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Tatyana Novoyatleva et al.
Communications biology, 4(1), 1002-1002 (2021-08-26)
Pulmonary arterial hypertension (PAH), is a fatal disease characterized by a pseudo-malignant phenotype. We investigated the expression and the role of the receptor tyrosine kinase Axl in experimental (i.e., monocrotaline and Su5416/hypoxia treated rats) and clinical PAH. In vitro Axl
Di Xiao et al.
iScience, 25(6), 104489-104489 (2022-06-21)
Myogenesis is governed by signaling networks that are tightly regulated in a time-dependent manner. Although different protein kinases have been identified, knowledge of the global signaling networks and their downstream substrates during myogenesis remains incomplete. Here, we map the myogenic
Tianliang Sun et al.
Cell stem cell, 26(1), 97-107 (2019-12-24)
The existence of specialized liver stem cell populations, including AXIN2+ pericentral hepatocytes, that safeguard homeostasis and repair has been controversial. Here, using AXIN2 lineage tracing in BAC-transgenic mice, we confirm the regenerative potential of intestinal stem cells (ISCs) but find
Zhe Yang et al.
Biomedicines, 11(7) (2023-07-29)
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the global coronavirus disease 2019 (COVID-19) pandemic, and the search for effective treatments has been limited. Furthermore, the rapid mutations of SARS-CoV-2 have posed challenges to existing
eIF4E phosphorylation recruits I?-catenin to mRNA cap and promotes Wnt pathway translation in dentate gyrus LTP maintenance.
Patil, et al.
iScience, 26, 106649-106649 (2023)
Sang-Won Park et al.
Autophagy, 19(5), 1424-1443 (2022-10-18)
A:C autophagic membrane:cytosol; ALS amyotrophic lateral sclerosis; ATG4 autophagy related 4; Atg8 autophagy related 8; BafA1 bafilomycin A1; BNIP3L/Nix BCL2 interacting protein 3 like; CALCOCO2/NDP52 calcium binding and coiled-coil domain 2; EBSS Earle's balanced salt solution; GABARAP GABA type A
Emmanuelle V LeBlanc et al.
Current protocols, 1(1), e17-e17 (2021-01-24)
Fungi infect over a billion people worldwide and contribute substantially to human morbidity and mortality despite all available therapies. New antifungal drugs are urgently needed. Decades of study have revealed numerous protein targets of potential therapeutic interest for which potent
Ikram Ullah et al.
Cell reports, 39(9), 110895-110895 (2022-06-02)
The ATP-dependent nucleosome remodeler Mi-2/CHD4 broadly modulates chromatin landscapes to repress transcription and to maintain genome integrity. Here we use individual nucleotide resolution crosslinking and immunoprecipitation (iCLIP) to show that Drosophila Mi-2 associates with thousands of mRNA molecules in vivo. Biochemical
Michael Landowski et al.
Scientific reports, 12(1), 756-756 (2022-01-16)
Aging is a significant factor in the development of age-related diseases but how aging disrupts cellular homeostasis to cause age-related retinal disease is unknown. Here, we further our studies on transmembrane protein 135 (Tmem135), a gene involved in retinal aging
Mai B Thayer et al.
Scientific reports, 10(1), 10425-10425 (2020-06-28)
Oligonucleotide therapeutics use short interfering RNA (siRNA) or antisense oligonucleotide (ASO) molecules to exploit endogenous systems-neutralizing target RNA to prevent subsequent protein translation. While the potential clinical application is vast, delivery efficiency and extrahepatic targeting is challenging. Bioanalytical assays are
Coline Arnould et al.
Methods in molecular biology (Clifton, N.J.), 2153, 427-438 (2020-08-26)
Among the types of damage, DNA double-strand breaks (DSBs) (provoked by various environmental stresses, but also during normal cell metabolic activity) are the most deleterious, as illustrated by the variety of human diseases associated with DSB repair defects. DSBs are
Chunsheng Hu et al.
International journal of molecular sciences, 23(21) (2022-11-12)
For patients exhibiting non-small-cell lung cancer (NSCLC) with activating epidermal growth factor receptor (EGFR) mutations, epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are a first-line treatment. However, most patients who initially responded to EGFR-TKIs eventually developed acquired resistance, limiting
Kevin Ao et al.
The New phytologist, 229(5), 2795-2811 (2020-11-07)
The unfoldase CDC48 (Cell Division Cycle 48) is highly conserved in eukaryotes, serving as an AAA + ATPase to extract ubiquitinated proteins from large protein complexes and membranes. Although its biochemical properties have been studied extensively in yeast and animal systems, the
Isac Lee et al.
Nature methods, 17(12), 1191-1199 (2020-11-25)
Probing epigenetic features on DNA has tremendous potential to advance our understanding of the phased epigenome. In this study, we use nanopore sequencing to evaluate CpG methylation and chromatin accessibility simultaneously on long strands of DNA by applying GpC methyltransferase
Yansheng Ye et al.
Nature communications, 14(1), 5503-5503 (2023-09-08)
Autophagosome formation, a crucial step in macroautophagy (autophagy), requires the covalent conjugation of LC3 proteins to the amino headgroup of phosphatidylethanolamine (PE) lipids. Atg3, an E2-like enzyme, catalyzes the transfer of LC3 from LC3-Atg3 to PEs in targeted membranes. Here
Lamp1 mediates lipid transport, but is dispensable for autophagy in Drosophila.
Chaudhry, et al.
Autophagy, 18, 2443-2458 (2023)
Victor L Bass et al.
Molecular systems biology, 17(7), e10127-e10127 (2021-07-22)
Cell-to-cell heterogeneity is a feature of the tumor necrosis factor (TNF)-stimulated inflammatory response mediated by the transcription factor NF-κB, motivating an exploration of the underlying sources of this noise. Here, we combined single-transcript measurements with computational models to study transcriptional
Dheva Setiaputra et al.
Molecular cell, 82(7), 1359-1371 (2022-02-27)
The chromatin-binding protein 53BP1 promotes DNA repair by orchestrating the recruitment of downstream effectors including PTIP, RIF1, and shieldin to DNA double-strand break sites. While we know how PTIP recognizes 53BP1, the molecular details of RIF1 recruitment to DNA-damage sites
Giulia Romano et al.
Bio-protocol, 11(23), e4250-e4250 (2022-01-11)
To determine the molecular and functional interactions between RNA-binding proteins (RBPs) and their targets RNAs, is of fundamental importance to understand the dynamic organization of the nervous system in health and disease. Nevertheless, this task has remained elusive due to
Natania S Field et al.
European journal of immunology, 50(10), 1468-1483 (2020-05-28)
To mount an antipathogen response, CD4 T cells must undergo rapid cell proliferation; however, poorly controlled expansion can result in diseases such as autoimmunity. One important regulator of T-cell activity is the E3 ubiquitin ligase Itch. Itch deficient patients suffer
Qingbo Chen et al.
Nature communications, 13(1), 7633-7633 (2022-12-11)
The signaling mechanisms underlying adipose thermogenesis have not been fully elucidated. Particularly, the involvement of adipokines that are selectively expressed in brown adipose tissue (BAT) and beige adipocytes remains to be investigated. Here we show that a previously uncharacterized adipokine
Narayanaiah Cheedarla et al.
iScience, 26(11), 108256-108256 (2023-11-15)
Traditional cellular and live-virus methods for detection of SARS-CoV-2 neutralizing antibodies (nAbs) are labor- and time-intensive, and thus not suited for routine use in the clinical lab to predict vaccine efficacy and natural immune protection. Here, we report the development
Kärt Mätlik et al.
Genes & development, 37(13-14), 570-589 (2023-07-26)
Developing neurons undergo a progression of morphological and gene expression changes as they transition from neuronal progenitors to mature neurons. Here we used RNA-seq and H3K4me3 and H3K27me3 ChIP-seq to analyze how chromatin modifications control gene expression in a specific
Jerome Mertens et al.
Cell stem cell, 28(9), 1533-1548 (2021-04-29)
Sporadic Alzheimer's disease (AD) exclusively affects elderly people. Using direct conversion of AD patient fibroblasts into induced neurons (iNs), we generated an age-equivalent neuronal model. AD patient-derived iNs exhibit strong neuronal transcriptome signatures characterized by downregulation of mature neuronal properties
Christopher J Terranova et al.
Cell reports, 36(3), 109410-109410 (2021-07-22)
The dynamic evolution of chromatin state patterns during metastasis, their relationship with bona fide genetic drivers, and their therapeutic vulnerabilities are not completely understood. Combinatorial chromatin state profiling of 46 melanoma samples reveals an association of NRAS mutants with bivalent
Soraya I Shehata et al.
RNA biology, 20(1), 444-456 (2023-07-07)
Nsp1 is a SARS-CoV-2 host shutoff factor that both represses cellular translation and promotes host RNA decay. However, it is unclear how these two activities are connected and interact with normal translation processes. Here, we performed mutational analyses of Nsp1
Takeshi Kameyama et al.
iScience, 26(10), 108010-108010 (2023-10-13)
Astrocytes interact with not only synapses but also brain blood vessels through perivascular astrocyte endfeet (PV-AEF) to form the neurovascular unit (NVU). However, PV-AEF components have not been fully identified. Here, we biochemically isolated blood vessels from mouse brain homogenates
Lin Yue et al.
Pathology international, 72(4), 242-251 (2022-01-29)
Malignant mesothelioma (MM) is still increasing worldwide. The pathogenesis depends on asbestos-induced iron accumulation, which eventually leads to ferroptosis-resistance of mesothelial cells via somatic mutations. Poly (rC)-binding proteins 1 and 2 (PCBP1/2) are recently recognized cytosolic Fe(II) chaperones. Here we
Roger S Zou et al.
Communications biology, 5(1), 290-290 (2022-04-02)
Nucleic acid detection is essential for numerous biomedical applications, but often requires complex protocols and/or suffers false-positive readouts. Here, we describe SENTINEL, an approach that combines isothermal amplification with a sequence-specific degradation method to detect nucleic acids with high sensitivity
Anna C Beck et al.
Molecular cancer research : MCR, 19(7), 1156-1167 (2021-03-24)
Activating protein 2 alpha (AP-2α; encoded by TFAP2A) functions as a tumor suppressor and influences response to therapy in several cancer types. We aimed to characterize regulation of the transcriptome by AP-2α in colon cancer. CRISPR-Cas9 and short hairpin RNA
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