Design, cohort profile and comparison of the KTD-Innov study: a prospective multidimensional biomarker validation study in kidney allograft rejection.

There is an unmet need for robust and clinically validated biomarkers of kidney allograft rejection. Here we present the KTD-Innov study (ClinicalTrials.gov, NCT03582436), an unselected deeply phenotyped cohort of kidney transplant recipients with a holistic approach to validate the clinical utility of precision diagnostic biomarkers. In 2018-2019, we prospectively enrolled consecutive adult patients who received a kidney allograft at seven French centers and followed them for a year. We performed multimodal phenotyping at follow-up visits, by collecting clinical, biological, immunological, and histological parameters, and analyzing a panel of 147 blood, urinary and kidney tissue biomarkers. The primary outcome was allograft rejection, assessed at each visit according to the international Banff 2019 classification. We evaluated the representativeness of participants by comparing them with patients from French, European, and American transplant programs transplanted during the same period. A total of 733 kidney transplant recipients (64.1% male and 35.9% female) were included during the study. The median follow-up after transplantation was 12.3 months (interquartile range, 11.9-13.1 months). The cumulative incidence of rejection was 9.7% at one year post-transplant. We developed a distributed and secured data repository in compliance with the general data protection regulation. We established a multimodal biomarker biobank of 16,736 samples, including 9331 blood, 4425 urinary and 2980 kidney tissue samples, managed and secured in a collaborative network involving 7 clinical centers, 4 analytical platforms and 2 industrial partners. Patients' characteristics, immune profiles and treatments closely resembled those of 41,238 French, European and American kidney transplant recipients. The KTD-Innov study is a unique holistic and multidimensional biomarker validation cohort of kidney transplant recipients representative of the real-world transplant population. Future findings from this cohort are likely to be robust and generalizable.

Comedications influence immune infiltration and pathological response to neoadjuvant chemotherapy in breast cancer.

Immunosurveillance plays an important role in breast cancer (BC) prognosis and progression, and can be geared by immunogenic chemotherapy. In a cohort of 1023 BC patients treated with neoadjuvant chemotherapy (NAC), 40% of the individuals took comedications mostly linked to aging and comorbidities. We systematically analyzed the off-target effects of 1178 concurrent comedications (classified according to the Anatomical Therapeutic Chemical (ATC) Classification System) on the density of tumor-infiltrating lymphocytes (TILs) and pathological complete responses (pCR). At level 1 of the ATC system, the main anatomical classes of drugs were those targeting the nervous system (class N, 39.1%), cardiovascular disorders (class C, 26.6%), alimentary and metabolism (class A, 16.9%), or hormonal preparations (class H, 6.5%). At level 2, the most frequent therapeutic classes were psycholeptics (N05), analgesics (N02), and psychoanaleptics (N06). Pre-NAC TIL density in triple-negative BC (TNBC) was influenced by medications from class H, N, and A, while TIL density in HER2+ BC was associated with the use of class C. Psycholeptics (N05) and agents acting on the renin-angiotensin system (C09) were independently associated with pCR in the whole population of BC or TNBC, and in HER2-positive BC, respectively. Importantly, level 3 hypnotics (N05C) alone were able to reduce tumor growth in BC bearing mice and increased the anti-cancer activity of cyclophosphamide in a T cell-dependent manner. These findings prompt for further exploration of drugs interactions in cancer, and for prospective drug-repositioning strategies to improve the efficacy of NAC in BC.

Domain-invariant features for mechanism of action prediction in a multi-cell-line drug screen.

MOTIVATION: High-content screening is an important tool in drug discovery and characterization. Often, high-content drug screens are performed on one single-cell line. Yet, a single-cell line cannot be thought of as a perfect disease model. Many diseases feature an important molecular heterogeneity. Consequently, a drug may be effective against one molecular subtype of a disease, but less so against another. To characterize drugs with respect to their effect not only on one cell line but on a panel of cell lines is therefore a promising strategy to streamline the drug discovery process. RESULTS: The contribution of this article is 2-fold. First, we investigate whether we can predict drug mechanism of action (MOA) at the molecular level without optimization of the MOA classes to the screen specificities. To this end, we benchmark a set of algorithms within a conventional pipeline, and evaluate their MOA prediction performance according to a statistically rigorous framework. Second, we extend this conventional pipeline to the simultaneous analysis of multiple cell lines, each manifesting potentially different morphological baselines. For this, we propose multi-task autoencoders, including a domain-adaptive model used to construct domain-invariant feature representations across cell lines. We apply these methods to a pilot screen of two triple negative breast cancer cell lines as models for two different molecular subtypes of the disease. AVAILABILITY AND IMPLEMENTATION: https://github.com/jcboyd/multi-cell-line or https://zenodo.org/record/2677923. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Flexible and expeditious assay for quantitative monitoring of alpha-amylase and amyloglucosidase activities.

The monitoring of the activity of alpha-amylase and amyloglucosidase is an important tool for studying their role in the hydrolysis of starch. Here we introduced an improved method capable to measure the activity of alpha-amylase and amyloglucosidase from different sources based on a quantitative starch-iodine assay. The developments of the assay sought the consistent preparation of the reagents, the rescale of the assay and the adjustment of the sensitivity. This was complemented by a glucose yield assay for amyloglucosidase that allowed a secondary source of information when insoluble starches were studied. The proposed method showed high precision in long-term use (RSD < 6.3%). Furthermore, all experimental conditions can be adapted according to the equipment available at each laboratory, transforming this method in a broadband analytical tool for screening alpha-amylase and amyloglucosidase activities. •Tailorable assay based on the starch-iodine staining for the determination of alpha-amylase and amyloglucosidase activities.•Enhanced consistence of reagent preparation.•High intra-day and inter-day reproducibility.

Author Correction: New insight for pharmacogenomics studies from the transcriptional analysis of two large-scale cancer cell line panels.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Extracellular vesicles: intelligent delivery strategies for therapeutic applications.

Extracellular vesicles (EV), in particular exosomes, have been the object of intense research, due to their potential to mediate intercellular communication, modulating the phenotype of target cells. The natural properties and functions of EV are being exploited as biomarkers for disease diagnosis and prognosis, and as nano-bio-carriers for the development of new therapeutic strategies. EV have been particularly examined in the field of cancer, but are also increasingly investigated in other areas, like immune-related diseases and regenerative medicine. In this review, the therapeutic use of EV as drug delivery systems is described, balancing the advantages and drawbacks of different routes for their in vivo administration. Systemic and local delivery of EV are discussed, tackling the persisting difficulties in the assessment of their pharmacokinetics, pharmacodynamics and biodistribution in vivo. Finally, we discuss the future perspectives for incorporating EV into delivery systems and their use for an improved and controlled release of EV in vivo.

The intensification of amyloglucosidase-based saccharification by ultrasound.

The present report studied the role of ultrasound (US) energy in the amyloglucosidase-based starch hydrolysis using two complementary approaches: (i) in the activity of six commercially-available amyloglucosidases (using soluble starch as substrate), and (ii) in the hydrolysis of four pure starches from different botanical sources. This corresponds to the first systematic evaluation of the role of US in starch hydrolysis mediated by amyloglucosidase, being a consequence of our previous report that assessed the effect of US in the activity of alpha-amylase (LWT - Food Science and Technology 84 (2017) 674-685). Regarding amlyloglucosidases, three enzymes obtained from Aspergillus niger (AN1-AN3), and Spirizyme Achieve (SPA), Spirizyme Fuel (SPF) and Spirizyme Ultra (SPU) were submitted to a Box-Behnken experimental design in order to establish the optimum conditions for their maximum activity. In the presence of US, we found both inactivation and activation, ranging from -88% (AN3) to 699% (SPA). The US promoted the enzyme activity when combined with lower temperatures (40-60 °C), with a marked effect in Spirizyme enzymes. Based on the optimum conditions established by the experimental design, we also evaluated the role of US in the glucose yield resulting from the hydrolysis of pure starches (corn, rice, potato, wheat). In this case, US led to higher glucose yields in all conditions tested. The enhancement factors observed ranged from 1.2 (AN1, rice starch) to 65 (SPA, potato starch) times. We compared these findings with previous reports, which highlighted the role of US in intensifying amyloglucosidase-based saccharification in mild conditions, by simultaneously influencing both enzyme and substrate. Hence, US power has to be fine-tuned for each particular enzyme in order to maximize process intensification.

Transmission of caprine arthritis encephalitis virus between sheep / Transmissão do vírus da artrite encefalite caprina entre ovinos

ABSTRACT: This study was conducted to evaluate caprine arthritis encephalitis virus (CAEV) transmission among sheep using 15 lambs that were distributed in 2 experimental groups. The exposed group consisted of 10 lambs that remained with their mothers, who were experimentally infected with CAEV. The non-exposed group was characterized as the control group and was comprised of 5 lambs that remained with their CAEV-negative mothers. Blood samples were collected monthly from birth until 1 year of life. To evaluate the transmission, an agar gel immunodiffusion test (AGID), enzyme immunoassay (ELISA), immunoblotting (IB), and nested polymerase chain reaction (nPCR) techniques were used. The non-exposed group was negative in all of the tests throughout the whole experiment. In the exposed group, 2 individuals had positive nPCR results. Positive nPCR samples were sequenced for comparison with the original goat strains and were shown to be similar to the CAEV-Cork strain. Seroconversion was not detected, and clinical manifestations were not observed. Thus, after 1 year of observation, it was verified that CAEV transmission among sheep is possible; however, with discreet frequency. This was an initial study, and other experiments are needed to analyze the adaptive capacity of the CAEV to remain in an infected sheep flock and cause the disease.

RESUMO: O estudo foi conduzido para avaliar a transmissão do vírus da artrite encefalite caprina (CAEV) entre ovinos, utilizando 15 cordeiros, distribuídos em dois grupos experimentais. O grupo exposto foi constituído por 10 cordeiros, mantidos com suas mães, que foram infectadas, experimentalmente, com CAEV. O grupo não exposto caracterizou-se como grupo controle e foi formado por cinco cordeiros, mantidos com suas matrizes, negativas para CAEV. Foram colhidas amostras de sangue mensalmente, do periodo que compreende o nascimento até um ano de vida. Para avaliar a transmissão, foram utilizadas as técnicas de imunodifusão em gel de agarose (IDGA), ensaio imunoenzimático (ELISA), immunoblotting (IB) e reação em cadeia da polimerase do tipo nested (nPCR). O grupo não exposto se manteve negativo aos testes durante todo o experimento. Já no grupo exposto, dois indivíduos apresentaram resultados positivos na nPCR. As amostras positivas na nPCR foram sequenciadas para serem comparadas com as cepas originais de caprinos, comprovando se tratar de lentivírus semelhante à cepa CAEV-Cork. A soroconversão não foi detectada e a manifestação clínica não foi observada. Sendo assim, após um ano de observação, verificou-se que a transmissão do CAEV entre ovinos é possível, entretanto, com discreta frequência. Este foi um estudo inicial, e outros experimentos são necessários para analisar a capacidade adaptativa do CAEV de permanecer em rebanho ovino infectado e, com isso, causar doença.

New insight for pharmacogenomics studies from the transcriptional analysis of two large-scale cancer cell line panels.

One of the most challenging problems in the development of new anticancer drugs is the very high attrition rate. The so-called "drug repositioning process" propose to find new therapeutic indications to already approved drugs. For this, new analytic methods are required to optimize the information present in large-scale pharmacogenomics datasets. We analyzed data from the Genomics of Drug Sensitivity in Cancer and Cancer Cell Line Encyclopedia studies. We focused on common cell lines (n = 471), considering the molecular information, and the drug sensitivity for common drugs screened (n = 15). We propose a novel classification based on transcriptomic profiles of cell lines, according to a biological network-driven gene selection process. Our robust molecular classification displays greater homogeneity of drug sensitivity than cancer cell line grouped based on tissue of origin. We then identified significant associations between cell line cluster and drug response robustly found between both datasets. We further demonstrate the relevance of our method using two additional external datasets and distinct sensitivity metrics. Some associations were still found robust, despite cell lines and drug responses' variations. This study defines a robust molecular classification of cancer cell lines that could be used to find new therapeutic indications to known compounds.

A Stromal Immune Module Correlated with the Response to Neoadjuvant Chemotherapy, Prognosis and Lymphocyte Infiltration in HER2-Positive Breast Carcinoma Is Inversely Correlated with Hormonal Pathways.

INTRODUCTION: HER2-positive breast cancer (BC) is a heterogeneous group of aggressive breast cancers, the prognosis of which has greatly improved since the introduction of treatments targeting HER2. However, these tumors may display intrinsic or acquired resistance to treatment, and classifiers of HER2-positive tumors are required to improve the prediction of prognosis and to develop novel therapeutic interventions. METHODS: We analyzed 2893 primary human breast cancer samples from 21 publicly available datasets and developed a six-metagene signature on a training set of 448 HER2-positive BC. We then used external public datasets to assess the ability of these metagenes to predict the response to chemotherapy (Ignatiadis dataset), and prognosis (METABRIC dataset). RESULTS: We identified a six-metagene signature (138 genes) containing metagenes enriched in different gene ontologies. The gene clusters were named as follows: Immunity, Tumor suppressors/proliferation, Interferon, Signal transduction, Hormone/survival and Matrix clusters. In all datasets, the Immunity metagene was less strongly expressed in ER-positive than in ER-negative tumors, and was inversely correlated with the Hormonal/survival metagene. Within the signature, multivariate analyses showed that strong expression of the "Immunity" metagene was associated with higher pCR rates after NAC (OR = 3.71[1.28-11.91], p = 0.019) than weak expression, and with a better prognosis in HER2-positive/ER-negative breast cancers (HR = 0.58 [0.36-0.94], p = 0.026). Immunity metagene expression was associated with the presence of tumor-infiltrating lymphocytes (TILs). CONCLUSION: The identification of a predictive and prognostic immune module in HER2-positive BC confirms the need for clinical testing for immune checkpoint modulators and vaccines for this specific subtype. The inverse correlation between Immunity and hormone pathways opens research perspectives and deserves further investigation.

Epigenomic alterations in breast carcinoma from primary tumor to locoregional recurrences.

INTRODUCTION: Epigenetic modifications such as aberrant DNA methylation has long been associated with tumorogenesis. Little is known, however, about how these modifications appear in cancer progression. Comparing the methylome of breast carcinomas and locoregional evolutions could shed light on this process. METHODS: The methylome profiles of 48 primary breast carcinomas (PT) and their matched axillary metastases (PT/AM pairs, 20 cases), local recurrences (PT/LR pairs, 17 cases) or contralateral breast carcinomas (PT/CL pairs, 11 cases) were analyzed. Univariate and multivariate analyzes were performed to determine differentially methylated probes (DMPs), and a similarity score was defined to compare methylation profiles. Correlation with copy-number based score was calculated and metastatic-free survival was compared between methods. RESULTS: 49 DMPs were found for the PT/AM set, but none for the others (FDR < 5%). Hierarchical clustering clustered 75% of the PT/AM, 47% of the PT/LR, and none of the PT/CL pairs together. A methylation-based score (MS) was defined as a clonality measure. The PT/AM set contained a high proportion of clonal pairs while PT/LR pairs were evenly split between high and low MS score, suggesting two groups: true recurrences (TR) and new primary tumors (NP). CL were classified as new tumors. MS score was significantly correlated with copy-number based scores. There was no significant difference between the metastatic-free survival of groups of patients based on different classifications. CONCLUSION: Epigenomic alterations are well suited to study clonality and track cancer progression. Methylation-based classification of TR and NP performed as well as clinical and copy-number based methods suggesting that these phenomenons are tightly linked.

Description of a large family with autosomal dominant hypercholesterolemia associated with the APOE p.Leu167del mutation.

Apolipoprotein (apo) E mutants are associated with type III hyperlipoproteinemia characterized by high cholesterol and triglycerides levels. Autosomal dominant hypercholesterolemia (ADH), due to the mutations in the LDLR, APOB, or PCSK9 genes, is characterized by an isolated elevation of cholesterol due to the high levels of low-density lipoproteins (LDLs). We now report an exceptionally large family including 14 members with ADH. Through genome-wide mapping, analysis of regional/functional candidate genes, and whole exome sequencing, we identified a mutation in the APOE gene, c.500_502delTCC/p.Leu167del, previously reported associated with sea-blue histiocytosis and familial combined hyperlipidemia. We confirmed the involvement of the APOE p.Leu167del in ADH, with (1) a predicted destabilization of an alpha-helix in the binding domain, (2) a decreased apo E level in LDLs, and (3) a decreased catabolism of LDLs. Our results show that mutations in the APOE gene can be associated with bona fide ADH.

Molecular spectrum of autosomal dominant hypercholesterolemia in France.

Autosomal Dominant Hypercholesterolemia (ADH), characterized by isolated elevation of plasmatic LDL cholesterol and premature cardiovascular complications, is associated with mutations in 3 major genes: LDLR (LDL receptor), APOB (apolipoprotein B) and PCSK9(proprotein convertase subtilisin-kexin type 9). Through the French ADH Research Network, we collected molecular data from 1358 French probands from eleven different regions in France.Mutations in the LDLR gene were identified in 1003 subjects representing 391 unique events with 46.0% missense, 14.6% frameshift, 13.6% splice, and 11.3% nonsense mutations, 9.7% major rearrangements, 3.8% small in frame deletions/insertions, and 1.0% UTR mutations. Interestingly,175 are novel mutational events and represent 45% of the unique events we identified, highlighting a specificity of the LDLR mutation spectrum in France. Furthermore, mutations in the APOB gene were identified in 89 probands and in the PCSK9 gene in 10 probands. Comparison of available clinical and biochemical data showed a gradient of severity for ADH-causing mutations:FH=PCSK9>FDB>«Others¼ genes. The respective contribution of each known gene to ADH inthis French cohort is: LDLR 73.9%, APOB 6.6%, PCSK9 0.7%. Finally, in 19.0% of the probands,no mutation was found, thus underscoring the existence of ADH mutations located in still unknown genes.

A fourth locus for autosomal dominant hypercholesterolemia maps at 16q22.1.

Autosomal dominant hypercholesterolemia (ADH) is characterized by isolated increase in plasmatic low-density lipoprotein (LDL) cholesterol levels associated with high risk of premature cardiovascular disease. Mutations in LDLR, APOB, and PCSK9 genes have been shown to cause ADH. We now report further genetic heterogeneity of ADH through the study of a large French family in which the involvement of these three genes was excluded. A genome-wide scan mapped the disease-causing gene, named HCHOLA4, at 16q22.1 in a 7.89-Mb interval containing 154 genes with a maximum LOD score of 3.9. To reduce the linked region, we genotyped 18 smaller non-LDLR/non-APOB/non-PCSK9-ADH families at the HCHOLA4 locus. Six families did not exclude linkage to the locus, but none allowed reduction of the disease interval. The 154 regional genes were sorted according to the function of the encoded protein and tissue expression profiles, and 57 genes were analyzed through sequencing of their coding region and close flanking intronic parts. No disease-causing mutation was identified in these families, particularly in the LCAT gene. Finally, our results also show the existence of other ADH genes as nine families were neither linked to LDLR, APOB, and PCSK9 genes nor to the new HCHOLA4 locus.

Novel LRP5 gene mutation in a patient with osteoporosis-pseudoglioma syndrome.

Osteoporosis-pseudoglioma syndrome (OPPG) is a rare autosomal recessive disorder characterised by severe juvenile-onset osteoporosis and congenital or early-onset blindness. This serious illness is due to mutations in the low-density lipoprotein receptor-related protein 5 (LRP5) that is a major actor in pathways involved in bone remodelling. Here, we report a novel frameshift mutation identified in a 22 year-old Tunisian boy of a consanguineous family. This patient had low bone mineral density (BMD), experienced multiple fractures during childhood and suffered ocular alterations with blindness. Direct DNA sequencing showed a homozygous 5 base pair insertion in exon 5 of the LRP5 gene. This new mutation is located in the first EGF-like domain and gives rise to a truncated protein of 384 amino acids. The functional significance of this mutation clearly indicates a loss-of-function mutation of the LRP5 gene leading to the observed OPPG phenotype. Rheumatologists must be aware of LRP5 gene that in addition to being a major gene in the mendelian disease that is OPPG syndrome seems to be involved in osteoporosis in the general population through some of its polymorphisms.