Exploring the tumor genomic landscape of aggressive prostate cancer by whole-genome sequencing of tissue or liquid biopsies

Treatment resistance remains a major issue in aggressive prostate cancer (PC), and novel genomic biomarkers may guide better treatment selection. Circulating tumor DNA (ctDNA) can provide minimally invasive information about tumor genomes, but the genomic landscape of aggressive PC based on whole-genome sequencing (WGS) of ctDNA remains incompletely characterized. Thus, we here performed WGS of tumor tissue (n = 31) or plasma ctDNA (n = 10) from a total of 41 aggressive PC patients, including 11 hormone-naïve, 15 hormone-sensitive, and 15 castration-resistant patients. Across all variant types, we found progressively more altered tumor genomic profiles in later stages of aggressive PC. The potential driver genes most frequently affected by single-nucleotide variants or insertions/deletions included the known PC-related genes TP53, CDK12, and PTEN and the novel genes COL13A1, KCNH3, and SENP3. Etiologically, aggressive PC was associated with age-related and DNA repair-related mutational signatures. Copy number variants most frequently affected 14q11.2 and 8p21.2, where no well-recognized PC-related genes are located, and also frequently affected regions near the known PC-related genes MYC, AR, TP53, PTEN, and BRCA1. Structural variants most frequently involved not only the known PC-related genes TMPRSS2 and ERG but also the less extensively studied gene in this context, PTPRD. Finally, clinically actionable variants were detected throughout all stages of aggressive PC and in both plasma and tissue samples, emphasizing the potential clinical applicability of WGS of minimally invasive plasma samples. Overall, our study highlights the feasibility of using liquid biopsies for comprehensive genomic characterization as an alternative to tissue biopsies in advanced/aggressive PC.

Rare case of Turner syndrome patient with metastatic dysgerminoma and no Y-chromosomal material with pathogenic variants found in KIT and MTOR

INTRODUCTION

The presence of Y-chromosomal material in females with Turner syndrome (TS) is a well-established risk factor for developing gonadoblastoma and malignant transformations hereof. However, these events are rarely seen in TS patients with no Y-chromosomal material. Thus, it is the current understanding that parts of the Y-chromosome are essential for malignant transformation of gonadoblastoma in the dysgenetic gonad.

METHODS

We report a case of a TS female with an apparent 46,X,idic(Xq) karyotype, who was diagnosed with a metastatic dysgerminoma. Whole exome sequencing of tumor and blood, along with RNA sequencing of the tumor, was performed to comprehensively search for cryptic Y-chromosomal material and pathogenic variants.

RESULTS

No Y-chromosomal material was detected in neither tumor nor blood. Whole exome sequencing of DNA and RNA revealed a pathogenic somatic gain-of-function mutation in KIT and a pathogenic missense mutation in MTOR. The patient underwent total hysterectomy with bilateral salpingo-oophorectomy, followed by adjuvant chemotherapy. Unfortunately, she died due to chemotherapy-induced pneumonitis seven months after initial diagnosis.

CONCLUSION

Females with TS can develop metastatic dysgerminoma even in the absence of Y-chromosomal material. This questions the current understanding of Y-chromosomal material being essential for the malignant transformation of a gonadoblastoma in the dysgenetic gonad.

Field Cancerization Is Associated with Tumor Development, T-cell Exhaustion, and Clinical Outcomes in Bladder Cancer

BACKGROUND

Field cancerization is characterized by areas of normal tissue affected by mutated clones. Bladder field cancerization may explain the development and recurrence of bladder cancer and may be associated with treatment outcomes.

OBJECTIVE

To investigate the predictive and prognostic roles of field cancerization in patients with high-risk non-muscle-invasive bladder cancer (NMIBC) treated with bacillus Calmette-Guérin (BCG).

DESIGN, SETTING, AND PARTICIPANTS

We conducted comprehensive genomic and proteomic analyses for 751 bladder biopsies and 234 urine samples from 136 patients with NMIBC. The samples were collected at multiple time points during the disease course. Field cancerization in normal-appearing bladder biopsies was measured using deep-targeted sequencing and error correction models.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

Endpoints included the rates of recurrence and progression. Cox regression and Wilcoxon rank-sum and Fisher's exact tests were used.

RESULTS AND LIMITATIONS

A high level of field cancerization was associated with high tumor mutational burden (p = 0.007), high tumor neoantigen load (p = 0.029), and high tumor-associated CD8 T-cell exhaustion (p = 0.017). In addition, high field cancerization was associated with worse short-term outcomes (p = 0.029). Nonsynonymous mutations in bladder cancer-associated genes such as KDM6A, ARID1A, and TP53 were identified as early disease drivers already found in normal-appearing bladder biopsies. Urinary tumor DNA (utDNA) levels reflected the bladder tumor burden and originated from tumors and field cancerization. High levels of utDNA after BCG were associated with worse clinical outcomes (p = 0.027) and with disease progression (p = 0.003). High field cancerization resulted in high urinary levels of proteins associated with angiogenesis and proliferation. Limitations include variation in the number of biopsies and time points analyzed.

CONCLUSIONS

Field cancerization levels are associated with tumor development, immune responses, and clinical outcomes. utDNA measurements can be used to monitor disease status and treatment response.

PATIENT SUMMARY

Molecular changes in the tissue lining the bladder result in tumor recurrence. Urinary measurements may be used to monitor bladder cancer status and treatment responses.

Improved protocol for single-nucleus RNA-sequencing of frozen human bladder tumor biopsies

This paper provides a laboratory workflow for single-nucleus RNA-sequencing (snRNA-seq) including a protocol for gentle nuclei isolation from fresh frozen tumor biopsies, making it possible to analyze biobanked material. To develop this protocol, we used non-frozen and frozen human bladder tumors and cell lines. We tested different lysis buffers (IgePal and Nuclei EZ) and incubation times in combination with different approaches for tissue and cell dissection: sectioning, semi-automated dissociation, manual dissociation with pestles, and semi-automated dissociation combined with manual dissociation with pestles. Our results showed that a combination of IgePal lysis buffer, tissue dissection by sectioning, and short incubation time was the best conditions for gentle nuclei isolation applicable for snRNA-seq, and we found limited confounding transcriptomic changes based on the isolation procedure. This protocol makes it possible to analyze biobanked material from patients with well-described clinical and histopathological information and known clinical outcomes with snRNA-seq.

Circular stable intronic RNAs possess distinct biological features and are deregulated in bladder cancer

Until recently, intronic lariats were regarded as short-lasting splicing byproducts with no apparent function; however, increasing evidence of stable derivatives suggests regulatory roles. Yet little is known about their characteristics, functions, distribution, and expression in healthy and tumor tissue. Here, we profiled and characterized circular stable intronic sequence RNAs (sisRNAs) using total RNA-Seq data from bladder cancer (BC; n = 457, UROMOL cohort), healthy tissue (n = 46), and fractionated cell lines (n = 5). We found that the recently-discovered full-length intronic circles and the stable lariats formed distinct subclasses, with a surprisingly high intronic circle fraction in BC (∼45%) compared to healthy tissues (0-20%). The stable lariats and their host introns were characterized by small transcript sizes, highly conserved BP regions, enriched BP motifs, and localization in multiple cell fractions. Additionally, circular sisRNAs showed tissue-specific expression patterns. We found nine circular sisRNAs as differentially expressed across early-stage BC patients with different prognoses, and sisHNRNPK expression correlated with progression-free survival. In conclusion, we identify distinguishing biological features of circular sisRNAs and point to specific candidates (incl. sisHNRNPK, sisWDR13 and sisMBNL1) that were highly expressed, had evolutionary conserved sequences, or had clinical correlations, which may facilitate future studies and further insights into their functional roles.

Single-nucleus and Spatially Resolved Intratumor Subtype Heterogeneity in Bladder Cancer

Background

Current bulk transcriptomic classification systems for bladder cancer do not consider the level of intratumor subtype heterogeneity.

Objective

To investigate the extent and possible clinical impact of intratumor subtype heterogeneity across early and more advanced stages of bladder cancer.

Design setting and participants

We performed single-nucleus RNA sequencing (RNA-seq) of 48 bladder tumors and additional spatial transcriptomics for four of these tumors. Total bulk RNA-seq and spatial proteomics data were available from the same tumors for comparison, along with detailed clinical follow-up of the patients.

Outcome measurements and statistical analysis

The primary outcome was progression-free survival for non-muscle-invasive bladder cancer. Cox regression analysis, log-rank tests, Wilcoxon rank-sum tests, Spearman correlation, and Pearson correlation were used for statistical analysis.

Results and limitations

We found that the tumors exhibited varying levels of intratumor subtype heterogeneity and that the level of subtype heterogeneity can be estimated from both single-nucleus and bulk RNA-seq data, with high concordance between the two. We found that a higher class 2a weight estimated from bulk RNA-seq data is associated with worse outcome for patients with molecular high-risk class 2a tumors. The sparsity of the data generated using the DroNc-seq sequencing protocol is a limitation.

Conclusions

Our results indicate that discrete subtype assignments from bulk RNA-seq data may lack biological granularity and that continuous class scores may improve clinical risk stratification of patients with bladder cancer.

Patient summary

We found that several molecular subtypes can exist within a single bladder tumor and that continuous subtype scores can be used to identify a subgroup of patients with poor outcomes. Use of these subtype scores may improve risk stratification for patients with bladder cancer, which can help in making decisions on treatment.

Cell-free urine- and plasma DNA mutational analysis predicts neoadjuvant chemotherapy response and outcome in patients with muscle invasive bladder cancer

PURPOSE

Investigate the use of plasma- and urine DNA mutation analysis for predicting neoadjuvant chemotherapy (NAC) response and oncological outcome in patients with muscle invasive bladder cancer.

EXPERIMENTAL DESIGN

Whole exome sequencing of tumor and germline DNA was performed for 92 patients treated with NAC followed by radical cystectomy (RC). A custom NGS-panel capturing approx. 50 mutations per patient was designed and utilized to track mutated tumor DNA in plasma and urine. A total of 447 plasma samples, 281 urine supernatants and 123 urine pellets collected before, during and after treatment were analyzed. Patients were enrolled from 2013-2019 with a median follow-up time of 41.3 months after RC.

RESULTS

We identified tumor DNA before NAC in 89% of urine supernatants, 85% of urine pellets and 43% of plasma samples. Tumor DNA levels were higher in urine supernatants and urine pellets compared to plasma samples (p<0.001). In plasma, detection of circulating tumor DNA (ctDNA) before NAC was associated with a lower NAC response rate (p<0.001). Detection of tumor DNA after NAC was associated with lower response rates in plasma, urine supernatant and urine pellet (p<0.001, p=0.03, p=0.002). Tumor DNA dynamics during NAC was predictive of NAC response and outcome in urine supernatant and plasma (p=0.006, p=0.002). A combined measure from plasma and urine supernatant tumor DNA dynamics stratified patients by outcome (p=0.003).

CONCLUSIONS

Analysis of tumor DNA in plasma and urine samples both separately and combined has potential to predict treatment response and outcome.

Noninvasive prenatal screening for cystic fibrosis using circulating trophoblasts: Detection of the 50 most common disease-causing variants

OBJECTIVES

Cystic fibrosis (CF) is one of the most common severe autosomal recessive disorders. Prenatal or preconception CF screening is offered in some countries. A maternal blood sample in early pregnancy can provide circulating trophoblasts and offers a DNA source for genetic analysis of both the mother and the fetus. This study aimed to develop a cell-based noninvasive prenatal test (NIPT) to screen for the 50 most common CF variants.

METHODS

Blood samples were collected from 30 pregnancies undergoing invasive diagnostics and circulating trophoblasts were harvested in 27. Cystic fibrosis testing was conducted using two different methods: by fragment length analysis and by our newly developed NGS-based CF analysis.

RESULTS

In all 27 cases, cell-based NIPT provided a result using both methods in agreement with the invasive test result.

CONCLUSION

This study shows that cell-based NIPT for CF screening provides a reliable result without the need for partner- and proband samples.

Classifying cGAS-STING Activity Links Chromosomal Instability with Immunotherapy Response in Metastatic Bladder Cancer

The cGAS-STING pathway serves a critical role in anticancer therapy. Particularly, response to immunotherapy is likely driven by both active cGAS-STING signaling that attracts immune cells, and by the presence of cancer neoantigens that presents as targets for cytotoxic T cells. Chromosomal instability (CIN) is a hallmark of cancer, but also leads to an accumulation of cytosolic DNA that in turn results in increased cGAS-STING signaling. To avoid triggering the cGAS-STING pathway, it is commonly disrupted by cancer cells, either through mutations in the pathway or through transcriptional silencing. Given its effect on the immune system, determining the cGAS-STING activation status prior to treatment initiation is likely of clinical relevance. Here, we used combined expression data from 2,307 tumors from five cancer types from The Cancer Genome Atlas to define a novel cGAS-STING activity score based on eight genes with a known role in the pathway. Using unsupervised clustering, four distinct categories of cGAS-STING activation were identified. In multivariate models, the cGAS-STING active tumors show improved prognosis. Importantly, in an independent bladder cancer immunotherapy-treated cohort, patients with low cGAS-STING expression showed limited response to treatment, while patients with high expression showed improved response and prognosis, particularly among patients with high CIN and more neoantigens. In a multivariate model, a significant interaction was observed between CIN, neoantigens, and cGAS-STING activation. Together, this suggests a potential role of cGAS-STING activity as a predictive biomarker for the application of immunotherapy.

Significance

The cGAS-STING pathway is induced by CIN, triggers inflammation and is often deficient in cancer. We provide a tool to evaluate cGAS-STING activity and demonstrate clinical significance in immunotherapy response.

Abstract 3483: Single-nucleus RNA-sequencing of human bladder tumors delineates intra-tumor cellular and subtype heterogeneity

Introduction: Single cell technologies now make it possible to study tumor ecosystems at single cell resolution and may improve our biological understanding of disease aggressiveness and tumor heterogeneity. Whereas single-cell RNA-sequencing of clinical tumor biopsies requires immediate processing after tissue acquisition, single-nucleus RNA-sequencing (snRNA-seq) allows profiling of single nuclei isolated from frozen tumor tissue from patients with long-term follow-up and known clinical outcomes.

Methods: We performed snRNA-seq of frozen tumors from 48 bladder cancer (BC) patients (10 Ta, 13 T1, 25 T2-4) using an optimized DroNc-seq protocol. Nuclei were isolated from frozen biopsies using IgePal lysis buffer and droplets were created using the Dolomite Bio platform followed by library generation and sequencing on an Illumina NovaSeq 6000. All epithelial nuclei were classified according to the UROMOL classes of non-muscle-invasive BC or the consensus classes of muscle-invasive BC. Bulk total RNA-sequencing (RNA-seq) was available for 44 of the tumors for comparison. Three tumors were additionally analyzed using 10x Chromium for validation and four tumors were analyzed using 10x Visium Spatial Transcriptomics.

Results: After pre-processing the raw sequencing data, we obtained data from 117,653 nuclei in total and 59,201 nuclei remained after quality control filtering (1,233 nuclei per tumor and 529 expressed genes per nuclei on average). We focused our analysis on the epithelial compartment, as it constituted the bulk of the tumors (99% of all nuclei). UMAP visualization and clustering of all tumors were mainly driven by patient origin indicating a high level of inter-tumor heterogeneity. To explore intra-tumor heterogeneity and the association to disease aggressiveness, we characterized the tumors individually using hallmark BC gene signatures. Finally, we explored the composition of transcriptomic classes for each tumor and found that 52% of tumors displayed profound intra-tumor class heterogeneity with less than 70% of all nuclei belonging to a single class. The dominating transcriptomic class of single nuclei was only consistent in 44% of the tumors when compared to the overall transcriptomic class from bulk RNA-seq. This may be explained by several levels of heterogeneity and method differences, including the technical challenges of applying a bulk classifier to single nuclei data. We are currently investigating whether specific epithelial subpopulations are associated to outcome and whether signatures derived from snRNA-seq data can be recovered in bulk RNA-seq data and used as prognostic predictors.

Conclusion: Our results highlight the biological complexity of bladder tumors and underline the importance of considering the extent of intra-tumor heterogeneity in the clinical management of BC patients.

Citation Format: Sia V. Lindskrog, Sofie S. Schmøkel, Iver Nordentoft, Philippe Lamy, Michael Knudsen, Jørgen B. Jensen, Lars Dyrskjøt. Single-nucleus RNA-sequencing of human bladder tumors delineates intra-tumor cellular and subtype heterogeneity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3483.

Abstract 3409: Whole genome sequencing of liquid tumor biopsies (ctDNA) from men with metastatic castration resistant prostate cancer

Background: Prostate cancer (PC) is the fifth most lethal male malignancy worldwide, as advanced metastatic castration resistant PC (mCRPC) remains incurable. Genomic biomarkers that can predict treatment response are urgently needed to facilitate personalized mCRPC treatment. Such biomarkers can be identified by whole genome sequencing (WGS) of tumor biopsies. Blood plasma can serve as a non-invasive liquid tumor biopsy as it contains cell free DNA (cfDNA), a subset of which in cancer patients is tumor-derived (circulating tumor DNA; ctDNA). The biomarker discovery potential of WGS of cfDNA in mCRPC remains largely undescribed, as most WGS studies to date have focused on tissue biopsies. Thus, we here aimed to characterize the genomic tumor landscape of mCRPC using WGS of cfDNA.

Methods: We previously performed low-pass WGS (mean coverage: 0.5X) of cfDNA sampled prior to initiation of first-line mCRPC treatment from 143 mCRPC patients (mean ctDNA fraction: 0.15). From these, 10 patients with high (&gt;0.35) ctDNA fractions who received enzalutamide as first-line mCRPC treatment were selected for deeper WGS here. Matched germline DNA from buffy coat (peripheral blood mononuclear cells) was also sequenced. Single-nucleotide variants (SNVs) were called with Mutect2 and CaVEMan, indels with Mutect2 and Pindel, copy-number variants (CNVs) with ASCAT, and structural variants (SVs) with BRASS. For the final analysis, we considered only SNVs and indels called by both tools.

Results: We sequenced germline samples to a mean coverage of 25X (range: 19-28X) and cfDNA samples to a mean coverage of 32X (range: 23-43X). We identified a median of 5,241 SNVs/indels (range: 3,422-48,314) per patient and the mean tumor mutation burden was 1.7 mutations/Mb. One sample had &gt;9 times more SNVs/indels than the median, suggesting microsatellite instability. Among the most recurrently mutated genes were LRP1B (7/10 patients), ARSB (5/10 patients), and TP53 (4/10 patients). COSMIC mutational signature analysis revealed that the clock-like signatures 1, 5, and 40 were most frequent. In contrast, the hypermutated sample was driven primarily by the defective DNA mismatch repair signatures 15, 26, and 44. CNVs affected a mean of 40.9% of the genome. Common PC CNVs were observed, including gains at chromosome 8 (MYC) in 8/10 patients and losses at chromosome 10 (PTEN) in 5/10 patients. Recurrent focal amplifications (defined as &gt;8 copies in regions &lt;3 Mb) affected chromosome 15q11.2 in 3/10 patients, chromosome 22q11.21 in 3/10 patients, and chromosome Xq12, where AR is located, in 3/10 patients. Finally, we identified a median of 241 SVs (range: 92-525) per patient. SVs affecting TMPRSS2 were observed in 3/10 patients.

Conclusion: This study highlights that WGS of cfDNA contributes to the identification of genomic aberrations that may serve as potential biomarkers to guide personalized treatment of mCRPC in the future.

Citation Format: Simone Weiss, Philippe Lamy, Maibritt Nørgaard, Michael Knudsen, Jørgen B. Jensen, Jakob S. Pedersen, Michael Borre, Karina D. Sørensen. Whole genome sequencing of liquid tumor biopsies (ctDNA) from men with metastatic castration resistant prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3409.

Circulating tumor DNA for prognosis assessment and postoperative management after curative-intent resection of colorectal liver metastases

The recurrence rate of colorectal liver metastases (CRLM) patients treated with curative intent is above 50%. Standard of care surveillance includes intensive computed tomographic (CT) imaging as well as carcinoembryonic antigen (CEA) measurements. Nonetheless, relapse detection often happens too late to resume curative treatment. This longitudinal cohort study enrolled 115 patients with plasma samples (N = 439) prospectively collected before surgery, postoperatively at day 30 and every third month for up to 3 years. Droplet digital PCR (ddPCR) was used to monitor serial plasma samples for somatic mutations. Assessment of ctDNA status either immediately after surgery, or serially during surveillance, stratified the patients into groups of high and low recurrence risk (hazard ratio [HR], 7.6; 95% CI, 3.0-19.7; P < .0001; and HR, 4.3; 95% CI, 2.3-8.1; P < .0001, respectively). The positive predictive value (PPV) of ctDNA was 100% in all postoperative analyses. In multivariable analyses, postoperative ctDNA status was the only consistently significant risk marker associated with relapse (P < .0001). Indeterminate CT findings were observed for 30.8% (21/68) of patients. All patients (9/21) that were ctDNA positive at the time of the indeterminate CT scan later relapsed, contrasting 42.6% (5/12) of those ctDNA negative (P = .0046). Recurrence diagnoses in patients with indeterminate CT findings were delayed (median 2.8 months, P < .0001). ctDNA status is strongly associated with detection of minimal residual disease and early detection of relapse. Furthermore, ctDNA status can potentially contribute to clinical decision-making in case of indeterminate CT findings, reducing time-to-intervention.

Molecular correlates of cisplatin-based chemotherapy response in muscle invasive bladder cancer by integrated multi-omics analysis

Overtreatment with cisplatin-based chemotherapy is a major issue in the management of muscle-invasive bladder cancer (MIBC), and currently none of the reported biomarkers for predicting response have been implemented in the clinic. Here we perform a comprehensive multi-omics analysis (genomics, transcriptomics, epigenomics and proteomics) of 300 MIBC patients treated with chemotherapy (neoadjuvant or first-line) to identify molecular changes associated with treatment response. DNA-based associations with response converge on genomic instability driven by a high number of chromosomal alterations, indels, signature 5 mutations and/or BRCA2 mutations. Expression data identifies the basal/squamous gene expression subtype to be associated with poor response. Immune cell infiltration and high PD-1 protein expression are associated with treatment response. Through integration of genomic and transcriptomic data, we demonstrate patient stratification to groups of low and high likelihood of cisplatin-based response. This could pave the way for future patient selection following validation in prospective clinical trials.

There are currently only a few biomarkers to predict the response of muscle invasive bladder cancer to therapy. Here, the authors analyse 300 tumors using exome and RNA sequencing and find that tumors with a high degree of genomic instability and a non-basal/squamous gene expression subtype are most likely to respond to treatment.

Validation of computational determination of microsatellite status using whole exome sequencing data from colorectal cancer patients

BACKGROUND

Microsatellite instability (MSI), resulting from a defective mismatch repair system, occurs in approximately 15% of sporadic colorectal cancers (CRC). Since MSI is associated with a poor response to 5-fluorouracile based chemotherapy and is a positive predictive marker of immunotherapy, it is routine practice to evaluate the MSI status of resected tumors in CRC patients. MSIsensor is a novel computational tool for determining MSI status using Next Generation Sequencing. However, it is not widely used in the clinic and has not been independently validated in exome data from CRC. To facilitate clinical implementation of computational determination of MSI status, we compared MSIsensor to current gold standard methods for MSI testing.

METHODS

MSI status was determined for 130 CRC patients (UICC stage I-IV) using immunohistochemistry, PCR based microsatellite stability testing and by applying MSIsensor to exome sequenced tumors and paired germline DNA. Furthermore, we investigated correlation between MSI status, mutational load and mutational signatures.

RESULTS

Eighteen out of 130 (13.8%) patients were microsatellite instable. We found a 100% agreement between MSIsensor and gold standard methods for MSI testing. All MSI tumors were hypermutated. In addition, two microsatellite stable (MSS) tumors were hypermutated, which was explained by a dominant POLE signature and pathogenic POLE mutations (p.Pro286Arg and p.Ser459Phe).

CONCLUSION

MSIsensor is a robust tool, which can be used to determine MSI status of tumor samples from exome sequenced CRC patients.

Hierarchical Classification of Cancers of Unknown Primary Using Multi-Omics Data

A cancer of unknown primary (CUP) is a metastatic cancer for which standard diagnostic tests fail to locate the primary cancer. As standard treatments are based on the cancer type, such cases are hard to treat and have very poor prognosis. Using molecular data from the metastatic cancer to predict the primary site can make treatment choice easier and enable targeted therapy. In this article, we first examine the ability to predict cancer type using different types of omics data. Methylation data lead to slightly better prediction than gene expression and both these are superior to classification using somatic mutations. After using 3 data types independently, we notice some differences between the classes that tend to be misclassified, suggesting that integrating the data might improve accuracy. In light of the different levels of information provided by different omics types and to be able to handle missing data, we perform multi-omics classification by hierarchically combining the classifiers. The proposed hierarchical method first classifies based on the most informative type of omics data and then uses the other types of omics data to classify samples that did not get a high confidence classification in the first step. The resulting hierarchical classifier has higher accuracy than any of the single omics classifiers and thus proves that the combination of different data types is beneficial. Our results show that using multi-omics data can improve the classification of cancer types. We confirm this by testing our method on metastatic cancers from the MET500 dataset.

Correlation between early dynamics in circulating tumour DNA and outcome from FOLFIRI treatment in metastatic colorectal cancer

Chemotherapy resistance remains a challenge in the clinical management of metastatic colorectal cancer (mCRC). Here, early changes in cell-free circulating tumour DNA (ctDNA) levels were explored as a marker of therapeutic efficacy. Twenty-four mCRC patients were enrolled and treated with FOLFIRI based first-line therapy. Blood samples collected pre-treatment, at day 7, 14, 21, 60 and at progression were analysed for cell-free DNA (cfDNA) and ctDNA levels using digital droplet PCR. A subset of samples were additionally analysed by targeted sequencing. Patients with high pre-treatment ctDNA or cfDNA levels (≥75^th centile) had significantly shorter progression free survival (PFS) than patients with lower levels. Despite an overall decline in ctDNA levels from pre-treatment to first CT-scan, serial analysis identified seven patients with temporary increases in ctDNA consistent with growth of resistant cells. These patients had shorter PFS and shorter overall survival. Targeted sequencing analyses of cfDNA revealed dramatic changes in the clonal composition in response to treatment. Our study suggests that increasing ctDNA levels during the first cycles of first-line FOLFIRI treatment is a predictor of incipient progressive disease and poorer survival. Thus, we demonstrate the importance of monitoring ctDNA levels as early as one week after treatment onset to enable early detection of treatment failure.

Analysis of Plasma Cell-Free DNA by Ultradeep Sequencing in Patients With Stages I to III Colorectal Cancer

Importance

Novel sensitive methods for detection and monitoring of residual disease can improve postoperative risk stratification with implications for patient selection for adjuvant chemotherapy (ACT), ACT duration, intensity of radiologic surveillance, and, ultimately, outcome for patients with colorectal cancer (CRC).

Objective

To investigate the association of circulating tumor DNA (ctDNA) with recurrence using longitudinal data from ultradeep sequencing of plasma cell-free DNA in patients with CRC before and after surgery, during and after ACT, and during surveillance.

Design, Setting, and Participants

In this prospective, multicenter cohort study, ctDNA was quantified in the preoperative and postoperative settings of stages I to III CRC by personalized multiplex, polymerase chain reaction-based, next-generation sequencing. The study enrolled 130 patients at the surgical departments of Aarhus University Hospital, Randers Hospital, and Herning Hospital in Denmark from May 1, 2014, to January 31, 2017. Plasma samples (n = 829) were collected before surgery, postoperatively at day 30, and every third month for up to 3 years.

Main Outcomes and Measures

Outcomes were ctDNA measurement, clinical recurrence, and recurrence-free survival.

Results

A total of 130 patients with stages I to III CRC (mean [SD] age, 67.9 [10.1] years; 74 [56.9%] male) were enrolled in the study; 5 patients discontinued participation, leaving 125 patients for analysis. Preoperatively, ctDNA was detectable in 108 of 122 patients (88.5%). After definitive treatment, longitudinal ctDNA analysis identified 14 of 16 relapses (87.5%). At postoperative day 30, ctDNA-positive patients were 7 times more likely to relapse than ctDNA-negative patients (hazard ratio [HR], 7.2; 95% CI, 2.7-19.0; P < .001). Similarly, shortly after ACT ctDNA-positive patients were 17 times (HR, 17.5; 95% CI, 5.4-56.5; P < .001) more likely to relapse. All 7 patients who were ctDNA positive after ACT experienced relapse. Monitoring during and after ACT indicated that 3 of the 10 ctDNA-positive patients (30.0%) were cleared by ACT. During surveillance after definitive therapy, ctDNA-positive patients were more than 40 times more likely to experience disease recurrence than ctDNA-negative patients (HR, 43.5; 95% CI, 9.8-193.5 P < .001). In all multivariate analyses, ctDNA status was independently associated with relapse after adjusting for known clinicopathologic risk factors. Serial ctDNA analyses revealed disease recurrence up to 16.5 months ahead of standard-of-care radiologic imaging (mean, 8.7 months; range, 0.8-16.5 months). Actionable mutations were identified in 81.8% of the ctDNA-positive relapse samples.

Conclusions and Relevance

Circulating tumor DNA analysis can potentially change the postoperative management of CRC by enabling risk stratification, ACT monitoring, and early relapse detection.

Early Detection of Metastatic Relapse and Monitoring of Therapeutic Efficacy by Ultra-Deep Sequencing of Plasma Cell-Free DNA in Patients With Urothelial Bladder Carcinoma

PURPOSE

Novel sensitive methods for early detection of relapse and for monitoring therapeutic efficacy may have a huge impact on risk stratification, treatment, and ultimately outcome for patients with bladder cancer. We addressed the prognostic and predictive impact of ultra-deep sequencing of cell-free DNA in patients before and after cystectomy and during chemotherapy.

PATIENTS AND METHODS

We included 68 patients with localized advanced bladder cancer. Patient-specific somatic mutations, identified by whole-exome sequencing, were used to assess circulating tumor DNA (ctDNA) by ultra-deep sequencing (median, 105,000×) of plasma DNA. Plasma samples (n = 656) were procured at diagnosis, during chemotherapy, before cystectomy, and during surveillance. Expression profiling was performed for tumor subtype and immune signature analyses.

RESULTS

Presence of ctDNA was highly prognostic at diagnosis before chemotherapy (hazard ratio, 29.1; P = .001). After cystectomy, ctDNA analysis correctly identified all patients with metastatic relapse during disease monitoring (100% sensitivity, 98% specificity). A median lead time over radiographic imaging of 96 days was observed. In addition, for high-risk patients (ctDNA positive before or during treatment), the dynamics of ctDNA during chemotherapy was associated with disease recurrence (P = .023), whereas pathologic downstaging was not. Analysis of tumor-centric biomarkers showed that mutational processes (signature 5) were associated with pathologic downstaging (P = .024); however, no significant correlation for tumor subtypes, DNA damage response mutations, and other biomarkers was observed. Our results suggest that ctDNA analysis is better associated with treatment efficacy compared with other available methods.

CONCLUSION

ctDNA assessment for early risk stratification, therapy monitoring, and early relapse detection in bladder cancer is feasible and provides a basis for clinical studies that evaluate early therapeutic interventions.

Abstract 3617: Prediction of irinotecan and flurouracil efficacy in metastatic colorectal cancer by early measurement of circulating tumor DNA

Background: Chemotherapy resistance in metastatic colorectal cancer (mCRC) is a major challenge, and development of biomarkers for determining therapy efficacy is vital to ensure optimal palliative treatment. Recently, quantification of changes in circulating tumor DNA (ctDNA) levels has attracted substantial attention as a predictive marker. Here, we provide evidence that ctDNA has the potential to be used as an early marker of therapeutic efficacy of irinotecan and fluorouracil (FOLFIRI).

Experimental Procedures: Patients diagnosed with mCRC, and with indication for first-line combination chemotherapy, were prospectively enrolled in this phase II study. Blood was drawn at baseline, day 7, 14, 21, 40 and then monthly until progression. Response evaluation was done at eight-week intervals by CT scanning using RECIST criteria. Chemotherapy was administered at day one and two every two weeks. The levels of cell-free DNA (cfDNA) and ctDNA were determined using sensitive digital droplet PCR assays. ctDNA assays were designed either to mutations identified by targeted sequencing or on basis of known tumor mutations detected in primary or metastatic lesions using a panel of mutation-specific qPCR based assays (KRAS, NRAS, BRAF).

Results: Twenty-four patients were enrolled. A KRAS, NRAS or BRAF mutation was observed in tumor tissue of 16 patients. In 12 of these the mutations were confirmed in baseline samples and used for assessing ctDNA. For the remaining 12 patients, a mutation for ctDNA quantification was identified by targeted tumor sequencing. Patients with high baseline ctDNA levels (75th centile) had significantly shorter progression-free survival (PFS) than patients with low baseline ctDNA levels. After first treatment cycle all patients experienced a decline in ctDNA levels demonstrating initial response to treatment; however, the reduction in ctDNA was not associated with prolonged PFS or overall survival (OS). Conversely, change in ctDNA levels from first to second cycle of treatment (three weeks after treatment start) predicted FOLFIRI efficacy. Patients with increasing ctDNA levels at this time point had a significantly shorter PFS and a shorter OS than patients with stable or decreasing ctDNA levels.

Conclusion: In agreement with the literature, we show that baseline tumor DNA levels predicted PFS. The initial observed decline in ctDNA levels upon administration of FOLFIRI indicates that all tumors had cancer cells sensitive to treatment; however, after elimination of these, resistant clones expanded, leading to treatment resistance. Importantly, our study demonstrates that FOLFIRI efficacy can be evaluated as early as three weeks after treatment initiation by measurement of ctDNA levels. This enables early detection of treatment failure and allows for rapid adaptation of the treatment strategy.

Citation Format: Iben Lyskjær, Camilla J. Kronborg, Mads H. Rasmussen, Boe S. Sørensen, Mona Rosenkilde, Michael Knudsen, Søren R. Krag, Karen-Lise G. Spindler, Claus L. Andersen. Prediction of irinotecan and flurouracil efficacy in metastatic colorectal cancer by early measurement of circulating tumor DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3617.

A Rare Case of Embryonal Carcinoma in a Patient with Turner Syndrome without Y Chromosomal Material but Mutations in KIT, AKT1, and ZNF358 Demonstrated Using Exome Sequencing

Gonadoblastoma and malignant transformations thereof can occur in females with Turner syndrome (TS) and Y chromosomal material. However, in females with TS and no Y chromosomal material, this is rarely seen. We report a female with an apparent 45,X karyotype (in blood and tumor) who was diagnosed with a metastatic embryonal carcinoma. Exome sequencing of blood and the tumor was done, and no Y chromosomal material was detected, while predicted deleterious mutations in KIT (likely driver), AKT1, and ZNF358 were identified in the tumor. The patient was treated with chemotherapy (first-line: cisplatin, etoposide, and bleomycin; second-line: paclitaxel and gemcitabine), and after that surgical debulking was performed. She is currently well and without signs of relapse. We conclude that embryonal carcinoma can apparently occur in 45,X TS without signs of Y chromosomal material.

Characterization of genetic intratumor heterogeneity in colorectal cancer and matching patient-derived spheroid cultures

Patient-derived in vitro cultures of colorectal cancer (CRC) may help guide treatment strategies prior to patient treatment. However, most previous studies have been performed on a single biopsy per tumor. The purpose of this study was to analyze multiple spatially distinct biopsies from CRCs and see how well intratumor heterogeneity (ITH) was recapitulated in matching patient-derived spheroids. Three to five biopsies were collected from six CRC tumors. Each biopsy was split in two; one half was used for spheroid culturing, while the other half was used for DNA and RNA purification. For two patients, lymph node metastases were analyzed. Somatic mutations were called from whole exome sequencing data. Each tumor contained mutations shared across all biopsies and spheroids, including major CRC drivers such as APC, KRAS, and TP53. At the same time, all tumors exhibited ITH on both mutation and copy number level. The concordance between biopsies and spheroids ranged between 40 and 70% for coding mutations. For three patients, the biopsy and spheroid from matching areas clustered together, meaning that the spheroid resembled the area of origin more than the other areas. However, all biopsies and spheroids contained private mutations. Therefore, multiple cultures from spatially distinct sites of the tumor increase the insight into the genetic profile of the entire tumor. Molecular subtypes were called from RNA sequencing data. When based on transcripts from both cancer and noncancerous cells, the subtypes were largely independent of sampling site. In contrast, subtyping based on cancer cell transcripts alone was dependent on sample site and genetic ITH. In conclusion, all examined CRC tumors showed genetic ITH. Spheroid cultures partly reflected this ITH, and having multiple cultures from distinct tumor sites improved the representation of the genetic tumor subclones. This should be taken into account when establishing patient-derived models for drug screening.

Abstract 2906: Characterization of genetic intratumor heterogeneity of colorectal cancer and matching organoids

Background: In the recent years it has become evident that intratumor heterogeneity of solid tumors, such as colorectal cancer (CRC), complicates development of efficient therapy strategies. A minor clone of the tumor might have the ability for treatment resistance and hence the ability for re-establishing the tumor. Organoid cultures derived from the patients’ tumors can be used for ex vivo drug screening prior to treatment of the patient. However this approach is only efficient if the organoids represent the heterogeneity of the tumor. In this study we aim to characterize the genetic intratumor heterogeneity of CRC by performing whole exome sequencing (WES) on multiple biopsies per tumor, and to see how well the heterogeneity is reflected in matching organoid cultures.

Methods: From five CRC patients, three biopsies were collected from separate areas of each tumor. Each biopsy was divided in two: one half was fresh frozen for DNA purification, and the other half was grown in vitro as organoid culture. When available, lymph node metastases (LNMs) were included. WES was performed using SeqCap EZ Exome v3.0, and Illumina NextSeq500. Matched germline DNA was used as reference to identify somatic mutations and copy number variations (CNVs) using Mutect2 and FACETS, respectively.

Results: Each tumor contained multiple mutations that were present in all biopsies and in the organoids as well, representing a common ancestral branch. However all tumor biopsies and organoids also contained private mutations. These constituted on average 10% of the mutations (range 3-18%) indicating spatial genetic heterogeneity in all tumors. Each organoid had private mutations not seen in the tumor area of origin and vice versa, indicating that each area contained multiple clones and only a subset was represented in the organoids. The extent of mutational differences between organoids and their area of origin was similar to the mutational differences between tumor areas. Implying that organoids do not reflect their local origin better than a single biopsy reflects the whole tumor. In one patient with LNMs it was observed that the mutational profile of the metastases resembled only one of the examined tumor areas. Surprisingly, not all the ancestral mutations found in the tumor biopsies were observed in the LNMs, suggesting that at least two clones co-existed in the area of origin and just one of these formed the metastases.

Conclusion: In the five patients studied; spatial genetic heterogeneity was observed, meaning that multiple biopsies are needed to picture the whole tumor. Genetic heterogeneity was also observed between primary tumor and metastases and our data support that the metastases were formed from a single cancer clone that did not dominate the primary tumor. From a genetic point of view, organoids do not seem to fully reflect the tumor area of origin and less so the whole tumor, indicating that care should be taken when using organoids as models of the primary tumor.

Citation Format: Sigrid S. Arnadottir, Maria Jeppesen, Philippe Lamy, Iver Nordentoft, Michael Knudsen, Søren Vang, Mogens R. Madsen, Jacob Thastrup, Ole Thastrup, Claus L. Andersen. Characterization of genetic intratumor heterogeneity of colorectal cancer and matching organoids [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2906. doi:10.1158/1538-7445.AM2017-2906

Clinical Implications of Monitoring Circulating Tumor DNA in Patients with Colorectal Cancer

Purpose: We investigated whether detection of ctDNA after resection of colorectal cancer identifies the patients with the highest risk of relapse and, furthermore, whether longitudinal ctDNA analysis allows early detection of relapse and informs about response to intervention.Experimental Design: In this longitudinal cohort study, we used massively parallel sequencing to identify somatic mutations and used these as ctDNA markers to detect minimal residual disease and to monitor changes in tumor burden during a 3-year follow-up period.Results: A total of 45 patients and 371 plasma samples were included. Longitudinal samples from 27 patients revealed ctDNA postoperatively in all relapsing patients (n = 14), but not in any of the nonrelapsing patients. ctDNA detected relapse with an average lead time of 9.4 months compared with CT imaging. Of 21 patients treated for localized disease, six had ctDNA detected within 3 months after surgery. All six later relapsed compared with four of the remaining patients [HR, 37.7; 95% confidence interval (CI), 4.2-335.5; P < 0.001]. The ability of a 3-month ctDNA analysis to predict relapse was confirmed in 23 liver metastasis patients (HR 4.9; 95% CI, 1.5-15.7; P = 0.007). Changes in ctDNA levels induced by relapse intervention (n = 19) showed good agreement with changes in tumor volume (κ = 0.41; Spearman ρ = 0.4).Conclusions: Postoperative ctDNA detection provides evidence of residual disease and identifies patients at very high risk of relapse. Longitudinal surveillance enables early detection of relapse and informs about response to intervention. These observations have implications for the postoperative management of colorectal cancer patients. Clin Cancer Res; 23(18); 5437-45. ©2017 AACR.

An Algebro-topological description of protein domain structure

The space of possible protein structures appears vast and continuous, and the relationship between primary, secondary and tertiary structure levels is complex. Protein structure comparison and classification is therefore a difficult but important task since structure is a determinant for molecular interaction and function. We introduce a novel mathematical abstraction based on geometric topology to describe protein domain structure. Using the locations of the backbone atoms and the hydrogen bonds, we build a combinatorial object – a so-called fatgraph. The description is discrete yet gives rise to a 2-dimensional mathematical surface. Thus, each protein domain corresponds to a particular mathematical surface with characteristic topological invariants, such as the genus (number of holes) and the number of boundary components. Both invariants are global fatgraph features reflecting the interconnectivity of the domain by hydrogen bonds. We introduce the notion of robust variables, that is variables that are robust towards minor changes in the structure/fatgraph, and show that the genus and the number of boundary components are robust. Further, we invesigate the distribution of different fatgraph variables and show how only four variables are capable of distinguishing different folds. We use local (secondary) and global (tertiary) fatgraph features to describe domain structures and illustrate that they are useful for classification of domains in CATH. In addition, we combine our method with two other methods thereby using primary, secondary, and tertiary structure information, and show that we can identify a large percentage of new and unclassified structures in CATH.

An algebraic approach to signaling cascades with N layers

Posttranslational modification of proteins is key in transmission of signals in cells. Many signaling pathways contain several layers of modification cycles that mediate and change the signal through the pathway. Here, we study a simple signaling cascade consisting of n layers of modification cycles such that the modified protein of one layer acts as modifier in the next layer. Assuming mass-action kinetics and taking the formation of intermediate complexes into account, we show that the steady states are solutions to a polynomial in one variable and in fact that there is exactly one steady state for any given total amounts of substrates and enzymes.We demonstrate that many steady-state concentrations are related through rational functions that can be found recursively. For example, stimulus-response curves arise as inverse functions to explicit rational functions. We show that the stimulus-response curves of the modified substrates are shifted to the left as we move down the cascade. Further, our approach allows us to study enzyme competition, sequestration, and how the steady state changes in response to changes in the total amount of substrates.Our approach is essentially algebraic and follows recent trends in the study of posttranslational modification systems.

The CATH database

The CATH database provides hierarchical classification of protein domains based on their folding patterns. Domains are obtained from protein structures deposited in the Protein Data Bank and both domain identification and subsequent classification use manual as well as automated procedures. The accompanying website http://www.cathdb.info provides an easy-to-use entry to the classification, allowing for both browsing and downloading of data. Here, we give a brief review of the database, its corresponding website and some related tools.

Preventing medication errors in community pharmacy: frequency and seriousness of medication errors

BACKGROUND

Medication errors are a widespread problem which can, in the worst case, cause harm to patients. Errors can be corrected if documented and evaluated as a part of quality improvement. The Danish community pharmacies are committed to recording prescription corrections, dispensing errors and dispensing near misses. This study investigated the frequency and seriousness of these errors.

METHODS

40 randomly selected Danish community pharmacies collected data for a defined period. The data included four types of written report of incidents, three of which already existed at the pharmacies: prescription correction, dispensing near misses and dispensing errors. Data for the fourth type of report, on adverse drug events, were collected through a web-based reporting system piloted for the project.

RESULTS

There were 976 cases of prescription corrections, 229 cases of near misses, 203 cases of dispensing errors and 198 cases of adverse drug events. The error rate was 23/10,000 prescriptions for prescription corrections, 1/10,000 for dispensing errors and 2/10,000 for near misses. The errors that reached the patients were pooled for separate analysis. Most of these errors, and the potentially most serious ones, occurred in the transcription stage of the dispensing process.

CONCLUSION

Prescribing errors were the most frequent type of error reported. Errors that reached the patients were not frequent, but most of them were potentially harmful, and the absolute number of medication errors was high, as provision of medicine is a frequent event in primary care in Denmark. Patient safety could be further improved by optimising the opportunity to learn from the incidents described.

Preventing medication errors in community pharmacy: root-cause analysis of transcription errors

BACKGROUND

Medication errors can have serious consequences for patients, and medication safety is essential to pharmaceutical care. Insight is needed into the vulnerability of the working process at community pharmacies to identify what causes error incidents, so that the system can be improved to enhance patient safety.

METHODS

40 randomly selected Danish community pharmacies collected data on medication errors. Cases that reached patients were analysed, and the most serious cases were selected for root-cause analyses by an interdisciplinary analysis team.

RESULTS

401 cases had reached patients and a substantial number of them had possible clinical significance. Most of these errors were made in the transcription stage, and the most serious were errors in strength and dosage. The analysis team identified four root causes: handwritten prescriptions; "traps" such as similarities in packaging or names, or strength and dosage stated in misleading ways; lack of effective control of prescription label and medicine; and lack of concentration caused by interruptions.

CONCLUSION

A substantial number of the medication errors identified at pharmacies that reach patients have possible clinical significance. Root-cause analysis shows potential for identifying the underlying causes of the incidents and for providing a basis for action to improve patient safety.

M-mode echocardiography in aortic stenosis. Clinical correlates and prognostic significance after valve replacement

To relate preoperative findings at M-mode echocardiography to preoperative clinical and haemodynamic status and to identify possible echocardiographic risk factors for mortality after aortic valve replacement (AVR), 250 patients with AVR for aortic stenosis (AS) were studied. In follow-up averaging 3.2 years there were 22 early (< 30 days) and 23 late deaths. Rising NYHA function class and cardiothoracic index, and left ventricular (LV) failure were related to rising LV end-diastolic and end-systolic diameter index (EDDI, ESDI), and to increasing LV muscle mass index and decreasing fractional shortening (FS). High peak-to-peak systolic aortic valve gradient and LV end-systolic pressure were related to small dimensions of LV with increased FS and posterior wall thickness (PWTh). EDDI < or = 20 mm/m2 and increasing PWTh were independent risk factors for early mortality. Patients with EDDI < or = 20 mm/m2 had normal or supranormal FS. PWTh was the only independent risk factor in long-term survival: 5-year rates being 81 +/- 6%, 94 +/- 3% and 85 +/- 7% for PWTh < or = 13, 14-17 and > or = 18 mm, respectively (p = 0.03). Prevalence of concomitant coronary artery disease (CAD) rose with decreasing PWTh. Angina pectoris in non-CAD patients was related to very high PWTh. Subnormal EDDI was associated with poor surgical outcome, and dilated, poorly contracting LV with congestive heart failure prior to AVR. The degree of LV hypertrophy seemed to be the dominant risk factor, but confounders included myocardial ischaemia due to CAD in low-grade hypertrophy or to hypertrophy per se. A hypothetically confounding factor is the reversibility potential of moderate or severe LV hypertrophy following AVR.

The potential for normal long term survival and morbidity rates after valve replacement for aortic stenosis

BACKGROUND AND AIM OF THE STUDY

The sequelae of early aortic valve replacement (AVR) for aortic stenosis (AS) are controversial, with an increasing body of opinion regarding the patient risk profile as having an influence on long term survival and prosthesis-related morbidity rates. We therefore undertook a comparison of the morbidity and mortality rates of the patients undergoing AVR at our institution over a 22 year period with those in the background population to establish whether early intervention leads to an increased incidence of either.

METHODS

A multivariate risk analysis of 630 consecutive patients with AS who were alive 30 days after AVR performed between January 1965 and December 1986 was completed. The patients had a mean age of 59 years (range 14-78 years), 98% received a mechanical prosthetic valve, and 71% were in functional classes III or IV preoperatively.

RESULTS

Relative to an age- and sex-matched background population, the patients suffered a slight excess mortality during the first postoperative year, and a significant excess mortality after the 12th year, which was primarily related to congestive heart failure (64% of deaths versus 25% during the first 12 years; p < 0.01). A multivariate Cox regression model allowed calculation of a prognostic index for each patient. The index divided the patients into three groups (from low to high index): group A (n = 195) had normal sex- and age-specific survival, group B (n = 165) had a slight late (> 12th year) excess mortality, while group C (n = 270) had significant excess mortality throughout the follow up. Multivariate risk analysis of thromboembolism (1.7%/pt-yr), anticoagulant related hemorrhage (1.5%/pt-yr), all prosthesis-related complications combined (4.2%/pt-yr), and sudden cardiac events (arrhythmia and myocardial infarct; 1.8%/pt-yr) identified variables underlying advanced preoperative heart disease, coronary artery disease and systemic hypertension as the decisive risk factors. The preoperative prevalence of these risk factors as well as the postoperative incidence of the complications differed significantly between the three patient groups; A < B < C. Incidence rates of stroke in the patients (95% confidence interval) and in sex- and age-matched background populations were: group A, 0.48 (0.13-0.83) and 0.34 %/pt-yr, respectively, group B, 1.07 (0.46-1.68) and 0.52%pt-yr, respectively, and group C, 2.28 (1.50-3.06) and 0.68%/pt-yr respectively. Similar results were obtained for incidence rates of myocardial infarct.

CONCLUSION

Operative intervention early in the course of AS, being equivalent to a favorable risk profile, may result in an age- and sex-specific normal long term survival, generally low rates of prosthesis-related complications and a normal incidence of the dominant thromboembolic and hemorrhagic events and of myocardial infarction.

Influence of pre-existing ischemia on recovery from chemical cardioplegia. A study on pig hearts in an isolated blood-perfused model

The impact of prior cardiac ischemia on recovery from chemical cardioplegia was investigated in pig hearts. Group I hearts were subjected to 9-min normothermic ischemia before the start of chemical cardioplegia. After 180 min of induced cardiac arrest, all hearts were reperfused and monitored for 120 min in a blood-perfused Langendorff model. Consistent with left ventricular performance, myocardial oxygen uptake was significantly lower in group I than in the other hearts during the first 60 min of reperfusion. Lactate elimination was significantly higher in group I at the start of reperfusion, but showed no intergroup difference after 25 min. Nor was intergroup difference found in left ventricular end-diastolic pressure, total myocardial flow or glucose extraction fraction during reperfusion. The mitochondrial ultrastructure was identical in the two groups before chemical cardioplegia. During cardioplegia it deteriorated in group I but normalized in group II. During reperfusion these circumstances were reversed. Although precardioplegic ischemia thus significantly impaired left ventricular performance during early recovery, with corresponding effects on metabolism and ultrastructure, stable performance during reperfusion indicated that the ischemic injury did not worsen.

Estimation of tissue blood flow from hyperthermia treatment data

During hyperthermia treatment of patients the delivered heat and the temperatures at several points in the tissue are often measured and recorded. These data contain information about thermal tissue parameters. A method for extracting this information, i.e. estimating the tissue parameters--in particular the blood perfusion rate--is described. The method applies a system identification technique, adjusting the unknown parameters in a thermal tissue model, until the predicted model output (temperature) coincides well with the measured temperature. Data from a number of patient treatments have been used to test the method, and although the accuracy of the method remains to be established conclusively it appears to give a good estimate of the model parameter representing blood flow. The obvious advantage of the method is that it requires no special transducers or experiments. The weak aspect is that it depends on the correctness of a thermal model of the perfused tissue.

Two-point control of temperature profile in tissue

A strategy for controlling the temperature profile in the tissue with a single applicator hyperthermia system is described. By manipulating the cooling water temperature as well as the heating power, the tissue temperatures in two selected locations can be controlled. By proper choice of these two locations and the corresponding temperature set-points, a temperature maximum can be obtained in a fairly superficial tumour. If the tissue composition and consequently the temperature distribution is fairly regular, a temperature profile above 43 degrees C in the tumour and below that in normal tissue can be obtained along an axis perpendicular to the surface. The controller is self-tuning and provides dynamic decoupling, bumpless transfer and anti-reset windup. Test of the controller by simulation and on a phantom indicates it is superior to the single point controller currently used.

State hospital review boards in Minnesota

For the past eight years Minnesota has had a review board for each state hospital serving the mentally ill and the mentally retarded. Each board consists of at least three individuals appointed by the commissioner of the department of public welfare. The board is an external review body in that members are not associated with the department or with the state hospital. It visits the hospital as frequently as required to review commitment papers and processes, assess the propriety of treatment procedures, ensure that each patient has an individualized treatment plan, interview patients and record their concerns, conduct a random review of patients' records, and meet with hospital staff. The board reports its findings to the commissioner and to the head of the hospital.