Geographic variation of mutagenic exposures in kidney cancer genomes

International differences in the incidence of many cancer types indicate the existence of carcinogen exposures that have not yet been identified by conventional epidemiology make a substantial contribution to cancer burden1. In clear cell renal cell carcinoma, obesity, hypertension and tobacco smoking are risk factors, but they do not explain the geographical variation in its incidence2. Underlying causes can be inferred by sequencing the genomes of cancers from populations with different incidence rates and detecting differences in patterns of somatic mutations. Here we sequenced 962 clear cell renal cell carcinomas from 11 countries with varying incidence. The somatic mutation profiles differed between countries. In Romania, Serbia and Thailand, mutational signatures characteristic of aristolochic acid compounds were present in most cases and but these were rare elsewhere. In Japan, a mutational signature of unknown cause was found in more than 70% of cases but in less than 2% elsewhere. A further mutational signature of unknown cause was ubiquitous but exhibited higher mutation loads in countries with higher incidence rates of kidney cancer. Known signatures of tobacco smoking correlated with tobacco consumption, but no signature was associated with obesity or hypertension, suggesting that non-mutagenic mechanisms of action underlie these risk factors. The results of this study indicate the existence of multiple, geographically variable, mutagenic exposures that potentially affect tens of millions of people and illustrate the opportunities for new insights into cancer causation through large-scale global cancer genomics.

Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator

BACKGROUND

All cancers harbor somatic mutations in their genomes. In principle, mutations affecting between one and fifty base pairs are generally classified as small mutational events. Conversely, large mutational events affect more than fifty base pairs, and, in most cases, they encompass copy-number and structural variants affecting many thousands of base pairs. Prior studies have demonstrated that examining patterns of somatic mutations can be leveraged to provide both biological and clinical insights, thus, resulting in an extensive repertoire of tools for evaluating small mutational events. Recently, classification schemas for examining large-scale mutational events have emerged and shown their utility across the spectrum of human cancers. However, there has been no computationally efficient bioinformatics tool that allows visualizing and exploring these large-scale mutational events.

RESULTS

Here, we present a new version of SigProfilerMatrixGenerator that now delivers integrated capabilities for examining large mutational events. The tool provides support for examining copy-number variants and structural variants under two previously developed classification schemas and it supports data from numerous algorithms and data modalities. SigProfilerMatrixGenerator is written in Python with an R wrapper package provided for users that prefer working in an R environment.

CONCLUSIONS

The new version of SigProfilerMatrixGenerator provides the first standardized bioinformatics tool for optimized exploration and visualization of two previously developed classification schemas for copy number and structural variants. The tool is freely available at https://github.com/AlexandrovLab/SigProfilerMatrixGenerator with an extensive documentation at https://osf.io/s93d5/wiki/home/ .

Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity

Malignant pleural mesothelioma (MPM) is an aggressive cancer with rising incidence and challenging clinical management. Through a large series of whole-genome sequencing data, integrated with transcriptomic and epigenomic data using multiomics factor analysis, we demonstrate that the current World Health Organization classification only accounts for up to 10% of interpatient molecular differences. Instead, the MESOMICS project paves the way for a morphomolecular classification of MPM based on four dimensions: ploidy, tumor cell morphology, adaptive immune response and CpG island methylator profile. We show that these four dimensions are complementary, capture major interpatient molecular differences and are delimited by extreme phenotypes that-in the case of the interdependent tumor cell morphology and adapted immune response-reflect tumor specialization. These findings unearth the interplay between MPM functional biology and its genomic history, and provide insights into the variations observed in the clinical behavior of patients with MPM.

Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator

Background

All cancers harbor somatic mutations in their genomes. In principle, mutations affecting between one and fifty base pairs are generally classified as small mutational events. Conversely, large mutational events affect more than fifty base pairs, and, in most cases, they encompass copy-number and structural variants affecting many thousands of base pairs. Prior studies have demonstrated that examining patterns of somatic mutations can be leveraged to provide both biological and clinical insights, thus, resulting in an extensive repertoire of tools for evaluating small mutational events. Recently, classification schemas for examining large-scale mutational events have emerged and shown their utility across the spectrum of human cancers. However, there has been no standard bioinformatics tool that allows visualizing and exploring these large-scale mutational events.

Results

Here, we present a new version of SigProfilerMatrixGenerator that now delivers integrated capabilities for examining large mutational events. The tool provides support for examining copy-number variants and structural variants under two previously developed classification schemas and it supports data from numerous algorithms and data modalities. SigProfilerMatrixGenerator is written in Python with an R wrapper package provided for users that prefer working in an R environment.

Conclusions

The new version of SigProfilerMatrixGenerator provides the first standardized bioinformatics tool for optimized exploration and visualization of two previously developed classification schemas for copy number and structural variants. The tool is freely available at https://github.com/AlexandrovLab/SigProfilerMatrixGenerator with an extensive documentation at https://osf.io/s93d5/wiki/home/ .

Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting signatures, and several novel mutational signatures, including one putatively attributed to direct tobacco smoking mutagenesis in bladder tissues.

Signatures of copy number alterations in human cancer

Gains and losses of DNA are prevalent in cancer and emerge as a consequence of inter-related processes of replication stress, mitotic errors, spindle multipolarity and breakage-fusion-bridge cycles, among others, which may lead to chromosomal instability and aneuploidy1,2. These copy number alterations contribute to cancer initiation, progression and therapeutic resistance3-5. Here we present a conceptual framework to examine the patterns of copy number alterations in human cancer that is widely applicable to diverse data types, including whole-genome sequencing, whole-exome sequencing, reduced representation bisulfite sequencing, single-cell DNA sequencing and SNP6 microarray data. Deploying this framework to 9,873 cancers representing 33 human cancer types from The Cancer Genome Atlas6 revealed a set of 21 copy number signatures that explain the copy number patterns of 97% of samples. Seventeen copy number signatures were attributed to biological phenomena of whole-genome doubling, aneuploidy, loss of heterozygosity, homologous recombination deficiency, chromothripsis and haploidization. The aetiologies of four copy number signatures remain unexplained. Some cancer types harbour amplicon signatures associated with extrachromosomal DNA, disease-specific survival and proto-oncogene gains such as MDM2. In contrast to base-scale mutational signatures, no copy number signature was associated with many known exogenous cancer risk factors. Our results synthesize the global landscape of copy number alterations in human cancer by revealing a diversity of mutational processes that give rise to these alterations.

Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA

Clustered somatic mutations are common in cancer genomes and previous analyses reveal several types of clustered single-base substitutions, which include doublet- and multi-base substitutions1-5, diffuse hypermutation termed omikli6, and longer strand-coordinated events termed kataegis3,7-9. Here we provide a comprehensive characterization of clustered substitutions and clustered small insertions and deletions (indels) across 2,583 whole-genome-sequenced cancers from 30 types of cancer10. Clustered mutations were highly enriched in driver genes and associated with differential gene expression and changes in overall survival. Several distinct mutational processes gave rise to clustered indels, including signatures that were enriched in tobacco smokers and homologous-recombination-deficient cancers. Doublet-base substitutions were caused by at least 12 mutational processes, whereas most multi-base substitutions were generated by either tobacco smoking or exposure to ultraviolet light. Omikli events, which have previously been attributed to APOBEC3 activity6, accounted for a large proportion of clustered substitutions; however, only 16.2% of omikli matched APOBEC3 patterns. Kataegis was generated by multiple mutational processes, and 76.1% of all kataegic events exhibited mutational patterns that are associated with the activation-induced deaminase (AID) and APOBEC3 family of deaminases. Co-occurrence of APOBEC3 kataegis and extrachromosomal DNA (ecDNA), termed kyklonas (Greek for cyclone), was found in 31% of samples with ecDNA. Multiple distinct kyklonic events were observed on most mutated ecDNA. ecDNA containing known cancer genes exhibited both positive selection and kyklonic hypermutation. Our results reveal the diversity of clustered mutational processes in human cancer and the role of APOBEC3 in recurrently mutating and fuelling the evolution of ecDNA.

Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence

Esophageal squamous cell carcinoma (ESCC) shows remarkable variation in incidence that is not fully explained by known lifestyle and environmental risk factors. It has been speculated that an unknown exogenous exposure(s) could be responsible. Here we combine the fields of mutational signature analysis with cancer epidemiology to study 552 ESCC genomes from eight countries with varying incidence rates. Mutational profiles were similar across all countries studied. Associations between specific mutational signatures and ESCC risk factors were identified for tobacco, alcohol, opium and germline variants, with modest impacts on mutation burden. We find no evidence of a mutational signature indicative of an exogenous exposure capable of explaining differences in ESCC incidence. Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like (APOBEC)-associated mutational signatures single-base substitution (SBS)2 and SBS13 were present in 88% and 91% of cases, respectively, and accounted for 25% of the mutation burden on average, indicating that APOBEC activation is a crucial step in ESCC tumor development.

Genomic and evolutionary classification of lung cancer in never smokers

Lung cancer in never smokers (LCINS) is a common cause of cancer mortality but its genomic landscape is poorly characterized. Here high-coverage whole-genome sequencing of 232 LCINS showed 3 subtypes defined by copy number aberrations. The dominant subtype (piano), which is rare in lung cancer in smokers, features somatic UBA1 mutations, germline AR variants and stem cell-like properties, including low mutational burden, high intratumor heterogeneity, long telomeres, frequent KRAS mutations and slow growth, as suggested by the occurrence of cancer drivers' progenitor cells many years before tumor diagnosis. The other subtypes are characterized by specific amplifications and EGFR mutations (mezzo-forte) and whole-genome doubling (forte). No strong tobacco smoking signatures were detected, even in cases with exposure to secondhand tobacco smoke. Genes within the receptor tyrosine kinase-Ras pathway had distinct impacts on survival; five genomic alterations independently doubled mortality. These findings create avenues for personalized treatment in LCINS.

Individual, interpersonal, and organisational factors of healthcare conflict: A scoping review

Unresolved conflicts among healthcare professionals can lead to difficult patient care consequences. This scoping review examines the current healthcare literature that reported sources and consequences of conflict associated with individual, interpersonal, and organisational factors. We identified 99 articles published between 2001 and 2015 from PubMed, Cumulative Index to Nursing and Allied Health Literature, and Excerpta Medical Database. Most reviewed studies relied on healthcare professionals' perceptions and beliefs associated with conflict sources and consequences, with few studies reporting behavioural or organisational change outcomes. Individual conflict sources included personal traits, such as self-focus, self-esteem, or worldview, as well as individuals' conflict management styles. These conflicts posed threats to one's physical, mental, and emotional health and to one's ability to perform at work. Interpersonal dynamics were hampered by colleagues' uncivil behaviours, such as low degree of support, to more destructive behaviours including bullying or humiliation. Perceptions of disrespectful working environment and weakened team collaboration were the main interpersonal conflict consequences. Organisational conflict sources included ambiguity in professional roles, scope of practice, reporting structure, or workflows, negatively affecting healthcare professionals' job satisfactions and intent to stay. Future inquiries into healthcare conflict research may target the following: shifting from research involving single professions to multiple professions; dissemination of studies via journals that promote interprofessional research; inquiries into the roles of unconscious or implicit bias, or psychological capital (i.e., resilience) in healthcare conflict; and diversification of data sources to include hospital or clinic data with implications for conflict sources.

Acute renal failure in a patient with non-fulminant hepatitis A infection

Acute viral hepatitis A is a common cause of jaundice with a very low mortality. Acute renal failure occurs very rarely in hepatitis A. We report a case of non-fulminant hepatitis A in a 45-year-old man complicated by acute renal failure. The patient was treated successfully with hemodialysis resulting in complete recovery. Kidney biopsy was not performed in view of improving clinical picture.

Video-assisted thoracic surgery: primary therapy for spontaneous pneumothorax?

OBJECTIVE:

To determine whether video-assisted thoracoscopic surgery is as effective as the traditional open method through axillary thoracotomy for the management of primary spontaneous pneumothorax in adults.

MATERIALS AND METHODS:

This retrospective study was conducted at King Hussein Medical Center in the period between March 2002 and March 2007. Eighty-two patients were included in this study. The patients were divided in two groups: group A, which included patients who underwent video-assisted thoracoscopic surgery; and group B, which included patients who underwent open technique through axillary thoracotomy. Efficiency of the procedure, operative time, postoperative complications, length of hospital stay, time to return to work and recurrence were compared between the two groups.

RESULTS:

There were 79 males (96.3%) and 3 females (3.7%) with a mean age of 23.7 ± 4.2 years for group A patients and 24.2 ± 4.6 years for group B patients (range 16–37 years). Forty-one patients (50%) underwent video-assisted thoracoscopic surgery (group A), and 41 patients (50%) underwent open surgical technique through axillary thoracotomy (group B). Postoperative complication occurred in 8 patients (19.3%) from among those who underwent open technique and 6 patients (14.6%) from among those who underwent thoracoscopic technique. There was no perioperative mortality in both groups. Postoperative pain, volume of blood loss, period of air leak and hospital stay were less in group A, although the operative time was less in group B.

CONCLUSION:

Video-assisted thoracoscopic surgery is an efficient and safe method for the treatment of patients with primary pneumothorax in the adults.

Video-assisted thoracic surgery: primary therapy for spontaneous pneumothorax?

BACKGROUND

This study assessed the role of video-assisted thoracic surgery (VATS) in current therapy for spontaneous pneumothorax.

METHODS

We compared a retrospective series of 89 patients treated conventionally with a consecutive group of 30 patients undergoing VATS pleural abrasion. The 89 earlier patients were predominantly male (81%). Treatment groups included observation/aspiration (7 or 17%), tube thoracostomy (32 or 36%), multiple tubes (7 or 9%), and thoracotomy (43 or 48%). Of the 30 patients treated with VATS, 18 (66%) were male. Primary indications for operation were recurrent pneumothorax (17) and persistent air leak (9).

RESULTS

Hospital lengths of stay (LOS) for the earlier group were 5 days for simple tube and 7 days for primary thoracotomy; LOS for initial intervention followed by thoractomy exceeded 15 days in all subgroups. The average LOS in the VATS group was 13 days; 6 patients treated with primary VATS (no chest tube) had a mean LOS of 6.5 days. Complications included 3 (10%) prolonged air leaks (more than 7 days) and 2 (7%) early recurrences.

CONCLUSIONS

We do not recommend VATS as primary therapy for spontaneous pneumothorax; tube thoracostomy remains the treatment of choice. However, we strongly support surgical intervention early (3 days) in patients with a persistent air leak, and as primary therapy in a nonurgent situation if standard indications exist. This study shows no advantage of VATS over conventional thoracotomy in hospital stay or complication rate.

Multiplex RT-PCR assay for the differential diagnosis of alveolar rhabdomyosarcoma and Ewing's sarcoma

Cytogenetic analysis has defined specific translocations associated with two of the most common small round cell tumors of childhood, t(11;22) in Ewing's sarcoma and t(2;13) in alveolar rhabdomyosarcoma. We and others have previously demonstrated the diagnostic utility of a reverse transcriptase polymerase chain reaction (RT-PCR) assay for the detection of the t(11;22) encoded EWS/FLI-1 chimeric message in Ewing's sarcoma. More recently, we have cloned the t(2;13)(q35;q14) translocation and have shown that it results in the fusion of the PAX3 gene on chromosome 2 to FKHR, a novel member of the fork-head family of transcription factors on chromosome 13. To define the morphological spectrum of childhood sarcomas that express the t(2;13) encoded PAX3/FKHR chimeric message, we have performed RT-PCR analysis on samples from 44 primary pediatric sarcomas and 8 sarcoma cell lines. PAX3/FKHR chimeric messages were detected in 24 of 27 alveolar, 2 of 12 embryonal, and 0 of 1 pleomorphic rhabdomyosarcoma and in 1 of 2 ectomesenchymomas. In contrast, none of 8 Ewing's sarcomas or 2 undifferentiated sarcomas expressed this message. Chimeric transcripts were detected in all cases with cytogenetic evidence of the (2;13) translocation, and in each case the chimeric PAX3/FKHR message had the identical junction sequence, suggesting that genomic chromosome breaks were clustered in a single intron in both genes. By combining the PAX3/FKHR RT-PCR assay with primers for detection of the Ewing's sarcoma t(11;22) encoded EWS/FLI-1 chimeric transcript, we have developed a multiplex RT-PCR reaction that allows the rapid and accurate identification of either translocation in a biopsy sample.

Does open lung biopsy affect treatment in patients with diffuse pulmonary infiltrates?

The decision to perform open lung biopsy in the evaluation of a diffuse pulmonary infiltrate is based on the probability that this examination will yield specific information that may lead to a change in treatment. The role of this procedure remains controversial and many clinicians are reluctant to allow this invasive procedure without assurances that results will lead to a change in therapy for a significant number. To evaluate the impact of open lung biopsy on diagnosis and treatment of diffuse pulmonary infiltrates, we conducted a retrospective review of 61 patients undergoing this procedure at three university-affiliated hospitals during a recent 7-year period. There were 37 men and 24 women; average age was 57 years. Biopsy yielded a specific diagnosis in 21 (34%) patients and a change in therapy in 33 (54%) patients. A complication developed in 11 (18%) patients, directly related to the biopsy procedure in six (10%). Eight patients died. The immune status in 22 (36%) patients was compromised. A specific diagnosis was obtained in 13 (59%) immunocompromised patients and a change in therapy occurred in 17 (77%) of these patients after biopsy. A specific diagnosis was obtained in only eight (21%) of the 39 noncompromised patients and therapy was changed in 16 (41%) patients in this group (p less than 0.02 compromised versus noncompromised). Morbidity and mortality were not significantly different between the two groups. A nonspecific diagnosis led to a change in therapy as frequently as a specific diagnosis in both compromised and noncompromised groups. Open lung biopsy in the patient with a diffuse pulmonary infiltrate is an accurate diagnostic tool and frequently leads to a change in patient treatment. The procedure can be performed with acceptable morbidity and mortality in immunocompromised and noncompromised patients.

Management of broncholithiasis: is thoracotomy necessary?

Endoscopic treatment of broncholithiasis is controversial. From 1953 through 1984, 66 operations were performed on 40 patients with broncholithiasis in an endemic area for histoplasmosis. They are reviewed here retrospectively. All patients had cough; wheeze, hemoptysis, and lithoptysis were present in 60%, 45%, and 26%, respectively. Bronchoscopic stone removal was successful in 19%, whereas 21% of patients required no treatment. The 25 patients who were affected more severely required thoracotomy and operations varying from simple lung wedge resection to repair of a bronchoesophageal fistula. Optimum preservation of lung function was a major treatment guideline. All survived, and most have returned to normal preoperative activity. For selected patients, bronchoscopy and stone removal may be all that is required for broncholithiasis.

Blastomycosis of the esophagus

A patient had clinical, endoscopic, and roentgenographic signs of esophageal carcinoma, but biopsies and brushings were negative. At operation he was found to have blastomycosis localized to the esophagogastric region and adjacent lymph nodes. There was no evidence of pulmonary disease. He was treated successfully by partial esophagectomy and amphotericin. The literature on esophageal blastomycosis is reviewed.

Traumatic rupture of the thoracic aorta

Our experience with 36 cases of traumatic rupture of the aorta has prompted an aggressive investigative and surgical approach. Age range, mechanism of injury, and associated injuries are quite variable. Aortogram is essential for diagnosis and should be done with any evidence of mediastinal abnormality following a deceleration injury. The preferred method of repair is graft interposition for the transected aorta, using femoral vein to femoral artery bypass with an oxygenator in the system. The salvage rate is good if an aggressive surgical approach is used.