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Lin S, Huang B, Zhao LL, Xu F, Pan D, Chen X, Lin S. A Python program to merge Sanger sequences: an update. PeerJ 2024; 12:e18363. [PMID: 39465179 PMCID: PMC11505972 DOI: 10.7717/peerj.18363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 09/29/2024] [Indexed: 10/29/2024] Open
Abstract
Gene cloning is an important step in investigating gene structure and function. To verify gene sequence, Sanger sequencing is used, which may produce several overlapping sequencing files that need to be merged before alignment to the target gene sequence is performed. Previously, we reported the Python program to Merge Sanger sequences (https://peerj.com/articles/11354/), which ran in command line and relied heavily on EMBOSS suite. In this updated version of the program, we have made several remarkable improvements. It provides a graphical user interface (GUI) written with tkinter, which is convenient and stable. It does not require users to rename the input sequences before performing merging. With regard to the implementation, the updated version utilizes Python function (Align.PairwiseAligner) to align adjacent sequences, which is more flexible (can adjust program parameter i.e., the number of first-time consecutive matching bases). The new version of the program makes merging Sanger sequences much more convenient and facilitates gene study.
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Affiliation(s)
- Shiming Lin
- School of Computing and Information Science, Fuzhou Institute of Technology, Fuzhou, Fujian, China
| | - Bifang Huang
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Li-li Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fei Xu
- College of Agronomy, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Danni Pan
- College of Agronomy, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xuanyang Chen
- College of Agronomy, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Shiqiang Lin
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Santangelo S, Invernizzi S, Sorce MN, Casiraghi V, Peverelli S, Brusati A, Colombrita C, Ticozzi N, Silani V, Bossolasco P, Ratti A. NEK1 haploinsufficiency worsens DNA damage, but not defective ciliogenesis, in C9ORF72 patient-derived iPSC-motoneurons. Hum Mol Genet 2024:ddae121. [PMID: 39222049 DOI: 10.1093/hmg/ddae121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
The hexanucleotide G4C2 repeat expansion (HRE) in C9ORF72 gene is the major cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), leading to both loss- and gain-of-function pathomechanisms. The wide clinical heterogeneity among C9ORF72 patients suggests potential modifying genetic and epigenetic factors. Notably, C9ORF72 HRE often co-occurs with other rare variants in ALS/FTD-associated genes, such as NEK1, which encodes for a kinase involved in multiple cell pathways, including DNA damage response and ciliogenesis. In this study, we generated induced pluripotent stem cells (iPSCs) and differentiated motoneurons (iPSC-MNs) from an ALS patient carrying both C9ORF72 HRE and a NEK1 loss-of-function mutation to investigate the biological effect of NEK1 haploinsufficiency on C9ORF72 pathology in a condition of oligogenicity. Double mutant C9ORF72/NEK1 cells showed increased pathological C9ORF72 RNA foci in iPSCs and higher DNA damage levels in iPSC-MNs compared to single mutant C9ORF72 cells, but no effect on DNA damage response. When we analysed the primary cilium, we observed a defective ciliogenesis in C9ORF72 iPSC-MNs which was not worsened by NEK1 haploinsufficiency in the double mutant iPSC-MNs. Altogether, our study shows that NEK1 haploinsufficiency influences differently DNA damage and cilia length, potentially acting as a modifier at biological level in an in vitro ALS patient-derived disease model of C9ORF72 pathology.
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Affiliation(s)
- Serena Santangelo
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Via Fratelli Cervi 93, Segrate, Milan 20054, Italy
| | - Sabrina Invernizzi
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Via Fratelli Cervi 93, Segrate, Milan 20054, Italy
| | - Marta Nice Sorce
- Department of Neuroscience - Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Via Zucchi 18, Cusano Milanino, Milan 20095, Italy
| | - Valeria Casiraghi
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Via Fratelli Cervi 93, Segrate, Milan 20054, Italy
| | - Silvia Peverelli
- Department of Neuroscience - Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Via Zucchi 18, Cusano Milanino, Milan 20095, Italy
| | - Alberto Brusati
- Department of Brain and Behavioral Sciences, University of Pavia, Via Bassi 21, Pavia 27100, Italy
| | - Claudia Colombrita
- Department of Neuroscience - Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Via Zucchi 18, Cusano Milanino, Milan 20095, Italy
| | - Nicola Ticozzi
- Department of Neuroscience - Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Via Zucchi 18, Cusano Milanino, Milan 20095, Italy
- "Dino Ferrari" Center, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Via Francesco Sforza 35, Milan 20122, Italy
| | - Vincenzo Silani
- Department of Neuroscience - Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Via Zucchi 18, Cusano Milanino, Milan 20095, Italy
- "Dino Ferrari" Center, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Via Francesco Sforza 35, Milan 20122, Italy
| | - Patrizia Bossolasco
- Department of Neuroscience - Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Via Zucchi 18, Cusano Milanino, Milan 20095, Italy
| | - Antonia Ratti
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Via Fratelli Cervi 93, Segrate, Milan 20054, Italy
- Department of Neuroscience - Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Via Zucchi 18, Cusano Milanino, Milan 20095, Italy
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Tang D, Bao H, Qi S. The C9orf72-SMCR8 complex suppresses primary ciliogenesis as a RAB8A GAP. Autophagy 2024; 20:1205-1207. [PMID: 38293807 PMCID: PMC11135869 DOI: 10.1080/15548627.2024.2311541] [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: 01/02/2024] [Revised: 01/03/2024] [Accepted: 01/24/2024] [Indexed: 02/01/2024] Open
Abstract
Approximately half of the familial cases of amyotrophic lateral sclerosis (ALS) and frontal temporal dementia (FTD) are attributed to the abnormal GGGGCC repeat expansion within the first intron of C9orf72, potentializing C9orf72 and its product as the most promising target for ALS therapeutics. Nevertheless, the biological function of C9orf72 remains unclear. Previously, we reported that C9orf72 and its binding partner, SMCR8, form a GTPase-activating protein (GAP) complex, which is proposed to regulate membrane trafficking and autophagy. Hereby, we found that the C9orf72-SMCR8 complex negatively regulates primary ciliogenesis and hedgehog (HH) signaling. Furthermore, the biochemical analysis and cell biology experiments identified C9orf72 as the RAB8A binding subunit and SMCR8 as the GAP subunit within the complex. Further, we discussed the relationship among the C9orf72-SMCR8 complex, primary ciliogenesis, and autophagy.
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Affiliation(s)
- Dan Tang
- Department of Urology, Institute of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University and National Collaborative Innovation Center, Chengdu, P.R. China
| | - Hui Bao
- Department of Urology, Institute of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University and National Collaborative Innovation Center, Chengdu, P.R. China
| | - Shiqian Qi
- Department of Urology, Institute of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University and National Collaborative Innovation Center, Chengdu, P.R. China
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