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At least 19 recordsLinked to original sources
PubMed1978

Initiation factor IF-3 and the binary complex between initiation factor IF-2 and formylmethionyl-tRNA are mutually exclusive on the 30-S ribosomal subunit.

The formation of 30-S initiation complexes depends strongly on initiation factor IF-3; at molar ratios of IF-3 to 30-S ribosomes up to one a stimulation is observed, whereas at ratios higher than one, initiation complex formation declines strongly. The target of the observed inhibition of fMet-tRNA binding at high concentrations of IF-3 is the 30-S initiation complex itself. On the one hand addition of IF-3 to preformed 30-S initiation complexes leads to a release of bound fMet-tRNA which is linear with the amount of factor added, whereas no effect on isolated 70-S initiation complexes is seen. The release of fMet-tRNA from preformed 30-S initiation complexes is accompanied by a release of IF-2 in a one-to-one molar ratio which is in agreement with our previous findings showing that binding of fMet-tRNA takes place via a binary complex: IF-2 . fMet-tRNA (Eur. J. Biochem. 66, 181--192 and 77, 69--75). On the other hand increasing amounts of both IF-2 and fMet-tRNA relieve the IF-3-induced inhibition of 30-S initiation complex formation. From these findings it is concluded that IF-3 and the IF-2 . fMet-tRNA complex are mutually exclusive on the 30-S ribosome. This implies that under our experimental conditions MS2 RNA binding precedes fMet-tRNA binding if one accepts that the presence of IF-3 on the 30-S subunit is obligatory for messenger binding.

Escherichia coli↗
PubMed2026

Interpreting Mutation Co-Occurrence in Cancer Genomics Under Biological Context.

Somatic mutation patterns observed in cancer genomes are widely used to generate hypotheses about functional relationships among cancer genes and signaling pathways. However, mutation co-occurrence and mutual exclusivity are assessed at multiple levels, including cohorts, bulk specimens, lesions, regions, clones, and individual cells, although each observational level supports a different scope of inference. In this structured narrative review, we clarify these inferential boundaries and distinguish marginal from conditional association, as well as negative association from complete mutual exclusivity. A hypothetical numerical example of Simpson's reversal illustrates how marginal and conditional associations can differ and why negative association with non-zero overlap should be distinguished from complete mutual exclusivity. We then synthesize evidence from bulk, multi-region, phylogenetic, and single-cell analyses to examine spatial and clonal localization, interclonal cooperation, single-cell error and detection power, and genetic versus non-genetic resistance. We also provide a decision guide for method selection and a staged framework for functional validation. Overall, statistical association, physical localization, and functional interaction are related but distinct inferential targets that require different data, assumptions, and forms of validation.

clonal evolution↗
PubMed2026

Cooccurrence of Homologous Recombination Deficiency and Mismatch Repair Deficiency in Colorectal Cancer.

Homologous recombination deficiency (HRD) in colorectal cancer (CRC) remains largely unexplored. In contrast, mismatch repair deficiency (dMMR) occurs in ∼15% of patients with CRC. Although HRD and dMMR have historically been regarded as mutually exclusive, emerging evidence suggests that this mutual exclusivity may not be absolute. Here, we conducted a retrospective cohort study utilizing genomic and transcriptomic data to define HRD status in a Chinese dMMR CRC cohort (n = 99). Multiple machine learning approaches were employed to analyze the expression profiles of these tumors and to develop a classifier distinguishing HRD from homologous recombination proficiency (HRP) in dMMR CRCs. In the Chinese dMMR CRC cohort, 66% of tumors were classified as HRD. Compared with the HRP group, the HRD group had a significantly higher tumor mutational burden and better outcomes. The derived expression signature, comprising eight genes, successfully predicted HRD status in dMMR tumors with high accuracy in the training set (AUC = 0.88, Naïve Bayes) and the test set (AUC = 0.87). In this study, a subset of dMMR CRC tumors with co-occurring HRD was identified, which may have potential implications for patient stratification and the application of targeted therapies, such as PARP inhibitors, in this molecular subgroup.

colorectal cancer↗
PubMed1978

Phenotypic exclusion in mouse melanoma-rat hepatoma hybrid cells: pigment and albumin production are not reexpressed simultaneously.

Hybridization of cells of defined and different histotypes has been carried out to investigate whether the expression (or reexpression) of parental functions is mutually exclusive, as is expected if the generally assumed rule of discreteness of differentiation applies to hybrid cells. A cross of pigmented mouse melanoma cells and albumin-producing rat hepatoma cells gave rise to hybrids containing essentially one set of chromosomes from each parent and producing neither melanin nor albumin. Cells of one hybrid clone are shown to retain the potential to reexpress both parental differentiations. Successive subclonings of this hybrid have shown that cells which reexpress one function may retain the potential to reexpress the other, and that freshly isolated, morphologically homogeneous subclones may produce pigment or albumin, but not both; there successive and exclusive shifts of phenotype are documented, and in these cases, chromosome loss is very slight. The use of immunoadsorbed antisera has revealed that most (if not all) of the albumin produced by the hybrid cells is of the mouse type. We conclude that both parental determinations are retained by the hybrid cells, and that the parental differentiations are reexpressed only in a mutually exclusive fashion.

Albumins↗
PubMed2026

Biochemical Insights Into the Conserved Interactions of NMD Factors From Budding Yeast to Humans.

Nonsense-mediated mRNA decay (NMD) is one of the most extensively studied pathways of cytoplasmic mRNA degradation. It plays a critical role in diverse cellular processes by eliminating aberrant transcripts containing premature stop codons and by regulating the stability of physiological mRNAs. NMD factors were initially identified through genetic screens in S. cerevisiae (UPF1, 2, 3) and C. elegans (SMG-1, SMG5-7). Subsequent biochemical and genetic studies revealed the composition of NMD complexes and identified additional factors. A major protein hub for NMD is Upf1, an ATP-dependent RNA helicase that is part of two mutually exclusive NMD assemblies, the Upf1-Upf2-Upf3 complex and the Upf1-decapping complex, which contains the decapping enzyme and its co-factors. Here, we discuss recent findings, primarily from budding yeast, on the protein-protein interactions driving NMD complexes dynamics and their similarities to human NMD. Together, the N-terminal cysteine and histidine rich (CH) and helicase domains (HD) of Upf1 act as a hub for binding multiple partners. Upf1 is required for binding to NMD substrates and for the initiation of RNA degradation through decapping (yeast) or endonucleolytic hydrolysis (humans). We focus on the interplay between Upf2, Dcp2 and Nmd4 (yeast SMG6), which ensures the mutually exclusive formation of Upf1-bound subcomplexes modulating Upf1's affinity for RNA. Thus, the study of NMD factors interactions in different organisms sheds new light on the remarkable conservation of NMD molecular mechanisms.

Nonsense Mediated mRNA Decay↗
PubMed2025

ProgModule: A novel computational framework to identify mutation driver modules for predicting cancer prognosis and immunotherapy response.

BACKGROUND: Cancer originates from dysregulated cell proliferation driven by driver gene mutations. Despite numerous algorithms developed to identify genomic mutational signatures, they often suffer from high computational complexity and limited clinical applicability. METHODS: Here, we presented ProgModule, an advanced computational framework designed to identify mutation driver modules for cancer prognosis and immunotherapy response prediction. In ProgModule, we introduced the Prognosis-Related Mutually Exclusive Mutation (PRMEM) score, which optimizes the balance between exclusive mutation coverage and the incorporation of mutation combination mechanisms critical for cancer prognosis. RESULTS: Applying to BLCA and HNSC cohorts, ProgModule successfully identified driver modules that stratify patients into distinct prognostic subgroups, and the combination of these modules could serve as an effective prognostic biomarker. Extending our method to diverse cancers, ProgModule presented robust prognostic performance and stability across model parameters, including stopping criteria and network topology. Moreover, our analysis suggested that driver modules can predict immunotherapeutic benefit more effectively than existing signatures. Further analyses based on published CRISPR data indicated that genes within these modules may serve as potential therapeutic targets. CONCLUSIONS: Altogether, ProgModule emerges as a powerful tool for identifying mutation driver modules as prognostic and immunotherapy response biomarkers, and genes within these modules may be used as potential therapeutic targets for cancer, offering new insights into precision oncology.

Humans↗
PubMedDate not supplied

Competition between oxalate and phosphate during active calcium accumulation by sarcoplasmic vesicles.

1. During ATP supported active calcium uptake oxalate as well as phosphate are accumulated with calcium. The uptake of calcium exceeds that of both anions by a small quantity--accounting for calcium binding to vesicular proteins and lipids. 2. From assay media containing phosphate and oxalate--nearly exclusively either oxalate or phosphate are taken up together with calcium by the sarcoplasmic reticulum vesicles. The mutual exclusion occurs in a very narrow concentration range of the anions. 3. In solutions containing phosphate and oxalate, calcium phosphate or calcium oxalate precipitates are formed according to their solubility properties. 4. When phosphate prevents oxalate from being taken up, calcium transport is inhibited. Inhibition occurs, because the concentration of ionized calcium inside the vesicles rises approximately 100-fold when oxalate is replaced by phosphate. The activity of the calcium dependent ATPase parallels the calcium uptake activity. 5. It is excluded that the inhibition of calcium uptake produced by phosphate is caused by an enhanced permeability of the sarcoplasmic reticulum membranes for calcium in the presence of phosphate.

Animals↗
PubMed2026

Genomic Characterization of ETV6::RUNX1-Positive Childhood B-ALL in a Chinese Cohort: Novel Fusion Partners, Co-Occurring Mutations, and Risk-Stratifying Biomarkers.

BACKGROUND: ETV6::RUNX1 is the most common genetic abnormality in pediatric B-cell acute lymphoblastic leukemia (ALL; ∼25%), yet the comprehensive genetic architecture and molecular predictors of intermediate-risk (IR) stratification remain incompletely characterized. METHODS: We performed whole-transcriptome sequencing (Illumina NovaSeq 6000, rRNA depletion, 41.70 Gb/sample) on bone marrow samples from 93 pediatric ETV6::RUNX1-positive B-ALL patients. Bioinformatics analysis included STAR alignment, MuTect2 variant calling, FusionCatcher fusion detection, and VEP annotation. The Jaccard index with permutation testing assessed mutation co-occurrence; logistic regression identified independent predictors of IR classification. RESULTS: Beyond ETV6::RUNX1, we identified 51 distinct fusion genes across the cohort, including the reciprocal RUNX1-ETV6 (73.1%), chr8::KLF1210 (38.7%), and KLF12-chr8 (34.4%). Somatic mutations in 249 genes were detected; the most frequent were KIAA1715 (17.2%), KRAS (11.8%), and NSD2 (10.8%). Network analysis revealed significant chromatin modifier co-occurrence (KIAA1715-KMT2C: J = 0.136, p = 0.015) and KRAS-NRAS mutual exclusivity (J = 0.000, p = 0.042). PTCH1 (OR = 3.50, 95% CI 0.21-58.49, p = 0.41) and GNB1 (OR = 6.5, 95% CI 1.2-34.8, p = 0.029) mutations independently predicted IR classification. chr8::KLF1210 fusion correlated with higher Day-19 MRD levels (p = 0.038). CONCLUSIONS: GNB1 mutation represents a novel independent predictor of IR stratification in ETV6::RUNX1-positive B-ALL. The chromatin modifier co-occurrence module and extensive fusion architecture reveal biological heterogeneity within this favorable-risk subtype, with potential implications for risk-adapted therapeutic strategies.

B‐ALL↗
PubMed1975

Motor-sensory cortex-corticospinal system and developing locomotion and placing in rats.

Normal and abnormal development of movement in the rat were studied by investigating the growth and organization of the motor-sensory cortexcorticospinal tract system (MSC-CST) and the functional and morphologic effects of ablating the MSC or quadrants of it at different ages. Major growth of the MSC outflow, the CST, in the brain stem and rostral cord occurred in the second and third weeks postnatally, coinciding approximately with the normal mid-week transition from infantile to mature locomotion. Ablation of the MSC at birth revealed that while the MSC-CST was not essential for ordinary locomotion on flat terrain, its presence hastened normal development of this kind of movement, and that it was absolutely essential for locomotion on difficult terrain. The MSC quadrants showed quite different, and in some domains mutually exclusive, CST projection patterns to forebrain, diencephalon, brain stem, and spinal destinations (determined by Fink-Heimer-Nauta fiber degeneration studies). Ablation of some quadrants produced distinctive syndromes of disordered movement: the posterolateral quadrant related to active grasping in positioning limbs, while the posteromedial quadrant related to tactile motor-sensory positioning of limbs. Thus in addition to the classic somatotopic organization of the MSC, there was another kind of organization into regions concerned with components of integrated movement of a number of parts of the body. Several forms of aberrant circuitry developed after MSC ablations in infants, but their possible roles in functional adaptation remain to be determined.

Age Factors↗
PubMed2026

Dysregulation of U12-Type Splicing in Lupus Neutrophils.

OBJECTIVE: Neutrophil dysfunction is a hallmark of systemic lupus erythematosus (SLE), but its molecular basis remains unclear. This study explores transcriptional and posttranscriptional changes in low-density granulocytes (LDGs), a proinflammatory neutrophil subset expanded in SLE, focusing on NADPH oxidase (Nox) function and minor intron splicing. METHODS: LDGs and normal-density granulocytes (NDGs) were isolated from patients with SLE and healthy controls (HCs). CYBA (p22phox) expression was evaluated at transcript and protein levels. Nox activity was measured using luminol assays. Bulk RNA sequencing (RNA-seq) and rMATS software were used to assess alternative splicing, particularly of U12-type intron-containing genes. RESULTS: CYBA expression was reduced in SLE LDGs (n = 11) compared to SLE and HC NDGs (n = 6), with levels resembling those in chronic granulomatous disease neutrophils. SLE LDGs exhibited impaired Nox activity (n = 7 SLE, n = 12 HC). CYBA is a U12 intron-containing gene, and transcriptomic analysis revealed broad down-regulation of this gene class in SLE LDGs, suggesting minor spliceosome dysfunction. rMATS analysis showed increased U12-type intron retention and widespread splicing defects-including exon skipping and mutually exclusive exon use-in genes such as GBP5, MAEA, and STX10. These abnormalities were validated in an independent long-read RNA-seq data set from SLE peripheral blood mononuclear cells. Importantly, splicing disruptions correlated with disease activity and autoantibody profiles. CONCLUSION: Impaired U12-dependent splicing may contribute to neutrophil dysfunction in SLE, potentially via defective oxidative burst and altered immune regulation. These findings highlight the minor spliceosome as a novel player in lupus pathogenesis.

Humans↗
PubMed2026

STK11 Mutations and Deletions Define an Aggressive Molecular Subgroup of Cervical Adenocarcinoma.

Cervical adenocarcinoma accounts for 15%-20% of cervical cancers and is associated with poorer survival and reduced response to screening and immunotherapy compared with squamous cell carcinoma (SCC). The genomic drivers underlying this molecular subgroup remain incompletely characterized. Whole-exome sequencing was performed on 302 invasive cervical cancers from Guatemala and Venezuela. Structural variation analysis was conducted using SNP-array and whole-genome sequencing data. Findings were replicated in more than 4600 additional cervical cancer samples from TCGA, AACR Project GENIE, MSKCC, and Caris datasets. TP53 mutations were more frequent in adenocarcinoma than SCC, particularly in HPV-negative tumors. STK11 alterations, including mutations and focal deletions, were significantly enriched in HPV-positive adenocarcinomas compared with SCC and affected 23% of adenocarcinomas overall. Whole-genome analyses identified recurrent focal deletions, inversions, chromosomal rearrangements, and breakage-fusion-bridge events involving chromosome 19p and STK11 that were not detected by exome sequencing alone. STK11 alterations were associated with younger age at diagnosis, poorer overall survival, and inferior outcomes following immune checkpoint inhibitor (ICI) therapy. STK11 alterations significantly co-occurred with YAP1 amplification but were largely mutually exclusive with PIK3CA mutation. Cervical adenocarcinomas also demonstrated significantly lower CD274 (PD-L1) expression than SCC. STK11 alterations define a distinct molecular subgroup of cervical adenocarcinoma characterized by structural disruption of chromosome 19p, younger age at onset, and poorer clinical outcomes. These findings have implications for molecular classification and future targeted therapeutic approaches in cervical cancer.

Humans↗
PubMed2026

Phenotypic and transcriptomic characterization of biallelic RNU2-2 developmental and epileptic encephalopathy.

OBJECTIVE: A significant proportion of individuals with suspected genetic developmental and epileptic encephalopathies (DEEs) remain unsolved following whole genome sequencing (WGS). Here we describe biallelic RNU2-2 variants causing a recently reported, severe, recessive DEE. METHODS: We screened individuals who have received WGS analyses at the Genomic Medicine Centre Karolinska for Rare Diseases for biallelic RNU2-2 variants. Deep phenotyping was performed through reviewing entire medical histories and phenotypic traits were transcribed to their corresponding Human Phenotype Ontology (HPO) term. HPO terms were used to generate pairwise phenotypic similarity scores and assess for significantly shared phenotype enrichment in the RNU2-2 sub-cohort. RNA sequencing analyses were performed in fibroblast and blood tissues to compare splicing events between RNU2-2 individuals and two independent control groups. RESULTS: We identified 14 individuals from nine families with 12 ultra-rare biallelic RNU2-2 variants clustering in the conserved 5' domains. Genotype data from 13 of 14 individuals has been reported previously as part of a larger cohort. All individuals presented with a highly concordant, severe DEE, characterized by severe to profound intellectual disability, inability to walk or communicate, hyperkinesia, and refractory seizures. Infantile spasms and tonic seizures were the predominant seizure types and a Lennox-Gastaut syndrome-like phenotype was common. These individuals had a significantly similar phenotypic signature when compared with 703 individuals with complex pediatric epilepsies (two-sided Monte Carlo permutation test, p = .005). RNA sequencing analyses showed aberrant splicing, with the most pronounced effects in fibroblast tissues in mutually exclusive exon and alternate 3' splice-site events, which were not detectable in blood. SIGNIFICANCE: We present deep phenotyping data and transcriptomic analyses that provide support for rare, 5' clustering biallelic RNU2-2 variants causing this novel, severe DEE. We propose an RNA sequencing methodology on fibroblast tissue for future validation of RNU2-2 variants.

autosomal recessive disease↗
PubMed1977

The characterization of SV40-transformed cell lines derived from mouse teratocarcinoma: growth properties and differentiated characteristics.

Mouse teratocarcinoma cells derived from embryoid bodies of 129SVsl mice were cultured in vitro to permit their differentiation. These cells were then infected with simiam virus 40 (SV40) and 31 cloned cell lines (SVTER) were derived from these cultures. All 31 SVTER cell lines contained the SV40 tumor (T) antigen and grew as permanent lines in culture. Mock-infected embryoid body cultures did not give rise to permanent cell lines. The morphology of each SVTER cell line was distinct and did not change during successive subclonings. The growth properties and tumorigenic potential of all 31 SVTER cell lines were investigated. None of these lines produced tumors in 129SVsl mice. Each cell line was tested for its ability to (1) grow in medium containing 1% serum, (2) plate on cell monolayer, and (3) form clones in methocel suspension. Only three of the SVTER cell lines were transformed with respect to all three of these criteria. Most of these cell lines were minimal transformants. The SVTER cell lines were tested for creatine phospholinase (CPK), an enzyme activity chracteristic of mouse brain and muscle tissue, and the protease, plasminogen activator (PA) which is found in embryoid bodies and several differentiated cell types. Some of the SVTER cell lines contained high levels of CPK, while others had high levels of PA and a third group of cells contained neither enzyme activity. No SVTER cell line was found with high levels of both these enzyme activities. This result suggests that mutually exclusive sets of genes are expressed in these cells as might be expected from the distinct tissue distribution of the two enzyme activities studied. These SVTER cell lines may be useful in reconstructing developmental pathways of differentiating teratomas in vitro.

Animals↗
PubMed1979

Correlation of liver growth and function during liver regeneration and hepatocarcinogenesis.

We have previously studied some parameters of rat liver activity and compared the kinetics of cell proliferation (normal growth or after partial hepatectomy) with some specific hepatic enzymes. The mutually exclusive relationship between division and tissue function, their specific circadian rhythm as well as the "chalone effect" have been used to characterize the normal homeostatic regulatory mechanism in the liver. The same parameters have been recently determined during chemical carcinogenesis. Adult rats, fed long term with diethylnitrosamine (DENA, 10 mg/kg/day) develop liver carcinoma after 90 days of carcinogen administration. The results show that the relationship between the above parameters is progressively disturbed during the second month of treatment. A minimum of 4 weeks of continuous DENA feeding is found to be necessary for the induction of liver cancers. Giving the carcinogen for a second month decreases the delay before death with cancer. Protracting the treatment after the second month has no further effect either on survival or on cancer induction. The mechanism of carcinogenesis is explained by postulating that preneoplastic lesions evolution would closely depend on the homeostatic control disturbances.

Animals↗
PubMed1979

Do the tightly linked structural genes for nitrate and nitrite reductases in Aspergillus nidulans form an operon? Evidence from an insertional translocation which separates them.

Previous work (Rand and Arst, 1977) led to the proposal that the nis-5 mutation results in a new low activity promoter for niiA, the structural gene for nitrite reductase in Aspergillus nidulans. Expression of niiA via this promoter differs from expression of niiA via its normal promoter/initiator in that expression by the new promoter is not subject to nitrate induction or ammonium repression. nis-5 reduces but does not abolish niiA expression mediated by the normal promoter/initiator. In this work we show that nis-5 is associated with and is probably identical to a non-reciprocal translocation in which a considerable portion of the centromere proximal region of the right arm of linkage group II is inserted into linkage group VIII between niiA and niaD, the tightly linked, probably contiguous structural genes for nitrate reductase. This implies that niiA, along with its normal promots yet unidentified by its normal role. Further, it indicates that niiA is transcribed from the niaD-proximal side. As niiA and niaD are separated by a large number of unrelated genes in nis-5 strains, we can safely conclude that expression of niiA does not occur solely by synthesis of a messenger which carries a niaD as well as a niiA transcript. Clearly, niiA and niaD do not form an operon for which a di- (or poly-) cistronic messenger by the only transcript. This is consistent with other experimental evidence which shows that the syntheses of nitrate and nitrite reductases are not coordinately regulated. Nevertheless, all of these data would also be consistent with a model in which niiA and niaD form an operon-type structure having overlapping transcripts, one being di- (or poly-) cistronic and including both niiA and niaD and another being monocistronic for niiA. The reduced niiA expression mediated by the normal promoter/initiator in nis-5 strains could be a consequence of the functioning or positioning of the new linkage group II niiA promoter. An alternative, but not mutually exclusive, explanation would be that the insertional translocation prevents synthesis of a niiA niaD dicistronic transcript so that only that component of niiA expression which is due to a monocistronic niiA messenger can be induced by nitrate (and nitrite) in nis-5 strains. The apparently low activity of the new linkage group II promoter in comparison to the normal niiA promoter/initiator might betoken considerable efficiency of the latter rather than any particular lack of efficiency of the former. In addition, this work has involved extensive new mapping in linkage group II, including both mitotic mapping of the centromere and meiotic mapping of previously unlocated markers. A series of crosses in cluding genotype combinations both heterozygous and homozygous for nis-5 has been used to map the break-points and orientation of the translocation. As one break-point is closer to the centromere of linkage group II than the most centromere proximal identified gene on the same (i.e...

Aspergillus nidulans↗
PubMed1979

Grooming and consort partner selection in a troop of Japanese monkeys (Macaca fuscata).

The Arashiyama West troop of Macaca fuscata consists of 150 monkeys transported from Kyoto, Japan, in February 1972 to their present location near Laredo, Texas. At this site the animals range over 108 acres and during the study period were only minimally provisioned and disturbed. In the report of a 3-year study of consort partner selection it was suggested that yearlong social bonds within the troop appeared to be distinct from consort bonds formed during mating season. Like Sade, we consider grooming to be a good measure of yearround affinitive bonding in macaques. This study compares the pairs formed for consorting with those formed for yearlong grooming activities, by the 94 individuals who formed consort relationships during the mating season of 1973--1974. It was found that yearlong grooming involved pairs of monkeys which were significantly different from those for consorting. Grooming was relatively frequent between related monkeys, while consort partners were seldom related. In addition, yearlong grooming patterns were not disrupted during mating season. These results suggest that consort and grooming activities are behavioral expressions of two important social networks, involving mutually exclusive social bonds.

Animals↗