Selection of endogenous control genes for normalising gene expression data derived from formalin-fixed paraffin-embedded tumour tissue (2020)

Type of publication:
Journal article

Author(s):
Smith T.A.D.; AbdelKarem O.A.; Irlam-Jones J.J.; Lane B.; Valentine H.; Bibby B.A.S.; Choudhury A.; West C.M.L.; *Denley H.

Citation:
Scientific reports; Oct 2020; vol. 10 (no. 1)

Abstract:
Quantitative real time polymerase chain reaction (qPCR) data are normalised using endogenous control genes. We aimed to: (1) demonstrate a pathway to identify endogenous control genes for qPCR analysis of formalinfixed paraffin-embedded (FFPE) tissue using bladder cancer as an exemplar; and (2) examine the influence of probe length and sample age on PCR amplification and co-expression of candidate genes on apparent expression stability. RNA was extracted from prospective and retrospective samples and subject to qPCR using TaqMan human endogenous control arrays or single tube assays. Gene stability ranking was assessed using coefficient of variation (CoV), GeNorm and NormFinder. Co-expressed genes were identified from The Cancer Genome Atlas (TCGA) using the on-line gene regression analysis tool GRACE. Cycle threshold (Ct) values were lower for prospective (19.49+/-2.53) vs retrospective (23.8+/-3.32) tissues (p<0.001) and shorter vs longer probes. Co-expressed genes ranked as the most stable genes in the TCGA cohort by GeNorm when analysed together but ranked lower when analysed individually omitting co-expressed genes indicating bias. Stability values were<1.5 for the 20 candidate genes in the prospective cohort. As they consistently ranked in the top ten by CoV, GeNorm and Normfinder, UBC, RPLP0, HMBS, GUSB, and TBP are the most suitable endogenous control genes for bladder cancer qPCR.

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Emerging concepts and spectrum of renal injury following Intravesical BCG for non-muscle invasive bladder cancer. (2017)

Type of publication:
Journal article

Author(s):
*Mohammed, Azharuddin; *Arastu, Zubair

Citation:
BMC urology; Dec 2017; vol. 17 (no. 1); p. 114

Abstract:
BACKGROUNDIntravesical Bacilli Calmette-Guerin (IVBCG) therapy for non-muscle invasive bladder cancer (NMIBC) has long been in use successfully. Albeit rarely, we still face with its safety concerns more than 25 years on since its approval by US Food and Drug Agency in 1990. Local and systemic infection following intravesical BCG is widely reported as compared to immune mediated local or systemic hypersensitivity reactions involving kidneys; acute kidney injury (AKI) and other renal manifestations are well reported but not of chronic kidney disease (CKD).CASEAn interesting case of a female was referred to nephrologists in advanced stages of CKD at an eGFR of 10 ml/min/1.732 following IVBCG for NMIBC. Our patient’s renal function plateaued when IVBCG was held; and worsened again when reinstilled. It introduces the concept of ‘repetitive’ immune mediated renal injury presenting as progressive CKD rather than AKI, as is generally reported. Although response was poor, corticosteroids stopped CKD progression to end stage renal disease.CONCLUSIONSWe highlight the need for increased awareness and early recognition of IVBCG renal complications by both urologists and nephrologists in order to prevent progressive and irreversible renal damage. Low incidence of IVBCG renal complications may also be due to under recognition in the era prior to CKD Staging and AKI Network (and AKI e-alerts) that defined AKI as a rise in serum creatinine of ≥26umol/L; hence an unmet need for urgent prospective studies. Major literature review focuses on emerging spectrum of histopathological IVBCG related renal complications and their outcomes.

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Interleukin-17-positive mast cells influence outcomes from BCG for patients with CIS: Data from a comprehensive characterisation of the immune microenvironment of urothelial bladder cancer (2017)

Type of publication:
Journal article

Author(s):
Dowell A.C.; Taylor G.S.; *Cobby E.; Wen K.; During V.; Anderson J.; James N.D.; Devall A.J.; Cheng K.K.; Zeegers M.P.; Bryan R.T.

Citation:
PloS one; 2017; vol. 12 (no. 9)

Abstract:

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