Rational Approach to Finding Genes Encoding Molecular Biomarkers: Focus on Breast Cancer.

Early detection of cancer facilitates treatment and improves patient survival. We hypothesized that molecular biomarkers of cancer could be rationally predicted based on even partial knowledge of transcriptional regulation, functional pathways and gene co-expression networks. To test our data mining approach, we focused on breast cancer, as one of the best-studied models of this disease. We were particularly interested to check whether such a 'guilt by association' approach would lead to pan-cancer markers generally known in the field or whether molecular subtype-specific 'seed' markers will yield subtype-specific extended sets of breast cancer markers. The key challenge of this investigation was to utilize a small number of well-characterized, largely intracellular, breast cancer-related proteins to uncover similarly regulated and functionally related genes and proteins with the view to predicting a much-expanded range of disease markers, especially that of extracellular molecular markers, potentially suitable for the early non-invasive detection of the disease. We selected 23 previously characterized proteins specific to three major molecular subtypes of breast cancer and analyzed their established transcription factor networks, their known metabolic and functional pathways and the existing experimentally derived protein co-expression data. Having started with largely intracellular and transmembrane marker 'seeds' we predicted the existence of as many as 150 novel biomarker genes to be associated with the selected three major molecular sub-types of breast cancer all coding for extracellularly targeted or secreted proteins and therefore being potentially most suitable for molecular diagnosis of the disease. Of the 150 such predicted protein markers, 114 were predicted to be linked through the combination of regulatory networks to basal breast cancer, 48 to luminal and 7 to Her2-positive breast cancer. The reported approach to mining molecular markers is not limited to breast cancer and therefore offers a widely applicable strategy of biomarker mining.

Bottom-Up Approach to the Discovery of Clinically Relevant Biomarker Genes: The Case of Colorectal Cancer.

Traditional approaches to genome-wide marker discovery often follow a common top-down strategy, where a large scale 'omics' investigation is followed by the analysis of functional pathways involved, to narrow down the list of identified putative biomarkers, and to deconvolute gene expression networks, or to obtain an insight into genetic alterations observed in cancer. We set out to investigate whether a reverse approach would allow full or partial reconstruction of the transcriptional programs and biological pathways specific to a given cancer and whether the full or substantially expanded list of putative markers could thus be identified by starting with the partial knowledge of a few disease-specific markers. To this end, we used 10 well-documented differentially expressed markers of colorectal cancer (CRC), analyzed their transcription factor networks and biological pathways, and predicted the existence of 193 new putative markers. Incredibly, the use of a validation marker set of 10 other completely different known CRC markers and the same procedure resulted in a very similar set of 143 predicted markers. Of these, 138 were identical to those found using the training set, confirming our main hypothesis that a much-expanded set of disease markers can be predicted by starting with just a small subset of validated markers. Further to this, we validated the expression of 42 out of 138 top-ranked predicted markers experimentally using qPCR in surgically removed CRC tissues. We showed that 41 out of 42 mRNAs tested have significantly altered levels of mRNA expression in surgically excised CRC tissues. Of the markers tested, 36 have been reported to be associated with aspects of CRC in the past, whilst only limited published evidence exists for another three genes (BCL2, PDGFRB and TSC2), and no published evidence directly linking genes to CRC was found for CCNA1, SHC1 and TGFB3. Whilst we used CRC to test and validate our marker discovery strategy, the reported procedures apply more generally to cancer marker discovery.

Pre-pregnancy BMI but not mild stress directly influences Interleukin-6 levels and insulin sensitivity during late pregnancy.

BACKGROUND: This study investigates the influence of maternal stress during pregnancy on maternal insulin sensitivity and Interleukin-6 (IL-6) levels in pregnant women (N = 277) in dependence of pre-pregnancy Body-Mass-Index (BMI). METHODS: Gestational diabetes was diagnosed in 80 women. We used the Patient Health Questionnaire (PHQ-D) to investigate maternal stress during pregnancy with a higher scoring indicating higher maternal stress level. IL-6 and cortisol were measured and maternal insulin sensitivity was assessed with the non-esterified fatty acid insulin sensitivity index (NEFA-ISI). Generalized Linear Model analysis was used to analyze effects within different stress groups. RESULTS: Maternal low stress symptoms during pregnancy showed no significant association with maternal insulin sensitivity or IL-6. Higher cortisol levels during pregnancy were associated with elevated IL-6 concentrations. Pre-pregnancy BMI had the strongest positive effect on IL-6 levels and was negatively associated with insulin sensitivity during pregnancy. CONCLUSIONS: Therefore, preconceptional interventions to reduce BMI are needed to improve maternal metabolism during pregnancy.

Acquired decrease of the C3b/C4b receptor (CR1, CD35) and increased C4d deposits on erythrocytes from ICU COVID-19 patients.

In order to study the mechanisms of COVID-19 damage following the complement activation phase occurring during the innate immune response to SARS-CoV-2, CR1 (the regulating complement activation factor, CD35, the C3b/C4b receptor), C4d deposits on Erythrocytes (E), and the products of complement activation C3b/C3bi, were assessed in 52 COVID-19 patients undergoing O2 therapy or assisted ventilation in ICU units in Rheims France. An acquired decrease of CR1 density on E from COVID-19 patients was observed (Mean = 418, SD = 162, N = 52) versus healthy individuals (Mean = 592, SD = 287, N = 400), Student's t-test p < 10-6, particularly among fatal cases, and in parallel with several parameters of clinical severity. Large deposits of C4d on E in patients were well above values observed in normal individuals, mostly without concomitant C3 deposits, in more than 80% of the patients. This finding is reminiscent of the increased C4d deposits on E previously observed to correlate with sub endothelial pericapillary deposits in organ transplant rejection, and with clinical SLE flares. Conversely, significant C3 deposits on E were only observed among » of the patients. The decrease of CR1/E density, deposits of C4 fragments on E and previously reported detection of virus spikes or C3 on E among COVID-19 patients, suggest that the handling and clearance of immune complex or complement fragment coated cell debris may play an important role in the pathophysiology of SARS-CoV-2. Measurement of C4d deposits on E might represent a surrogate marker for assessing inflammation and complement activation occurring in organ capillaries and CR1/E decrease might represent a cumulative index of complement activation in COVID-19 patients. Taken together, these original findings highlight the participation of complement regulatory proteins and indicate that E are important in immune pathophysiology of COVID-19 patients. Besides a potential role for monitoring the course of disease, these observations suggest that novel therapies such as the use of CR1, or CR1-like molecules, in order to down regulate complement activation and inflammation, should be considered.

[Clinical and biological features of haptoglobin phenotypes]. / Phénotypes d'haptoglobine : impacts cliniques et biologiques.

Haptoglobin is a late positive acute phase protein of inflammation. Haptoglobin binds to free hemoglobin released from erythrocytes during intravascular hemolysis to form a complex which is removed shortly. Other properties like inhibition of oxidative stress and prostaglandin synthesis have been described. Three main phenotypes of haptoglobin have been identified: Hp1-1, Hp2-1, Hp2-2, which may have an impact in different diseases such as cardiovascular or infectious diseases. Haptoglobins of different phenotypes can be separated by capillary electrophoresis. They may induce a split of the alpha 2-globulin zone in the electrophoretic pattern. Hp1-1 and Hp2-1 phenotypes induce an important and a moderate split of the α2 globulin zone, respectively, whereas Hp2-2 does not. In vitro hemolysis and migration of a monoclonal component (i.e. immunoglobulin free light chain) may also induce a split of the alpha 2-globulin zone. In daily practice, Hp2-1 or Hp1-1 phenotypes could be notified in the electrophoresis report to alert the clinician about the possible physiopathological consequences.

[An acute monoclonal gammopathy?]. / Une gammapathie monoclonale d'apparition brutale ?

Serum protein electrophoresis is commonly used in case of acute or chronic renal failure. It can lead to the etiologic diagnosis by detecting monoclonal gammopathies which are frequently complicated by renal failure, such as cast nephropathy, Randall's disease or amyloidosis, or to explore an associated inflammatory syndrome. We report the occurrence of two monoclonal components in a patient without any monoclonal component 10 days earlier. The sudden appearance of these two monoclonal components associated to the context of sepsis of urinary origin suggested the diagnosis of transient monoclonal gammopathy. This hypothesis was confirmed by monitoring serum protein electrophoresis that showed a gradual decrease of these two monoclonal components few weeks after the resolution of the infectious disease. The main etiological factors of transient monoclonal gammopathies are infectious or autoimmune diseases. In this context, it is important to delay the achievement of serum protein electrophoresis after the acute episode, in order to avoid to falsely conclude to hematologic malignancy diagnosis. This can prevent costly biological examinations of these transient monoclonal gammopathies and invasive procedures like bone marrow examination.

[Urinary investigations in the diagnosis and monitoring of monoclonal gammopathies in daily practice]. / Place des explorations urinaires dans le diagnostic et le suivi des gammapathies monoclonales en pratique quotidienne.

The management of monoclonal gammopathies remains a public health issue with an incidence greater than 3% of the population over 50 years. Laboratory investigations, including urinary investigations play a key role in the diagnosis and monitoring of the patients. Urinary investigations are not recommended when screening monoclonal gammopathies. However, the initial laboratory evaluation of the monoclonal gammopathies systematically relies on renal function and proteinuria assessment. Urinary proteins electrophoresis combined with urinary proteins immunofixation are also recommended in the initial evaluation, with the exception of the Waldenström's disease. In some cases, serum investigations remain negative whereas urinary investigations confirm the presence of a monoclonal component. National and international recommendations have also been published about the monitoring of monoclonal gammopathies. The biological monitoring of monoclonal gammopathy of undetermined significance is mostly done by serum tests. Urinary investigations are commonly included in the response criteria in case of multiple myeloma or AL amyloidosis. Laboratory investigations like serum free light chain assay tend to decrease the need of urinary investigations in the monoclonal gammopathies. However, these urinary investigations currently maintain a leading role in the diagnosis and monitoring of monoclonal gammopathies.

[Comparative analysis of immunoglobulin free light chains quantification by Freelite™ (The Binding Site) and N Latex FLC (Siemens) methods]. / Étude comparative du dosage des chaînes légères libres d'immunoglobulines par technique Freelite™ (The Binding Site) et N Latex FLC (Siemens).

Serum immunoglobulin free light chain assay has proved to be an invaluable biological tool for diagnosis and monitoring of monoclonal gammopathies including multiple myeloma, primary amyloidosis, solitary plasmocytoma or monoclonal gammopathy of undetermined significance. Free light chain quantification, although essential, cannot be achieved by serum protein electrophoresis either because there is no monoclonal peak or because the peak is hidden in beta or alpha-globulin fraction. As for serum protein immunofixation, this major test allows the typing of the paraprotein but does not provide any quantitative evaluation. Hence, the development of free light chain assays constitutes a significant improvement in the management of these patients. In this context, we compared the results of serum free light chains quantification and of calculation of the ratio kappa/lambda, indicator of monoclonality, in forty samples performed on BN ProSpec(®) analyzer, with the two methods available on the European market. This comparative analysis provided evidence of a good correlation of results between the two methods. However, we noticed clinically significant differences in four samples. In addition, this evaluation highlighted the fact that all free light chain results must be biologically validated on the light of different criteria such as serum protein electrophoresis, serum protein immunofixation, presence of proteinuria, presence of renal failure, and additional clinical data, in order to ascertain the best interpretation for clinical use.

Noninvasive assessment of hepatic fibrosis in patients with chronic hepatitis C using serum Fourier transform infrared spectroscopy.

Assessment of liver fibrosis is of paramount importance to guide the therapeutic strategy in patients with chronic hepatitis C (CHC). In this pilot study, we investigated the potential of serum Fourier transform infrared (FTIR) spectroscopy for differentiating CHC patients with extensive hepatic fibrosis from those without fibrosis. Twenty-three serum samples from CHC patients were selected according to the degree of hepatic fibrosis as evaluated by the FibroTest: 12 from patients with no hepatic fibrosis (F0) and 11 from patients with extensive fibrosis (F3-F4). The FTIR spectra (ten per sample) were acquired in the transmission mode and data homogeneity was tested by cluster analysis to exclude outliers. After selection of the most discriminant wavelengths using an ANOVA-based algorithm, the support vector machine (SVM) method was used as a supervised classification model to classify the spectra into two classes of hepatic fibrosis, F0 and F3-F4. Given the small number of samples, a leave-one-out cross-validation algorithm was used. When SVM was applied to all spectra (n = 230), the sensitivity and specificity of the classifier were 90.1% and 100%, respectively. When SVM was applied to the subset of 219 spectra, i.e., excluding the outliers, the sensitivity and specificity of the classifier were 95.2% and 100%, respectively. This pilot study strongly suggests that the serum from CHC patients exhibits infrared spectral characteristics, allowing patients with extensive fibrosis to be differentiated from those with no hepatic fibrosis.

Diagnosing microalbuminuria and consequences for the drug treatment of patients with type 2 diabetes: a European survey in primary care.

AIMS: To assess general practitioners (GPs) knowledge of guideline recommendations on diagnosing microalbuminuria (MA) and to evaluate how this diagnosis influences drug treatment of diabetes patients. METHODS: A postal case-history based questionnaire describing a male patient (previously not tested for MA) with type 2 diabetes who had several risk markers for cardiovascular disease. RESULTS: 2078GPs from nine European countries were included, with response rates varying from 7% to 43%. Almost all GPs recommended annual testing for MA. Forty-five to 77% (depending on country) of GPs required more than one positive test to diagnose MA. The absolute increase in the percentages of GPs who would supplement the patient's drug treatment if MA developed was: for anginotensin converting enzyme inhibitors (ACEIs) or angiotensin II receptor blockers (ARBs) 23-50% (depending on country), for statins 0-19%, for acetylsalicylic acid 2-13%, and for hypoglycemic agents (tablets and insulin) 0-33%. The proportion of GPs recommending all four possible treatment modalities was low. CONCLUSIONS: Guidelines for diagnosing MA were partly followed. ACEIs and ARBs were recommended when MA was present, but the recommended multifactorial treatment of cardiovascular risk markers was not implemented.

Postanalytical external quality assessment of urine albumin in primary health care: an international survey.

BACKGROUND: Microalbuminuria (MA) is recognized as an important risk factor for cardiovascular and renal complications in diabetes. We sought to evaluate how screening for MA is conducted and how urine albumin (UA) results are interpreted in primary care internationally. METHODS: General practitioners (GPs) received a case history-based questionnaire depicting a male type 2 diabetes patient in whom UA testing had not been performed. Questions were related to type of urine sample used for UA testing, need for a repeat test, whether UA testing was performed in the office laboratory, and what changes in UA results were considered clinically important [critical difference (CD)]. Participants received national benchmarking feedback reports. RESULTS: We included 2078 GPs from 9 European countries. Spot urine samples were used most commonly for first time office-based testing, whereas timed collections were used to a larger extent for hospital-based repeat tests. Repeat tests were requested by 45%-77% of GPs if the first test was positive. Four different measurement units were used by 70% of participants in estimating clinically important changes in albumin values. Stated CDs varied considerably among GPs, with similar variations in each country. A median CD of 33% was considered clinically important for both improvement and deterioration in MA, corresponding to an achievable analytical imprecision of 14%, when UA is reported as an albumin/creatinine ratio. CONCLUSIONS: Guidelines on diagnosing MA are followed only partially, and should be made more practicable, addressing issues such as type of samples, measurement units, and repeat tests.

Comparison of two hemolysis procedures prior to an automated HbA(1c) immunoassay.

BACKGROUND: Hemoglobin A(1c) (HbA(1c)) is widely accepted as the most important biological parameter reflecting glycemic control in diabetic patients. Its measurement in clinical chemistry necessitates the use of reliable and robust methods. We studied here the influence of two hemolysis procedures on an automated HbA(1c) immunoassay using the Mira Plus analyzer. METHODS AND RESULTS: Whole blood was hemolyzed either manually, using an external manual procedure, or automatically on-board the analyzer. The results of imprecision studies showed comparable performance of both procedures, coefficients of variation (CVs) being slightly higher with the automated procedure (2.2-2.7% versus 1.7-2.1% in within-run experiments, and 2.4-3.5% versus 2.1-3.0% in between-run experiments). Comparison of results in 100 fresh samples showed acceptable correlation between the two procedures (r(2) = 0.94, y = 0.98x+0.43). Sedimentation of whole blood in sample tubes prior to automatic hemolysis did not alter the results. CONCLUSION: These data demonstrate that both procedures are suitable for routine use, with a higher practicability of the automated one. However, the values are not directly comparable, pointing out the critical role of every analytical step and the need for standardization and strict quality control of HbA(1c) assays.