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

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

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

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

Chromosome 17 aneusomy is associated with poor prognostic factors in invasive breast carcinoma

Aberrations of chromosome 17 are common in breast cancer. Fluorescence in situ hybridization (FISH) enables gene or chromosome copy number to be assessed in situ in archival tissues and related to morphology and clinical outcome. In this study direct labeled DNA probes for the chromosome 17 alpha satellite and the HER2/neu gene were applied simultaneously to 5 micron sections of 214 formalin-fixed paraffin-embedded invasive primary breast carcinomas. A high proportion (54%) of invasive breast carcinomas displayed aneusomy of chromosome 17. Polysomy 17 correlated with multiple copies of HER2/neu (p=less than 0.001), but not with HER2/neu amplification. Eighty-six patients without HER2/neu amplification had aneusomy 17. Fifty-eight of the 86 patients that had aneusomy 17 had high HER2/neu copy number. Twelve patients with normal copy number for chromosome 17 had amplification of HER2/neu and 30 patients had amplification of HER2/neu with aneusomy 17. Aneusomy 17 was associated with grade 3 carcinoma (p=0.008), ER negativity (p=0.0032) and a Nottingham prognostic index of greater than 5.4 (p=0.039) but was not associated with survival by univariate analysis. In conclusion, the determination of chromosome 17 copy number should be incorporated in assessment of HER2/neu status, as this will give an accurate measure of amplification of HER2/neu and may also be helpful in determining suitability for breast carcinoma trials

Genetic aberrations of NAT2 and chromosome 8: Their association with progression in transitional cell carcinoma of the urinary bladder

Introduction/Objective: N-acetyltransferase 2 (NAT2), mapped to 8p22, is a polymorphic enzyme which metabolizes aromatic amines. Loss of heterozygosity of 8p22 is associated with an increased risk of bladder cancer. This study evaluated NAT2 and chromosome 8 in sequential tumours from bladder cancer patients to determine if NAT2 alterations increase the risk of progression. Materials and Methods: Thirty-seven sequential carcinomas from 19 patients were assessed using fluorescence in situ hybridization. Results: Five carcinomas showed loss of NAT2; 4 of these were from pTa/pT1 tumours. Polysomy 8 was observed in 4 of 14 (29%) primary carcinomas (pTa/pT1), in 4 of 12 (33%) pTa/pT1 recurrences, and in 90% (9/10) of the detrusor muscle invasive tumours (pT2+). 6 of 8 (75%) locally invasive tumours with polysomy 8 were from patients who subsequently developed disease progression (pT2+). In total, 13.5% (5/37) of the carcinomas were abnormal for NAT2, and 46% (17/37) were abnormal for chromosome 8 copy number. Polysomy 8 was associated with high grade (p = 0.01) and stage (p = 0.03) and disease progression (p = 0.03). Conclusion: Whilst there does not appear to be an association between loss of NAT2 and risk of progression in transitional cell carcinoma, the high rate of polysomy of chromosome 8 implies that other genes on this chromosome significantly influence disease progression

Evaluating HER2 amplification and overexpression in breast cancer

The development of Herceptin (Trazumatab) makes testing for HER2 status important for choosing optimal therapy in breast cancer. This study addresses the precision, accuracy, and reproducibility of HER2 assays. HER2 was assessed retrospectively by immunohistochemistry (IHC) with Dako 'Herceptest', by IHC with the monoclonal antibody CB11, and by fluorescence in situ hybridization (FISH, PathVysion), in a series of 216 formalin-fixed breast carcinomas including 191 for which quantitative HER2 data from radioimmunohistochemistry (Q-IHC) were available. All tests were scored independently by two observers. Positivity rates varied between Herceptest (12.6%), FISH (19.4%), and CB11 IHC (28.5%). Kappa values showed that IHC-based tests were more susceptible to inter- observer variation (kappa = 0.67 and 0.74 for Herceptest and CB11, respectively) than FISH (kappa = 0.973). Overall test accuracy (see the Materials and methods section) for CB11 IHC (83.8%) was lower than Herceptest (87.4%) or FISH (93.2%,,). FISH predicted p185 HER2 overexpression (determined by Q-IHC) better (concordance index C.Ind. 0.90) than CB11 IHC (C.Ind. = 0.85) or Herceptest (C.Ind. = 0.81). Of 42 cases with gene amplification by FISH, 67%, were positive in the Herceptest (2 + or 3 +) vs. 83% with CB11. Of 174 cases negative by FISH, 96%, were negative in the Herceptest and 68% with CB11. conclusion, FISH is the most accurate, reproducible, and precise predictor of HER2 overexpression in routine diagnostic laboratories