References of "JOSSE, Claire"
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See detailPrevalence of Histological Characteristics of Breast Cancer in Rwanda in Relation to Age and Tumor Stages
Uyisenga, Jeanne ULiege; Butera, Yvan ULiege; Debit, Ahmed ULiege et al

in Hormones and Cancer (2020)

Breast cancer is a complex disease, and it is the most common cause of morbidity and mortality among women worldwide. In Sub-Saharan Africa, the clinical characteristics and tumor profiles of breast ... [more ▼]

Breast cancer is a complex disease, and it is the most common cause of morbidity and mortality among women worldwide. In Sub-Saharan Africa, the clinical characteristics and tumor profiles of breast cancer are still unknown. In the present study we aimed to determine breast tumor profiles of the Rwandan patients in relation to age and tumor stages. We compare our findings to related results from other sub-Saharan Africa studies. Data on age at diagnosis, tumor stage, and hormonal profiles of 138 patients diagnosed between January 2015 and December 2018 were retrospectively retrieved from electronic medical records at three referral hospitals in Rwanda. We compared our results to related findings reported in other Sub-Saharan African countries. All statistical analyses were done using SPSS Inc., Chicago, IL, USA, version 20 and R software languages. The mean age at diagnosis was 49.7 years (SD = 13) and ranged from 17 to 86 years. The majority of patients (57.2%) were diagnosed before 50 years of age compared with 42.8% aged > 50 years. Tumor stage III was the commonest accounting for 62% followed by stage II with 24.8%. The distribution of breast tumor subtypes was ER−, PR−, HER2−: 37.7%; ER+, PR+, HER2−: 31.2%; ER−, PR−, HER2+: 14.5%; ER+, PR+, HER2+: 5.1%; and other subtypes represented 11.6%. There was no statistically significant difference in age and tumor stages between the molecular subtypes. Our findings revealed the predominance of hormonal negative tumors among Rwandan patients with breast cancer. Triple negative was found to be the most common breast tumor subtype regardless of age and tumor stage. Larger prospective studies could examine genetics and environmental factors that may play a role in the differences of tumor characteristics in Sub-Saharan populations. © 2020, Springer Science+Business Media, LLC, part of Springer Nature. [less ▲]

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See detailGREB1L variants in familial and sporadic hereditary urogenital adysplasia and Mayer-Rokitansky-Kuster-Hauser syndrome
Jacquinet, Adeline ULiege; Boujemla, Bouchra ULiege; FASQUELLE, Corinne ULiege et al

in Clinical Genetics (2020), 98(2), 126-137

Congenital uterine anomalies (CUA) may have major impacts on the health and social well-being of affected individuals. Their expressivity is variable, with the most severe end of the spectrum being the ... [more ▼]

Congenital uterine anomalies (CUA) may have major impacts on the health and social well-being of affected individuals. Their expressivity is variable, with the most severe end of the spectrum being the absence of any fully or unilaterally developed uterus (aplastic uterus), which is a major feature in Mayer-Rokitansky-Kuster-Hauser syndrome (MRKH). So far, etiologies of CUA remain largely unknown. As reports of familial occurrences argue for strong genetic contributors in some cases, we performed whole exome sequencing in nine multiplex families with recurrence of uterine and kidney malformations, a condition called hereditary urogenital adysplasia. Heterozygous likely causative variants in the gene GREB1L were identified in four of these families, confirming GREB1L as an important gene for proper uterine and kidney development. The apparent mode of inheritance was autosomal dominant with incomplete penetrance. The four families included fetuses with uterovaginal aplasia and bilateral renal agenesis, highlighting the importance to investigate GREB1L in such phenotypes. Subsequent sequencing of the gene in a cohort of 68 individuals with MRKH syndrome or uterine malformation (mostly sporadic cases) identified six additional variants of unknown significance. We therefore conclude that heterozygous GREB1L variants contribute to MRKH syndrome and this probably requires additional genetic or environmental factors for full penetrance. © 2020 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd [less ▲]

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See detailBlood eosinophilic relative count is prognostic for breast cancer and associated with the presence of tumor at diagnosis and at time of relapse
ONESTI, Concetta Elisa ULiege; JOSSE, Claire ULiege; Boulet, Delphine ULiege et al

in Oncoimmunology (2020)

Background: Cancer outcome is associated with circulating immune cells, including eosinophils. Here we analyze the relative eosinophil count (REC) in different breast cancer subtypes. Methods: Stage I–III ... [more ▼]

Background: Cancer outcome is associated with circulating immune cells, including eosinophils. Here we analyze the relative eosinophil count (REC) in different breast cancer subtypes. Methods: Stage I–III breast cancer patients were included in the study and classified as REC-high vs low (cutoff 1.5%) or relative lymphocyte count (RLC)-high vs low (cutoff 17.5%). The co-primary endpoints were the breast cancer-specific survival (BCSS) or the time to treatment failure (TTF) in the REC groups. Results: Overall 930 patients were included in the study. We observed a benefit for REC-high vs REC-low in TTF (HR 0.610, 95% CI 0.458–0.812), and in BCSS (HR 0.632, 95% CI 0.433–0.923). Similarly, we observed a better TTF (HR 0.421, 95% CI 0.262–0.677) and BCSS (HR 0.350, 95% CI 0.200–0.614) in RLC-high vs low. A lower relapse rate was observed in the REC-high vs REC-low group (17.1% vs 24.7%, p = 0.005), not confirmed in the multivariate analysis. A lower median REC at baseline and at relapse was observed compared to REC after surgery and during cancer-free follow-up (p < .0001). Conclusions: REC could be a new promising, affordable and accessible predictive and prognostic biomarker in all breast cancer subtypes. [less ▲]

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See detailTOWARDS AN ACCURATE CANCER DIAGNOSIS MODELIZATION:COMPARISON OF RANDOM FOREST STRATEGIES
Debit, Ahmed ULiege; Poulet, Christophe ULiege; JOSSE, Claire ULiege et al

Poster (2019, March 15)

Machine learning approaches are heavily used to produce models that will one day support clinical decisions. To be reliably used as a medical decision, such diagnosis and prognosis tools have to harbor a ... [more ▼]

Machine learning approaches are heavily used to produce models that will one day support clinical decisions. To be reliably used as a medical decision, such diagnosis and prognosis tools have to harbor a high-level of precision. Random Forests have been already used in cancer diagnosis, prognosis, and screening. Numerous Random Forests methods have been derived from the original random forest algorithm from Breiman et al. in 2001. Nevertheless, the precision of their generated models remains unknown when facing biological data. The precision of such models can be therefore too variable to produce models with the same accuracy of classification, making them useless in daily clinics. Here, we perform an empirical comparison of Random Forest based strategies, looking for their precision in model accuracy and overall computational time. An assessment of 15 methods is carried out for the classification of paired normal -tumor patients, from 3 TCGA RNA-Seq datasets: BRCA (Breast Invasive Carcinoma), LUSC (Lung Squamous Cell Carcinoma), and THCA (Thyroid Carcinoma). Results demonstrate noteworthy differences in the precisions of the model accuracy and the overall time processing, between the strategies for one dataset, as well as between datasets for one strategy. Therefore, we highly recommend to test each random forest strategy prior to modelization. This will certainly improve the precision in model accuracy while revealing the method of choice for the candidate data. [less ▲]

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See detailTryptophan catabolism increases in breast cancer patients compared to healthy controls without affecting the cancer outcome or response to chemotherapy
ONESTI, Concetta Elisa ULiege; BOEMER, François ULiege; JOSSE, Claire ULiege et al

in Journal of Translational Medicine (2019), 17

Background: Indoleamine 2,3-dioxygenase catalyzes the conversion of tryptophan to kynurenine, an immunosuppressive metabolite involved in T regulatory cell differentiation. Indoleamine 2,3-dioxygenase is ... [more ▼]

Background: Indoleamine 2,3-dioxygenase catalyzes the conversion of tryptophan to kynurenine, an immunosuppressive metabolite involved in T regulatory cell differentiation. Indoleamine 2,3-dioxygenase is expressed in many cancer types, including breast cancer. Here, we analyze kynurenine and tryptophan and their ratio in breast cancer patients and healthy controls. Methods: Breast cancer patients and healthy controls were prospectively enrolled in our study. All subjects underwent blood sample withdrawal at diagnosis or on the day of screening mammography for the healthy controls. Plasmatic kynurenine and tryptophan were determined on a TQ5500 tandem mass spectrometer after chromatographic separation. Results: We enrolled 146 healthy controls and 202 women with stages I–III breast cancer of all subtypes. All patients underwent surgery, 126 underwent neoadjuvant chemotherapy with 43 showing a pathological complete response, and 43 underwent adjuvant chemotherapy. We observed significantly higher plasmatic kynurenine, tryptophan and their ratio for the healthy controls compared to patients with breast cancer. We observed a lower plasmatic tryptophan and a higher kynurenine/tryptophan ratio in hormone receptor-negative patients compared to hormone receptor-positive cancers. Lobular cancers showed a lower ratio than any other histologies. Advanced cancers were associated with a lower tryptophan level and higher grades with an increased kynurenine/tryptophan ratio. Pathological complete response was associated with higher kynurenine values. The plasmatic kynurenine, tryptophan and kynurenine/tryptophan ratios were not predictive of survival. Conclusions: The plasmatic kynurenine, tryptophan and kynurenine/tryptophan ratio could differentiate breast cancer patients from healthy controls. The Kyn/Trp ratio and Trp also showed different values according to hormone receptor status, TNM stage, T grade and histology. These results suggest a rapid metabolism in breast cancer, but no associations with outcome or sensitivity to chemotherapy were observed. [less ▲]

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See detailTowards an accurate cancer diagnosis modelization: Comparison of Random Forest strategies
Debit, Ahmed ULiege; Poulet, Christophe ULiege; JOSSE, Claire ULiege et al

Poster (2018, October 05)

Machine learning approaches are heavily used to produce models that will one day support clinical decisions. To be reliably used as a medical decision, such diagnosis and prognosis tools have to harbor a ... [more ▼]

Machine learning approaches are heavily used to produce models that will one day support clinical decisions. To be reliably used as a medical decision, such diagnosis and prognosis tools have to harbor a high-level of precision. Random Forests have been already used in cancer diagnosis, prognosis, and screening. Numerous Random Forests methods have been derived from the original random forest algorithm from Breiman et al. in 2001. Nevertheless, the precision of their generated models remains unknown when facing biological data. The precision of such models can be therefore too variable to produce models with the same accuracy of classification, making them useless in daily clinics. Here, we perform an empirical comparison of Random Forest based strategies, looking for their precision in model accuracy and overall computational time. An assessment of 15 methods is carried out for the classification of paired normal - tumor patients, from 3 TCGA RNA-Seq datasets: BRCA (Breast Invasive Carcinoma), LUSC (Lung Squamous Cell Carcinoma), and THCA (Thyroid Carcinoma). Results demonstrate noteworthy differences in the precisions of the model accuracy and the overall time processing, between the strategies for one dataset, as well as between datasets for one strategy. Therefore, we highly recommend to test each random forest strategy prior to modelization. This will certainly improve the precision in model accuracy while revealing the method of choice for the candidate data. [less ▲]

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See detailPredictive and prognostic role of peripheral blood eosinophil count in triple-negative and hormone receptor-negative/HER2-positive breast cancer patients undergoing neoadjuvant treatment
ONESTI, Concetta Elisa ULiege; JOSSE, Claire ULiege; Poncin, Aurélie ULiege et al

in Oncotarget (2018)

In current clinical practices, up to 27% of all breast cancer patients receive neoadjuvant chemotherapy. High pathological complete response rate is frequently associated with tumor-infiltrating ... [more ▼]

In current clinical practices, up to 27% of all breast cancer patients receive neoadjuvant chemotherapy. High pathological complete response rate is frequently associated with tumor-infiltrating lymphocytes. Additionally, circulating immune cells are also often linked to chemotherapy response. We performed a retrospective analysis on a cohort of 112 breast cancer patients (79 triple-negative, 33 hormone receptor-negative/HER2-positive) treated with standard neoadjuvant chemotherapy. Eosinophil and lymphocyte counts were collected from whole blood at baseline and during follow-ups and their associations with pathological complete response, relapse, disease-free and breast cancer-specific survival were analyzed. We observed a higher pathological complete response rate in patients who presented at baseline a relative eosinophil count ≥ 1.5% (55.6%) than in those with a relative eosinophil count < 1.5% (36.2%)(p = 0.04). An improvement in breast cancerspecific survival in patients with high relative eosinophil count (p = 0.05; HR = 0.336; 95% CI = 0.107–1.058) or with high relative lymphocyte count (threshold = 17.5%, p = 0.01; HR = 0.217; 95% CI = 0.060–0.783) were also observed. Upon combining the two parameters into the eosinophil x lymphocyte product with a threshold at 35.8, associations with pathological complete response (p = 0.002), relapse (p = 0.028), disease-free survival (p = 0.012) and breast cancer-specific survival (p = 0.001) were also recorded. In conclusion, the relative eosinophil count and eosinophil x lymphocyte product could be promising, affordable and accessible new biomarkers that are predictive for neoadjuvant chemotherapy response and prognostic for longer survival in triplenegative and hormone receptors-negative/HER2-positive breast cancers. Confirmation of these results in a larger patient population is needed. [less ▲]

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See detailTowards an accurate cancer diagnosis modelization:Comparison of Random Forest strategies
Debit, Ahmed ULiege; JOSSE, Claire ULiege; JERUSALEM, Guy ULiege et al

Poster (2018, September 13)

Machine learning approaches are heavily used to produce models that will one day support clinical decisions. To be reliably used as a medical decision, such diagnosis and prognosis tools have to harbor a ... [more ▼]

Machine learning approaches are heavily used to produce models that will one day support clinical decisions. To be reliably used as a medical decision, such diagnosis and prognosis tools have to harbor a high-level of precision. Random Forests have been already used in cancer diagnosis, prognosis, and screening. Numerous Random Forests methods have been derived from the original random forest algorithm from Breiman et al. in 2001. Nevertheless, the precision of their generated models remains unknown when facing biological data. The precision of such models can be therefore too variable to produce models with the same accuracy of classification, making them useless in daily clinics. Here, we perform an empirical comparison of Random Forest based strategies, looking for their precision in model accuracy and over all computational time. An assessment of 15 methods is carried out for the classification of paired normal - tumor patients, from 3 TCGA RNA-Seq datasets: BRCA (Breast Invasive Carcinoma), LUSC (Lung Squamous Cell Carcinoma), and THCA (Thyroid Carcinoma).Results demonstrate noteworthy differences in the precision of the model accuracy and the overall time processing, between the strategies for one dataset, as well as between datasets for one strategy. Therefore, we highly recommend to test each random forest strategy prior to modelization. This will certainly improve the precision in model accuracy while revealing the method of choice for the candidate data. [less ▲]

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See detailRole of DNA methylation in INK4a-ARF-INK4b locus expression in breast cancer
Latgé, Guillaume ULiege; JOSSE, Claire ULiege; Poulet, Christophe ULiege et al

Poster (2018, September 13)

Breast cancer is a public health problem : one woman in 9 will suffer of it during her lifetime. The estrogen receptor expressing sub-type (ER+) is the most frequent, with 75 % of the cases. Those tumors ... [more ▼]

Breast cancer is a public health problem : one woman in 9 will suffer of it during her lifetime. The estrogen receptor expressing sub-type (ER+) is the most frequent, with 75 % of the cases. Those tumors frequently become resistant to hormonotherapy and spread as metastasis. In this case, chemotherapy needs to be administrated. The CDK4/6 inhibitors in combination with hormonotherapy appears as the new standard treatment for metastatic disease and allows to postpone the chemotherapy. Those drugs play the same role as the endogenous p16-p15 proteins, and it is expected that the patients who have lost their protein expression are also those who will present the best response to treatment. However, none of the currently tested biomarkers turns out to be predictive of treatment response. The INK locus, where p16/p14-p15 proteins are encoded, is often altered in cancers and is involved in cell cycle regulation. The p16/p14-p15 expression is negatively regulated by a non-coding RNA called ANRIL. My aim is to explore the molecular mechanisms linked to the non-coding RNA of the INK locus and involved in the expression regulation of the proteins p16/p14-p15, and to highlight potential biomarkers of the CDK4/6 inhibitors treatment response in ER+ breast cancer. To this end, I already collected In Vitro expression data by RT-qPCR in some cell lines with different expression patterns. DNA methylation are investigated thanks to a Deoxyazacytidine treatment, a DNA methylation inhibitor then by ImmunoPrecipitation of methylated DNA. So, the first links between the expression of the locus and its methylation can be done. In future, other treamtents, protein and RNA interactions will be studied to explain the potential links and molecular mechanisms. [less ▲]

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See detailPredictive and prognostic role of peripheral blood eosinophil count in triple negative and hormone receptor negative/HER2 positive breast cancers patients undergoing neoadjuvant treatment.
ONESTI, Concetta Elisa ULiege; JOSSE, Claire ULiege; PONCIN, Aurélie ULiege et al

Scientific conference (2018, September 13)

Introduction: In clinical practices, up to 27% of breast cancer (BC) patients receive neoadjuvant chemotherapy (NAC). In this context, a pathological complete response (pCR) is the most commonly used end ... [more ▼]

Introduction: In clinical practices, up to 27% of breast cancer (BC) patients receive neoadjuvant chemotherapy (NAC). In this context, a pathological complete response (pCR) is the most commonly used end-point. High pCR rate is frequently associated with tumor infiltrating lymphocytes. Besides, circulating immune cells are also often linked to chemotherapy response. Materials and methods: We performed a retrospective analysis on 112 BC patients (79 triple negative, 33 HR-/HER2+), treated with standard NAC. The median follow-up was 37.5 months (range 9-156). Eosinophil and lymphocyte count were collected at baseline, after surgery, at 1 year of follow-up and at relapse. The primary end-point is the association between the relative eosinophil count (REC) and pCR. The secondary end-points are the associations of REC, relative lymphocyte count (RLC) and eosinophil/lymphocyte product (ELP) with relapse, disease free (DFS) and breast cancer specific (BCSS) survival and to study the variation of REC and RLC during follow-up. Results: We observed a higher pCR rate in patients with REC≥1.5% vs patients with REC <1.5% (55.6% vs 36.2%, p = 0.04), and a higher median REC in patients with pCR (1.9% vs 1.2%, p 0.042). No statistically significant associations were detected with relapse, nor between RLC with pCR or relapse. We observed a 3-year BCSS of 91% vs 80% for high and low REC respectively (p 0.05; HR 0.336, 95% CI 0.107-1.058) and of 88% vs 49% in RLC≥17.5% and <17.5% respectively (p 0.01; HR 0.217, 95% CI 0.060-0.783). No significant differences were detected for DFS. Combining the two parameters in the ELP, we observed an association with pCR (59.6% in ELP≥35.8 vs 30.9% in ELP<35.8, p 0.002), relapse (12.3% vs 29.1% in high and low ELP, p 0.028), DFS (3-year DFS 90% vs 69% in high and low ELP, p 0.012; HR 0.337, 95% CI 0.138-0.823) and BCSS (3-year BCSS 95% vs 75% in high and low ELP, p 0.001; HR 0.129, 95% CI 0.029-0.573). Moreover, we observed a raise of REC after surgery from 1.4% to 2.6% (p 0.0001) and a significant reduction at relapse from 2.8% to 1.7% (p 0.021). Conversely, a reduction of RLC from 26.9% at baseline to 20.45% after surgery (p 0.0001), without significant variation at relapse, was detected. Conclusion: REC, RLC and ELP could be new promising, affordable and accessible biomarkers predictive for NAC response and prognostic for longer survival in TNBC and HR-/HER2+ BC. Confirmation in a larger cohort is needed. [less ▲]

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See detailInnovative methodology for the identification of soluble biomarkers in fresh tissues.
Costanza, Brunella ULiege; Turtoi, Andrei ULiege; Bellahcene, Akeila ULiege et al

in Oncotarget (2018), 9(12), 10665-10680

The identification of diagnostic and prognostic biomarkers from early lesions, measurable in liquid biopsies remains a major challenge, particularly in oncology. Fresh human material of high quality is ... [more ▼]

The identification of diagnostic and prognostic biomarkers from early lesions, measurable in liquid biopsies remains a major challenge, particularly in oncology. Fresh human material of high quality is required for biomarker discovery but is often not available when it is totally required for clinical pathology investigation. Hence, all OMICs studies are done on residual and less clinically relevant biological samples. Here after, we present an innovative, simple, and non-destructive, procedure named EXPEL that uses rapid, pressure-assisted, interstitial fluid extrusion, preserving the specimen for full routine clinical pathology investigation. In the meantime, the technique allows a comprehensive OMICs analysis (proteins, metabolites, miRNAs and DNA). As proof of concept, we have applied EXPEL on freshly collected human colorectal cancer and liver metastases tissues. We demonstrate that the procedure efficiently allows the extraction, within a few minutes, of a wide variety of biomolecules holding diagnostic and prognostic potential while keeping both tissue morphology and antigenicity unaltered. Our method enables, for the first time, both clinicians and scientists to explore identical clinical material regardless of its origin and size, which has a major positive impact on translation to the clinic. [less ▲]

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See detailVariations of circulating cardiac biomarkers during and after anthracycline-containing chemotherapy in breast cancer patients
Freres, Pierre ULiege; Bouznad, N.; Servais, Laurence ULiege et al

in BMC Cancer (2018), 18(1),

Background: Over time, the chance of cure after the diagnosis of breast cancer has been increasing, as a consequence of earlier diagnosis, improved diagnostic procedures and more effective treatment ... [more ▼]

Background: Over time, the chance of cure after the diagnosis of breast cancer has been increasing, as a consequence of earlier diagnosis, improved diagnostic procedures and more effective treatment options. However, oncologists are concerned by the risk of long term treatment side effects, including congestive heart failure (CHF). Methods: In this study, we evaluated innovative circulating cardiac biomarkers during and after anthracycline-based neoadjuvant chemotherapy (NAC) in breast cancer patients. Levels of cardiac-specific troponins T (cTnT), N-terminal natriuretic peptides (NT-proBNP), soluble ST2 (sST2) and 10 circulating microRNAs (miRNAs) were measured. Results: Under chemotherapy, we observed an elevation of cTnT and NT-proBNP levels, but also the upregulation of sST2 and of 4 CHF-related miRNAs (miR-126-3p, miR-199a-3p, miR-423-5p, miR-34a-5p). The elevations of cTnT, NT-proBNP, sST2 and CHF-related miRNAs were poorly correlated, suggesting that these molecules could provide different information. Conclusions: Circulating miRNA and sST2 are potential biomarkers of the chemotherapy-related cardiac dysfunction (CRCD). Nevertheless, further studies and long-term follow-up are needed in order to evaluate if these new markers may help to predict CRCD and to identify the patients at risk to later develop CHF. © 2018 The Author(s). [less ▲]

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See detailNatural Antisense Transcripts: Molecular Mechanisms and Implications in Breast Cancers.
Latge, Guillaume ULiege; Poulet, Christophe ULiege; Bours, Vincent ULiege et al

in International Journal of Molecular Sciences (2018), 19(1),

Natural antisense transcripts are RNA sequences that can be transcribed from both DNA strands at the same locus but in the opposite direction from the gene transcript. Because strand-specific high ... [more ▼]

Natural antisense transcripts are RNA sequences that can be transcribed from both DNA strands at the same locus but in the opposite direction from the gene transcript. Because strand-specific high-throughput sequencing of the antisense transcriptome has only been available for less than a decade, many natural antisense transcripts were first described as long non-coding RNAs. Although the precise biological roles of natural antisense transcripts are not known yet, an increasing number of studies report their implication in gene expression regulation. Their expression levels are altered in many physiological and pathological conditions, including breast cancers. Among the potential clinical utilities of the natural antisense transcripts, the non-coding|coding transcript pairs are of high interest for treatment. Indeed, these pairs can be targeted by antisense oligonucleotides to specifically tune the expression of the coding-gene. Here, we describe the current knowledge about natural antisense transcripts, their varying molecular mechanisms as gene expression regulators, and their potential as prognostic or predictive biomarkers in breast cancers. [less ▲]

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See detailNormalization and correction for batch effects via RUV for RNA-seq data: practical implications for Breast Cancer Research
Debit, Ahmed ULiege; Wenric, Stéphane ULiege; JOSSE, Claire ULiege et al

Poster (2017, May)

The whole transcriptome contains information about nonsense, missense, silent, in-frame and frameshift mutations, as observed at whole-exome level, as well as splicing and (allelic) gene-expression ... [more ▼]

The whole transcriptome contains information about nonsense, missense, silent, in-frame and frameshift mutations, as observed at whole-exome level, as well as splicing and (allelic) gene-expression changes which are missed by DNA analysis. One important step in the analysis of gene expression data arising from RNA-seq is the detection of differential expression (DE) levels. Several methods are available and the choice is sometimes controversial. For a reliable DE analysis that reduces False Positive DE genes, and accurate estimation of gene expression levels, a good and suitable normalization approach (including correction for confounders) is mandatory. Several normalization methods have been proposed to correct for both within-sample and between-sample biases. RUV (Removing Unwanted Variation) is one of them and has the advantage to correct for batch effects including potentially unknown unwanted variation in gene expression. In this study, we present a comparison on real-life Illumina paired-end sequencing data for Estrogen-Receptor-Positive (ER+) Breast Cancer tissues versus matched controls between RUV (RUVg using in silico negative control genes) and more commonly used methods for RNA-seq data normalization, such as DESeq2, edgeR, and UQ. The set of in silico empirical negative control genes for RUVg was defined as the set of least significant DE genes obtained after a first DE analysis performed prior to RUVg correction. Box plots of relative log expression (RLE) among the samples and PCA plots show that RUVg performs well and leads to a stabilization of read count across samples with a clear clustering of biological replicates. [less ▲]

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See detailTranscriptome wide analysis of natural antisense transcripts shows potential role in breast cancer
Wenric, Stéphane ULiege; El Guendi, Sonia ULiege; CABERG, Jean-Hubert ULiege et al

Poster (2017, May)

Non-coding RNAs (ncRNA) represent at least 1/5 of the mammalian transcript amount, and about 90% of the genome length is actively transcribed. Many ncRNAs have been demonstrated to play a role in cancer ... [more ▼]

Non-coding RNAs (ncRNA) represent at least 1/5 of the mammalian transcript amount, and about 90% of the genome length is actively transcribed. Many ncRNAs have been demonstrated to play a role in cancer. Among them, natural antisense transcripts (NAT) are RNA sequences which are complementary and overlapping to those of protein-coding transcripts (PCT). NATs were punctually described as regulating gene expression, and are expected to act more frequently in cis than other ncRNAs that commonly function in trans. In this work, 22 breast cancers expressing estrogen receptors and their paired healthy tissues were analyzed by strand-specific RNA sequencing. To highlight the potential role of NATs in gene regulations occurring in breast cancer, three different gene extraction methods were used: differential expression analysis of NATs between tumor and healthy tissues, differential correlation analysis of paired NAT/PCT between tumor and healthy tissues, and NAT/PCT read count ratio variation between tumor and healthy tissues. Each of these methods yielded lists of NAT/PCT pairs that were demonstrated to be enriched in survival-associated genes on an independent cohort (TCGA). This work allows to highlight NAT lists that display a strong potential to affect the expression of genes involved in the breast cancer pathology. [less ▲]

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See detailGenomic Studies of Multiple Myeloma Reveal an Association between X Chromosome Alterations and Genomic Profile Complexity.
Sticca, Tiberio ULiege; CABERG, Jean-Hubert ULiege; Wenric, Stéphane ULiege et al

in Genes, Chromosomes and Cancer (2017), 56

The genomic profile of multiple myeloma (MM) has prognostic value by dividing patients into a good prognosis hyperdiploid group and a bad prognosis non-hyperdiploid group with a higher incidence of IgH ... [more ▼]

The genomic profile of multiple myeloma (MM) has prognostic value by dividing patients into a good prognosis hyperdiploid group and a bad prognosis non-hyperdiploid group with a higher incidence of IgH translocations. This classification, however, is inadequate and many other parameters like mutations, epigenetic modifications and genomic heterogeneity may influence the prognosis. We performed a genomic study by array-based comparative genomic hybridization (aCGH) on a cohort of 162 patients to evaluate the frequency of genomic gains and losses. We identified a high frequency of X chromosome alterations leading to partial Xq duplication, often associated with Xi deletion in female patients. This partial X duplication could be a cytogenetic marker of aneuploidy as it is correlated with a high number of chromosomal breakages. Patient with high level of chromosomal breakage had reduced survival regardless the region implicated. A higher transcriptional level was shown for genes with potential implication in cancer and located in this altered region. Among these genes, IKBKG and IRAK1 are members of the NFKB pathway which plays an important role in MM and is a target for specific treatments. [less ▲]

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See detailTranscriptome-wide analysis of natural antisense transcripts shows their potential role in breast cancer.
Wenric, Stéphane ULiege; ElGuendi, Sonia; CABERG, Jean-Hubert ULiege et al

in Scientific Reports (2017), 7(1), 17452

Non-coding RNAs (ncRNA) represent 1/5 of the mammalian transcript number, and 90% of the genome length is transcribed. Many ncRNAs play a role in cancer. Among them, non-coding natural antisense ... [more ▼]

Non-coding RNAs (ncRNA) represent 1/5 of the mammalian transcript number, and 90% of the genome length is transcribed. Many ncRNAs play a role in cancer. Among them, non-coding natural antisense transcripts (ncNAT) are RNA sequences that are complementary and overlapping to those of either protein-coding (PCT) or non-coding transcripts. Several ncNATs were described as regulating protein coding gene expression on the same loci, and they are expected to act more frequently in cis compared to other ncRNAs that commonly function in trans. In this work, 22 breast cancers expressing estrogen receptors and their paired adjacent non-malignant tissues were analyzed by strand-specific RNA sequencing. To highlight ncNATs potentially playing a role in protein coding gene regulations that occur in breast cancer, three different data analysis methods were used: differential expression analysis of ncNATs between tumor and non-malignant tissues, differential correlation analysis of paired ncNAT/PCT between tumor and non-malignant tissues, and ncNAT/PCT read count ratio variation between tumor and non-malignant tissues. Each of these methods yielded lists of ncNAT/PCT pairs that were enriched in survival-associated genes. This work highlights ncNAT lists that display potential to affect the expression of protein-coding genes involved in breast cancer pathology. [less ▲]

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See detailA next-generation newborn screening pilot study: NGS on dried blood spots detects causal mutations in patients with inherited metabolic diseases.
BOEMER, François ULiege; Fasquelle, Corinne ULiege; D'OTREPPE DE BOUVETTE, Stéphanie ULiege et al

in Scientific Reports (2017), 7(1), 17641

The range of applications performed on dried blood spots (DBS) widely broadened during the past decades to now include next-generation sequencing (NGS). Previous publications provided a general overview ... [more ▼]

The range of applications performed on dried blood spots (DBS) widely broadened during the past decades to now include next-generation sequencing (NGS). Previous publications provided a general overview of NGS capacities on DBS-extracted DNA but did not focus on the identification of specific disorders. We thus aimed to demonstrate that NGS was reliable for detecting pathogenic mutations on genomic material extracted from DBS. Assuming the future implementation of NGS technologies into newborn screening (NBS), we conducted a pilot study on fifteen patients with inherited metabolic disorders. Blood was collected from DBS. Whole-exome sequencing was performed, and sequences were analyzed with a specific focus on genes related to NBS. Results were compared to the known pathogenic mutations previously identified by Sanger sequencing. Causal mutations were readily characterized, and multiple polymorphisms have been identified. According to variant database prediction, an unexplained homozygote pathogenic mutation, unrelated to patient's disorder, was also found in one sample. While amount and quality of DBS-extracted DNA are adequate to identify causal mutations by NGS, bioinformatics analysis revealed critical drawbacks: coverage fluctuations between regions, difficulties in identifying insertions/deletions, and inconsistent reliability of database-referenced variants. Nevertheless, results of this study lead us to consider future perspectives regarding "next-generation" NBS. [less ▲]

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