Sci Rep. 2021 Feb 12;11(1):3739. doi: 10.1038/s41598-021-83274-1.

ABSTRACT

This study addressed the hypothesis that epoxyeicosatrienoic acids (EETs) synthesized by CYP450 and catabolized by soluble epoxide hydrolase (sEH) are involved in the maintenance of renal allograft function, either directly or through modulation of cardiovascular function. The impact of single nucleotide polymorphisms (SNPs) in the sEH gene EPHX2 and CYP450 on renal and vascular function, plasma levels of EETs and peripheral blood monuclear cell sEH activity was assessed in 79 kidney transplant recipients explored at least one year after transplantation. Additional experiments in a mouse model mimicking the ischemia-reperfusion (I/R) injury suffered by the transplanted kidney evaluated the cardiovascular and renal effects of the sEH inhibitor t-AUCB administered in drinking water (10 mg/l) during 28 days after surgery. There was a long-term protective effect of the sEH SNP rs6558004, which increased EET plasma levels, on renal allograft function and a deleterious effect of K55R, which increased sEH activity. Surprisingly, the loss-of-function CYP2C9*3 was associated with a better renal function without affecting EET levels. R287Q SNP, which decreased sEH activity, was protective against vascular dysfunction while CYP2C8*3 and 2C9*2 loss-of-function SNP, altered endothelial function by reducing flow-induced EET release. In I/R mice, sEH inhibition reduced kidney lesions, prevented cardiac fibrosis and dysfunction as well as preserved endothelial function. The preservation of EET bioavailability may prevent allograft dysfunction and improve cardiovascular disease in kidney transplant recipients. Inhibition of sEH appears thus as a novel therapeutic option but its impact on other epoxyfatty acids should be carefully evaluated.

PMID:33580125 | PMC:PMC7881112 | DOI:10.1038/s41598-021-83274-1

NPJ Genom Med. 2020 Aug 3;5(1):30. doi: 10.1038/s41525-020-0135-2.

ABSTRACT

Genetic variation in genes encoding cytochrome P450 enzymes has important clinical implications for drug metabolism. Bioinformatics algorithms for genotyping these highly polymorphic genes using high-throughput sequence data and automating phenotype prediction have recently been developed. The CYP2D6 gene is often used as a model during the validation of these algorithms due to its clinical importance, high polymorphism, and structural variations. However, the validation process is often limited to common star alleles due to scarcity of reference datasets. In addition, there has been no comprehensive benchmark of these algorithms to date. We performed a systematic comparison of three star allele calling algorithms using 4618 simulations as well as 75 whole-genome sequence samples from the GeT-RM project. Overall, we found that Aldy and Astrolabe are better suited to call both common and rare diplotypes compared to Stargazer, which is affected by population structure. Aldy was the best performing algorithm in calling CYP2D6 structural variants followed by Stargazer, whereas Astrolabe had limitations especially in calling hybrid rearrangements. We found that ensemble genotyping, characterised by taking a consensus of genotypes called by all three algorithms, has higher haplotype concordance but it is prone to ambiguities whenever complete discrepancies between the tools arise. Further, we evaluated the effects of sequencing coverage and indel misalignment on genotyping accuracy. Our account of the strengths and limitations of these algorithms is extremely important to clinicians and researchers in the pharmacogenomics and precision medicine communities looking to haplotype CYP2D6 and other pharmacogenes using high-throughput sequencing data.

PMID:33579996 | DOI:10.1038/s41525-020-0135-2

NPJ Genom Med. 2020 Mar 5;5(1):9. doi: 10.1038/s41525-020-0119-2.

ABSTRACT

The genomic inter-individual heterogeneity remains a significant challenge for both clinical decision-making and the design of clinical trials. Although next-generation sequencing (NGS) is increasingly implemented in drug development and clinical trials, translation of the obtained genomic information into actionable clinical advice lags behind. Major reasons are the paucity of sufficiently powered trials that can quantify the added value of pharmacogenetic testing, and the considerable pharmacogenetic complexity with millions of rare variants with unclear functional consequences. The resulting uncertainty is reflected in inconsistencies of pharmacogenomic drug labels in Europe and the United States. In this review, we discuss how the knowledge gap for bridging pharmacogenomics into the clinics can be reduced. First, emerging methods that allow the high-throughput experimental characterization of pharmacogenomic variants combined with novel computational tools hold promise to improve the accuracy of drug response predictions. Second, tapping of large biobanks of therapeutic drug monitoring data allows to conduct high-powered retrospective studies that can validate the clinical importance of genetic variants, which are currently incompletely characterized. Combined, we are confident that these methods will improve the accuracy of drug response predictions and will narrow the gap between variant identification and its utilization for clinical decision-support.

PMID:33579994 | DOI:10.1038/s41525-020-0119-2

Mol Cancer. 2021 Feb 12;20(1):32. doi: 10.1186/s12943-021-01327-5.

ABSTRACT

In the "precision oncology" era the characterization of tumor genetic features is a pivotal step in cancer patients' management. Liquid biopsy approaches, such as analysis of cell-free DNA from plasma, represent a powerful and noninvasive strategy to obtain information about the genomic status of the tumor. Sequencing-based analyses of cell-free DNA, currently performed with second generation sequencers, are extremely powerful but poorly scalable and not always accessible also due to instrumentation costs. Third generation sequencing platforms, such as Nanopore sequencers, aim at overcoming these obstacles but, unfortunately, are not designed for cell-free DNA analysis.Here we present a customized workflow to exploit low-coverage Nanopore sequencing for the detection of copy number variations from plasma of cancer patients. Whole genome molecular karyotypes of 6 lung cancer patients and 4 healthy subjects were successfully produced with as few as 2 million reads, and common lung-related copy number alterations were readily detected.This is the first successful use of Nanopore sequencing for copy number profiling from plasma DNA. In this context, Nanopore represents a reliable alternative to Illumina sequencing, with the advantages of minute instrumentation costs and extremely short analysis time.The availability of protocols for Nanopore-based cell-free DNA analysis will make this analysis finally accessible, exploiting the full potential of liquid biopsy both for research and clinical purposes.

PMID:33579306 | PMC:PMC7881593 | DOI:10.1186/s12943-021-01327-5

NUTRITION AND MINERAL CONTENT IN HUMAN TEETH THROUGH THE CENTURIES.

Arch Oral Biol. 2021 Feb 04;124:105075

Authors: Nedoklan S, Knezovic Z, Knezovic N, Sutlovic D

Abstract
OBJECTIVES: The objectives of the study were: (i) to compare mineral values of calcium, phosphorus, magnesium, zinc and their ratios, in teeth from Croatian populations that lived in different historical periods, namely the Medieval period, the early 20th century, and the 21 st century; and (ii) to elucidate the influence of diet and lifestyle on tooth quality in these groups.
DESIGN: Determination of mineral content (Ca, Mg, P and Zn) in 294 teeth from three different periods of history (Medieval Period [G1], Second World War period [G2] and the contemporary period [G3]) using atomic absorption spectrometer and UV/VIS spectrometer methods.
RESULTS: Our results showed that the mineral content in teeth has changed over the centuries. Between analysed samples from all groups, there were significant differences in the elemental content as well as in the interrelationship of the elements. The largest differences were observed in the mean values of magnesium and zinc concentrations while smaller differences were observed for changes in calcium and phosphorus.
CONCLUSIONS: From the obtained results, it is evident that there are changes in the tooth mineral composition in specimens centuries apart that could be a reflection of changes in eating habits, food quality and the environment. In addition to differences in individual elements, differences in their mutual ratios were also observed.

PMID: 33571733 [PubMed - as supplied by publisher]

Exogenous activation of toll-like receptor 5 signaling mitigates acetaminophen-induced hepatotoxicity in mice.

Toxicol Lett. 2021 Feb 08;:

Authors: Zhou Z, Qi J, Yang D, Yang MS, Jeong H, Lim CW, Kim JW, Kim B

Abstract
Acetaminophen (APAP) poisoning is the most common cause of drug-induced acute liver injury (ALI). Our results showed that toll-like receptor 5 (TLR5) was abundantly expressed in hepatocytes and dramatically downregulated in the toxic mouse livers. Hence, we herein investigated the role of TLR5 signaling after APAP overdose. Mice were intraperitoneally (i.p.) injected with APAP to induce ALI, and then injected with flagellin at one hour after APAP administration. Flagellin attenuated APAP-induced ALI based on decreased histopathologic lesions, serum biochemical, oxidative stress, and inflammation. Furthermore, the protective effects of flagellin were abolished by TH1020 (a TLR5 antagonist) treatment. These results suggest that flagellin exerted protective effects on ALI via TLR5 activation. Mechanistically, flagellin injection promoted the translocation of nuclear factor erythroid 2-related factor 2 (Nrf2) to the nucleus in hepatocytes. Consistent with the in vivo results, flagellin increased the activation of Nrf2 in hepatocytes, resulting in decreased APAP toxicity. ML385, a selective inhibitor of Nrf2, abolished the flagellin-mediated hepatoprotective effects in damaged livers and hepatocytes. Additionally, the flagellin-induced Nrf2 translocation was dependent upon the activation of TLR5-JNK/p38 pathways. These findings suggest that TLR5 signaling-induced Nrf2 activation, at least partially, contributed to the protection against APAP-induced ALI by flagellin treatment.

PMID: 33571619 [PubMed - as supplied by publisher]

Circulating nuclear DNA structural features, origins, and complete size profile revealed by fragmentomics.

JCI Insight. 2021 Feb 11;:

Authors: Sanchez C, Roch B, Mazard T, Blache P, Al Amir Dache Z, Pastor B, Pisareva E, Tanos R, Thierry AR

Abstract
To unequivocally address their unresolved intimate structures in blood, we scrutinized the size distribution of circulating cell-free DNA (cfDNA) using whole genome sequencing (WGS) from both double- and single-strand DNA library preparations (DSP and SSP), as well as using Q-PCR. The size profile in healthy individuals was remarkably homogenous when using either DSP sequencing (DSP-S) or SSP sequencing (SSP-S). Our findings also confirmed that cfDNA size profile shows a characteristic nucleosome fragmentation pattern. Overall, our data indicate that the proportion of cfDNA inserted in mono-nucleosomes, di-nucleosomes and chromatin of higher molecular size (>1,000bp) can be estimated as 67.5-80%, 9.4-11.5% and 8.5-21.0%, respectively. Thus, our data on WGS (N=7) and Q-PCR (N=116 taken together suggests that only a minor proportion of cfDNA is bigger than that existing in mono-nucleosome or transcription factor complexes circulating in blood. Although DNA on single chromatosomes or mono-nucleosomes is detectable, our data revealed that cfDNA is highly nicked (97-98%) on those structures, which appear to be subjected to continuous nuclease activity in the bloodstream. Fragments analysis allows the distinction of cfDNA of different origins: first, cfDNA size profile analysis may be useful in cfDNA extract quality control; second, subtle but reliable differences between healthy metastatic colorectal cancer (mCRC) patients and healthy individuals vary with the proportion of malignant cell-derived cfDNA in plasma extracts, pointing to a higher degree of cfDNA fragmentation and nuclease activity in samples with high malignant cell cfDNA content. Size profile analysis, or 'fragmentomics', has shown significant potential to improve diagnostics and cancer screening.

PMID: 33571170 [PubMed - as supplied by publisher]

GH deficiency and insensitivity in children and adults.

Rev Endocr Metab Disord. 2021 Feb 10;:

Authors: Johannsson G, Kopchick JJ

Abstract
This thematic review includes short reviews on GH deficiency and insensitivity in children and adults from basic science to clinical significance.

PMID: 33569699 [PubMed - as supplied by publisher]

Pharmacogenetics Guidelines: Overview and Comparison of the DPWG, CPIC, CPNDS, and RNPGx Guidelines.

Front Pharmacol. 2020;11:595219

Authors: Abdullah-Koolmees H, van Keulen AM, Nijenhuis M, Deneer VHM

Abstract
Many studies have shown that the efficacy and risk of side effects of drug treatment is influenced by genetic variants. Evidence based guidelines are essential for implementing pharmacogenetic knowledge in daily clinical practice to optimize pharmacotherapy of individual patients. A literature search was performed to select committees developing guidelines with recommendations being published in English. The Dutch Pharmacogenetics Working Group (DPWG), the Clinical Pharmacogenetics Implementation Consortium (CPIC), the Canadian Pharmacogenomics Network for Drug Safety (CPNDS), and the French National Network (Réseau) of Pharmacogenetics (RNPGx) were selected. Their guidelines were compared with regard to the methodology of development, translation of genotypes to predicted phenotypes, pharmacotherapeutic recommendations and recommendations on genotyping. A detailed overview of all recommendations for gene-drug combinations is given. The committees have similar methodologies of guideline development. However, the objectives differed at the start of their projects, which have led to unique profiles and strengths of their guidelines. DPWG and CPIC have a main focus on pharmacotherapeutic recommendations for a large number of drugs in combination with a patient's genotype or predicted phenotype. DPWG, CPNDS and RNPGx also recommend on performing genetic testing in daily clinical practice, with RNPGx even describing specific clinical settings or medical conditions for which genotyping is recommended. Discordances exist, however committees also initiated harmonizing projects. The outcome of a consensus project was to rename "extensive metabolizer (EM)" to "normal metabolizer (NM)". It was decided to translate a CYP2D6 genotype with one nonfunctional allele (activity score 1.0) into the predicted phenotype of intermediate metabolizer (IM). Differences in recommendations are the result of the methodologies used, such as assessment of dose adjustments of tricyclic antidepressants. In some cases, indication or dose specific recommendations are given for example for clopidogrel, codeine, irinotecan. The following drugs have recommendations on genetic testing with the highest level: abacavir (HLA), clopidogrel (CYP2C19), fluoropyrimidines (DPYD), thiopurines (TPMT), irinotecan (UGT1A1), codeine (CYP2D6), and cisplatin (TPMT). The guidelines cover many drugs and genes, genotypes, or predicted phenotypes. Because of this and their unique features, considering the totality of guidelines are of added value. In conclusion, many evidence based pharmacogenetics guidelines with clear recommendations are available for clinical decision making by healthcare professionals, patients and other stakeholders.

PMID: 33568995 [PubMed]

LincRNA-immunity landscape analysis identifies EPIC1 as a regulator of tumor immune evasion and immunotherapy resistance.

Sci Adv. 2021 Feb;7(7):

Authors: Guo W, Wang Y, Yang M, Wang Z, Wang Y, Chaurasia S, Wu Z, Zhang M, Yadav GS, Rathod S, Concha-Benavente F, Fernandez C, Li S, Xie W, Ferris RL, Kammula US, Lu B, Yang D

Abstract
Through an integrative analysis of the lincRNA expression and tumor immune response in 9,626 tumor samples across 32 cancer types, we developed a lincRNA-based immune response (LIMER) score that can predict the immune cells infiltration and patient prognosis in multiple cancer types. Our analysis also identified tumor-specific lincRNAs, including EPIC1, that potentially regulate tumor immune response in multiple cancer types. Immunocompetent mouse models and in vitro co-culture assays demonstrated that EPIC1 induces tumor immune evasion and resistance to immunotherapy by suppressing tumor cell antigen presentation. Mechanistically, lincRNA EPIC1 interacts with the histone methyltransferase EZH2, leading to the epigenetic silencing of IFNGR1, TAP1/2, ERAP1/2, and MHC-I genes. Genetic and pharmacological inhibition of EZH2 abolish EPIC1's immune-related oncogenic effect and its suppression of interferon-γ signaling. The EPIC1-EZH2 axis emerges as a potential mechanism for tumor immune evasion that can serve as therapeutic targets for immunotherapy.

PMID: 33568470 [PubMed - in process]

DRUGPATH: The Drug Gene Pathway Meta-Database.

Int J Mol Sci. 2020 Apr 30;21(9):

Authors: Jaundoo R, Craddock TJA

Abstract
The complexity of modern-day diseases often requires drug treatment therapies consisting of multiple pharmaceutical interventions, which can lead to adverse drug reactions for patients. A priori prediction of these reactions would not only improve the quality of life for patients but also save both time and money in regards to pharmaceutical research. Consequently, the drug-gene-pathway (DRUGPATH) meta-database was developed to map known interactions between drugs, genes, and pathways among other information in order to easily identify potential adverse drug events. DRUGPATH utilizes expert-curated sources such as PharmGKB, DrugBank, and the FDA's NDC database to identify known as well as previously unknown/overlooked relationships, and currently contains 12,940 unique drugs, 3933 unique pathways, 5185 unique targets, and 3662 unique genes. Moreover, there are 59,561 unique drug-gene interactions, 77,808 unique gene-pathway interactions, and over 1 million unique drug-pathway interactions.

PMID: 32365960 [PubMed - indexed for MEDLINE]

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pharmacogenomics

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11 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

pharmacogenomics

These pubmed results were generated on 2021/02/11

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Front Pharmacol. 2021 Jan 11;11:612573. doi: 10.3389/fphar.2020.612573. eCollection 2020.

ABSTRACT

Chronic myeloid leukemia (CML) is a myeloid stem cell neoplasm characterized by an expansion of myeloid progenitor cells and the presence of BCR-ABL1 oncoprotein. Since the introduction of specific BCR-ABL1 tyrosine kinase inhibitors (TKI), overall survival has improved significantly. However, under long-term therapy patients may have residual disease that originates from TKI-resistant leukemic stem cells (LSC). In this work, we analyzed the miRNome of LSC-enriched CD34+CD38-CD26+ and normal hematopoietic stem cells (HSC) fractions obtained from the same chronic phase (CP) CML patients, and stem and progenitor cells obtained from healthy donors (HD) by next-generation sequencing. We detected a global decrease of microRNA levels in LSC-enriched CD34+CD38-CD26+ and HSC fractions from CML-CP patients, and decreased levels of microRNAs and snoRNAs from a genomic cluster in chromosome 14, suggesting a mechanism of silencing of multiple non-coding RNAs. Surprisingly, HSC from CML-CP patients, despite the absence of BCR-ABL1 expression, showed an altered miRNome. We confirmed by RT-qPCR that the levels of miR-196a-5p were increased more than nine-fold in CD26+ (BCR-ABL1 + ) vs. CD26- (BCR-ABL1 -) CD34+CD38- fractions from CML-CP patients at diagnosis, and in silico analysis revealed a significant association to lipid metabolism and hematopoiesis functions. In the light of recent descriptions of increased oxidative metabolism in CML LSC-enriched fractions, these results serve as a guide for future functional studies that evaluate the role of microRNAs in this process. Metabolic vulnerabilities in LSCs open the road for new therapeutic strategies. This is the first report of the miRNome of CML-CP CD34+CD38- fractions that distinguishes between CD26+ (BCR-ABL1 + ) and their CD26- (BCR-ABL1 - ) counterparts, providing valuable data for future studies.

PMID:33569005 | PMC:PMC7869017 | DOI:10.3389/fphar.2020.612573

Publisher Correction: Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability.

Nat Commun. 2021 Feb 08;12(1):995

Authors: Lagou V, Mägi R, Hottenga JJ, Grallert H, Perry JRB, Bouatia-Naji N, Marullo L, Rybin D, Jansen R, Min JL, Dimas AS, Ulrich A, Zudina L, Gådin JR, Jiang L, Faggian A, Bonnefond A, Fadista J, Stathopoulou MG, Isaacs A, Willems SM, Navarro P, Tanaka T, Jackson AU, Montasser ME, O'Connell JR, Bielak LF, Webster RJ, Saxena R, Stafford JM, Pourcain BS, Timpson NJ, Salo P, Shin SY, Amin N, Smith AV, Li G, Verweij N, Goel A, Ford I, Johnson PCD, Johnson T, Kapur K, Thorleifsson G, Strawbridge RJ, Rasmussen-Torvik LJ, Esko T, Mihailov E, Fall T, Fraser RM, Mahajan A, Kanoni S, Giedraitis V, Kleber ME, Silbernagel G, Meyer J, Müller-Nurasyid M, Ganna A, Sarin AP, Yengo L, Shungin D, Luan J, Horikoshi M, An P, Sanna S, Boettcher Y, Rayner NW, Nolte IM, Zemunik T, Iperen EV, Kovacs P, Hastie ND, Wild SH, McLachlan S, Campbell S, Polasek O, Carlson O, Egan J, Kiess W, Willemsen G, Kuusisto J, Laakso M, Dimitriou M, Hicks AA, Rauramaa R, Bandinelli S, Thorand B, Liu Y, Miljkovic I, Lind L, Doney A, Perola M, Hingorani A, Kivimaki M, Kumari M, Bennett AJ, Groves CJ, Herder C, Koistinen HA, Kinnunen L, Faire U, Bakker SJL, Uusitupa M, Palmer CNA, Jukema JW, Sattar N, Pouta A, Snieder H, Boerwinkle E, Pankow JS, Magnusson PK, Krus U, Scapoli C, de Geus EJCN, Blüher M, Wolffenbuttel BHR, Province MA, Abecasis GR, Meigs JB, Hovingh GK, Lindström J, Wilson JF, Wright AF, Dedoussis GV, Bornstein SR, Schwarz PEH, Tönjes A, Winkelmann BR, Boehm BO, März W, Metspalu A, Price JF, Deloukas P, Körner A, Lakka TA, Keinanen-Kiukaanniemi SM, Saaristo TE, Bergman RN, Tuomilehto J, Wareham NJ, Langenberg C, Männistö S, Franks PW, Hayward C, Vitart V, Kaprio J, Visvikis-Siest S, Balkau B, Altshuler D, Rudan I, Stumvoll M, Campbell H, van Duijn CM, Gieger C, Illig T, Ferrucci L, Pedersen NL, Pramstaller PP, Boehnke M, Frayling TM, Shuldiner AR, Peyser PA, Kardia SLR, Palmer LJ, Penninx BW, Meneton P, Harris TB, Navis G, Harst PV, Smith GD, Forouhi NG, Loos RJF, Salomaa V, Soranzo N, Boomsma DI, Groop L, Tuomi T, Hofman A, Munroe PB, Gudnason V, Siscovick DS, Watkins H, Lecoeur C, Vollenweider P, Franco-Cereceda A, Eriksson P, Jarvelin MR, Stefansson K, Hamsten A, Nicholson G, Karpe F, Dermitzakis ET, Lindgren CM, McCarthy MI, Froguel P, Kaakinen MA, Lyssenko V, Watanabe RM, Ingelsson E, Florez JC, Dupuis J, Barroso I, Morris AP, Prokopenko I, Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC)

PMID: 33558525 [PubMed]

Integrative Genomic-Epigenomic Analysis of Clozapine-Treated Patients with Refractory Psychosis.

Pharmaceuticals (Basel). 2021 Feb 04;14(2):

Authors: Mayén-Lobo YG, Martínez-Magaña JJ, Pérez-Aldana BE, Ortega-Vázquez A, Genis-Mendoza AD, Dávila-Ortiz de Montellano DJ, Soto-Reyes E, Nicolini H, López-López M, Monroy-Jaramillo N

Abstract
Clozapine (CLZ) is the only antipsychotic drug that has been proven to be effective in patients with refractory psychosis, but it has also been proposed as an effective mood stabilizer; however, the complex mechanisms of action of CLZ are not yet fully known. To find predictors of CLZ-associated phenotypes (i.e., the metabolic ratio, dosage, and response), we explore the genomic and epigenomic characteristics of 44 patients with refractory psychosis who receive CLZ treatment based on the integration of polygenic risk score (PRS) analyses in simultaneous methylome profiles. Surprisingly, the PRS for bipolar disorder (BD-PRS) was associated with the CLZ metabolic ratio (pseudo-R2 = 0.2080, adjusted p-value = 0.0189). To better explain our findings in a biological context, we assess the protein-protein interactions between gene products with high impact variants in the top enriched pathways and those exhibiting differentially methylated sites. The GABAergic synapse pathway was found to be enriched in BD-PRS and was associated with the CLZ metabolic ratio. Such interplay supports the use of CLZ as a mood stabilizer and not just as an antipsychotic. Future studies with larger sample sizes should be pursued to confirm the findings of this study.

PMID: 33557049 [PubMed]

Pharmacogenomic Biomarkers of Follicle-Stimulating Hormone Receptor Malfunction in Females with Impaired Ovarian Response-A Genetic Survey.

J Clin Med. 2021 Jan 06;10(2):

Authors: Tafazoli A, Wołczyński S, Wawrusiewicz-Kurylonek N, Esmaeili SA, Miltyk W

Abstract
Follicle-stimulating hormone receptor (FSHR) plays an essential role as one of the most important molecules in response to some of infertility related medications. Impaired ovarian reserve and poor response to such treatments are partially dependent on the FSHR molecule itself. However, the function and drug sensitivity for this receptor may change due to various allele and polymorphisms in the FSHR gene. Studies indicated some of the FSHR-mediated treatments utilized in clinical centers display different outcomes in specific populations, which may arise from FSHR altered genotypes in certain patients. To support the increased demands for reaching the personalized drug and hormone therapy in clinics, focusing on actionable variants through Pharmacogenomic analysis of this receptor may be necessary. The current study tries to display a perspective view on genetic assessments for Pharmacogenomic profiling of the FSHR gene via providing a systematic and critical overview on the genetics of FSHR and its diverse responses to ligands for infertility treatment in females with impaired ovarian responses and show the potential effects of the patient genetic make-up on related binding substances efficacy. All identified functional drug-related alleles were selected through a comprehensive literature search and analyzed. Advanced technologies for the genetic evaluation of them are also discussed properly.

PMID: 33561079 [PubMed - as supplied by publisher]

AI-aided Precision Medicine against COVID-19: Strategic Areas of Research and Development.

J Med Internet Res. 2021 Jan 31;:

Authors: Santus E, Marino N, Cirillo D, Chersoni E, Montagud A, Santuccione Chada A, Valencia A, Hughes K, Lindvall C

Abstract
UNSTRUCTURED: Modern Artificial Intelligence (AI) technologies can play a key role in preventing and monitoring the present and the future epidemics. Here, we provide an overview of recently published literature on the COVID-19 pandemics in four strategic areas: (1) triage, diagnosis and risk prediction; (2) drug repurposing and development; (3) pharmacogenomics and vaccines; (4) mining of medical literature. In accordance to the newly proposed value-based care paradigm, we notice that AI-powered healthcare is essential to make public health systems able to efficiently handle future outbreaks and improve patient outcomes.

PMID: 33560998 [PubMed - as supplied by publisher]

Pharmacogenomics of the Efficacy and Safety of Colchicine in COLCOT.

Circ Genom Precis Med. 2021 Feb 09;:

Authors: Dubé MP, Legault MA, Lemaçon A, Lemieux Perreault LP, Fouodjio R, Waters DD, Kouz S, Pinto FJ, Maggioni AP, Diaz R, Berry C, Koenig W, Lopez-Sendon J, Gamra H, Kiwan GS, Asselin G, Provost S, Barhdadi A, Sun M, Cossette M, Blondeau L, Mongrain I, Dubois A, Rhainds D, Bouabdallaoui N, Samuel M, de Denus S, L'Allier PL, Guertin MC, Roubille F, Tardif JC

Abstract
Background - The randomized, placebo-controlled COLchicine Cardiovascular Outcomes Trial (COLCOT) has shown the benefits of colchicine 0.5 mg daily to lower the rate of ischemic cardiovascular events in patients with a recent myocardial infarction. Here, we conducted a post-hoc pharmacogenomic study of COLCOT with the aim to identify genetic predictors of the efficacy and safety of treatment with colchicine. Methods - There were 1522 participants of European descent from the COLCOT trial available for the pharmacogenomic study of COLCOT trial. The pharmacogenomic study's primary cardiovascular (CV) endpoint was defined as for the main trial, as time to first occurrence of CV death, resuscitated cardiac arrest, myocardial infarction, stroke or urgent hospitalization for angina requiring coronary revascularization. The safety endpoint was time to the first report of gastrointestinal events. Patients' DNA was genotyped using the Illumina Global Screening array followed by imputation. We performed a genome-wide association study (GWAS) in colchicine-treated patients. Results - None of the genetic variants passed the GWAS significance threshold for the primary CV endpoint conducted in 702 patients in the colchicine arm who were compliant to medication. The GWAS for gastrointestinal events was conducted in all 767 patients in the colchicine arm and found two significant association signals, one with lead variant rs6916345 (hazard ratio (HR)=1.89, 95% confidence interval (CI) 1.52-2.35, P=7.41×10-9) in a locus which colocalizes with Crohn's disease, and one with lead variant rs74795203 (HR= 2.51, 95% CI 1.82-3.47; P=2.70×10-8), an intronic variant in gene SEPHS1. The interaction terms between the genetic variants and treatment with colchicine versus placebo were significant. Conclusions - We found two genomic regions associated with gastrointestinal events in patients treated with colchicine. Those findings will benefit from replication to confirm that some patients may have genetic predispositions to lower tolerability of treatment with colchicine.

PMID: 33560138 [PubMed - as supplied by publisher]

Epigenetic Mechanisms of Resistance to Immune Checkpoint Inhibitors.

Biomolecules. 2020 07 16;10(7):

Authors: Perrier A, Didelot A, Laurent-Puig P, Blons H, Garinet S

Abstract
Immune checkpoint inhibitors (ICIs) have demonstrated to be highly efficient in treating solid tumors; however, many patients have limited benefits in terms of response and survival. This rapidly led to the investigation of combination therapies to enhance response rates. Moreover, predictive biomarkers were assessed to better select patients. Although PD-L1 expression remains the only validated marker in clinics, molecular profiling has brought valuable information, showing that the tumor mutation load and microsatellite instability (MSI) status were associated to higher response rates in nearly all cancer types. Moreover, in lung cancer, EGFR and MET mutations, oncogene fusions or STK11 inactivating mutations were associated with low response rates. Cancer progression towards invasive phenotypes that impede immune surveillance relies on complex regulatory networks and cell interactions within the tumor microenvironment. Epigenetic modifications, such as the alteration of histone patterns, chromatin structure, DNA methylation status at specific promoters and changes in microRNA levels, may alter the cell phenotype and reshape the tumor microenvironment, allowing cells to grow and escape from immune surveillance. The objective of this review is to make an update on the identified epigenetic changes that target immune surveillance and, ultimately, ICI responses, such as histone marks, DNA methylation and miR signatures. Translational studies or clinical trials, when available, and potential epigenetic biomarkers will be discussed as perspectives in the context of combination treatment strategies to enhance ICI responses in patients with solid tumors.

PMID: 32708698 [PubMed - indexed for MEDLINE]