bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intracellular Retention of Estradiol is Mediated by GRAM Domain-Containing Protein ASTER-B in Breast Cancer Cells
Authors: Kim Hyung Bum , Kraus W. Lee 
Published: May 2024

AbstractElevated blood levels of estrogens have been associated with poor prognosis in estrogen receptor-positive (ER+) breast cancers, but the relationship between circulating hormone levels in the blood and intracellular hormone concentrations are not well characterized. We observed that MCF-7 cells treated acutely with 17β-estradiol (E2) retain a substantial amount of the hormone even upon removal of the hormone from the culture medium. Moreover, global patterns of E2-dependent gene expression are sustained for hours after acute E2 treatment and hormone removal. While circulating E2 is sequestered by sex hormone binding globulin (SHBG), the potential mechanisms of intracellular E2 retention are poorly understood. We found that a mislocalization of a steroid-binding GRAM-domain containing protein, ASTER-B, to the nucleus, which is observed in a subset of breast cancer patients, is associated with higher cellular E2 retention. Accumulation and retention of E2 are related to the steroidal properties of E2, and require nuclear localization and steroid binding by ASTER-B, as shown using a panel of mutant ASTER-B proteins. Finally, we observed that nuclear ASTER-B-mediated E2 retention is required for sustained hormone-induced ERα chromatin occupancy at enhancers and gene expression, as well as subsequent cell growth responses. Our results add intracellular hormone retention as a mechanism controlling E2-dependent gene expression and downstream biological outcomes.SignificanceThis study demonstrates how E2 can be accumulated and retained intracellularly to drive a pro-proliferative gene expression program in ER+ breast cancer cells. Mechanistically, intracellular E2 retention is mediated in part by mislocalized nuclear ASTER-B, which binds estradiol to support the functions of ER, including E2-mediated gene expression
Beyond the phloem: A general role of the ArabidopsisOCTOPUSgene family in controlling plant growth vigour
Authors: Crivelli Simona , Bartusch Kai , Ruiz-Sola M. Aguila , Coiro Mario , Schmidt Kjølner Hansen Signe , Truernit Elisabeth 
Published: May 2024

SummaryOCTOPUS(OPS) andOCTOPUS-LIKE 2(OPL2), two homologous genes, were previously identified as important regulators of phloem differentiation in Arabidopsis roots, impacting root growth when their function is lost. Here, we investigated the roles of the other threeOPShomologs in Arabidopsis,OPL1,OPL3, andOPL4. We employed promoter activity analyses, protein localisation studies, functional complementation assays, analysis of single and multiple mutant combinations, and growth assays, including exposure to CLE45 and brassinosteroid pathway modulators. TheOPS/OPLgenes exhibit overlapping expression patterns and functions. Multiple mutant combinations revealed a high degree of redundancy, withOPSand the phloem domain playing a major role in controlling plant growth. While phloem phenotypes are not exacerbated in higher-order mutants, plant growth vigour is nevertheless more severely impacted than inops opl2. Our results suggest a novel role of theOPS/OPLgenes in broadly controlling plant growth and development, potentially through the modulation of meristematic activity via brassinosteroid pathways.
Investigation of the isomerization oftrans- andcis-cinnamic acid in Arabidopsis using stable-isotope-labeled cinnamic acid isomers
Authors: Tsuzuki Kei , Suzuki Taiki , Nishiyama Kotaro , Seto Yoshiya 
Published: May 2024

AbstractCinnamic acid (CA) is a widely distributed metabolite in plant species and is a precursor of many important plant molecules, including lignin, flavonoids, and coumarins. CA exists as bothtransandcisisomers; thetransisomer is more stable and common in nature. Previous reports have revealed that thecisisomer of CA (cis-CA) has auxin-like activity when exogenously applied. However, it has also been reported thatcis-CA does not function as an auxin but affects its transport. Although these reports suggest a crucial role forcis-CA as an endogenous signaling molecule, its exact function and mechanism of isomerization fromtrans-CA remain unclear. Here, we report the chemical synthesis of stable-isotope-labeledtrans- andcis-CA. Using these labeled compounds as internal standards, we developed a quantification method of CA using LC–MS/MS. Moreover, we monitored the endogenous conversion fromtrans-tocis-CA using the labeled compounds, demonstrating the UV-dependent and UV-independent CA isomerization in Arabidopsis. Additionally, we identifiedcis-CA in diverse plant species, including liverwort.
Experimental myositis: an optimised version of C-protein-induced myositis
Authors: Giannini M , Rovito D , Oulad-Abdelghani M , Messaddeq N , Debrut L , Kessler P , Charles AL , Geny B , Metzger D , Laverny G , Meyer A 
Published: May 2024

IntroductionInflammatory myopathies (IM) are a group of severe autoimmune diseases, sharing some similarities, whose cause is unknown and treatment is empirical. While C-protein-induced myositis (CIM), the most currently used model of IM, has removed some roadblock to understand and improve the treatment of IM, it has only been partially characterised and its generation limited by reproducibility issues. This study aimed at optimising the generation and the characterisation of CIM.MethodsIn silicoanalysis was run to identify the top-3 specific and immunogenic regions of C-protein. The cognate polypeptides were synthetised and used to immunise C57BL/6N mice. Grip strength, walking ability, serum creatine-kinase levels and muscle pathology (histological and electron microscopic features) were assessed. Immune cell proportions and interferon signature in muscles were also determined.ResultsAmong the three C-protein polypeptides with the highest immunogenic score, amino acids 965-991 induced the most severe phenotype (i.e., 37% decrease in strength, 36% increase in hind base width, 45% increase in serum creatine-kinase level, 80% increase in histological inflammatory score) from day (D) 14 to at least D31 after immunisation [experimental myositis (EM)]. Optical and electron microscopy revealed mononuclear cell infiltrate, myofibre necrosis, atrophy, MHC-I expression as well as sarcolemmal, sarcomeric and mitochondrial abnormalities. Proinflammatory T-lymphocytes, macrophages, type-I and II interferon-stimulated transcripts were found within the muscle of EM mice.ConclusionEM recapitulates the common hallmarks of IM. This costless, high throughput, reproducible and stable model, generated in the most commonly used background for genetically engineered mice, may foster pre-clinical research in IM.Key messagesWhat is already known on this topicC-protein-induced myositis is currently the most used model of inflammatory myopathies but has been partially characterised and its generation is limited by reproducibility issues.What this study adds.Immunisation against the polypeptide encompassing C-protein amino acids 965-991 induces a costless, high throughput, reproducible and stable model of myositis (experimental myositis) that recapitulates the common hallmarks of inflammatory myopathies.How this study might affect research, practice or policyExperimental myositis, generated in the most used background for genetically engineered mice (C57BL/6N), might foster pre-clinical research in IM.
Triptolide sensitizes cancer cells to nucleoside DNA methyltransferase inhibitors through inhibition of DCTPP1-mediated cell-intrinsic resistance
Authors: Liu Jianyong , He Qing-Li , Zhou Jianya , Chikarmane Roshan , Hauk Glenn , Rachakonda Archana , Vaghasia Ajay M. , Castagna Nicole , Steinberg Ruchama C. , Pham Minh-Tam , Anders Nicole M. , Wanjiku Teresia M. , Nuhn Philipp , Shim Joong Sup , Giovinazzo Hugh , Esopi David M. , Kim Kunhwa , Coulter Jonathan , Wang Rulin , Zhou Jianying , Rudek Michelle A. , Berger James M. , Liu Jun O. , Nelson William G. , Yegnasubramanian Srinivasan 
Published: May 2024

SUMMARYWhile nucleoside DNA methyltransferase inhibitors (DNMTi) such as decitabine and azacitidine are effective in treating myelodysplatic syndrome (MDS)/leukemia, they have had limited utility for the majority of other cancers. Through a chemical library screen, we identified that triptolide, a diterpenoid epoxide fromTripterygium wilfordii, or analogs significantly augmented the epigenetic and anti-cancer effects of decitabinein vitroandin vivo. These effects were attributable to inhibition of DCTPP1-mediated cleavage of 5-aza-deoxycytidine triphosphate, the convergent activated metabolite of nucleoside DNMTi, leading to enhanced drug incorporation into genomic DNA, increased DNMT degradation, enhanced global DNA demethylation and associated transcriptional reprogramming. We show that high DCTPP1 expression was associated with cell-intrinsic resistance to nucleoside DNMTi, and that triptolide and its analogs could overcome this resistance.SIGNIFICANCEWe screened a library of existing drugs to identify those capable of enhancing the anti-cancer effects of the nucleoside DNMTi decitabine. The combination of triptolide and decitabine synergistically inhibited cancer cell growth and survivalin vitro, and was highly effective in inhibiting xenograft growthin vivo. Biochemical, genetic and structural biology studies with triptolide and its analogs revealed that this synergy was due to their inhibition of DCTPP1-mediated pyrophosphate cleavage from 5-aza-deoxycytidine triphosphate, the active metabolite of DNMTi. The genomic incorporation and efficacy of decitabine in cancer cell lines were significantly correlated with DCTPP1 expression more so than those of other nucleoside metabolizing genes. Triptolide and its analogs comprise rational adjuncts to nucleoside DNMTi ripe for further pre-clinical/clinical translation.HIGHLIGHTSTriptolide synergistically sensitizes cancer cells to DNMTiin vitro.Triptolide and decitabine combination shows favorable efficacy and safetyin vivo.Synergy of triptolide and decitabine is mediated through inhibition of DCTPP1.High DCTPP1 expression confers cell intrinsic resistance to DNMTi.
Novel and Efficient Plasmid Transfection Protocols for Functional Analysis of Genetic Elements in Human Cardiac Fibroblasts
Authors: Makoto MATSUYAMA , Takahiro IWAMIYA 
Published: May 2024

AbstractCardiac fibroblasts, have lower gene transfer efficiency compared to dermal fibroblasts, posing challenges for plasmid-based gene transfer methods. A higher transfer efficiency could enable improved insight into heart pathology and development of novel therapeutic targets.In this study we compared eleven commercially available transfection reagents and eight plasmid purification methods. Finally, we systematically evaluated 150 unique transfection conditions (incubation times, addition of innate immune inhibitors, reagent to plasmid ratios etc) to optimize the methodology.The aim was to develop an optimized plasmid transfection protocol specifically tailored for primary human cardiac fibroblasts with high efficiency and minimal toxicity. Leveraging our newly developed methodology, we could perform comprehensive profiling of nine viral and native enhancer/promoters, revealing regulatory sequences governing classical fibroblast marker (VIM) and resident cardiac fibroblast marker (TCF21) expression. We believe that these findings can help advance many aspects of cardiovascular research.In conclusion, we here report for the first time a plasmid transfection protocol for cardiac fibroblasts with minimal cell toxicity.
Transcriptional control of central T cell tolerance by NR4A family nuclear receptors
Authors: Nielsen Hailyn V. , Mueller James L. , Hiwa Ryosuke , Yang Letitia , Proekt Irena , Rackaityte Elze , Aylard Dominik , Scharer Christopher D. , Anderson Mark , Au-Yeung Byron , Zikherman Julie 
Published: May 2024

AbstractAlthough deletion of self-reactive thymocytes and their diversion into regulatory T cell (Treg) lineage are critical for immune tolerance and homeostasis, the molecular pathways that link antigen recognition to these fates are incompletely understood. The Nr4a nuclear hormone receptors are transcriptionally upregulated in response to TCR signaling in the thymus and are implicated in both deletion and diversion, but the mechanisms by which they operate are not clear. Redundancy among the family members and their requirement for Treg generation and maintenance have obscured their role in negative selection. Here we take advantage of competitive bone marrow chimeras and the OT-II/RIPmOVA model to demonstrate thatNr4a1andNr4a3are essential for upregulation ofBcl2l11/BIM and negative selection by tissue-restricted model self-antigen (TRA). Moreover, we reveal that the Nr4a family is absolutely required for full induction of a broad transcriptional program triggered in self-reactive thymocytes by TRA recognition, and conserved across model systems and the natural repertoire. Importantly, both model self antigen-specific TCR Tg and polyclonal thymocytes lackingNr4a1/3that escape negative selection acquire an anergy-like program that persists in the periphery and is also evident among wild-type recent thymic emigrants (RTEs). We propose that the Nr4a family transduces TCR signals during thymic development to enforce the fates of highly self-reactive clones, mediating not only deletion and Treg diversion, but also contributing to a cell-intrinsic, persistent anergy-like program that may operate at the margins of canonical thymic tolerance mechanisms to restrain self-reactive T cells after thymic egress.
Cholesterol Restriction Primes RIG-I Antiviral Responses Through a Noncanonical Type I IFN Pathway
Authors: Nishimura Tasuku , Kouwaki Takahisa , Takashima Ken , Ochi Akie , Mtali Yohana S , Oshiumi Hiroyuki 
Published: May 2024

AbstractCholesterol metabolism is associated with innate immune responses; however, the mechanisms underlying this have not been fully elucidated. Here, we performed a chemical screening to isolate small molecules affecting the activity of RIG-I, a cytoplasmic viral RNA sensor, and found that statins, which inhibit cholesterol synthesis, dramatically enhanced RIG-I-dependent antiviral responses in specific cell types. The restriction of cholesterol synthesis induced the expression of noncanonical type I interferons (IFNs), such as IFN-ω, in an SREBP1 transcription factor-dependent manner. This noncanonical type I IFN expression pathway subsequently enhanced RIG-I-mediated signaling following viral infection. Administration of statins in mice augmented RIG-I-dependent cytokine expression in the lungs. Conversely, a mouse obesity model exhibited reduced RIG-I response in the lungs compared to wild-type mice. Single-cell transcriptome analyses revealed a subset of alveolar macrophages that increased the RIG-I expression in response to inhibited cholesterol synthesis in vivo. This study revealed the noncanonical type I IFN pathway linking cholesterol metabolism and RIG-I signaling. Targeting this pathway could offer valuable insights for developing novel treatment approaches to address future viral pandemics.
Health Disparities and Reporting Gaps in Artificial Intelligence (AI) Enabled Medical Devices: A Scoping Review of 692 U.S. Food and Drug Administration (FDA) 510k Approvals
Authors: Muralidharan Vijaytha , Adewale Boluwatife Adeleye , Huang Caroline J , Nta Mfon Thelma , Ademiju Peter Oluwaduyilemi , Pathmarajah Pirunthan , Hang Man Kien , Adesanya Oluwafolajimi , Abdullateef Ridwanullah Olamide , Babatunde Abdulhammed Opeyemi , Ajibade Abdulquddus , Onyeka Sonia , Cai Zhou Ran , Daneshjou Roxana , Olatunji Tobi 
Published: May 2024

AbstractMachine learning and artificial intelligence (AI/ML) models in healthcare may exacerbate health biases. Regulatory oversight is critical in evaluating the safety and effectiveness of AI/ML devices in clinical settings. We conducted a scoping review on the 692 FDA 510k-approved AI/ML-enabled medical devices to examine transparency, safety reporting, and sociodemographic representation. Only 3.6% of approvals reported race/ethnicity, 99.1% provided no socioeconomic data. 81.6% did not report the age of study subjects. Only 46.1% provided comprehensive detailed results of performance studies; only 1.9% included a link to a scientific publication with safety and efficacy data. Only 9.0% contained a prospective study for post-market surveillance. Despite the growing number of market-approved medical devices, our data shows that FDA reporting data remains inconsistent. Demographic and socioeconomic characteristics are underreported, exacerbating the risk of algorithmic bias and health disparity.
Genetic Variants and Therapeutic Approaches in Maturity-Onset Diabetes of the Young: A Retrospective Analysis
Authors: Deng Lily , Shah Amy S. , Krishnamurthy Mansa 
Published: May 2024

AbstractContextIdentifying Maturity-Onset Diabetes of the Young (MODY) in patients with diabetes is essential because treatment differs significantly from other forms of diabetes. We identified patients with MODY gene variants and evaluated their clinical characteristics and responses to treatment.Evidence AcquisitionWe identified 106 patients with genetic MODY variants. Demographics, islet autoantibodies at diabetes diagnosis, co-morbidities, and response to treatment by genetic variant were evaluated.Evidence SynthesisPatients diagnosed with MODY variants comprised 4% of the total population with diabetes. Mean age and HbA1c of patients with MODY at diagnosis were 10.5 years and 8.2%, respectively. Surprisingly, diabetic ketoacidosis was a presenting feature for some (n=7, 6.8%), and others with MODY had positive islet cell autoantibodies (n= 7, 6.6%). Variants in HNF1A, GCK, and HNF1B were frequently observed (20%, 22%, and 17% respectively), while rare variants in PDX1, RFX6, BLK, and CNOT1 were uncovered. Initial and follow up treatment of patients with MODY were compared. For each medication (Insulin, Metformin, Sulfonylureas, and GLP-1 receptor agonists), a reduction in HbA1c was observed at follow-up (0.3-21%). Insulin and sulfonylureas were associated with an increase in average BMI (insulin: +8.23%, n=21, sulfonylurea: +0.63%, n=12) at follow-up, metformin was intermediate (−2.46%, n=4), and GLP-1 receptor agonists demonstrated the greatest decrease in BMI (−4.79%, n=4).ConclusionsThe presence of islet autoantibodies or diabetic ketoacidosis does not preclude the diagnosis of MODY. Given the observed improvements in BMI and HbA1c, further investigation into the use of GLP-1 receptor agonists as treatment for MODY should be considered.
Human TRMT1 and TRMT1L paralogs ensure the proper modification state, stability, and function of tRNAs
Authors: Zhang Kejia , Manning Aidan C. , Lentini Jenna M. , Howard Jonathan , Dalwigk Felix , Maroofian Reza , Efthymiou Stephanie , Chan Patricia , Eliseev Sergei I. , Yang Zi , Chang Hayley , Karimiani Ehsan Ghayoor , Bakhshoodeh Behnoosh , Houlden Henry , Kaiser Stefanie M. , Lowe Todd M. , Fu Dragony 
Published: May 2024

SummaryThe tRNA methyltransferase 1 (TRMT1) enzyme catalyzes m2,2G modification in tRNAs. Intriguingly, vertebrates encode an additional tRNA methyltransferase 1-like (TRMT1L) paralog. Here, we use a comprehensive tRNA sequencing approach to decipher targets of human TRMT1 and TRMT1L. We find that TRMT1 methylates all known tRNAs containing guanosine at position 26 while TRMT1L represents the elusive enzyme catalyzing m2,2G at position 27 in tyrosine tRNAs. Surprisingly, TRMT1L is also necessary for maintaining acp3U modifications in a subset of tRNAs through a process that can be uncoupled from methyltransferase activity. We also demonstrate that tyrosine and serine tRNAs are dependent upon m2,2G modifications for their stability and function in translation. Notably, human patient cells with disease-associated TRMT1 variants exhibit reduced levels of tyrosine and serine tRNAs. These findings uncover unexpected roles for TRMT1 paralogs, decipher functions for m2,2G modifications, and pinpoint tRNAs dysregulated in human disorders caused by tRNA modification deficiency.
Automated Xeno-Free Chondrogenic Differentiation from Human Embryonic Stem Cells: Enhancing Efficiency and Ensuring High-Quality Mass Production
Authors: Chen JunLong , Kataoka Oki , Tsuchiya Kazeto , Oishi Yoshie , Takao Ayumi , Huang Yen-Chih , Komura Hiroko , Akiyama Saeko , Itou Ren , Inui Masafumi , Enosawa Shin , Akutsu Hidenori , Komura Makoto , Fuchimoto Yasushi , Umezawa Akihiro 
Published: May 2024

AbstractIntroductionRepairing damaged cartilage poses significant challenges, particularly in cases of congenital cartilage defects such as microtia or congenital tracheal stenosis, or as a consequence of traumatic injury, as the regenerative potential of cartilage is inherently limited. Stem cell therapy and tissue engineering offer promising approaches to overcome these limitations in cartilage healing. However, the challenge lies in the size of cartilage-containing organs, which necessitates a large quantity of cells to fill the damaged areas. Therefore, pluripotent stem cells that can proliferate indefinitely are highly desirable as a cell source. This study aims to delineate the differentiation conditions for cartilage derived from human embryonic stem cells (ESCs) and to develop an automated cell culture system to facilitate mass production for therapeutic applications.MethodsCartilage cell sheets were derived from human ESCs (SEES2, clinical trial-compatible line) by forming embryoid bodies (EBs) with either conventional manual culture or a benchtop multi-pipetter and an automated medium exchange integrated cell incubator, using xeno-free media. Cell sheets were implanted into the subcutaneous tissue of immunodeficient NOG mice to obtain cartilage tissue. The properties of cartilage tissues were examined by histological staining and quantitative PCR analysis.ResultsWe have optimized an efficient xeno-free system for cartilage production with the conventional culture method and successfully transitioned to an automated system. Differentiated cartilage was histologically uniform with cartilage-specific elasticity and strength. The cartilage tissues were stained by alcian blue, safranin O, and toluidine blue, and quantitative PCR showed an increase in differentiation markers such as ACAN, COL2A1, and Vimentin. Automation significantly enhanced the efficiency of human ESC-derived chondrocyte differentiation. The number of constituent cells within EBs and the seeding density of EBs were identified as key factors influencing chondrogenic differentiation efficiency. By automating the process of chondrogenic differentiation, we achieved scalable production of chondrocytes.ConclusionsBy integrating the differentiation protocol with an automated cell culture system, there is potential to produce cartilage of sufficient size for clinical applications in humans. The resulting cartilage tissue holds promise for clinical use in repairing organs such as the trachea, joints, ears, and nose.