Chromosomal aberrations in benign and malignant bilharzia-associated bladder lesions analyzed by comparative genomic hybridization

A Review of Cancer Genetics and Genomics Studies in Africa

Cancer is the second leading cause of death globally and is projected to overtake infectious disease as the leading cause of mortality in Africa within the next two decades. Cancer is a group of genomic diseases that presents with intra- and inter-population unique phenotypes, with Black populations having the burden of morbidity and mortality for most types. At large, the prevention and treatment of cancers have been propelled by the understanding of the genetic make-up of the disease of mostly non-African populations. By the same token, there is a wide knowledge gap in understanding the underlying genetic causes of, and genomic alterations associated with, cancer among black Africans. Accordingly, we performed a review of the literature to survey existing studies on cancer genetics/genomics and curated findings pertaining to publications across multiple cancer types conducted on African populations. We used PubMed MeSH terms to retrieve the relevant publications from 1990 to December 2019. The metadata of these publications were extracted using R text mining packages: RISmed and Pubmed.mineR. The data showed that only 0.329% of cancer publications globally were on Africa, and only 0.016% were on cancer genetics/genomics from Africa. Although the most prevalent cancers in Africa are cancers of the breast, cervix, uterus, and prostate, publications representing breast, colorectal, liver, and blood cancers were the most frequent in our review. The most frequently reported cancer genes were BRCA1, BRCA2, and TP53. Next, the genes reported in the reviewed publications’ abstracts were extracted and annotated into three gene ontology classes. Genes in the cellular component class were mostly associated with cell part and organelle part, while those in biological process and molecular function classes were mainly associated with cell process, biological regulation, and binding, and catalytic activity, respectively. Overall, this review highlights the paucity of research on cancer genomics on African populations, identified gaps, and discussed the need for concerted efforts to encourage more research on cancer genomics in Africa.

Urinary schistosomiasis and the associated bladder cancer: update

Background

Urinary schistosomiasis and its severe complications, mainly bladder cancer, are scarce in non-endemic areas. The deficiency in knowledge and clinical experience of schistosomiasis may lead to inadequate management. Highlighting these topics may be of value, especially with the increased immigration from endemic low-/middle-income countries (LMIC) to non-endemic high-income countries (HIC). Schistosomiasis is a parasitic infection endemic in many low- and middle-income countries. It can affect various systems but is best known for its effect on the urinary system.

Main Body

PubMed, Scopus, Google Scholar, and the Cochrane Library databases were searched for urinary schistosomiasis and its related bladder cancer published from 1980 till 2020.

Schistosoma haematobium (SH) infecting the urinary bladder was considered by the IARC as group 1 definitive biological carcinogenic agent. Several carcinogenic pathways have been postulated but the exact mechanism(s) are not defined yet. A more thorough understanding of the parasite life cycle was explored to help eradicate the infection especially for the immigrants from endemic areas. This may prevent or slow down the process of carcinogenesis that leads to Schistosoma-associated bladder cancer (SA-BC), which is usually, but not conclusively, squamous cell carcinoma. Treatment of SA-BC generally follows the same guidelines as urothelial Schistosoma-non-associated bladder cancer (SNA-BC) management; however, prospective trials to confirm and refine the treatment approach for SA-BC have been relatively limited.

Conclusion

The available data showed that despite some etiologic and carcinogenic differences, the oncologic outcomes are generally comparable for SA-BC and NSA-BC when adjusting for stage, risk status, and comorbidities.

Urine biomarkers of schistosomiais and its associated bladder cancer

Schistosomiasis (SCH) is the second only to malaria among the parasitic diseases affecting humans regarding the prevalence of infection worldwide. In this nonsystematic review, we summarize the existing data on commercially available and promising investigational urine markers for the detection of SCH and its associated bladder cancer (BC). We searched PubMed, Scopus and Cochran without time limits. We reviewed the recent literatures on urine-based markers for SCH and its associated BC. Many studies identified several urine biomarkers of Schistosoma haematobium and Schistosoma mansoni worms and their associated BC using automated, inexpensive, quantitative assays in urine. These markers may aid in early detection of bladder carcinoma and have the potential to reduce the number of follow-up cystoscopy, thus reducing healthcare costs and patient discomfort, at the same time. Nevertheless, clinical evidence is insufficient to warrant the substitution of the cystoscopic follow-up scheme by any of the currently available urine marker tests.

Schistosomiasis and cancer in egypt: review

Schistosomiasis is not known to be associated with any malignant disease other than bladder cancer. Bladder cancer is still the most common malignant tumor among males in Egypt and some African and Middle East countries. However, the frequency rate of bladder cancer has declined significantly during the last 25 years. This drop is mainly related to the control of Schistosomiasis. Many studies have elucidated the pathogenic events of Schistosomal-related bladder cancer with a suggested theory of pathogenesis. Furthermore, the disease presents with a distinct clinicopathologic profile that is quite different from bladder cancer elsewhere with younger age at presentation, more male predominance, more invasive stages, and occurrence of squamous cell carcinoma pathologic subtype. However, recent data suggest that this profile has been dramatically changed over the past 25 years leading to minimization of the differences between its features in Egypt and that in Western countries. Management of muscle-invasive localized disease is mainly surgery with 5-year survival rates of 30-50%. Although still a debatable issue, adjuvant and neoadjuvant chemotherapy and radiotherapy have improved treatment outcomes including survival and bladder preservation rates in most studies. This controversy emphasizes the need of individualized treatment options based on a prognostic index or other factors that can define the higher risk groups where more aggressive therapy is needed. The treatment for locally advanced and/or metastatic disease has passed through a series of clinical trials since 1970s. These phase II and III trials have included the use of single agent and combination of chemotherapy and radiotherapy regimens. The current standard of systemic chemotherapy of generally fit patients is now the gemcitabine-cisplatin combination. In conclusion, a changing pattern of bladder cancer in Egypt is clearly observed. This is mainly due to the success in the control of Schistosomiasis. It may also be due to increased exposure to other etiologic factors that include smoking, pesticides, and/or other causative agents. This change will ultimately affect disease management.

Identification of prefoldin amplification (1q23.3-q24.1) in bladder cancer using comparative genomic hybridization (CGH) arrays of urinary DNA

BACKGROUND

Array-CGH represents a comprehensive tool to discover genomic disease alterations that could potentially be applied to body fluids. In this report, we aimed at applying array-CGH to urinary samples to characterize bladder cancer.

METHODS

Urinary DNA from bladder cancer patients and controls were hybridized on 44K oligonucleotide arrays. Validation analyses of identified regions and candidates included fluorescent in situ hybridization (FISH) and immunohistochemistry in an independent set of bladder tumors spotted on custom-made tissue arrays (n = 181).

RESULTS

Quality control of array-CGH provided high reproducibility in dilution experiments and when comparing reference pools. The most frequent genomic alterations (minimal recurrent regions) among bladder cancer urinary specimens included gains at 1q and 5p, and losses at 10p and 11p. Supervised hierarchical clustering identified the gain at 1q23.3-q24.1 significantly correlated to stage (p = 0.011), and grade (p = 0.002). The amplification and overexpression of Prefoldin (PFND2), a selected candidate mapping to 1q23.3-q24.1, correlated to increasing stage and tumor grade by means of custom-designed and optimized FISH (p = 0.013 and p = 0.023, respectively), and immunohistochemistry (p ≤0.0005 and p = 0.011, respectively), in an independent set of bladder tumors included in tissue arrays. Moreover, PFND2 overexpression was significantly associated with poor disease-specific survival (p ≤0.0005). PFND2 was amplified and overexpressed in bladder tumors belonging to patients providing urinary specimens where 1q23.3q24.1 amplification was detected by array-CGH.

CONCLUSIONS

Genomic profiles of urinary DNA mirrowed bladder tumors. Molecular profiling of urinary DNA using array-CGH contributed to further characterize genomic alterations involved in bladder cancer progression. PFND2 was identified as a tumor stratification and clinical outcome prognostic biomarker for bladder cancer patients.

Bladder cancer and schistosomiasis

Schistosoma-associated bladder cancer was believed, for several decades, to be a completely unique entity of disease, different from urothelial cancer. This was probably due to its distinct clinicopathologic and demographic features that varied from those of urothelial entity. The carcinogenesis is an extremely complex process resulting from the accumulation of many genetic and epigenetic changes leading to alterations in the cell proliferation regulation process. In bladder cancer, many of these carcinogenic cascades were not fully documented or somewhat conflicting. Inspite of the efforts performed, much is still needed to explore the presence or absence of the carcinogenic difference with a different etiology. The control of schistosomiasis in certain countries and the subsequent decrease in the intensity of infestation showed changing of features approaching that of urothelial tumors. However the schistosoma-associated bladder cancer presented in more advanced stages than schistosoma-non associated urothelial cancer. More recently, data are gathered that, upon applying the same treatment protocol and management care, stage by stage comparison of the treatment end-results were found to be similar in bladder cancer patients with a different etiology. All treatment options; including radical cystectomy with or without adjuvant or neoadjuvant chemo- or radiotherapy or trimodality bladder preserving treatment seem to lead to similar end-results regardless of etiologic factor(s) implicated in bladder cancer development.

The role of helminth infections in carcinogenesis

This review examines the significant literature on the role of helminth infections in carcinogenesis. Both parasitic infections and cancer have complex natural histories and long latent periods during which numerous exogenous and endogenous factors interact to obfuscate causality. Although only two helminths, Schistosoma haematobium and Opisthorchis viverrini, have been proven to be definitely carcinogenic to humans, others have been implicated in facilitating malignant transformation. The known mechanisms of helminth-induced cancer include chronic inflammation, modulation of the host immune system, inhibition of intracellular communication, disruption of proliferation-antiproliferation pathways, induction of genomic instability and stimulation of malignant stem cell progeny. Approximately 16% of all cancer cases worldwide are attributable to pathogenic agents, including schistosomes and liver flukes. This equates to 1,375,000 preventable cancer deaths per year. Means to reduce the incidence of helminth-associated malignancies are discussed.

Genomic imbalances in Schistosoma-associated and non–Schistosoma-associated bladder carcinoma. An array comparative genomic hybridization analysis

Carcinoma of the urinary bladder is the most common malignancy in many tropical and subtropical countries due to endemic infection by Schistosoma hematobium (bilharzia). In the current study, we performed a high-resolution analysis of gene copy number amplifications using array comparative genomic hybridization to compare DNA copy number changes in pools of Schistosoma-associated (SA) and non-Schistosoma-associated (NSA) bladder cancer (BC). Many DNA copy number changes were detected in all studies, with multiple gains and losses of genetic material. The most frequent alterations were gains on 5p15.2 approximately p15.33, 8q13.1, and 11q13, and losses on 8p21.3 approximately p22 and 22q13. Even when SA pools showed no Schistosoma-specific gene copy number profiling as compared to NSA pools, some genes seemed to be gained (ELN on 7q11.23) and some lost (PRKAG3 on 2q35 and PRDM6 on 5q23.2) in SA-SCC. The following genes were gained in all histopathologic categories: SRC (20q11.23), CEBPB (20q13.13), and GPR9 (Xq13.1). Our study did not provide clear evidence of differences in carcinogenesis of SA-BC and NSA-BC.

EAU guidelines for the management of urogenital schistosomiasis

More than 100 million people worldwide are affected by bilharziasis, caused by Schistosoma haematobium. For travellers precaution is most important. For the population in endemic areas, an integrated approach including health education is necessary. Effective pharmacologic treatment is available.

Bladder tumor markers beyond cytology: International Consensus Panel on bladder tumor markers

This is the first of 2 articles that summarize the findings of the International Consensus Panel on cytology and bladder tumor markers. The objectives of our panel were to reach a consensus on the areas where markers are needed, to define the attributes of an ideal tumor marker, and to identify which marker(s) would be suitable for diagnosis and/or surveillance of bladder cancer. Our panel consisted of urologists and researchers from Europe, Asia, and the United States who reviewed original articles, reviews, and book chapters on individual bladder tumor markers published in the English language mainly using the PubMed search engine. Panel members also met during 3 international meetings to write recommendations regarding bladder tumor markers. The panel found that the most practical use of noninvasive tests is to monitor bladder cancer recurrence, thereby reducing the number of surveillance cystoscopies performed each year. Markers also may be useful in the screening of high-risk individuals for early detection of bladder cancer. However, more prospective studies are needed to strengthen this argument. Case-control and cohort studies show that several markers have a higher sensitivity to detect bladder cancer. However, cytology is the superior marker in terms of specificity, although some markers in limited numbers of studies have shown specificity equivalent to that of cytology. Our panel believes that several bladder tumor markers are more accurate in detecting bladder cancer than prostate-specific antigen (PSA) is in detecting prostate cancer. However, bladder tumor markers are held to a higher standard than PSA. Therefore, use of bladder tumor markers in the management of patients with bladder cancer will require the willingness of both urologists and clinicians to accept them.

High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID)

BACKGROUND

We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. The original version of GoMiner was oriented toward visualization and interpretation of the results from a single microarray (or other high-throughput experimental platform), using a graphical user interface. Although that version can be used to examine the results from a number of microarrays one at a time, that is a rather tedious task, and original GoMiner includes no apparatus for obtaining a global picture of results from an experiment that consists of multiple microarrays. We wanted to provide a computational resource that automates the analysis of multiple microarrays and then integrates the results across all of them in useful exportable output files and visualizations.

RESULTS

We now introduce a new tool, High-Throughput GoMiner, that has those capabilities and a number of others: It (i) efficiently performs the computationally-intensive task of automated batch processing of an arbitrary number of microarrays, (ii) produces a human-or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories, (iii) integrates the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories, (iv) provides a fast form of 'false discovery rate' multiple comparisons calculation, and (v) provides annotations and visualizations for relating transcription factor binding sites to genes and GO categories.

CONCLUSION

High-Throughput GoMiner achieves the desired goal of providing a computational resource that automates the analysis of multiple microarrays and integrates results across all of the microarrays. For illustration, we show an application of this new tool to the interpretation of altered gene expression patterns in Common Variable Immune Deficiency (CVID). High-Throughput GoMiner will be useful in a wide range of applications, including the study of time-courses, evaluation of multiple drug treatments, comparison of multiple gene knock-outs or knock-downs, and screening of large numbers of chemical derivatives generated from a promising lead compound.

Advanced molecular cytogenetics in human and mouse

Fluorescence in situ hybridization, spectral karyotyping, multiplex fluorescence in situ hybridization, comparative genomic hybridization, and more recently array comparative genomic hybridization, represent advancements in the field of molecular cytogenetics. The application of these techniques for the analysis of specimens from humans, or mouse models of human diseases, enables one to reliably identify and characterize complex chromosomal rearrangements resulting in alterations of the genome. As each of these techniques has advantages and limitations, a comprehensive analysis of cytogenetic aberrations can be accomplished through the utilization of a combination approach. As such, analyses of specific tumor types have proven invaluable in the identification of new tumor-specific chromosomal aberrations and imbalances (aneuploidy), as well as regions containing tumor-specific gene targets. Application of these techniques has already improved the classification of tumors into distinct categories, with the hope that this will lead to more tailored treatment strategies. These techniques, in particular the application of tumor-specific fluorescence in situ hybridization probes to interphase nuclei, are also powerful tools for the early identification of premalignant lesions.

Malignant Non-Urothelial Neoplasms of the Urinary Bladder: A Review

OBJECTIVES

Non-urothelial bladder tumors frequently present a diagnostic and therapeutic challenge. We review the peer-reviewed literature to summarize the available evidence on the etiology, diagnosis and optimal management of malignant non-urothelial bladder tumors.

METHODS

A comprehensive MEDLINE database search was performed. In addition, the proceedings of recent national and international urological and cancer society meetings were reviewed.

RESULTS

Primary non-urothelial bladder tumors are rare in Europe and North America representing less than 5% of all bladder lesions combined. A large number of risk factors have been implicated in the etiology of non-schistosomiasis-related squamous cell carcinoma, yet their exact pathomechanism remains poorly defined. Squamous cell carcinoma, adenocarcinoma, small cell carcinoma, sarcoma and carcinosarcoma/sarcomatoid tumors share an unfavorable prognosis despite aggressive surgical management that relates both to an aggressive biological behaviour as well as to an often times advanced stage at the time of diagnosis. Inflammatory pseudotumors are benign tumors of uncertain histogenesis that may mimic sarcomas. Paraganglioma, primary melanoma and lymphoma represent additional, exceedingly rare bladder tumors.

CONCLUSIONS

The systematic investigation of most non-urothelial bladder tumors is limited by the rarity of these lesions. A concerted effort of multiple institutions linked together in a national or international tumor registry will be necessary to advance our understanding of these tumors, evaluate treatment strategies and optimize patient outcome in the future.