Epigenetic Regulation Of Gene Expression Research Articles

Development of trofinetide for the treatment of Rett syndrome: from bench to bedside.

Rett syndrome (RTT) is rare neurodevelopmental disorder caused by mutations in the MECP2 gene that encodes methyl-CpG-binding protein 2 (MeCP2), a DNA-binding protein with roles in epigenetic regulation of gene expression. Functional loss of MeCP2 results in abnormal neuronal maturation and plasticity, characterized by loss of verbal communication and loss of fine and gross motor function, among others. Trofinetide, a synthetic analog of glycine-proline-glutamate, was approved by the US Food and Drug Administration for the treatment of RTT in adult and pediatric patients aged 2years and older. Here, we present the development of trofinetide from bench research to clinical studies and emphasize how the collaboration between academia, the pharmaceutical industry, and patient advocacy led to the recent approval. The bench-to-bedside development of trofinetide underscores the value of collaboration between these groups in the development and approval of treatments for rare diseases.

Histone deacetylase OsHDA716 represses rice chilling tolerance by deacetylating OsbZIP46 to reduce its transactivation function and protein stability.

Low temperature is a major environmental factor limiting plant growth and crop production. Epigenetic regulation of gene expression is important for plant adaptation to environmental changes, whereas the epigenetic mechanism of cold signaling in rice (Oryza sativa) remains largely elusive. Here, we report that the histone deacetylase (HDAC) OsHDA716 represses rice cold tolerance by interacting with and deacetylating the transcription factor OsbZIP46. The loss-of-function mutants of OsHDA716 exhibit enhanced chilling tolerance, compared with the wild-type plants, while OsHDA716 overexpression plants show chilling hypersensitivity. On the contrary, OsbZIP46 confers chilling tolerance in rice through transcriptionally activating OsDREB1A and COLD1 to regulate cold-induced calcium influx and cytoplasmic calcium elevation. Mechanistic investigation showed that OsHDA716-mediated OsbZIP46 deacetylation in the DNA-binding domain reduces the DNA-binding ability and transcriptional activity as well as decreasing OsbZIP46 protein stability. Genetic evidence indicated that OsbZIP46 deacetylation mediated by OsHDA716 reduces rice chilling tolerance. Collectively, these findings reveal that the functional interplay between the chromatin regulator and transcription factor fine-tunes the cold response in plant and uncover a mechanism by which HDACs repress gene transcription through deacetylating nonhistone proteins and regulating their biochemical functions.

Revealing the transitory and local effect of zebularine on development and on proteome dynamics of Salix purpurea.

DNA methylation plays major roles in the epigenetic regulation of gene expression, transposon and transcriptional silencing, and DNA repair, with implications in developmental processes and phenotypic plasticity. Relevantly for woody species, DNA methylation constitutes a regulative layer in cell wall dynamics associated with xylogenesis. The use of methyltransferase and/or demethylase inhibitors has been proven informative to shed light on the methylome dynamics behind the regulation of these processes. The present work employs the cytidine analog zebularine to inhibit DNA methyltransferases and induce DNA hypomethylation in Salix purpurea plantlets grown in vitro and in soil. An integrative approach was adopted to highlight the effects of zebularine on proteomic dynamics, revealing age-specific (3 weeks of in vitro culture and 1 month of growth in soil) and tissue-specific (stem and root) effects. After 3 weeks of recovery from zebularine treatment, a decrease of 5-mC levels was observed in different genomic contexts in the roots of explants that were exposed to zebularine, whereas a functionally heterogeneous subset of protein entries was differentially accumulated in stem samples, including entries related to cell wall biosynthesis, tissue morphogenesis, and hormonal regulation. Significant proteomic remodeling was revealed in the development from in vitro to in-soil culture, but no significant changes in 5-mC levels were observed. The identification of tissue-specific proteomic hallmarks in combination with hypomethylating agents provides new insights into the role of DNA methylation and proteome in early plant development in willow species. Proteomic data are available via ProteomeXchange with identifier PXD045653. WGBS data are available under BioProject accession PRJNA889596.

Cold-induced deposition of bivalent H3K4me3-H3K27me3 modification and nucleosome depletion in Arabidopsis.

Epigenetic regulation of gene expression plays a crucial role in plant development and environmental adaptation. The H3K4me3 and H3K27me3 have not only been discovered in the regulation of gene expression in multiple biological processes but also in responses to abiotic stresses in plants. However, evidence for the presence of both H3K4me3 and H3K27me3 on the same nucleosome is sporadic. Cold-induced deposition of bivalent H3K4me3-H3K27me3 modifications and nucleosome depletion over a considerable number of active genes is documented in potato tubers and provides clues on an additional role of the bivalent modifications. Limited by the available information of genes encoding PcG/TrxG proteins as well as their corresponding mutants in potatoes, the molecular mechanism underlying the cold-induced deposition of the bivalent mark remains elusive. In this study, we found a similar deposition of the bivalent H3K4me3-H3K27me3 mark over 2129 active genes in cold-treated Arabidopsis Col-0 seedlings. The expression levels of the bivalent mark-associated genes tend to be independent of bivalent modification levels. However, these genes were associated with greater chromatin accessibility, presumably to provide a distinct chromatin environment for gene expression. In mutants clf28 and lhp1, failure to deposit H3K27me3 in active genes upon cold treatment implies that the CLF is potentially involved in cold-induced deposition of H3K27me3, with assistance from LHP1. Failure to deposit H3K4me3 during cold treatment in atx1-2 suggests a regulatory role of ATX1 in the deposition of H3K4me3. In addition, we observed a cold-induced global reduction in nucleosome occupancy, which is potentially mediated by LHP1 in an H3K27me3-dependent manner.

Preventing retinal homocysteine dysregulation protects against retinal ganglion cell death

Glaucoma, the most common cause of irreversible blindness, is characterized by progressive dysfunction and loss of retinal ganglion cells. There are no neuroprotective therapies. Metabolic dysfunction is an emerging pathophysiological mechanism in glaucoma with widespread changes to energy homeostasis, yet little is known about non‐energy metabolism. We recently identified elevated retinal homocysteine as a strong early metabolomic signature in a rat model of glaucoma. We tested whether local elevation of homocysteine to the retina compounded glaucoma in the rat model by artificially rising homocysteine through intravitreal injection. Short‐term elevation of homocysteine (from 1 to 15 μM, as has been detected in the vitreous of diabetic retinopathy patients) either alone or in addition to glaucoma does not worsen retinal ganglion cell death, suggesting that local elevation of homocysteine does not contribute to retinal ganglion cell degeneration, but may be an indicator of wider metabolic dysfunction. Homocysteine is central to one‐carbon metabolism, an anabolic pathway with an essential role in generation of methionine and methyl donors (necessary for the epigenetic regulation of gene expression), and glutathione (antioxidant). In a mouse model of glaucoma, we identified early‐ and sustained‐dysregulation of genes involved in one‐carbon metabolism in whole retina. In retinal ganglion cells, a number of these genes change prior to detectable neurodegeneration. These pathways require vitamin B6 and B12 as essential cofactors, and folic acid (B9) and choline are essential precursors, for the metabolism of homocysteine. Genes involved in the transport and utilization of these cofactors and precursors were also significantly dysregulated in the retina, further supporting dysfunctional homocysteine metabolism. Dietary deficiency in these leads to homocysteine accumulation and are well associated with optic neuropathies. We hypothesize that local retinal deficiency in these may contribute to dysfunction in one‐carbon metabolism and impact wider retinal ganglion cell homeostasis. To test this hypothesis, we first supplemented the drinking water of mice with B6 (4.5 mg/kg), folic acid (B9) (1.5 mg/kg), cobalamin (B12) (20 μg/kg), and choline (750 mg/kg) as a prophylactic treatment 7 days prior to intravitreal homocysteine injection. We used a supraphysiological dose of homocysteine (500 μM) that causes spontaneous death of ~10% of retinal ganglion cell death after 7 days in untreated animals. Pre‐treated animals were completely protected from retinal ganglion cell death. Next, we pre‐treated rats in the same way for 7 days prior to induction of our glaucoma model. In untreated rats there was a ~ 40% loss of retinal ganglion cells after 14 days, and this was significantly mitigated in pre‐treated rats (only ~25% loss), demonstrating that these cofactors can provide moderate neuroprotection in a complex, multifactorial neurodegenerative context.

DNA methylation differences in genes associated with human personal disorders and deviant behavior.

Epigenetic regulation of gene expression is involved in the progression of mental disorders, including deviant behavior, brain developmental, and personality disorders. The large number of genes has been studied for their activity association with stress and depression; however, the obtained results for the majority of these genes are contradictory. The aim of our study was to investigate the possible contribution of methylation level changes to the development of personality disorders and deviant behavior. A systematic study of CpG Islands in 21 target regions, including the promoter and intron regions of the 12 genes was performed in DNA samples extracted from peripheral blood cells, to obtain an overview of their methylation status. High-throughput sequencing of converted DNA samples was performed and calling of the methylation sites on the "original top strand" in CpG islands was carried out in the Bismark pipeline. The initial methylation profile of 77 patients and 48 controls samples revealed a significant difference in 7 CpG sites in 6 genes. The most significant hypermethylation was found for the target sites of the HTR2A (p-value = 1.2 × 10-13) and OXTR (p-value = 2.3 × 10-7) genes. These data support the previous reports that alterations in DNA methylation may play an important role in the dysregulation of gene expression associated with personality disorders and deviant behavior, and confirm their potential use as biomarkers to improve thediagnosis, prognosis, and assessment of response to treatment.

Regulatory mechanisms of circular RNAs during human mesenchymal stem cell osteogenic differentiation.

Human osteogenic differentiation is a complex and well-orchestrated process which involves a plethora of molecular players and cellular processes. A growing number of studies have underlined that circular RNAs (circRNAs) play an important regulatory role during human osteogenic differentiation. CircRNAs are single-stranded, covalently closed non-coding RNA molecules that are acquiring increased attention as epigenetic regulators of gene expression. Given their intrinsic high conformational stability, abundance, and specificity, circRNAs can undertake various biological activities in order to regulate multiple cellular processes, including osteogenic differentiation. The most recent evidence indicates that circRNAs control human osteogenesis by preventing the inhibitory activity of miRNAs on their downstream target genes, using a competitive endogenous RNA mechanism. The aim of this review is to draw attention to the currently known regulatory mechanisms of circRNAs during human osteogenic differentiation. Specifically, we provide an understanding of recent advances in research conducted on various human mesenchymal stem cell types that underlined the importance of circRNAs in regulating osteogenesis. A comprehensive understanding of the underlying regulatory mechanisms of circRNA in osteogenesis will improve knowledge on the molecular processes of bone growth, resulting in the potential development of novel preclinical and clinical studies and the discovery of novel diagnostic and therapeutic tools for bone disorders.

Epigenetic perspective on atherosclerotic cardiovascular diseases: The holistic principle of systems biology and epigenetic reasoning

Atherosclerosis and coronary artery disease are the main causes of impairment and cardiac death, placing a significant burden on our health-care system. This review focuses on elucidating the involvement of various epigenetic mechanisms in the genesis and progression of cardiovascular diseases (CVDs), particularly chronic CVDs. The deregulation of epigenetic mechanisms plays a crucial role in the progression of CVDs, prompting exploration into novel preventive approaches. Advancements in molecular procedures, network-based approaches, and data analysis have identified new targets in CVDs, permitting the utilization of individualized epigenetic factors for personalized diagnosis and treatment. While promising for improving diagnostic and prognostic assessments, the clinical implementation of epigenetic biomarkers lags behind. Multicenter clinical documentation in a large sample population is crucial to confidently ascertain the clinical utility of specific epigenetic biomarkers. Of particular interest is the interplay between epigenetics and the conflict between the gene-based reductionist theory and the holistic principle of systems biology (SB). The holistic principle analyzes the structural organization and regulation of biological networks, influencing the genesis and progression of complex cardiac diseases like CVDs. This review emphasizes the complexity of CVDs, elucidates the interrelationship between disease networks and epigenetic mechanisms, and highlights the importance of the holistic principle of SB, coupled with artificial intelligence, in clarifying this interrelationship. The constant and uninterrupted epigenetic impact holds immense potential for advancing our understanding of disease progression and treatment across cells and tissues. Despite these advancements, the full integration of the epigenetic impact into medical practice remains incomplete, with limited utilization in clinical applications. Nevertheless, it is likely that in the near future, the epigenetic regulation of gene expression, with its lifelong and extended effects on health, will become an integral part of everyday clinical practice.

Study of the association of polymorphisms of the folate cycle enzyme gene with the degree of cognitive and affective disorders in patients in the post-covid period

Recently, molecular genetic studies have become widespread, and demonstrated the importance of DNA and histone methylation processes in the epigenetic regulation of gene expression. The aim of this study was to detect the association of polymorphisms of the folate cycle enzyme gene methylenetetrahydrofolate reductase (MTHGFR) with the degree of cognitive and affective disorders and the serum level of homocysteine and folic acid in 41 post-covid patients. Hematological and laboratory indices, serum concentration of C-reactive protein, D-dimer, homocysteine and folic acid were determined. MTHGFR polymorphisms for C677T and A1298C mutations were determined by polymerase chain reaction in real time. According to the MTHGFR C677T genotype variant, the examined patients were divided into 3 groups: 1) 21 persons (male/female 10/11) with homozygous CC genotype; 2) 17 ones (male/female 12/5) with heterozygous CT genotype; 3) 3 persons with a recessive homozygous TT genotype (all men). Six months after the end of the acute phase of the coronavirus disease, patients were surveyed using questionnaires to assess the psycho-emotional state: cognitive function, anxiety and depression. No significant difference was found in the average scores of cognitive function, anxiety and depression in patients of group 1 and 2. Individuals of the group 1 C677C, who had an additional recessive homozygous C1298C mutation (group 1a, n=6), were characterized by an elevated level of homocysteine, which showed a high negative correlation with serum folate (r= -0.95). A small group of individuals with the recessive homozygous T677T genotype (group 3, all men) was distinguished by an older age, the presence of cardiovascular diseases, type 2 diabetes (2 cases out of 3), more severe manifestations of COVID-19, which forces us to pay attention to potentially increased risk of complications in such patients and requires further investigation. Correlation relationships between assessments of cognitive function, anxiety, depression and serum levels of homocysteine and folate in patients with different genotypes of MTHGFR C677T were recorded. Therefore, the use of a molecular genetic approach made it possible to pay attention to the possible predisposition to hyperhomocysteinemia in individuals who have a folic acid deficiency, and different combination of alleles of the MTHGFR gene C677T and A1298C.

Metabiotics - a new direction in the effectiveness of disease prevention and treatment

The authors consider the symbiotic microbiota of the human body as a leading factor in the health of the entire body, which should be managed in order to prevent and treat various diseases and possibilities of metabiotics and targeted metabiotics used for this purpose as the most promising direction for the treatment and prevention of diseases of various organs. It was noted that Russia is one of the first countries to assess biotechnological prospects and the importance of creating metabiotics for various purposes, capable of preventing, restoring and regulating physiological functions, biochemical and behavioral responses, signaling intra and intercellular communications, epigenetic regulation of gene expression and post-translational modification of their final products.

Histone methyltransferases as a new target for the epigenetic action by vorinostat

Aberrant methylation and acetylation of histones are characteristic changes in the system of epigenetic regulation of gene expression accompanying the process of malignant transformation of the cell. Vorinostat is the epigenetic modulator that actively used in clinical oncology practice. The antitumor activity of vorinostat is considered to be associated with only with the inhibition of histone deacetylases. The effects of this drug on histone methylation have not been sufficiently studied. Using the HeLa TI test system, which allows evaluating the integral effect of epigenetically active compounds by activating the expression of the reporter gene GFP, and knockdown of genes by small interfering RNAs, we showed that the inhibitory effect of vorinostat is directed not only at HDAC1, but also at EZH2, SUV39H1, SUV39H2, SUV420H1. Using Western blotting, the ability of vorinostat to suppress the expression of enzymes EZH2, SUV39H1/2, SUV420H1 was confirmed and, in addition, its ability to inhibit the expression of enzymes SUV420H2 and DOT1L was revealed. The data obtained expand the understanding of the epigenetic effects of vorinostat and demonstrate the need for a large-scale analysis of its activity in relation to other epigenetic enzymes. A detailed understanding of the mechanism of epigenetic action of vorinostat will contribute to its more adequate use in the treatment of tumors with an aberrant epigenetic profile.

Study of the role of chromatin-remodeling factor SWI/SNF in neuronal processes in Drosophila

SWI/SNF complexes are ATP-dependent chromatin remodeling complexes that regulate the expression of numerous genes through the use of at least 15 subunits. The composition of these complexes is diverse, a result of combinatory assembly of subunits from homologous families with a variety of additional functions. During neurogenesis, researchers have identified distinctive SWI/SNF complexes that are specific to various stages of development. These complexes were detected in stem cells, neuronal progenitor cells, and postmitotic differentiated neurons. Notably, SWI/SNF complexes specific to neuronal progenitor cells are essential for regulating their division. SWI/SNF complexes are critical for adult brain plasticity in neurons and contribute to the regulatory genetic mechanisms that underlie higher neural activity, especially in learning and memory processes. However, the epigenetic regulation of gene expression in neurons remains insufficiently understood. Mutations in complex subunits result in the development of pathologies. For instance, ARID1A and ARID1B subunit mutations in humans cause Coffin–Siris syndrome, which is a rare congenital multisystem genetic disease primarily characterized by developmental disabilities and intellectual disability. Currently, there are challenges in creating model systems to study Coffin–Siris syndrome. Drosophila has shown promise as a model organism due to its extensive research and suitability in studying neurodevelopmental pathologies. It is a cost-effective species that facilitates tracking of both species-specific features and general patterns for abnormality types. Additionally, Drosophila serves as a model organism due to its abundance of orthologous genes that lead to neuronal developmental abnormalities in humans. Notably, the knockdown of genes that encode subunit complexes in Drosophila produces a noticeable decline in long-term memory formation. In this study, we examine the involvement of SAYP and osa complex subunits in different molecular mechanisms in Drosophila brain neurons. We use multiple strategies to alter the levels of SAYP and osa factors, such as tissue-specific knockdown, tissue-specific protein degradation, and null allele production. Using the CRISPR/Cas9 technique, we generated novel alleles of the osa and SAYP genes that encode operational proteins which can be selectively degraded at specific times and in specific tissues. We examine the changes in gene expression profiles, chromatin states, and the participation of transcription factors on chromatin, as well as DNA integrity alterations, upon removal of these factors from neurons. We are conducting research on the long-term memory of adult flies and neurogenesis at different developmental stages. Our aim is to gain insight into the role of the epigenetic regulator SWI/SNF in the development of nervous system pathologies and its involvement in the development and functioning of higher eukaryotic nervous systems.

Effect of lipotoxicity on mitochondrial function and epigenetic programming during bovine in vitro embryo production

Maternal metabolic disorders may cause lipotoxic effects on the developing oocyte. Understanding the timing at which this might disrupt embryo epigenetic programming and how this is linked with mitochondrial dysfunction is crucial for improving assisted reproductive treatments, but has not been investigated before. Therefore, we used a bovine in vitro model to investigate if pathophysiological palmitic acid (PA) concentrations during in vitro oocyte maturation and in vitro embryo culture alter embryo epigenetic patterns (DNA methylation (5mC) and histone acetylation/methylation (H3K9ac/H3K9me2)) compared to control (CONT) and solvent control (SCONT), at the zygote and morula stage. Secondly, we investigated if these epigenetic alterations are associated with mitochondrial dysfunction and changes in ATP production rate, or altered expression of epigenetic regulatory genes. Compared to SCONT, H3K9ac and H3K9me2 levels were increased in PA-derived zygotes. Also, 5mC and H3K9me2 levels were increased in PA-exposed morulae compared to SCONT. This was associated with complete inhibition of glycolytic ATP production in oocytes, increased mitochondrial membrane potential and complete inhibition of glycolytic ATP production in 4-cell embryos and reduced SOD2 expression in PA-exposed zygotes and morulae. For the first time, epigenetic alterations in metabolically compromised zygotes and morulae have been observed in parallel with mitochondrial dysfunction in the same study.

MICRO-RNA AS POTENTIAL NON-INVASIVE MARKERS OF PATHOLOGICAL CONDITIONS OF THE LIVER

The state of the cell (and the organism as a whole) is determined not only by the genotype, but by the ratio of turned on and off genes as well. Epigenetic regulation of gene expression plays a key role in the control of many cellular processes. Being important molecules of such regulation microRNAs are involved in post-transcriptional turning about half of human genes off. Abnormal expression of microRNAs, leading to changes in their concentration, can contribute to the development of many pathophysiological processes, diseases as well as cancer, and therefore microRNAs can be regarded as biomarkers for identifying various types of diseases. This mini-review presents the biogenesis, subcellular and exosomal localization of microRNAs and the mechanisms by which they regulate transcription and cellular homeostasis.

CBP and RAD21 Proteins Bind at the Termini of Forum Domains in Human Chromosomes.

Forum domains are 50-100-kb stretches of DNA delimited by the hotspots of double-strand breaks (DSBs). These domains possess coordinately expressed genes. However, molecular mechanisms of such regulation are not clear. It is assumed that the proteins specifically binding at the termini of domains can be involved in coordinated regulation of expression. In this study, we used the results of precise mapping of hotspots of DSBs and ChIP-Seq data for ten nuclear proteins in HEK293T cell line for a search of proteins specifically binding at forum-domain termini. We detected that two proteins, CBP and RAD24, which are known to be involved in epigenetic regulation of gene expression and formation of 3D chromosomal structures, bind at the termini. We assume that these proteins may be involved in coordinated expression of genes in forum domains.

Iadademstat and Gilteritinib for the Treatment of FLT3-Mutated Relapsed/Refractory Acute Myeloid Leukemia: The Frida Study

Background: Frontline and relapsed /refractory (R/R) acute myeloid leukemia (AML) patients carrying fms-related tyrosine kinase 3 [FLT3]-mutations (FLT3 mut+) benefit from FLT3 inhibitors (FLT3i) that have emerged as active therapeutic agents for this subset of AML encompassing up to 30-40% of all AML cases. The FLT3i gilteritinib, as monotherapy for R/R AML pts, has improved outcomes but the duration of remission achieved is transient and often brief. The Phase 3 randomized ADMIRAL trial of gilteritinib demonstrated a 20% CR rate and 2.8 months event-free-survival (EFS) (Perl, et al., NEJM 2019). The development of new targeted agents which synergize with FLT3 inhibitors, and ideally also inhibit the emergence of resistance, is therefore a major medical need in AML. Iadademstat (iada/ORY-1001) is a specific, oral, potent, covalent inhibitor of the epigenetic Lysine-Specific Demethylase 1 (LSD1/KDMA1) enzyme. Epigenetic dysregulation is a hallmark of AML. Up to 70% of recurring mutations in AML patients target epigenetic regulators of gene expression, resulting in myeloid differentiation blockade and enhanced leukemic stem cell renewal, underscoring the potential of epigenetic therapies to change the natural history of the disease. Preclinically, iada produces striking synergy with FLT3is, particularly gilteritinib in FLT3 wild-type and FLT3 mut+ AML cells and in derived cell lines resistant to venetoclax, azacitidine and other FLT3is (Sacilotto et al., 2022 Eur J. of Cancer 174S1). The novel MOAs generating this synergy in combinations include activation of a pro-differentiating epigenetic transcriptional program with simultaneous suppression of MYC-driven target genes (Yashar, et al. 2023, Mol. Cancer Res). The recently completed Phase 2 study of iada in combination with azacitidine (ALICE) produced a high rate of composite remission, including complete remission (CR) and CR with incomplete count recovery (CRi) (mostly MRD negative), as well as durable responses, in treatment naïve, unfit AML patients (pts), without exacerbating the toxicity profile of azacitidine (Salamero et al., 2022, Blood S1). The FRIDA study (NCT05546580) aims to establish the safety, tolerability, and the recommended phase 2 dose (RP2D) of the combination of iada plus gilteritinib in FLT3 mut+ R/R AML. Methods: Adult pts with body weight ≥50 Kg and ECOG 0-2, with FLT3 mut+ R/R AML, after no more than 2 prior lines of therapy, are enrolling. Certain patients with prior exposure to FLT3is including gilteritinib may be eligible. Up to 18 pts, in a 3+3 escalation phase, will receive iada at doses of 75 to 150 ug, orally, in 5 days ON - 2 days OFF schedule, with continuous gilteritinib, at 120 mg/day orally. In the expansion phase, up to 14 pts at the selected safe and pharmacologically active dose/s (determined based on all available data from escalation pts including PK, target engagement (TE), safety, tolerability, and emerging activity) will be enrolled. Primary endpoints of the study are safety and RP2D determination, based on the same 5 criteria outlined above. Bayesian posterior probability efficacy monitoring will be performed periodically for each dose cohort in the expansion phase. Bayesian efficacy futility and early stopping boundary will be applied during the monitoring. Posterior probability criterion (Prob (CR>0.3) ≥ 0.60) at the end of the study will warrant additional development. The safety of the combination treatment will also be continuously evaluated during expansion following a Bayesian design stopping rule.Secondary endpoints include overall survival, EFS, CR, CR/CR with partial hematologic recovery (CRh), overall response rates, time to response, duration of response, and transfusion rate. Exploratory endpoints include measurable residual disease and gene mutational analysis. At the time of the submission, FRIDA is enrolling a second dose level cohort in escalation phase and plans to have the 15 sites open to accrual in the US by the end of 2023. Additional sites will be added for a subsequent randomized controlled double-blinded FRIDA 2 study to assess the efficacy of the iada and gilteritinib combination in R/R FLT3 mut+ AML.

Genetic Subtyping Using Whole Exome Sequencing across Large B Cell Lymphoma Entities in a Series of 109 DLBCL and Plasmablastic Lymphoma Cases

Background: Diffuse Large B Cell Lymphomas are still a significantly heterogeneous disease with few molecularly defined entities. Recently genomic based algorithms have been proposed for DBCL NOS disease classification, including the Lymphgen tool 1. Other large B cell lymphoma entities, including High Grade BCL Dual Hit or plasmablastic lymphoma remain poorly characterized according to this molecular based clustering methods. Here we sought to apply this tool for disease classification in a series of 109 large B cell lymphoma cases derived from GELTAMO clinical trials (NCT01848132 and NCT2015-005390-21) and retrospective multicentric series to confirm its application across different large B cell lymphoma entities. Methods: We retrieved FFPE and liquid biopsy diagnostic samples from 109 cases and performed histopathological confirmation, FISH testing and whole exome sequencing (Agilent Sureselect v6) by NGS. Sequencing data and available fusion data for BCL2 and BCL6 were used to classify the cases according to Lymphgen (https://llmpp.nih.gov/lymphgen). Results: 109 cases were classified as different large B cell lymphoma entities, including 31 DLBCL NOS GCB type, 8 HGBCL/DLBCL DH/NOS, 41 DLBCL NOS non-GCB type, 22 plasmablastic lymphoma, 3 THRLBCL, 1 PMBL, 2 DLBCL NOS and 1 3B Follicular Lymphoma. After WES median Tumor Mutation Burden was 972. Overall genetic classification by Lymphgen was obtained in 53 cases (49%) with the remaining 56 cases considered unclassified (molecular subtype other/NOS). Of the genetically identified cases, 18 were classified as ST2 (33%), 15 were considered EZB (28%), 5 BN2 (10%) and 3 MCD (5%). Interestingly 12 (22%, overall, 11%) were genetically composite, including 8, ST2/EZB; 1, ST2/BN2; 1, ST2/MCD and 2 ST2/EZB/MCD. According to histopathological subtype 17 GCB type DLBCL were classified as EZB (8, 47%), ST2 (5, 30%) and BN2 (1, 6%). 3 cases (17%) were genetically composite. 6 out of 8 cases of HGBCL/DLBCL DH/NOS were classified as either EZB (2), ST2 (2) or composite EZB/ST2 (2). 19 non-GCB type DLBCL were classified as ST2 (5, 26%), BN2 (4, 21 %), EZB (3, 16 %) and MCD (3, 16%). 4 cases were genetically composite (21%). Interestingly, plasmablastic lymphomas showed ST2 genetic features, found in 5 out of 22 (23%) and composite ST2/EZB in 2 cases. Genes overrepresented in the ST2 cluster include TET2, PRRC2C, STAT3,DOCK8 and CLTC. Plasmablastic Lymphomas classified as other showed recurrent mutations in PRRC2C, PABPC1, TRRAP, PRKCB, EP300 and TP53. Conclusions: ST2 and EZB genetic groups stand as the most frequent genetic subtypes of DLBCL NOS. While ST2 is found in either GCB and non-GCB subtypes, EZB is found preferentially in cases with the GCB phenotype, including GCB type DLBCL and HGBCL/DLBCL DH. In comparison with already published series we found a relatively higher prevalence of the ST2 genetic subtype among DLBCL NOS. MCD and BN2 genetic subtypes are restricted to the non-GCB subtype, but its prevalence is relatively low. Importantly, a significant fraction of cases (~50%) is still genetically unclassified (molecular subtype NOS) using WES and FISH-derived fusion data. Proper identification of the A53 cluster and relevant dysregulated pathways in the molecular NOS group require more research. Specific large B cell lymphoma entities such as plasmablastic lymphoma show features of ST2 genetic subtype in a significant fraction of tumors. These features include JAK/STAT3 pathway activation related genes and fit well with already published data 2,3. In addition, recurrent mutations in TET2, involved in epigenetic regulation of gene expression and TRRAP, target of C-MYC transcriptional activation, were enriched in this molecular subtype of plasmablastic lymphoma. Importantly ~70% remained unclassified. Mutations in this group are recurrently found in PRRC2C as well as PABPC1, both involved in VEGFA-VEGFR2 signaling. In summary, DLBCL NOS molecular subtyping supplies exact molecular classification in ~50% of our cohort. ST2 and EZB subtypes constitute ~60% of the cases with a fraction of ~15% of composite ST2/EZB. Application of the molecular classifier to plasmablastic lymphomas shows intraspecific genetic diversity and points toward dysregulation of JAK/STAT, MAPK/Erk and VEGFA-VEGFR2 signaling as well as MYC transcriptional activation. REFERENCES 1. PMID: 32289277 2. PMID: 33225311 3. PMID: 32273478

HCV and HCC Tango-Deciphering the Intricate Dance of Disease: A Review Article.

Hepatitis C virus (HCV) is a major cause of hepatocellular carcinoma (HCC) accounting for around one-third of all HCC cases. Prolonged inflammation in chronic hepatitis C (CHC), maintained through a variety of pro- and anti-inflammatory mediators, is one of the aspects of carcinogenesis, followed by mitochondrial dysfunction and oxidative stress. Immune response dysfunction including the innate and adaptive immunity also plays a role in the development, as well as in the recurrence of HCC after treatment. Some of the tumor suppressor genes inhibited by the HCV proteins are p53, p73, and retinoblastoma 1. Mutations in the telomerase reverse transcriptase promoter and the oncogene catenin beta 1 are two more important carcinogenic signaling pathways in HCC associated with HCV. Furthermore, in HCV-related HCC, numerous tumor suppressor and seven oncogenic genes are dysregulated by epigenetic changes. Epigenetic regulation of gene expression is considered as a lasting "epigenetic memory", suggesting that HCV-induced changes persist and are associated with liver carcinogenesis even after cure. Epigenetic changes and immune response dysfunction are recognized targets for potential therapy of HCC.

PSV-4 Effects of Asprosin on Nuclear Sirtuins Expression in Bovine Granulosa Cells

Abstract Asprosin is an adipokine that regulates steroid production in granulosa cells (GC). Sirtuins are a family of NAD+-dependent deacetylases associated with GC function. In the nucleus, sirtuins are epigenetic regulators of gene expression. Although the literature shows that sirtuins and asprosin affect GC steroidogenesis and proliferation, studies are required to investigate whether their actions are linked. The aims of this study are to determine the influence of asprosin on mRNA expression of nuclear sirtuins and their association with steroidogenic regulators in bovine GC. GC were isolated from small antral follicles (1 to 5mm) of bovine ovaries, cultured in vitro, and treated with or without asprosin (200 ng/mL) in combination with FSH (30 ng/mL) or IGF1 (30 ng/mL). Cells were cultured for 24 h and submitted to RNA extraction (n = 5 pools). Relative mRNA abundance of SIRTs 1, 2, 6, 7, aromatase (CYP19A1), IGF1 receptor (IGF1r), and FSH receptor (FSHr) were determined via RT-qPCR using 18S as a housekeeping gene. Data were analyzed via factorial ANOVA with GLM procedures of SAS for Windows (SAS Institute Inc., Cary, NC). Normality was tested using the Shapiro-Wilk test. Data sets that showed non-gaussian distribution (P >0.05) after log-transformation were analyzed via the Kruskal-Wallis test followed by Dunn’s post hoc test using GraphPad Prism 9.2.0. Differences among treatments were considered significant at P < 0.05, and a tendency at 0.05< P < 0.10. Pearson correlation was performed using PROC CORR procedures of SAS for Windows (version 9.4, SAS Institute Inc., Cary, NC). SIRT1 (P < 0.05) mRNA abundance increased after Asprosin treatment in comparison with FSH alone and in combination with asprosin as well as to IGF1 alone. Also, SIRT1 under asprosin treatment showed a tendency (P < 0.06) to be increased in comparison with negative control. Additionally, a very high correlation (r = 0.999; P < 0.05) between CYP19A1 and SIRT1 was observed in the treatment with asprosin. SIRT2 had a tendency (P < 0.08) to increase after treatment with asprosin in comparison with FSH alone. Moreover, SIRT2 has a very high (r = 0.995; P < 0.005) correlation to CYP19A1 after treatment of FSH in combination with asprosin and a significant (r = 0.676; P < 0.05) correlation with IGF1r. Asprosin treatment led to a very high (r = 0.997; P < 0.05) correlation of SIRT6 with FSHr. Also, when asprosin was combined with FSH, a very high (r = 0.993, P < 0.01) correlation between SIRT6 and CYP19A1 was observed. SIRT7 mRNA relative abundance decreased (P < 0.05) after treatment with IGF1 in comparison to the negative control. No significant correlation was observed between SIRT7 and CYP19A1 or receptors. In summary, asprosin increases expression of SIRT1 and increases the correlation between SIRTs 1, 2, 6, and aromatase. These results indicate that the actions of asprosin on steroidogenesis involve sirtuins regulation.

Dysregulation of MicroRNAs in Adult Osteogenesis Imperfecta: The miROI Study.

As epigenetic regulators of gene expression, circulating micro-RiboNucleic Acids(miRNAs) have been described in several bone diseases as potential prognostic markers. The aim of our study was to identify circulating miRNAs potentially associated with the severity of osteogenesis imperfecta (OI) in three steps. We have screened by RNA sequencing for the miRNAs that were differentially expressed in sera of a small group of OI patients versus controls and then conducted a validation phase by RT-qPCR analysis of sera of a larger patient population. In the first phase of miROI, we found 79 miRNAs that were significantly differentially expressed. We therefore selected 19 of them as the most relevant. In the second phase, we were able to validate the significant overexpression of 8 miRNAs in the larger OI group. Finally, we looked for a relationship between the level of variation of the validated miRNAs and the clinical characteristics of OI. We found a significant difference in the expression of two microRNAs in those patients with dentinogenesis imperfecta. After reviewing the literature, we found 6 of the 8 miRNAs already known to have a direct action on bone homeostasis. Furthermore, the use of a miRNA-gene interaction prediction model revealed a 100% probability of interaction between 2 of the 8 confirmed miRNAs and COL1A1 and/or COL1A2. This is the first study to establish the miRNA signature in OI, showing a significant modification of miRNA expression potentially involved in the regulation of genes involved in the physiopathology of OI. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).