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Nature Biotechnology Jun 2024Oxidative modification of 5-methylcytosine (5mC) by ten-eleven translocation (TET) DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of...
Oxidative modification of 5-methylcytosine (5mC) by ten-eleven translocation (TET) DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of oxidized 5mC. Existing single-cell bisulfite sequencing methods cannot resolve 5mC and 5hmC, leaving the cell-type-specific regulatory mechanisms of TET and 5hmC largely unknown. Here, we present joint single-nucleus (hydroxy)methylcytosine sequencing (Joint-snhmC-seq), a scalable and quantitative approach that simultaneously profiles 5hmC and true 5mC in single cells by harnessing differential deaminase activity of APOBEC3A toward 5mC and chemically protected 5hmC. Joint-snhmC-seq profiling of single nuclei from mouse brains reveals an unprecedented level of epigenetic heterogeneity of both 5hmC and true 5mC at single-cell resolution. We show that cell-type-specific profiles of 5hmC or true 5mC improve multimodal single-cell data integration, enable accurate identification of neuronal subtypes and uncover context-specific regulatory effects on cell-type-specific genes by TET enzymes.
Topics: 5-Methylcytosine; Single-Cell Analysis; Animals; Mice; DNA Methylation; Gene Expression Regulation; Epigenesis, Genetic; Brain; Humans
PubMed: 37640946
DOI: 10.1038/s41587-023-01909-2 -
European Journal of Heart Failure Jan 2024In the EXPLORER-HCM trial, mavacamten reduced left ventricular outflow tract obstruction (LVOTO) and improved functional capacity of symptomatic hypertrophic obstructive... (Clinical Trial)
Clinical Trial
AIMS
In the EXPLORER-HCM trial, mavacamten reduced left ventricular outflow tract obstruction (LVOTO) and improved functional capacity of symptomatic hypertrophic obstructive cardiomyopathy (HOCM) patients. We sought to define the potential use of mavacamten by comparing real-world HOCM patients with those enrolled in EXPLORER-HCM and assessing their eligibility to treatment.
METHODS AND RESULTS
We collected information on HOCM patients followed up at 25 Italian HCM outpatient clinics and with significant LVOTO (i.e. gradient ≥30 mmHg at rest or ≥50 mmHg after Valsalva manoeuvre or exercise) despite pharmacological or non-pharmacological therapy. Pharmacological or non-pharmacological therapy resolved LVOTO in 1044 (61.2%) of the 1706 HOCM patients under active follow-up, whereas 662 patients (38.8%) had persistent LVOTO. Compared to the EXPLORER-HCM trial population, these real-world HOCM patients were older (62.1 ± 14.3 vs. 58.5 ± 12.2 years, p = 0.02), had a lower body mass index (26.8 ± 5.3 vs. 29.7 ± 4.9 kg/m , p < 0.0001) and a more frequent history of atrial fibrillation (21.5% vs. 9.8%, p = 0.027). At echocardiography, they had lower left ventricular ejection fraction (LVEF, 66 ± 7% vs. 74 ± 6%, p < 0.0001), higher left ventricular outflow tract gradients at rest (60 ± 27 vs. 52 ± 29 mmHg, p = 0.003), and larger left atrial volume index (49 ± 16 vs. 40 ± 12 ml/m , p < 0.0001). Overall, 324 (48.9%) would have been eligible for enrolment in the EXPLORER-HCM trial and 339 (51.2%) for treatment with mavacamten according to European guidelines.
CONCLUSIONS
Real-world HOCM patients differ from the EXPLORER-HCM population for their older age, lower LVEF and larger atrial volume, potentially reflecting a more advanced stage of the disease. About half of real-world HOCM patients were found eligible to mavacamten.
Topics: Humans; Benzylamines; Cardiomyopathy, Hypertrophic; Heart Failure; Stroke Volume; Uracil; Ventricular Function, Left
PubMed: 38131253
DOI: 10.1002/ejhf.3120 -
Organic & Biomolecular Chemistry Dec 2023Uracil has been modified at the 5-position to derive a small library of nucleobase-chromophores which were inspired by green fluorescent protein (GFP). The key steps in...
Uracil has been modified at the 5-position to derive a small library of nucleobase-chromophores which were inspired by green fluorescent protein (GFP). The key steps in the syntheses were Erlenmeyer azlactone synthesis followed by amination by use of hexamethyl disilazane (HMDS) to produce the imidazolinone derivatives. The uracil analogues displayed emission in the green region of visible spectrum and exhibited microenvironmental sensitivity exemplified by polarity-based solvatochromism and viscosity-dependent emission enhancement. Solid-state quantum yields of approximately 0.2 and solvent dependent emission wavelengths beyond 500 nm were observed. Select analogues were incorporated into peptide nucleic acid (PNA) strands which upon duplex formation with DNA showed good response ranging from a turn-off of fluorescence in presence of an opposing mismatched residue to a greater than 3-fold turn-on of fluorescence upon binding to fully complementary DNA strand.
Topics: Green Fluorescent Proteins; Uracil; Molecular Structure; Fluorescence; DNA
PubMed: 37997774
DOI: 10.1039/d3ob01539d -
Virology Aug 2023With no approved antiviral therapies, the continuous emergence and re-emergence of tick-borne encephalitis virus (TBEV) and yellow fever virus (YFV) is a rising concern....
With no approved antiviral therapies, the continuous emergence and re-emergence of tick-borne encephalitis virus (TBEV) and yellow fever virus (YFV) is a rising concern. We performed head-to-head comparisons of the antiviral activity of available nucleos(t)ide analogs (nucs) using relevant human cell lines. Eight existing nucs inhibited TBEV and/or YFV with differential activity between cell lines and viruses. Remdesivir, uprifosbuvir and sofosbuvir were the most potent drugs against TBEV and YFV in liver cells, but they had reduced activity in neural cells, whereas galidesivir retained uniform activity across cell lines and viruses. Ribavirin, valopicitabine, molnupiravir and GS-6620 exhibited only moderate antiviral activity. We found antiviral activity for drugs previously reported as inactive, demonstrating the importance of using human cell lines and comparative experimental assays when screening the activity of nucs. The relatively high antiviral activity of remdesivir, sofosbuvir and uprifosbuvir against TBEV and YFV merits further investigation in clinical studies.
Topics: Humans; Sofosbuvir; Encephalitis, Tick-Borne; Yellow Fever; Cell Line; Encephalitis Viruses, Tick-Borne; Yellow fever virus; Antiviral Agents
PubMed: 37356253
DOI: 10.1016/j.virol.2023.06.002 -
Current Pharmaceutical Biotechnology 2024Monkeypox is a disease caused by the monkeypox virus, which is a type of orthopox virus that comes from the virus family Poxviridae. Its first case reported in animals... (Review)
Review
Monkeypox is a disease caused by the monkeypox virus, which is a type of orthopox virus that comes from the virus family Poxviridae. Its first case reported in animals and humans was in 1958 and 1970, respectively. It is a viral zoonosis disease with two modes of transmission: animal to human (via direct contact or eating the meat of an infected animal) and human to human (via contact or contact with skin lesions, body fluids, and infected person's contaminated objects). The literature depicts that monkeypox is less contagious among individuals in contrast to smallpox; the infection chain of monkeypox is nearly five to six patients approximately. It has two clades, the West African and the Central African (the Congo basin). The Congo basin subgroup of monkeypox is highly transmissible and severe. The symptoms of monkeypox include fever, lethargy, headache, lymphadenopathy, myalgia, myodynia, fainting, shivers, backache, and rashes on the face and extremities. The most common symptom of monkeypox is lymphatic hyperplasia or, lymph adenopathy or swollen lymph nodes. It is proven to be very useful in the diagnosis of monkeypox. The antiviral drugs that are used for its treatment are tecovirimat, brincidofovir and cidofovir. Tecovirimat has fewer side effects and it shows better therapeutic action in comparison to brincidofovir and cidofovir. For the prevention of monkeypox, the Center for Disease Control and Prevention recommends the administration of the same vaccine used for smallpox named INVAMUNE, which is currently in its third generation. Its first and second generations have adverse side effects in patients having HIV or atopic dermatitis.
Topics: Humans; Cidofovir; Cytosine; Mpox (monkeypox); Organophosphonates; Smallpox; Variola virus
PubMed: 37711132
DOI: 10.2174/1389201025666230914094444 -
Nucleic Acids Research Jun 2024Dihydrouridine (D) is a common modified base found predominantly in transfer RNA (tRNA). Despite its prevalence, the mechanisms underlying dihydrouridine biosynthesis,...
Dihydrouridine (D) is a common modified base found predominantly in transfer RNA (tRNA). Despite its prevalence, the mechanisms underlying dihydrouridine biosynthesis, particularly in prokaryotes, have remained elusive. Here, we conducted a comprehensive investigation into D biosynthesis in Bacillus subtilis through a combination of genetic, biochemical, and epitranscriptomic approaches. Our findings reveal that B. subtilis relies on two FMN-dependent Dus-like flavoprotein homologs, namely DusB1 and DusB2, to introduce all D residues into its tRNAs. Notably, DusB1 exhibits multisite enzyme activity, enabling D formation at positions 17, 20, 20a and 47, while DusB2 specifically catalyzes D biosynthesis at positions 20 and 20a, showcasing a functional redundancy among modification enzymes. Extensive tRNA-wide D-mapping demonstrates that this functional redundancy impacts the majority of tRNAs, with DusB2 displaying a higher dihydrouridylation efficiency compared to DusB1. Interestingly, we found that BsDusB2 can function like a BsDusB1 when overexpressed in vivo and under increasing enzyme concentration in vitro. Furthermore, we establish the importance of the D modification for B. subtilis growth at suboptimal temperatures. Our study expands the understanding of D modifications in prokaryotes, highlighting the significance of functional redundancy in this process and its impact on bacterial growth and adaptation.
Topics: Bacillus subtilis; Bacterial Proteins; RNA, Bacterial; RNA, Transfer; Uridine; Gene Expression
PubMed: 38682613
DOI: 10.1093/nar/gkae325 -
PloS One 2023Tetrahymena are ciliated protists that have been used to study the effects of toxic chemicals, including anticancer drugs. In this study, we tested the inhibitory...
Tetrahymena are ciliated protists that have been used to study the effects of toxic chemicals, including anticancer drugs. In this study, we tested the inhibitory effects of six pyrimidine analogs (5-fluorouracil, floxuridine, 5'-deoxy-5-fluorouridine, 5-fluorouridine, gemcitabine, and cytarabine) on wild-type CU428 and conditional mutant NP1 Tetrahymena thermophila at room temperature and the restrictive temperature (37°C) where NP1 does not form the oral apparatus. We found that phagocytosis was not required for pyrimidine analog entry and that all tested pyrimidine analogs inhibited growth except for cytarabine. IC50 values did not significantly differ between CU428 and NP1 for the same analog at either room temperature or 37°C. To investigate the mechanism of inhibition, we used two pyrimidine bases (uracil and thymine) and three nucleosides (uridine, thymidine, and 5-methyluridine) to determine whether the inhibitory effects from the pyrimidine analogs were reversible. We found that the inhibitory effects from 5-fluorouracil could be reversed by uracil and thymine, from floxuridine could be reversed by thymidine, and from 5'-deoxy-5-fluorouridine could be reversed by uracil. None of the tested nucleobases or nucleosides could reverse the inhibitory effects of gemcitabine or 5-fluorouridine. Our results suggest that the five pyrimidine analogs act on different sites to inhibit T. thermophila growth and that nucleobases and nucleosides are metabolized differently in Tetrahymena.
Topics: Tetrahymena thermophila; Floxuridine; Nucleosides; Thymine; Antimetabolites; Gemcitabine; Pyrimidines; Uracil; Fluorouracil; Cytarabine
PubMed: 37708236
DOI: 10.1371/journal.pone.0284309 -
Hepatology (Baltimore, Md.) Dec 2023Chronic HEV infections remain a serious problem in immunocompromised patients, as specifically approved antiviral drugs are unavailable. In 2020, a 24-week multicenter...
BACKGROUND AND AIMS
Chronic HEV infections remain a serious problem in immunocompromised patients, as specifically approved antiviral drugs are unavailable. In 2020, a 24-week multicenter phase II pilot trial was carried out, evaluating the nucleotide analog sofosbuvir by treating nine chronically HEV-infected patients with sofosbuvir (Trial Number NCT03282474). During the study, antiviral therapy reduced virus RNA levels initially but did not lead to a sustained virologic response. Here, we characterize the changes in HEV intrahost populations during sofosbuvir treatment to identify the emergence of treatment-associated variants.
APPROACH AND RESULTS
We performed high-throughput sequencing on RNA-dependent RNA polymerase sequences to characterize viral population dynamics in study participants. Subsequently, we used an HEV-based reporter replicon system to investigate sofosbuvir sensitivity in high-frequency variants. Most patients had heterogenous HEV populations, suggesting high adaptability to treatment-related selection pressures. We identified numerous amino acid alterations emerging during treatment and found that the EC 50 of patient-derived replicon constructs was up to ~12-fold higher than the wild-type control, suggesting that variants associated with lower drug sensitivity were selected during sofosbuvir treatment. In particular, a single amino acid substitution (A1343V) in the finger domain of ORF1 could reduce susceptibility to sofosbuvir significantly in 8 of 9 patients.
CONCLUSIONS
In conclusion, viral population dynamics played a critical role during antiviral treatment. High population diversity during sofosbuvir treatment led to the selection of variants (especially A1343V) with lower sensitivity to the drug, uncovering a novel mechanism of resistance-associated variants during sofosbuvir treatment.
Topics: Humans; Sofosbuvir; Antiviral Agents; Hepatitis E; Sustained Virologic Response; Drug Therapy, Combination; Hepacivirus; Genotype; Treatment Outcome
PubMed: 37334496
DOI: 10.1097/HEP.0000000000000514 -
Clinical Cancer Research : An Official... Jun 2024Bruton's tyrosine kinase (BTK) is central to the survival of malignant and normal B lymphocytes and has been a crucial therapeutic target of several generations of... (Review)
Review
Bruton's tyrosine kinase (BTK) is central to the survival of malignant and normal B lymphocytes and has been a crucial therapeutic target of several generations of kinase inhibitors and newly developed degraders. These new means for targeting BTK have added additional agents to the armamentarium for battling cancers dependent on B-cell receptor (BCR) signaling, including chronic lymphocytic leukemia and other non-Hodgkin lymphomas. However, the development of acquired resistance mutations to each of these classes of BTK inhibitors has led to new challenges in targeting BTK as well as novel insights into BCR signaling. The first-generation covalent BTK inhibitor ibrutinib is susceptible to mutations affecting the covalent binding site, cysteine 481 (C481). Newer noncovalent BTK inhibitors, such as pirtobrutinib, overcome C481 mutation-mediated resistance but are susceptible to other kinase domain mutations, particularly at residues Threonine 474 and Leucine 528. In addition, these novel BTK inhibitor resistance mutations have been shown biochemically and in patients to cause cross-resistance to some covalent BTK inhibitors. Importantly, newer generation covalent BTK inhibitors zanubrutinib and acalabrutinib are susceptible to the same mutations that confer resistance to noncovalent inhibitors. The BTK L528W mutation is of particular interest as it disrupts the kinase activity of BTK, rendering it kinase dead. This observation suggests that BTK may act independently of its kinase activity as a scaffold. Thus, the timely development of BTK degrading proteolysis targeting drugs has allowed for degradation, rather than just enzymatic inhibition, of BTK in B-cell lymphomas, and early clinical trials to evaluate BTK degraders are underway.
Topics: Humans; Agammaglobulinaemia Tyrosine Kinase; Protein Kinase Inhibitors; Pyrimidines; Pyrazoles; Drug Resistance, Neoplasm; Piperidines; Mutation; Adenine; Molecular Targeted Therapy; Signal Transduction; Antineoplastic Agents; Leukemia, Lymphocytic, Chronic, B-Cell; Animals
PubMed: 38578606
DOI: 10.1158/1078-0432.CCR-23-0409 -
Heart Failure Reviews Mar 2024Hypertrophic cardiomyopathy (HCM) is the most common heritable myocardial disorder worldwide. Current pharmacological treatment options are limited. Mavacamten, a... (Meta-Analysis)
Meta-Analysis Review
Hypertrophic cardiomyopathy (HCM) is the most common heritable myocardial disorder worldwide. Current pharmacological treatment options are limited. Mavacamten, a first-in-class cardiac myosin inhibitor, targets the main underlying pathology of HCM. We conducted a systematic review and meta-analysis to evaluate the efficacy and safety of Mavacamten in patients with HCM. PRISMA flow chart was utilized using PubMed, SCOPUS, and Cochrane databases for all up-to-date studies using pre-defined keywords. Pre-specified efficacy outcomes comprised several parameters, including an improvement in peak oxygen consumption (pVO2) and ≥ 1 NYHA class, the need for septal reduction therapy (SRT), change from baseline in Kansas City Cardiomyopathy Questionnaire (KCCQ), changes in biochemical markers and LVEF, along with peak left ventricular outflow tract gradient at rest and after Valsalva maneuver. Safety outcomes included morbidity and serious adverse events. This systematic review included five studies, four RCTs and one non-randomized control trial comprised a total of 524 (Mavacamten [273, 54.3%] vs placebo [230, 45.7%] adult (≥ 18 years) patients with a mean age of 56 years. The study. comprised patients with Caucasian and Chinese ethnicity and patients with obstructive (oHCM) and non-obstructive (nHCM) HCM. Most baseline characteristics were similar between the treatment and placebo groups. Mavacamten showed a statistically significant increase in the frequency of the primary composite endpoint (RR = 1.92, 95% CI [1.28, 2.88]), ≥ 1 NYHA class improvement (RR = 2.10, 95% CI [1.66, 2.67]), a significant decrease in LVEF, peak left ventricular outflow tract gradient at rest and after Valsalva maneuver. Mavacamten also showed a significant reduction in SRT rates (RR = 0.29, 95% CI [0.21, 0.40], p < 0.00001), KCCQ clinical summary scores (MD = 8.08, 95% CI [4.80, 11.37], P < 0.00001) troponin levels and N-terminal pro-B-type natriuretic peptide levels. However, there was no statistically significant difference between Mavacamten and placebo regarding the change from baseline peak oxygen consumption. Mavacamten use resulted in a small increase in adverse events but no statistically significant increment in serious adverse events. Our study showed that Mavacamten is a safe and effective treatment option for Caucasian and Chinese patients with HCM on the short-term. Further research is needed to explore the long-term safety and efficacy of Mavacamten with HCM. In addition, adequately powered studies including patients with nHCM is needed to ascertain befits of Mavacamten in those patients.
Topics: Adult; Humans; Middle Aged; Cardiomyopathy, Hypertrophic; Heart; Benzylamines; Myocardium; Uracil
PubMed: 38112937
DOI: 10.1007/s10741-023-10375-6