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1.
Mol Cell ; 84(9): 1711-1726.e11, 2024 May 02.
Artículo en Inglés | MEDLINE | ID: mdl-38569554

RESUMEN

N6-methyladenosine (m6A) is a crucial RNA modification that regulates diverse biological processes in human cells, but its co-transcriptional deposition and functions remain poorly understood. Here, we identified the RNA helicase DDX21 with a previously unrecognized role in directing m6A modification on nascent RNA for co-transcriptional regulation. DDX21 interacts with METTL3 for co-recruitment to chromatin through its recognition of R-loops, which can be formed co-transcriptionally as nascent transcripts hybridize onto the template DNA strand. Moreover, DDX21's helicase activity is needed for METTL3-mediated m6A deposition onto nascent RNA following recruitment. At transcription termination regions, this nexus of actions promotes XRN2-mediated termination of RNAPII transcription. Disruption of any of these steps, including the loss of DDX21, METTL3, or their enzymatic activities, leads to defective termination that can induce DNA damage. Therefore, we propose that the R-loop-DDX21-METTL3 nexus forges the missing link for co-transcriptional modification of m6A, coordinating transcription termination and genome stability.


Asunto(s)
Adenosina , Adenosina/análogos & derivados , ARN Helicasas DEAD-box , Exorribonucleasas , Inestabilidad Genómica , Metiltransferasas , Estructuras R-Loop , ARN Polimerasa II , Terminación de la Transcripción Genética , Humanos , ARN Helicasas DEAD-box/metabolismo , ARN Helicasas DEAD-box/genética , Metiltransferasas/metabolismo , Metiltransferasas/genética , Adenosina/metabolismo , Adenosina/genética , Exorribonucleasas/metabolismo , Exorribonucleasas/genética , ARN Polimerasa II/metabolismo , ARN Polimerasa II/genética , Células HEK293 , Cromatina/metabolismo , Cromatina/genética , Daño del ADN , Células HeLa , ARN/metabolismo , ARN/genética , Transcripción Genética , Metilación de ARN
2.
Nature ; 591(7850): 413-419, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-33618348

RESUMEN

The deep population history of East Asia remains poorly understood owing to a lack of ancient DNA data and sparse sampling of present-day people1,2. Here we report genome-wide data from 166 East Asian individuals dating to between 6000 BC and AD 1000 and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan Plateau are linked by a deeply splitting lineage that probably reflects a coastal migration during the Late Pleistocene epoch. We also follow expansions during the subsequent Holocene epoch from four regions. First, hunter-gatherers from Mongolia and the Amur River Basin have ancestry shared by individuals who speak Mongolic and Tungusic languages, but do not carry ancestry characteristic of farmers from the West Liao River region (around 3000 BC), which contradicts theories that the expansion of these farmers spread the Mongolic and Tungusic proto-languages. Second, farmers from the Yellow River Basin (around 3000 BC) probably spread Sino-Tibetan languages, as their ancestry dispersed both to Tibet-where it forms approximately 84% of the gene pool in some groups-and to the Central Plain, where it has contributed around 59-84% to modern Han Chinese groups. Third, people from Taiwan from around 1300 BC to AD 800 derived approximately 75% of their ancestry from a lineage that is widespread in modern individuals who speak Austronesian, Tai-Kadai and Austroasiatic languages, and that we hypothesize derives from farmers of the Yangtze River Valley. Ancient people from Taiwan also derived about 25% of their ancestry from a northern lineage that is related to, but different from, farmers of the Yellow River Basin, which suggests an additional north-to-south expansion. Fourth, ancestry from Yamnaya Steppe pastoralists arrived in western Mongolia after around 3000 BC but was displaced by previously established lineages even while it persisted in western China, as would be expected if this ancestry was associated with the spread of proto-Tocharian Indo-European languages. Two later gene flows affected western Mongolia: migrants after around 2000 BC with Yamnaya and European farmer ancestry, and episodic influences of later groups with ancestry from Turan.


Asunto(s)
Genoma Humano/genética , Genómica , Migración Humana/historia , China , Producción de Cultivos/historia , Femenino , Haplotipos/genética , Historia Antigua , Humanos , Japón , Lenguaje/historia , Masculino , Mongolia , Nepal , Oryza , Polimorfismo de Nucleótido Simple/genética , Siberia , Taiwán
3.
Proc Natl Acad Sci U S A ; 120(18): e2221352120, 2023 05 02.
Artículo en Inglés | MEDLINE | ID: mdl-37094160

RESUMEN

T cell activation stimulates substantially increased protein synthesis activity to accumulate sufficient biomass for cell proliferation. The protein synthesis is fueled by the amino acids transported from the environment. Steroid nuclear receptor coactivator 2 (SRC2) is a member of a family of transcription coactivators. Here, we show that SRC2 recruited by c-Myc enhances CD4+ T cell activation to stimulate immune responses via upregulation of amino acid transporter Slc7a5. Mice deficient of SRC2 in T cells (SRC2fl/fl/CD4Cre) are resistant to the induction of experimental autoimmune encephalomyelitis (EAE) and susceptible to Citrobacter rodentium (C. rodentium) infection. Adoptive transfer of naive CD4+ T cells from SRC2fl/fl/CD4Cre mice fails to elicit EAE and colitis in Rag1/ recipients. Further, CD4+ T cells from SRC2fl/fl/CD4Cre mice display defective T cell proliferation, cytokine production, and differentiation both in vitro and in vivo. Mechanically, SRC2 functions as a coactivator to work together with c-Myc to stimulate the expression of amino acid transporter Slc7a5 required for T cell activation. Slc7a5 fails to be up-regulated in CD4+ T cells from SRC2fl/fl/CD4Cre mice, and forced expression of Slc7a5 rescues proliferation, cytokine production, and the ability of SRC2fl/fl/CD4Cre CD4+ T cells to induce EAE. Therefore, SRC2 is essential for CD4+ T cell activation and, thus, a potential drug target for controlling CD4+ T cell-mediated autoimmunity.


Asunto(s)
Encefalomielitis Autoinmune Experimental , Linfocitos T , Animales , Ratones , Linfocitos T CD4-Positivos , Citocinas/metabolismo , Ratones Endogámicos C57BL , Ratones Noqueados , Coactivador 2 del Receptor Nuclear/metabolismo , Regulación hacia Arriba
4.
Prostate ; 84(6): 605-619, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38375594

RESUMEN

BACKGROUND: Metastatic castration-resistant prostate cancer (CRPC), the most refractory prostate cancer, inevitably progresses and becomes unresponsive to hormone therapy, revealing a pressing unmet need for this disease. Novel agents targeting HDAC6 and microtubule dynamics can be a potential anti-CRPC strategy. METHODS: Cell proliferation was examined in CRPC PC-3 and DU-145 cells using sulforhodamine B assay and anchorage-dependent colony formation assay. Flow cytometric analysis of propidium iodide staining was used to determine cell-cycle progression. Cell-based tubulin polymerization assay and confocal immunofluorescence microscopic examination determine microtubule assembly/disassembly status. Protein expressions were determined using Western blot analysis. RESULTS: A total of 82 novel derivatives targeting HDAC6 were designed and synthesized, and Compound 25202 stood out, showing the highest efficacy in blocking HDAC6 (IC50, 3.5 nM in enzyme assay; IC50, 1.0 µM in antiproliferative assay in CRPC cells), superior to tubastatin A (IC50, 5.4 µM in antiproliferative assay). The selectivity and superiority of 25202 were validated by examining the acetylation of both α-tubulin and histone H3, detecting cell apoptosis and HDACs enzyme activity assessment. Notably, 25202 but not tubastatin A significantly decreased HDAC6 protein expression. 25202 prolonged mitotic arrest through the detection of cyclin B1 upregulation, Cdk1 activation, mitotic phosphoprotein levels, and Bcl-2 phosphorylation. Compound 25202 did not mimic docetaxel in inducing tubulin polymerization but disrupted microtubule organization. Compound 25202 also increased the phosphorylation of CDC20, BUB1, and BUBR1, indicating the activation of the spindle assembly checkpoint (SAC). Moreover, 25202 profoundly sensitized cisplatin-induced cell death through impairment of cisplatin-evoked DNA damage response and DNA repair in both ATR-Chk1 and ATM-Chk2 pathways. CONCLUSION: The data suggest that 25202 is a novel selective and potent HDAC6 inhibitor. Compound 25202 blocks HDAC6 activity and interferes microtubule dynamics, leading to SAC activation and mitotic arrest prolongation that eventually cause apoptosis of CRPC cells. Furthermore, 25202 sensitizes cisplatin-induced cell apoptosis through impeding DNA damage repair pathways.


Asunto(s)
Cisplatino , Neoplasias de la Próstata Resistentes a la Castración , Masculino , Humanos , Cisplatino/farmacología , Neoplasias de la Próstata Resistentes a la Castración/patología , Tubulina (Proteína)/metabolismo , Puntos de Control de la Fase M del Ciclo Celular , Línea Celular Tumoral , Apoptosis , Proliferación Celular , Microtúbulos/metabolismo , Microtúbulos/patología , Histona Desacetilasa 6/metabolismo
5.
Environ Res ; 245: 117995, 2024 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-38145731

RESUMEN

BACKGROUND: The increasing problem of bacterial resistance, particularly with quinolone-resistant Escherichia coli (QnR eco) poses a serious global health issue. METHODS: We collected data on QnR eco resistance rates and detection frequencies from 2014 to 2021 via the China Antimicrobial Resistance Surveillance System, complemented by meteorological and socioeconomic data from the China Statistical Yearbook and the China Meteorological Data Service Centre (CMDC). Comprehensive nonparametric testing and multivariate regression models were used in the analysis. RESULT: Our analysis revealed significant regional differences in QnR eco resistance and detection rates across China. Along the Hu Huanyong Line, resistance rates varied markedly: 49.35 in the northwest, 54.40 on the line, and 52.30 in the southeast (P = 0.001). Detection rates also showed significant geographical variation, with notable differences between regions (P < 0.001). Climate types influenced these rates, with significant variability observed across different climates (P < 0.001). Our predictive model for resistance rates, integrating climate and healthcare factors, explained 64.1% of the variance (adjusted R-squared = 0.641). For detection rates, the model accounted for 19.2% of the variance, highlighting the impact of environmental and healthcare influences. CONCLUSION: The study found higher resistance rates in warmer, monsoon climates and areas with more public health facilities, but lower rates in cooler, mountainous, or continental climates with more rainfall. This highlights the strong impact of climate on antibiotic resistance. Meanwhile, the predictive model effectively forecasts these resistance rates using China's diverse climate data. This is crucial for public health strategies and helps policymakers and healthcare practitioners tailor their approaches to antibiotic resistance based on local environmental conditions. These insights emphasize the importance of considering regional climates in managing antibiotic resistance.


Asunto(s)
Proteínas de Escherichia coli , Quinolonas , Escherichia coli , China/epidemiología , Farmacorresistencia Bacteriana , Antibacterianos/farmacología
6.
Surg Endosc ; 38(7): 3520-3530, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38816620

RESUMEN

BACKGROUND: There are few available studies that compare the feasibility, efficacy, and safety of robotic pelvic lateral lymph node dissection compared to laparoscopic pelvic lateral lymph node dissection (LPLND) in advanced rectal cancer. This meta-analysis aims to compare perioperative outcomes between robotic and LPLND. METHODS: We performed a systemic literature review of PubMed, Embase, and Web of Science databases. Perioperative parameters were extracted and pooled for analysis. This meta-analysis provided an analysis of heterogeneity and prediction intervals. RESULTS: Five studies were included: 567 patients divided between 266 robotic and 301 LPLND. Overall operation time was longer in the robotic group than laparoscopic group (difference in means = 67.11, 95% CI [30.80, 103.42], p < 0.001) but the difference in the pelvic lateral lymph dissection time was not statistically significant (difference in means = - 1.212, 95% CI [ - 11.594, 9.171], p = 0.819). There were fewer overall complications in the robotic than in the laparoscopic group (OR = 1.589, 95% CI [1.009, 2.503], p = 0.046), especially with respect to urinary retention (OR = 2.23, 95% CI [1.277, 3.894], p = 0.005). More pelvic lateral lymph nodes were harvested by robotic surgery than by laparoscopy (differences in means = - 1.992, 95% CI [ - 2.421, 1.563], p < 0.001). CONCLUSIONS: In this meta-analysis, robotic pelvic lateral lymph node dissection was associated with more pelvic lateral lymph nodes harvested and lower overall complications, especially urinary retention when compared to LPLND. Further studies are needed to reinforce these findings.


Asunto(s)
Laparoscopía , Escisión del Ganglio Linfático , Pelvis , Neoplasias del Recto , Procedimientos Quirúrgicos Robotizados , Humanos , Escisión del Ganglio Linfático/métodos , Procedimientos Quirúrgicos Robotizados/métodos , Laparoscopía/métodos , Neoplasias del Recto/cirugía , Neoplasias del Recto/patología , Tempo Operativo , Complicaciones Posoperatorias/epidemiología , Complicaciones Posoperatorias/etiología
7.
Gerontology ; 2024 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-38857585

RESUMEN

INTRODUCTION: Existing evidence evaluating the impact of change in body mass index (BMI) on the risk of all-cause and cardiovascular disease (CVD)-related mortality in older people is limited and inconsistent. This population-based cohort study evaluated the association of changes in BMI over time with all-cause and CVD-related mortality in older adults. METHODS: We recruited 55,351 adults aged over 65 years between 2006-2011 from Taipei Elderly Health Examination Program who underwent repeated annual health examinations at 3.2 year-intervals and were followed-up for mortality over 5.5 years. Cox proportional hazard and Fine-Gray sub-distribution hazard models with death from non-CVD causes as the competing risk were used to determine the impact of changes in BMI status on the risk of all-cause or CVD-related mortality, respectively. RESULTS: Over 227,967 person-years of follow-up, 4,054 participants died, including 940 (23.2%) CVD-related deaths. After adjusting for other covariates, >10% decrease of BMI was significantly associated with a higher risk of all-cause (adjusted hazard ratio [AHR]= 1.93; 95% confidence interval [CI]: 1.74-2.13) and CVD-related mortality (AHR= 1.96; 95%CI: 1.60-2.40), compared with stable BMI. Sensitivity analysis showed that a >10% decrease in BMI was significantly associated with a high risk of all-cause and CVD-related mortality in participants with normal weight, underweight, overweight, or obesity at baseline. DISCUSSION/CONCLUSION: Older adults with >10% decrease in BMI are at high risk of all-cause and CVD-related mortality. Our findings suggest that older individuals experiencing a substantial reduction in BMI should undergo a thorough evaluation to minimize the risks associated with mortality.

8.
BMC Public Health ; 24(1): 549, 2024 Feb 21.
Artículo en Inglés | MEDLINE | ID: mdl-38383321

RESUMEN

BACKGROUND: The temporality of household income level with overweight/obesity in children has not been extensively studied. Little research has been conducted to determine the impact of household income on the risk of childhood overweight/obesity over time. This population-based cohort study aimed to investigate the impact of household income on the risk of overweight/obesity over time among preschool-aged children in Taiwan. METHODS: From 2009 to 2018, we recruited 1,482 preschool-aged children ( ≦ 7 y of age) from low-income households and selected age- and sex-matched controls from non-low-income households for comparison; All participants were selected from those who consistently participated in the Taipei Child Development Screening Program and were monitored for overweight/obesity using body mass index (BMI) until December 31, 2018. Low-income households were defined as those with an average monthly disposable income < 60% of the minimum standard of living expense in Taiwan. The primary outcome was childhood overweight or obesity in study participants, defined as BMI (kg/m2) ≥ 85th percentile or ≥ 95th percentile, respectively. The generalized estimating equations (GEE) model was used to determine the impact of low-income households on the risk of overweight/obesity in study participants. RESULTS: Over 21,450 person-years of follow-up, 1,782 participants developed overweight /obesity, including 452 (30.5%) and 1,330 (22.4%) children from low- and non-low-income households, respectively. The GEE model showed that the first group had a significantly higher risk of becoming overweight/obese than the other during the follow-up period (adjusted odds ratio [aOR] = 1.44, 95% CI: 1.29-1.60). Moreover, children of foreign mothers had a higher risk of becoming overweight/obese than those of Taiwanese mothers during the follow-up period (aOR = 1.51, 95% CI: 1.24-1.8). The subgroup analysis revealed a significant association between low-income households and an increased risk of overweight/obesity in children aged 2-7 years (P =.01). However, this association was not observed in children aged 0-1 years (P >.999). CONCLUSIONS: During the follow-up period, there was a notable correlation between low-income households and an increased risk of preschool-aged children developing overweight or obesity. Implementing health promotion initiatives aimed at reducing overweight and obesity in this demographic is crucial.


Asunto(s)
Sobrepeso , Obesidad Infantil , Niño , Femenino , Preescolar , Humanos , Sobrepeso/epidemiología , Obesidad Infantil/epidemiología , Estudios de Cohortes , Índice de Masa Corporal , Madres , Renta
9.
J Formos Med Assoc ; 2024 May 12.
Artículo en Inglés | MEDLINE | ID: mdl-38740535

RESUMEN

BACKGROUND/PURPOSE: Vaccination is the most important preventive measure to protect people from coronavirus disease 2019 (COVID-19). Governments worldwide have prioritized their vaccination policy against COVID-19. However, there is a lack of relevant research on Taiwanese attitudes and considerations toward COVID-19 vaccination. This study aimed to investigate the cognition, preventive behaviors, and attitudes toward COVID-19 vaccines that influence people's willingness to get vaccinated in Taiwan. METHODS: From October 1 to 31, 2021, a computer-assisted telephone interview system was used to randomly select Taiwanese people to investigate their COVID-19 preventive behaviors, knowledge, and willingness to be vaccinated. RESULTS: We included 2000 participants of whom 96.45% showed vaccination willingness. The overall mean age and knowledge scores were 48.6 years and 5.78, respectively. All of the participants chose to wear masks, and 80% chose to be vaccinated to prevent COVID-19. Compared with the non-willing vaccination participants, those with younger ages, higher incomes, and higher knowledge scores regarding masks and vaccination were more likely to be vaccinated. Furthermore, apprehensions about vaccine side effects and negative news about COVID-19 vaccines were the major reasons for vaccination hesitancy. CONCLUSION: To improve people's willingness to get vaccinated, the government should strive to deliver correct knowledge and refute inappropriate negative information about COVID-19 vaccination. Moreover, recommendation by physicians was an important factor for older individuals to decide on receiving the COVID-19 vaccine, and policies could be implemented from this aspect.

10.
Chem Soc Rev ; 52(24): 8699-8720, 2023 Dec 11.
Artículo en Inglés | MEDLINE | ID: mdl-38014465

RESUMEN

We define the anisotropic structure building unit that encompasses diverse chemical bonds (ABUCB). The ABUCB is highly likely to cause anisotropy in both crystallographic structure and spatial electron distribution, ultimately resulting in enhanced macroscopic optical anisotropy. Accordingly, the (PO3F)2- or (SO3F)- tetrahedron involving the unique P-F or S-F bond serves as such an ABUCB. The distinct chemical bond effectively alters the microscopic nature of the structure building unit, such as polarizability anisotropy, hyperpolarizability, and geometry distortion; this consequently changes the macroscopic second-order nonlinear optical (2nd-NLO) properties of the materials. In this review, we summarize both typical and newly emerged compounds containing ABUCBs. These compounds encompass approximately 90 examples representing six distinct categories, including phosphates, borates, sulfates, silicates, chalcogenides and oxyhalides. Furthermore, we demonstrate that the presence of ABUCBs in DUV/UV NLO compounds contributes to an increase in birefringence and retention of a large band gap, facilitating phase matching in high-energy short-wavelength spectral ranges. On the other hand, the inclusion of ABUCBs in IR NLO compounds offers a feasible method for increasing the band gap and consequently enhancing the larger laser-induced damage threshold. This review consolidates various trial-and-error explorations and presents a novel strategy for designing 2nd-NLO compounds, potentially offering an opportunity for the development of high-performance 2nd-NLO materials.

11.
J Am Chem Soc ; 145(27): 14981-14993, 2023 Jul 12.
Artículo en Inglés | MEDLINE | ID: mdl-37382475

RESUMEN

Thermoelectric copper selenides are highly attractive owing to not only their constituent nontoxic, abundant elements but also their ultralow liquid-like lattice thermal conductivity (κlat). For the first time, the promising thermoelectric properties of the new KCu5Se3 are reported herein, showing a high power factor (PF = 9.0 µWcm-1 K-2) and an intrinsically ultralow κlat = 0.48 Wm-1 K-1. The doped K1-xBaxCu5Se3 (x = 0.03) realizes a figure-of-merit ZT = 1.3 at 950 K. The crystallographic structure of KCu5Se3 allows complex lattice dynamics that obey a rare dual-phonon transport model well describing a high scattering rate and an extremely short phonon lifetime that are attributed to interband phonon tunneling, confinement of the transverse acoustic branches, and temperature-dependent anharmonic renormalization, all of which generate an unprecedently high contribution of the diffusive phonons (70% at 300 K). The overall weak chemical bonding feature of KCu5Se3 gives K+ cations a quiescence behavior that further blocks the heat flux transfer. In addition, the valence band edge energy dispersion of KCu5Se3 is quasilinear that allows a large Seebeck coefficient even at high hole concentrations. These in-depth understandings of the ultralow lattice thermal conductivity provide new insights into the property-oriented design and synthesis of advanced complex chalcogenide materials.

12.
Prostate ; 83(16): 1549-1563, 2023 12.
Artículo en Inglés | MEDLINE | ID: mdl-37583103

RESUMEN

BACKGROUND: Castration-resistant prostate cancer (CRPC) is refractory to hormone treatment and the therapeutic options are continuously advancing. This study aims to discover the anti-CRPC effects and underlying mechanisms of small-molecule compounds targeting topoisomerase (TOP) II and cellular components of DNA damage repair. METHODS: Cell proliferation was determined in CRPC PC-3 and DU-145 cells using anchorage-dependent colony formation, sulforhodamine B assay and flow cytometric analysis of CFSE staining. Flow cytometric analyses of propidium iodide staining and JC-1 staining were used to examine the population of cell-cycle phases and mitochondrial membrane potential, respectively. Nuclear extraction was performed to detect the nuclear localization of cellular components in DNA repair pathways. Protein expressions were determined using Western blot analysis. RESULTS: A series of azathioxanthone-based derivatives were synthesized and examined for bioactivities in which WC-A13, WC-A14, WC-A15, and WC-A16 displayed potent anti-CRPC activities in both PC-3 and DU-145 cell models. These WC-A compounds selectively downregulated both TOP IIα and TOP IIß but not TOP I protein expression. WC-A13, WC-A14, and WC-A15 were more potent than WC-A16 on TOP II inhibition, mitochondrial dysfunction, and induction of caspase cascades indicating the key role of amine-containing side chain of the compounds in determining anti-CRPC activities. Furthermore, WC-A compounds induced an increase of γH2AX and activated ATR-Chk1 and ATM-Chk2 signaling pathways. P21 protein expression was also upregulated by WC-A compounds in which WC-A16 showed the least activity. Notably, WC-A compounds exhibited different regulation on Rad51, a major protein in homologous recombination of DNA in double-stranded break repair. WC-A13, WC-A14, and WC-A15 inhibited, whereas WC-A16 induced, the nuclear translocation of Rad51. CONCLUSION: The data suggest that WC-A compounds exhibit anti-CRPC effects through the inhibition of TOP II activities, leading to mitochondrial stress-involved caspase activation and apoptosis. Moreover, WC-A13, WC-A14, and WC-A15 but not WC-A16 display inhibitory activities of Rad51-mediated DNA repair pathway which may increase apoptotic effect of CRPC cells.


Asunto(s)
Antineoplásicos , Neoplasias de la Próstata Resistentes a la Castración , Masculino , Humanos , Antineoplásicos/uso terapéutico , Neoplasias de la Próstata Resistentes a la Castración/tratamiento farmacológico , Neoplasias de la Próstata Resistentes a la Castración/metabolismo , Línea Celular Tumoral , Apoptosis , Proliferación Celular , Caspasas/metabolismo , Caspasas/farmacología , Caspasas/uso terapéutico , Reparación del ADN , ADN-Topoisomerasas de Tipo II/metabolismo , ADN-Topoisomerasas de Tipo II/farmacología , ADN-Topoisomerasas de Tipo II/uso terapéutico
13.
Bioinformatics ; 38(16): 3877-3884, 2022 08 10.
Artículo en Inglés | MEDLINE | ID: mdl-35766808

RESUMEN

MOTIVATION: MinION, a third-generation sequencer from Oxford Nanopore Technologies, is a portable device that can provide long-nucleotide read data in real-time. It primarily aims to deduce the makeup of nucleotide sequences from the ionic current signals generated when passing DNA/RNA fragments through nanopores charged with a voltage difference. To determine nucleotides from measured signals, a translation process known as basecalling is required. However, compared to NGS basecallers, the calling accuracy of MinION still needs to be improved. RESULTS: In this work, a simple but powerful neural network architecture called multi-scale recurrent caller (MSRCall) is proposed. MSRCall comprises a multi-scale structure, recurrent layers, a fusion block and a connectionist temporal classification decoder. To better identify both short-and long-range dependencies, the recurrent layer is redesigned to capture various time-scale features with a multi-scale structure. The results show that MSRCall outperforms other basecallers in terms of both read and consensus accuracies. AVAILABILITY AND IMPLEMENTATION: MSRCall is available at: https://github.com/d05943006/MSRCall. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Nanoporos , Análisis de Secuencia de ADN/métodos , Redes Neurales de la Computación , ADN , Secuencia de Bases , Secuenciación de Nucleótidos de Alto Rendimiento/métodos
14.
Blood ; 138(23): 2337-2346, 2021 12 09.
Artículo en Inglés | MEDLINE | ID: mdl-34320162

RESUMEN

Myeloid leukemia in children with Down syndrome (ML-DS) is associated with young age and somatic GATA1 mutations. Because of high event-free survival (EFS) and hypersensitivity of the leukemic blasts to chemotherapy, the prior Children's Oncology Group protocol ML-DS protocol (AAML0431) reduced overall treatment intensity but lacking risk stratification, retained the high-dose cytarabine course (HD-AraC), which was highly associated with infectious morbidity. Despite high EFS of ML-DS, survival for those who relapse is rare. AAML1531 introduced therapeutic risk stratification based on the previously identified prognostic factor, measurable residual disease (MRD) at the end of the first induction course. Standard risk (SR) patients were identified by negative MRD using flow cytometry (<0.05%) and did not receive the historically administered HD-AraC course. Interim analysis of 114 SR patients revealed a 2-year EFS of 85.6% (95% confidence interval [CI], 75.7-95.5), which was significantly lower than for MRD- patients treated with HD-AraC on AAML0431 (P = .0002). Overall survival at 2 years was 91.0% (95% CI, 83.8-95.0). Twelve SR patients relapsed, mostly within 1 year from study entry and had a 1-year OS of 16.7% (95% CI, 2.7-41.3). Complex karyotypes were more frequent in SR patients who relapsed compared with those who did not (36% vs 9%; P = .0248). MRD by error-corrected sequencing of GATA1 mutations was piloted in 18 SR patients and detectable in 60% who relapsed vs 23% who did not (P = .2682). Patients with SR ML-DS had worse outcomes without HD-AraC after risk classification based on flow cytometric MRD.


Asunto(s)
Antimetabolitos Antineoplásicos/uso terapéutico , Citarabina/uso terapéutico , Síndrome de Down/complicaciones , Leucemia Mieloide/complicaciones , Leucemia Mieloide/tratamiento farmacológico , Antimetabolitos Antineoplásicos/administración & dosificación , Antimetabolitos Antineoplásicos/efectos adversos , Preescolar , Citarabina/administración & dosificación , Citarabina/efectos adversos , Relación Dosis-Respuesta a Droga , Síndrome de Down/genética , Femenino , Humanos , Lactante , Leucemia Mieloide/diagnóstico , Leucemia Mieloide/genética , Masculino , Neoplasia Residual/diagnóstico , Neoplasia Residual/genética , Pronóstico , Resultado del Tratamiento
15.
Opt Express ; 31(8): 12634-12644, 2023 Apr 10.
Artículo en Inglés | MEDLINE | ID: mdl-37157419

RESUMEN

We study a systematic formation of continuous exceptional points (EPs) in a fully-asymmetric optical microdisk. A parametric generation of chiral EP modes is investigated by analyzing asymmetricity-dependent coupling elements in an effective Hamiltonian. It is shown that given the external perturbation, the frequency splitting around EPs is scaled by the fundamental "strength" of EPs [J. Wiersig, Phys. Rev. Res.4, 023121 (2022)10.1103/PhysRevResearch.4.023121] multiplied by the extra responding strength of the newly added perturbation. Our finding demonstrates that the sensitivity of EP-based sensors can be maximized by carefully examining the continuous formation of EPs.

16.
Phys Rev Lett ; 130(4): 043201, 2023 Jan 27.
Artículo en Inglés | MEDLINE | ID: mdl-36763419

RESUMEN

The Floquet engineering opens the way to create new topological states without counterparts in static systems. Here, we report the experimental realization and characterization of new anomalous topological states with high-precision Floquet engineering for ultracold atoms trapped in a shaking optical Raman lattice. The Floquet band topology is manipulated by tuning the driving-induced band crossings referred to as band inversion surfaces (BISs), whose configurations fully characterize the topology of the underlying states. We uncover various exotic anomalous topological states by measuring the configurations of BISs that correspond to the bulk Floquet topology. In particular, we identify an unprecedented anomalous Floquet valley-Hall state that possesses anomalous helical-like edge modes protected by valleys and a chiral state with high Chern number.

17.
Eur J Nucl Med Mol Imaging ; 50(10): 3072-3083, 2023 08.
Artículo en Inglés | MEDLINE | ID: mdl-37191679

RESUMEN

PURPOSE: Clinical studies on the use of ascorbic acid (AA) have become a hot spot in cancer research. There remains an unmet need to assess AA utilization in normal tissues and tumors. 6-Deoxy-6-[18F]fluoro-L-ascorbic acid ([18F]DFA) displayed distinctive tumor localization and similar distribution as AA in mice. In this study, to evaluate the distribution, tumor detecting ability and radiation dosimetry of [18F]DFA in humans, we performed the first-in-human PET imaging study. METHODS: Six patients with a variety of cancers underwent whole-body PET/CT scans after injection of 313-634 MBq of [18F]DFA. Five sequential dynamic emission scans in each patient were acquired at 5-60 min. Regions of interest (ROI) were delineated along the edge of the source-organ and tumor on the transverse PET slice. Tumor-to-background ratio (TBR) was obtained using the tumor SUVmax to background SUVmean. Organ residence times were calculated via time-activity curves, and human absorbed doses were estimated from organ residence time using the medical internal radiation dosimetry method. RESULTS: [18F]DFA was well tolerated in all subjects without serious adverse event. The high uptake was found in the liver, adrenal glands, kidneys, choroid plexus, and pituitary gland. [18F]DFA accumulated in tumor rapidly and the TBR increased over time. The average SUVmax of [18F]DFA in tumor lesions was 6.94 ± 3.92 (range 1.62-22.85, median 5.94). The organs with the highest absorbed doses were the liver, spleen, adrenal glands, and kidneys. The mean effective dose was estimated to be 1.68 ± 0.36 E-02 mSv/MBq. CONCLUSIONS: [18F]DFA is safe to be used in humans. It showed a similar distribution pattern as AA, and displayed high uptake and retention in tumors with appropriate kinetics. [18F]DFA might be a promising radiopharmaceutical in identifying tumors with high affinity for SVCT2 and monitoring AA distribution in both normal tissues and tumors. TRIAL REGISTRATION: Chinese Clinical Trial Registry; Registered Number: ChiCTR2200057842 (registered 19 March 2022).


Asunto(s)
Neoplasias , Tomografía Computarizada por Tomografía de Emisión de Positrones , Humanos , Animales , Ratones , Tomografía Computarizada por Tomografía de Emisión de Positrones/métodos , Distribución Tisular , Neoplasias/diagnóstico por imagen , Radiometría , Tomografía de Emisión de Positrones/métodos
18.
J Biomed Sci ; 30(1): 30, 2023 May 03.
Artículo en Inglés | MEDLINE | ID: mdl-37138292

RESUMEN

The coronavirus disease 2019 (COVID-19) pandemic has impacted human lifestyles around the world, causing huge distress in terms of public health systems, emergency response capacity and economic development. The causative agent of COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is associated with respiratory involvement, cardiovascular-related diseases, and ultimately causes multiple organ failure and death in severely affected individuals. Thus, effective prevention or early treatment of COVID-19 is critical. An effective vaccine offers a way out of the pandemic for governments, the scientific community and people worldwide, but we still lack effective drug therapies, including treatments for the prevention and treatment of COVID-19. This had led to a high global demand for many complementary and alternative medicines (CAMs). Moreover, many healthcare providers are now requesting information about CAMs that prevent, relieve, or treat the symptoms of COVID-19 and even alleviate vaccine-related side effects. Experts and scholars must therefore become familiar with the use of CAMs in COVID-19, current research directions and effectiveness of CAMs for COVID-19. This narrative review updates the current status and research worldwide on the use of CAMs for COVID-19. The review provides reliable evidence on theoretical viewpoints and therapeutic efficacies of CAM combinations, and evidence in support of the therapeutic strategy of Taiwan Chingguan Erhau (NRICM102) against moderate-to-severe novel coronavirus infectious disease in Taiwan.


Asunto(s)
COVID-19 , Humanos , COVID-19/terapia , SARS-CoV-2 , Taiwán
19.
J Biomed Sci ; 30(1): 32, 2023 May 22.
Artículo en Inglés | MEDLINE | ID: mdl-37217939

RESUMEN

BACKGROUND: Nutrient limitations often lead to metabolic stress during cancer initiation and progression. To combat this stress, the enzyme heme oxygenase 1 (HMOX1, commonly known as HO-1) is thought to play a key role as an antioxidant. However, there is a discrepancy between the level of HO-1 mRNA and its protein, particularly in cells under stress. O-linked ß-N-acetylglucosamine (O-GlcNAc) modification of proteins (O-GlcNAcylation) is a recently discovered cellular signaling mechanism that rivals phosphorylation in many proteins, including eukaryote translation initiation factors (eIFs). The mechanism by which eIF2α O-GlcNAcylation regulates translation of HO-1 during extracellular arginine shortage (ArgS) remains unclear. METHODS: We used mass spectrometry to study the relationship between O-GlcNAcylation and Arg availability in breast cancer BT-549 cells. We validated eIF2α O-GlcNAcylation through site-specific mutagenesis and azido sugar N-azidoacetylglucosamine-tetraacylated labeling. We then evaluated the effect of eIF2α O-GlcNAcylation on cell recovery, migration, accumulation of reactive oxygen species (ROS), and metabolic labeling during protein synthesis under different Arg conditions. RESULTS: Our research identified eIF2α, eIF2ß, and eIF2γ, as key O-GlcNAcylation targets in the absence of Arg. We found that O-GlcNAcylation of eIF2α plays a crucial role in regulating antioxidant defense by suppressing the translation of the enzyme HO-1 during Arg limitation. Our study showed that O-GlcNAcylation of eIF2α at specific sites suppresses HO-1 translation despite high levels of HMOX1 transcription. We also found that eliminating eIF2α O-GlcNAcylation through site-specific mutagenesis improves cell recovery, migration, and reduces ROS accumulation by restoring HO-1 translation. However, the level of the metabolic stress effector ATF4 is not affected by eIF2α O-GlcNAcylation under these conditions. CONCLUSIONS: Overall, this study provides new insights into how ArgS fine-tunes the control of translation initiation and antioxidant defense through eIF2α O-GlcNAcylation, which has potential biological and clinical implications.


Asunto(s)
Arginina , Factor 2 Eucariótico de Iniciación , Hemo-Oxigenasa 1 , Antioxidantes , Factor 2 Eucariótico de Iniciación/genética , Factor 2 Eucariótico de Iniciación/metabolismo , Hemo-Oxigenasa 1/genética , Homeostasis , Especies Reactivas de Oxígeno/metabolismo , Humanos
20.
Pharmacol Res ; 192: 106781, 2023 06.
Artículo en Inglés | MEDLINE | ID: mdl-37119880

RESUMEN

Targeting single tumor antigens makes it difficult to provide sufficient tumor selectivity for T cell engagers (TCEs), leading to undesirable toxicity and even treatment failure, which is particularly serious in solid tumors. Here, we designed novel trispecific TCEs (TriTCEs) to improve the tumor selectivity of TCEs by logic-gated dual tumor-targeting. TriTCE can effectively redirect and activate T cells to kill tumor cells (∼18 pM EC50) by inducing the aggregation of dual tumor antigens, which was ∼70- or 750- fold more effective than the single tumor-targeted isotype controls, respectively. Further in vivo experiments indicated that TriTCE has the ability to accumulate in tumor tissue and can induce circulating T cells to infiltrate into tumor sites. Hence, TriTCE showed a stronger tumor growth inhibition ability and significantly prolonged the survival time of the mice. Finally, we revealed that this concept of logic-gated dual tumor-targeted TriTCE can be applied to target different tumor antigens. Cumulatively, we reported novel dual tumor-targeted TriTCEs that can mediate a robust T cell response by simultaneous recognition of dual tumor antigens at the same cell surface. TriTCEs allow better selective T cell activity on tumor cells, resulting in safer TCE treatment.


Asunto(s)
Neoplasias , Linfocitos T , Ratones , Animales , Neoplasias/metabolismo , Antígenos de Neoplasias
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