Chromosomal aberrations in transitional cell carcinoma that are predictive of disease outcome are independent of polyploidy

Objective To determine whether aneusomy for chromosomes 7, 9 and 17 (reported to predict recurrence in up to 65% of patients with superficial transitional cell bladder cancer and thus providing the opportunity for early and effective treatment) reflects specific genetic events on these chromosomes or merely wider unspecific genetic damage to the cell, e.g. that increased copy numbers for 7 and 17 reflect tumour polyploidy. Materials and methods The study comprised 25 primary tumours; 6 mu m thick sections from formalin-fixed and paraffin-embedded tumours were analysed. Chromosome copy numbers were determined by fluorescence in situ hybridization (FISH) using pericentromeric probes for chromosomes 7, 8, 9, 10, 11 and 17. A minimum of 200 nuclei per tumour area were scored by two independent observers. Results Eight of the 25 tumours examined (32%) showed no evidence of chromosomal abnormalities as detected by FISH for any chromosomes analysed. Twelve tumours (48%) showed abnormalities for one or two chromosomes, five tumours (20%) showed abnormalities for multiple chromosomes and one tumour showed abnormalities for all chromosomes analysed, suggestive of polyploidy. Conclusions Chromosomal abnormalities predictive of recurrence occur largely in the absence of other gross chromosomal lesions. In a small proportion of cases other chromosomes are affected, but this is almost always distinct from tumour polyploidy

Amplification of the androgen receptor may not explain the development of androgen-independent prostate cancer

Objective To examine the role of androgen receptor (AR) gene amplification and aneusomy of the X chromosome in the development of antiandrogen-resistant prostate cancer. Patients and methods Twenty patients with prostate cancer resistant to androgen-deprivation therapy were selected for study. The records of patients with tumours before and after antiandrogen therapy, and with a full clinical follow-up, were retrieved. AR gene amplification and X chromosome copy number were assessed by fluorescence in situ hybridization using a labelled probe at locus Xq11-13 for the AR gene and a labelled a-satellite probe for the X chromosome. At least 20 nuclei were scored over three tumour areas by two independent observers. Results Aneusomy of the X chromosome was reported respectively in seven (35%) and 11 (55%) tumours before and after hormone relapse, the AR gene copy number was increased in seven (35%) and 13 (65%), respectively, and AR gene amplification was detected in one (5%) and three (15%), respectively. Neither increased AR copy number nor AR amplification in primary tumours precluded a biological response to androgen-deprivation therapy. Conclusion The rate of AR gene amplification is too low to be solely responsible for the development of antiandrogen-resistant prostate cancer. Also, the presence of amplified AR and cells aneusomic for the X chromosome in primary tumours that respond to androgen-deprivation therapy suggests that an increase in AR gene copy number does not prevent a tumour from responding to this therapy. Therefore other mechanisms which could cause hormone-refractory prostate cancer must be investigated before it is understood why so many patients relapse with this disease

Gene amplification and overexpression of HER2 in renal cell carcinoma

Objective To determine the frequency of HER2 genetic abnormalities in renal cell carcinoma (RCC) and hence assess the potential suitability of Herceptin(TM) immunotherapy. Patients and methods Tumours from 2 7 patients with RCC were assessed: all patients had undergone nephrectomy. Benign renal tissue from the nephrectomy specimens was studied in seven patients. Gene amplification was assessed using fluorescent in- situ hybridization, and protein over-expression using immunohistochemistry. Results Twenty-four patients had clear cell renal carcinoma, two had papillary renal carcinoma and one a sarcomatoid variant carcinoma. There was no HER2 amplification in the tumours or the benign renal tissue. Polysomy 17 was detected in 11 of 27 tumours (41%) and increased HER2 copy number in seven (26%). Both polysomy 17 and increased HER2 copy number were absent in the benign renal tissue. Three tumours (11%) and six of the seven benign renal tissue samples over-expressed the HER2 protein. Conclusions HER2 amplification is absent and protein over-expression uncommon in RCC. This casts doubt on the suitability of Herceptin(TM) in the treatment of RCC

Aneusomy of chromosomes 7 and 17 predicts the recurrence of transitional cell carcinoma of the urinary bladder

Objective To determine if changes in chromosome 7 and 17 copy number can be used to predict recurrence in patients with primary noninvasive (pTa) or superficially invasive (pT1) transitional cell carcinoma (TCC) of the urinary bladder. Patients and methods Tissue specimens for 129 tumours from 52 patients (38 men and 14 women) with pTa/pT1 TCC at first diagnosis were retrieved from pathology archives. All patient notes were accessed and disease outcome documented for superficial (pTa/ pT1) recurrence or progression to detrusor muscle invasion (greater than or equal to pT2). The rumours were examined for chromosomal copy number of chromosomes 7 and 17 using fluorescence in situ hybridization (PISH) with chromosome-specific probes. The copy number of chromosomes 7 and 17 was determined in interphase nuclei on intact 6 mu m tissue sections. Results Aneusomy of chromosomes 7 and 17 was detected in the index primary tumours of 10 of 32 (31%) patients with subsequent recurrent disease. No aneusomy for these chromosomes was detected in primary tumours from 20 patients with no detectable recurrence (P = 0.0082). The relative risk of recurrence was 3.62 times greater (95% confidence interval 1.6-8.1, Cox's multiple regression P = 0.0019) for patients with chromosomal aneusomy in primary TCC. Neither stage nor grade of the primary tumours was associated with recurrence in these patients, nor was there a significant association with increased grade (G2/3) or stage (greater than or equal to pT2) at recurrence. Conclusion These results suggest that the measurement of aneusomy by FISH, using markers for chromosomes 7 and 17, predict recurrence in a subgroup of patients with pTa/pT1 tumours at presentation. This finding may offer a new objective and quantitative test for patients destined to recur

Prevention of tracheal cartilage injury with modified Griggs technique during percutaneous tracheostomy - Randomized controlled cadaver study

Introduction: Tracheal stenosis is the most common severe late complication of percutaneous tracheostomy causing significant decrease in quality of life. Applying modified Griggs technique reduced the number of late tracheal stenoses observed in our clinical study. The aim of this study was to investigate the mechanism of this relationship. Materials and methods: Forty-six cadavers were randomized into two groups according to the mode of intervention during 2006-2008. Traditional versus modified Griggs technique was applied in the two groups consequently. Wider incision, surgical preparation, and bidirectional forceps dilation of tracheal wall were applied in modified technique. Injured cartilages were inspected by sight and touch consequently. Age, gender, level of intervention, and number of injured tracheal cartilages were registered. Results: Significantly less frequent tracheal cartilage injury was observed after modified (9%) than original (91%) Griggs technique (p<0.001). A moderate association between cartilage injury and increasing age was observed, whereas the level of intervention (p=0.445) and to gender (p=0.35) was not related to injury. Risk of cartilage injury decreased significantly (OR: 0.0264, 95%, CI: 0.005-0.153) with modified Griggs technique as determined in adjusted logistic regression model. Discussion: Modified Griggs technique decreased the risk of tracheal cartilage injury significantly in our cadaver study. This observation may explain the decreased number of late tracheal stenosis after application of the modified Griggs method. © 2012 Akadémiai Kiadó, Budapes

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Fluorescence in situ hybridization in paraffin tissue sections - Pretreatment protocol

Fluorescence in situ hybridization has found wide application in the enumeration of gene and chromosome copy number both in isolated cells and in tissue sections. However, the technique has been less widely used than would be expected in formalin- fixed paraffin processed (archival) tissue. This article describes a method for assessing archival tissue sections, following pretreatment, before applying DNA probes, that gives consistent, reliable results

A modified Nick translation method used with FISH that produces reliable results with archival tissue sections

Nick translation is used to label DNA and RNA to produce probes for in situ hybridization and Northern and Southern blotting. Fluorescence in situ hybridization (FISH) is a widely applied technique used to determine chromosomal and genetic anomalies in many biological samples. Initially the technique was applied to metaphase preparations, but the usefulness of detecting genetic anomalies in solid tumors in situ has resulted in the development of modified protocols. Formalin fixed paraffin processed tissue sections present novel challenges when applying FISH; the probes must be small (between 200 and 600 base pairs) and pretreatment is necessary before the probes can be applied to tissue sections, to promote probe access to target DNA. Here we report on a modification of a nick translation method to produce a probe that can reliably be used with FISH in paraffin processed tissue sections

Progression to detrusor-muscle invasion in bladder carcinoma is associated with polysomy of chromosomes 1 and 8 in recurrent pTa/pT1 tumours

Transitional cell carcinoma (TCC) provides a unique model of cancer recurrence and progression. Sequential tumours (n = 100) from 57 patients with an index pTa or pT1 TCC were studied using fluorescence in situ hybridisation (FISH), to determine aberrations of chromosomes 1 and 8. Thirty-seven patients experienced recurrences; eleven developed muscle invasive tumours (pT2+). Polysomy of chromosomes I or 8 was associated with pT1 TCC (P = 0.0017 and P = 0.0037, respectively), but not with recurrence. Progression was associated with polysomy of chromosomes I (P = 0.003) and 8 (P = 0.011) in pTa/pT1 recurrences, but not with stage. In conclusion, patients who subsequently developed invasive TCC (pT2+) had significantly higher rates of ancusomy (90%) in their superficial cancers than those patients who did not progress (P = 0.009). Investigation of sequential tumours in patients with recurrent and progressive TCC showed that polysomy of chromosomes I and 8 were linked to subsequent detrusor muscle invasion, but not recurrence per se