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1.
Front Immunol ; 15: 1399975, 2024.
Article in English | MEDLINE | ID: mdl-38774882

ABSTRACT

Recently, targeted therapy and immunotherapy have emerged as effective treatment options for non-small cell lung cancer (NSCLC). This progress has been facilitated by the rapid development of diagnostic and therapeutic technologies and the continuous research and development of new drugs, leading to a new era in precision medicine for NSCLC. This is a breakthrough for patients with common mutations in the human epidermal growth factor receptor (EGFR) gene in NSCLC. Consequently, the use of targeted drugs has significantly improved survival. Nevertheless, certain rare genetic mutations are referred to as EGFR exon 20 insertion (ex20ins) mutations, which differ in structure from conventional EGFR gene mutations, namely, exon 19 deletion mutations (19-Del) and exon 21 point mutations. Owing to their distinct structural characteristics, patients harboring these EGFR ex20ins mutations are unresponsive to traditional tyrosine kinase inhibitor (TKI) therapy. This particular group of patients did not fall within the scope of their applicability. However, the activating A763_Y764insFQEA mutation elicits a more pronounced response than mutations in the near and far regions of the C-helix immediately following it and should, therefore, be treated differently. Currently, there is a lack of effective treatments for EGFR ex20ins mutations NSCLC. The efficacy of chemotherapy has been relatively favorable, whereas the effectiveness of immunotherapy remains ambiguous owing to inadequate clinical data. In addition, the efficacy of the first- and second-generation targeted drugs remains limited. However, third-generation and novel targeted drugs have proven to be effective. Although novel EGFR-TKIs are expected to treat EGFR ex20ins mutations in patients with NSCLC, they face many challenges. The main focus of this review is on emerging therapies that target NSCLC with EGFR ex20ins and highlight major ongoing clinical trials while also providing an overview of the associated challenges and research advancements in this area.


Subject(s)
Carcinoma, Non-Small-Cell Lung , ErbB Receptors , Exons , Lung Neoplasms , Humans , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/drug therapy , Carcinoma, Non-Small-Cell Lung/therapy , Lung Neoplasms/genetics , Lung Neoplasms/drug therapy , Lung Neoplasms/therapy , ErbB Receptors/genetics , ErbB Receptors/antagonists & inhibitors , Exons/genetics , Protein Kinase Inhibitors/therapeutic use , Immunotherapy/methods , Mutagenesis, Insertional , Molecular Targeted Therapy , Mutation , Animals
2.
Microb Ecol ; 87(1): 63, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38691135

ABSTRACT

Bacterial azoreductases are enzymes that catalyze the reduction of ingested or industrial azo dyes. Although azoreductase genes have been well identified and characterized, the regulation of their expression has not been systematically investigated. To determine how different factors affect the expression of azoR, we extracted and analyzed transcriptional data from the Gene Expression Omnibus (GEO) resource, then confirmed computational predictions by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Results showed that azoR expression was lower with higher glucose concentration, agitation speed, and incubation temperature, but higher at higher culture densities. Co-expression and clustering analysis indicated ten genes with similar expression patterns to azoR: melA, tpx, yhbW, yciK, fdnG, fpr, nfsA, nfsB, rutF, and chrR (yieF). In parallel, constructing a random transposon library in E. coli K-12 and screening 4320 of its colonies for altered methyl red (MR)-decolorizing activity identified another set of seven genes potentially involved in azoR regulation. Among these genes, arsC, relA, plsY, and trmM were confirmed as potential azoR regulators based on the phenotypic decolorization activity of their transposon mutants, and the expression of arsC and relA was confirmed, by qRT-PCR, to significantly increase in E. coli K-12 in response to different MR concentrations. Finally, the significant decrease in azoR transcription upon transposon insertion in arsC and relA (as compared to its expression in wild-type E. coli) suggests their probable involvement in azoR regulation. In conclusion, combining in silico analysis and random transposon mutagenesis suggested a set of potential regulators of azoR in E. coli.


Subject(s)
DNA Transposable Elements , Escherichia coli Proteins , Escherichia coli , Gene Expression Regulation, Bacterial , Nitroreductases , DNA Transposable Elements/genetics , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Nitroreductases/genetics , Nitroreductases/metabolism , NADH, NADPH Oxidoreductases/genetics , NADH, NADPH Oxidoreductases/metabolism , Mutagenesis , Genome, Bacterial , Computational Biology , Mutagenesis, Insertional
3.
Commun Biol ; 7(1): 586, 2024 May 16.
Article in English | MEDLINE | ID: mdl-38755285

ABSTRACT

Bats serve as reservoirs for numerous zoonotic viruses, yet they typically remain asymptomatic owing to their unique immune system. Of particular significance is the MHC-I in bats, which plays crucial role in anti-viral response and exhibits polymorphic amino acid (AA) insertions. This study demonstrated that both 5AA and 3AA insertions enhance the thermal stability of the bat MHC-I complex and enrich the diversity of bound peptides in terms of quantity and length distribution, by stabilizing the 310 helix, a region prone to conformational changes during peptide loading. However, the mismatched insertion could diminish the stability of bat pMHC-I. We proposed that a suitable insertion may help bat MHC-I adapt to high body temperatures during flight while enhancing antiviral responses. Moreover, this site-specific insertions may represent a strategy of evolutionary adaptation of MHC-I molecules to fluctuations in body temperature, as similar insertions have been found in other lower vertebrates.


Subject(s)
Chiroptera , Histocompatibility Antigens Class I , Animals , Histocompatibility Antigens Class I/metabolism , Histocompatibility Antigens Class I/chemistry , Histocompatibility Antigens Class I/genetics , Protein Stability , Peptides/chemistry , Peptides/metabolism , Amino Acids/chemistry , Amino Acids/metabolism , Antigen Presentation , Mutagenesis, Insertional
4.
Nat Commun ; 15(1): 3844, 2024 May 07.
Article in English | MEDLINE | ID: mdl-38714690

ABSTRACT

Multiple myeloma (MM) is a heterogeneous disease characterized by frequent MYC translocations. Sporadic MYC activation in the germinal center of genetically engineered Vk*MYC mice is sufficient to induce plasma cell tumors in which a variety of secondary mutations are spontaneously acquired and selected over time. Analysis of 119 Vk*MYC myeloma reveals recurrent copy number alterations, structural variations, chromothripsis, driver mutations, apolipoprotein B mRNA-editing enzyme, catalytic polypeptide (APOBEC) mutational activity, and a progressive decrease in immunoglobulin transcription that inversely correlates with proliferation. Moreover, we identify frequent insertional mutagenesis by endogenous retro-elements as a murine specific mechanism to activate NF-kB and IL6 signaling pathways shared with human MM. Despite the increased genomic complexity associated with progression, advanced tumors remain dependent on MYC. In summary, here we credential the Vk*MYC mouse as a unique resource to explore MM genomic evolution and describe a fully annotated collection of diverse and immortalized murine MM tumors.


Subject(s)
Multiple Myeloma , Proto-Oncogene Proteins c-myc , Animals , Multiple Myeloma/genetics , Multiple Myeloma/pathology , Humans , Mice , Proto-Oncogene Proteins c-myc/genetics , Proto-Oncogene Proteins c-myc/metabolism , Cell Transformation, Neoplastic/genetics , Mutation , Signal Transduction/genetics , Mice, Transgenic , NF-kappa B/metabolism , NF-kappa B/genetics , Mutagenesis, Insertional , DNA Copy Number Variations/genetics , Genomics/methods , Translocation, Genetic
5.
Virology ; 595: 110066, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38574415

ABSTRACT

Avian influenza virus (AIV) is a constant threat to animal health with recent global outbreaks resulting in the death of hundreds of millions of birds with spillover into mammals. Myxovirus-resistance (Mx) proteins are key mediators of the antiviral response that block virus replication. Mouse (Mu) Mx (Mx1) is a strong antiviral protein that interacts with the viral nucleoprotein to inhibit polymerase function. The ability of avian Mx1 to inhibit AIV is unclear. In these studies, Mu Mx1 was stably introduced into chicken DF1 cells to enhance the immune response against AIV. Following infection, titers of AIV were significantly decreased in cells expressing Mu Mx1. In addition, considerably less cytopathic effect (CPE) and matrix protein staining was observed in gene-edited cells expressing Mu Mx1, suggesting Mu Mx1 is broadly effective against multiple AIV subtypes. This work provides foundational studies for use of gene-editing to enhance innate disease resistance against AIV.


Subject(s)
Chickens , Immunity, Innate , Influenza in Birds , Myxovirus Resistance Proteins , Virus Replication , Animals , Myxovirus Resistance Proteins/genetics , Myxovirus Resistance Proteins/metabolism , Cell Line , Influenza in Birds/virology , Influenza in Birds/immunology , Influenza in Birds/genetics , Mice , Mutagenesis, Insertional , Influenza A virus/immunology , Influenza A virus/genetics
6.
PLoS One ; 19(4): e0301120, 2024.
Article in English | MEDLINE | ID: mdl-38687753

ABSTRACT

Determining the exact type of epidermal growth factor receptor (EGFR) exon 20 insertion (ex20ins) mutation in lung cancer has become important. We found that not all ex20ins mutations reported by cobas EGFR test v2 could be validated by Sanger sequencing even using surgical specimens with high tumor contents. This study aimed to validate the ex20ins results reported by the cobas test and to determine whether there were clinicopathological factors associated with aberrant cobas ex20ins report. In total, 123 cobas-reported cases with ex20ins were retrospectively collected and validated by Sanger sequencing and Idylla assay. Clinicopathological features between ex20ins cobas+/Sanger+ group (n = 71) and cobas+/Sanger- group (n = 52) were compared. The Idylla assay detected ex20ins in 82.6% of cobas+/Sanger+ cases but only in 4.9% of cobas+/Sanger- cases. The cobas+/Sanger- group was significantly associated with higher tumor contents, poorly differentiated patterns, tumor necrosis, and a lower internal control cycle threshold value reported by the Idylla which suggesting the presence of increased EGFR gene copy numbers. EGFR fluorescence in situ hybridization (FISH) revealed the majority of cobas+/Sanger- group had EGFR high copy number gain (16%) or amplification (76%) according to the Colorado criteria. Among cases reported to have concomitant classic EGFR and ex20ins mutations by the cobas, the classic EGFR mutations were all detected by Sanger sequencing and Idylla, while the ex20ins mutations were undetected by Sanger sequencing (0%) or rarely reported by Idylla assay (3%). FISH revealed high EGFR copy number gain (17.9%) and amplification (79.5%) in cases reported having concomitant classic EGFR and ex20ins mutations by the cobas. This study demonstrated an unusually high frequency of EGFR amplification in cases with aberrant cobas ex20ins report which could not be validated by Sanger sequencing or Idylla assay. Ex20ins reported by the cobas test should be validated using other methods especially those reported having concomitant ex20ins and classic EGFR mutations.


Subject(s)
ErbB Receptors , Exons , Lung Neoplasms , Humans , ErbB Receptors/genetics , Male , Female , Middle Aged , Exons/genetics , Aged , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Lung Neoplasms/diagnosis , Retrospective Studies , Mutagenesis, Insertional , Gene Amplification , Adult , Mutation , Aged, 80 and over , DNA Mutational Analysis/methods
7.
Microb Biotechnol ; 17(5): e14453, 2024 May.
Article in English | MEDLINE | ID: mdl-38683670

ABSTRACT

Soluble di-iron monooxygenases (SDIMOs) are multi-component enzymes catalysing the oxidation of various substrates. These enzymes are characterized by high sequence and functional diversity that is still not well understood despite their key role in biotechnological processes including contaminant biodegradation. In this study, we analysed a mutant of Rhodoccocus aetherivorans BCP1 (BCP1-2.10) characterized by a transposon insertion in the gene smoA encoding the alpha subunit of the plasmid-located SDIMO SmoABCD. The mutant BCP1-2.10 showed a reduced capacity to grow on propane, lost the ability to grow on butane, pentane and n-hexane and was heavily impaired in the capacity to degrade chloroform and trichloroethane. The expression of the additional SDIMO prmABCD in BCP1-2.10 probably allowed the mutant to partially grow on propane and to degrade it, to some extent, together with the other short-chain n-alkanes. The complementation of the mutant, conducted by introducing smoABCD in the genome as a single copy under a constitutive promoter or within a plasmid under a thiostreptone-inducible promoter, allowed the recovery of the alkanotrophic phenotype as well as the capacity to degrade chlorinated n-alkanes. The heterologous expression of smoABCD allowed a non-alkanotrophic Rhodococcus strain to grow on pentane and n-hexane when the gene cluster was introduced together with the downstream genes encoding alcohol and aldehyde dehydrogenases and a GroEL chaperon. BCP1 smoA gene was shown to belong to the group 6 SDIMOs, which is a rare group of monooxygenases mostly present in Mycobacterium genus and in a few Rhodococcus strains. SmoABCD originally evolved in Mycobacterium and was then acquired by Rhodococcus through horizontal gene transfer events. This work extends the knowledge of the biotechnologically relevant SDIMOs by providing functional and evolutionary insights into a group 6 SDIMO in Rhodococcus and demonstrating its key role in the metabolism of short-chain alkanes and degradation of chlorinated n-alkanes.


Subject(s)
Alkanes , Mixed Function Oxygenases , Alkanes/metabolism , Mixed Function Oxygenases/metabolism , Mixed Function Oxygenases/genetics , Genetic Complementation Test , Mutagenesis, Insertional , Biotransformation , DNA Transposable Elements , Hydrocarbons, Chlorinated/metabolism
8.
Lung Cancer ; 191: 107798, 2024 May.
Article in English | MEDLINE | ID: mdl-38669727

ABSTRACT

OBJECTIVES: In this study, we explored the clinical outcomes of non-small cell lung cancer (NSCLC) patients with EGFR Exon20 in-frame insertions (Exon20ins), and the impact of the location of Exon20ins on these clinical outcomes. MATERIALS AND METHODS: The efficacies of current systemic therapies in NSCLC patients harboring Exon20ins were investigated using a large-scale clinico-genomic database of LC-SCRUM-Asia, and compared with that of amivantamab in the CHRYSALIS trial. RESULTS: Of the 11,397 patients enrolled in LC-SCRUM-Asia, Exon20ins were detected in 189 patients (1.7 %). Treatment with classical EGFR tyrosine-kinase inhibitors (classical TKIs) was associated with a significantly shorter progression-free survival (PFS) in NSCLC patients with Exon20ins as compared with Exon19 deletions and L858R. Post platinum-based chemotherapy, classical TKIs and immune checkpoint inhibitors (ICIs) were associated with a shorter PFS than with docetaxel in patients with Exon20ins (HR [95 % CI]; TKIs vs docetaxel, 2.16 [1.35-3.46]; ICIs vs docetaxel, 1.49 [1.21-1.84]). Patients treated with amivantamab in the CHRYSALIS trial showed a risk reduction in PFS and overall survival as compared with LC-SCRUM-Asia patients treated with docetaxel, classical TKIs, or ICIs. Among the 189 patients, Exon20ins were classified as near-loop or far-loop insertions in 115 (61 %) and 56 (30 %) patients, respectively. Treatment with osimertinib was associated with a longer PFS in patients with Exon20ins in near-loop as compared with far-loop (median, 5.6 vs. 2.0 months; HR [95 % CI], 0.22 [0.07-0.64]). CONCLUSIONS: After platinum-based chemotherapy, classical TKIs and ICIs are less effective in NSCLC patients with Exon20ins, and amivantamab may be a promising targeted therapy. There is a possibility that the location of Exon20ins has an impact on the efficacy of TKIs.


Subject(s)
Carcinoma, Non-Small-Cell Lung , ErbB Receptors , Exons , Lung Neoplasms , Protein Kinase Inhibitors , Humans , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/drug therapy , Carcinoma, Non-Small-Cell Lung/mortality , Carcinoma, Non-Small-Cell Lung/pathology , Lung Neoplasms/genetics , Lung Neoplasms/drug therapy , Lung Neoplasms/mortality , Lung Neoplasms/pathology , Male , Female , ErbB Receptors/genetics , Middle Aged , Exons/genetics , Aged , Protein Kinase Inhibitors/therapeutic use , Mutagenesis, Insertional , Adult , Aniline Compounds/therapeutic use , Treatment Outcome , Aged, 80 and over
9.
Microbiol Res ; 284: 127731, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38653011

ABSTRACT

Aeromonas veronii, a significant pathogen in aquatic environments, poses a substantial threat to both human and animal health, particularly in aquaculture. In this study, we isolated A. veronii strain GD2019 from diseased largemouth bass (Micropterus salmoides) during a severe outbreak of aeromonad septicemia in Guangdong Province, China. The complete genome sequence of A. veronii GD2019 revealed that GD2019 contains a single chromosome of 4703,168 bp with an average G+C content of 58.3%. Phylogenetic analyses indicated that GD2019 forms a separate sub-branch in A. veronii and comparative genomic analyses identified the existence of an intact Type III secretion system. Moreover, to investigate the genes that are required for the conditional fitness of A. veronii under various stresses, a high-density transposon insertion library in GD2019 was generated by a Tn5-based transposon and covers 6311 genomic loci including 4155 genes and 2156 intergenic regions. Leveraging this library, 630 genes were classified as essential genes for growth in rich-nutrient LB medium. Furthermore, the genes GE001863/NtrC and GE002550 were found to confer tolerance to sodium hypochlorite in A. veronii. GE002562 and GE002614 were associated with the resistance to carbenicillin. Collectively, our results provide abundant genetic information on A. veronii, shedding light on the pathogenetic mechanisms of Aeromonas.


Subject(s)
Aeromonas veronii , DNA Transposable Elements , Drug Resistance, Bacterial , Fish Diseases , Genome, Bacterial , Phylogeny , Sodium Hypochlorite , Whole Genome Sequencing , Aeromonas veronii/genetics , Aeromonas veronii/drug effects , DNA Transposable Elements/genetics , Animals , Sodium Hypochlorite/pharmacology , Drug Resistance, Bacterial/genetics , Fish Diseases/microbiology , China , Gram-Negative Bacterial Infections/microbiology , Bass/microbiology , Anti-Bacterial Agents/pharmacology , Base Composition , Mutagenesis, Insertional
10.
JAMA Netw Open ; 7(4): e247034, 2024 Apr 01.
Article in English | MEDLINE | ID: mdl-38630472

ABSTRACT

Importance: Cerebral small vessel diseases (CSVDs) account for one-fifth of stroke cases. Numerous familial cases remain unresolved after routine screening of known CSVD genes. Objective: To identify novel genes and mechanisms associated with familial CSVD. Design, Setting, and Participants: This 2-stage study involved linkage analysis and a case-control study; linkage analysis and whole exome and genome sequencing were used to identify candidate gene variants in 2 large families with CSVD (9 patients with CSVD). Then, a case-control analysis was conducted on 246 unrelated probands, including probands from these 2 families and 244 additional probands. All probands (clinical onset

Subject(s)
3' Untranslated Regions , Cerebral Small Vessel Diseases , Collagen Type IV , Adult , Female , Humans , Middle Aged , 3' Untranslated Regions/genetics , Alleles , Case-Control Studies , Cerebral Small Vessel Diseases/genetics , Collagen Type IV/metabolism , Protein Isoforms , Mutagenesis, Insertional
11.
Microb Biotechnol ; 17(5): e14472, 2024 May.
Article in English | MEDLINE | ID: mdl-38683679

ABSTRACT

The availability of an alternative and efficient genetic editing technology is critical for fundamental research and strain improvement engineering of Streptomyces species, which are prolific producers of complex secondary metabolites with significant pharmaceutical activities. The mobile group II introns are retrotransposons that employ activities of catalytic intron RNAs and intron-encoded reverse transcriptase to precisely insert into DNA target sites through a mechanism known as retrohoming. We here developed a group II intron-based gene editing tool to achieve precise chromosomal gene insertion in Streptomyces. Moreover, by repressing the potential competition of RecA-dependent homologous recombination, we enhanced site-specific insertion efficiency of this tool to 2.38%. Subsequently, we demonstrated the application of this tool by screening and characterizing the secondary metabolite biosynthetic gene cluster (BGC) responsible for synthesizing the red pigment in Streptomyces roseosporus. Accompanied with identifying and inactivating this BGC, we observed that the impair of this cluster promoted cell growth and daptomycin production. Additionally, we applied this tool to activate silent jadomycin BGC in Streptomyces venezuelae. Overall, this work demonstrates the potential of this method as an alternative tool for genetic engineering and cryptic natural product mining in Streptomyces species.


Subject(s)
Introns , Multigene Family , Streptomyces , Streptomyces/genetics , Streptomyces/metabolism , Introns/genetics , Gene Editing/methods , Mutagenesis, Insertional/methods , Secondary Metabolism/genetics , Biosynthetic Pathways/genetics , Homologous Recombination
12.
Clin Neurol Neurosurg ; 240: 108261, 2024 05.
Article in English | MEDLINE | ID: mdl-38599043

ABSTRACT

This report presents a case of Alexander disease showing clinical characteristics mimicking progressive supranuclear palsy (PSP). A 67-year-old woman complaining of motor disturbance exhibited severe atrophy of medulla, spinal cord, and midbrain tegmentum, as well as periventricular hyperintensity on cerebral MRI. Genetic analysis identified a novel in-frame deletion/insertion mutation in the exon 3 of the GFAP gene. Interestingly, neurological findings and decreased striatal uptake in dopamine transporter SPECT were suggestive of PSP. A novel GFAP gene mutation found in the present case may cause the unique clinical phenotype, which should be differentiated from PSP.


Subject(s)
Alexander Disease , Glial Fibrillary Acidic Protein , Magnetic Resonance Imaging , Supranuclear Palsy, Progressive , Humans , Alexander Disease/genetics , Alexander Disease/diagnostic imaging , Alexander Disease/diagnosis , Female , Supranuclear Palsy, Progressive/genetics , Supranuclear Palsy, Progressive/diagnostic imaging , Aged , Glial Fibrillary Acidic Protein/genetics , Diagnosis, Differential , Tomography, Emission-Computed, Single-Photon , Brain/diagnostic imaging , Brain/pathology , Mutagenesis, Insertional/genetics
13.
J Virol Methods ; 327: 114936, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38583808

ABSTRACT

A Tn7-transposition approach was utilized for site-specific insertion of foreign genes into the genome of simian varicella virus (SVV), the causative agent of simian varicella in nonhuman primates. The severe acute respiratory syndrome coronavirus (SARS-CoV-2) nucleocapsid (N) gene and receptor binding domain (RBD) of the spike gene were inserted into the ORF 14 region of the SVV genome cloned into a bacterial artificial chromosome and then transfected into Vero cells to generate the infectious recombinant SVV (rSVV). The rSVV replicated efficiently in infected Vero cells and expressed the N and RBD antigens as indicated by immunoblot and immunofluorescence assays. Tn7-mediated transposition provides a rapid and efficient method for constructing rSVVs which may be evaluated as live-attenuated vaccines.


Subject(s)
Genome, Viral , Animals , Chlorocebus aethiops , Vero Cells , DNA Transposable Elements , SARS-CoV-2/genetics , Mutagenesis, Insertional , Spike Glycoprotein, Coronavirus/genetics , Virus Replication , Varicellovirus/genetics , Chromosomes, Artificial, Bacterial/genetics , Nucleocapsid Proteins/genetics
14.
J Biol Chem ; 300(5): 107266, 2024 May.
Article in English | MEDLINE | ID: mdl-38583864

ABSTRACT

We describe molecular-level functional changes in the α4ß2 nicotinic acetylcholine receptor by a leucine residue insertion in the M2 transmembrane domain of the α4 subunit associated with sleep-related hyperkinetic epilepsy. Measurements of agonist-elicited single-channel currents reveal the primary effect is to stabilize the open channel state, while the secondary effect is to promote reopening of the channel. These dual effects prolong the durations of bursts of channel openings equally for the two major stoichiometric forms of the receptor, (α4)2(ß2)3 and (α4)3(ß2)2, indicating the functional impact is independent of mutant copy number per receptor. Altering the location of the residue insertion within M2 shows that functionally pivotal structures are confined to a half turn of the M2 α-helix. Residue substitutions within M2 and surrounding α-helices reveal that both intrasubunit and intersubunit interactions mediate the increase in burst duration. These interactions impacting burst duration depend linearly on the size and hydrophobicity of the substituting residue. Together, the results reveal a novel structural region of the α4ß2 nicotinic acetylcholine receptor in which interhelical interactions tune the stability of the open channel state.


Subject(s)
Ion Channel Gating , Receptors, Nicotinic , Receptors, Nicotinic/metabolism , Receptors, Nicotinic/genetics , Receptors, Nicotinic/chemistry , Humans , Animals , HEK293 Cells , Xenopus laevis , Mutagenesis, Insertional , Protein Domains
15.
Sci Rep ; 14(1): 6756, 2024 03 21.
Article in English | MEDLINE | ID: mdl-38514891

ABSTRACT

Transposon directed insertion-site sequencing (TraDIS), a variant of transposon insertion sequencing commonly known as Tn-Seq, is a high-throughput assay that defines essential bacterial genes across diverse growth conditions. However, the variability between laboratory environments often requires laborious, time-consuming modifications to its protocol. In this technical study, we aimed to refine the protocol by identifying key parameters that can impact the complexity of mutant libraries. Firstly, we discovered that adjusting electroporation parameters including transposome concentration, transposome assembly conditions, and cell densities can significantly improve the recovery of viable mutants for different Escherichia coli strains. Secondly, we found that post-electroporation conditions, such as recovery time and the use of different mediums for selecting mutants may also impact the complexity of viable mutants in the library. Finally, we developed a simplified sequencing library preparation workflow based on a Nextera-TruSeq hybrid design where ~ 80% of sequenced reads correspond to transposon-DNA junctions. The technical improvements presented in our study aim to streamline TraDIS protocols, making this powerful technique more accessible for a wider scientific audience.


Subject(s)
DNA Transposable Elements , Genes, Bacterial , Mutagenesis, Insertional , DNA Transposable Elements/genetics , Cost-Benefit Analysis , Base Sequence , Escherichia coli/genetics , High-Throughput Nucleotide Sequencing/methods , Gene Library
16.
J Integr Plant Biol ; 66(4): 645-659, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38450982

ABSTRACT

ChinaMu is the largest sequence-indexed Mutator (Mu) transposon insertional library in maize (Zea mays). In this study, we made significant improvements to the size and quality of the ChinaMu library. We developed a new Mu-tag isolation method Mu-Tn5-seq (MuT-seq). Compared to the previous method used by ChinaMu, MuT-seq recovered 1/3 more germinal insertions, while requiring only about 1/14 of the sequencing volume and 1/5 of the experimental time. Using MuT-seq, we identified 113,879 germinal insertions from 3,168 Mu-active F1 families. We also assembled a high-quality genome for the Mu-active line Mu-starter, which harbors the initial active MuDR element and was used as the pollen donor for the mutation population. Using the Mu-starter genome, we recovered 33,662 (15.6%) additional germinal insertions in 3,244 (7.4%) genes in the Mu-starter line. The Mu-starter genome also improved the assignment of 117,689 (54.5%) germinal insertions. The newly upgraded ChinaMu dataset currently contains 215,889 high-quality germinal insertions. These insertions cover 32,224 pan-genes in the Mu-starter and B73Ref5 genomes, including 23,006 (80.4%) core genes shared by the two genomes. As a test model, we investigated Mu insertions in the pentatricopeptide repeat (PPR) superfamily, discovering insertions for 92% (449/487) of PPR genes in ChinaMu, demonstrating the usefulness of ChinaMu as a functional genomics resource for maize.


Subject(s)
Chromosomes , DNA Transposable Elements , Humans , DNA Transposable Elements/genetics , Mutagenesis, Insertional/genetics , Base Sequence , Mutation , Zea mays/genetics
17.
Hum Mol Genet ; 33(11): 1001-1014, 2024 May 18.
Article in English | MEDLINE | ID: mdl-38483348

ABSTRACT

The CEL gene encodes carboxyl ester lipase, a pancreatic digestive enzyme. CEL is extremely polymorphic due to a variable number tandem repeat (VNTR) located in the last exon. Single-base deletions within this VNTR cause the inherited disorder MODY8, whereas little is known about VNTR single-base insertions in pancreatic disease. We therefore mapped CEL insertion variants (CEL-INS) in 200 Norwegian patients with pancreatic neoplastic disorders. Twenty-eight samples (14.0%) carried CEL-INS alleles. Most common were insertions in repeat 9 (9.5%), which always associated with a VNTR length of 13 repeats. The combined INS allele frequency (0.078) was similar to that observed in a control material of 416 subjects (0.075). We performed functional testing in HEK293T cells of a set of CEL-INS variants, in which the insertion site varied from the first to the 12th VNTR repeat. Lipase activity showed little difference among the variants. However, CEL-INS variants with insertions occurring in the most proximal repeats led to protein aggregation and endoplasmic reticulum stress, which upregulated the unfolded protein response. Moreover, by using a CEL-INS-specific antibody, we observed patchy signals in pancreatic tissue from humans without any CEL-INS variant in the germline. Similar pancreatic staining was seen in knock-in mice expressing the most common human CEL VNTR with 16 repeats. CEL-INS proteins may therefore be constantly produced from somatic events in the normal pancreatic parenchyma. This observation along with the high population frequency of CEL-INS alleles strongly suggests that these variants are benign, with a possible exception for insertions in VNTR repeats 1-4.


Subject(s)
Minisatellite Repeats , Pancreas, Exocrine , Humans , Minisatellite Repeats/genetics , Animals , Mice , Pancreas, Exocrine/metabolism , Pancreas, Exocrine/enzymology , HEK293 Cells , Mutagenesis, Insertional/genetics , Alleles , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/pathology , Pancreatic Neoplasms/enzymology , Gene Frequency , Male , Female , Lipase/genetics
18.
Evolution ; 78(5): 1022-1023, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38437634

ABSTRACT

Transposable elements can exhibit a predilection for specific insertion regions. In a recent study, Munasinghe et al. (2023) consider how variation in where TE families prefer to insert within the genome influences their copy number evolution. The study emphasizes how a preference for neutral insertion sites is only advantageous in conjunction with host restriction mechanisms, which suggests that insertion preference may be a strategy to mitigate genetic conflicts with the host.


Subject(s)
DNA Transposable Elements , Animals , Evolution, Molecular , Mutagenesis, Insertional
19.
BioDrugs ; 38(3): 369-385, 2024 May.
Article in English | MEDLINE | ID: mdl-38489061

ABSTRACT

The remarkable advance in gene editing technology presents unparalleled opportunities for transforming medicine and finding cures for hereditary diseases. Human trials of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 nuclease (Cas9)-based therapeutics have demonstrated promising results in disrupting or deleting target sequences to treat specific diseases. However, the potential of targeted gene insertion approaches, which offer distinct advantages over disruption/deletion methods, remains largely unexplored in human trials due to intricate technical obstacles and safety concerns. This paper reviews the recent advances in preclinical studies demonstrating in vivo targeted gene insertion for therapeutic benefits, targeting somatic solid tissues through systemic delivery. With a specific emphasis on hemophilia as a prominent disease model, we highlight advancements in insertion strategies, including considerations of DNA repair pathways, targeting site selection, and donor design. Furthermore, we discuss the complex challenges and recent breakthroughs that offer valuable insights for progressing towards clinical trials.


Subject(s)
CRISPR-Cas Systems , Drug Development , Gene Editing , Genetic Therapy , Hemophilia A , Humans , Hemophilia A/genetics , Hemophilia A/therapy , Gene Editing/methods , Drug Development/methods , Genetic Therapy/methods , Animals , Mutagenesis, Insertional
20.
Target Oncol ; 19(2): 277-288, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38416376

ABSTRACT

BACKGROUND: Data from studies looking at both EGFR and ERBB2 exon 20 insertion mutations (-20ins) in the same cohort of patients with non-small cell lung cancer (NSCLC) are limited. OBJECTIVE: The purpose of this study was to analyze EGFR/ERBB2-20ins in all-stage NSCLC patients to reveal their histological and molecular features, and to retrospectively evaluate the results of first-line real-world systemic treatments in patients with advanced-stage disease. PATIENTS AND METHODS: We collected 13,920 formalin-fixed paraffin-embedded NSCLC specimens. Clinicopathological features were recorded and DNA-based next-generation sequencing was performed. First-line systemic treatment data were obtained via chart review. RESULTS: In total, 414 (2.97%) EGFR-20ins cases and 666 (4.78%) ERBB2-20ins cases were identified. Both were more common in women, non-smokers, and patients with adenocarcinoma. The incidence of EGFR/ERBB2-20ins in adenocarcinoma is inversely proportional to the degree of invasion; 77 and 26 variants were detected in EGFR-20ins and ERBB2-20ins cases, respectively. The most common concurrently mutated genes were TP53 and RB1. In invasive adenocarcinoma, lepidic components were more common in EGFR/ERBB2-20ins-alone cases than in those with other concurrent mutated genes. In EGFR-/ERBB2-20ins patients, there was no significant difference in progression-free survival (PFS) or treatment response to first-line systemic treatments in this study. There was no significant difference in PFS or treatment response among patients with different EGFR/ERBB2-20ins variants and those with or without concurrent mutated genes. CONCLUSIONS: EGFR/ERBB2-20ins is more common in early lung adenocarcinoma. EGFR-20ins had more variants. In both cohorts, the results for first-line systemic treatments showed no significant difference.


Subject(s)
Adenocarcinoma , Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Humans , Female , Carcinoma, Non-Small-Cell Lung/drug therapy , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/pathology , Lung Neoplasms/drug therapy , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Retrospective Studies , Mutagenesis, Insertional , Adenocarcinoma/pathology , Exons , China , Mutation , Receptor, ErbB-2/genetics , ErbB Receptors/genetics
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