3%) amino acid changes, the E6 consensus sequence showed 1/150 (0.7%) changes and the E7 consensus sequence showed 1/98 (1.0%) changes. Since many of the early gene sequences from biopsy material were more similar to the HPV-6a subtype than HPV-6b, this data supports the use of HPV-6a as the HPV-6 prototype.

The incidence and detection of HPV in the upper aerodigestive tract using brush and biopsy techniques.

The association between human papillomavirus (HPV) and squamous carcinoma is well established. In the polymerase chain reaction (PCR) we have an effective technique for detecting small quantities of viral DNA, but the assay requires tissue taken at endoscopy to reveal the presence or absence of HPV. Brushings have been used effectively elsewhere in the body to obtain cytological material. This study set out to ascertain if sufficient viral DNA could be obtained, using a laryngeal brushing and the PCR, to detect the presence or absence of HPV. Six patients with squamous carcinoma of the larynx and seven controls who were having laryngoscopy for other reasons underwent laryngeal biopsy. In addition, in the patients with carcinoma, biopsies were taken at the tumour margins and brushings from both sites. The samples were tested for the presence of HPV types 6, 11, 16, 18 and 31 by means of the PCR. The distribution of HPV types was as expected in the biopsy specimens, but only one brushing detected any HPV type at all. We conclude that laryngeal brushing is an inadequate technique for assessing the presence of HPV in the larynx.

Gas chromatographic determination of eugenol in ethanol extract of cloves.

An ethanolic extract of cloves was analyzed by gas chromatography directly to identify eugenol and other major phenolic compounds without previous separation of other components. Separation was performed on a fused-silica capillary column of 30 m x 0.53 mm I.D., 0.53 microns film thickness. The detector was a flame ionization detector. Helium gas at a flow-rate of 3 ml/min was used as a carrier gas. The analysis were performed with linear temperature programming. Nine components were detected and special attention was given to the major phenolic compound, eugenol.

The presence of Epstein-Barr virus in multiple organs in a fatal case of virus-associated haemophagocytic syndrome.

We describe a case report of a 21-year-old male with fatal Epstein-Barr virus-associated haemophagocytic syndrome. Virus is detected in multiple organs by polymerase chain reaction and in the tissue-specific cells of those organs by in situ hybridisation. It is suggested that organ failure may be a direct response to infection.

Detection of human papillomavirus types in balanitis xerotica obliterans and other penile conditions.

OBJECTIVES: To determine the prevalence of human papillomavirus (HPV) types 6, 11, 16 and 18 in foreskin biopsies from patients with balanitis xerotica obliterans (BXO) and other penile conditions. MATERIALS AND METHODS: Foreskin biopsy specimens from 24 patients with penile lesions and 5 control patients were analysed by type-specific polymerase chain reaction (PCR). RESULTS: HPV6 or HPV16 were not detected in patients with BXO. HPV6 was detected in 2 controls. CONCLUSIONS: Genital papillomaviruses do not have a strong association with BXO.

Gastrointestinal adenovirus infections in a tertiary referral centre in Saudi Arabia.

To determine the prevalence of adenovirus and its serotypes in diarrhoeal stools in Saudi Arabia, 3,000 stool specimens were collected prospectively from subjects of all ages over a 28-month period. A total of 220 positive isolates were obtained. Fifteen serotypes were found, serotypes 40 and 41 being the most prevalent. Underlying disorders were found in the majority of patients, leukaemia being the most common single underlying condition. This investigation represents the first detailed study of the epidemiology of gastrointestinal adenovirus infections in Saudi Arabia.

Biphasic synovial sarcoma in the small intestinal mesentery.

BACKGROUND: A 46-year-old man presented with recurrent anemia and polyarthralgia. Investigations revealed a mass in the ileal mesentery, which was resected. Results of routine histologic examination suggested a diagnosis of synovial sarcoma, a rare malignancy usually not reported at this site. METHODS: Tissue was examined immunohistochemically, ultrastructurally, and by fluorescent in situ hybridization to confirm the diagnosis. RESULTS: Immunohistochemical studies revealed widespread labeling for cytokeratins and focal labeling for desmin and vimentin in the epithelial component, with labeling for epithelial membrane antigen in the epithelial and spindle-cell components. Fluorescent in situ hybridization analysis showed the characteristic t(X;18) translocation of synovial sarcoma. CONCLUSIONS: This is a unique case of synovial sarcoma in the small intestinal mesentery. Immunohistochemical labeling confirmed the diagnosis, although, to the authors' knowledge, the pattern of desmin labeling has not been described previously. The clinical association with polyarthralgia, which resolved after removal of the neoplasm, also has not been described previously.

Comparison of paediatric viral gastroenteritis at large medical centres in Saudi Arabia and the United Kingdom.

A comparison of the prevalence of viral diarrhoeas in children was made between the United Kingdom and Saudi Arabia over a three-year period. Laboratory data from Saudi Arabia were compared with those of a large medical centre in the UK. The prevalence ratios of virus-associated diarrhoea as a fraction of all diarrhoeal cases over three years were found to be 23% in the UK and 14% in Saudi Arabia. The relative proportion due to rotavirus and adenovirus was higher in the UK than in Saudi Arabia, but small round viruses were comparable at the two centres.

Non-uniform dwell times in line source high dose rate brachytherapy: physical and radiobiological considerations.

The ability to vary source dwell times in high dose rate (HDR) brachytherapy allows for the use of non-uniform dwell times along a line source. This may have advantages in the radical treatment of tumours depending on individual tumour geometry. This study investigates the potential improvements in local tumour control relative to adjacent normal tissue isoeffects when intratumour source dwell times are increased along the central portion of a line source (technique A) in radiotherapy schedules which include a relatively small component of HDR brachytherapy. Such a technique is predicted to increase the local control for tumours of diameters ranging between 2 cm and 4 cm by up to 11% compared with a technique in which there are uniform dwell times along the line source (technique B). There is no difference in the local control rates for the two techniques when used to treat smaller tumours. Normal tissue doses are also modified by the technique used. Technique A produces higher normal tissue doses at points perpendicular to the centre of the line source and lower doses at points nearer the ends of the line source if the prescription point is not in the central plane of the line source. Alternatively, if the dose is prescribed at a point in the central plane of the line source, the dose at all the normal tissue points are lower when technique A is used.

Aetiology of gastroenteritis at a major referral centre in Saudi Arabia.

To determine the causes of gastroenteritis at a major referral centre in Saudi Arabia, retrospective study was carried out on 58,110 fresh stools from 42,035 patients. Examination of stool specimens for pathogens was based on the clinical judgement of the physician responsible, so that all specimens were not tested for the presence of all pathogen groups. Bacterial enteropathogens were found in 7.7% of patients; Salmonella species (51.7%) were found to be the most frequent pathogens followed by Campylobacter jejuni (28%) and Shigella species (14.9%). Protozoan or metazoan parasites were detected in 27.8% of patients examined, the most common being Giardia lamblia and Hymenolepsis nana. Of the patients tested for viruses in stool, 14.1% had rotavirus, 5.3% adenovirus, 1.2% small round viruses and 0.3% coronavirus. Clostridium difficile toxin was also found in 9.5% of patients examined.

In vitro culture for the detection of infectious human parvovirus B19 and B19-specific antibodies using foetal haematopoietic precursor cells.

The inability to culture human parvovirus B19 in standard cell lines has rendered investigation of clinical samples for the presence of infectious virus problematic. Using haematopoietic precursors derived from first trimester foetal liver as targets for infection, and non-isotopic in situ hybridization to detect intracellular viral DNA, we have assessed infectivity in stored serum samples taken from nine volunteers at different stages following intranasal inoculation with parvovirus B19. Infectious virus was detected as early as 3 days after inoculation, the cessation of infectivity correlating with the rise in specific IgM. In all but two samples, infectivity correlated with the detection of B19 DNA by dot-blot hybridization, although in vitro culture was 10-fold more sensitive than dot-blot hybridization. B19 DNA was detected by the polymerase chain reaction in serum from one volunteer up to 36 days after inoculation, although samples containing specific antibody were non-infectious. Infection of erythroid precursors was completely inhibited by preincubation of virus with serum containing high titre B19-specific IgM and IgG. Unexpectedly, this was associated with a strong B19 DNA hybridization signal within the cytoplasm of phagocytic macrophages. This culture and detection system is a rapid and sensitive means of detecting infectious virus in serum samples, and of assessing the neutralizing ability of B19-specific antibodies.

Accelerated fast neutron therapy: a pilot study.

The clinical role of fast neutron therapy has been limited by excessive late normal tissue damage. A pilot study of accelerated fractionation of fast neutron therapy was performed, based on the rationale that this should result in an increase in the response in acute reacting tissues (normal and malignant), with no change in late damage and a consequent increase in the therapeutic ratio. Further accelerated fractionation should improve the local control of rapidly proliferating tumour, without the potential problem of inadequate reoxygenation inherent in accelerated photon schedules. 6 or 12 fractions of 62 MeV (p-Be) neutrons were given over 12 days to 27 sites in 23 patients with locally advanced tumours. With a dose reduction of 12% (18 Gy), acceptable skin and oral mucosa early reactions were obtained. A larger dose reduction (15%) was required at pelvic sites. The incidence of late EORTC/RTOG grade 4 toxicity was 46%. The overall response rate was 76% with a complete response rate of 16%. For locally advanced breast cancer, the complete response rate was 9%, which compares unfavourably with previous results with conventional neutron fractionation schedules. The combination of a low overall complete response rate and excessive late normal tissue toxicity suggests that accelerated fractionation of fast neutrons does not lead to an improvement in the therapeutic ratio, and that late normal tissue damage will continue to be dose limiting.