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Article
Open AccessMechanism of ERBB2 gene overexpression by the formation of super-enhancer with genomic structural abnormalities in lung adenocarcinoma without clinically actionable genetic alterations
In an extensive genomic analysis of lung adenocarcinomas (LUADs), driver mutations have been recognized as potential targets for molecular therapy. However, there remain cases where target genes are not identi...
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Article
Open AccessGenomic profiles of Japanese patients with vulvar squamous cell carcinoma
The incidence of vulvar carcinoma varies by race; however, it is a rare disease, and its genomic profiles remain largely unknown. This study examined the characteristics of vulvar squamous cell carcinoma (VSCC...
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Article
Open AccessAdvances in cancer DNA methylation analysis with methPLIER: use of non-negative matrix factorization and knowledge-based constraints to enhance biological interpretability
DNA methylation is an epigenetic modification that results in dynamic changes during ontogenesis and cell differentiation. DNA methylation patterns regulate gene expression and have been widely researched. Whi...
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Article
Open AccessIntegrative analysis reveals early epigenetic alterations in high-grade serous ovarian carcinomas
High-grade serous ovarian carcinoma (HGSOC) is the most lethal gynecological malignancy. To date, the profiles of gene mutations and copy number alterations in HGSOC have been well characterized. However, the ...
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Article
Open AccessUtility of molecular subtypes and genetic alterations for evaluating clinical outcomes in 1029 patients with endometrial cancer
We investigated the utility of a molecular classifier tool and genetic alterations for predicting prognosis in Japanese patients with endometrial cancer.
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Article
Open AccessThe UFM1 system regulates ER-phagy through the ufmylation of CYB5R3
Protein modification by ubiquitin-like proteins (UBLs) amplifies limited genome information and regulates diverse cellular processes, including translation, autophagy and antiviral pathways. Ubiquitin-fold mod...
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Article
Open AccessRepression of the PRELP gene is relieved by histone deacetylase inhibitors through acetylation of histone H2B lysine 5 in bladder cancer
Proline/arginine-rich end leucine-rich repeat protein (PRELP) is a member of the small leucine-rich proteoglycan family of extracellular matrix proteins, which is markedly suppressed in the majority of early-s...
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Article
Open AccessPredictive model for the preoperative assessment and prognostic modeling of lymph node metastasis in endometrial cancer
Lymph node metastasis (LNM) is a well-established prognostic factor in endometrial cancer (EC). We aimed to construct a model that predicts LNM and prognosis using preoperative factors such as myometrial invas...
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Article
Author Correction: LC3 lipidation is essential for TFEB activation during the lysosomal damage response to kidney injury
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Article
Open AccessIntroducing AI to the molecular tumor board: one direction toward the establishment of precision medicine using large-scale cancer clinical and biological information
Since U.S. President Barack Obama announced the Precision Medicine Initiative in his New Year’s State of the Union address in 2015, the establishment of a precision medicine system has been emphasized worldwid...
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Article
Impaired GATE16-mediated exocytosis in exocrine tissues causes Sjögren’s syndrome-like exocrinopathy
Sjögren’s syndrome (SjS) is a chronic autoimmune disease characterized by immune cell infiltration of the exocrine glands, mainly the salivary and lacrimal glands. Despite recent advances in the clinical and m...
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Article
Open AccessThe metabolic stress-activated checkpoint LKB1-MARK3 axis acts as a tumor suppressor in high-grade serous ovarian carcinoma
High-grade serous ovarian carcinoma (HGSOC) is the most aggressive gynecological malignancy, resulting in approximately 70% of ovarian cancer deaths. However, it is still unclear how genetic dysregulations and...
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Article
Open AccessTP53 mutants and non-HPV16/18 genotypes are poor prognostic factors for concurrent chemoradiotherapy in locally advanced cervical cancer
Targeted sequencing for somatic mutations across the hotspots of 50 cancer-related genes was performed using biopsy specimens to investigate whether clinicopathological factors and genomic alterations correlat...
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Article
Membrane perturbation by lipidated Atg8 underlies autophagosome biogenesis
Autophagosome biogenesis is an essential feature of autophagy. Lipidation of Atg8 plays a critical role in this process. Previous in vitro studies identified membrane tethering and hemi-fusion/fusion activitie...
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Article
Open AccessEssential role of autophagy in protecting neonatal haematopoietic stem cells from oxidative stress in a p62-independent manner
Autophagy is a cellular degradation system contributing to homeostasis of tissue stem cells including haematopoietic stem cells (HSCs). It plays pleiotropic roles in HSC characteristics throughout life, but it...
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Article
Open Accessp62/SQSTM1-droplet serves as a platform for autophagosome formation and anti-oxidative stress response
Autophagy contributes to the selective degradation of liquid droplets, including the P-Granule, Ape1-complex and p62/SQSTM1-body, although the molecular mechanisms and physiological relevance of selective degr...
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Article
LC3 lipidation is essential for TFEB activation during the lysosomal damage response to kidney injury
Sensing and clearance of dysfunctional lysosomes is critical for cellular homeostasis. Here we show that transcription factor EB (TFEB)—a master transcriptional regulator of lysosomal biogenesis and autophagy—...
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Article
Open AccessAutophagy regulates lipid metabolism through selective turnover of NCoR1
Selective autophagy ensures the removal of specific soluble proteins, protein aggregates, damaged mitochondria, and invasive bacteria from cells. Defective autophagy has been directly linked to metabolic disor...
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Article
Open AccessAutophagy attenuates tubulointerstital fibrosis through regulating transforming growth factor-β and NLRP3 inflammasome signaling pathway
Renal fibrosis is the final common pathway of various renal injuries and it leads to chronic kidney disease. Autophagy is a cellular process of degradation of damaged cytoplasmic components and regulates cell ...
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Protocol
Measuring Nonselective and Selective Autophagy in the Liver
Administration of leupeptin, a specific inhibitor of lysosomal cysteine proteinases, to starved rats or mice inhibits autolysosomal protein degradation and results in accumulation of autolysosomes in their liv...
