Long noncoding RNAs (lncRNAs) regulate the expression of protein-coding genes and have been shown to play important roles in inflammatory skin diseases. However, we still have limited understanding of the functional impact of lncRNAs in skin, partly due to their tissue specificity and lower expression levels compared with protein-coding genes. We compiled a comprehensive list of 18,517 lncRNAs from different sources and studied their expression profiles in 834 RNA-Seq samples from multiple inflammatory skin conditions and cytokine-stimulated keratinocytes. Applying a balanced random forest to predict involvement in biological functions, we achieved a median AUROC of 0.79 in 10-fold cross-validation, identifying significant DNA binding domains (DBDs) for 39 lncRNAs. G18244, a skin-expressing lncRNA predicted for IL-4/IL-13 signaling in keratinocytes, was highly correlated in expression with F13A1, a protein-coding gene involved in macrophage regulation, and we further identified a significant DBD in F13A1 for G18244. Reflecting clinical implications, AC090198.1 (predicted for IL-17 pathway) and AC005332.6 (predicted for IFN-γ pathway) had significant negative correlation with the SCORAD metric for atopic dermatitis. We also utilized single-cell RNA and spatial sequencing data to validate cell type specificity. Our research demonstrates lncRNAs have important immunological roles and can help prioritize their impact on inflammatory skin diseases.
Matthew T. Patrick, Sutharzan Sreeskandarajan, Alanna Shefler, Rachael Wasikowski, Mrinal K. Sarkar, Jiahan Chen, Tingting Qin, Allison C. Billi, J. Michelle Kahlenberg, Errol Prens, Alain Hovnanian, Stephan Weidinger, James T. Elder, Chao-Chung Kuo, Johann E. Gudjonsson, Lam C. Tsoi
Weaver syndrome is a Mendelian disorder of the epigenetic machinery (MDEM) caused by germline pathogenic variants in EZH2, which encodes the predominant H3K27 methyltransferase and key enzymatic component of Polycomb repressive complex 2 (PRC2). Weaver syndrome is characterized by striking overgrowth and advanced bone age, intellectual disability, and distinctive facies. We generated a mouse model for the most common Weaver syndrome missense variant, EZH2 p.R684C. Ezh2R684C/R684C mouse embryonic fibroblasts (MEFs) showed global depletion of H3K27me3. Ezh2R684C/+ mice had abnormal bone parameters indicative of skeletal overgrowth, and Ezh2R684C/+ osteoblasts showed increased osteogenic activity. RNA-seq comparing osteoblasts differentiated from Ezh2R684C/+ and Ezh2+/+ bone marrow mesenchymal stem cells (BM-MSCs) indicated collective dysregulation of the BMP pathway and osteoblast differentiation. Inhibition of the opposing H3K27 demethylases KDM6A/6B substantially reversed the excessive osteogenesis in Ezh2R684C/+ cells both at the transcriptional and phenotypic levels. This supports both the ideas that writers and erasers of histone marks exist in a fine balance to maintain epigenome state, and that epigenetic modulating agents have therapeutic potential for the treatment of MDEMs.
Christine W. Gao, WanYing Lin, Ryan C. Riddle, Priyanka Kushwaha, Leandros Boukas, Hans T. Björnsson, Kasper D. Hansen, Jill A. Fahrner
HNF1A haploinsufficiency underlies the most common form of human monogenic diabetes (HNF1A-MODY) and hypomorphic HNF1A variants confer type 2 diabetes risk, but a lack of experimental systems for interrogating mature human islets has limited our understanding of how the transcription factor HNF1α regulates adult islet function. Here, we combined conditional genetic targeting in human islet cells, RNA sequencing, chromatin mapping with Cleavage Under Targets & Release Using Nuclease (CUT&RUN), and transplantation-based assays to determine HNF1α-regulated mechanisms in adult human pancreatic α and β cells. Short hairpin RNA-mediated (shRNA) suppression of HNF1A in primary human pseudoislets led to blunted insulin output and dysregulated glucagon secretion after transplantation in mice, recapitulating phenotypes observed in diabetic patients. These deficits corresponded with altered expression of genes encoding factors critical for hormone secretion, including calcium channel subunits, ATPase transporters and extracellular matrix constituents. Additionally, HNF1A loss led to upregulation of transcriptional repressors, providing evidence for a mechanism of transcriptional de-repression through HNF1α. CUT&RUN mapping of HNF1α DNA-binding sites in primary human islets imputed a subset of HNF1α-regulated genes as direct targets. These data elucidate mechanistic links between HNF1A loss and diabetic phenotypes in mature human α and β cells.
Mollie F. Qian, Romina J. Bevacqua, Vy M.N. Coykendall, Xiong Liu, Weichen Zhao, Charles A. Chang, Xueying Gu, Xiao-Qing Dai, Patrick E. MacDonald, Seung K. Kim
Poly (ADP-ribose) polymerase inhibitors (PARPis) are approved for cancer therapy according to their synthetic lethal interactions, and clinical trials have been applied in non–small cell lung cancer. However, the therapeutic efficacy of PARPis in lung adenocarcinoma (LUAD) is still unknown. We explored the effect of a mutated retinoblastoma gene (RB1) on PARPi sensitivity in LUAD. Bioinformatic screening was performed to identify PARPi-sensitive biomarkers. Here, we showed that viability of LUAD cell lines with mutated RB1 was significantly decreased by PARPis (niraparib, rucaparib, and olaparib). RB1 deficiency induced genomic instability, prompted cytosolic double-stranded DNA (dsDNA) formation, activated the cGAS/STING pathway, and upregulated downstream chemokines CCL5 and CXCL10, triggering immune cell infiltration. Xenograft experiments indicated that PARPi treatment reduced tumorigenesis in RB1-KO mice. Additionally, single-cell RNA sequencing analysis showed that malignant cells with downregulated expression of RB1 had more communications with other cell types, exhibiting activation of specific signaling such as GAS, IFN response, and antigen-presenting and cytokine activities. Our findings suggest that RB1 mutation mediates the sensitivity to PARPis through a synthetic lethal effect by triggering the cGAS/STING pathway and upregulation of immune infiltration in LUAD, which may be a potential therapeutic strategy.
Qi Dong, Tong Yu, Bo Chen, Mingyue Liu, Xiang Sun, Huiying Cao, Kaidong Liu, Huanhuan Xu, Yuquan Wang, Shuping Zhuang, Zixin Jin, Haihai Liang, Yang Hui, Yunyan Gu
Microcephalic osteodysplastic primordial dwarfism type II (MOPDII) is caused by biallelic loss-of-function variants in pericentrin (PCNT), and premature coronary artery disease (CAD) is a complication of the syndrome. Histopathology of coronary arteries from patients with MOPDII who died of CAD in their 20s showed extensive atherosclerosis. Hyperlipidemic mice with smooth muscle cell–specific (SMC-specific) Pcnt deficiency (PcntSMC–/–) exhibited significantly greater atherosclerotic plaque burden compared with similarly treated littermate controls despite similar serum lipid levels. Loss of PCNT in SMCs induced activation of heat shock factor 1 (HSF1) and consequently upregulated the expression and activity of HMG-CoA reductase (HMGCR), the rate-limiting enzyme in cholesterol biosynthesis. The increased cholesterol biosynthesis in PcntSMC–/– SMCs augmented PERK signaling and phenotypic modulation compared with control SMCs. Treatment with the HMGCR inhibitor, pravastatin, blocked the augmented SMC modulation and reduced plaque burden in hyperlipidemic PcntSMC–/– mice to that of control mice. These data support the notion that Pcnt deficiency activates cellular stress to increase SMC modulation and plaque burden, and targeting this pathway with statins in patients with MOPDII has the potential to reduce CAD in these individuals. The molecular mechanism uncovered further emphasizes SMC cytosolic stress and HSF1 activation as a pathway driving atherosclerotic plaque formation independently of cholesterol levels.
Suravi Majumder, Abhijnan Chattopadhyay, Jamie M. Wright, Pujun Guan, L. Maximilian Buja, Callie S. Kwartler, Dianna M. Milewicz
Overactive fibroblast growth factor receptor 3 (FGFR3) signaling drives pathogenesis in a variety of cancers and a spectrum of short-limbed bone dysplasias, including the most common form of human dwarfism, achondroplasia (ACH). Targeting FGFR3 activity holds great promise as a therapeutic approach for treatment of these diseases. Here, we established a receptor/adaptor translocation assay system that can specifically monitor FGFR3 activation, and we applied it to identify FGFR3 modulators from complex natural mixtures. An FGFR3-suppressing plant extract of Amaranthus viridis was identified from the screen, and two bioactive porphyrins, pheophorbide a (Pa) and pyropheophorbide a (PyroPa) were sequentially isolated from the extract and functionally characterized. Further analysis showed that Pa reduced excessive FGFR3 signaling by decreasing its half-life in FGFR3-overactivated multiple myeloma (MM) cells and chondrocytes. In an ex vivo culture system, Pa alleviated defective long bone growth in humanized ACH mice (FGFR3ACH mice). Overall, our study presents a novel approach to discovery and validation of plant extracts or drug candidates that target FGFR3 activation. The compounds identified by this approach may have potential applications as therapeutics for FGFR3-associated cancers and skeletal dysplasias.
Yun-Wen Lin, Hsiao-Jung Kao, Wei-Ting Chen, Cheng-Fu Kao, Jer-Yuarn Wu, Yuan-Tsong Chen, Yi-Ching Lee
MAD2L1BP-encoded p31comet mediates Trip13-dependent disassembly of Mad2- and Rev7-containing complexes and, through this antagonism, promotes timely spindle assembly checkpoint (SAC) silencing, faithful chromosome segregation, insulin signaling and homology-directed repair (HDR) of DNA double-strand breaks. We identified a homozygous MAD2L1BP nonsense variant, R253*, in two siblings with microcephaly, epileptic encephalopathy and juvenile granulosa cell tumors of ovary and testis. Patient-derived cells exhibited high-grade mosaic variegated aneuploidy, slowed-down proliferation, and instability of truncated p31comet mRNA and protein. Corresponding recombinant p31comet was defective in Trip13-, Mad2- and Rev7-binding and unable to support SAC silencing or HDR. Furthermore, C-terminal truncation abrogated a newly identified interaction of p31comet with tp53. Another homozygous truncation, R227*, detected in an early deceased patient with low-level aneuploidy, severe epileptic encephalopathy and frequent blood glucose elevations likely corresponds to complete loss-of-function, as in Mad2l1bp–/– mice. Thus, human mutations of p31comet are linked to aneuploidy and tumor predisposition.
Ghada M. H. Abdel-Salam, Susanne Hellmuth, Elise Gradhand, Stephan Käseberg, Jennifer Winter, Ann-Sophie Pabst, Maha M. Eid, Holger Thiele, Peter Nürnberg, Birgit S. Budde, Mohammad Reza Toliat, Ines B. Brecht, Christopher Schroeder, Axel Gschwind, Stephan Ossowski, Friederike Häuser, Heidi Rossmann, Mohamed S. Abdel-Hamid, Ibrahim Hegazy, Ahmed G. Mohamed, Dominik T. Schneider, Aida M. Bertoli-Avella, Peter Bauer, Jillian N. Pearring, Rolph Pfundt, Alexander Hoischen, Christian Gilissen, Dennis Strand, Ulrich Zechner, Soha A. Tashkandi, Eissa A. Faqeih, Olaf Stemmann, Susanne Strand, Hanno J. Bolz
Retinitis pigmentosa (RP) is the most common inherited retinal disease (IRD) and is characterized by photoreceptor degeneration and progressive loss of vision. We report here four patients who presented with RP from three unrelated families with variants in TBC1D32, which to date has never been associated with an IRD. To validate TBC1D32 as a putative RP causative gene, we combined Xenopus in vivo approaches and human iPSC-derived retinal models. Our data showed that TBC1D32 was expressed during retinal development and that it played an important role in retinal pigment epithelium (RPE) differentiation. Furthermore, we identified a role for TBC1D32 in ciliogenesis of the RPE. We demonstrated elongated ciliary defects that resulted in disrupted apical tight junctions, loss of functionality (delayed retinoid cycling and altered secretion balance), and the onset of an epithelial-mesenchymal transition-like phenotype. Lastly, our results also suggested photoreceptor differentiation defects, including connecting cilium anomalies, that resulted in impaired trafficking to the outer segment in both cones and rods in TBC1D32 iPSC-derived retinal organoids. Overall, our data not only highlight a critical role for TBC1D32 in the retina but demonstrate that TBC1D32 mutations lead to RP. We thus identify TBC1D32 as an IRD causative gene.
Béatrice Bocquet, Caroline Borday, Nejla Erkilic, Daria Mamaeva, Alicia Donval, Christel Masson-Garcia, Karine Parain, Karolina Kaminska, Mathieu Quinodoz, Irene Perea-Romero, Gema Garcia-Garcia, Carla Jimenez-Medina, Hassan Boukhaddaoui, Arthur Coget, Nicolas Leboucq, Giacomo Calzetti, Stefano A. Gandolfi, Antonio Percesepe, Valeria Barili, Vera Uliana, Marco Delsante, Francesca Bozzetti, Hendrik P.N. Scholl, Marta Corton, Carmen Ayuso, Jose M. Millan, Carlo Rivolta, Isabelle Meunier, Muriel Perron, Vasiliki Kalatzis
Application of classic liver-directed gene replacement strategies is limited in genetic diseases characterized by liver injury due to hepatocyte proliferation resulting in decline of therapeutic transgene expression and potential genotoxic risk. Wilson disease (WD) is a life-threating autosomal disorder of copper homeostasis caused by pathogenic variants in copper transporter ATP7B and characterized by toxic copper accumulation, resulting in severe liver and brain diseases. Genome editing holds promise for the treatment of WD, nevertheless to rescue copper homeostasis ATP7B function must be restored in at least 25% of the hepatocytes, which surpasses by far genome editing correction rates. We applied a liver-directed nuclease-free genome editing approach, based on adeno-associated viral vector (AAV) -mediated targeted integration of a promoterless mini-ATP7B cDNA into the Alb locus. Administration of AAV-Alb-mini-ATP7B in two WD mouse models resulted in extensive liver repopulation by genome edited hepatocytes holding a proliferative advantage over non-edited ones, and ameliorated liver injury and copper metabolism. Furthermore, combination of genome editing with a copper chelator currently used for WD treatment, achieved greater disease improvement compared to chelation therapy alone. Nuclease-free genome editing provided therapeutic efficacy and may represent a safer and longer lasting alternative to classic gene replacement strategies for WD.
Agnese Padula, Michele Spinelli, Edoardo Nusco, Xabier Bujanda Cundin, Filomena Capolongo, Severo Campione, Claudia Perna, Amy Bastille, Megan E. Ericson, Chih-Chieh Wang, Shengwen Zhang, Angela Amoresano, Mariana Nacht, Pasquale Piccolo
Sialidosis is an ultrarare multisystemic lysosomal disease caused by mutations in the neuraminidase 1 (NEU1) gene. The severe Type II form of the disease, manifests with a prenatal/infantile or juvenile onset, bone abnormalities, severe neuropathology and visceromegaly. A subset of these patients presents with nephrosialidosis, characterized by abrupt onset of fulminant glomerular nephropathy. We studied the pathophysiological mechanism of the disease in two NEU1-deficient mouse models, a constitutive Neu1 knockout Neu1∆Ex3 and a conditional phagocyte-specific knockout Neu1Cx3cr1ΔEx3. Mice of both strains exhibited terminal urinary retention and severe kidney damage with elevated urinary albumin levels, loss of nephrons, renal fibrosis, presence of storage vacuoles and dysmorphic mitochondria in the intraglomerular and tubular cells. Glycoprotein sialylation in glomeruli, proximal and distal tubules was drastically increased including that of an endocytic reabsorption receptor megalin. The pool of megalin bearing O-linked glycans with terminal galactose residues, essential for protein targeting and activity, was reduced to below detection levels. Megalin levels were severely reduced, and the protein was directed to lysosomes instead of the apical membrane. Together, our results demonstrated that desialylation by NEU1 plays a crucial role in processing and cellular trafficking of megalin and that NEU1 deficiency in sialidosis impairs megalin-mediated protein reabsorption.
Ikhui Kho, Ekaterina P. Demina, Xuefang Pan, Irene Londono, Christopher W. Cairo, Luisa Sturiale, Angelo Palmigiano, Angela Messina, Domenico Garozzo, Roth-Visal Ung, Fabrice Mac‐Way, Éric Bonneil, Pierre Thibault, Mathieu Lemaire, Carlos R. Morales, Alexey V. Pshezhetsky
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