Comprehensive multi-omics analysis of breast cancer reveals distinct long-term prognostic subtypes.

Breast cancer (BC) is a leading cause of cancer-related death worldwide. The diverse nature and heterogeneous biology of BC pose challenges for survival prediction, as patients with similar diagnoses often respond differently to treatment. Clinically relevant BC intrinsic subtypes have been established through gene expression profiling and are implemented in the clinic. While these intrinsic subtypes show a significant association with clinical outcomes, their long-term survival prediction beyond 5 years often deviates from expected clinical outcomes. This study aimed to identify naturally occurring long-term prognostic subgroups of BC based on an integrated multi-omics analysis. This study incorporates a clinical cohort of 335 untreated BC patients from the Oslo2 study with long-term follow-up (>12 years). Multi-Omics Factor Analysis (MOFA+) was employed to integrate transcriptomic, proteomic, and metabolomic data obtained from the tumor tissues. Our analysis revealed three prominent multi-omics clusters of BC patients with significantly different long-term prognoses (p = 0.005). The multi-omics clusters were validated in two independent large cohorts, METABRIC and TCGA. Importantly, a lack of prognostic association to long-term follow-up above 12 years in the previously established intrinsic subtypes was shown for these cohorts. Through a systems-biology approach, we identified varying enrichment levels of cell-cycle and immune-related pathways among the prognostic clusters. Integrated multi-omics analysis of BC revealed three distinct clusters with unique clinical and biological characteristics. Notably, these multi-omics clusters displayed robust associations with long-term survival, outperforming the established intrinsic subtypes.

Quantification of multiple steroid hormones in serum and human breast cancer tissue by liquid chromatography-tandem mass spectrometry analysis.

Introduction: Systemic and local steroid hormone levels may function as novel prognostic and predictive biomarkers in breast cancer patients. We aimed at developing a novel liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the simultaneous measurement of multiple, biologically pivotal steroid hormones in human serum and breast cancer tissue. Methods: The quantitative method consisted of liquid-liquid extraction, Sephadex LH-20 chromatography for tissue extracts, and analysis of steroid hormones by liquid-chromatography-tandem mass spectrometry. We analyzed serum and tissue steroid hormone levels in 16 and 40 breast cancer patients, respectively, and assessed their correlations with clinical parameters. Results: The method included quantification of nine steroid hormones in serum [including cortisol, cortisone, corticosterone, estrone (E1), 17ß-estradiol (E2), 17α-hydroxyprogesterone, androstenedione (A4), testosterone and progesterone) and six (including cortisone, corticosterone, E1, E2, A4, and testosterone) in cancer tissue. The lower limits of quantification were between 0.003-10 ng/ml for serum (250 µl) and 0.038-125 pg/mg for tissue (20 mg), respectively. Accuracy was between 98%-126%, intra-assay coefficient of variations (CV) was below 15%, and inter-assay CV were below 11%. The analytical recoveries for tissue were between 76%-110%. Tissue levels of E1 were positively correlated with tissue E2 levels (p<0.001), and with serum levels of E1, E2 and A4 (p<0.01). Tissue E2 levels were positively associated with serum E1 levels (p=0.02), but not with serum E2 levels (p=0.12). The levels of tissue E2 and ratios of E1 to A4 levels (an index for aromatase activity) were significantly higher in patients with larger tumors (p=0.03 and p=0.02, respectively). Conclusions: The method was convenient and suitable for a specific and accurate profiling of clinically important steroid hormones in serum. However, the sensitivity of the profile method in steroid analysis in tissue samples is limited, but it can be used for the analysis of steroids in breast cancer tissues if the size of the sample or its steroid content is sufficient.

Profiling of serum metabolome of breast cancer: multi-cancer features discriminate between healthy women and patients with breast cancer.

Introduction: The progression of solid cancers is manifested at the systemic level as molecular changes in the metabolome of body fluids, an emerging source of cancer biomarkers. Methods: We analyzed quantitatively the serum metabolite profile using high-resolution mass spectrometry. Metabolic profiles were compared between breast cancer patients (n=112) and two groups of healthy women (from Poland and Norway; n=95 and n=112, respectively) with similar age distributions. Results: Despite differences between both cohorts of controls, a set of 43 metabolites and lipids uniformly discriminated against breast cancer patients and healthy women. Moreover, smaller groups of female patients with other types of solid cancers (colorectal, head and neck, and lung cancers) were analyzed, which revealed a set of 42 metabolites and lipids that uniformly differentiated all three cancer types from both cohorts of healthy women. A common part of both sets, which could be called a multi-cancer signature, contained 23 compounds, which included reduced levels of a few amino acids (alanine, aspartate, glutamine, histidine, phenylalanine, and leucine/isoleucine), lysophosphatidylcholines (exemplified by LPC(18:0)), and diglycerides. Interestingly, a reduced concentration of the most abundant cholesteryl ester (CE(18:2)) typical for other cancers was the least significant in the serum of breast cancer patients. Components present in a multi-cancer signature enabled the establishment of a well-performing breast cancer classifier, which predicted cancer with a very high precision in independent groups of women (AUC>0.95). Discussion: In conclusion, metabolites critical for discriminating breast cancer patients from controls included components of hypothetical multi-cancer signature, which indicated wider potential applicability of a general serum metabolome cancer biomarker.

Diagnostic accuracy of anti-3-[18F]-FACBC PET/MRI in gliomas.

PURPOSE: The primary aim was to evaluate whether anti-3-[18F]FACBC PET combined with conventional MRI correlated better with histomolecular diagnosis (reference standard) than MRI alone in glioma diagnostics. The ability of anti-3-[18F]FACBC to differentiate between molecular and histopathological entities in gliomas was also evaluated. METHODS: In this prospective study, patients with suspected primary or recurrent gliomas were recruited from two sites in Norway and examined with PET/MRI prior to surgery. Anti-3-[18F]FACBC uptake (TBRpeak) was compared to histomolecular features in 36 patients. PET results were then added to clinical MRI readings (performed by two neuroradiologists, blinded for histomolecular results and PET data) to assess the predicted tumor characteristics with and without PET. RESULTS: Histomolecular analyses revealed two CNS WHO grade 1, nine grade 2, eight grade 3, and 17 grade 4 gliomas. All tumors were visible on MRI FLAIR. The sensitivity of contrast-enhanced MRI and anti-3-[18F]FACBC PET was 61% (95%CI [45, 77]) and 72% (95%CI [58, 87]), respectively, in the detection of gliomas. Median TBRpeak was 7.1 (range: 1.4-19.2) for PET positive tumors. All CNS WHO grade 1 pilocytic astrocytomas/gangliogliomas, grade 3 oligodendrogliomas, and grade 4 glioblastomas/astrocytomas were PET positive, while 25% of grade 2-3 astrocytomas and 56% of grade 2-3 oligodendrogliomas were PET positive. Generally, TBRpeak increased with malignancy grade for diffuse gliomas. A significant difference in PET uptake between CNS WHO grade 2 and 4 gliomas (p < 0.001) and between grade 3 and 4 gliomas (p = 0.002) was observed. Diffuse IDH wildtype gliomas had significantly higher TBRpeak compared to IDH1/2 mutated gliomas (p < 0.001). Adding anti-3-[18F]FACBC PET to MRI improved the accuracy of predicted glioma grades, types, and IDH status, and yielded 13.9 and 16.7 percentage point improvement in the overall diagnoses for both readers, respectively. CONCLUSION: Anti-3-[18F]FACBC PET demonstrated high uptake in the majority of gliomas, especially in IDH wildtype gliomas, and improved the accuracy of preoperatively predicted glioma diagnoses. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov ID: NCT04111588, URL: https://clinicaltrials.gov/study/NCT04111588.

Randomised controlled trial of exercise training during lactation on breast milk composition in breastfeeding people with overweight/obesity: a study protocol for the MILKSHAKE trial.

Breast milk from people with overweight/obesity may differ in composition compared with that from normal-weight people. Exercise training can modify breast milk composition in rodent models, with a beneficial impact demonstrated on the offspring's metabolism, but whether these findings translate to humans is unclear. This trial aims to determine the effect of an exercise intervention on breast milk composition and whether an exercise-induced modification of breast milk impacts the infants' growth and body composition. Effect of Exercise Training on Breastmilk Composition is a randomised, controlled trial with two parallel groups, one exercise group and one control group, with a 1:1 allocation. We will include a minimum of 62 exclusively breastfeeding participants, 6 weeks postpartum. The exercise intervention lasts 8 weeks and comprises 25 supervised endurance exercise sessions with moderate or high intensity. The primary outcome measure is the change in the relative concentration of the human milk oligosaccharide 3'sialyllactose in breast milk from baseline at 6 weeks postpartum to the end of the intervention period. Secondary outcomes include breast milk concentrations of other metabolites, cytokines, hormones and microRNA, maternal health outcomes, infant growth, infant gut microbiome and infant circulating microRNA. Maternal and infant outcomes will be measured before, during and after the intervention period, with a follow-up of the infants until they are 24 months old. Trial registration number NCT05488964.

The impact of pre-processing and disease characteristics on reproducibility of T2-weighted MRI radiomics features.

PURPOSE: To evaluate the reproducibility of radiomics features derived via different pre-processing settings from paired T2-weighted imaging (T2WI) prostate lesions acquired within a short interval, to select the setting that yields the highest number of reproducible features, and to evaluate the impact of disease characteristics (i.e., clinical variables) on features reproducibility. MATERIALS AND METHODS: A dataset of 50 patients imaged using T2WI at 2 consecutive examinations was used. The dataset was pre-processed using 48 different settings. A total of 107 radiomics features were extracted from manual delineations of 74 lesions. The inter-scan reproducibility of each feature was measured using the intra-class correlation coefficient (ICC), with ICC values > 0.75 considered good. Statistical differences were assessed using Mann-Whitney U and Kruskal-Wallis tests. RESULTS: The pre-processing parameters strongly influenced the reproducibility of radiomics features of T2WI prostate lesions. The setting that yielded the highest number of features (25 features) with high reproducibility was the relative discretization with a fixed bin number of 64, no signal intensity normalization, and outlier filtering by excluding outliers. Disease characteristics did not significantly impact the reproducibility of radiomics features. CONCLUSION: The reproducibility of T2WI radiomics features was significantly influenced by pre-processing parameters, but not by disease characteristics. The selected pre-processing setting yielded 25 reproducible features.

Sexual functioning, sexual enjoyment, and body image in Norwegian breast cancer survivors: a 12-year longitudinal follow-up study and comparison with the general female population.

BACKGROUND: Given the scarcity of evidence concerning the long-term sexual health of breast cancer (BC) survivors (BC-Pop), we aimed to assess how BC treatments affect short- and long-term sexual functioning, sexual enjoyment, and body image, and compare with aged-matched women in the Norwegian general population (F-GenPop). MATERIAL AND METHODS: The 349 patients in BC-Pop treated at Trondheim University Hospital in 2007-2014, were assessed in clinical controls at the hospital; before starting radiotherapy (T1, baseline), immediately after ending radiotherapy (T2), and after 3, 6, and 12 months (T3-T5), and at a long-term follow-up 7-12 years after baseline (T6). Meanwhile, F-GenPop included 2254 age-matched women in the Norwegian general population. The impact of BC treatment on sexual functioning was examined using a Linear Mixed Model. Sexual functioning, sexual enjoyment, and body image were assessed with the EORTC's QLQ-BR23 scales and compared between the populations in the four age groups (30-49, 50-59, 60-69, and 70+ years) using means with 95% confidence intervals and Student t-test. Linear regression, adjusted for age and comorbidity was applied to estimate individual scores. RESULT: BC survivors treated with mastectomy had overall lower sexual functioning than patients who had received breast-conserving surgery (p = 0.017). Although BC survivors treated with chemotherapy had lower sexual functioning than those treated without chemotherapy at T1-T5 (p = 0.044), both groups showed the same level of functioning at T6. BC-Pop exhibited significantly poorer sexual functioning (p < 0.001), lower sexual enjoyment (p < 0.05), and better body image (p < 0.001) than F-GenPop in all age groups. CONCLUSION: The impact of specific BC treatments on sexual functioning was modest; only mastectomy had a persistent negative influence. Nevertheless, all age groups in BC-Pop displayed significantly poorer sexual functioning than F-GenPop at both 12 months and up to 12 years after treatment.

Colorectal cancer detected by liquid biopsy 2 years prior to clinical diagnosis in the HUNT study.

BACKGROUND: Colorectal cancer (CRC) is often diagnosed in advanced stages. Circulating tumour DNA (ctDNA) has been proposed as an early diagnostic biomarker. However, as a screening tool, ctDNA has mainly been studied in selected populations at the time of clinical diagnosis. The aim of this study was to detect CRC by known ctDNA markers up to 2 years prior to clinical diagnosis. METHODS: In this case-control study, methylated ctDNA markers were detected in plasma samples from 106 healthy controls and 106 individuals diagnosed with CRC within 24 months following participation in The Trøndelag Health Study. RESULTS: The most specific single markers were BMP3, FLI1, IKZF1, SFRP1, SFRP2, NPTX2, SLC8A1 and VIM (specificity >70%). When combining these into a panel, the CRC sensitivity was 43% (95% CI 42.7-43.4) and the CRC specificity was 86% (95% CI 85.7-86.2). The findings were reproduced in an independent validation set of samples. CONCLUSIONS: Detection of known methylated ctDNA markers of CRC is possible up to 2 years prior to the clinical diagnosis in an unselected population resembling the screening setting. This study supports the hypothesis that some patients could be diagnosed earlier, if ctDNA detection was part of the CRC screening programme.

Association of serum cortisol and cortisone levels and risk of recurrence after endocrine treatment in breast cancer.

Metabolic reprogramming in breast cancer involves changes in steroid hormone synthesis and metabolism. Alterations in estrogen levels in both breast tissue and blood may influence carcinogenesis, breast cancer growth, and response to therapy. Our aim was to examine whether serum steroid hormone concentrations could predict the risk of recurrence and treatment-related fatigue in patients with breast cancer. This study included 66 postmenopausal patients with estrogen receptor-positive breast cancer who underwent surgery, radiotherapy, and adjuvant endocrine treatment. Serum samples were collected at six different time points [before the start of radiotherapy (as baseline), immediately after radiotherapy, and then 3, 6, 12 months, and 7-12 years after radiotherapy]. Serum concentrations of eight steroid hormones (cortisol, cortisone, 17α-hydroxyprogesterone, 17ß-estradiol, estrone, androstenedione, testosterone, and progesterone) were measured using a liquid chromatography-tandem mass spectrometry-based method. Breast cancer recurrence was defined as clinically proven relapse/metastatic breast cancer or breast cancer-related death. Fatigue was assessed with the QLQ-C30 questionnaire. Serum steroid hormone concentrations measured before and immediately after radiotherapy differed between relapse and relapse-free patients [(accuracy 68.1%, p = 0.02, and 63.2%, p = 0.03, respectively, partial least squares discriminant analysis (PLS-DA)]. Baseline cortisol levels were lower in patients who relapsed than in those who did not (p < 0.05). The Kaplan-Meier analysis showed that patients with high baseline concentrations of cortisol (≥ median) had a significantly lower risk of breast cancer recurrence than patients with low cortisol levels (

Association of serum metabolome profile with the risk of breast cancer in participants of the HUNT2 study.

Background: The serum metabolome is a potential source of molecular biomarkers associated with the risk of breast cancer. Here we aimed to analyze metabolites present in pre-diagnostic serum samples collected from healthy women participating in the Norwegian Trøndelag Health Study (HUNT2 study) for whom long-term information about developing breast cancer was available. Methods: Women participating in the HUNT2 study who developed breast cancer within a 15-year follow-up period (BC cases) and age-matched women who stayed breast cancer-free were selected (n=453 case-control pairs). Using a high-resolution mass spectrometry approach 284 compounds were quantitatively analyzed, including 30 amino acids and biogenic amines, hexoses, and 253 lipids (acylcarnitines, glycerides, phosphatidylcholines, sphingolipids, and cholesteryl esters). Results: Age was a major confounding factor responsible for a large heterogeneity in the dataset, hence age-defined subgroups were analyzed separately. The largest number of metabolites whose serum levels differentiated BC cases and controls (82 compounds) were observed in the subgroup of younger women (<45 years old). Noteworthy, increased levels of glycerides, phosphatidylcholines, and sphingolipids were associated with reduced risk of cancer in younger and middle-aged women (≤64 years old). On the other hand, increased levels of serum lipids were associated with an enhanced risk of breast cancer in older women (>64 years old). Moreover, several metabolites could be detected whose serum levels were different between BC cases diagnosed earlier (<5 years) and later (>10 years) after sample collecting, yet these compounds were also correlated with the age of participants. Current results were coherent with the results of the NMR-based metabolomics study performed in the cohort of HUNT2 participants, where increased serum levels of VLDL subfractions were associated with reduced risk of breast cancer in premenopausal women. Conclusions: Changes in metabolite levels detected in pre-diagnostic serum samples, which reflected an impaired lipid and amino acid metabolism, were associated with long-term risk of breast cancer in an age-dependent manner.

Effect of high-fat diet and morning or evening exercise on lipoprotein subfraction profiles: secondary analysis of a randomised trial.

We investigated the effect of a high-fat diet (HFD) on serum lipid subfractions in men with overweight/obesity and determined whether morning or evening exercise affected these lipid profiles. In a three-armed randomised trial, 24 men consumed an HFD for 11 days. One group of participants did not exercise (n = 8, CONTROL), one group trained at 06:30 h (n = 8, EXam), and one group at 18:30 h (n = 8, EXpm) on days 6-10. We assessed the effects of HFD and exercise training on circulating lipoprotein subclass profiles using NMR spectroscopy. Five days of HFD induced substantial perturbations in fasting lipid subfraction profiles, with changes in 31/100 subfraction variables (adjusted p values [q] < 0.05). Exercise training induced a systematic change in lipid subfraction profiles, with little overall difference between EXam and EXpm. Compared with CONTROL, exercise training reduced serum concentrations of > 20% of fasting lipid subfractions. EXpm reduced fasting cholesterol concentrations in three LDL subfractions by ⁓30%, while EXam only reduced concentration in the largest LDL particles by 19% (all q < 0.05). Lipid subfraction profiles changed markedly after 5 days HFD in men with overweight/obesity. Both morning and evening exercise training impacted subfraction profiles compared with no exercise.

Immunomodulatory Effects of Metformin Treatment in Pregnant Women With PCOS.

CONTEXT: Polycystic ovary syndrome (PCOS) is a common endocrine disorder associated with low-grade systemic inflammation and increased risk of pregnancy complications. Metformin treatment reduces the risk of late miscarriage and preterm birth in pregnant women with PCOS. Whether the protective effect of metformin involves immunological changes has not been determined. OBJECTIVE: To investigate the effect of metformin on the maternal immunological status in women with PCOS. METHODS: A post-hoc analysis was performed of two randomized controlled trials, PregMet and PregMet2, including longitudinal maternal serum samples from 615 women with PCOS. Women were randomized to metformin or placebo from first trimester to delivery. Twenty-two cytokines and C-reactive protein were measured in serum sampled at gestational weeks 5 to 12, 19, 32, and 36. RESULTS: Metformin treatment was associated with higher serum levels of several multifunctional cytokines throughout pregnancy, with the strongest effect on eotaxin (P < .001), interleukin-17 (P = .03), and basic fibroblast growth factor (P = .04). Assessment of the combined cytokine development confirmed the impact of metformin on half of the 22 cytokines. The immunomodulating effect of metformin was more potent in normal weight and overweight women than in obese women. Moreover, normoandrogenic women had the strongest effect of metformin in early pregnancy, whereas hyperandrogenic women presented increasing effect throughout pregnancy. CONCLUSION: It appears that metformin has immunomodulating rather than anti-inflammatory properties in pregnancy. Its effect on the serum levels of many multifunctional cytokines demonstrates robust, persisting, and body mass-dependent immune mobilization in pregnant women with PCOS.

High-intensity exercise increases breast milk adiponectin concentrations: a randomised cross-over study.

Introduction: Adiponectin plays a role in glucose and fat metabolism and is present in human breast milk. It has been postulated that higher breast milk adiponectin concentrations may prevent rapid weight gain in infancy. Prior research indicates that circulating adiponectin increases acutely after endurance exercise, but no prior research has investigated the effect of exercise on breast milk adiponectin concentrations. The purpose of this randomised, cross-over study was to determine the acute effects of endurance exercise on adiponectin concentrations in human breast milk. Methods: Participants who were exclusively breastfeeding a 6-12 week-old term infant (N = 20) completed three conditions in the laboratory: (1) Moderate-intensity continuous training (MICT), (2) High-intensity interval training (HIIT), and (3) No activity (REST). At each condition, we collected breast milk at 07:00 h (before exercise/rest), 11:00 h (immediately after exercise/rest), 12:00 h (1 h after exercise/rest), and 15:00 h (4 h after exercise/rest) and determined adiponectin concentrations using enzyme-linked immunosorbent assay. We compared changes in adiponectin concentrations after MICT and HIIT, adjusted for the morning concentration on each test day, with those after REST, using paired t-tests. Results: Adiponectin concentrations increased 1 h after HIIT, from 4.6 (± 2.2) µg/L in the 07:00 h sample to 5.6 (± 2.6) µg/L. This change was 0.9 µg/L (95% confidence interval 0.3 to 1.5) greater than the change between these two timepoints in the REST condition (p = 0.025). There were no other statistically significant changes in adiponectin concentrations. Conclusion: HIIT may increase adiponectin concentrations in breast milk acutely after exercise. Further studies should determine the impact of exercise-induced elevations in breast milk adiponectin concentrations on growth and metabolism in infancy.

Effect of Delayed Centrifugation on the Levels of NMR-Measured Lipoproteins and Metabolites in Plasma and Serum Samples.

Metabolic profiling is widely used for large-scale association studies, based on biobank material. The main obstacle to the translation of metabolomic findings into clinical application is the lack of standardization, making validation in independent cohorts challenging. One reason for this is sensitivity of metabolites to preanalytical conditions. We present a systematic investigation of the effect of delayed centrifugation on the levels of NMR-measured metabolites and lipoproteins in serum and plasma samples. Blood was collected from 20 anonymous donors, of which 10 were recruited from an obesity clinic. Samples were stored at room temperature until centrifugation after 30 min, 1, 2, 4, or 8 h, which is within a realistic time scenario in clinical practice. The effect of delaying centrifugation on plasma and serum metabolic concentrations, and on concentrations of lipoprotein subfractions, was investigated. Our results show that lipoproteins are only minimally affected by a delay in centrifugation while metabolite levels are more sensitive to a delay. Metabolites significantly increased or decreased in concentration depending on delay duration. Further, we describe differences in the stability of serum and plasma, showing that plasma is more stable for metabolites, while lipoprotein subfractions are equally stable for both types of matrices.

Prognostic value of combined MTV and ADC derived from baseline FDG PET/MRI in aggressive non-Hodgkins lymphoma.

PURPOSE: The aim of this prospective study was to investigate the prognostic value of metabolic tumor volume (MTV) and apparent diffusion coefficient (ADC) from baseline FDG PET/MRI compared to established clinical risk factors in terms of progression free survival (PFS) at 2 years in a cohort of diffuse large B-cell Lymphoma (DLBCL) and high-grade-B-cell lymphoma (HGBCL). METHODS: Thirty-three patients and their baseline PET/MRI examinations were included. Images were read by two pairs of nuclear medicine physicians and radiologists for defining lymphoma lesions. MTV was computed on PET, and up to six lymphoma target lesions with restricted diffusion was defined for each PET/MRI examination. Minimum ADC (ADCmin) and the corresponding mean ADC (ADCmean) from the target lesion with the lowest ADCmin were included in the analyses. For the combined PET/MRI parameters, the ratio between MTV and the target lesion with the lowest ADCmin (MTV/ADCmin) and the corresponding ADCmean (MTV/ADCmean) was calculated for each patient. Clinical, histological, and PET/MRI parameters were compared between the treatment failure and treatment response group, while survival analyses for each variable was performed by using univariate Cox regression. In case of significant variables in the Cox regression analyses, Kaplan-Meier survival analyses with log-rank test was used to study the effect of the variables on PFS. RESULTS: ECOC PS scale ≥2 (p = 0.05) and ADCmean (p = 0.05) were significantly different between the treatment failure group (n = 6) and those with treatment response (n = 27). Survival analyses showed that ADCmean was associated with PFS (p = 0.02, [HR 2.3 for 1 SD increase]), while combining MTV and ADC did not predict outcome. In addition, ECOG PS ≥2 (p = 0.01, [HR 13.3]) and histology of HGBCL (p = 0.02 [HR 7.6]) was significantly associated with PFS. CONCLUSIONS: ADCmean derived from baseline MRI could be a prognostic imaging biomarker for DLBCL and HGBCL. Baseline staging with PET/MRI could therefore give supplementary prognostic information compared to today's standard PET/CT.

ALASCA: An R package for longitudinal and cross-sectional analysis of multivariate data by ASCA-based methods.

The increasing availability of multivariate data within biomedical research calls for appropriate statistical methods that can describe and model complex relationships between variables. The extended ANOVA simultaneous component analysis (ASCA+) framework combines general linear models and principal component analysis (PCA) to decompose and visualize the separate effects of experimental factors. It has recently been demonstrated how linear mixed models can be included in the framework to analyze data from longitudinal experimental designs with repeated measurements (RM-ASCA+). The ALASCA package for R makes the ASCA+ framework accessible for general use and includes multiple methods for validation and visualization. The package is especially useful for longitudinal data and the ability to easily adjust for covariates is an important strength. This paper demonstrates how the ALASCA package can be applied to gain insights into multivariate data from interventional as well as observational designs. Publicly available data sets from four studies are used to demonstrate the methods available (proteomics, metabolomics, and transcriptomics).

Lipoprotein and metabolite associations to breast cancer risk in the HUNT2 study.

BACKGROUND: The aim of this study was to gain an increased understanding of the aetiology of breast cancer, by investigating possible associations between serum lipoprotein subfractions and metabolites and the long-term risk of developing the disease. METHODS: From a cohort of 65,200 participants within the Trøndelag Health Study (HUNT study), we identified all women who developed breast cancer within a 22-year follow-up period. Using nuclear magnetic resonance (NMR) spectroscopy, 28 metabolites and 89 lipoprotein subfractions were quantified from prediagnostic serum samples of future breast cancer patients and matching controls (n = 1199 case-control pairs). RESULTS: Among premenopausal women (554 cases) 14 lipoprotein subfractions were associated with long-term breast cancer risk. In specific, different subfractions of VLDL particles (in particular VLDL-2, VLDL-3 and VLDL-4) were inversely associated with breast cancer. In addition, inverse associations were detected for total serum triglyceride levels and HDL-4 triglycerides. No significant association was found in postmenopausal women. CONCLUSIONS: We identified several associations between lipoprotein subfractions and long-term risk of breast cancer in premenopausal women. Inverse associations between several VLDL subfractions and breast cancer risk were found, revealing an altered metabolism in the endogenous lipid pathway many years prior to a breast cancer diagnosis.

Longitudinal Changes in Circulating Metabolites and Lipoproteins After Breast Cancer Treatment.

The multimodal treatment of breast cancer may induce long term effects on the metabolic profile and increase the risk of future cardiovascular disease. In this study, we characterized longitudinal changes in serum lipoprotein subfractions and metabolites after breast cancer treatment, aiming to determine the long-term effect of different treatment modalities. Further, we investigated the prognostic value of treatment-induced changes in breast cancer-specific and overall 10-year survival. In this study, serum samples from breast cancer patients (n = 250) were collected repeatedly before and after radiotherapy, and serum metabolites and lipoprotein subfractions were quantified by NMR spectroscopy. Longitudinal changes were assessed by univariate and multivariate data analysis methods applicable for repeated measures. Distinct changes were detectable in levels of lipoprotein subfractions and circulating metabolites during the first year, with similar changes despite large differences in treatment regimens. We detect increased free cholesterol and decreased esterified cholesterol levels of HDL subfractions, a switch towards larger LDL particles and higher total LDL-cholesterol, in addition to a switch in the glutamine-glutamate ratio. Non-survivors had different lipid profiles from survivors already at baseline. To conclude, our results show development towards an atherogenic lipid profile in breast cancer patients with different treatment regimens.