Identification of stably expressed microRNAs in plasma from high-grade serous ovarian carcinoma and benign tumor patients

BACKGROUND

Ovarian cancer is a lethal gynecological cancer and no reliable minimally invasive early diagnosis tools exist. High grade serous ovarian carcinoma (HGSOC) is often diagnosed at advanced stages, resulting in poorer outcome than those diagnosed in early stage. Circulating microRNAs have been investigated for their biomarker potential. However, due to lack of standardization methods for microRNA detection, there is no consensus, which microRNAs should be used as stable endogenous controls. We aimed to identify microRNAs that are stably expressed in plasma of HGSOC and benign ovarian tumor patients.

METHODS AND RESULTS

We isolated RNA from plasma samples of 60 HGSOC and 48 benign patients. RT-qPCR was accomplished with a custom panel covering 40 microRNAs and 8 controls. Stability analysis was performed using five algorithms: Normfinder, geNorm, Delta-Ct, BestKeeper and RefFinder using an R-package; RefSeeker developed by our study group [1]. Among 41 analyzed RNAs, 13 were present in all samples and eligible for stability analysis. Differences between stability rankings were observed across algorithms. In HGSOC samples, hsa-miR-126-3p and hsa-miR-23a-3p were identified as the two most stable miRNAs. In benign samples, hsa-miR-191-5p and hsa-miR-27a-3p were most stable. In the combined HGSOC and benign group, hsa-miR-23a-3p and hsa-miR-27a-3p were identified by both the RefFinder and Normfinder analysis as the most stable miRNAs.

CONCLUSIONS

Consensus regarding normalization approaches in microRNA studies is needed. The choice of endogenous microRNAs used for normalization depends on the histological content of the cohort. Furthermore, normalization also depends on the algorithms used for stability analysis.

The influence of insulin-related genetic variants on fetal growth, fetal blood flow, and placental weight in a prospective pregnancy cohort

The fetal insulin hypothesis proposes that low birthweight and type 2 diabetes (T2D) in adulthood may be two phenotypes of the same genotype. In this study we aimed to explore this theory further by testing the effects of GWAS-identified genetic variants related to insulin release and sensitivity on fetal growth and blood flow from week 20 of gestation to birth and on placental weight at birth. We calculated genetic risk scores (GRS) of first phase insulin release (FPIR), fasting insulin (FI), combined insulin resistance and dyslipidaemia (IR + DLD) and insulin sensitivity (IS) in a study population of 665 genotyped newborns. Two-dimensional ultrasound measurements with estimation of fetal weight and blood flow were carried out at week 20, 25, and 32 of gestation in all 665 pregnancies. Birthweight and placental weight were registered at birth. Associations between the GRSs and fetal growth, blood flow and placental weight were investigated using linear mixed models. The FPIR GRS was directly associated with fetal growth from week 20 to birth, and both the FI GRS, IR + DLD GRS, and IS GRS were associated with placental weight at birth. Our findings indicate that insulin-related genetic variants might primarily affect fetal growth via the placenta.

Expression Stability Analysis of Candidate References for Normalization of RT-qPCR Data Using RefSeeker R package

When performing expression analysis either for coding RNA (e.g., mRNA) or non-coding RNA (e.g., miRNA), reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a widely used method. To normalize these data, one or more stable endogenous references must be identified. RefFinder is an online web-based tool using four almost universally used algorithms for assessing candidate endogenous references-delta-Ct, BestKeeper, geNorm, and Normfinder. However, the online interface is presently cumbersome and time consuming. We developed an R package, RefSeeker, which performs easy and straightforward RefFinder analysis by enabling raw data import and calculation of stability from each of the algorithms and provides data output tools to create graphs and tables. This protocol uses RefSeeker R package for fast and simple RefFinder stability analysis. Key features Perform stability analysis using five algorithms: Normfinder, geNorm, delta-Ct, BestKeeper, and RefFinder. Identification of endogenous references for normalization of RT-qPCR data. Create publication-ready graphs and tables output. Step-by-step guide dialog window for novice R users.

Randomised phase II trial of stereotactic body radiotherapy in combination with point inhibitors in metastatic castration-resistant state cancer (CheckPRO): a study protocol

INTRODUCTION

Immunotherapy with checkpoint inhibitors (CPIs) has revolutionised cancer treatment but has no convincing effect in metastatic castration-resistant prostate cancer (mCRPC). It has been suggested that a combination of CPI and hypofractionated stereotactic body radiotherapy (SBRT) may work synergistically, and recent trials have supported this. We hypothesise that adding SBRT to CPI treatment can improve response rates in patients with mCRPC.

METHODS AND ANALYSIS

The CheckPRO trial is an open-label, randomised, two-stage, phase II trial. We aim to enrol and randomise 80 evaluable patients with mCRPC who progressed following ≥2 lines of treatment. Enrolment started in November 2019 with 38 months expected enrolment period. The participants receive treatment for 52 weeks including four cycles of ipilimumab and nivolumab with or without concomitant SBRT (24 Gray in three fractions) to a single soft tissue or bone metastasis, followed by 10 cycles of nivolumab. Participants are followed until progression, death, or for 12 months after the end of treatment.Co-primary endpoints are the objective response rate and prostate-specific antigen (PSA) response rate. Secondary endpoints include safety, radiographic progression-free survival, clinical benefit rate, duration of response, PSA-progression-free survival beyond 12 weeks, quality of life and overall survival. Exploratory endpoints include translational analyses of tumour biopsies and consecutive blood samples. Biopsies from metastatic sites are collected at baseline, before the third treatment and at the end of treatment. Blood sampling for immune monitoring and circulating tumour DNA is performed consecutively at baseline and every radiographic assessment.

ETHICS AND DISSEMINATION

This study follows the Helsinki Declaration and is approved by the Danish Ethics Committee System (journal no. H-19016100). All participants must receive written and oral information and provide a signed informed consent document prior to inclusion. The study results will be published in an international peer-review journal.

TRIAL REGISTRATION NUMBER

EudraCT number: 2018-003461-34.

CLINICALTRIALS

gov ID NCT05655715.

Strategies for data normalization and missing data imputation and consequences for potential diagnostic microRNA biomarkers in epithelial ovarian cancer

MicroRNAs (miRNAs) are small non-coding RNA molecules regulating gene expression with diagnostic potential in different diseases, including epithelial ovarian carcinomas (EOC). As only a few studies have been published on the identification of stable endogenous miRNA in EOC, there is no consensus which miRNAs should be used aiming standardization. Currently, U6-snRNA is widely adopted as a normalization control in RT-qPCR when investigating miRNAs in EOC; despite its variable expression across cancers being reported. Therefore, our goal was to compare different missing data and normalization approaches to investigate their impact on the choice of stable endogenous controls and subsequent survival analysis while performing expression analysis of miRNAs by RT-qPCR in most frequent subtype of EOC: high-grade serous carcinoma (HGSC). 40 miRNAs were included based on their potential as stable endogenous controls or as biomarkers in EOC. Following RNA extraction from formalin-fixed paraffin embedded tissues from 63 HGSC patients, RT-qPCR was performed with a custom panel covering 40 target miRNAs and 8 controls. The raw data was analyzed by applying various strategies regarding choosing stable endogenous controls (geNorm, BestKeeper, NormFinder, the comparative ΔCt method and RefFinder), missing data (single/multiple imputation), and normalization (endogenous miRNA controls, U6-snRNA or global mean). Based on our study, we propose hsa-miR-23a-3p and hsa-miR-193a-5p, but not U6-snRNA as endogenous controls in HGSC patients. Our findings are validated in two external cohorts retrieved from the NCBI Gene Expression Omnibus database. We present that the outcome of stability analysis depends on the histological composition of the cohort, and it might suggest unique pattern of miRNA stability profiles for each subtype of EOC. Moreover, our data demonstrates the challenge of miRNA data analysis by presenting various outcomes from normalization and missing data imputation strategies on survival analysis.

Genomic Sub-Classification of Ovarian Clear Cell Carcinoma Revealed by Distinct Mutational Signatures

Ovarian clear cell carcinoma (OCCC) is characterized by dismal prognosis, partially due to its low sensitivity to standard chemotherapy regimen. It is also well-known for presenting unique molecular features in comparison to other epithelial ovarian cancer subtypes. Here, we aim to identify potential subgroups of patients in order to (1) determine their molecular features and (2) characterize their mutational signature. Furthermore, we sought to perform the investigation based on a potentially clinically relevant setting. To that end, we assessed the mutational profile and genomic instability of 55 patients extracted from the Gynecologic Cancer Database (DGCD) by using a panel comprised of 409 cancer-associated genes and a microsatellite assay, respectively; both are currently used in our routine environment. In accordance with previous findings, ARID1A and PIK3CA were the most prevalent mutations, present in 49.1% and 41.8%, respectively. From those, the co-occurrence of ARID1A and PIK3CA mutations was observed in 36.1% of subjects, indicating that this association might be a common feature of OCCC. The microsatellite instability frequency was low across samples. An unbiased assessment of signatures identified the presence of three subgroups, where "PIK3CA" and "Double hit" (with ARID1A and PIK3CA double mutation) subgroups exhibited unique signatures, whilst "ARID1A" and "Undetermined" (no mutations on ARID1A nor PIK3CA) subgroups showed similar profiles. Those differences were further indicated by COSMIC signatures. Taken together, the current findings suggest that OCCC presents distinct mutational landscapes within its group, which may indicate different therapeutic approaches according to its subgroup. Although encouraging, it is noteworthy that the current results are limited by sample size, and further investigation on a larger group would be crucial to better elucidate them.

Integrated microRNA and mRNA signatures associated with overall survival in epithelial ovarian cancer

Ovarian cancer (OC), the eighth-leading cause of cancer-related death among females worldwide, is mainly represented by epithelial OC (EOC) that can be further subdivided into four subtypes: serous (75%), endometrioid (10%), clear cell (10%), and mucinous (3%). Major reasons for high mortality are the poor biological understanding of the OC mechanisms and a lack of reliable markers defining each EOC subtype. MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression primarily by targeting messenger RNA (mRNA) transcripts. Their aberrant expression patterns have been associated with cancer development, including OC. However, the role of miRNAs in tumorigenesis is still to be determined, mainly due to the lack of consensus regarding optimal methodologies for identification and validation of miRNAs and their targets. Several tools for computational target prediction exist, but false interpretations remain a problem. The experimental validation of every potential miRNA-mRNA pair is not feasible, as it is laborious and expensive. In this study, we analyzed the correlation between global miRNA and mRNA expression patterns derived from microarray profiling of 197 EOC patients to identify the signatures of miRNA-mRNA interactions associated with overall survival (OS). The aim was to investigate whether these miRNA-mRNA signatures might have a prognostic value for OS in different subtypes of EOC. The content of our cohort (162 serous carcinomas, 15 endometrioid carcinomas, 11 mucinous carcinomas, and 9 clear cell carcinomas) reflects a real-world scenario of EOC. Several interaction pairs between 6 miRNAs (hsa-miR-126-3p, hsa-miR-223-3p, hsa-miR-23a-5p, hsa-miR-27a-5p, hsa-miR-486-5p, and hsa-miR-506-3p) and 8 mRNAs (ATF3, CH25H, EMP1, HBB, HBEGF, NAMPT, POSTN, and PROCR) were identified and the findings appear to be well supported by the literature. This indicates that our study has a potential to reveal miRNA-mRNA signatures relevant for EOC. Thus, the evaluation on independent cohorts will further evaluate the performance of such findings.

DNA Methylation in Ovarian Tumors-a Comparison Between Fresh Tissue and FFPE Samples

Among women, ovarian cancer (OC) is one of the most severe forms of malignancy, accounting for a low 5-year survival rate, of approximately 52%. Early symptoms are unspecific and hence hard to detect. The origin of OC and its subtypes are still unclear, underlying the need for efficient diagnostic biomarkers. In that regard, epigenetics studies are emerging in cancer diagnostics, with encouraging outcomes. Among them, DNA methylation profiling has shown that the origins of the cancer epigenome are associated with molecular factors that are crucial to carcinogenesis, such as regulation of oncogenes and tumor suppressors. Furthermore, those events have been detected in abnormal cell morphology before neoplastic formation, indicating its potential crucial use in the OC diagnostics in the future. Nonetheless, studies are limited, and whether methylation analysis can be performed optimally in formalin-fixed paraffin-embedded (FFPE) preparations of OC cases is still elusive. In the present report, we investigated the performance of DNA methylation analysis in FFPE samples, compared to their matched fresh frozen tissue in a small cohort of OC samples. We found that the overall DNA methylation profile in FFPE tissue showed high concordance to that found in fresh frozen tissue, and accounting for the small cohort size, the differentially methylated sites found primarily in frozen tissue, compared to benign samples, were also reproducible in FFPE. Overall, by using samples from our current clinical setting of tissue preservation, these preliminary observations might provide insights into the clinical use of FFPE tissues in methylation studies without critically compromising the outcome.

Gene expression profile association with poor prognosis in epithelial ovarian cancer patients

Ovarian cancer (OC) is the eighth most common type of cancer for women worldwide. The current diagnostic and prognostic routine available for OC management either lack specificity or are very costly. Gene expression profiling has shown to be a very effective tool in exploring new molecular markers for patients with OC, although association of such markers with patient survival and clinical outcome is still elusive. Here, we performed gene expression profiling of different subtypes of OC to evaluate its association with patient overall survival (OS) and aggressive forms of the disease. By global mRNA microarray profiling in a total of 196 epithelial OC patients (161 serous, 15 endometrioid, 11 mucinous, and 9 clear cell carcinomas), we found four candidates-HSPA1A, CD99, RAB3A and POM121L9P, which associated with OS and poor clinicopathological features. The overexpression of all combined was correlated with shorter OS and progression-free survival (PFS). Furthermore, the combination of at least two markers were further associated with advanced grade, chemotherapy resistance, and progressive disease. These results indicate that a panel comprised of a few predictors that associates with a more aggressive form of OC may be clinically relevant, presenting a better performance than one marker alone.

Exome sequencing of 22 genes using tissue from patients with biliary tract cancer

Biliary tract cancers (BTC) are a rare heterogeneous disease group with a dismal prognosis and limited treatment options. The mutational landscape consists of genetic aberrations both shared by and characteristic for anatomical location. Here, we present exome sequencing data on 22 genes from a phase 2 trial using a clinically validated panel used in patients with colorectal cancer. A total of 56 patients were included in a one-armed phase 2 trial investigating the treatment combination of capecitabine, gemcitabine, oxaliplatin, and cetuximab. Tissue DNA yield and quality allowed analysis of 30 patients on our panel including 22 genes. ARID1A (33%) and TP53 (33%) were found to be most frequently mutated followed by KRAS mutations found in 20% of the patients. Mutational aberrations in ARID1A were found more prevalent than expected, whereas TP53 and KRAS were in concordance with earlier reported data. Mutation in CTNNB1 was significantly associated with poor prognosis. Our panel is clinically validated and suitable for a high volume of samples to detect mutations in patients with BTC. However, it is reasonable to assume that the clinical utility could be optimized in this patient group by extending the panel to include BTC specific mutations with potential therapeutic consequences such as IDH1/2, FGFR fusions, ERBB3, and BRCA1/2.

Diagnostic plasma miRNA-profiles for ovarian cancer in patients with pelvic mass

Background

Ovarian cancer is the fifth most common cancer in women worldwide. Moreover, there are no reliable minimal invasive tests to secure the diagnosis of malignant pelvic masses. Cell-free, circulating microRNAs have the potential as diagnostic biomarkers in cancer. Here, we performed and validated a miRNA panel with the potential to distinguish OC from benign pelvic masses.

Methods

The profile of plasma microRNA was determined with a panel of 46 candidates in a discovery group and a validation group, each consisting of 190 pre-surgery plasma samples from age-matched patients with malignant (n = 95) and benign pelvic mass (n = 95), by real time RT-qPCR.

Results

Four up-regulated (miR-200c-3p, miR-221-3p, miR-21-5p, and miR-484) and two down-regulated (miR-195-5p and miR-451a) microRNAs were discovered. From those, miR-200c-3p and miR-221-3p were further confirmed in a validation cohort. A combination of these 2 microRNAs together with CA-125 yielded an overall diagnostic accuracy of AUC = 0.96.

Conclusions

We showed consistent plasma microRNA profiles that provide independent diagnostic information of late stage OC.

Methylation and ovarian cancer: Can DNA methylation be of diagnostic use?

Ovarian cancer is a silent killer and, due to late diagnosis and frequent chemo resistance in patients, the primary cause of fatality amongst the various types of gynecological cancer. The discovery of a specific and sensitive biomarker for ovarian cancer could improve early diagnosis, thereby saving lives. Biomarkers could also improve treatment, by predicting which patients will benefit from specific treatment strategies. DNA methylation is an epigenetic mechanism, and 'methylation imbalance' is characteristic of cancer. Previous research suggests that changes in DNA methylation can be used diagnostically, and that they may predict resistance to treatment. This paper gives an up-to-date overview of research investigating the potential of DNA methylation-based markers for diagnostics, prognostics, screening and prediction of drug resistance for ovarian cancer patients. DNA methylation cancer-biomarkers may be useful for cancer treatment, particularly since they are chemically stable and since cancer-associated changes in methylation typically precedes tumor growth. DNA methylation markers could improve diagnosis and treatment and might even be used for screening in the future. Furthermore, DNA methylation biomarkers could facilitate the development of precision medicine. However, at this point no biomarkers for ovarian cancer have a sufficient combination of sensitivity and specificity in a clinical setting. A reason for this is that most studies have focused on a single or a few methylation sites. More large screenings and genome-wide studies must be performed to increase the chance of identifying a DNA methylation marker which can identify ovarian cancer.

Discovery of microRNAs in tumor tissue predictive of time to progression and overall survival in patients with colorectal cancer treated with first-line capecitabine, oxaliplatin, and bevacizumab

461

Background: The aim was to identify predictive and prognostic microRNAs (miRNAs) in cancer tissue samples from patients with metastatic colorectal cancer (mCRC) treated with 1.-line capecitabine, oxaliplatin, and bevacizumab (CapOxBev).

Methods: Patients with mCRC treated with 1.-line CapOxBev were identified from 7 hospital databases and clinical and pathological data was extracted retrospectively. Formalin-fixed paraffin-embedded (FFPE) tissue samples from primary tumors were collected and RNA was purified from 3 x 10 µm sections, without micro-dissection. MiRNA expression was measured using TaqMan® Array Human MicroRNA A and B cards (Applied Biosystems) profiling 754 miRNAs. Raw miRNA expression values were checked for outliers and data was corrected using spike-in values. In a univariate selection method, each miRNA was related to time-to-progression (TTP) and overall survival (OS) using Cox proportional hazards model (threshold p < 0.001). Candidate miRNAs were tested using Akaike’s Information Criterion in a multivariate analysis corrected for age, sex, histology, number of metastatic sites, primary location, and prior adjuvant treatment.

Results: Samples from 212 patients were profiled and 205 and 192 had acceptable miRNA and outcome data available for final analysis of OS and TTP, respectively. Four miRNAs were found to be predictive for TTP and two for OS. Higher expression of miRNAs A, B, and C and lower expression of miRNA D was predictive of longer TTP, and higher expression of miRNAs E and F predicted longer OS.

Conclusions: Four miRNAs measured in archival FFPE samples of primary CRC tumors from patients treated with 1.-line CapOxBev were predictors of TTP and two others of OS. Three of the miRNAs found have reported roles in angiogenesis pathways indicating that they may be biomarkers for bevacizumab efficacy. A validation study in 500 patients is on-going.

[Table: see text]

Impact of microRNA miR-345 in blood on survival and response in 144 patients with metastatic colorectal cancer treated with third-line cetuximab and irinotecan

451

Background: MicroRNAs (miR) are small non-coding RNAs regulating gene expression at a posttranscriptional level. A prognostic potential of miRs in cancer tissue, whole blood or serum/plasma has been proposed in a small subset of cancers. MiR-345 has been reported up-regulated in cancer tissue and involved in malignant transformation in cancer cells. The aim of the study was to describe the ability of miR-345 to predict OS and response in patients with metastatic colorectal cancer (mCRC) treated with 3. line cetuximab and irinotecan independent of their KRAS status.

Methods: A total of 144 patients with mCRC were included in a prospective phase II study of 3. line treatment with cetuximab and irinotecan. All patients had progressed on 5-FU, oxaliplatin and irinotecan prior to the protocol. MiRs were isolated from whole blood collected in PAXgene Blood RNA tubes (Qiagen), and miRNA profiling was performed using TaqMan MicroRNA Array v2.0 (Applied Biosystems). Cox proportional hazard model was applied to study the correlation between baseline miR-345 expression and OS. Logistic regression analysis was applied to study response (PR (n=25) vs. PD (n=38)) and clinical benefit (PR+SD > 9 months (n=32)) vs. no clinical benefit (PD+SD < 4 months (n=87)). Hazard ratios (HR) and odds ratios are per inter quartile range.

Results: High expression of miR-345 was associated with poor treatment response with an odds ratio of 1.43 (p= 0.002) for progressive disease as best overall response and 2.04 (p=0.01) for no clinical benefit. High expression of miR-345 was significantly associated with short OS (HR =5.01, 95% Confidence Interval (CI): 2.39-10.50) when adjusted for KRAS status and performance status. This finding was confirmed in the subgroup of patients with KRAS wild type (n=87) (HR=3.02, 95% CI: 1.00-9.07).

Conclusions: High expression of miR-345 in whole blood is correlated to lack of response and short OS in mCRC patients treated with cetuximab and irinotecan. This suggests that miR-345 may be a new predictive and prognostic biomarker for treatment with cetuximab and irinotecan.

Gene expression profiles as prognostic markers in women with ovarian cancer

The purpose was to find a gene expression profile that could distinguish short-term from long-term survivors in our collection of serous epithelial ovarian carcinomas. Furthermore, it should be able to stratify in an external validation set. Such a classifier profile will take us a step forward toward investigations for more individualized therapies and the use of gene expression profiles in the clinical practice. RNA from tumor tissue from 43 Danish patients with serous epithelial ovarian carcinoma (11 International Federation of Gynecology and Obstetrics [FIGO] stage I/II, 32 FIGO stage III/IV) was analyzed using Affymetrix U133 plus 2.0 microarrays. A multistep statistical procedure was applied to the data to find the gene set that optimally split the patients into short-term and long-term survivors in a Kaplan-Meier plot. A 14-gene prognostic profile with the ability to distinguish short-term survivors (median overall survival of 32 months) from long-term survivors (median overall survival not yet reached after a median follow-up of 76 months) with a P value of 3.4 x 10 was found. The prognostic gene set was also able to distinguish short-term from long-term survival in patients with advanced disease. Furthermore, its ability to classify in an external validation set was demonstrated. The identified 14-gene prognostic profile was able to predict survival (short- vs long-term survival) with a strength that is better than any other prognostic factor in epithelial ovarian cancer including FIGO stage. This stratification method may form the basis of determinations for new therapeutic approaches, as patients with poor prognosis could obtain the biggest advantage from new treatment modalities.

Distribution of microsatellite instability in Danish ovarian tumor patients and the prognostic value in ovarian cancer patients

The repeated frequency of microsatellite instability (MSI) in ovarian cancer (OC) ranges from 0% to 50%. Most MSI studies including OC patients have involved relatively small number of tumors, a wide range of different MSI markers, different patient characteristics, and varying criteria for defining tumors as MSI positive. Thus, no conclusive evidence about MSI occurrence in OC has been provided and the large variation has made interpretation of these previous studies difficult. The majority of MSI studies have been performed on OC cases with few borderline ovarian tumor (BOT) cases included. Few BOT studies showed no evidence of MSI, but in one study the frequency of MSI was 27.7% with all tumors of serous type, suggesting that MSI may play a role in the development of serous BOT. The aim of our study was to determine the frequency of MSI using a panel of 16 dinucleotide markers: TP53, D17S250, CACNLB1, D18S58, D19S49, DXS538, DXS454, D5S117, D5S107, D6S284, D6S305, D9S171, D9S15, D11S554, D11S29, and D13S272 in tissue from patients with OC or BOT and to correlate the presence of MSI at these markers with the clinical information, such as FIGO stage, histological type, age, and survival in OC. The overall frequencies of MSI were within 2-10%. We observed MSI at different loci and with different extent (2.3-9.8%) in the different histopathological types. In both BOT and OC cases, we observed that all high MSI (MSI-H) were of serous type. No significant difference in disease specific survival was found between stage III/IV OC patients who presented MSI compared to patients being microsatellite stable (MSS) (p = 0.72). In conclusion, we found no association to any of the clinical parameters evaluated, although a tendency of a higher frequency of MSI was observed among serous OC.

Sample handling for mass spectrometric proteomic investigations of human sera

Proteomic investigations of sera are potentially of value for diagnosis, prognosis, choice of therapy, and disease activity assessment by virtue of discovering new biomarkers and biomarker patterns. Much debate focuses on the biological relevance and the need for identification of such biomarkers while less effort has been invested in devising standard procedures for sample preparation and storage in relation to model building based on complex sets of mass spectrometric (MS) data. Thus, development of standardized methods for collection and storage of patient samples together with standards for transportation and handling of samples are needed. This requires knowledge about how sample processing affects MS-based proteome analyses and thereby how nonbiological biased classification errors are avoided. In this study, we characterize the effects of sample handling, including clotting conditions, storage temperature, storage time, and freeze/thaw cycles, on MS-based proteomics of human serum by using principal components analysis, support vector machine learning, and clustering methods based on genetic algorithms as class modeling and prediction methods. Using spiking to artificially create differentiable sample groups, this integrated approach yields data that--even when working with sample groups that differ more than may be expected in biological studies--clearly demonstrate the need for comparable sampling conditions for samples used for modeling and for the samples that are going into the test set group. Also, the study emphasizes the difference between class prediction and class comparison studies as well as the advantages and disadvantages of different modeling methods.

Unravelling in vitro variables of major importance for the outcome of mass spectrometry-based serum proteomics

The use of mass spectrometry (MS) for analysing low-molecular weight proteins and peptides from biological fluids has a great, yet not fully realized, potential for biomarker discovery. To prune MS-data as much as possible for non-relevant non-biological variation the development of standardized protocols for handling and processing the samples before MS and adjusting data after MS to compensate for method-induced variability are warranted. This calls for knowledge about how different variables contribute to MS-based proteome analyses. In addition, identification of the peptides involved in pre-analytical variation will be helpful in evaluating the clinical significance of predictive models derived from MS data. Using human sera, extraction by weak cation-exchange magnetic beads, and analysis by MALDI-TOF MS we here evaluated pre-analytical variation and identify peptides involved in this. The influences of humidity, temperature, and time for preparation of sera on spectral changes were evaluated. Also, the reproducibility of the methods and the effect of a baseline correction procedure were examined. Low temperatures, short handling times, and a baseline correction procedure minimize the contribution of artifacts to sample variability as observed by MS. The complement split product C3f and fragments thereof appear to be sensitive indicators of sample handling induced modifications. Other peptides that are indicative of such variability are fibrin and kininogen fragments. Using strict experimental guidelines as well as standardized sample collection procedures it is possible to obtain reproducible peak intensities and positions in serum mass profiling using magnetic bead-based fractionation and MALDI-TOF MS.

Smoking and Overweight: Negative Prognostic Factors in Stage III Epithelial Ovarian Cancer

OBJECTIVE

Smoking and overweight are associated with poorer prognosis in several cancer types. The prognostic effect of smoking and body mass index (BMI) on ovarian cancer is unknown.

METHODS

Ovarian cancer cases were from the Danish MALOVA (MALignant OVArian cancer) study. Information on smoking status and BMI was obtained from a personal interview conducted closely after primary surgery. Cox regression models were used to estimate adjusted hazard ratios (HR) and 95% confidence intervals (95% CI) for ovarian cancer-specific death in relation to smoking variables and BMI.

RESULTS

A total of 295 women with stage III epithelial ovarian cancer were identified and followed to death or for a median of 7.3 years (range, 5.4-9.5 years). Median survival time for normal-weight never smokers was 2.8 years (95% CI, 2.3-3.2) compared with 1.2 years (95% CI, 0.8-2.3) for overweight current smokers. Current smokers had a significantly increased risk of ovarian cancer death compared with never smokers in multivariate Cox analysis (HR, 1.65; 95% CI, 1.22-2.24). The negative effect of smoking diminished with increasing time since a former smoker had stopped smoking (HR, 0.89; 95% CI, 0.80-0.98 per 5 years since stop of smoking). Overweight women also had an increased risk of ovarian cancer death (HR, 1.83; 95% CI, 1.38-2.42) compared with normal-weight women.

CONCLUSION

Smoking at the time of diagnosis and premorbid overweight were negative prognostic factors for ovarian cancer-specific survival. The negative effect of smoking decreased with increasing time since stop of smoking.

Do risk factors for epithelial ovarian cancer have an impact on prognosis? Focus on previous pelvic surgery and reproductive variables

OBJECTIVES

The prognostic impact of risk factors for ovarian cancer development is sparsely explored, but previous sterilisation has been shown to have a negative impact on survival.

METHODS

Ovarian cancer cases were from the Danish MALOVA study. Information on previous pelvic surgery as well as reproductive variables was obtained from a personal interview conducted closely after primary surgery. Cox regression models were used to estimate adjusted hazard ratios (HR) and 95% confidence intervals (95% CI) for ovarian cancer specific death in relation to previous pelvic surgery and reproductive variables including lifetime number of ovulation years.

RESULTS

A total of 295 women with Stage III ovarian carcinomas were identified and followed to death or for a median of 7.3 years (range 5.4-9.5 years). Previously sterilised or hysterectomised women seemed to have a slightly decreased risk of ovarian cancer death (HR = 0.62; 95% CI: 0.36-1.08 and HR = 0.82; 95% CI: 0.55-1.21), although none of these associations reached statistical significance. The prognostic impacts of the individual reproductive variables followed the same pattern as the impact of the variables on ovarian cancer development, although significance was only reached for age at menarche (HR = 0.91 per year; 95% CI: 0.84-0.99). By accumulation of the possible minor effects of the reproductive variables in calculation of the total lifetime number of ovulation years, we found that survival decreased significantly with increasing number of ovulations (HR = 1.53 per 10 years; 95% CI: 1.09-2.14).

CONCLUSION

Increasing lifetime number of ovulations was a negative prognostic factor for ovarian cancer specific survival. Previous sterilisation or hysterectomy seemed to be associated with improved survival.

Evaluation of a polymorphism in intron 2 of the p53 gene in ovarian cancer patients. From the Danish "Malova" Ovarian Cancer Study

BACKGROUND

The p53 gene is frequently mutated in various human tumours. In addition, single nucleotide polymorphisms are often observed in exons and introns of the p53 gene in normal tissues and tumours.

MATERIALS AND METHODS

A total of 210 blood and tissue samples from 182 ovarian cancers (OC) and 28 ovarian borderline tumours, in addition to blood samples from 72 healthy women, were analysed. The used analyses were PCR and SSCP. The distinguishable SSCP patterns were confirmed by DNA sequencing.

RESULTS

A polymorphism located at position 38 in intron 2 of the p53 gene was studied in blood and tumour tissues from Danish ovarian tumour patients and in blood from controls. Significant differences were found between the distributions of the genotypes in blood samples compared to the corresponding tissue samples (p = 0.0002). A tendency towards a significant difference in survival was observed between OC stage II patients with a shift from one genotype in the blood to another genotype in the tissue and patients with no shift (p = 0.05). In multivariate COX regression analysis restricted to stage III OC patients, the only independent factors found were shift, serum-tetranectin and age.

CONCLUSION

A shift from one p53 intron 2 genotype in the blood to another genotype in the tissue may be a prognostic factor in ovarian cancer patients.

The variation of risk estimates through pregnancy in second trimester maternal serum screening for Down syndrome

The variation of risk estimates in second trimester maternal serum screening for Down's syndrome has been shown to be considerable in quality control schemes, i.e. UKNEQAS. We studied the biological variation of risk estimates in 16 women through pregnancy. The maternal serum markers alpha-fetoprotein (AFP), human chorionic gonadotrophin (hCG), unconjugated estriol (uE3) and beta-hCG were determined six times during late first to late second trimester, and the associated likelihood ratios for Down syndrome were calculated. The interpersonal variation of markers, as well as that of the likelihood ratio, was much greater than the intrapersonal variation. The average intrapersonal standard deviation (SD) of the triple test log likelihood ratio was 0.2291, corresponding to a central 95-percentile interval 0.36-2.81 of the likelihood ratio. The interpersonal SD of the log likelihood ratio was 0.5482, corresponding to a central 95-percentile interval 0.08-11.87 of the likelihood ratio. The large difference between the intra- and interpersonal variation makes it unlikely that biological variation through pregnancy is a major contributor to the variation of risk estimates obtained several times in the same pregnancy. Rather, improvements in analytical quality and laboratory management must be expected to result in reduced variation and, in consequence, better performance of screening.

The prognostic value of pretherapeutic tetranectin and CA-125 in patients with relapse of ovarian cancer

OBJECTIVE

The aim of the study was to examine the prognostic values of, respectively, tetranectin (TN) and CA-125 measured in serum from patients presenting with relapse of ovarian cancer (OC).

METHODS

TN and CA-125 were measured in serum samples from 75 patients with relapse of OC before the start of second-line chemotherapy. The endpoint used was death of OC. The variables were analyzed by univariate life table analysis and multivariate Cox analysis.

RESULTS

A significantly shortened survival was found for patients with low serum TN values compared to patients with serum TN levels above one of the cutoff levels. The survivals are illustrated by life tables. No prognostic function was found for CA-125. TN and relapse </=12 months after primary treatment were the only significant independent prognostic variables among the following variables tested in the Cox analyses: primary and second-line treatment, CA-125, age, histology, performance score, tumor localization, and size.

CONCLUSION

Serum TN determination may be valuable in the selection of patients with relapse of OC for new treatment strategies in future studies.

Stability of YKL-40 concentration in blood samples

The stability of YKL-40, a mammalian member of the family of 18 glycosylhydrolases, in blood samples handled under different temperatures and different time intervals before centrifugation was studied in paired serum and plasma samples from 25 healthy premenopausal Danish women. Significant elevations of YKL-40 were found in 8 paired serum samples left on the clot for more than 3 h at room temperature compared to paired serum samples left on the clot for 3 h or less. Significant elevations of YKL-40 were found in 8 paired plasma (EDTA) samples left on the blood cells for more than 8 h at room temperature compared to paired plasma (EDTA) samples left on the blood cells for 8 h or less. No elevations were found in YKL-40 levels in serum samples left on the clot at 4 degrees C for 24 h or in plasma (EDTA) samples left on the blood cells for 72 h before centrifugation. Significantly lower concentrations of YKL-40 were measured in plasma (EDTA) compared with paired serum samples with a serum/plasma ratio of 1.4 in samples left on the clot or on blood cells at 4 degrees C for up to 24 h. Repetitive freezing and thawing had no significant effect on the measured YKL-40 concentrations. In conclusion, we have shown that YKL-40 is very dependent on the handling procedures. All the blood samples must be processed into plasma (EDTA) within 8 h at room temperature or into serum in less than 3 h at room temperature. If this is not possible, the blood samples must be stored at 4 degrees C until processed.

Alpha-fetoprotein in human fetal cerebrospinal fluid

Alpha-fetoprotein (AFP) is a fetal glycoprotein. It has been ascribed a regulatory function of growth factor responses and immune functions. The concentrations of AFP and albumin (ALB) are highly variable in fetal serum and CSF and change with gestational age. The AFP index=[AFP(CSF)/AFP(SERUM)]/[ALB(CSF)/ALB(SERUM)] was determined in six normal fetuses at gestational age 17-23 weeks and found to be independent of gestational age and close to unity, mean 0.90+/-0.11 (S.D.). The ratio of CSF-serum concentrations of AFP and ALB both decreased significantly (p<0.05) with gestational age. The mean fraction of AFP being non-reactive with concanavalin A was 1.7% in serum and 1.9% in CSF, suggesting a common hepatic origin of AFP in both compartments. In conclusion, the concentration of AFP in CSF seems to be determined largely by the serum-CSF concentration gradient in normal fetuses. This finding, combined with the remarkable constancy of the AFP index compared to the highly variable absolute concentrations of AFP in both serum and CSF should make the AFP index the marker of choice when analyzing for intrathecal AFP synthesis during development and in pathological conditions.

Structure and tissue-specific expression of genes encoding bovine copper amine oxidases

A cDNA coding for an enzyme belonging to the family of copper amine oxidases was cloned from a bovine lung cDNA library using a PCR approach. The nucleotide sequence of this cDNA was found to be different from that of the previously published liver cDNA encoding bovine serum amine oxidase, another copper amine oxidase. Analyses using reverse transcription followed by PCR of RNA extracted from different bovine tissues confirmed that the copper amine oxidase gene expressed in bovine liver is closely related to, but different from, the copper amine oxidase gene expressed in bovine lung, kidney, spleen and heart. Northern blotting data showed that the level of copper amine oxidase expression in liver is considerably higher than in the other tissues tested. Southern blotting analyses of bovine chromosomal DNA suggested the existence of at least three copper amine oxidase genes. Two of these genes are apparently expressed in a tissue-specific manner as outlined above. A fragment of a third copper amine oxidase gene is identified. The exon-intron organization of the bovine copper amine oxidase genes analyzed is similar to that of the related human diamine oxidase gene, except that no intron in the position equivalent to that of the third intron in the human gene is found. In the third gene, a complete replacement of the third intron of the bovine copper amine oxidase gene (equivalent to the fourth intron of the human gene) has occurred.

Use of tetranectin, CA-125 and CASA to predict residual tumor and survival at second- and third-look operations for ovarian cancer

Tetranectin (TN), CA-125 and CASA were measured in serum prior to 63 second-look and 5 third-look operations for ovarian cancer. Patients with residual tumor had significantly lower levels of TN and higher levels of CASA and CA-125 compared with tumor-free patients. The predictive values PVPos = 100% and PVNeg = 50.9% were found for TN at 9.3 mg/l. For CASA, a predictive value PVPos = 100% was found at 10 U/ml with a corresponding PVNeg = 52.7%. At the cut-off 35 U/ml for CA-125, the PVPos was 100% and the PVNeg = 53.6%. By combining the markers, PVNeg increased to 61.7% with a PVPos on 100%. Significantly differences in survival were found by lifetable analysis between patients tested as positive and negative respectively for any of the markers. Using multivariate Cox analyses, it was found that every marker had an independent prognostic function for survival.

[Screening of newborn infants for cystic fibrosis. A combined analysis of immunoreactive trypsin and delta F508 mutation--a screening without false positive results]

A total of 1081 blood screening cards taken from newborn babies, were anonymously selected for cystic fibrosis (CF) screening by quantitation of immunoreactive trypsin (IRT, Delfia) and by delta F508 mutational analyses using polymerase chain reaction followed by a time resolved fluorescence hybridization assay (Delfia). The IRT values showed a log normal distribution and were significantly higher in girls than boys and in 28 carriers compared with 1052 normals. In 12 newborns, corresponding to 1.02%, an IRT concentration greater than 70 micrograms/l was found. One of these was a delta F508 homozygote with an IRT concentration of 380 micrograms/l. delta F508 mutational analyses showed 1052 normals, 28 heterozygotes, and one homozygote, i.e., a carrier frequency of this mutation for delta F508 of 1:39. In future newborn CF-screening programmes we therefore recommend Delfia IRT followed by Delfia delta F508 analyses for IRT values greater than 70 micrograms/l.

Pre-operative plasma tetranectin as a prognostic marker in ovarian cancer patients

Plasma tetranectin (TN) was tested as a biochemical prognostic marker in ovarian cancer on 39 patients. In stage I + II the 5-year survival was 33% (2/6) if plasma TN was < or = 6.7 mg l-1 and 100% (15/15) with plasma TN > 6.7 mg l-1. For stage III + IV the survival was 0% (0/11) at 26 months for patients with plasma TN < or = 6.7 mg l-1 and 29% (2/7) after 5 years with plasma TN > 6.7 mg l-1. By multivariate testing the relative hazard (RH) of death was found to be 73 times higher in patients with plasma TN < or = 6.7 mg l-1 compared to patients with values above 6.7 mg l-1 (p < 0.001). For comparison, the maximal RH for the other tested variables were: 15 for advanced stage, 2.5 for grade, four for residual tumour and 2.5 for younger age.

Changes in plasma tetranectin following hip surgery with or without thrombotic complications

The fibrinolytic system seems to play a role in the development of postoperative thromboembolic complications (DVT). The newly described tetrameric protein tetranectin (TN), which has been found to enhance the activation of plasminogen to plasmin, therefore was studied in 55 patients who had total hip replacement and solely elastic stockings as physical thromboprophylaxis. No significant difference in plasma TN was found between the 5 patients with DVT and those without DVT, neither preoperatively or postoperatively at day 0, 1, 3, 7 or 10. A significant decrease in plasma TN was found from preoperative to postoperative values, indicating that TN may be a possible marker for other postoperative events. Because of the observed postoperative decrease it is important to consider the sampling time in the future research with TN.

CA-125 as a maternal serum marker for Down's syndrome in the first and second trimesters

CA-125, alpha-fetoprotein (AFP), and human chorionic gonadotropin (HCG) were determined in maternal serum in the first trimester from 14 women with a Down's syndrome fetus and 61 women with a healthy fetus. In the second trimester, 15 and 60 serum samples were determined from women with a Down's syndrome and a healthy fetus respectively. In both trimesters, maternal serum CA-125 was found to be elevated in Down's syndrome pregnancies compared with controls. Using discrimination functions, our preliminary results indicate that CA-125 is a better marker than AFP and HCG respectively for a Down's syndrome fetus in the first trimester and improves the detection rate in the second trimester.

Plasma tetranectin and ovarian neoplasms

Plasma tetranectin was measured in 67 controls, 121 patients with a benign or malignant ovarian tumor, and 24 patients with another benign gynecologic disease to evaluate the predictive value of plasma tetranectin. A significant reduction of plasma tetranectin was found in every malignant tumor type except for mucinous tumors. Further a significant correlation was found between stage of tumors and plasma tetranectin. Depending on the cutoff level the sensitivity for stage 1 cancer ranged from 52 to 71%. In stage 1 + 2 the sensitivity ranged from 58 to 75% and for advanced cancer (stage 3 + 4) from 80 to 95%. The corresponding specificities ranged from 97 to 84%. Plasma tetranectin may be a useful tool for detecting early stages of ovarian cancer.

Tetranectin in amniotic fluid, maternal serum and fetal fluids

The concentration of the newly discovered protein tetranectin has been measured in different fetal and maternal compartments. In amniotic fluid a significant, positive correlation between the tetranectin concentration and gestational age was found (a mean of 0.2 mg l-1 at week 14 to a mean of 0.5 mg l-1 at week 21). In maternal serum a slight negative correlation was found between tetranectin concentration and gestational week (a mean of 6.17 mg l-1 at week 14 to a mean of 5.79 mg l-1 at week 21). In-term cord blood collected at delivery a mean level of 6.0 mg l-1 was found, and no difference was found between arterial- and venous-blood tetranectin concentration. In fetal serum the overall mean level was 2.6 mg l-1 and a significant positive correlation between tetranectin concentration and gestational age was found. The mean level was 1.1 mg l-1 in fetal cerebrospinal fluid and no correlation to gestational age was found. Fetal tetranectin may, therefore, be correlated to fetal maturation.