Sainte-Foy-lès-Lyon, France
Sainte-Foy-lès-Lyon, France

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Burska A.N.,University of Leeds | Roget K.,TcLand Expression | Blits M.,VU University Amsterdam | Soto Gomez L.,University of Leeds | And 7 more authors.
Pharmacogenomics Journal | Year: 2014

Gene expression has recently been at the forefront of advance in personalized medicine, notably in the field of cancer and transplantation, providing a rational for a similar approach in rheumatoid arthritis (RA). RA is a prototypic inflammatory autoimmune disease with a poorly understood etiopathogenesis. Inflammation is the main feature of RA; however, many biological processes are involved at different stages of the disease. Gene expression signatures offer management tools to meet the current needs for personalization of RA patient's care. This review analyses currently available information with respect to RA diagnostic, prognostic and prediction of response to therapy with a view to highlight the abundance of data, whose comparison is often inconclusive due to the mixed use of material source, experimental methodologies and analysis tools, reinforcing the need for harmonization if gene expression signatures are to become a useful clinical tool in personalized medicine for RA patients. © 2014 Macmillan Publishers Limited.


Dantan E.,University of Nantes | Combescure C.,University of Geneva | Lorent M.,University of Nantes | Ashton-Chess J.,TcLand Expression | And 4 more authors.
Journal of Clinical Epidemiology | Year: 2014

Objectives: Predicting chronic disease evolution from a prognostic marker is a key field of research in clinical epidemiology. However, the prognostic capacity of a marker is not systematically evaluated using the appropriate methodology. We proposed the use of simple equations to calculate time-dependent sensitivity and specificity based on published survival curves and other time-dependent indicators as predictive values, likelihood ratios, and posttest probability ratios to reappraise prognostic marker accuracy. Study Design and Setting: The methodology is illustrated by back calculating time-dependent indicators from published articles presenting a marker as highly correlated with the time to event, concluding on the high prognostic capacity of the marker, and presenting the Kaplan-Meier survival curves. The tools necessary to run these direct and simple computations are available online at http://www.divat.fr/en/online-calculators/evalbiom. Results: Our examples illustrate that published conclusions about prognostic marker accuracy may be overoptimistic, thus giving potential for major mistakes in therapeutic decisions. Conclusion: Our approach should help readers better evaluate clinical articles reporting on prognostic markers. Time-dependent sensitivity and specificity inform on the inherent prognostic capacity of a marker for a defined prognostic time. Time-dependent predictive values, likelihood ratios, and posttest probability ratios may additionally contribute to interpret the marker's prognostic capacity. © 2014 Elsevier Inc. All rights reserved.


Miller I.,European Personalised Medicine Association | Miller I.,bioMerieux | Ashton-Chess J.,European Personalised Medicine Association | Spolders H.,European Personalised Medicine Association | And 10 more authors.
Personalized Medicine | Year: 2011

The clinical utility and medico-economic value of several personalized diagnostic tests has been well described in the literature. Development of such tests, including generation of the necessary supportive clinical validation data, is a complex and expensive endeavor. In general, sponsors of such tests lack sufficient clarity on appropriate reimbursement and regulatory pathways to provide the clear development framework necessary to incentivize the required level of investment. In the USA, an imperfect reimbursement paradigm has evolved to accommodate a small number of 'value-priced' laboratory-developed tests, although major structural barriers remain to broader implementation. In Europe, by contrast, there is virtually no precedent for value-based public sector pricing, and even such procedurally based pricing as currently exists is administered by a complex network of largely decentralized bodies. As a consequence, patient access is limited and health-economic savings are not realized. This article explores some of the European market entry barriers, with a focus on reimbursement challenges, and highlights some collaborative proposals to address such. © 2011 Future Medicine Ltd.


PubMed | University of Nantes, TcLand Expression, The Surgical Center, University of Geneva and Nantes University Hospital Center
Type: Journal Article | Journal: Journal of clinical epidemiology | Year: 2014

Predicting chronic disease evolution from a prognostic marker is a key field of research in clinical epidemiology. However, the prognostic capacity of a marker is not systematically evaluated using the appropriate methodology. We proposed the use of simple equations to calculate time-dependent sensitivity and specificity based on published survival curves and other time-dependent indicators as predictive values, likelihood ratios, and posttest probability ratios to reappraise prognostic marker accuracy.The methodology is illustrated by back calculating time-dependent indicators from published articles presenting a marker as highly correlated with the time to event, concluding on the high prognostic capacity of the marker, and presenting the Kaplan-Meier survival curves. The tools necessary to run these direct and simple computations are available online at http://www.divat.fr/en/online-calculators/evalbiom.Our examples illustrate that published conclusions about prognostic marker accuracy may be overoptimistic, thus giving potential for major mistakes in therapeutic decisions.Our approach should help readers better evaluate clinical articles reporting on prognostic markers. Time-dependent sensitivity and specificity inform on the inherent prognostic capacity of a marker for a defined prognostic time. Time-dependent predictive values, likelihood ratios, and posttest probability ratios may additionally contribute to interpret the markers prognostic capacity.


Berthelot L.,French Institute of Health and Medical Research | Miqueu P.,French Institute of Health and Medical Research | Pettre S.,French Institute of Health and Medical Research | Guillet M.,TcLand Expression | And 8 more authors.
Clinical Immunology | Year: 2010

Glatiramer acetate (GA) is a random copolymer used as an immunomodulatory treatment in relapsing-remitting multiple sclerosis (RR-MS). Its mechanisms of action are poorly understood, and several hypotheses have been put forward, the majority of which rely on in vitro studies. It has been hypothesised that further to processing by APC, GA could provide a large number of different epitopes with a possible sequence similarity to auto-antigens, which are able to stimulate a large proportion of T cells. Given that in a previous study we showed that the circulating T cells of MS patients present more alterations of the Vβ T cell receptor (TCR) usage than normal individuals, we explored the possible effect of GA on the ex vivo T cell repertoire of MS patients. Here we used quantitative PCR and electrophoresis to longitudinally analyse (and without any ex vivo stimulation), the CDR3 length distribution (LD) and the amount of Vβ TCR, as well as various cytokines, in the blood T cells of 10 RR-MS patients before and after 3 months and 2 years of GA treatment. In addition, we also determined the status of responder and non-responder patients after 24 months of GA treatment based on clinical and radiological criteria. We found no significant modification of cytokine production, Vβ TCR mRNA accumulation or CDR3-LD in the patients after short-term and long-term treatment. In addition, we did not observe any difference in CDR3-LD in the GA responder patients (n = 6) compared to non-responder patients (n = 4). Focusing our study on responder patients, we performed TCR repertoire analysis in the CD4+ and CD8+ compartment. Alterations of CDR3-LD were predominantly found in the CD8+ compartment, without any significant influence of GA treatment. Finally, the T cell repertoire variations in MS patients treated with GA and healthy controls were equivalent. Collectively, our data suggest that GA therapy does not induce significant variations in cytokine production or TCR usage in MS patients. © 2009 Elsevier Inc. All rights reserved.


Brouard S.,French Institute of Health and Medical Research | Brouard S.,Nantes University Hospital Center | Brouard S.,University of Nantes | Giral M.,French Institute of Health and Medical Research | And 6 more authors.
Transplantation | Year: 2011

Successful kidney transplant management throughout the graft lifespan depends on adequate diagnosis (i.e., recognition of a particular type of graft rejection or injury) and prognosis (i.e., predicting future events or outcome). The currently used methods (mainly graft histology, immunosuppressive drug level monitoring, measurement of renal function, and DSA) have proven highly useful on a population level by indicating good or bad outcome, but are difficult to translate into meaningful tests for individual patients. There is thus a need for diagnostic and predictive tests that add value by being more informative to each patient, more powerful, addressing more specific questions or providing less invasive interventions. Gene expression profiling using microarrays or quantitative PCR has become a benchmark in research into novel and informative monitoring assays for transplantation. A wealth of gene expression studies are reported in the literature spanning two decades. There is now a need for clinical validation so that such tests can become standardized and approved for widespread integration into the standard of care to improve outcome for kidney transplant recipients. © 2011 by Lippincott Williams & Wilkins.


Brouard S.,French Institute of Health and Medical Research | Puig-Pey I.,University of Barcelona | Pallier A.,French Institute of Health and Medical Research | Braud C.,TcLand Expression | And 9 more authors.
American Journal of Transplantation | Year: 2010

Due to its low level of nephrotoxicity and capacity to harness tolerogenic pathways, sirolimus (SRL) has been proposed as an alternative to calcineurin inhibitors in transplantation. The exact mechanisms underlying its unique immunosuppressive profile in humans, however, are still not well understood. In the current study, we aimed to depict the in vivo effects of SRL in comparison with cyclosporin A (CSA) by employing gene expression profiling and multiparameter flow cytometry on blood cells collected from stable kidney recipients under immunosuppressant monotherapy. SRL recipients displayed an increased frequency of CD4 + CD25highFoxp3 + T cells. However, this was accompanied by an increased number of effector memory T cells and by enrichment in NFkB-related pro-inflammatory expression pathways and monocyte and NK cell lineage-specific transcripts. Furthermore, measurement of a transcriptional signature characteristic of operationally tolerant kidney recipients failed to detect differences between SRL and CSA-treated recipients. In conclusion, we show here that the blood transcriptional profile induced by SRL monotherapy in vivo does not resemble that of operationally tolerant recipients and is dominated by innate immune cells and NFkB-related pro-inflammatory events. These data provide novel insights on the complex effects of SLR on the immune system in clinical transplantation. © 2010 The American Society of Transplantation and the American Society of Transplant Surgeons.


Dugast E.,French Institute of Health and Medical Research | Kiss-Toth E.,University of Sheffield | Soulillou J.-P.,French Institute of Health and Medical Research | Soulillou J.-P.,Institute Of Recherche En Transplantation | And 5 more authors.
Current Molecular Medicine | Year: 2013

This review describes the key role of the serine-threonine kinase like protein Tribbles-1 in health as well as in diverse human pathologies. Tribbles-1 is a homolog protein of the Drosophila Tribbles. In Drosophila, the Tribbles protein is involved in the cell-cycle progression during mitosis and in mammals initial data showed TRIB1 to be involved in cell proliferation. In mammals, TRIB1 lacks a catalytic domain and thus acts as an adaptor protein by interacting with several partners. The activity of TRIB1 seems to be very specific to the environment and the cells type in which it is expressed, and a role for this molecule has been mainly described in several pathological states including various cancers such as acute myeloid leukemia and ovarian cancer. Further evidence has also linked TRIB1 to the control of plasmalipid homeostasis thus indicating the role of this molecule as a risk factor for myocardial infarction. Finally, TRIB1 is shown to be up-regulated during inflammatory events such as chronic inflammation of atherosclerotic arteries or chronic antibody-mediated rejection of transplanted organs. Here we provide a review of the current state of the scientific literature for TRIB1, highlighting its role in diverse pathologies and inflammatory states. A better understanding of the role of this protein as both a target as well as a biological marker in diseases should drive the development of new therapeutic strategies. © 2013 Bentham Science Publishers.


Ashton-Chess J.,TcLand Expression | Cervino A.C.L.,TcLand Expression
Personalized Medicine | Year: 2011

Many scientific articles have been published that use gene-expression-based technologies to discriminate a trait of interest, typically a disease subgroup, within a patient population. However, few gene-expression-based signatures have at present reached the market and become a financially and clinically successful product. The technological, scientific and medical challenges, the regulatory environment and the financial considerations are all essential parts of the development process. Here we discuss the scientific aspects of successfully developing a gene-expression-based signature and review the global strategy of six products that made it to the market. We also present a point-to-point guide that should help researchers to successfully develop genomic signatures, thus paving the way towards personalized medicine. © 2011 Future Medicine Ltd.


Grant
Agency: European Commission | Branch: H2020 | Program: SME-2 | Phase: PHC-12-2014 | Award Amount: 5.00M | Year: 2015

The aim of the RABIOPRED project is to take the final steps to bring an innovative set of biomarkers that is able to predict response to treatment with TNF- inhibitors in Rheumatoid Arthritis (RA) to the market and clinical practice. Millions of RA patients are treated with TNF- inhibiting agents, currently one of the main second-line treatment strategies for RA. These expensive biological RA therapies represent a multibillion market. However, the TNF- inhibiting agents are not effective in 30-40% of the patients. Clinicians are currently unable to predict the response to this treatment beforehand. The ability to predict response to treatment would greatly improve clinical decision-making, improve health outcomes for RA patients, and contribute to cost reduction and sustainability of the health care system. The RABIOPRED assay is based on a novel gene expression signature and a predictive model, that have been identified and developed by TcLand Expression SA and that have been patented. Proof-of-concept has already been obtained for the prototype biomarker assay. The analytical validation and clinical performance evaluation of the RABIOPRED assay in the current project are the final development steps towards market introduction and clinical application. At the end of this 3.5 year project, a validated and CE registered IVD biomarker assay will be available that is ready for clinical application, initial market introduction and further commercialization and implementation. TcLand Expression SA is a French SME developing biomarkers for personalized medicine and companion diagnostics in immune mediated disorders. TcLand focusses on development and validation of noninvasive multi-gene molecular diagnostic blood tests. TcLand is embedded in an international network of collaborating pharmaceutical companies and clinical centers throughout Europe, facilitating clinical performance evaluation and enhancing subsequent market uptake of novel biomarkers assays.

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