ABSTRACT
Progressive familial intrahepatic cholestasis (PFIC) is a rare childhood manifested disease associated with impaired bile secretion with severe pruritus yellow stool, and sometimes hepatosplenomegaly. PFIC is caused by mutations in ATP8B1, ABCB11, ABCB4, TJP2, NR1H4, SLC51A, USP53, KIF12, ZFYVE19, and MYO5B genes depending on its type. ABCB11 mutations lead to PFIC2 that encodes the bile salt export pump (BSEP). Different mutations of ABCB11 have been reported in different population groups but no data available in Pakistani population being a consanguineous one. We sequenced coding exons of the ABCB11 gene along with its flanking regions in 66 unrelated Pakistani children along with parents with PFIC2 phenotype. We identified 20 variations of ABCB11: 12 in homozygous form, one compound heterozygous, and seven heterozygous. These variants include 11 missenses, two frameshifts, two nonsense mutations, and five splicing variants. Seven variants are novel candidate variants and are not detected in any of the 120 chromosomes from normal ethnically matched individuals. Insilico analysis revealed that four homozygous missense variations have high pathogenic scores. Minigene analysis of splicing variants showed exon skipping and the addition of exon. This data is a useful addition to the disease variants genomic database and would be used in the future to build a diagnostic algorithm.
Subject(s)
ATP Binding Cassette Transporter, Subfamily B, Member 11 , Cholestasis, Intrahepatic , Humans , ATP Binding Cassette Transporter, Subfamily B, Member 11/genetics , Cholestasis, Intrahepatic/genetics , Pakistan , Male , Female , Child , Child, Preschool , Infant , Mutation , Exons/genetics , Cohort Studies , HomozygoteABSTRACT
The new HLA-DRB3*03:69 allele differs from DRB3*03:01:01:03 by change of C â G in exon 3.
Subject(s)
Alleles , Exons , HLA-DRB3 Chains , High-Throughput Nucleotide Sequencing , Histocompatibility Testing , Humans , Base Sequence , Codon , High-Throughput Nucleotide Sequencing/methods , Histocompatibility Testing/methods , HLA-DRB3 Chains/genetics , Sequence Alignment , Sequence Analysis, DNA/methodsABSTRACT
A missense nucleotide substitution at codon 95 of HLA-C*18:01:01:01 creates a novel allele HLA-C*18:20.
Subject(s)
Alleles , Exons , HLA-C Antigens , High-Throughput Nucleotide Sequencing , Histocompatibility Testing , Humans , HLA-C Antigens/genetics , Histocompatibility Testing/methods , Codon , Mutation, Missense , Base Sequence , Sequence Analysis, DNA/methods , Tissue DonorsABSTRACT
HLA-A*24:630 differs from HLA-A*24:20:01:01 by one nucleotide substitution in codon 131 in exon 3.
Subject(s)
Alleles , Base Sequence , Exons , Histocompatibility Testing , Sequence Analysis, DNA , Humans , Codon , Histocompatibility Testing/methods , HLA-A24 Antigen/genetics , HLA-A24 Antigen/immunology , Polymorphism, Single Nucleotide , Sequence Alignment , Sequence Analysis, DNA/methodsABSTRACT
The coding sequence of HLA-B*40:540N differs from HLA-B*40:02:01:01 by a non-synonymous nucleotide substitution in exon 3.
Subject(s)
Alleles , Base Sequence , Exons , Humans , Codon , Histocompatibility Testing , HLA-B Antigens/genetics , HLA-B40 Antigen/genetics , Sequence Alignment , Sequence Analysis, DNA , Tissue Donors , Male , Middle AgedABSTRACT
Full genomic sequence shows HLA-G*01:19 differs from HLA-G*01:04:01:01 only at position 99 in exon 2.
Subject(s)
Alleles , Exons , HLA-G Antigens , Humans , Base Sequence , Histocompatibility Testing , HLA-G Antigens/genetics , Sequence Analysis, DNA/methodsABSTRACT
BACKGROUND: The ubiquitously expressed Guanine nucleotide exchange factor, RAPGEF1 (C3G), is essential for early development of mouse embryos. It functions to regulate gene expression and cytoskeletal reorganization, thereby controlling cell proliferation and differentiation. While multiple transcripts have been predicted, their expression in mouse tissues has not been investigated in detail. METHODS & RESULTS: Full length RAPGEF1 isoforms primarily arise due to splicing at two hotspots, one involving exon-3, and the other involving exons 12-14 incorporating amino acids immediately following the Crk binding region of the protein. These isoforms vary in expression across embryonic and adult organs. We detected the presence of unannotated, and unpredicted transcripts with incorporation of cassette exons in various combinations, specifically in the heart, brain, testis and skeletal muscle. Isoform switching was detected as myocytes in culture and mouse embryonic stem cells were differentiated to form myotubes, and embryoid bodies respectively. The cassette exons encode a serine-rich polypeptide chain, which is intrinsically disordered, and undergoes phosphorylation. In silico structural analysis using AlphaFold indicated that the presence of cassette exons alters intra-molecular interactions, important for regulating catalytic activity. LZerD based docking studies predicted that the isoforms with one or more cassette exons differ in interaction with their target GTPase, RAP1A. CONCLUSIONS: Our results demonstrate the expression of novel RAPGEF1 isoforms, and predict cassette exon inclusion as an additional means of regulating RAPGEF1 activity in various tissues and during differentiation.
Subject(s)
Exons , Guanine Nucleotide Exchange Factors , Protein Isoforms , Animals , Exons/genetics , Mice , Guanine Nucleotide Exchange Factors/genetics , Guanine Nucleotide Exchange Factors/metabolism , Protein Isoforms/genetics , Protein Isoforms/metabolism , Organ Specificity/genetics , Cell Differentiation/genetics , Alternative Splicing/genetics , Gene Expression Regulation, Developmental/genetics , Male , Mouse Embryonic Stem Cells/metabolismABSTRACT
Hemophilia B (HB) is an inherited bleeding disorder caused by defects in the Fâ ¨ gene, leading to severe coagulation dysfunction. This study designed eight pairs of primers covering eight exons of the Fâ ¨ gene and used PCR and DNA sequencing to detect Fâ ¨ gene mutations in 31 HB patients. Sequencing results were compared with normal sequences using Chromas software on Blast to identify mutation sites. Findings revealed the CpG dinucleotide region as a mutation hotspot and the 192nd nucleotide (Fâ ¨192) as a dinucleotide polymorphism site in the Chinese population. Pathogenic mutations included point mutations, deletions, insertions, and mutations affecting amino acids or splicing sites. For cases with only polymorphic sites, further exon sequencing is needed. This study adds new mutation data to the global HB database, supports research on racial differences in Fâ ¨ gene mutations, and contributes to domestic HB statistics. The results aid in understanding the Fâ ¨ gene's role in coagulation, elucidating HB pathogenesis, and providing a basis for future gene therapy.
Subject(s)
Hemophilia B , Mutation , Humans , Hemophilia B/genetics , Male , Factor IX/genetics , Female , ExonsABSTRACT
Alternative splicing is crucial for cancer progression and can be targeted pharmacologically, yet identifying driver exons genome-wide remains challenging. We propose identifying such exons by associating statistically gene-level cancer dependencies from knockdown viability screens with splicing profiles and gene expression. Our models predict the effects of splicing perturbations on cell proliferation from transcriptomic data, enabling in silico RNA screening and prioritizing targets for splicing-based therapies. We identified 1,073 exons impacting cell proliferation, many from genes not previously linked to cancer. Experimental validation confirms their influence on proliferation, especially in highly proliferative cancer cell lines. Integrating pharmacological screens with splicing dependencies highlights the potential driver exons affecting drug sensitivity. Our models also allow predicting treatment outcomes from tumor transcriptomes, suggesting applications in precision oncology. This study presents an approach to identifying cancer driver exon and their therapeutic potential, emphasizing alternative splicing as a cancer target.
Subject(s)
Alternative Splicing , Cell Proliferation , Computer Simulation , Exons , Neoplasms , Humans , Exons/genetics , Alternative Splicing/genetics , Neoplasms/genetics , Neoplasms/drug therapy , Cell Line, Tumor , Cell Proliferation/drug effects , Cell Proliferation/genetics , RNA Isoforms/genetics , Gene Expression Regulation, Neoplastic , TranscriptomeABSTRACT
BACKGROUND: The Alpe-DPD study (NCT02324452) demonstrated that prospective genotyping and dose-individualization using four alleles in DPYD (DPYD*2A/rs3918290, c.1236G > A/rs75017182, c.2846A > T/rs67376798 and c.1679 T > G/rs56038477) can mitigate the risk of severe fluoropyrimidine toxicity. However, this could not prevent all toxicities. The goal of this study was to identify additional genetic variants, both inside and outside DPYD, that may contribute to fluoropyrimidine toxicity. METHODS: Biospecimens and data from the Alpe-DPD study were used. Exon sequencing was performed to identify risk variants inside DPYD. In silico and in vitro analyses were used to classify DPYD variants. A genome-wide association study (GWAS) with severe fluoropyrimidine-related toxicity was performed to identify variants outside DPYD. Association with severe toxicity was assessed using matched-pair analyses for the exon sequencing and logistic, Cox, and ordinal regression analyses for GWAS. RESULTS: Twenty-four non-synonymous, frameshift, and splice site DPYD variants were detected in ten of 986 patients. Seven of these variants (c.1670C > T, c.1913 T > C, c.1925 T > C, c.506delC, c.731A > C, c.1740 + 1G > T, c.763 - 2A > G) were predicted to be deleterious. The carriers of either of these variants showed a trend towards a 2.14-fold (95% CI, 0.41-11.3, P = 0.388) increased risk of severe toxicity compared to matched controls (N = 30). After GWAS of 942 patients, no individual single nucleotide polymorphisms achieved genome-wide significance (P ≤ 5 × 10-8), however, five variants were suggestive of association (P < 5 × 10-6) with severe toxicity. CONCLUSIONS: Results from DPYD exon sequencing and GWAS analysis did not identify additional genetic variants associated with severe toxicity, which suggests that testing for single markers at a population level currently has limited clinical value. Identifying additional variants on an individual level is still promising to explain fluoropyrimidine-related severe toxicity. In addition, studies with larger samples sizes, in more diverse cohorts are needed to identify potential clinically relevant genetic variants related to severe fluoropyrimidine toxicity.
Subject(s)
Dihydrouracil Dehydrogenase (NADP) , Humans , Dihydrouracil Dehydrogenase (NADP)/genetics , Female , Male , Middle Aged , Genome-Wide Association Study , Germ-Line Mutation , Aged , Polymorphism, Single Nucleotide , Adult , Fluorouracil/adverse effects , Pyrimidines/adverse effects , Antimetabolites, Antineoplastic/adverse effects , ExonsABSTRACT
INTRODUCTION: This retrospective study aimed to investigate treatment patterns and outcomes in patients with NSCLC harboring EGFR20ins in China. EGFR20ins mutations are associated with poor responses to EGFR-TKIs, and limited real-world data exist regarding the efficacy of various treatment modalities. METHODS: In this retrospective, single-center study, treatment outcomes, including PFS and ORR, were evaluated for different treatment regimens based on imaging assessments. The impact of mutation heterogeneity on treatment efficacy was also explored. RESULTS: Data from 302 patients diagnosed with NSCLC with EGFR20ins were analyzed. EGFR-TKI monotherapy demonstrated suboptimal PFS compared to platinum-based chemotherapy in the first-line setting (3.00 m vs. 6.83 m, HR = 3.674, 95%CI = 2.48-5.44, p < 0.001). Platinum plus pemetrexed plus bevacizumab combination therapy showed improved PFS and ORR compared to platinum plus pemetrexed (7.50m vs. 5.43 m, HR = 0.593, 95%CI = 0.383-0.918, p = 0.019). In later-line treatments, monotherapy with EGFR-TKIs or ICIs exhibited suboptimal efficacy. The specific EGFR20ins subtype, A763_Y764insFQEA, showed favorable responses to EGFR-TKIs in real-world settings. CONCLUSIONS: This large-scale real-world study provides valuable insights into the treatment patterns and outcomes of NSCLC patients with EGFR20ins mutations in China. These findings contribute to the understanding of EGFR20ins treatment and provide real-world benchmark for future clinical trials and drug development.
Subject(s)
Antineoplastic Combined Chemotherapy Protocols , 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/pathology , Male , Female , ErbB Receptors/genetics , Lung Neoplasms/genetics , Lung Neoplasms/drug therapy , Lung Neoplasms/pathology , Middle Aged , Retrospective Studies , Aged , China , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Treatment Outcome , Adult , Pemetrexed/therapeutic use , Pemetrexed/administration & dosage , Protein Kinase Inhibitors/therapeutic use , Mutagenesis, Insertional , Mutation , Aged, 80 and over , East Asian PeopleSubject(s)
Acrylamides , Adenocarcinoma of Lung , Afatinib , Aniline Compounds , Drug Resistance, Neoplasm , ErbB Receptors , Exons , Lung Neoplasms , Mutation , Humans , ErbB Receptors/genetics , Afatinib/therapeutic use , Afatinib/pharmacology , Acrylamides/therapeutic use , Acrylamides/pharmacology , Mutation/genetics , Drug Resistance, Neoplasm/genetics , Lung Neoplasms/genetics , Lung Neoplasms/drug therapy , Lung Neoplasms/pathology , Adenocarcinoma of Lung/genetics , Adenocarcinoma of Lung/drug therapy , Adenocarcinoma of Lung/pathology , Aniline Compounds/therapeutic use , Aniline Compounds/pharmacology , Exons/genetics , Female , Piperazines/therapeutic use , Piperazines/pharmacology , Male , Indoles , PyrimidinesSubject(s)
Exons , Humans , Exons/genetics , RNA Editing , Genetic Therapy/methods , CRISPR-Cas SystemsABSTRACT
HLA-A*24:617 differs from HLA-A*24:02:01:01 by one nucleotide in exon 4.
Subject(s)
Alleles , Asian People , Base Sequence , Exons , HLA-A24 Antigen , Histocompatibility Testing , Sequence Analysis, DNA , Humans , HLA-A24 Antigen/genetics , Asian People/genetics , Sequence Analysis, DNA/methods , Sequence Alignment , Codon , Polymorphism, Single Nucleotide , East Asian PeopleABSTRACT
HLA-A*02:1146 differs from HLA-A*02:01:01:01 by one nucleotide in exon 1.
Subject(s)
Alleles , Asian People , Base Sequence , Exons , HLA-A2 Antigen , Histocompatibility Testing , Sequence Analysis, DNA , Humans , Asian People/genetics , Sequence Analysis, DNA/methods , HLA-A2 Antigen/genetics , Sequence Alignment , Codon , East Asian PeopleABSTRACT
Two novel HLA class II, HLA-DRB1*13:357 and HLA-DQB1*03:525, characterised in Russian individuals.
Subject(s)
Alleles , HLA-DQ beta-Chains , HLA-DRB1 Chains , High-Throughput Nucleotide Sequencing , Humans , High-Throughput Nucleotide Sequencing/methods , HLA-DRB1 Chains/genetics , HLA-DQ beta-Chains/genetics , Exons , Russia , Histocompatibility Testing/methods , Base Sequence , Sequence Analysis, DNA/methodsABSTRACT
We report the first two cases of EGFR exon20ins SCLC, treated with amivantamab and TKIs.
Subject(s)
ErbB Receptors , Exons , Lung Neoplasms , Small Cell Lung Carcinoma , Humans , Lung Neoplasms/genetics , Lung Neoplasms/drug therapy , Small Cell Lung Carcinoma/genetics , Small Cell Lung Carcinoma/drug therapy , ErbB Receptors/genetics , Exons/genetics , Male , Middle Aged , Treatment Outcome , Female , AgedABSTRACT
Genomic sequence of HLA-DQB1*03:01:01:60, -DQB1*03:01:01:61, -DQB1*03:01:01:62, -DQB1*03:01:01:63, -DQB1*03:02:01:23, -DQB1*03:02:01:24, -DQB1*03:02:01:25 and -DQB1*03:03:02:14 alleles in Spanish individuals.
Subject(s)
Alleles , HLA-DQ beta-Chains , High-Throughput Nucleotide Sequencing , Humans , HLA-DQ beta-Chains/genetics , High-Throughput Nucleotide Sequencing/methods , Histocompatibility Testing/methods , Exons , Spain , Sequence Analysis, DNA/methods , Genetic VariationABSTRACT
The novel allele, HLA-DQB1*03:517, differs by a single nucleotide substitution in exon 3 to HLA-DQB1*03:02:01:02.