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North L, Olivier M, Runge CL. Cochlear Implant Outcomes in Patients With TMTC2 -Associated Sensorineural Hearing Loss and Auditory Neuropathy/Auditory Dys-Synchrony. Otol Neurotol 2024; 45:e478-e482. [PMID: 38769084 PMCID: PMC11168879 DOI: 10.1097/mao.0000000000004208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
OBJECTIVE To investigate the outcomes of cochlear implantation in patients with TMTC2 -associated sensorineural hearing loss and auditory neuropathy/auditory dys-synchrony. PATIENTS Adult and pediatric cochlear implant (CI) patients followed in an academic center who tested positive for TMTC2 genetic variant rs35725509. INTERVENTION Cochlear implantation. MAIN OUTCOME MEASURES Speech perception scores in quiet. RESULTS Ten CI patients were identified with TMTC2 variant rs35725509 out of 157 patients who underwent genetic testing (i.e., 6.3% of patients tested). All demonstrated progressive, bilateral hearing loss with severe-to-profound audiometric thresholds preoperatively. Pre-CI and 1-year post-CI speech recognition percent correct scores were compared. Post-CI speech perception (mean 61.0%, standard deviation 31.4%) was significantly higher than pre-CI speech perception (mean 21.0%, standard deviation 27.0%) ( p = 0.002). Individually, 9 of the 10 subjects experienced significant improvements in speech perception pre- to post-CI ( p < 0.05). Electrically evoked compound action potential measures were available for five patients, and all showed normal electrically evoked compound action potential thresholds. CONCLUSION Patients with TMTC2 -associated sensorineural hearing loss and auditory neuropathy/auditory dys-synchrony have significantly improved speech perception outcomes with cochlear implantation and should be considered candidates for this intervention if there are no other contraindications.
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Affiliation(s)
- Lauren North
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Michael Olivier
- Department of Internal Medicine-Section of Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Christina L Runge
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee, Wisconsin
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2
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Deng W, Fu J, Lin S, Wen Q, Fu L, Chen X. Hsa_circRNA_101036 aggravates hypoxic-induced endoplasmic reticulum stress via the miR-21-3p/TMTC1 axis in oral squamous cell carcinoma. Heliyon 2024; 10:e32969. [PMID: 38994041 PMCID: PMC11238011 DOI: 10.1016/j.heliyon.2024.e32969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 07/13/2024] Open
Abstract
Objective Circular RNAs (circRNAs) have been identified as potential biomarkers and therapeutic targets for various types of cancer, including Oral squamous cell carcinoma (OSCC). Hsa_circRNA_101036 was found to function as a cancer suppressor gene in OSCC; however, the underlying regulatory mechanism remains unclear. We investigated the role of hsa_circRNA_101036 in OSCC development and progression and explored its potential as a therapeutic target. Methods We performed a bioinformatics analysis and used experimental approaches to investigate the regulatory mechanism of hsa_circRNA_101036. The database StarBase v.2.0 was used to predict potential target-miRNAs of hsa_circRNA_101036. The levels of hsa_circRNA_101036, miR-21-3p, and TMTC2 expression in samples of OSCC cancer tissue (n = 15) and adjacent tissue (n = 15) were determined. We also examined the effects of hsa_circRNA_101036 overexpression on OSCC cell lines by using cell viability, migration, and invasion assays. The proportions of apoptotic cells and the reactive oxygen species (ROS) levels were analyzed by flow cytometry. We also investigated how hsa_circRNA_101036 overexpression affected the levels of miR-21-3p and TMTC2, and endoplasmic reticulum (ER) stress in OSCC cells. Results The levels of hsa_circRNA_101036 and TMTC2 expression were significantly lower, while miR-21-3p expression was higher in tumor tissues and OSCC cells when compared to adjacent tissues and normal oral fibroblasts, respectively. The levels of HIF-1α and miR-21-3p expression were significantly increased under conditions of hypoxia, while the levels of hsa_circRNA_101036 and TMTC2 were decreased. The expression levels of proteins associated with ER stress, the proportions of apoptotic cells, and the levels of ROS were all increased by hypoxia stimulation. In addition, overexpression of hsa_circRNA_101036, but not mutant hsa_circRNA_101036, was found to enhance the effect of hypoxia on HSC3 and OECM-1 cells. Hsa_circRNA_101036 overexpression suppressed tumor growth and induced ER stress. Finally, knockdown of miR-21-3p had the same effect as overexpression of hsa_circRNA_101036. Conclusion Our findings suggest that hsa_circRNA_101036 plays a critical role in the development and progression of OSCC. Overexpression of hsa_circRNA_101036 aggravated ER stress, and increased cell apoptosis and ROS production in OSCC under hypoxic conditions. Hsa_circRNA_101036 up-regulated TMTC2 expression by sponging miR-21-3p in OSCC.
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Affiliation(s)
- Wei Deng
- Department of Oral and Maxillofacial Surgery, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China
| | - Juan Fu
- Department of Infectious Diseases, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China
| | - Shigeng Lin
- Department of Oral and Maxillofacial Surgery, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China
| | - Qitao Wen
- Department of Oral and Maxillofacial Surgery, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China
| | - Liangbin Fu
- Department of Oral and Maxillofacial Surgery, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China
| | - Xiaoze Chen
- Department of Oral and Maxillofacial Surgery, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China
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3
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Manoharan A, Ballambattu VB, Palani R. Genetic architecture of preeclampsia. Clin Chim Acta 2024; 558:119656. [PMID: 38583550 DOI: 10.1016/j.cca.2024.119656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/04/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Affiliation(s)
- Aarthi Manoharan
- Department of Medical Biotechnology, Kirumampakkam, Puducherry 607403, India.
| | | | - Ramya Palani
- Department of Obstetrics and Gynecology, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission's Research Foundation (DU), Kirumampakkam, Puducherry 607403, India
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4
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Viana Neto AM, Guerreiro DD, Martins JAM, Vasconcelos FÁR, Melo RÉBF, Velho ALMCS, Neila-Montero M, Montes-Garrido R, Nagano CS, Araújo AA, Moura AA. Sperm traits and seminal plasma proteome of locally adapted hairy rams subjected to intermittent scrotal insulation. Anim Reprod Sci 2024; 263:107439. [PMID: 38447240 DOI: 10.1016/j.anireprosci.2024.107439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024]
Abstract
The present study evaluated the effects of heat stress on reproductive parameters of hairy rams. Six animals were subjected to scrotal insulation during four consecutive nights (6 PM - 6 AM). Day (D) 0 was the first day of insulation. Scrotal circumference increased from 30.5 ± 0.3 cm (at pre-insulation) to 31.8 ± 0.4 cm on D4, decreased 3.9 cm on D28, returning to 30.6 ± 0.6 cm on D57. Sperm concentration decreased from 3.7 ± 0.12 ×109 sperm/mL before insulation to 2.6 ± 0.1 ×109 on D23, returning to normal on D57. Sperm motility averaged 75 ± 2.9% before insulation, was undetectable on D23, and became normal on D77. Sperm with normal morphology reached 5.9 ± 2.6% on D35 but recovered (86.8 ± 2.1%) on D91. Sperm DNA integrity decreased from 86.5 ± 4.7% before insulation to 11.1 ± 3.7% on D63, returning to pre-insulation values on D120. Sperm BSP immunostaining was reduced after scrotal insulation. Variations in seminal protein abundances coincided with changes in sperm parameters. Seminal plasma superoxide dismutase, carboxypeptidase Q-precursor and NPC intracellular cholesterol transporter 2 decreased on D18, returning to normal after D28. Albumin, inhibitor of carbonic anhydrase precursor, EGF-like repeat and discoid I-like domain-containing protein 3 and polymeric immunoglobulin receptor increased after insulation. In summary, intermittent scrotal insulation drastically altered ram sperm attributes and seminal proteins, especially those associated with oxidative stress. Knowledge of animal´s response to thermal stress is vital in the scenario of climate changes.
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Affiliation(s)
| | - Denise D Guerreiro
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | - Jorge A M Martins
- School of Veterinary Medicine, Federal University of Cariri, Juazeiro do Norte, Brazil
| | | | - R Évila B F Melo
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | | | - Marta Neila-Montero
- Itra-ULE, Animal Reproduction and Obstetrics, Department of Veterinary Medicine, Surgery and Anatomy, University of León, León, Spain
| | - Rafael Montes-Garrido
- Itra-ULE, Animal Reproduction and Obstetrics, Department of Veterinary Medicine, Surgery and Anatomy, University of León, León, Spain
| | - Celso S Nagano
- Department of Fisheries Engineering, Federal University of Ceará, Fortaleza, Brazil
| | - Airton A Araújo
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil; School of Veterinary Medicine, Ceará State University, Fortaleza, Brazil
| | - Arlindo A Moura
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil.
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5
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Koff M, Monagas-Valentin P, Novikov B, Chandel I, Panin V. Protein O-mannosylation: one sugar, several pathways, many functions. Glycobiology 2023; 33:911-926. [PMID: 37565810 PMCID: PMC10859634 DOI: 10.1093/glycob/cwad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 07/23/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Recent research has unveiled numerous important functions of protein glycosylation in development, homeostasis, and diseases. A type of glycosylation taking the center stage is protein O-mannosylation, a posttranslational modification conserved in a wide range of organisms, from yeast to humans. In animals, protein O-mannosylation plays a crucial role in the nervous system, whereas protein O-mannosylation defects cause severe neurological abnormalities and congenital muscular dystrophies. However, the molecular and cellular mechanisms underlying protein O-mannosylation functions and biosynthesis remain not well understood. This review outlines recent studies on protein O-mannosylation while focusing on the functions in the nervous system, summarizes the current knowledge about protein O-mannosylation biosynthesis, and discusses the pathologies associated with protein O-mannosylation defects. The evolutionary perspective revealed by studies in the Drosophila model system are also highlighted. Finally, the review touches upon important knowledge gaps in the field and discusses critical questions for future research on the molecular and cellular mechanisms associated with protein O-mannosylation functions.
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Affiliation(s)
- Melissa Koff
- Department of Biochemistry and Biophysics, AgriLife Research, Texas A&M University, College Station, College Station, TX 77843, United States
| | - Pedro Monagas-Valentin
- Department of Biochemistry and Biophysics, AgriLife Research, Texas A&M University, College Station, College Station, TX 77843, United States
| | - Boris Novikov
- Department of Biochemistry and Biophysics, AgriLife Research, Texas A&M University, College Station, College Station, TX 77843, United States
| | - Ishita Chandel
- Department of Biochemistry and Biophysics, AgriLife Research, Texas A&M University, College Station, College Station, TX 77843, United States
| | - Vladislav Panin
- Department of Biochemistry and Biophysics, AgriLife Research, Texas A&M University, College Station, College Station, TX 77843, United States
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6
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Canniff NP, Graham JB, Guay KP, Lubicki DA, Eyles SJ, Rauch JN, Hebert DN. TTC17 is an endoplasmic reticulum resident TPR-containing adaptor protein. J Biol Chem 2023; 299:105450. [PMID: 37949225 PMCID: PMC10783571 DOI: 10.1016/j.jbc.2023.105450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/11/2023] [Accepted: 10/29/2023] [Indexed: 11/12/2023] Open
Abstract
Protein folding, quality control, maturation, and trafficking are essential processes for proper cellular homeostasis. Around one-third of the human proteome is targeted to the endoplasmic reticulum (ER), the organelle that serves as entrance into the secretory pathway. Successful protein trafficking is paramount for proper cellular function and to that end there are many ER resident proteins that ensure efficient secretion. Here, biochemical and cell biological analysis was used to determine that TTC17 is a large, soluble, ER-localized protein that plays an important role in secretory trafficking. Transcriptional analysis identified the predominantly expressed protein isoform of TTC17 in various cell lines. Further, TTC17 localizes to the ER and interacts with a wide variety of chaperones and cochaperones normally associated with ER protein folding, quality control, and maturation processes. TTC17 was found to be significantly upregulated by ER stress and through the creation and use of TTC17-/- cell lines, quantitative mass spectrometry identified secretory pathway wide trafficking defects in the absence of TTC17. Notably, trafficking of insulin-like growth factor type 1 receptor, glycoprotein nonmetastatic melanoma protein B, clusterin, and UDP-glucose:glycoprotein glucosyltransferase 1 were significantly altered in H4 neuroglioma cells. This study defines a novel ER trafficking factor and provides insight into the protein-protein assisted trafficking in the early secretory pathway.
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Affiliation(s)
- Nathan P Canniff
- Program in Molecular and Cellular Biology, University of Massachusetts Amherst, USA
| | - Jill B Graham
- Program in Molecular and Cellular Biology, University of Massachusetts Amherst, USA
| | - Kevin P Guay
- Program in Molecular and Cellular Biology, University of Massachusetts Amherst, USA
| | - Daniel A Lubicki
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, USA
| | - Stephen J Eyles
- Program in Molecular and Cellular Biology, University of Massachusetts Amherst, USA; Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, USA; Institute for Applied Life Sciences, Mass Spectrometry Center, University of Massachusetts Amherst, USA
| | - Jennifer N Rauch
- Program in Molecular and Cellular Biology, University of Massachusetts Amherst, USA; Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, USA
| | - Daniel N Hebert
- Program in Molecular and Cellular Biology, University of Massachusetts Amherst, USA; Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, USA.
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7
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Yeh TC, Lin NY, Chiu CY, Hsu TW, Wu HY, Lin HY, Chen CH, Huang MC. TMTC1 promotes invasiveness of ovarian cancer cells through integrins β1 and β4. Cancer Gene Ther 2023; 30:1134-1143. [PMID: 37221403 PMCID: PMC10425284 DOI: 10.1038/s41417-023-00625-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/20/2023] [Accepted: 05/04/2023] [Indexed: 05/25/2023]
Abstract
Ovarian cancer is the most lethal gynecological malignancy and is characterized by peritoneal disseminated metastasis. Although O-mannosyltransferase TMTC1 is highly expressed by ovarian cancer, its pathophysiological role in ovarian cancer remains unclear. Here, immunohistochemistry showed that TMTC1 was overexpressed in ovarian cancer tissues compared with adjacent normal ovarian tissues, and high TMTC1 expression was associated with poor prognosis in patients with ovarian cancer. Silencing TMTC1 reduced ovarian cancer cell viability, migration, and invasion in vitro, as well as suppressed peritoneal tumor growth and metastasis in vivo. Moreover, TMTC1 knockdown reduced cell-laminin adhesion, which was associated with the decreased phosphorylation of FAK at pY397. Conversely, TMTC1 overexpression promoted these malignant properties in ovarian cancer cells. Glycoproteomic analysis and Concanavalin A (ConA) pull-down assays showed that integrins β1 and β4 were novel O-mannosylated protein substrates of TMTC1. Furthermore, TMTC1-mediated cell migration and invasion were significantly reversed by siRNA-mediated knockdown of integrin β1 or β4. Collectively, these results suggest that TMTC1-mediated invasive behaviors are primarily through integrins β1 and β4 and that TMTC1 is a potential therapeutic target for ovarian cancer.
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Affiliation(s)
- Ting-Chih Yeh
- Graduate Institute of Anatomy and Cell Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Neng-Yu Lin
- Graduate Institute of Anatomy and Cell Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chin-Yu Chiu
- Graduate Institute of Anatomy and Cell Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tzu-Wen Hsu
- Graduate Institute of Anatomy and Cell Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsin-Yi Wu
- Instrumentation Center, National Taiwan University, Taipei, Taiwan
| | - Hsuan-Yu Lin
- Graduate Institute of Anatomy and Cell Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chi-Hau Chen
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan.
| | - Min-Chuan Huang
- Graduate Institute of Anatomy and Cell Biology, College of Medicine, National Taiwan University, Taipei, Taiwan.
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8
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Larsen ISB, Povolo L, Zhou L, Tian W, Mygind KJ, Hintze J, Jiang C, Hartill V, Prescott K, Johnson CA, Mullegama SV, McConkie-Rosell A, McDonald M, Hansen L, Vakhrushev SY, Schjoldager KT, Clausen H, Worzfeld T, Joshi HJ, Halim A. The SHDRA syndrome-associated gene TMEM260 encodes a protein-specific O-mannosyltransferase. Proc Natl Acad Sci U S A 2023; 120:e2302584120. [PMID: 37186866 PMCID: PMC10214176 DOI: 10.1073/pnas.2302584120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023] Open
Abstract
Mutations in the TMEM260 gene cause structural heart defects and renal anomalies syndrome, but the function of the encoded protein remains unknown. We previously reported wide occurrence of O-mannose glycans on extracellular immunoglobulin, plexin, transcription factor (IPT) domains found in the hepatocyte growth factor receptor (cMET), macrophage-stimulating protein receptor (RON), and plexin receptors, and further demonstrated that two known protein O-mannosylation systems orchestrated by the POMT1/2 and transmembrane and tetratricopeptide repeat-containing proteins 1-4 gene families were not required for glycosylation of these IPT domains. Here, we report that the TMEM260 gene encodes an ER-located protein O-mannosyltransferase that selectively glycosylates IPT domains. We demonstrate that disease-causing TMEM260 mutations impair O-mannosylation of IPT domains and that TMEM260 knockout in cells results in receptor maturation defects and abnormal growth of 3D cell models. Thus, our study identifies the third protein-specific O-mannosylation pathway in mammals and demonstrates that O-mannosylation of IPT domains serves critical functions during epithelial morphogenesis. Our findings add a new glycosylation pathway and gene to a growing group of congenital disorders of glycosylation.
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Affiliation(s)
- Ida Signe Bohse Larsen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Lorenzo Povolo
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Luping Zhou
- Faculty of Medicine, Institute of Pharmacology, University of Marburg, 35043Marburg, Germany
| | - Weihua Tian
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Kasper Johansen Mygind
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - John Hintze
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Chen Jiang
- Faculty of Medicine, Institute of Pharmacology, University of Marburg, 35043Marburg, Germany
| | - Verity Hartill
- Leeds Institute of Medical Research, University of Leeds, St James’ University Hospital, LeedsLS2 9JT, United Kingdom
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, LeedsLS7 4SA, United Kingdom
| | - Katrina Prescott
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, LeedsLS7 4SA, United Kingdom
| | - Colin A. Johnson
- Leeds Institute of Medical Research, University of Leeds, St James’ University Hospital, LeedsLS2 9JT, United Kingdom
| | | | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC27710
| | - Marie McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC27710
| | - Lars Hansen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Sergey Y. Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Katrine T. Schjoldager
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Thomas Worzfeld
- Faculty of Medicine, Institute of Pharmacology, University of Marburg, 35043Marburg, Germany
- Max-Planck-Institute for Heart and Lung Research, 61231Bad Nauheim, Germany
| | - Hiren J. Joshi
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
| | - Adnan Halim
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200Copenhagen N, Denmark
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9
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Ribeiro-dos-Santos A, de Brito LM, de Araújo GS. The fusiform gyrus exhibits differential gene-gene co-expression in Alzheimer's disease. Front Aging Neurosci 2023; 15:1138336. [PMID: 37255536 PMCID: PMC10225579 DOI: 10.3389/fnagi.2023.1138336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/21/2023] [Indexed: 06/01/2023] Open
Abstract
Alzheimer's Disease (AD) is an irreversible neurodegenerative disease clinically characterized by the presence of β-amyloid plaques and tau deposits in various regions of the brain. However, the underlying factors that contribute to the development of AD remain unclear. Recently, the fusiform gyrus has been identified as a critical brain region associated with mild cognitive impairment, which may increase the risk of AD development. In our study, we performed gene co-expression and differential co-expression network analyses, as well as gene-expression-based prediction, using RNA-seq transcriptome data from post-mortem fusiform gyrus tissue samples collected from both cognitively healthy individuals and those with AD. We accessed differential co-expression networks in large cohorts such as ROSMAP, MSBB, and Mayo, and conducted over-representation analyses of gene pathways and gene ontology. Our results comprise four exclusive gene hubs in co-expression modules of Alzheimer's Disease, including FNDC3A, MED23, NRIP1, and PKN2. Further, we identified three genes with differential co-expressed links, namely FAM153B, CYP2C8, and CKMT1B. The differential co-expressed network showed moderate predictive performance for AD, with an area under the curve ranging from 0.71 to 0.76 (+/- 0.07). The over-representation analysis identified enrichment for Toll-Like Receptors Cascades and signaling pathways, such as G protein events, PIP2 hydrolysis and EPH-Epherin mechanism, in the fusiform gyrus. In conclusion, our findings shed new light on the molecular pathophysiology of AD by identifying new genes and biological pathways involved, emphasizing the crucial role of gene regulatory networks in the fusiform gyrus.
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Affiliation(s)
- Arthur Ribeiro-dos-Santos
- Programa de Pós-graduação em Genética e Biologia Molecular, Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Leonardo Miranda de Brito
- Programa de Pós-graduação em Genética e Biologia Molecular, Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
- Centro de Informática, Universidade Federal de Pernambuco, Recife, Brazil
| | - Gilderlanio Santana de Araújo
- Programa de Pós-graduação em Genética e Biologia Molecular, Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
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10
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Sørensen DM, Büll C, Madsen TD, Lira-Navarrete E, Clausen TM, Clark AE, Garretson AF, Karlsson R, Pijnenborg JFA, Yin X, Miller RL, Chanda SK, Boltje TJ, Schjoldager KT, Vakhrushev SY, Halim A, Esko JD, Carlin AF, Hurtado-Guerrero R, Weigert R, Clausen H, Narimatsu Y. Identification of global inhibitors of cellular glycosylation. Nat Commun 2023; 14:948. [PMID: 36804936 PMCID: PMC9941569 DOI: 10.1038/s41467-023-36598-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
Small molecule inhibitors of glycosylation enzymes are valuable tools for dissecting glycan functions and potential drug candidates. Screening for inhibitors of glycosyltransferases are mainly performed by in vitro enzyme assays with difficulties moving candidates to cells and animals. Here, we circumvent this by employing a cell-based screening assay using glycoengineered cells expressing tailored reporter glycoproteins. We focused on GalNAc-type O-glycosylation and selected the GalNAc-T11 isoenzyme that selectively glycosylates endocytic low-density lipoprotein receptor (LDLR)-related proteins as targets. Our screen of a limited small molecule compound library did not identify selective inhibitors of GalNAc-T11, however, we identify two compounds that broadly inhibited Golgi-localized glycosylation processes. These compounds mediate the reversible fragmentation of the Golgi system without affecting secretion. We demonstrate how these inhibitors can be used to manipulate glycosylation in cells to induce expression of truncated O-glycans and augment binding of cancer-specific Tn-glycoprotein antibodies and to inhibit expression of heparan sulfate and binding and infection of SARS-CoV-2.
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Affiliation(s)
- Daniel Madriz Sørensen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Christian Büll
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Thomas D Madsen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Erandi Lira-Navarrete
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- The Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, 50018, Zaragoza, Spain
- Fundación ARAID, 50018, Zaragoza, Spain
| | - Thomas Mandel Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alex E Clark
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Aaron F Garretson
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Richard Karlsson
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Johan F A Pijnenborg
- Institute for Molecules and Materials, Department of Synthetic Organic Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Xin Yin
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Rebecca L Miller
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Sumit K Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Thomas J Boltje
- Institute for Molecules and Materials, Department of Synthetic Organic Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Aaron F Carlin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ramon Hurtado-Guerrero
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark
- The Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, 50018, Zaragoza, Spain
- Fundación ARAID, 50018, Zaragoza, Spain
| | - Roberto Weigert
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark.
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen, Denmark.
- GlycoDisplay ApS, Copenhagen, Denmark.
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11
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Hu X, Guo B, Sun T, Wang W. Inhibition of glycolysis represses the growth and alleviates the endoplasmic reticulum stress of breast cancer cells by regulating TMTC3. Open Med (Wars) 2023; 18:20230635. [PMID: 37069941 PMCID: PMC10105522 DOI: 10.1515/med-2023-0635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/05/2022] [Accepted: 12/11/2022] [Indexed: 04/19/2023] Open
Abstract
Considering the role of glycolysis inhibition as a novel therapeutic strategy for cancer, including breast cancer (BC), we wondered whether glycolysis could affect BC progression by regulating transmembrane O-mannosyltransferase-targeting cadherins 3 (TMTC3). Following the intervention, lactic acid production in BC cells was monitored, and viability, proliferation, and apoptosis assays were performed. The expressions of TMTC3 and endoplasmic reticulum (ER) stress- and apoptosis-related factors Caspase-12, C/EBP homologous protein (CHOP), glucose-regulated protein 78 (GRP78), B-cell lymphoma-2 (Bcl-2), and Bcl-2 associated X (Bax) were quantified. TMTC3 was lowly expressed in BC tissue and cell. The promotion of glycolysis via glucose represses TMTC3 expression and apoptosis yet enhances lactic acid production and growth of BC cell, along with promoted levels of Caspase-12, CHOP, GRP78, and Bcl-2 yet repressed level of Bax, while the contrary results were evidenced after 2-deoxyglycouse intervention. Overexpressed TMTC3 additionally abrogated the effects of glycolysis on increasing the viability and proliferation yet inhibiting the apoptosis of BC cells, with the increased expressions of Caspase-12, CHOP, and GRP78, and Bcl-2 yet decreased level of Bax. Collectively, inhibiting glycolysis restrained the growth and attenuated the ER stress of BC cell by regulating TMTC3.
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Affiliation(s)
- Xue Hu
- Department of Breast Surgery, China-Japan Union Hospital of Jilin University, Changchun City, Jilin Province, 130033, China
| | - Baoliang Guo
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin City, Heilongjiang Province, China
| | - Tong Sun
- Department of Breast Surgery, China-Japan Union Hospital of Jilin University, Changchun City, Jilin Province, 130033, China
| | - Wan Wang
- Department of Breast Surgery, China-Japan Union Hospital of Jilin University, No. 126 Xiantai
Avenue, Nanguan District, Changchun City, Jilin Province, 130033, China
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12
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Integrative QTL mapping and selection signatures in Groningen White Headed cattle inferred from whole-genome sequences. PLoS One 2022; 17:e0276309. [PMID: 36288367 PMCID: PMC9605288 DOI: 10.1371/journal.pone.0276309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/04/2022] [Indexed: 11/04/2022] Open
Abstract
Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle, and in particular to identify candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used to evaluate the genetic structure of the GWH in relation to other cattle breeds by carrying out principal components and model-based clustering analyses. Secondly, the candidate genomic regions were identified by integrating the findings from: a) a genome-wide association study using GWH, other white headed breeds (Hereford and Simmental), and breeds with a non-white headed phenotype (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel, Dutch Belted, and Holstein Friesian); b) scans for specific signatures of selection in GWH cattle by comparison with four other Dutch traditional breeds (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel and Dutch Belted) and the commercial Holstein Friesian; and c) detection of candidate genes identified via these approaches. The alignment of the filtered reads to the reference genome (ARS-UCD1.2) resulted in a mean depth of coverage of 8.7X. After variant calling, the lowest number of breed-specific variants was detected in Holstein Friesian (148,213), and the largest in Deep Red (558,909). By integrating the results, we identified five genomic regions under selection on BTA4 (70.2-71.3 Mb), BTA5 (10.0-19.7 Mb), BTA20 (10.0-19.9 and 20.0-22.7 Mb), and BTA25 (0.5-9.2 Mb). These regions contain positional and functional candidate genes associated with retinal degeneration (e.g., CWC27 and CLUAP1), ultraviolet protection (e.g., ERCC8), and pigmentation (e.g. PDE4D) which are probably associated with the GWH specific pigmentation and/or eye-protective phenotypes, e.g. Ambilateral Circumocular Pigmentation (ACOP). Our results will assist in characterizing the molecular basis of GWH phenotypes and the biological implications of its adaptation.
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13
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Feng Z, Su X, Wang T, Guo S. Identification of Biomarkers That Modulate Osteogenic Differentiation in Mesenchymal Stem Cells Related to Inflammation and Immunity: A Bioinformatics-Based Comprehensive Study. Pharmaceuticals (Basel) 2022; 15:ph15091094. [PMID: 36145314 PMCID: PMC9504288 DOI: 10.3390/ph15091094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/23/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Inducing mesenchymal stem cells (MSCs) osteogenesis may be beneficial in a number of clinical applications. The aim of this study is to identify key novel biomarkers of this process and to analyze the possible regulatory effects on inflammation and immunity. Results: Seven datasets (GSE159137, GSE159138, GSE114117, GSE88865, GSE153829, GSE63754, GSE73087) were obtained from the Gene Expression Omnibus database and were assigned to either the training or the validation dataset. The least absolute shrinkage and selection operator (LASSO) logistic regression model was applied to the training data to select biomarkers of osteogenesis, which were then confirmed using the validation dataset. FK506 binding protein 5 (FKBP5), insulin-like growth factor binding protein (IGFBP2), prostaglandin E receptor 2 (PTGER2), SAM domain and HD domain-containing protein 1 (SAMHD1), and transmembrane tetratricopeptide 1 (TMTC1) were highlighted as potential biomarkers. In addition, the differential expressions of immunity and inflammation-related genes were examined and their correlations with the five identified biomarkers were analyzed. The results from performing RT-qPCR and Western blots confirmed that the levels of each of these biomarkers were all significantly increased following osteogenic differentiation of MSCs. Conclusions: Our results identify five biomarkers related to MSCs osteogenesis and allow us to identify their potential roles in immunoregulation and inflammation. Each biomarker was verified by in vitro experiments.
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14
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Oe S, Hayashi S, Tanaka S, Koike T, Hirahara Y, Seki-Omura R, Kakizaki R, Sakamoto S, Nakano Y, Noda Y, Yamada H, Kitada M. Cytoplasmic Polyadenylation Element-Binding Protein 1 Post-transcriptionally Regulates Fragile X Mental Retardation 1 Expression Through 3′ Untranslated Region in Central Nervous System Neurons. Front Cell Neurosci 2022; 16:869398. [PMID: 35496917 PMCID: PMC9051318 DOI: 10.3389/fncel.2022.869398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
Fragile X syndrome (FXS) is an inherited intellectual disability caused by a deficiency in Fragile X mental retardation 1 (Fmr1) gene expression. Recent studies have proposed the importance of cytoplasmic polyadenylation element-binding protein 1 (CPEB1) in FXS pathology; however, the molecular interaction between Fmr1 mRNA and CPEB1 has not been fully investigated. Here, we revealed that CPEB1 co-localized and interacted with Fmr1 mRNA in hippocampal and cerebellar neurons and culture cells. Furthermore, CPEB1 knockdown upregulated Fmr1 mRNA and protein levels and caused aberrant localization of Fragile X mental retardation protein in neurons. In an FXS cell model, CPEB1 knockdown upregulated the mRNA levels of several mitochondria-related genes and rescued the intracellular heat shock protein family A member 9 distribution. These findings suggest that CPEB1 post-transcriptionally regulated Fmr1 expression through the 3′ untranslated region, and that CPEB1 knockdown might affect mitochondrial function.
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Affiliation(s)
- Souichi Oe
- Department of Anatomy, Kansai Medical University, Hirakata, Japan
- *Correspondence: Souichi Oe,
| | - Shinichi Hayashi
- Department of Anatomy, Kansai Medical University, Hirakata, Japan
| | - Susumu Tanaka
- Department of Anatomy, Kansai Medical University, Hirakata, Japan
| | - Taro Koike
- Department of Anatomy, Kansai Medical University, Hirakata, Japan
| | - Yukie Hirahara
- Department of Anatomy, Kansai Medical University, Hirakata, Japan
| | | | - Rio Kakizaki
- Department of Anatomy, Kansai Medical University, Hirakata, Japan
| | - Sumika Sakamoto
- Department of Anatomy, Kansai Medical University, Hirakata, Japan
| | - Yosuke Nakano
- Department of Anatomy, Kansai Medical University, Hirakata, Japan
| | - Yasuko Noda
- Department of Anatomy, Bio-Imaging and Neuro-Cell Science, Jichi Medical University, Shimotsuke, Japan
| | - Hisao Yamada
- Biwako Professional University of Rehabilitation, Higashiomi, Japan
| | - Masaaki Kitada
- Department of Anatomy, Kansai Medical University, Hirakata, Japan
- Masaaki Kitada,
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15
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Heat Shock-Binding Protein 21 Regulates the Innate Immune Response to Viral Infection. J Virol 2022; 96:e0000122. [DOI: 10.1128/jvi.00001-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The innate immune system is the first-line host defense against microbial pathogen invasion. The physiological functions of molecular chaperones, involving cell differentiation, migration, proliferation and inflammation, have been intensively studied.
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16
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Hang J, Wang J, Lu M, Xue Y, Qiao J, Tao L. Protein O-mannosylation across kingdoms and related diseases: From glycobiology to glycopathology. Biomed Pharmacother 2022; 148:112685. [PMID: 35149389 DOI: 10.1016/j.biopha.2022.112685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 11/18/2022] Open
Abstract
The post-translational glycosylation of proteins by O-linked α-mannose is conserved from bacteria to humans. Due to advances in high-throughput mass spectrometry-based approaches, a variety of glycoproteins are identified to be O-mannosylated. Various proteins with O-mannosylation are involved in biological processes, providing essential necessity for proper growth and development. In this review, we summarize the process and regulation of O-mannosylation. The multi-step O-mannosylation procedures are quite dynamic and complex, especially when considering the structural and functional inspection of the involved enzymes. The widely studied O-mannosylated proteins in human include α-Dystroglycan (α-DG), cadherins, protocadherins, and plexin, and their aberrant O-mannosylation are associated with many diseases. In addition, O-mannosylation also contributes to diverse functions in lower eukaryotes and prokaryotes. Finally, we present the relationship between O-mannosylation and gut microbiota (GM), and elucidate that O-mannosylation in microbiome is of great importance in the dynamic balance of GM. Our study provides an overview of the processes of O-mannosylation in mammalian cells and other organisms, and also associated regulated enzymes and biological functions, which could contribute to the understanding of newly discovered O-mannosylated glycoproteins.
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Affiliation(s)
- Jing Hang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Jinpeng Wang
- Department of Orthopedics, First Hospital of China Medical University, Shenyang 110001, China
| | - Minzhen Lu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Yuchuan Xue
- The First Department of Clinical Medicine, China Medical University, Shenyang 110001, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China.
| | - Lin Tao
- Department of Orthopedics, First Hospital of China Medical University, Shenyang 110001, China.
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17
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Cheng JY, Stern AJ, Racimo F, Nielsen R. Detecting Selection in Multiple Populations by Modeling Ancestral Admixture Components. Mol Biol Evol 2022; 39:msab294. [PMID: 34626111 PMCID: PMC8763095 DOI: 10.1093/molbev/msab294] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
One of the most powerful and commonly used approaches for detecting local adaptation in the genome is the identification of extreme allele frequency differences between populations. In this article, we present a new maximum likelihood method for finding regions under positive selection. It is based on a Gaussian approximation to allele frequency changes and it incorporates admixture between populations. The method can analyze multiple populations simultaneously and retains power to detect selection signatures specific to ancestry components that are not representative of any extant populations. Using simulated data, we compare our method to related approaches, and show that it is orders of magnitude faster than the state-of-the-art, while retaining similar or higher power for most simulation scenarios. We also apply it to human genomic data and identify loci with extreme genetic differentiation between major geographic groups. Many of the genes identified are previously known selected loci relating to hair pigmentation and morphology, skin, and eye pigmentation. We also identify new candidate regions, including various selected loci in the Native American component of admixed Mexican-Americans. These involve diverse biological functions, such as immunity, fat distribution, food intake, vision, and hair development.
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Affiliation(s)
- Jade Yu Cheng
- Lundbeck GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Aaron J Stern
- Graduate Group in Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Fernando Racimo
- Lundbeck GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Nielsen
- Lundbeck GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
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18
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María Irene CC, Juan Germán RC, Gamaliel LL, Dulce Adriana ME, Estela Isabel B, Brenda Nohemí M, Payan Jorge B, Zyanya Lucía ZB, Myriam BDV, Fernanda CG, Adrian OL, Martha Isabel M, Rogelio HP. Profiling the immune response to Mycobacterium tuberculosis Beijing family infection: a perspective from the transcriptome. Virulence 2021; 12:1689-1704. [PMID: 34228582 PMCID: PMC8265813 DOI: 10.1080/21505594.2021.1936432] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 03/24/2021] [Accepted: 05/14/2021] [Indexed: 01/15/2023] Open
Abstract
Tuberculosis continues to be an important public health problem. Particularly considering Beijing-family strains of Mycobacterium tuberculosis, which have been associated with drug-resistance and hypervirulence. The Beijing-like SIT190 (BL) is the most prevalent Beijing strain in Colombia. The pathogenic mechanism and immune response against this pathogen is unknown. Thus, we compared the course of pulmonary TB in BALB/c mice infected with Classical-Beijing strain 391 and BL strain 323. The disease course was different among infected animals with Classical-Beijing and BL strain. Mice infected with BL had a 100% mortality at 45 days post-infection (dpi), with high bacillary loads and massive pneumonia, whereas infected animals with Classical-Beijing survived until 60 dpi and showed extensive pneumonia and necrosis. Lung RNA extraction was carried out at early (day 3 dpi), intermediate (day 14 dpi), and late (days 28 and 60 dpi) time points of infection. Transcriptional analysis of infected mice with Classical-Beijing showed several over-expressed genes, associated with a pro-inflammatory profile, including those for coding for CCL3 and CCL4 chemokines, both biomarkers of disease severity. Conversely, mice infected with BL displayed a profile which included the over-expression of several genes associated with immune-suppression, including Nkiras, Dleu2, and Sphk2, highlighting an anti-inflammatory milieu which would allow high bacterial replication followed by an intense inflammatory response. In summary, both Beijing strains induced a non-protective immune response which induced extensive tissue damage, BL strain induced rapidly extensive pneumonia and death, whereas Classical-Beijing strain produced slower extensive pneumonia later associated with extensive necrosis.
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Affiliation(s)
- Cerezo-Cortés María Irene
- Universidad Nacional De Colombia, Facultad De Medicina, Departamento De Microbiología, Laboratorio De Micobacterias
| | | | - López-Leal Gamaliel
- Departamento De Microbiología Molecular, Instituto De Biotecnología, Universidad Nacional Autónoma De México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, México
| | - Mata-Espinosa Dulce Adriana
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Bini Estela Isabel
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Marquina–Casitllo Brenda Nohemí
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Barrios Payan Jorge
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Zatarain-Barrón Zyanya Lucía
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
| | - Bobadilla del Valle Myriam
- Departamento De Microbiología Clínica, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán Ciudad De México, México
| | - Cornejo-Granados Fernanda
- Departamento De Microbiología Molecular, Instituto De Biotecnología, Universidad Nacional Autónoma De México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, México
| | - Ochoa-Leyva Adrian
- Departamento De Microbiología Molecular, Instituto De Biotecnología, Universidad Nacional Autónoma De México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, México
| | - Murcia Martha Isabel
- Universidad Nacional De Colombia, Facultad De Medicina, Departamento De Microbiología, Laboratorio De Micobacterias
| | - Hernández-Pando Rogelio
- Sección De Patología Experimental, Departamento De Patología, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Ciudad De México, México
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19
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Raman D, Tay P, Hirpara JL, Liu D, Pervaiz S. TRAIL sensitivity of nasopharyngeal cancer cells involves redox dependent upregulation of TMTC2 and its interaction with membrane caspase-3. Redox Biol 2021; 48:102193. [PMID: 34839142 PMCID: PMC8636823 DOI: 10.1016/j.redox.2021.102193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/12/2021] [Accepted: 11/19/2021] [Indexed: 12/09/2022] Open
Abstract
AIMS Preferential expression of receptors for TNF-family related apoptosis inducing ligand (TRAIL), DR4 and DR5 makes TRAIL an attractive anti-cancer therapeutic. However, the efficacy of targeting death receptors has not been extensively studied in nasopharyngeal cancer (NPC). Here we investigated TRAIL sensitivity and its underlying mechanism in NPC cell lines, and assessed the potential of TRAIL as a therapeutic option against NPC. RESULTS Using two established NPC cell lines, we report the expression of DR4 and DR5, which respond to TRAIL ligation by triggering efficient Type II apoptosis. Mechanistically, early activation of caspase-3 and its membrane recruitment is identified in NPC cell lines, which is associated with, hitherto unreported, interaction with transmembrane and tetratricopeptide repeat containing 2 (TMTC2) in the lipid raft domains. TMTC2 expression is induced upon exposure to TRAIL and involves intracellular increase in peroxynitrite (ONOO-) production. While ONOO- increase is downstream of caspase-8 activation, it is involved in the upregulation of TMTC2, gene knockdown of which abrogated TRAIL-induced apoptotic execution. Bioinformatics analyses also provide evidence for a strong correlation between TMTC2 and DR4 or caspase-3 as well as a significantly better disease-free survival in patients with high TMTC2 expression. INNOVATION AND CONCLUSION Collectively, redox-dependent execution of NPC cells upon ligation of TRAIL receptors reintroduces the possible therapeutic use of TRAIL in NPC as well as underscores the potential of using TMTC2 as a biomarker of TRAIL sensitivity.
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Affiliation(s)
- Deepika Raman
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Patricia Tay
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Dan Liu
- Integrated Science and Engineering Program (ISEP), NUS Graduate School, National University of Singapore, Singapore
| | - Shazib Pervaiz
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cancer Science Institute, National University of Singapore, Singapore; NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; National University Cancer Institute, National University Health System, Singapore; Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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20
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Dubon MAC, Pedrosa VB, Feitosa FLB, Costa RB, de Camargo GMF, Silva MR, Pinto LFB. Identification of novel candidate genes for age at first calving in Nellore cows using a SNP chip specifically developed for Bos taurus indicus cattle. Theriogenology 2021; 173:156-162. [PMID: 34392169 DOI: 10.1016/j.theriogenology.2021.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 01/08/2023]
Abstract
The age at first calving has a great economic impact on the beef cattle system and calving at 24 months is an objective of selection for a more efficient herd. However, an age at first calving around 36 months has been observed for Nellore cattle in Brazil. Thus, a genome-wide association study (GWAS) was carried out with 8376 records of age at first calving and 3239 animals genotyped with the GGP-Indicus 35K, which has been developed specifically for Bos taurus indicus. The weighted single-step genomic best linear unbiased prediction method was used, with adjacent SNPs (single nucleotide polymorphisms) in genomic windows of 1.0 Mb. After quality control, 3239 (2161 males and 1078 females) animals genotyped for 30,519 SNPs were used in GWAS analysis. The average and standard deviation of age at first calving were 1041.7 and 140.6 days, respectively. The heritability estimate was 0.10 ± 0.02. The GWAS analysis found seven genomic regions in BTA1, 2, 5, 12, 18, 21, and 24, which explained a total of 11.24% of the additive genetic variance of age at first calving. In these regions were found 62 protein coding genes, and the genes HSD17B2, SERPINA14, SERPINA1, SERPINA5, STAT1, NFATC1, ATP9B, CTDP1, THPO, ECE2, PSMD2, EIF4G1, EIF2B2, DVL3, POLR2H, TMTC2, and GPC6 are possible candidates for age at first birth due their function. Moreover, two molecular functions ("serine-type endopeptidase inhibitor activity" and "negative regulation of endopeptidase activity") were significant, which depend on several serpin genes. The use of a SNP chip developed especially for Bos taurus indicus allowed to find genomic regions for age at first calving, which are close to QTLs previously reported for other reproduction-related traits. Future studies can reveal the causal variants and their effects on reproductive precocity of Nellore cows.
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Affiliation(s)
| | - Victor Breno Pedrosa
- State University of Ponta Grossa, 4748, Av. General Carlos Cavalcanti, Ponta Grossa, PR, 84030900, Brazil.
| | | | - Raphael Bermal Costa
- Federal University of Bahia, 500, Av. Adhemar de Barros, Salvador, BA, 40170110, Brazil.
| | | | - Marcio Ribeiro Silva
- Melhore Animal and Katayama Agropecuaria Lda, Guararapes, SP, 16700-000, Brazil.
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21
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Makboul R, Abdelkawi IF, Badary DM, Hussein MRA, Rhim JS, Toraih EA, Zerfaoui M, Abd Elmageed ZY. Transmembrane and Tetratricopeptide Repeat Containing 4 Is a Novel Diagnostic Marker for Prostate Cancer with High Specificity and Sensitivity. Cells 2021; 10:cells10051029. [PMID: 33925440 PMCID: PMC8146280 DOI: 10.3390/cells10051029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 11/17/2022] Open
Abstract
The histopathologic diagnosis of prostate cancer (PCa) from biopsies is a current challenge if double or triple staining is needed. Therefore, there is an urgent need for development of a new reliable biomarker to diagnose PCa patients. We aimed to explore and compare the expression of TMTC4 in PCa cells and tissue specimens and evaluate its sensitivity and specificity. The expression of TMTC4 in PCa and normal prostate epithelial cells was determined by real-time PCR and Western blot analyses. Immunohistochemical (IHC) staining of TMTC4 was performed on tissues collected from PCa and benign prostatic hyperplasia (BPH). Our results show a high expression of TMTC4 on mRNA and protein levels in PCa versus BPH1 and normal cells (p < 0.05). IHC results show strong cytoplasmic expressions in PCa cases (p < 0.001) as compared to BPH cases. The overall accuracy as measured by the AUC was 1.0 (p < 0.001). The sensitivity and specificity of the protein were 100% and 96.6%, respectively. Taken together, we report a high TMTC4 expression in PCa cells and tissues and its ability to differentiate between PCa and BPH with high sensitivity and specificity. This finding can be carried over to clinical practice after its confirmation by further studies.
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Affiliation(s)
- Rania Makboul
- Department of Pathology and Urology, Faculty of Medicine, Assiut University, Assiut 71111, Egypt; (R.M.); (D.M.B.); (M.R.A.H.)
| | - Islam F. Abdelkawi
- Department of Urology, Faculty of Medicine, Assiut University, Assiut 71111, Egypt;
| | - Dalia M. Badary
- Department of Pathology and Urology, Faculty of Medicine, Assiut University, Assiut 71111, Egypt; (R.M.); (D.M.B.); (M.R.A.H.)
| | - Mahmoud R. A. Hussein
- Department of Pathology and Urology, Faculty of Medicine, Assiut University, Assiut 71111, Egypt; (R.M.); (D.M.B.); (M.R.A.H.)
| | - Johng S. Rhim
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA;
| | - Eman A. Toraih
- Department of Surgery, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70112, USA; (E.A.T.); (M.Z.)
| | - Mourad Zerfaoui
- Department of Surgery, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70112, USA; (E.A.T.); (M.Z.)
| | - Zakaria Y. Abd Elmageed
- Department of Pharmacology, Edward Via College of Osteopathic Medicine, University of Louisiana at Monroe, Monroe, LA 71203, USA
- Correspondence:
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22
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Vassalli QA, Colantuono C, Nittoli V, Ferraioli A, Fasano G, Berruto F, Chiusano ML, Kelsh RN, Sordino P, Locascio A. Onecut Regulates Core Components of the Molecular Machinery for Neurotransmission in Photoreceptor Differentiation. Front Cell Dev Biol 2021; 9:602450. [PMID: 33816460 PMCID: PMC8012850 DOI: 10.3389/fcell.2021.602450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/11/2021] [Indexed: 11/13/2022] Open
Abstract
Photoreceptor cells (PRC) are neurons highly specialized for sensing light stimuli and have considerably diversified during evolution. The genetic mechanisms that underlie photoreceptor differentiation and accompanied the progressive increase in complexity and diversification of this sensory cell type are a matter of great interest in the field. A role of the homeodomain transcription factor Onecut (Oc) in photoreceptor cell formation is proposed throughout multicellular organisms. However, knowledge of the identity of the Oc downstream-acting factors that mediate specific tasks in the differentiation of the PRC remains limited. Here, we used transgenic perturbation of the Ciona robusta Oc protein to show its requirement for ciliary PRC differentiation. Then, transcriptome profiling between the trans-activation and trans-repression Oc phenotypes identified differentially expressed genes that are enriched in exocytosis, calcium homeostasis, and neurotransmission. Finally, comparison of RNA-Seq datasets in Ciona and mouse identifies a set of Oc downstream genes conserved between tunicates and vertebrates. The transcription factor Oc emerges as a key regulator of neurotransmission in retinal cell types.
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Affiliation(s)
- Quirino Attilio Vassalli
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Chiara Colantuono
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Valeria Nittoli
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Anna Ferraioli
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Giulia Fasano
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Federica Berruto
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Maria Luisa Chiusano
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Agriculture, Università degli Studi di Napoli Federico II, Portici, Italy
| | - Robert Neil Kelsh
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, University of Bath, London, United Kingdom
| | - Paolo Sordino
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Annamaria Locascio
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
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23
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Eisenhaber B, Sinha S, Jadalanki CK, Shitov VA, Tan QW, Sirota FL, Eisenhaber F. Conserved sequence motifs in human TMTC1, TMTC2, TMTC3, and TMTC4, new O-mannosyltransferases from the GT-C/PMT clan, are rationalized as ligand binding sites. Biol Direct 2021; 16:4. [PMID: 33436046 PMCID: PMC7801869 DOI: 10.1186/s13062-021-00291-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/04/2021] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The human proteins TMTC1, TMTC2, TMTC3 and TMTC4 have been experimentally shown to be components of a new O-mannosylation pathway. Their own mannosyl-transferase activity has been suspected but their actual enzymatic potential has not been demonstrated yet. So far, sequence analysis of TMTCs has been compromised by evolutionary sequence divergence within their membrane-embedded N-terminal region, sequence inaccuracies in the protein databases and the difficulty to interpret the large functional variety of known homologous proteins (mostly sugar transferases and some with known 3D structure). RESULTS Evolutionary conserved molecular function among TMTCs is only possible with conserved membrane topology within their membrane-embedded N-terminal regions leading to the placement of homologous long intermittent loops at the same membrane side. Using this criterion, we demonstrate that all TMTCs have 11 transmembrane regions. The sequence segment homologous to Pfam model DUF1736 is actually just a loop between TM7 and TM8 that is located in the ER lumen and that contains a small hydrophobic, but not membrane-embedded helix. Not only do the membrane-embedded N-terminal regions of TMTCs share a common fold and 3D structural similarity with subgroups of GT-C sugar transferases. The conservation of residues critical for catalysis, for binding of a divalent metal ion and of the phosphate group of a lipid-linked sugar moiety throughout enzymatically and structurally well-studied GT-Cs and sequences of TMTCs indicates that TMTCs are actually sugar-transferring enzymes. We present credible 3D structural models of all four TMTCs (derived from their closest known homologues 5ezm/5f15) and find observed conserved sequence motifs rationalized as binding sites for a metal ion and for a dolichyl-phosphate-mannose moiety. CONCLUSIONS With the results from both careful sequence analysis and structural modelling, we can conclusively say that the TMTCs are enzymatically active sugar transferases belonging to the GT-C/PMT superfamily. The DUF1736 segment, the loop between TM7 and TM8, is critical for catalysis and lipid-linked sugar moiety binding. Together with the available indirect experimental data, we conclude that the TMTCs are not only part of an O-mannosylation pathway in the endoplasmic reticulum of upper eukaryotes but, actually, they are the sought mannosyl-transferases.
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Affiliation(s)
- Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.
- Genome Institute of Singapore (BII), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
| | - Swati Sinha
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Chaitanya K Jadalanki
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Vladimir A Shitov
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
- Siberian State Medical University, Moskovskiy Trakt, 2, Tomsk, Tomsk Oblast, 634050, Russia
| | - Qiao Wen Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
- School of Biological Science (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Fernanda L Sirota
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore.
- Genome Institute of Singapore (BII), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
- School of Biological Science (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
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24
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Hosseinipour M, Shahbazi S, Roudbar-Mohammadi S, Khorasani M, Marjani M. Differential genes expression analysis of invasive aspergillosis: a bioinformatics study based on mRNA/microRNA. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2020; 9:173-180. [PMID: 33344664 PMCID: PMC7731968 DOI: 10.22099/mbrc.2020.37432.1509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Invasive aspergillosis is a severe opportunistic infection with high mortality in immunocompromised patients. Recently, the roles of microRNAs have been taken into consideration in the immune system and inflammatory responses. Using bioinformatics approaches, we aimed to study the microRNAs related to invasive aspergillosis to understand the molecular pathways involved in the disease pathogenesis. Data were extracted from the gene expression omnibus (GEO) database. We proposed 3 differentially expressed genes; S100B, TDRD9 and TMTC1 related to pathogenesis of invasive aspergillosis. Using miRWalk 2.0 predictive tool, microRNAs that targeted the selected genes were identified. The roles of microRNAs were investigated by microRNA target prediction and molecular pathways analysis. The significance of combined expression changes in selected genes was analyzed by ROC curves study. Thirty-three microRNAs were identified as the common regulator of S100B, TDRD9 and TMTC1 genes. Several of them were previously reported in the pathogenesis of fungal infections including miR-132. Predicted microRNAs were involved in innate immune response as well as toll-like receptor signaling. Most of the microRNAs were also linked to platelet activation. The ROC chart in the combination mode of S100B/TMTC1, showed the sensitivity of 95.65 percent and the specificity of 69.23 percent. New approaches are needed for rapid and accurate detection of invasive aspergillosis. Given the pivotal signaling pathways involved, predicted microRNAs can be considered as the potential candidates of the disease diagnosis. Further investigation of the microRNAs expression changes and related pathways would lead to identifying the effective biomarkers for IA detection.
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Affiliation(s)
- Maryam Hosseinipour
- Department of Medical Mycology, Faculty of Medical Science, Tarbiat Modares University, Tehran Iran
| | - Shirin Shahbazi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Shahla Roudbar-Mohammadi
- Department of Medical Mycology, Faculty of Medical Science, Tarbiat Modares University, Tehran Iran
| | - Maryam Khorasani
- Molecular Medicine Department, Pasteur Institute of Iran, Tehran, Iran
| | - Majid Marjani
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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25
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Mealer RG, Williams SE, Daly MJ, Scolnick EM, Cummings RD, Smoller JW. Glycobiology and schizophrenia: a biological hypothesis emerging from genomic research. Mol Psychiatry 2020; 25:3129-3139. [PMID: 32377000 PMCID: PMC8081046 DOI: 10.1038/s41380-020-0753-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/09/2020] [Accepted: 04/22/2020] [Indexed: 12/12/2022]
Abstract
Advances in genomics are opening new windows into the biology of schizophrenia. Though common variants individually have small effects on disease risk, GWAS provide a powerful opportunity to explore pathways and mechanisms contributing to pathophysiology. Here, we highlight an underappreciated biological theme emerging from GWAS: the role of glycosylation in schizophrenia. The strongest coding variant in schizophrenia GWAS is a missense mutation in the manganese transporter SLC39A8, which is associated with altered glycosylation patterns in humans. Furthermore, variants near several genes encoding glycosylation enzymes are unambiguously associated with schizophrenia: FUT9, MAN2A1, TMTC1, GALNT10, and B3GAT1. Here, we summarize the known biological functions, target substrates, and expression patterns of these enzymes as a primer for future studies. We also highlight a subset of schizophrenia-associated proteins critically modified by glycosylation including glutamate receptors, voltage-gated calcium channels, the dopamine D2 receptor, and complement glycoproteins. We hypothesize that common genetic variants alter brain glycosylation and play a fundamental role in the development of schizophrenia. Leveraging these findings will advance our mechanistic understanding of disease and may provide novel avenues for treatment development.
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Affiliation(s)
- Robert G. Mealer
- Massachusetts General Hospital, Department of Psychiatry.,The Stanley Center for Psychiatric Research at Broad Institute.,Department of Surgery, Beth Israel Deaconess Medical Center. Harvard Medical School, Boston MA.,Corresponding Author: Robert Gene Mealer, M.D., Ph.D., Richard B. Simches Research Center, 185 Cambridge St, 6th Floor, Boston, MA 02114, Tel: +1 (617) 724-9076,
| | - Sarah E. Williams
- Massachusetts General Hospital, Department of Psychiatry.,Department of Surgery, Beth Israel Deaconess Medical Center. Harvard Medical School, Boston MA
| | - Mark J. Daly
- Massachusetts General Hospital, Department of Psychiatry.,The Stanley Center for Psychiatric Research at Broad Institute
| | - Edward M. Scolnick
- Massachusetts General Hospital, Department of Psychiatry.,The Stanley Center for Psychiatric Research at Broad Institute
| | - Richard D. Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center. Harvard Medical School, Boston MA
| | - Jordan W. Smoller
- Massachusetts General Hospital, Department of Psychiatry.,The Stanley Center for Psychiatric Research at Broad Institute
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26
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Martinez R, Huang W, Samadani R, Mackowiak B, Centola G, Chen L, Conlon IL, Hom K, Kane MA, Fletcher S, Shapiro P. Mechanistic Analysis of an Extracellular Signal-Regulated Kinase 2-Interacting Compound that Inhibits Mutant BRAF-Expressing Melanoma Cells by Inducing Oxidative Stress. J Pharmacol Exp Ther 2020; 376:84-97. [PMID: 33109619 PMCID: PMC7788356 DOI: 10.1124/jpet.120.000266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/06/2020] [Indexed: 11/22/2022] Open
Abstract
Constitutively active extracellular signal–regulated kinase (ERK) 1/2 signaling promotes cancer cell proliferation and survival. We previously described a class of compounds containing a 1,1-dioxido-2,5-dihydrothiophen-3-yl 4-benzenesulfonate scaffold that targeted ERK2 substrate docking sites and selectively inhibited ERK1/2-dependent functions, including activator protein-1–mediated transcription and growth of cancer cells containing active ERK1/2 due to mutations in Ras G-proteins or BRAF, Proto-oncogene B-RAF (Rapidly Acclerated Fibrosarcoma) kinase. The current study identified chemical features required for biologic activity and global effects on gene and protein levels in A375 melanoma cells containing mutant BRAF (V600E). Saturation transfer difference-NMR and mass spectrometry analyses revealed interactions between a lead compound (SF-3-030) and ERK2, including the formation of a covalent adduct on cysteine 252 that is located near the docking site for ERK/FXF (DEF) motif for substrate recruitment. Cells treated with SF-3-030 showed rapid changes in immediate early gene levels, including DEF motif–containing ERK1/2 substrates in the Fos family. Analysis of transcriptome and proteome changes showed that the SF-3-030 effects overlapped with ATP-competitive or catalytic site inhibitors of MAPK/ERK Kinase 1/2 (MEK1/2) or ERK1/2. Like other ERK1/2 pathway inhibitors, SF-3-030 induced reactive oxygen species (ROS) and genes associated with oxidative stress, including nuclear factor erythroid 2–related factor 2 (NRF2). Whereas the addition of the ROS inhibitor N-acetyl cysteine reversed SF-3-030–induced ROS and inhibition of A375 cell proliferation, the addition of NRF2 inhibitors has little effect on cell proliferation. These studies provide mechanistic information on a novel chemical scaffold that selectively regulates ERK1/2-targeted transcription factors and inhibits the proliferation of A375 melanoma cells through a ROS-dependent mechanism.
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Affiliation(s)
- Ramon Martinez
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Ramin Samadani
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Bryan Mackowiak
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Garrick Centola
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Lijia Chen
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Ivie L Conlon
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Kellie Hom
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
| | - Paul Shapiro
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore- School of Pharmacy, Baltimore, Maryland
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27
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Inoue M, Sakuta N, Watanabe S, Zhang Y, Yoshikaie K, Tanaka Y, Ushioda R, Kato Y, Takagi J, Tsukazaki T, Nagata K, Inaba K. Structural Basis of Sarco/Endoplasmic Reticulum Ca 2+-ATPase 2b Regulation via Transmembrane Helix Interplay. Cell Rep 2020; 27:1221-1230.e3. [PMID: 31018135 DOI: 10.1016/j.celrep.2019.03.106] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/28/2019] [Accepted: 03/27/2019] [Indexed: 12/31/2022] Open
Abstract
Sarco/endoplasmic reticulum (ER) Ca2+-ATPase 2b (SERCA2b) is a ubiquitously expressed membrane protein that facilitates Ca2+ uptake from the cytosol to the ER. SERCA2b includes a characteristic 11th transmembrane helix (TM11) followed by a luminal tail, but the structural basis of SERCA regulation by these C-terminal segments remains unclear. Here, we determined the crystal structures of SERCA2b and its C-terminal splicing variant SERCA2a, both in the E1-2Ca2+-adenylyl methylenediphosphonate (AMPPCP) state. Despite discrepancies with the previously reported structural model of SERCA2b, TM11 was found to be located adjacent to TM10 and to interact weakly with a part of the L8/9 loop and the N-terminal end of TM10, thereby inhibiting the SERCA2b catalytic cycle. Accordingly, mutational disruption of the interactions between TM11 and its neighboring residues caused SERCA2b to display SERCA2a-like ATPase activity. We propose that TM11 serves as a key modulator of SERCA2b activity by fine-tuning the intramolecular interactions with other transmembrane regions.
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Affiliation(s)
- Michio Inoue
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Kawaguchi, Japan
| | - Nanami Sakuta
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Kawaguchi, Japan
| | - Satoshi Watanabe
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Kawaguchi, Japan
| | - Yuxia Zhang
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Kawaguchi, Japan
| | - Kunihito Yoshikaie
- Graduate School of Biological Sciences, NARA Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Yoshiki Tanaka
- Graduate School of Biological Sciences, NARA Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Ryo Ushioda
- Graduate School of Biological Sciences, NARA Institute of Science and Technology, Ikoma 630-0192, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Kawaguchi, Japan
| | - Yukinari Kato
- Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, Suita 565-0871, Japan
| | - Tomoya Tsukazaki
- Graduate School of Biological Sciences, NARA Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kazuhiro Nagata
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Kawaguchi, Japan
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Kawaguchi, Japan.
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28
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Wu Q, Finley SD. Mathematical Model Predicts Effective Strategies to Inhibit VEGF-eNOS Signaling. J Clin Med 2020; 9:jcm9051255. [PMID: 32357492 PMCID: PMC7287924 DOI: 10.3390/jcm9051255] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/12/2020] [Accepted: 04/20/2020] [Indexed: 12/27/2022] Open
Abstract
The endothelial nitric oxide synthase (eNOS) signaling pathway in endothelial cells has multiple physiological significances. It produces nitric oxide (NO), an important vasodilator, and enables a long-term proliferative response, contributing to angiogenesis. This signaling pathway is mediated by vascular endothelial growth factor (VEGF), a pro-angiogenic species that is often targeted to inhibit tumor angiogenesis. However, inhibiting VEGF-mediated eNOS signaling can lead to complications such as hypertension. Therefore, it is important to understand the dynamics of eNOS signaling in the context of angiogenesis inhibitors. Thrombospondin-1 (TSP1) is an important angiogenic inhibitor that, through interaction with its receptor CD47, has been shown to redundantly inhibit eNOS signaling. However, the exact mechanisms of TSP1's inhibitory effects on this pathway remain unclear. To address this knowledge gap, we established a molecular-detailed mechanistic model to describe VEGF-mediated eNOS signaling, and we used the model to identify the potential intracellular targets of TSP1. In addition, we applied the predictive model to investigate the effects of several approaches to selectively target eNOS signaling in cells experiencing high VEGF levels present in the tumor microenvironment. This work generates insights for pharmacologic targets and therapeutic strategies to inhibit tumor angiogenesis signaling while avoiding potential side effects in normal vasoregulation.
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Affiliation(s)
- Qianhui Wu
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA 90089, USA;
| | - Stacey D. Finley
- Department of Biomedical Engineering, Mork Family Department of Chemical Engineering and Materials Science, and Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Correspondence: ; Tel.: +1-213-740-8788
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29
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Metastasizing Pleomorphic Adenoma: Recurrent PLAG1/HMGA2 Rearrangements and Identification of a Novel HMGA2-TMTC2 Fusion. Am J Surg Pathol 2020; 43:1145-1151. [PMID: 31094927 DOI: 10.1097/pas.0000000000001280] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Pleomorphic adenoma (PA) is the most common salivary gland neoplasm. On a molecular level PA is characterized by a translocation involving PLAG1 or HMGA2. PA is considered to be a benign tumor although it can undergo malignant transformation. Alternatively, cases of histologically benign PA "metastasizing" to lymph nodes or distant body sites are well documented. Several theories have been proposed to explain this behavior. However, there is a lack of molecular data available to assess the relationship of metastasizing PA (MPA) and their benign counterparts. In this study we describe 4 cases of MPAs and perform the first molecular study linking them to conventional PA. The index case was identified in the course of routine clinical practice, while the other cases were retrieved from the archives of the authors. Slides were reviewed to confirm the diagnosis of both the primary/recurrent tumor and the metastasis. Fluorescence in situ hybridization (FISH) was performed in all cases and RNA sequencing was performed on the index case. In all cases there was a history of recurrent PA involving the parotid. Lymph node metastases were identified in 2 cases; non-lymph node metastases were identified in 3 cases. All the metastases were histologically benign. RNA sequencing performed on the index case demonstrated a novel HMGA2-TMTC2 translocation, which was confirmed by separate FISH break-apart assays for both genes. FISH performed on the remaining cases demonstrated rearrangement of PLAG1 in all 3 cases. This study demonstrates that MPA harbors the same disease-defining molecular hallmark as their benign counterparts.
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30
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Graham JB, Sunryd JC, Mathavan K, Weir E, Larsen ISB, Halim A, Clausen H, Cousin H, Alfandari D, Hebert DN. Endoplasmic reticulum transmembrane protein TMTC3 contributes to O-mannosylation of E-cadherin, cellular adherence, and embryonic gastrulation. Mol Biol Cell 2020; 31:167-183. [PMID: 31851597 PMCID: PMC7001481 DOI: 10.1091/mbc.e19-07-0408] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/29/2019] [Accepted: 12/12/2019] [Indexed: 01/17/2023] Open
Abstract
Protein glycosylation plays essential roles in protein structure, stability, and activity such as cell adhesion. The cadherin superfamily of adhesion molecules carry O-linked mannose glycans at conserved sites and it was recently demonstrated that the transmembrane and tetratricopeptide repeat-containing proteins 1-4 (TMTC1-4) gene products contribute to the addition of these O-linked mannoses. Here, biochemical, cell biological, and organismal analysis was used to determine that TMTC3 supports the O-mannosylation of E-cadherin, cellular adhesion, and embryonic gastrulation. Using genetically engineered cells lacking all four TMTC genes, overexpression of TMTC3 rescued O-linked glycosylation of E-cadherin and cell adherence. The knockdown of the Tmtcs in Xenopus laevis embryos caused a delay in gastrulation that was rescued by the addition of human TMTC3. Mutations in TMTC3 have been linked to neuronal cell migration diseases including Cobblestone lissencephaly. Analysis of TMTC3 mutations associated with Cobblestone lissencephaly found that three of the variants exhibit reduced stability and missence mutations were unable to complement TMTC3 rescue of gastrulation in Xenopus embryo development. Our study demonstrates that TMTC3 regulates O-linked glycosylation and cadherin-mediated adherence, providing insight into its effect on cellular adherence and migration, as well the basis of TMTC3-associated Cobblestone lissencephaly.
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Affiliation(s)
- Jill B. Graham
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Amherst, MA 01003
| | - Johan C. Sunryd
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Amherst, MA 01003
| | - Ketan Mathavan
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Amherst, MA 01003
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Amherst, MA 01003
| | - Emma Weir
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Amherst, MA 01003
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Amherst, MA 01003
| | - Ida Signe Bohse Larsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200, Denmark
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Adnan Halim
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200, Denmark
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Henrik Clausen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200, Denmark
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen 2200, Denmark
| | - Hélène Cousin
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Amherst, MA 01003
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Amherst, MA 01003
| | - Dominque Alfandari
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Amherst, MA 01003
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Amherst, MA 01003
| | - Daniel N. Hebert
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Amherst, MA 01003
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Calcium Signaling in Endothelial Colony Forming Cells in Health and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1131:1013-1030. [PMID: 31646543 DOI: 10.1007/978-3-030-12457-1_40] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Endothelial colony forming cells (ECFCs) represent the only known truly endothelial precursors. ECFCs are released in peripheral circulation to restore the vascular networks dismantled by an ischemic insult or to sustain the early phases of the angiogenic switch in solid tumors. A growing number of studies demonstrated that intracellular Ca2+ signaling plays a crucial role in driving ECFC proliferation, migration, homing and neovessel formation. For instance, vascular endothelial growth factor (VEGF) triggers intracellular Ca2+ oscillations and stimulates angiogenesis in healthy ECFCs, whereas stromal derived factor-1α promotes ECFC migration through a biphasic Ca2+ signal. The Ca2+ toolkit endowed to circulating ECFCs is extremely plastic and shows striking differences depending on the physiological background of the donor. For instance, inositol-1,4,5-trisphosphate-induced Ca2+ release from the endoplasmic reticulum is downregulated in tumor-derived ECFCs, while agonists-induced store-operated Ca2+ entry is up-regulated in renal cellular carcinoma and is unaltered in breast cancer and reduced in infantile hemangioma. This remodeling of the Ca2+ toolkit prevents VEGF-induced pro-angiogenic Ca2+ oscillations in tumor-derived ECFCs. An emerging theme of research is the dysregulation of the Ca2+ toolkit in primary myelofibrosis-derived ECFCs, as this myeloproliferative disorder may depend on a driver mutation in the calreticulin gene. In this chapter, I provide a comprehensive, but succinct, description on the architecture and role of the intracellular Ca2+ signaling toolkit in ECFCs derived from umbilical cord blood and from peripheral blood of healthy donors, cancer patients and subjects affected by primary myelofibrosis.
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Graham JB, Canniff NP, Hebert DN. TPR-containing proteins control protein organization and homeostasis for the endoplasmic reticulum. Crit Rev Biochem Mol Biol 2019; 54:103-118. [PMID: 31023093 DOI: 10.1080/10409238.2019.1590305] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The endoplasmic reticulum (ER) is a complex, multifunctional organelle comprised of a continuous membrane and lumen that is organized into a number of functional regions. It plays various roles including protein translocation, folding, quality control, secretion, calcium signaling, and lipid biogenesis. Cellular protein homeostasis is maintained by a complicated chaperone network, and the largest functional family within this network consists of proteins containing tetratricopeptide repeats (TPRs). TPRs are well-studied structural motifs that mediate intermolecular protein-protein interactions, supporting interactions with a wide range of ligands or substrates. Seven TPR-containing proteins have thus far been shown to localize to the ER and control protein organization and homeostasis within this multifunctional organelle. Here, we discuss the roles of these proteins in controlling ER processes and organization. The crucial roles that TPR-containing proteins play in the ER are highlighted by diseases or defects associated with their mutation or disruption.
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Affiliation(s)
- Jill B Graham
- a Molecular Cellular Biology Program , University of Massachusetts , Amherst , MA , USA.,b Biochemistry and Molecular Biology Department , University of Massachusetts , Amherst , MA , USA
| | - Nathan P Canniff
- a Molecular Cellular Biology Program , University of Massachusetts , Amherst , MA , USA.,b Biochemistry and Molecular Biology Department , University of Massachusetts , Amherst , MA , USA
| | - Daniel N Hebert
- a Molecular Cellular Biology Program , University of Massachusetts , Amherst , MA , USA.,b Biochemistry and Molecular Biology Department , University of Massachusetts , Amherst , MA , USA
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Larsen ISB, Narimatsu Y, Clausen H, Joshi HJ, Halim A. Multiple distinct O-Mannosylation pathways in eukaryotes. Curr Opin Struct Biol 2019; 56:171-178. [PMID: 30999272 DOI: 10.1016/j.sbi.2019.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 12/29/2022]
Abstract
Protein O-mannosylation (O-Man), originally discovered in yeast five decades ago, is an important post-translational modification (PTM) conserved from bacteria to humans, but not found in plants or nematodes. Until recently, the homologous family of ER-located protein O-mannosyl transferases (PMT1-7 in yeast; POMT1/POMT2 in humans), were the only known enzymes involved in directing O-Man biosynthesis in eukaryotes. However, recent studies demonstrate the existence of multiple distinct O-Man glycosylation pathways indicating that the genetic and biosynthetic regulation of O-Man in eukaryotes is more complex than previously envisioned. Introduction of sensitive glycoproteomics strategies provided an expansion of O-Man glycoproteomes in eukaryotes (yeast and mammalian cell lines) leading to the discovery of O-Man glycosylation on important mammalian cell adhesion (cadherin superfamily) and signaling (plexin family) macromolecules, and to the discovery of unique nucleocytoplasmic O-Man glycosylation in yeast. It is now evident that eukaryotes have multiple distinct O-Man glycosylation pathways including: i) the classical PMT1-7 and POMT1/POMT2 pathway conserved in all eukaryotes apart from plants; ii) a yet uncharacterized nucleocytoplasmic pathway only found in yeast; iii) an ER-located pathway directed by the TMTC1-4 genes found in metazoans and protists and primarily dedicated to the cadherin superfamily; and iv) a yet uncharacterized pathway found in metazoans primarily dedicated to plexins. O-Man glycosylation is thus emerging as a much more widespread and evolutionary diverse PTM with complex genetic and biosynthetic regulation. While deficiencies in the POMT1/POMT2 O-Man pathway underlie muscular dystrophies, the TMTC1-4 pathway appear to be involved in distinct congenital disorders with neurodevelopmental phenotypes. Here, we review and discuss the recent discoveries of the new non-classical O-Man glycosylation pathways, their substrates, functions and roles in disease.
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Affiliation(s)
- Ida Signe Bohse Larsen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
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Kondkar AA, Azad TA, Almobarak FA, Abu-Amero KK, Al-Obeidan SA. Polymorphism rs7961953 in TMTC2 gene is not associated with primary open-angle glaucoma in a Saudi cohort. Ophthalmic Genet 2019; 40:74-76. [PMID: 30729851 DOI: 10.1080/13816810.2019.1576210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Altaf A Kondkar
- a Department of Ophthalmology, Glaucoma Research Chair, College of Medicine , King Saud University , Riyadh , Saudi Arabia
| | - Taif A Azad
- a Department of Ophthalmology, Glaucoma Research Chair, College of Medicine , King Saud University , Riyadh , Saudi Arabia
| | - Faisal A Almobarak
- a Department of Ophthalmology, Glaucoma Research Chair, College of Medicine , King Saud University , Riyadh , Saudi Arabia
| | - Khaled K Abu-Amero
- a Department of Ophthalmology, Glaucoma Research Chair, College of Medicine , King Saud University , Riyadh , Saudi Arabia
| | - Saleh A Al-Obeidan
- a Department of Ophthalmology, Glaucoma Research Chair, College of Medicine , King Saud University , Riyadh , Saudi Arabia
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35
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Liu X, Chen J, Guan T, Yao H, Zhang W, Guan Z, Wang Y. miRNAs and target genes in the blood as biomarkers for the early diagnosis of Parkinson's disease. BMC SYSTEMS BIOLOGY 2019; 13:10. [PMID: 30665415 PMCID: PMC6341689 DOI: 10.1186/s12918-019-0680-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 01/04/2019] [Indexed: 01/26/2023]
Abstract
Background Parkinson’s disease (PD) is the second most common neurodegenerative disease, and it is a multifactorial disease with no definite diagnostic index. The aim of this study is to construct a molecular network to find molecules that play important roles in the progression of PD with the goal of using them diagnostically and for early intervention. Results We downloaded two gene expression profiles (GSE54536 and GSE100054) from the Expression Omnibus (GEO) database to analyze possible markers. The Genes were analyzed with GEO2R. There were 1790 and 967 differentially expressed genes (DEGs) in GSE54536 and GSE100054 respectively. A total of 125 genes co-exist in the DEGs of the two data sets. KEGG pathway analysis showed that 125 DEGs were enriched in Aldosterone synthesis and secretion, Gap junctions, Platelet activation, Rap1 signaling pathway, and Estrogen signaling pathway. There were 20 hub genes among 125 DEGs analyzed by PPI that involved in Platelet activation, Inflammatory response, Innate immune response, B cell receptor signaling, Stimulatory C-type lectin receptor signaling, Lipopolysaccharide response, Leukocyte migration, and Regulation of cell proliferation. Additionally, 42 differences in miRNAs were found in GSE100054. We constructed a miRNA-mRNA regulatory network depicting interactions between the predicted genes and the 125 DEGs. 34 miRNA-mRNA pairs were obtained. We found GNAQ and TMTC2 were the most important mRNAs in the network analyzed by Cytoscape APP centiscape, and their degrees in centiscape2.2 were all 10. has-miR-142 was the most important miRNA (the highest degree is 4 in centiscape2.2), which forms miRNA-mRNA pairs with GNAQ, TMTC2, BEND2, and KYNU. Conclusions This study provides data of potential biomarkers and therapeutic targets for PD diagnosis and treatment. Among them, hsa-miR-142 is a critical miRNA in the PD network, and may be involved in PD progression by regulating GNAQ, TMTC2, BEND2, and KYNU.
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Affiliation(s)
- Xiaoting Liu
- Department of Physiology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jinhu Chen
- Department of Endocrinology, Hebei General Hospital, Shijiazhuang, China
| | - Tianyuan Guan
- Department of Neurology, Hebei General Hospital, Shijiazhuang, China
| | - Hui Yao
- Department of Physiology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Wenpei Zhang
- Department of Physiology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Zhenlong Guan
- Department of Physiology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yanqin Wang
- Department of Physiology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.
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36
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Li J, Akil O, Rouse SL, McLaughlin CW, Matthews IR, Lustig LR, Chan DK, Sherr EH. Deletion of Tmtc4 activates the unfolded protein response and causes postnatal hearing loss. J Clin Invest 2018; 128:5150-5162. [PMID: 30188326 DOI: 10.1172/jci97498] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 08/30/2018] [Indexed: 12/16/2022] Open
Abstract
Hearing loss is a significant public health concern, affecting over 250 million people worldwide. Both genetic and environmental etiologies are linked to hearing loss, but in many cases the underlying cellular pathophysiology is not well understood, highlighting the importance of further discovery. We found that inactivation of the gene Tmtc4 (transmembrane and tetratricopeptide repeat 4), which was broadly expressed in the mouse cochlea, caused acquired hearing loss in mice. Our data showed Tmtc4 enriched in the endoplasmic reticulum, and that it functioned by regulating Ca2+ dynamics and the unfolded protein response (UPR). Given this genetic linkage of the UPR to hearing loss, we demonstrated a direct link between the more common noise-induced hearing loss (NIHL) and the UPR. These experiments suggested a novel approach to treatment. We demonstrated that the small-molecule UPR and stress response modulator ISRIB (integrated stress response inhibitor), which activates eIF2B, prevented NIHL in a mouse model. Moreover, in an inverse genetic complementation approach, we demonstrated that mice with homozygous inactivation of both Tmtc4 and Chop had less hearing loss than knockout of Tmtc4 alone. This study implicated a novel mechanism for hearing impairment, highlighting a potential treatment approach for a broad range of human hearing loss disorders.
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Affiliation(s)
| | - Omar Akil
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco (UCSF), San Francisco, California, USA
| | - Stephanie L Rouse
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco (UCSF), San Francisco, California, USA
| | - Conor W McLaughlin
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco (UCSF), San Francisco, California, USA
| | - Ian R Matthews
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco (UCSF), San Francisco, California, USA
| | - Lawrence R Lustig
- Department of Otolaryngology - Head and Neck Surgery, College of Physicians and Surgeons, Columbia University and New York Presbyterian Hospital, New York, New York, USA
| | - Dylan K Chan
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco (UCSF), San Francisco, California, USA
| | - Elliott H Sherr
- Department of Neurology and.,Department of Pediatrics, Institute of Human Genetics, Weill Institute for Neurosciences, UCSF, San Francisco, California, USA
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Poletto V, Rosti V, Biggiogera M, Guerra G, Moccia F, Porta C. The role of endothelial colony forming cells in kidney cancer's pathogenesis, and in resistance to anti-VEGFR agents and mTOR inhibitors: A speculative review. Crit Rev Oncol Hematol 2018; 132:89-99. [PMID: 30447930 DOI: 10.1016/j.critrevonc.2018.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 08/07/2018] [Accepted: 09/08/2018] [Indexed: 12/22/2022] Open
Abstract
Renal cell carcinoma (RCC) is highly dependent on angiogenesis, due to the overactivation of the VHL/HIF/VEGF/VEGFRs axis; this justifies the marked sensitivity of this neoplasm to antiangiogenic agents which, however, ultimately fail to control tumor growth. RCC also frequently shows alterations in the mTOR signaling pathway, and mTOR inhibitors have shown a similar pattern of initial activity/late failure as pure antiangiogenic agents. Understanding mechanisms of resistance to these agents would be key to improve the outcome of our patients. Circulating endothelial cells are a family of mainly bone marrow-derived progenitors, which have been postulated to be responsible of the reactivation of angiogenesis in different tumors. In this review, we shall discuss the complex nature and function of these cells, the evidence pro and contra their contribution to tumor vascularization, especially as far as RCC is concerned, and their possible role in determining resistance to presently available treatments.
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Affiliation(s)
- Valentina Poletto
- Center for the Study of Myelofibrosis, Research and Experimental Biotechnology Laboratory Area, Istituto di Ricovero e Cura a Carattere Scientifico (I.R.C.C.S.) Policlinico San Matteo Foundation, Piazzale Golgi 19, 27100, Pavia, Italy.
| | - Vittorio Rosti
- Center for the Study of Myelofibrosis, Research and Experimental Biotechnology Laboratory Area, Istituto di Ricovero e Cura a Carattere Scientifico (I.R.C.C.S.) Policlinico San Matteo Foundation, Piazzale Golgi 19, 27100, Pavia, Italy.
| | - Marco Biggiogera
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Italy.
| | - Germano Guerra
- Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy.
| | - Francesco Moccia
- Laboratory of Physiology, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, via Forlanini 6, 27100, Pavia, Italy.
| | - Camillo Porta
- Medical Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (I.R.C.C.S.) Policlinico San Matteo Foundation, Piazzale Golgi 19, 27100, Pavia, Italy; present address: Department of Internal Medicine, University of Pavia, and Division of Translational Oncology, IRCCS Istituti Clinici Scientifici Maugeri, via S. Maugeri 10, 27100 Pavia, Italy.
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38
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Guillen‐Ahlers H, Erbe CB, Chevalier FD, Montoya MJ, Zimmerman KD, Langefeld CD, Olivier M, Runge CL. TMTC2 variant associated with sensorineural hearing loss and auditory neuropathy spectrum disorder in a family dyad. Mol Genet Genomic Med 2018; 6:653-659. [PMID: 29671961 PMCID: PMC6081214 DOI: 10.1002/mgg3.397] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 02/02/2018] [Accepted: 03/09/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Sensorineural hearing loss (SNHL) is a common form of hearing loss that can be inherited or triggered by environmental insults; auditory neuropathy spectrum disorder (ANSD) is a SNHL subtype with unique diagnostic criteria. The genetic factors associated with these impairments are vast and diverse, but causal genetic factors are rarely characterized. METHODS A family dyad, both cochlear implant recipients, presented with a hearing history of bilateral, progressive SNHL, and ANSD. Whole-exome sequencing was performed to identify coding sequence variants shared by both family members, and screened against genes relevant to hearing loss and variants known to be associated with SNHL and ANSD. RESULTS Both family members are successful cochlear implant users, demonstrating effective auditory nerve stimulation with their devices. Genetic analyses revealed a mutation (rs35725509) in the TMTC2 gene, which has been reported previously as a likely genetic cause of SNHL in another family of Northern European descent. CONCLUSION This study represents the first confirmation of the rs35725509 variant in an independent family as a likely cause for the complex hearing loss phenotype (SNHL and ANSD) observed in this family dyad.
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Affiliation(s)
- Hector Guillen‐Ahlers
- Department of GeneticsTexas Biomedical Research InstituteSan AntonioTXUSA
- Present address:
Department of Internal MedicineSection of Molecular MedicineWake Forest University School of MedicineWinston‐SalemNCUSA
| | - Christy B. Erbe
- Department of Otolaryngology and Communication SciencesMedical College of WisconsinMilwaukeeWIUSA
| | | | - Maria J. Montoya
- Department of GeneticsTexas Biomedical Research InstituteSan AntonioTXUSA
| | - Kip D. Zimmerman
- Department of Biostatistical SciencesWake Forest University School of MedicineWinston‐SalemNCUSA
| | - Carl D. Langefeld
- Department of Biostatistical SciencesWake Forest University School of MedicineWinston‐SalemNCUSA
| | - Michael Olivier
- Department of GeneticsTexas Biomedical Research InstituteSan AntonioTXUSA
- Present address:
Department of Internal MedicineSection of Molecular MedicineWake Forest University School of MedicineWinston‐SalemNCUSA
| | - Christina L. Runge
- Department of Otolaryngology and Communication SciencesMedical College of WisconsinMilwaukeeWIUSA
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Farhan SMK, Nixon KCJ, Everest M, Edwards TN, Long S, Segal D, Knip MJ, Arts HH, Chakrabarti R, Wang J, Robinson JF, Lee D, Mirsattari SM, Rupar CA, Siu VM, Poulter MO, Hegele RA, Kramer JM. Identification of a novel synaptic protein, TMTC3, involved in periventricular nodular heterotopia with intellectual disability and epilepsy. Hum Mol Genet 2018; 26:4278-4289. [PMID: 28973161 PMCID: PMC5886076 DOI: 10.1093/hmg/ddx316] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/08/2017] [Indexed: 12/30/2022] Open
Abstract
Defects in neuronal migration cause brain malformations, which are associated with intellectual disability (ID) and epilepsy. Using exome sequencing, we identified compound heterozygous variants (p.Arg71His and p. Leu729ThrfsTer6) in TMTC3, encoding transmembrane and tetratricopeptide repeat containing 3, in four siblings with nocturnal seizures and ID. Three of the four siblings have periventricular nodular heterotopia (PVNH), a common brain malformation caused by failure of neurons to migrate from the ventricular zone to the cortex. Expression analysis using patient-derived cells confirmed reduced TMTC3 transcript levels and loss of the TMTC3 protein compared to parental and control cells. As TMTC3 function is currently unexplored in the brain, we gathered support for a neurobiological role for TMTC3 by generating flies with post-mitotic neuron-specific knockdown of the highly conserved Drosophila melanogaster TMTC3 ortholog, CG4050/tmtc3. Neuron-specific knockdown of tmtc3 in flies resulted in increased susceptibility to induced seizures. Importantly, this phenotype was rescued by neuron-specific expression of human TMTC3, suggesting a role for TMTC3 in seizure biology. In addition, we observed co-localization of TMTC3 in the rat brain with vesicular GABA transporter (VGAT), a presynaptic marker for inhibitory synapses. TMTC3 is localized at VGAT positive pre-synaptic terminals and boutons in the rat hypothalamus and piriform cortex, suggesting a role for TMTC3 in the regulation of GABAergic inhibitory synapses. TMTC3 did not co-localize with Vglut2, a presynaptic marker for excitatory neurons. Our data identified TMTC3 as a synaptic protein that is involved in PVNH with ID and epilepsy, in addition to its previously described association with cobblestone lissencephaly.
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Affiliation(s)
- Sali M K Farhan
- Molecular Medicine Research Group, Robarts Research Institute, London, ON, Canada, N6A 5B7.,Department of Biochemistry
| | - Kevin C J Nixon
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Michelle Everest
- Molecular Medicine Research Group, Robarts Research Institute, London, ON, Canada, N6A 5B7.,Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Tara N Edwards
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Shirley Long
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Dmitri Segal
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Maria J Knip
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Heleen H Arts
- Molecular Medicine Research Group, Robarts Research Institute, London, ON, Canada, N6A 5B7.,Division of Genetics and Development, Children's Health Research Institute, London, ON, Canada, N6A 5W9.,Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre Nijmegen, The Netherlands
| | - Rana Chakrabarti
- Division of Genetics and Development, Children's Health Research Institute, London, ON, Canada, N6A 5W9.,Department of Pediatrics
| | - Jian Wang
- Molecular Medicine Research Group, Robarts Research Institute, London, ON, Canada, N6A 5B7
| | - John F Robinson
- Molecular Medicine Research Group, Robarts Research Institute, London, ON, Canada, N6A 5B7
| | | | - Seyed M Mirsattari
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1.,Departments of Clinical Neurological Sciences, Medical Biophysics, Medical Imaging and Psychology
| | - C Anthony Rupar
- Department of Biochemistry.,Division of Genetics and Development, Children's Health Research Institute, London, ON, Canada, N6A 5W9.,Department of Pediatrics.,Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Victoria M Siu
- Department of Biochemistry.,Division of Genetics and Development, Children's Health Research Institute, London, ON, Canada, N6A 5W9.,Department of Pediatrics
| | | | - Michael O Poulter
- Molecular Medicine Research Group, Robarts Research Institute, London, ON, Canada, N6A 5B7.,Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Robert A Hegele
- Molecular Medicine Research Group, Robarts Research Institute, London, ON, Canada, N6A 5B7.,Department of Biochemistry
| | - Jamie M Kramer
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1.,Division of Genetics and Development, Children's Health Research Institute, London, ON, Canada, N6A 5W9.,Department of Biology, Faculty of Science, Western University, London, ON, Canada, N6A 5B7
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40
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Endothelial Ca 2+ Signaling and the Resistance to Anticancer Treatments: Partners in Crime. Int J Mol Sci 2018; 19:ijms19010217. [PMID: 29324706 PMCID: PMC5796166 DOI: 10.3390/ijms19010217] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 02/06/2023] Open
Abstract
Intracellular Ca2+ signaling drives angiogenesis and vasculogenesis by stimulating proliferation, migration, and tube formation in both vascular endothelial cells and endothelial colony forming cells (ECFCs), which represent the only endothelial precursor truly belonging to the endothelial phenotype. In addition, local Ca2+ signals at the endoplasmic reticulum (ER)-mitochondria interface regulate endothelial cell fate by stimulating survival or apoptosis depending on the extent of the mitochondrial Ca2+ increase. The present article aims at describing how remodeling of the endothelial Ca2+ toolkit contributes to establish intrinsic or acquired resistance to standard anti-cancer therapies. The endothelial Ca2+ toolkit undergoes a major alteration in tumor endothelial cells and tumor-associated ECFCs. These include changes in TRPV4 expression and increase in the expression of P2X7 receptors, Piezo2, Stim1, Orai1, TRPC1, TRPC5, Connexin 40 and dysregulation of the ER Ca2+ handling machinery. Additionally, remodeling of the endothelial Ca2+ toolkit could involve nicotinic acetylcholine receptors, gasotransmitters-gated channels, two-pore channels and Na⁺/H⁺ exchanger. Targeting the endothelial Ca2+ toolkit could represent an alternative adjuvant therapy to circumvent patients' resistance to current anti-cancer treatments.
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41
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Discovery of an O-mannosylation pathway selectively serving cadherins and protocadherins. Proc Natl Acad Sci U S A 2017; 114:11163-11168. [PMID: 28973932 DOI: 10.1073/pnas.1708319114] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The cadherin (cdh) superfamily of adhesion molecules carry O-linked mannose (O-Man) glycans at highly conserved sites localized to specific β-strands of their extracellular cdh (EC) domains. These O-Man glycans do not appear to be elongated like O-Man glycans found on α-dystroglycan (α-DG), and we recently demonstrated that initiation of cdh/protocadherin (pcdh) O-Man glycosylation is not dependent on the evolutionary conserved POMT1/POMT2 enzymes that initiate O-Man glycosylation on α-DG. Here, we used a CRISPR/Cas9 genetic dissection strategy combined with sensitive and quantitative O-Man glycoproteomics to identify a homologous family of four putative protein O-mannosyltransferases encoded by the TMTC1-4 genes, which were found to be imperative for cdh and pcdh O-Man glycosylation. KO of all four TMTC genes in HEK293 cells resulted in specific loss of cdh and pcdh O-Man glycosylation, whereas combined KO of TMTC1 and TMTC3 resulted in selective loss of O-Man glycans on specific β-strands of EC domains, suggesting that each isoenzyme serves a different function. In addition, O-Man glycosylation of IPT/TIG domains of plexins and hepatocyte growth factor receptor was not affected in TMTC KO cells, suggesting the existence of yet another O-Man glycosylation machinery. Our study demonstrates that regulation of O-mannosylation in higher eukaryotes is more complex than envisioned, and the discovery of the functions of TMTCs provide insight into cobblestone lissencephaly caused by deficiency in TMTC3.
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42
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Lodola F, Laforenza U, Cattaneo F, Ruffinatti FA, Poletto V, Massa M, Tancredi R, Zuccolo E, Khdar DA, Riccardi A, Biggiogera M, Rosti V, Guerra G, Moccia F. VEGF-induced intracellular Ca 2+ oscillations are down-regulated and do not stimulate angiogenesis in breast cancer-derived endothelial colony forming cells. Oncotarget 2017; 8:95223-95246. [PMID: 29221123 PMCID: PMC5707017 DOI: 10.18632/oncotarget.20255] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/12/2017] [Indexed: 01/08/2023] Open
Abstract
Endothelial colony forming cells (ECFCs) represent a population of truly endothelial precursors that promote the angiogenic switch in solid tumors, such as breast cancer (BC). The intracellular Ca2+ toolkit, which drives the pro-angiogenic response to VEGF, is remodelled in tumor-associated ECFCs such that they are seemingly insensitive to this growth factor. This feature could underlie the relative failure of anti-VEGF therapies in cancer patients. Herein, we investigated whether and how VEGF uses Ca2+ signalling to control angiogenesis in BC-derived ECFCs (BC-ECFCs). Although VEGFR-2 was normally expressed, VEGF failed to induce proliferation and in vitro tubulogenesis in BC-ECFCs. Likewise, VEGF did not trigger robust Ca2+ oscillations in these cells. Similar to normal cells, VEGF-induced intracellular Ca2+ oscillations were triggered by inositol-1,4,5-trisphosphate-dependent Ca2+ release from the endoplasmic reticulum (ER) and maintained by store-operated Ca2+ entry (SOCE). However, InsP3-dependent Ca2+ release was significantly lower in BC-ECFCs due to the down-regulation of ER Ca2+ levels, while there was no remarkable difference in the amplitude, pharmacological profile and molecular composition of SOCE. Thus, the attenuation of the pro-angiogenic Ca2+ response to VEGF was seemingly due to the reduction in ER Ca2+ concentration, which prevents VEGF from triggering robust intracellular Ca2+ oscillations. However, the pharmacological inhibition of SOCE prevented BC-ECFC proliferation and in vitro tubulogenesis. These findings demonstrate for the first time that BC-ECFCs are insensitive to VEGF, which might explain at cellular and molecular levels the failure of anti-VEGF therapies in BC patients, and hint at SOCE as a novel molecular target for this disease.
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Affiliation(s)
- Francesco Lodola
- Laboratory of General Physiology, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia 27100, Italy.,Current address: Italian Institute of Technology, Center for Nano Science and Technology, Milano 20133, Italy
| | - Umberto Laforenza
- Department of Molecular Medicine, University of Pavia, Pavia 27100, Italy
| | - Fabio Cattaneo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples 80131, Italy
| | | | - Valentina Poletto
- Laboratory of Biochemistry, Biotechnology and Advanced Diagnosis, Foundation IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Margherita Massa
- Laboratory of Immunology Transplantation, Foundation IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Richard Tancredi
- Medical Oncology Unit, Foundation IRCCS Salvatore Maugeri, Pavia 27100, Italy
| | - Estella Zuccolo
- Laboratory of General Physiology, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia 27100, Italy
| | - Dlzar Alì Khdar
- Laboratory of General Physiology, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia 27100, Italy
| | - Alberto Riccardi
- Medical Oncology Unit, Foundation IRCCS Salvatore Maugeri, Pavia 27100, Italy.,Department of Internal Medicine, University of Pavia, Pavia 27100, Italy
| | - Marco Biggiogera
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia 27100, Italy
| | - Vittorio Rosti
- Laboratory of Biochemistry, Biotechnology and Advanced Diagnosis, Foundation IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Germano Guerra
- Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso 86100, Italy
| | - Francesco Moccia
- Laboratory of General Physiology, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia 27100, Italy
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43
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Runge CL, Indap A, Zhou Y, Kent JW, King E, Erbe CB, Cole R, Littrell J, Merath K, James R, Rüschendorf F, Kerschner JE, Marth G, Hübner N, Göring HHH, Friedland DR, Kwok WM, Olivier M. Association of TMTC2 With Human Nonsyndromic Sensorineural Hearing Loss. JAMA Otolaryngol Head Neck Surg 2017; 142:866-72. [PMID: 27311106 DOI: 10.1001/jamaoto.2016.1444] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
IMPORTANCE Sensorineural hearing loss (SNHL) is commonly caused by conditions that affect cochlear structures or the auditory nerve, and the genes identified as causing SNHL to date only explain a fraction of the overall genetic risk for this debilitating disorder. It is likely that other genes and mutations also cause SNHL. OBJECTIVE To identify a candidate gene that causes bilateral, symmetric, progressive SNHL in a large multigeneration family of Northern European descent. DESIGN, SETTING, AND PARTICIPANTS In this prospective genotype and phenotype study performed from January 1, 2006, through April 1, 2016, a 6-generation family of Northern European descent with 19 individuals having reported early-onset hearing loss suggestive of an autosomal dominant inheritance were studied at a tertiary academic medical center. In addition, 179 unrelated adult individuals with SNHL and 186 adult individuals reporting nondeafness were examined. MAIN OUTCOMES AND MEASURES Sensorineural hearing loss. RESULTS Nine family members (5 women [55.6%]) provided clinical audiometric and medical records that documented hearing loss. The hearing loss is characterized as bilateral, symmetric, progressive SNHL that reached severe to profound loss in childhood. Audiometric configurations demonstrated a characteristic dip at 1000 to 2000 Hz. All affected family members wear hearing aids or have undergone cochlear implantation. Exome sequencing and linkage and association analyses identified a fully penetrant sequence variant (rs35725509) on chromosome 12q21 (logarithm of odds, 3.3) in the TMTC2 gene region that segregates with SNHL in this family. This gene explains the SNHL occurrence in this family. The variant is also associated with SNHL in a cohort of 363 unrelated individuals (179 patients with confirmed SNHL and 184 controls, P = 7 × 10-4). CONCLUSIONS AND RELEVANCE A previously uncharacterized gene, TMTC2, has been identified as a candidate for causing progressive SNHL in humans. This finding identifies a novel locus that causes autosomal dominant SNHL and therefore a more detailed understanding of the genetic basis of SNHL. Because TMTC2 has not been previously reported to regulate auditory function, the discovery reveals a potentially new, uncharacterized mechanism of hearing loss.
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Affiliation(s)
- Christina L Runge
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee
| | - Amit Indap
- Department of Biology, Boston College, Chestnut Hill, Massachusetts
| | - Yifan Zhou
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee
| | - Jack W Kent
- Department of Genetics, Texas Biomedical Research Institute, San Antonio
| | - Ericka King
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee
| | - Christy B Erbe
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee
| | - Regina Cole
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee
| | - Jack Littrell
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee
| | - Kate Merath
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee
| | - Roland James
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee
| | | | - Joseph E Kerschner
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee
| | - Gabor Marth
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City
| | - Norbert Hübner
- Max Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Harald H H Göring
- Department of Genetics, Texas Biomedical Research Institute, San Antonio
| | - David R Friedland
- Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin, Milwaukee
| | - Wai-Meng Kwok
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee8Department of Anesthesiology, Medical College of Wisconsin, Milwaukee
| | - Michael Olivier
- Department of Genetics, Texas Biomedical Research Institute, San Antonio5Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee
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44
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Geng F, Wang J, Liu D, Jin Y, Ma M. Identification of N-Glycosites in Chicken Egg White Proteins Using an Omics Strategy. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:5357-5364. [PMID: 28587447 DOI: 10.1021/acs.jafc.7b01706] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Chicken egg white (CEW) is a perfect source of natural proteins that possesses outstanding functional properties and various bioactivities. The glycosylation structure of CEW proteins plays important roles in their functions, bioactivities, and allergies. The present work attempted to identify N-glycosites of CEW proteins using an omics strategy. CEW proteins were digested with trypsin and chymotrypsin; glycopeptides were enriched and deglycosylated using PNGase F in H218O water, followed by analysis using high-performance liquid chromatography/tandem mass spectrometry (HPLC-MS/MS). A total of 71 N-glycosites in 26 CEW glycoproteins were identified. Web-Logo analysis showed that most of the N-glycosites were at N-X-T (55%) and N-X-S (32%). Furthermore, two-dimensional electrophoresis of CEW clusterin demonstrated a series of spots horizontally distributed at 35-37 kDa with an extremely wide isoelectric point range of 4.54-6.68, indicating the heterogeneity of glycosylation of CEW clusterin. These results provided important information for the understanding of the structures, functions, and bioactivities of CEW glycoproteins.
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Affiliation(s)
- Fang Geng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture, College of Pharmacy and Biological Engineering, Chengdu University , No. 1 Upper Section of Shiling Street, Chengdu 610106, P. R. China
| | - Jinqiu Wang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture, College of Pharmacy and Biological Engineering, Chengdu University , No. 1 Upper Section of Shiling Street, Chengdu 610106, P. R. China
| | - Dayu Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture, College of Pharmacy and Biological Engineering, Chengdu University , No. 1 Upper Section of Shiling Street, Chengdu 610106, P. R. China
| | - Yongguo Jin
- National R&D Center for Egg Processing, College of Food Science and Technology, Huazhong Agricultural University , No. 1 Shizishan Street, Wuhan 430070, P. R. China
| | - Meihu Ma
- National R&D Center for Egg Processing, College of Food Science and Technology, Huazhong Agricultural University , No. 1 Shizishan Street, Wuhan 430070, P. R. China
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45
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Moccia F, Fotia V, Tancredi R, Della Porta MG, Rosti V, Bonetti E, Poletto V, Marchini S, Beltrame L, Gallizzi G, Da Prada GA, Pedrazzoli P, Riccardi A, Porta C, Zambelli A, D'Incalci M. Breast and renal cancer—Derived endothelial colony forming cells share a common gene signature. Eur J Cancer 2017; 77:155-164. [DOI: 10.1016/j.ejca.2017.01.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 12/22/2016] [Accepted: 01/23/2017] [Indexed: 12/25/2022]
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46
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Li Q, Li J, Dai W, Li YX, Li YY. Differential regulation analysis reveals dysfunctional regulatory mechanism involving transcription factors and microRNAs in gastric carcinogenesis. Artif Intell Med 2017; 77:12-22. [PMID: 28545608 DOI: 10.1016/j.artmed.2017.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/23/2017] [Accepted: 02/23/2017] [Indexed: 12/12/2022]
Abstract
Gastric cancer (GC) is one of the most incident malignancies in the world. Although lots of featured genes and microRNAs (miRNAs) have been identified to be associated with gastric carcinogenesis, underlying regulatory mechanisms still remain unclear. In order to explore the dysfunctional mechanisms of GC, we developed a novel approach to identify carcinogenesis relevant regulatory relationships, which is characterized by quantifying the difference of regulatory relationships between stages. Firstly, we applied the strategy of differential coexpression analysis (DCEA) to transcriptomic datasets including paired mRNA and miRNA of gastric samples to identify a set of genes/miRNAs related to gastric cancer progression. Based on these genes/miRNAs, we constructed conditional combinatorial gene regulatory networks (cGRNs) involving both transcription factors (TFs) and miRNAs. Enrichment of known cancer genes/miRNAs and predicted prognostic genes/miRNAs was observed in each cGRN. Then we designed a quantitative method to measure differential regulation level of every regulatory relationship between normal and cancer, and the known cancer genes/miRNAs proved to be ranked significantly higher. Meanwhile, we defined differentially regulated link (DRL) by combining differential regulation, differential expression and the regulation contribution of the regulator to the target. By integrating survival analysis and DRL identification, three master regulators TCF7L1, TCF4, and MEIS1 were identified and testable hypotheses of dysfunctional mechanisms underlying gastric carcinogenesis related to them were generated. The fine-tuning effects of miRNAs were also observed. We propose that this differential regulation network analysis framework is feasible to gain insights into dysregulated mechanisms underlying tumorigenesis and other phenotypic changes.
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Affiliation(s)
- Quanxue Li
- School of biotechnology, East China University of Science and Technology, Shanghai, China; Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Junyi Li
- Shanghai Center for Bioinformation Technology, Shanghai, China; Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wentao Dai
- Shanghai Center for Bioinformation Technology, Shanghai, China; Shanghai Industrial Technology Institute, Shanghai, China; Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai, China
| | - Yi-Xue Li
- School of biotechnology, East China University of Science and Technology, Shanghai, China; Shanghai Center for Bioinformation Technology, Shanghai, China; Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Shanghai Industrial Technology Institute, Shanghai, China; Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai, China.
| | - Yuan-Yuan Li
- Shanghai Center for Bioinformation Technology, Shanghai, China; Shanghai Industrial Technology Institute, Shanghai, China; Shanghai Engineering Research Center of Pharmaceutical Translation, Shanghai, China.
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47
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Zhou Y, He Q, Chen J, Liu Y, Mao Z, Lyu Z, Ni D, Long Y, Ju P, Liu J, Gu Y, Zhou Q. The expression patterns of Tetratricopeptide repeat domain 36 (Ttc36). Gene Expr Patterns 2016; 22:37-45. [PMID: 27826126 DOI: 10.1016/j.gep.2016.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/20/2016] [Accepted: 11/02/2016] [Indexed: 02/05/2023]
Abstract
Tetratricopeptide repeat domain 36 (Ttc36), whose coding protein belongs to tetratricopeptide repeat (TPR) motif family, has not been studied extensively. We for the first time showed that Ttc36 is evolutionarily conserved across mammals by bioinformatics. Rabbit anti-mouse Ttc36 polyclonal antibody was generated by injecting synthetic full-length peptides through "antigen intersection" strategy. Subsequently, we characterized Ttc36 expression profile in mouse, showing its expression in liver and kidney both from embryonic day 15.5 (E15.5) until adult, as well as in testis. Immunofluorescence staining showed that Ttc36 is diffusely expressed in liver, however, specifically in kidney cortex. Thus, we further compare Ttc36 with proximal tubules (PT) marker Lotus Tetragonolobus Lectin (LTL) and distal tubules (DT) marker Calbindin-D28k respectively by double immunofluorescence staining. Results showed the co-localization of Ttc36 with LTL rather than Calbindin-D28k. Collectively, on the basis of the expression pattern, Ttc36 is specifically expressed in proximal distal tubules.
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Affiliation(s)
- Yuru Zhou
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China; The Seventh Class of 2012 Year Entry, The Third Clinical College, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Qingling He
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Jihui Chen
- Department of Dermatology, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, 610041, PR China.
| | - Yunhong Liu
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Zhaomin Mao
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Zhongshi Lyu
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Dongsheng Ni
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Yaoshui Long
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Pan Ju
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Jianing Liu
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Yuping Gu
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Qin Zhou
- Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
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48
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Jerber J, Zaki MS, Al-Aama JY, Rosti RO, Ben-Omran T, Dikoglu E, Silhavy JL, Caglar C, Musaev D, Albrecht B, Campbell KP, Willer T, Almuriekhi M, Çağlayan AO, Vajsar J, Bilgüvar K, Ogur G, Abou Jamra R, Günel M, Gleeson JG. Biallelic Mutations in TMTC3, Encoding a Transmembrane and TPR-Containing Protein, Lead to Cobblestone Lissencephaly. Am J Hum Genet 2016; 99:1181-1189. [PMID: 27773428 PMCID: PMC5097947 DOI: 10.1016/j.ajhg.2016.09.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 09/13/2016] [Indexed: 12/13/2022] Open
Abstract
Cobblestone lissencephaly (COB) is a severe brain malformation in which overmigration of neurons and glial cells into the arachnoid space results in the formation of cortical dysplasia. COB occurs in a wide range of genetic disorders known as dystroglycanopathies, which are congenital muscular dystrophies associated with brain and eye anomalies and range from Walker-Warburg syndrome to Fukuyama congenital muscular dystrophy. Each of these conditions has been associated with alpha-dystroglycan defects or with mutations in genes encoding basement membrane components, which are known to interact with alpha-dystroglycan. Our screening of a cohort of 25 families with recessive forms of COB identified six families affected by biallelic mutations in TMTC3 (encoding transmembrane and tetratricopeptide repeat containing 3), a gene without obvious functional connections to alpha-dystroglycan. Most affected individuals showed brainstem and cerebellum hypoplasia, as well as ventriculomegaly. However, the minority of the affected individuals had eye defects or elevated muscle creatine phosphokinase, separating the TMTC3 COB phenotype from typical congenital muscular dystrophies. Our data suggest that loss of TMTC3 causes COB with minimal eye or muscle involvement.
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Affiliation(s)
- Julie Jerber
- Laboratory for Pediatric Brain Disease, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12311, Egypt
| | - Jumana Y Al-Aama
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21453, Saudi Arabia; Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah 21453, Saudi Arabia
| | - Rasim Ozgur Rosti
- Laboratory for Pediatric Brain Disease, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Tawfeg Ben-Omran
- Clinical and Metabolic Genetics Section, Department of Pediatrics, Hamad Medical Corporation, PO Box 3050, Doha, Qatar; Weill Cornell Medical College, Qatar, Education City, PO Box 24144, Doha, Qatar
| | - Esra Dikoglu
- Laboratory for Pediatric Brain Disease, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Jennifer L Silhavy
- Laboratory for Pediatric Brain Disease, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Caner Caglar
- Laboratory for Pediatric Brain Disease, The Rockefeller University, New York, NY 10065, USA
| | - Damir Musaev
- Laboratory for Pediatric Brain Disease, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Beate Albrecht
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, 45122 Essen, Germany
| | - Kevin P Campbell
- Howard Hughes Medical Institute, Departments of Neurology, Internal Medicine, and Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1101, USA
| | - Tobias Willer
- Howard Hughes Medical Institute, Departments of Neurology, Internal Medicine, and Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1101, USA
| | - Mariam Almuriekhi
- Clinical and Metabolic Genetics Section, Department of Pediatrics, Hamad Medical Corporation, PO Box 3050, Doha, Qatar; Weill Cornell Medical College, Qatar, Education City, PO Box 24144, Doha, Qatar
| | - Ahmet Okay Çağlayan
- Department of Medical Genetics, School of Medicine, Istanbul Bilim University, Istanbul 34394, Turkey
| | - Jiri Vajsar
- Division of Neurology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Kaya Bilgüvar
- Yale Program on Neurogenetics, Departments of Neurosurgery, Neurobiology, and Genetics, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Gonul Ogur
- Department of Genetics, School of Medicine, Ondokuz Mayis University, 55000 Samsun, Turkey
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Philipp-Rosenthal-Str. 55, 04103 Leipzig, Germany; Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Murat Günel
- Yale Program on Neurogenetics, Departments of Neurosurgery, Neurobiology, and Genetics, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Joseph G Gleeson
- Laboratory for Pediatric Brain Disease, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, CA 92093, USA.
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Madsen MB, Kogelman LJA, Kadarmideen HN, Rasmussen HB. Systems genetics analysis of pharmacogenomics variation during antidepressant treatment. THE PHARMACOGENOMICS JOURNAL 2016; 18:144-152. [PMID: 27752142 DOI: 10.1038/tpj.2016.68] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/17/2016] [Accepted: 08/25/2016] [Indexed: 12/24/2022]
Abstract
Selective serotonin reuptake inhibitors (SSRIs) are the most widely used antidepressants, but the efficacy of the treatment varies significantly among individuals. It is believed that complex genetic mechanisms play a part in this variation. We have used a network based approach to unravel the involved genetic components. Moreover, we investigated the potential difference in the genetic interaction networks underlying SSRI treatment response over time. We found four hub genes (ASCC3, PPARGC1B, SCHIP1 and TMTC2) with different connectivity in the initial SSRI treatment period (baseline to week 4) compared with the subsequent period (4-8 weeks after initiation), suggesting that different genetic networks are important at different times during SSRI treatment. The strongest interactions in the initial SSRI treatment period involved genes encoding transcriptional factors, and in the subsequent period genes involved in calcium homeostasis. In conclusion, we suggest a difference in genetic interaction networks between initial and subsequent SSRI response.
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Affiliation(s)
- M B Madsen
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Capital Region of Denmark, Roskilde, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - L J A Kogelman
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - H N Kadarmideen
- Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - H B Rasmussen
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Capital Region of Denmark, Roskilde, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
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50
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Mariappa D, Zheng X, Schimpl M, Raimi O, Ferenbach AT, Müller HAJ, van Aalten DMF. Dual functionality of O-GlcNAc transferase is required for Drosophila development. Open Biol 2016; 5:150234. [PMID: 26674417 PMCID: PMC4703063 DOI: 10.1098/rsob.150234] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Post-translational modification of intracellular proteins with O-linked N-acetylglucosamine (O-GlcNAc) catalysed by O-GlcNAc transferase (OGT) has been linked to regulation of diverse cellular functions. OGT possesses a C-terminal glycosyltransferase catalytic domain and N-terminal tetratricopeptide repeats that are implicated in protein-protein interactions. Drosophila OGT (DmOGT) is encoded by super sex combs (sxc), mutants of which are pupal lethal. However, it is not clear if this phenotype is caused by reduction of O-GlcNAcylation. Here we use a genetic approach to demonstrate that post-pupal Drosophila development can proceed with negligible OGT catalysis, while early embryonic development is OGT activity-dependent. Structural and enzymatic comparison between human OGT (hOGT) and DmOGT informed the rational design of DmOGT point mutants with a range of reduced catalytic activities. Strikingly, a severely hypomorphic OGT mutant complements sxc pupal lethality. However, the hypomorphic OGT mutant-rescued progeny do not produce F2 adults, because a set of Hox genes is de-repressed in F2 embryos, resulting in homeotic phenotypes. Thus, OGT catalytic activity is required up to late pupal stages, while further development proceeds with severely reduced OGT activity.
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Affiliation(s)
- Daniel Mariappa
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Xiaowei Zheng
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Marianne Schimpl
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Olawale Raimi
- Division of Molecular Microbiology, University of Dundee, Dundee, UK
| | - Andrew T Ferenbach
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - H-Arno J Müller
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee, UK
| | - Daan M F van Aalten
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK Division of Molecular Microbiology, University of Dundee, Dundee, UK
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