H-2 mutations: their genetics and effect on immune functions.
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Amino Acid Sequence↗
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Genetic insight into lung neuroendocrine tumors: Notch and Wnt signaling pathways as potential targets.
BACKGROUND: The molecular landscape of lung neuroendocrine neoplasms is still poorly characterized, making it difficult to develop a molecular classification and personalized therapeutic approaches. Significant clinical heterogeneity of these malignancies has been highlighted among poorly differentiated histotypes and within the subgroup of well-differentiated neuroendocrine tumors (NET). Currently, the main prognostic factors of lung NET include stage, histotype, grade, peripheral location, and demographic parameters. To gain deeper insights into the genomic underpinnings of lung NETs, we conducted a pilot investigation to uncover potential genetic mutations and copy number variations (CNVs) implicated in their pathogenesis. METHODS: Formalin-fixed, paraffin-embedded intraoperative tumor biopsies and matched peripheral blood mononuclear cell samples were collected from six consecutive patients with lung NETs. The whole exome sequencing (WES) was performed to profile germline and somatic mutations, identify novel genetic alterations, and detect CNVs. Clinical and pathological data were systematically documented at diagnosis and during follow-up. RESULTS: The WES analysis identified a subset of mutations shared between germline and somatic; some were of particular clinical interest as they were associated with tumor proliferation and potential therapeutic targets such as the genes KDM5C, ATR, COL7A1, NOTCH4, PTPRS, SMO, SPEN, SPTA1, TAF1. These mutations were predominantly linked to chromatin remodeling and were involved in critical oncogenic pathways such as Notch and Wnt signaling. CONCLUSIONS: This pilot study highlights the potential role of NGS analysis on solid biopsy in the assessment of the mutational profile of lung NET. A comparison of germline and somatic mutations is critical to identifying putative tumor driver mutations. In perspective, the enrichment of a subpopulation of cancer cells in the blood, with one or more specific mutations, is information of enormous clinical relevance, either for prognosis or therapeutic decisions. Translational studies on large prospective series are required to establish the role of liquid biopsy in lung NET.
Humans↗
Mitochondrial genetics. XI. Mutations at the mitochondrial locus omega affecting the recombination of mitochondrial genes in Saccharomyces cerevisiae.
1. A series of CS revertants has been selected from various strains (both omega+ and omega-) carrying a CR mitochondrial mutation at the RIB1 locus. The properties of mitochondrial recombination exhibited by these CS revertants in various crosses, have been examined systematically. The omega allele of the CS revertants has been defined in crosses with omega+ and omega- tester strains using two criteria: the polarity of recombination and a new criterium called relative output coefficient. We found that mutations of omega appear frequently associated with the mutations at the RIB1 locus selected from omega- strains but not with those selected from omega+ strains. A new allelic form of omega (omega n) which had not been found amongst wild type yeast strains is characterised. Similarly omega n mutation was found frequently associated with CR mutants at the RIB1 locus selected from omega- CS strains but not with those selected from omega+ CS strains. The omega n mutants, and the omega+ and omega- strains, explain the groups of polarity previously observed by Coen et al. (1970). 2. Main features of mitochondrial crosses with omega n strains (omega+ x omega n, omega- x omega n and omega n x omega n) are analysed. Recombination is possible between the different mitochondrial genetic markers. No high polarity of recombination is observed and the frequency of recombinants are similar to those found in homosexual crosses (omega+ x omega+ and omega- x omega-). A striking property, observed for the first time, exists in crosses between zota+ omega n CS strains and some zota- CREO mutants: the zota- CREO are unable to integrate by recombination their CR allele into the zota+ mit-DNA of omega n CS strains while being capable of integrating it into omega+ CS or omega- CS genomes. 3. It is proposed that the omega locus is the site of initiation of non reciprocal recombination events, the omega+/omega- pairing specifically initiates the non-reciprocal act while omega+/omega n or omega-/omega n pairings do not. 4. The molecular nature of the omega n mutation and its bearing on the structure of the omega locus are discussed. It is suggested that omega n mutations correspond to macrolesions (probably deletions) of a segment of the mit-DNA covering the omega and RIB1 loci. If omega n is a partial deletions of the omega- sequence the omega+ could be an additionnal deletion of the omega n sequence. 5. The occurrence of spontaneous CR and ER mitochondrial mutations has been analysed by the Luria and Delbrück fluctuation test in omega- and omega n isonuclear strains. Results of these tests indicate that an intracellular selection of resistant copies preexisting the action of the anttibiotic occurs.
Alleles↗
Targeted Forward Genetics: Saturating Mutational Analyses of Specific Target Loci Within the Genome.
Precise allele replacement by homologous recombination (also known as "gene targeting" or "genome editing") allows scientists to engineer altered DNA sequences, insertions, or deletions at specific locations in the genome. Such reverse genetics provides powerful tools to elucidate the structure and function of regulatory DNA elements, genes, RNAs, and proteins within their natural, endogenous context. Here, we describe in detail the methodology for Targeted Forward Genetics (TFG), which supports population-scale, saturating screens of allele replacements spanning thousands of base pairs at a specific target locus in the genome. The overall approach and detailed protocols, developed for the fission yeast Schizosaccharomyces pombe, are extensible to other organisms in which gene targeting is feasible.
Schizosaccharomyces↗
The two-mutational-event theory in medullary thyroid cancer.
Comparisons are presented of the ages of onset of 20 cases of hereditary medullary carcinoma of the thyroid (MCT) and of 22 sporadic cases of this same type of cancer. These data are compatible with what might be expected by the two-mutational-event theory of the initiation of cancer postulated by Knudson. It had been previously postulated that C-cell hyperplasia of the thyroid was a premalignant change resulting from the first or genetic mutational event in the initiation of this type of cancer. The finding of C-cell hyperplasia in thyroid glands of each of the 10 patients with the hereditary condition and in none of the 10 sporadic patients is compatible with this theory. The C-cell hyperplasia is believed to be the expression of the genetic mutation, which requires a subsequent somatic mutation to transform the initially mutated cell into a cancer cell.
Adolescent↗
The genetic relationship of abetalipoproteinemia and hypobetalipoproteinemia: a report of the occurence of both diseases within the same family.
A new case of abetalipoproteinemia (ABL) is reported after its recognition during an acquired hemorrhagic disthesis at parturition in a 37-year-old female. The new born infant of that delivery and 4 other first-degree relatives were subsequently studied and found to have hypobetalipoproteinemia (HBL). ABL and HBL, while sharing many clinical and biochemical similarities have, but rarely, been demonstrated within the same kindred and have, therefore, been regarded as different genetic mutations. Analysis of the data in the present and two other reported families indicates that ABL can result from the homozygous inheritance of the same gene which, when present in the heterozygous state, results in HBL't is concluded, therefore, that these cases of ABL have apparently been inherited via a different genetic mutation than most previously reported cases of ABL,and is likely the same gene involved in HBL. The clinical presentation of this form of ABL, that is, familial homozygous hypobetalipoproteinemia, is compared to that of the classical form of ABL.
Abetalipoproteinemia↗
Mutational mosaicism and genetic counseling in retinoblastoma.
Mutations may arise throughout an organism's life cycle. Typically, sporadic meiotic mutations give rise to individuals with all their germinal and somatic cells bearing the mutant gene. These mutations may be amorphs (with full penetrance and expressivity) or hypomorphs (with reduced penetrance and expressivity). Mutational mosaicism, however, involves the origin of mutations occurring during mitosis, whether in the parent at some stage prior to reproductive maturity or in the offspring at some time following fertilization. The phenotypic expression and transmission of these new mutations are dependent on the proportion of cells bearing the mutant gene as well as the location of these cells in somatic and/or germinal tissues. Mutational mosaicism was used as a developmental model to analyze 1,500 sporadic and 179 familial cases of retinoblastoma from the world literature. This model provided an interpretation for the origin, onset, and transmissibility of the sporadic unilateral retinoblastoma cases, which represent over 60% of all retinoblastoma patients. The model also permits a reclassification of all transmissible types of retinoblastoma; based on this classification, more accurate risk figures for genetic counseling can be offered. In addition, mutational mosaicism can be extended as a model to other autosomal dominant and X-linked mutations.
Animals↗
Single-cell mutational burden distributions in birth-death processes.
Genetic mutations are footprints of cancer evolution and reveal critical dynamic parameters of tumour growth, which otherwise are hard to measure in vivo. The mutation accumulation in tumour cell populations has been described by various statistics, such as site frequency spectra (SFS), single-cell division distributions (DD) and mutational burden distributions (MBD). While DD and SFS have been intensively studied in phylogenetics especially after the development of whole genome sequencing technology of bulk samples, MBD has drawn attention more recently with the single-cell sequencing data. Although those statistics all arise from the same somatic evolutionary process, an integrated understanding of these distributions is missing and requires novel mathematical tools to better inform the ecological and evolutionary dynamics of tumours. Here we introduce dynamical matrices to analyse and unite the SFS, DD and MBD and derive recurrence relations for the expectations of these three distributions. While we successfully recover classic exact results in pure-birth cases for the SFS and the DD through our new framework, we derive a new expression for the MBD and approximate all three distributions when death is introduced. We demonstrate a natural link between the SFS and the single-cell MBD, and show that the MBD can be regenerated through the DD. Counter-intuitively, the single-cell MBD is mainly driven by the stochasticity arising in the DD, rather than the extra stochasticity in the number of mutations at each cell division.
Single-Cell Analysis↗
Targeting cancer-specific mutations with RNA-triggered chromatin shredding.
Genetic mutations that drive cancer often occur in tumour-suppressor proteins such as the p53 transcription factor, which is altered in 40-50% of cases1,2. However, current therapies often fail to target these mutations because the mutant proteins typically lack defined drug-binding pockets and restoring their endogenous function has proven challenging. Here we program Cas12a2, an RNA-guided CRISPR nuclease with trans-nucleolytic cleavage activity3,4, to kill cancer cells selectively by targeting cancer-specific transcripts. This approach limited cell growth by inducing trans shredding of chromatin and triggering DNA-damage responses and cell death. In contrast to existing methods, RNA-guided Cas12a2 senses cellular RNA signatures, enabling precise targeting of undruggable mutations. Transcript-activated chromatin shredding provides an innovative approach to precision disease treatments for undruggable targets.
Animals↗
BRCA1 Exon 11 Mutations in Breast Cancer: A Study From Pakistan.
Breast cancer ranks among the top causes of cancer-related deaths in women around the globe, with genetic mutations in the BRCA1 gene being a frequent cause of breast or ovarian cancer. This study investigates hotspot mutations in exon 11 of the BRCA1 gene among Pakistani women diagnosed with breast cancer. Thirty clinically diagnosed breast cancer patients, all women, were enrolled in the current study, and high-quality DNA was extracted from peripheral blood samples. Two of the twenty-five successfully sequenced samples had a homozygous missense variant (c.2312T > C: p.Leu771Ser) detected by Sanger sequencing after PCR amplification. Upon investigation in the ClinVar database, the identified variant showed conflicting interpretations of pathogenicity. Demographic data highlighted an early disease onset, showing that 56% of patients were under 50 years of age. The need for genetic screening was further supported by the fact that 24% of the patients had a positive family history of cancer. Our study emphasizes the necessity of screening BRCA1 gene mutations to better understand the pathogenic potential of the identified variants in the Pakistani population.
Humans↗
Escherichia coli mutants overproducing phenylalanyl- and threonyl-tRNA synthetase.
The structural genes for threonyl-tRNA synthetase (ThrRS) and phenylalanyl-tRNA synthetase (PheRS) are closely linked on the Escherichia coli chromosome. To study whether these enzymes share a common regulatory element, we have investigated their synthesis in mutants which were selected for overproduction of either ThrRS or PheRS. It was found that mutants isolated previously for overproduction of ThrRS as strains resistant to the antibiotic borrelidin (strains Bor Res 3 and Bor Res 15) did not show an elevated level of PheRS. PheRS-overproducing strains were then isolated as revertants of strains with structurally altered enzymes. Strain S1 is a temperature-resistant derivative of a temperature-sensitive PheRS mutant, and strain G118 is a prototrophic derivative of a PheRS mutant which shows phenylalanine auxotrophy as a consequence of an altered K(m) of this enzyme for the amino acid. In both kinds of revertants, S1 and G118, the concentration of PheRS and ThrRS was increased by factors of about 2.5 and 1.8, respectively, whereas the level of other aminoacyl-tRNA synthetases was not affected by the mutations. Genetic studies showed that the simultaneous overproduction of PheRS and ThrRS in revertants G118 and S1 is based upon gene amplification, since this property was easily lost after growing the cells in the absence of the selective stimulus, and since this loss could be prevented by the presence of the recA allele. By similar criteria, the four- and eightfold overproduction of ThrRS in strains Bor Res 3 and Bor Res 15, respectively, was very stable genetically, indicating that it is caused by a mutational event other than gene amplification. From these results, we conclude that the concomitant increase of PheRS and ThrRS in strains G118 and S1 is an expression of gene duplication and not of a joint regulation of these two aminoacyl-tRNA synthetases. This conclusion is further supported by the result that, in mutant G118 as well as in its parental strain G1, growth in minimal medium lacking phenylalanine led to an additional twofold increase of their PheRS concentration. This increase was restricted to the PheRS, since the level of other aminoacyl-tRNA synthetases, including the ThrRS, stayed unchanged.
Amino Acyl-tRNA Synthetases↗
Reduced ferrochelatase activity: a defect common to porphyria variegata and protoporphyria.
Erythroid ferrochelatase activity has been studied in the normoblasts of patients with porphyria variegata and protoporphyria. Two methods were used for the investigation: one using intact cells and the other lysed cells, each measuring the amount of haem synthesized by normoblasts. In patients with porphyria variegata, ferrochelatase activity estimated by both methods was approximately 50% of the normal, and in protoporphyria the ferrochelatase activity was normal in intact normoblasts but was 20% of the normal in sonicated normoblasts (marrow lysates). It is suggested therefore that in porphyria variegata a dominantly inherited structural gene mutation results in an active ferrochelatase whereas in protoporphyria the genetic mutation results in an unstable ferrochelatase. The mechanism of the enzyme instability is not known though a number of postulates are discussed.
Adolescent↗
[Early diagnosis of neoplasms].
Cancer is a generic term for a variant manifestation of life caused by genetic mutations of somatic cells. It is not only carcinogenesis which is basically a genetic phenomenon, but also tumor progression which can be influenced by various genetic factors. A group of tumors is known to be inherited in a Mendelian fashion. In addition a great number of single gene disorders is associated with the development of maligne tumors. The further study of these diseases will allow new insights into the fundamental mechanisms leading to clinical cancer. In this respect a series of immunodeficiency diseases is of particular interest. Several organ tumors which seem to occur more frequently in relatives of tumor patients are of practical importance. A more sophisticated classification of these tumors may illuminate their genetic behavior. The geneticist cannot only define groups of individuals with a high cancer risk, but he can identify genetic, e.g. chromosomal, aberrations of cancerous cells which enables him the early detection of neoplasia.
Chromosome Aberrations↗
Assessment the carrier frequency of monogenic diseases in populations requiring assisted reproductive technology.
PURPOSE: The objective of this study is to assess the carrier frequency and pathogenic variation of monogenetic diseases in a population of 114 subjects in Han Chinese from Hebei province who are undergoing assisted reproductive technology through the utilization of Expanded Carrier Screening (ECS). METHODS: The study utilized a panel consisting of 155 severe monogenic recessive genetic diseases for ECS. Next-generation sequencing technology was employed to identify specific variants associated with ECS in a cohort of 114 subjects from 97 couples, comprising 97 females and 17 male spouses. RESULTS: A total of 114 individuals received ECS. The carrier rate of pathogenic genes in the enrolled population was 44.74% (51/114). Among the 97 females, the carrier rate of pathogenic genes was higher in those without assisted reproduction indicators than in those with assisted reproduction indicators (59.09% vs. 41.33%). However, the carrier rate of pathogenic genes in males without assisted reproductive technology was slightly lower than that with assisted reproductive technology (40% vs. 41.67%). Among both female and male participants, the carrier rate of pathogenic genes between individuals without indicators of assisted reproduction and those with such indicators was 55.55% vs. 41.38%. In 51 carriers, 72.55% (37/51) carried one genetic variant, 25.49% (13/51) carried two genetic variants, and 1.96% (1/51) carried three genetic variants. A total of 38 pathogenic genes were detected in this study, and GJB2 and MMACHC were most common. The carrier rates of the two genes were both 5.26% (6/114). A total of 55 variations were detected, and c.235delC was most frequently found. The carrier rate was 3.51% (4/114). The incidence of couples carrying the same pathogenic genes was 1.03% (1/97). CONCLUSIONS: The findings elucidate the carrier rate of pathogenic genes among 155 severe monogenic recessive genetic diseases and underscore the significance of ECS as a preventive measure against congenital anomalies. When both partners carry the same genetic mutation for a monogenic disease, preventive strategies can be taken in offspring through preimplantation genetic testing (PGT), prenatal genetic testing, or the utilization of donor gametes. ECS is instrumental in assessing reproductive risk, guiding fertility-related decisions, and reducing the prevalence of monogenic recessive genetic disorders in subsequent generations.
Humans↗
MYO5B gene mutations may promote the occurrence of very early onset inflammatory bowel disease: a case report.
BACKGROUND: With recent advances in gene sequencing technology, more than 60 genetic mutations associated with very early onset inflammatory bowel disease (VEO-IBD) have been reported. Most of the genes are associated with immune deficiencies. The Myosin 5B (MYO5B) gene is primarily involved in cell motility and material transport which is associated with congenital intractable diarrhea and cholestasis. No studies have examined the relationship between the MYO5B gene and VEO-IBD. We report a case of a child with a mutation in the MYO5B gene who was diagnosed with VEO-IBD, then we investigated the association between the MYO5B gene and VEO-IBD. CASE PRESENTATION: A 7-month-old baby girl with a chief complaint of "blood in the stool for more than 4 months and vaginal pus and blood discharge for 3 weeks" was diagnosed with VEO-IBD, and her symptoms improved after treatment with mesalazine. The whole-exome sequencing was performed with peripheral blood. Immunohistochemistry was performed on the terminal ileal tissue. Western blotting, quantitative polymerase chain reaction (Q-PCR) and immunofluorescence were performed with cultured organoid tissue from the terminal ileum. Whole-exome sequencing identified heterozygous missense of MYO5B variant of unknown significance (p. [I769N]; [T1546M]). Immunohistochemistry revealed a significant decrease in the expression of MYO5B protein in the terminal ileum of the child with MYO5B mutation; Q-PCR revealed a decrease in the mRNA levels of occludin and ZO-1 and both the mRNA levels and protein levels of MYO5B was downregulated in the patient. Immunofluorescence images showed that MYO5B gene mutation disrupted the apical delivery of transporters SGLT1, NHE3 and AQP7. CONCLUSIONS: MYO5B gene mutation leading to the downregulation of MYO5B protein may promote the occurrence of VEO-IBD by decreasing mRNA and protein levels of intestinal tight junction genes and dislocating the apical transporters.
Humans↗
Mutation, recombination and genetic organization in Drosophila hydei, compared to other Drosophila species.
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Animals↗
Post-Hoc Long-Read Sequencing Links Leukemic Mutation Status to Single-Cell Transcriptomes.
Single-cell RNA-sequencing-based characterization of cells that belong to the neoplastic clone is a major challenge in hematologic neoplasms, where malignant and normal cells coexist. Confident molecular profiling requires simultaneous analysis of gene expression and genetic mutations in individual cells, an ability that is not supported by the standard 10X Genomics workflow. Here, we systematically evaluated the potential and limitations of repurposing amplified cDNA generated during the 10X Genomics 3' workflow for post hoc genotyping of individual cells. We first established a mixed leukemic cell line system comprising one cell line with KIT point mutations and another with the BCR::ABL1 fusion gene. Targeted long-read PacBio sequencing enabled post hoc assignment of mutation data to transcriptionally profiled cells, but recovery differed between targets. Consistent with ambient RNA in microfluidics-based single-cell workflows, mutation-associated transcripts were detected in cells not expected to carry the corresponding mutations, illustrating how transcript recovery complicates cell-level genotype assignment. Target-specific thresholds mitigated this source of misclassification. In primary chronic myeloid leukemia samples, the post hoc approach detected BCR::ABL1-positive cells at diagnosis, but not during imatinib treatment. Together, we present a framework for adding mutation status to cells already profiled using the 10X Genomics workflow and highlight broader considerations for transcript-based single-cell genotyping.
BCR::ABL1↗
Complementation of a human disease phenotype by intercellular mRNA transfer.
There is growing evidence that mRNAs undergo intercellular transfer through cytoplasmic connections called tunneling nanotubes (TNTs), but whether transferred mRNAs are translated and affect cellular changes post-transfer is unknown. Using multiple lines of evidence, we show that transferred mRNAs undergo translation and can complement the phenotype of genetic mutations in vitro. For example, the human peroxisome biogenesis disorder, Zellweger Syndrome, results from mutations in genes such as PEX5 and PEX6. We demonstrate that the co-culture of patient-derived PEX6 mutant fibroblasts or PEX5 knockout cells with wild-type cells leads to de novo peroxisome biogenesis. We provide additional examples of genetic complementation via transfer of mRNAs encoding the HSF1 transcription factor or CRE recombinase. Complementation occurs by TNT-mediated mRNA transfer and translation in acceptor cells, but not by exosomes, nor by protein or peroxisome transfer. Our study provides evidence for the physiological significance of mRNA transfer and suggests another approach for mRNA therapeutics.
CP: cell biology↗